All File Changes

v504_base to v505_preview (2026-09-21 to 2026-10-05) v505

• confs/hgwbeta.hg.conf
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    9b01cd88c13e54301f06f7ae447f5cf071961a61 Sun Sep 27 01:11:16 2026 -0700
    Installing updated hg.conf files from UCSC servers
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    e095dfb2c98560a92e59e9956c3a7ca215073378 Sun Oct 4 01:11:15 2026 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
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    2450d99ee7e6173eff5045678d0c3d60463ff508 Sat Sep 26 21:48:03 2026 -0700
    hgwdev hg.conf: turn on showGenbankDownload, the GenBank output in the track download dialog, refs #38433
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    9b01cd88c13e54301f06f7ae447f5cf071961a61 Sun Sep 27 01:11:16 2026 -0700
    Installing updated hg.conf files from UCSC servers
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    e095dfb2c98560a92e59e9956c3a7ca215073378 Sun Oct 4 01:11:15 2026 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cgilib/cartJson.c
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    beb596d6144e0deb9ce96c5955c71e6d5f4eaec9 Sat Sep 26 13:01:02 2026 -0700
    trackHub: add an hg.conf switch for hub description page handling, refs #38126 hubHtmlSanitizeOn() in trackHub.c reads the hg.conf setting hubHtmlSanitize, default off, and the description page code in lib and cgilib asks it. With the setting off, that code behaves as it did in v503. hubCheck follows the same setting.
• src/hg/cgilib/tests/expected/bedItemRgbTest
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    5f6b4fa86cd975502de93a57756260ea22f15a22 Thu Oct 1 09:45:34 2026 -0700
    bedItemRgbTest: the on run sets alwaysItemRgb on by name, refs #36212, #38185 The on conf only included ~/.hg.conf and relied on the default. A developer whose conf chain turns alwaysItemRgb off got it off in both runs, and the test failed.
• src/hg/cgilib/tests/makefile
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    5f6b4fa86cd975502de93a57756260ea22f15a22 Thu Oct 1 09:45:34 2026 -0700
    bedItemRgbTest: the on run sets alwaysItemRgb on by name, refs #36212, #38185 The on conf only included ~/.hg.conf and relied on the default. A developer whose conf chain turns alwaysItemRgb off got it off in both runs, and the test failed.
• src/hg/hgGateway/hgGateway.c
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    81a04805893ab59c954464ac449abe65da05ac7f Mon Sep 21 16:28:30 2026 -0700
    highlight NCBI "reference" assemblies in the search result and hg.conf gated with hgGateway.showRefBadge=on default is off refs #38401
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    7b3bd7a453e354dc0d4003bc7c65b073866f16f4 Tue Sep 29 13:35:06 2026 -0700
    hgGateway: read a hub assembly's description the way other hub pages are read, refs #38430
• src/hg/hgGeneGraph/hgGeneGraph
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    d27769317be7f92e199f69d75b10a7421eecf770 Sat Sep 26 21:57:15 2026 -0700
    hgGeneGraph: require a form submission and a checked answer to file a feedback report
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    b6f15357f432f1c218fabcb0d53777322e357c00 Tue Sep 29 15:43:57 2026 -0700
    hgGeneGraph: bind the feedback-form arithmetic check to its target and a real secret Reuses a per-render hash instead of a fixed public constant, and ties it to the specific gene pair rather than just the answer, refs #38399
• src/hg/hgHubConnect/tests/makefile
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    a3dbceed952bbbfbd67e73148714bb3a828a0ec8 Mon Sep 21 15:24:52 2026 -0700
    Add some uiTests for hubspace, mostly checking that file metadata editing works when a hub.txt is in a batch. This test does not actually test uploading anything, refs #38398
• src/hg/hgHubConnect/tests/pages/hgHubConnect.js
  • lines changed 130, context: html, text, full: html, text
    a3dbceed952bbbfbd67e73148714bb3a828a0ec8 Mon Sep 21 15:24:52 2026 -0700
    Add some uiTests for hubspace, mostly checking that file metadata editing works when a hub.txt is in a batch. This test does not actually test uploading anything, refs #38398
• src/hg/hgHubConnect/tests/t01-hubTxtGenome.js
  • lines changed 80, context: html, text, full: html, text
    a3dbceed952bbbfbd67e73148714bb3a828a0ec8 Mon Sep 21 15:24:52 2026 -0700
    Add some uiTests for hubspace, mostly checking that file metadata editing works when a hub.txt is in a batch. This test does not actually test uploading anything, refs #38398
• src/hg/hgLogin/hgLogin.c
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    e3d5f0b1474ba392a87b2f65dc9701db3e88bfa2 Sat Sep 26 21:54:08 2026 -0700
    hgLogin: require POST and a per-page token to change the pending-signup address
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    b9bd7488e55a3124bb617290eccee4b544ce8600 Sun Sep 27 16:03:24 2026 -0700
    Updating hgLogin's change-recovery-email description wording: adding GitHub and CILogon and dropping ORCID from the sign-in options it names, and matching existing "sign-in options" phrasing instead of "buttons", refs #38197
• src/hg/hgSession/hgSession.c
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    8c0ef9e7b8633c0994cdaf8030d9c49c8b402016 Sat Sep 26 21:53:54 2026 -0700
    cart/hgSession: fix the session-load notice to always name the session actually loaded
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    8afc792afaf50aab2d6b83a33ba41b47dbf1df4a Tue Sep 29 15:51:16 2026 -0700
    hgSession: also clear the pending session-load marker before a local-file save The named-session save path already did this; the "save as local file" export path did not, so the marker (and the session name/owner it points at) could ride along into an exported file and resurface on re-import, refs #38399
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    35c5facfb9e64030b6eeb70aadd2026bd9296c21 Wed Sep 30 17:11:59 2026 -0700
    hgSession: a Save request without the share flag or the name no longer ends in a stack dump, refs #38456 doNewSession() read the session name with cartString() and the share flag with cartBoolean(), and both abort when the variable is missing. The Save form always sends both, so only a hand-made request reached this. doReSaveSession() read the name the same way, and outDefaultTracks() read db the same way, which a brand-new cart does not have. The name and db now have defaults, and a missing name gets the existing "without a name" message. For the share flag the code asks the request, not the cart, because the cart keeps hgS_newSessionShare on purpose. When the request carries neither the flag nor the checkbox's shadow, an existing session keeps its own sharing level and a new one is saved private.
• src/hg/hgSession/tests/makefile
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    384180e37487b4818cf7a98ca43479dda0bb282d Wed Sep 30 18:11:33 2026 -0700
    backupParseTest, mallocTopPadTest: the off run sets its gate off by name, refs #38185, #38225 Each off conf only included ~/.hg.conf. A developer whose conf chain reaches one that sets the gated variable got the gate on in both runs, and the test failed.
• src/hg/hgTablesTest/hgTablesTest.c
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    d48a1f1935917a45b20ae782f4a0ab53da13e6a9 Tue Sep 15 12:53:04 2026 -0700
    hgTablesTest: skip an oversized page instead of dying inside the allocator, refs #38359 A dense file-backed track can hand back hundreds of megabytes for a single five-megabyte test region. hg38 hgdp returned 602MB, which took carefulAlloc past its 500MB ceiling, and carefulAlloc exits the process where it stands rather than errAborting, on the grounds that errAbort itself allocates. So the run ended with one line on stderr, nothing in the log, and every table still to come forfeited. The arm in quickSubmit meant to catch exactly this and name the track had never once run. htmlPage now takes an optional ceiling on the response it will read into memory. Past it the fetch frees what it has read and errAborts naming the url, which the robot's errCatch turns back into an ordinary return of no page. The ceiling defaults to none, which leaves hgNearTest, hgBlatTest and htmlCheck exactly as they were. hgTablesTest sets it to 100MB, a fifth of the allocator ceiling: the dyString roughly doubles as it grows and the old buffer is still live while the new one fills, and the parsed page then sits alongside its text. An oversized page is logged and skipped, not counted as an error. A track that answers a 5Mb region with 600MB is one this robot cannot test, which is the same situation the row count screen already catches before submitting; counting it would put a failure in every weekly run and leave the summary as useless a gate as the one that never failed. The log is line buffered now as well. Finding out that a run died partway through is what this robot is for, and a block of buffered lines lost on the way out is part of how the old failure left no trace of which track it was on. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/hgTrackUi/hgTrackUi.c
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    6256dc2c93839878b3faef3ee64214d0abcd6d4e Tue Sep 22 11:32:49 2026 -0700
    used sameOk instead of sameString to protect agaisnt NULL dereference
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    b5af24c744cd0f5571634a863c34f208bbd0a199 Wed Sep 23 11:15:40 2026 -0700
    hgTrackUi: better error when a faceted composite's metadata file is refused, refs #29344 The 400 error now says which URL was refused and for which track, and that a hub's metaDataUrl or colorSettingsUrl has to point inside the hub's directory. facetedComposite.js now shows that text instead of just "HTTP Status: 400". Also in facetedComposite.js: facet values with a count of zero are hidden, unless they are checked, and there is a new "Clear all filters" button that unchecks all facets and empties the search boxes.
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    b3a26a6aff3896d7577be7f42ce94a7d841c91c7 Wed Sep 23 16:41:09 2026 -0700
    hgTrackUi: let a faceted composite load its metadata from any curated hub copy, refs #29344 Each sandbox attaches its own copy of a curated hub like hs1 (/gbdb/hs1/hubs/<curatedHubPrefix>/hub.txt), so a link to another sandbox's copy arrived on other servers with that hub missing from the cart, and the metadata file was refused. Now any copy in the curated directory from dbDb is accepted. A hub that is not in the cart is checked by its URL in hubStatus only, without fetching it.
• src/hg/hgTracks/bigBedTrack.c
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    2521d696f5073ce8cee3f59f423f161fdb77d550 Fri Sep 25 02:48:37 2026 -0700
    VCF tracks: the bigBed trackDb filters (filter.*, filterByRange, filterLimits, filterValues, filterType, filterText, filterLabel) now work on INFO fields, plus ID and QUAL. The field list and types come from the VCF header; the bigBed filter code is reused, bigBed behavior unchanged, refs #37617
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    c9d17a52b6b5663c7175b01f801d23198b675f7e Fri Sep 25 12:03:55 2026 -0700
    Revert all bigBed-filters for VCF changes, as Chris did that earlier already. This reverts commit 2521d696f5073ce8cee3f59f423f161fdb77d550.
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    de6d2d4e5d0106a57d1ada79e9e36005676c260e Fri Sep 25 12:39:18 2026 -0700
    Add trackDb defined filters, coloring, and mouseovers for vcf tracks, using INFO fields or sub INFO fields, like vep.Consequence, refs #37617, #37618
• src/hg/hgTracks/chainTrack.c
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    2727d941e00bc74cc9fe53851ccc16172965646d Tue Sep 29 22:35:07 2026 -0700
    a track name too long caused a buffer overflow, claude advice here fixes this problem, track to test is in GenArk assembly GCA_020740595.1 in the "LiftOver Ring-tailed lemur (2021-11-04) minimap2 Lift Over Chained Alignments" track refs #34360
• src/hg/hgTracks/halSnakeTrack.c
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    2727d941e00bc74cc9fe53851ccc16172965646d Tue Sep 29 22:35:07 2026 -0700
    a track name too long caused a buffer overflow, claude advice here fixes this problem, track to test is in GenArk assembly GCA_020740595.1 in the "LiftOver Ring-tailed lemur (2021-11-04) minimap2 Lift Over Chained Alignments" track refs #34360
• src/hg/hgTracks/hgTracks.c
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    18125243f8a0d219285fe081ed3f1eb8cd558ff2 Sat Sep 26 17:59:16 2026 -0700
    hgTracks: GenBank as a fourth format in the "Download Current Track Data" dialog The file holds the DNA of the region in view plus the selected track items as a GenBank feature table, so a region opens in the sequence editors people already use: SnapGene, Benchling, ApE and the rest. Blocks become join() locations, thickStart..thickEnd a CDS for the types that really carry a gene model, and an item running off the edge of the view gets the partial markers. Written in javascript beside the existing JSON/CSV/TSV converters, because the dialog is entirely client side: it adds one getData/sequence call to the getData/track call it already makes. Behind showGenbankDownload in hg.conf, default off, registered as a release gate in hgConfCatalog.py. Wiggle-type tracks have no GenBank equivalent and are greyed out while the format is selected, and the region is capped at 100 Mbp because the web browser has to build the whole file in memory. The dialog itself is reworked at the same time, for every format: the output format comes first, then the file name, the track list and the check-all buttons; it uses the page's font size and normal-height buttons instead of jquery-ui's smaller ones; and the position sits on its own line with the strand the Reverse button is showing. hgTracks.c adds organism and scientificName to jsonForClient, which the GenBank header needs. refs #38433
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    e061eee76c1c9e8c8161f99379273aa0d1146c1f Sat Sep 26 21:52:35 2026 -0700
    hgTracks: quickLifted superTracks keep their own bare-name visibility A quickLifted superTrack's cart visibility var should always be read under its own (undecorated) name, the same as its source assembly used, even when the target assembly happens to have a native superTrack of the same name.
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    92c5b9ee733e28d68fbb180b26d175b46776a27e Sat Sep 26 21:59:16 2026 -0700
    hgTracks: fix hub genome dropdown's db-field collision, add real labels and position lookup The groupDropdown "Genomes:" select shared name='db' with TrackForm's own hidden db field, so submitting any button in the form (e.g. Hide all) sent two values for db and the hub's own genome silently won it. Give the select its own id instead, and switch genomes via an onchange handler that sets the real db field and resubmits. Also label each option via hOrganism()/hFreezeFromDb() (the same lookup hgTracks already uses for the page title), so native UCSC assemblies get a readable label too, not just GenArk-style hub genomes; and reset position to the target genome's own default position via hDbDb() before resubmitting, since a coordinate from the current assembly usually doesn't exist in the next one. refs #38434
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    dba11b63364870388011d5f04c6563ed440eb2a1 Thu Sep 24 13:49:56 2026 -0700
    quickLift: a container set back to show no longer stays hidden on the target, refs #38198 When hgTracks arrives from a lift (hideTracks), it read a quickLifted superTrack's state from the cart. It copied the source's bare cart value, such as wgEncodeReg4, to hub_NNN_wgEncodeReg4 and then removed the bare one. That had two effects. A container hidden before one lift kept the stored hide after every later lift. This happened because hgTracks prunes a container value that equals its default, so a container set back to show left nothing to carry over. Visiting the target also deleted the source's own setting. The cart read was added for #37535, when the lifted stanza still ended with the source's "superTrack on hide". #37969 removed that line, so the stanza is now correct. On a lift the stanza decides again: any hub_ value for the container is dropped, and the source's value is left alone. Also write "visibility show" for the container rather than "visibility hide". walkTree passed "tvShow" to hTvFromString, which does not know that string and returns hide. With this change, a container hidden on the source keeps its earlier stanza on the target, the same as a hidden track.
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    32eec44ad3147d1c9912002e586662d199f78974 Tue Sep 29 15:33:05 2026 -0700
    labelTrackAsDensityWindowSize fires on winTooBigDoWiggle, which compares the window width against maxWindowCoverage and never looks at a count, so "too many items" named the wrong cause: evaSnp sets maxWindowCoverage 250000 alongside maxItems 1000000, so a 400 kb window holding a single variant claimed there were too many items to draw. Say "window too large" instead. Caught in code review of 07f0635. refs #38407
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    6743564c0d16d85e588d5a9d80097e4690b91666 Tue Sep 29 15:37:43 2026 -0700
    hgTracks: tell the user when a track download is incomplete or still being prepared, and put the GenBank size limit under hg.conf Four things in the "Download Current Track Data" dialog, all of them about a download that quietly does the wrong thing. The api stops at a limit on how many items it will return and says so with maxItemsLimit in the reply, which the dialog ignored. Worse, a truncated reply carries two extra top level fields, maxItemsLimit and dataDownloadUrl, and the CSV/TSV converter took every top level field it did not recognise for a track: the string one was iterated one character per row, and the conversion threw before writing anything. A truncated CSV or TSV download therefore produced no file and no message at all. A track's value is always the array of its rows, so that is now the test for what is a track, rather than a list of field names that the api will keep outgrowing. All formats now say plainly that the file is incomplete, and the GenBank file carries the same warning in its COMMENT block, where it outlives the dialog. Nothing showed that anything was happening between the click and the browser's download, which is one second for two tracks and four for twenty, on a 20 kb region. The Download button now goes disabled with a line beside it while the file is prepared. It is in the button pane rather than the dialog body because the body scrolls once the track list is long. The GenBank region limit drops from 100 Mbp to 25 Mbp. 50 Mbp of chr1 with 24 tracks answers with 340 MB of track json and 50 MB of sequence, which the web browser parses, copies into the file text and copies again into the Blob, so the tab needs several times the region in memory. The limit is now the hg.conf setting maxGenbankRegion, registered in hgConfCatalog.py as a knob: the ceiling belongs to the machine and its users. It is read only when showGenbankDownload is on, and a value that is not a positive number falls back to the default rather than aborting the CGI. refs #38433
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    1a9c722ad341c178dc418034e51a1d015507db9b Fri Oct 2 20:23:47 2026 -0700
    Let superTracks nest inside superTracks. refs #38460 A superTrack given a parent used to pass tdbQuery -check -strict and then be dropped at load, with no warning: the browser reported the outer folder as not found. Seven places each looked exactly one level up the parent chain, which is what trackDb.h means by "Folders are superTracks. Currently only one level deep". trackDbSuperMarkup skipped any track that was itself a superTrack when resolving parent, so the link was never made rFindTrack looked "to the sky" one level, so the outer super could not be found by name addChildRefsToParents only walked tdbList, which excludes superTracks, so an inner super never reached its parent's children list findSuperTrack matched tdb->parent->track only, so hgTrackUi could not find the outer folder of a hub assembly flatten rescued the immediate super parent only, so the outer one was never written to the table polishSupers polished the immediate parent only, so the outer super reached the write with a NULL shortLabel and segfaulted groupTrackListAddSuper made a track for one super above a member setSuperTrackHasVisibleMembers marked one level visible Each now walks the chain. The group list still shows only the outermost folder, since superTrack members are not listed there; the inner folders appear on its page with their own controls, as members always have. Walking the chain makes a parent loop fatal where it used to be harmless, so trackDbSuperMarkup now checks that the supertracks form a tree once every link is set, and breaks a loop at the supertrack that closes it, naming that track. Verified by planting a loop: before, hgTrackDb spun in trackDbSetting and had to be killed; now it warns and loads. The same hazard in composite parents is untouched and filed as #38471. Regression: trackDb built with this and with the released hgTrackDb is byte-identical on mm39 (20377 rows) and, on a tree with no nesting, on hg38 (55629) and hs1 (782). With a nested trackDb the only difference on hg38 is the one rescued container row. hgTracks on hg38 renders the same 32 rows and the same 10 supertrack controls as dev, and the wgEncodeReg member list is unchanged. Note for whoever deploys this: trackDbToTxt also has to be rebuilt. It writes the curated hub trackDb.txt from the table, and a released one emits a member whose parent stanza is missing, which breaks the hub.
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    314d1a9a41231220ae79fc971758da141c21f233 Fri Oct 2 21:36:10 2026 -0700
    Revert the superTrack nesting fix on master; it lives on superTrackNesting. refs #38460 Taken off master with its only consumer, the TSS trackDb change reverted in the previous commit. It is a library change every CGI links, in trackDbCustom.c, hdb.c, hubConnect.c and hgTracks.c, and nothing on master needs it until the TSS tracks nest again. Kept on the superTrackNesting branch with its regression evidence. Note for whoever lands it: trackDbToTxt has to be rebuilt too, or the curated hub it writes names a parent stanza it did not emit.
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    93a3129444064c4d19b4cb49e24b6de4bd0e06a6 Fri Oct 2 21:41:15 2026 -0700
    Restore the superTrack nesting fix. refs #38460 Taking this off master was over-cautious. It is wanted on its own: #38460 is a real bug, a superTrack given a parent passes tdbQuery -check -strict and is then silently dropped at load, and the fix should get into a release rather than wait on a trackDb change that uses it. Nothing on master nests yet, and the fix is behaviour-identical where nothing does: trackDb built with it and with the released hgTrackDb is byte-identical on hg38, hs1 and mm39, and hgTracks renders the same rows and supertrack controls as dev. The TSS trackDb change that uses this stays reverted, on superTrackNesting, until this ships. Whoever releases it: trackDbToTxt has to be rebuilt too, or the curated hub it writes names a parent stanza it did not emit.
• src/hg/hgTracks/imageV2.c
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    2cdae04ddc1e46cdfc2e5e8cf479cbbbb616ad10 Tue Sep 22 15:55:10 2026 -0700
    htmlSanitize tooltips before printing them into the page, refs #38226
• src/hg/hgTracks/simpleTracks.c
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    2cdae04ddc1e46cdfc2e5e8cf479cbbbb616ad10 Tue Sep 22 15:55:10 2026 -0700
    htmlSanitize tooltips before printing them into the page, refs #38226
• src/hg/hgTracks/vcfTrack.c
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    2521d696f5073ce8cee3f59f423f161fdb77d550 Fri Sep 25 02:48:37 2026 -0700
    VCF tracks: the bigBed trackDb filters (filter.*, filterByRange, filterLimits, filterValues, filterType, filterText, filterLabel) now work on INFO fields, plus ID and QUAL. The field list and types come from the VCF header; the bigBed filter code is reused, bigBed behavior unchanged, refs #37617
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    c9d17a52b6b5663c7175b01f801d23198b675f7e Fri Sep 25 12:03:55 2026 -0700
    Revert all bigBed-filters for VCF changes, as Chris did that earlier already. This reverts commit 2521d696f5073ce8cee3f59f423f161fdb77d550.
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    de6d2d4e5d0106a57d1ada79e9e36005676c260e Fri Sep 25 12:39:18 2026 -0700
    Add trackDb defined filters, coloring, and mouseovers for vcf tracks, using INFO fields or sub INFO fields, like vep.Consequence, refs #37617, #37618
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    da43847aab52991e91bfec700b16038710710038 Sat Sep 26 21:56:05 2026 -0700
    VCF tracks: new trackDb setting excludeFilterValues, a comma-separated list of FILTER values that are hidden by default; they show up pre-checked in the existing Exclude variants with these FILTER values list, refs #38424
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    7bf9ad5d27f838f39326f49e9670da152f51e1c6 Wed Sep 30 15:02:37 2026 -0700
    vcfTabix tracks: trackDb setting maxItems now also sets the maximum number of VCF records loaded for the window, overriding the hg.conf setting vcfMaxItems (default 10000), refs #37306
• src/hg/hgTracks/wigMafTrack.c
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    0ef19267989fe032759da765ca5475bebf2803bd Thu Sep 24 17:13:21 2026 -0700
    hgTracks: no codon translation on a quickLifted maf track at base level, refs #38249 The base-level view opened its connections for codon translation on the reference assembly and read the frames table there. For a lifted track both belong to the other assembly. When the reference is a hub assembly such as hs1 there is no database of that name, and the page aborted. A lifted maf now shows bases without codon translation.
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    8de67388be9a67cb94ba95615b7643b4ddc385da Thu Sep 24 17:48:19 2026 -0700
    quickLift: give a lifted maf block the reference's own bases, refs #38249 Inside a chain block the two assemblies run in step but need not agree base for base, and the first row of a lifted block still carried the other assembly's letters. The details page showed hg19's base in the human row of a block lifted onto hg38. quickLiftMafs now reads the reference sequence once over the span of the lifted blocks and writes it into that row, leaving the gaps where they are. The lifted blocks are also sorted by position now. On a chain that turns the alignment over they came back last to first, and the details page listed them in that order.
• src/hg/hgTracks/wigTrack.c
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    e3084c1bf7cea3aa7f2bbe90d298adbae603b5e2 Fri Oct 2 09:33:46 2026 -0700
    hgTracks: keep the fraction when negateValues swaps a pixel's min and max, refs #38462 preDrawWindowFunction swapped min and max through an int, so the old min lost its fraction on the way into the new max. With mean+whiskers the top whisker, and the autoscale upper limit, were then drawn at a whole number.
• src/hg/hgc/hgc.c
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    4decf5fbe82051b2d5aff9cabce3feae9dfafae1 Sat Sep 26 18:48:55 2026 -0700
    uniprot: stop declaring the alignments as amino acid coordinates, and show them properly The bigPsl seqType field describes the coordinates, not the letters stored beside them, and the UniProt query side is in bases: these proteins reach the genome through transcripts, so a query runs three bases to a residue. Declaring amino acids made pslFromBigPsl divide the block sizes by three and leave the query coordinates alone, so every reader got an alignment measured in two units at once. That fed a heap overflow in the alignment page, drew blocks short in hgTracks, and loaded sub-codon blocks as size 0, which aborted pslTransMap and took down the lifted SwissProt track (#38249). pslProtFromNaLike() converts such a psl to one counted in residues. Blocks are trimmed to whole codons, and a residue whose codon straddles an exon junction sits in two places in the genome at once, so it gets no column and the page says how many are missing rather than dropping them silently: 0.9% of residues, though 87% of alignments have at least one. A bigPsl also keeps the reference strand where a psl reads the query strand, so minus-strand items arrived claiming the protein was reversed and were rendered as reverse complemented nucleotide ambiguity codes; pslRc moves them to the convention blat uses, query forward and the strand on the target. Checked on hg38 against the translated genome: 210,416 residues over both strands, 99.86% identical, the remainder real protein-vs-reference variation. All 29 items of a test region render the stored protein at the right residues. Files already published still say amino acid and must keep working until they are rebuilt, so the conversion also requires the blocks to measure the target the way the target is measured; verified that separates the two shapes on 3000 records each way, and that all 29 render without crashing in the old format, where they now say plainly that the coordinates and the sequence do not match. refs #38300
• src/hg/hgc/mafClick.c
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    8de67388be9a67cb94ba95615b7643b4ddc385da Thu Sep 24 17:48:19 2026 -0700
    quickLift: give a lifted maf block the reference's own bases, refs #38249 Inside a chain block the two assemblies run in step but need not agree base for base, and the first row of a lifted block still carried the other assembly's letters. The details page showed hg19's base in the human row of a block lifted onto hg38. quickLiftMafs now reads the reference sequence once over the span of the lifted blocks and writes it into that row, leaving the gaps where they are. The lifted blocks are also sorted by position now. On a chain that turns the alignment over they came back last to first, and the details page listed them in that order.
• src/hg/htdocs/FAQ/FAQblat.html
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    09360ed5d9de0f031b6f62924852b533c8fda23a Sat Sep 26 18:45:33 2026 -0700
    Fixing typo in zip name, no refs
• src/hg/htdocs/FAQ/FAQdownloads.html
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    fa272dac584b8d450211f426b50c5e9e6de114c8 Tue Sep 22 08:40:34 2026 -0700
    New FAQ page on regulation and cis-regulatory tracks, refs #24610 Adds FAQ/FAQregulation.html, the page requested in this ticket since 2019: where to find transcription factor binding site data, and how the various cis-regulatory tracks relate to each other. The page is organized around the measured vs predicted distinction, which is what most of the mailing list questions turn on, and then covers which TFBS tracks to use, what to do when a factor is in none of them, loading ENCODE portal data through the portal's own Visualize button, promoters, enhancers, cCREs, restricting to a cell type, and working outward from a gene. It ends with a summary table of 16 tracks. Assembly coverage is given per track and every assembly name is a link to that track's description page on that assembly, since coverage varies a lot (mm39 carries only three of these tracks, and TFBS Conserved was never built for hg38). Also adds the category to FAQ/index.html and a cross-link from the promoter sequence question in FAQ/FAQdownloads.html. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/FAQ/FAQregulation.html
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    fa272dac584b8d450211f426b50c5e9e6de114c8 Tue Sep 22 08:40:34 2026 -0700
    New FAQ page on regulation and cis-regulatory tracks, refs #24610 Adds FAQ/FAQregulation.html, the page requested in this ticket since 2019: where to find transcription factor binding site data, and how the various cis-regulatory tracks relate to each other. The page is organized around the measured vs predicted distinction, which is what most of the mailing list questions turn on, and then covers which TFBS tracks to use, what to do when a factor is in none of them, loading ENCODE portal data through the portal's own Visualize button, promoters, enhancers, cCREs, restricting to a cell type, and working outward from a gene. It ends with a summary table of 16 tracks. Assembly coverage is given per track and every assembly name is a link to that track's description page on that assembly, since coverage varies a lot (mm39 carries only three of these tracks, and TFBS Conserved was never built for hg38). Also adds the category to FAQ/index.html and a cross-link from the promoter sequence question in FAQ/FAQdownloads.html. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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    5fd99d465a31d5bd38320ac85ff1969ab9515014 Wed Sep 23 15:44:06 2026 -0700
    Regulation FAQ: correct assembly coverage, add variant effect section, refs #24610 Corrections found by checking the page against our own release announcements, which I should have done before the first commit: - ENCODE4 Regulation is on mm10 as well as hg38. The track symbol differs by assembly (wgEncodeReg4 on hg38, encode4Reg on mm10), so a search by name missed it. - JASPAR 2026 covers hg38, mm39, danRer11, galGal6, dm6, ce11, ci3 and sacCer3. hg19 and mm10 stop at JASPAR 2024. The page had implied all ten were 2026. Also notes that the track holds several releases as subtracks, so the version depends on which one is turned on. - TFBS Conserved is on hg17 as well as hg18 and hg19. - ENCODE4 replaced ENCODE3 as the default in July 2026 and ENCODE3 is kept for archival use. Said in the text and marked in the summary table. - The cell type section described the old subtrack list for the large collections, which now use the faceted interface. - Dropped "composite" and "superTrack", which users should not see. New section on what a single variant does to regulation, covering MPRAVarDB for variants that were actually tested in a reporter assay, and AlphaGenome and PromoterAI for predictions. These live under Phenotype and Disease Associations rather than Regulation, which is worth saying since that is where a reader would otherwise fail to find them. Links to goldenPath/help/hgRegMotifHelp.html from the motif definition and from the JASPAR entry, and the definition now matches the wording there. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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    4fa04b06c8c9e1627bb6bedef9e78a02fc4ceb60 Sat Sep 26 16:25:41 2026 -0700
    minor tewaks to wording; removing oreganno refs; removing params from hgTracks links so they use users cart, refs #24610
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    9687a91909838021ee4ca314e2a29c0cccd845c8 Sat Sep 26 16:32:35 2026 -0700
    commenting out the section about loading ENCODE files as CTs, refs #24610
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    3814d8eec23ed1c9f539f669383099eb605dbbcd Sat Sep 26 18:18:00 2026 -0700
    Regulation FAQ: link hgCustom as well as the custom track help, refs #24610
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    b3aef6de6abdf2356bf7d4a64fd5d857726eea6b Sun Oct 4 09:57:49 2026 -0700
    Regulation FAQ: cis-regulation background and six interpretive questions Max asked for a short introduction to cis-regulation, and Lou noted that the page leaned towards listing datasets rather than explaining how to read them. This covers both. A new opening question walks through the kinds of evidence the Browser carries for regulation: open chromatin, histone marks, DNA methylation, transcription factor binding, conservation and physical contact. It is adapted from Max's draft, trimmed where it repeated the sections below it. The top of the page now says when the track list was last checked, and CADD 1.7 goes ahead of AlphaGenome among the variant scores, since it has been stable for years. Six questions are new, each one chosen because people keep asking it on the genome list: why a motif turns up across a whole gene, what a GeneHancer arc does and does not claim, what the scores and grey shading mean (which differs from track to track), whether signal heights can be compared (ENCODE4 auto-scales and ENCODE3 does not, which nothing else documents), what an empty region means, and what to do when your tissue was never assayed. The three "Which tracks show ..." headings become "How do I find ...", which is the form the other FAQ pages use. The Single-cell ATAC-seq row leaves the summary table because singleCellSignalsPeaks is still release alpha and those links error anywhere but hgwdev; the row is kept in a comment to restore when the track is released. refs #24610 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/FAQ/index.html
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    fa272dac584b8d450211f426b50c5e9e6de114c8 Tue Sep 22 08:40:34 2026 -0700
    New FAQ page on regulation and cis-regulatory tracks, refs #24610 Adds FAQ/FAQregulation.html, the page requested in this ticket since 2019: where to find transcription factor binding site data, and how the various cis-regulatory tracks relate to each other. The page is organized around the measured vs predicted distinction, which is what most of the mailing list questions turn on, and then covers which TFBS tracks to use, what to do when a factor is in none of them, loading ENCODE portal data through the portal's own Visualize button, promoters, enhancers, cCREs, restricting to a cell type, and working outward from a gene. It ends with a summary table of 16 tracks. Assembly coverage is given per track and every assembly name is a link to that track's description page on that assembly, since coverage varies a lot (mm39 carries only three of these tracks, and TFBS Conserved was never built for hg38). Also adds the category to FAQ/index.html and a cross-link from the promoter sequence question in FAQ/FAQdownloads.html. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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    4d3e56eaa15bfc5d19ee528c03777244d9e1033b Thu Oct 1 15:27:35 2026 -0700
    Add a mailing list search box to the FAQ and Search page The page already linked to the genome mailing list archive, but a link out to Google Groups is easy to miss next to the four search boxes in the same column, and you still have to start the search once you get there. This adds a box alongside the others that hands the query to the group's own search. refs #38438 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/apple-touch-icon.png
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    de9c4a994c80701abb407a64634cfc4f419a4e67 Tue Sep 29 13:13:27 2026 -0700
    New Genome Browser favicon designs for dev, beta and RR, now 16x16 plus 32x32 instead of 16x16 only. Each host still serves a hand-placed copy of its own faviconDev/Beta/RR.ico as favicon.ico, which is not in the tree. Also adds apple-touch-icon.png, which iOS already requests and was getting a 404 for; it is the same on every host, so it is committed under its real name. refs #36625
• src/hg/htdocs/contacts.html
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    dbc8dc013509561c1a9612491c0c84358c1db182 Tue Sep 29 17:26:25 2026 -0700
    Home page and contacts page search box did nothing when the text matched a position regex (chr1:1000000-1001000, BED-style, single base): searchBarClick only navigated in the non-position branch, after the hgSearch getChromName lookup. Now a position goes straight to hgTracks, as hgSearch.js already does. Broken since 258a0a679dd. refs #38449
• src/hg/htdocs/faviconBeta.ico
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    de9c4a994c80701abb407a64634cfc4f419a4e67 Tue Sep 29 13:13:27 2026 -0700
    New Genome Browser favicon designs for dev, beta and RR, now 16x16 plus 32x32 instead of 16x16 only. Each host still serves a hand-placed copy of its own faviconDev/Beta/RR.ico as favicon.ico, which is not in the tree. Also adds apple-touch-icon.png, which iOS already requests and was getting a 404 for; it is the same on every host, so it is committed under its real name. refs #36625
• src/hg/htdocs/faviconDev.ico
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    de9c4a994c80701abb407a64634cfc4f419a4e67 Tue Sep 29 13:13:27 2026 -0700
    New Genome Browser favicon designs for dev, beta and RR, now 16x16 plus 32x32 instead of 16x16 only. Each host still serves a hand-placed copy of its own faviconDev/Beta/RR.ico as favicon.ico, which is not in the tree. Also adds apple-touch-icon.png, which iOS already requests and was getting a 404 for; it is the same on every host, so it is committed under its real name. refs #36625
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    b6447cadc83582018d1241b1d3336e844b8b086e Tue Sep 29 13:26:29 2026 -0700
    Lighten the new dev favicon from #B54A4A to #DA7C25, halfway to the old helix's yellow-orange strand. refs #36625
• src/hg/htdocs/faviconRR.ico
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    de9c4a994c80701abb407a64634cfc4f419a4e67 Tue Sep 29 13:13:27 2026 -0700
    New Genome Browser favicon designs for dev, beta and RR, now 16x16 plus 32x32 instead of 16x16 only. Each host still serves a hand-placed copy of its own faviconDev/Beta/RR.ico as favicon.ico, which is not in the tree. Also adds apple-touch-icon.png, which iOS already requests and was getting a 404 for; it is the same on every host, so it is committed under its real name. refs #36625
• src/hg/htdocs/goldenPath/help/api.html
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    795eb665503d576544d47e863b6a4d30df48b568 Sat Sep 26 18:48:11 2026 -0700
    point three help pages at public hosts instead of genome-test, refs #37641
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    619d7563efb2f65ce421d9e40cb1965584ef1d78 Sun Oct 4 05:51:58 2026 -0700
    api.html: document the /blat endpoint (query types, apiKey, parameters, limits, output formats), refs #36315
• src/hg/htdocs/goldenPath/help/assemblyHubHelp.html
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    a8900aeeb2ac10fba9a4c772f270d15c54279b87 Sat Sep 26 18:55:12 2026 -0700
    rewrite the example assembly hub sections around GenArk instead of genome-test, refs #37641
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    215d7a575ff21f96f5bf8d3d4a3d20f95bd1d95a Sat Sep 26 19:57:36 2026 -0700
    assembly hub docs: fix broken twoBit and BLAT examples, correct mirror IPs, lead with the short hub URL, document hubCheck, refs #37641
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    63c0f6234dbcc0c3fdc9bc2d0e673c8313bd6443 Sun Sep 27 11:57:25 2026 -0700
    two minor fixes from automated CR, #37641
• src/hg/htdocs/goldenPath/help/barChart.html
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    2353ec21c6649e1de33b43bd1b3b304603ac71f1 Thu Oct 1 15:31:50 2026 -0700
    Document how to set the order of the bars on a barChart track, refs #37619 Adds a "Setting the order of the bars" section to the barChart format page. It explains that the order is a property of the data file rather than of the display, that barChartBars, barChartCategoryUrl, barChartColors and the barChartStatsUrl rows are all positional and have to move together, and then gives three recipes: barChartReorder on a barChart file, the same wrapped in bigBedToBed and bedToBigBed for a bigBarChart, and expMatrixToBarchartBed --groupOrderFile for anyone who is still at the matrix stage and can get the order right the first time. The barChartBars entry in trackDbLibrary.shtml gains a line saying the labels are positional, with a link to the new section. Also corrects the bedToBigBed command in Example 4 to pass -sort. expMatrixToBarchartBed writes its rows in item-name order, since it joins on name, so bedToBigBed rejects the file as unsorted as soon as the two orders disagree. The example has always worked on the three-row file we host, whose rows happen to be in position order already, and fails on real data. Checked the claims against the code rather than against the existing prose: barChartTrack.c walks expScores and the category list in step at increasing x with no sort anywhere, createCategs numbers the categories in label order, facetedTableSelectOffsets hands back the stats row index as the expScores offset, and getSampleValsFromFile matches samples to categories by name, which is why the matrix and sample files need no changes. Every command and both example orderings were run against the files already published under goldenPath/help/examples/barChart. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/goldenPath/help/bigPsl.html
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    4d43b746e730f4cf9df40e70d715e75b33ed6fca Tue Sep 22 14:43:59 2026 -0700
    Explain the bigPsl o-prefixed field names on the help page, refs #37155 The autoSql field comments now name the PSL field each o-prefixed field corresponds to, but nothing on the page said what the o fields are or why they are named after chromosomes when the aligned sequence is usually a transcript or protein. Add a paragraph under the schema block. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
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    795eb665503d576544d47e863b6a4d30df48b568 Sat Sep 26 18:48:11 2026 -0700
    point three help pages at public hosts instead of genome-test, refs #37641
• src/hg/htdocs/goldenPath/help/hic.html
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    795eb665503d576544d47e863b6a4d30df48b568 Sat Sep 26 18:48:11 2026 -0700
    point three help pages at public hosts instead of genome-test, refs #37641
• src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
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    a8900aeeb2ac10fba9a4c772f270d15c54279b87 Sat Sep 26 18:55:12 2026 -0700
    rewrite the example assembly hub sections around GenArk instead of genome-test, refs #37641
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    215d7a575ff21f96f5bf8d3d4a3d20f95bd1d95a Sat Sep 26 19:57:36 2026 -0700
    assembly hub docs: fix broken twoBit and BLAT examples, correct mirror IPs, lead with the short hub URL, document hubCheck, refs #37641
• src/hg/htdocs/goldenPath/help/trackDb/changes.html
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    da43847aab52991e91bfec700b16038710710038 Sat Sep 26 21:56:05 2026 -0700
    VCF tracks: new trackDb setting excludeFilterValues, a comma-separated list of FILTER values that are hidden by default; they show up pre-checked in the existing Exclude variants with these FILTER values list, refs #38424
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    d19b85083618569a8b3400a8d17a3d2028ef223d Tue Sep 29 15:38:31 2026 -0700
    The itemRgb doc said a color setting "in the same stanza" loses to an explicit itemRgb on, which is narrower than bedItemRgb() behaves: both settings go through trackDbSetting(), which walks the parent chain, and the two lookups are independent, so a parent's itemRgb on beats a color set on the child itself. Reworded that and the matching colorFields sentence, and added the changes.html row this should have had. Caught by CR of 64adf565f28. refs #36212
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    6aca098fdf7765a7122271fdcc18d5ddfe468edc Sun Oct 4 09:59:09 2026 -0700
    trackDb docs: maxItems now also sets the VCF record limit of vcfTabix tracks, refs #37306
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
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    2521d696f5073ce8cee3f59f423f161fdb77d550 Fri Sep 25 02:48:37 2026 -0700
    VCF tracks: the bigBed trackDb filters (filter.*, filterByRange, filterLimits, filterValues, filterType, filterText, filterLabel) now work on INFO fields, plus ID and QUAL. The field list and types come from the VCF header; the bigBed filter code is reused, bigBed behavior unchanged, refs #37617
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    c9d17a52b6b5663c7175b01f801d23198b675f7e Fri Sep 25 12:03:55 2026 -0700
    Revert all bigBed-filters for VCF changes, as Chris did that earlier already. This reverts commit 2521d696f5073ce8cee3f59f423f161fdb77d550.
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    da43847aab52991e91bfec700b16038710710038 Sat Sep 26 21:56:05 2026 -0700
    VCF tracks: new trackDb setting excludeFilterValues, a comma-separated list of FILTER values that are hidden by default; they show up pre-checked in the existing Exclude variants with these FILTER values list, refs #38424
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
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    da43847aab52991e91bfec700b16038710710038 Sat Sep 26 21:56:05 2026 -0700
    VCF tracks: new trackDb setting excludeFilterValues, a comma-separated list of FILTER values that are hidden by default; they show up pre-checked in the existing Exclude variants with these FILTER values list, refs #38424
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
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    2521d696f5073ce8cee3f59f423f161fdb77d550 Fri Sep 25 02:48:37 2026 -0700
    VCF tracks: the bigBed trackDb filters (filter.*, filterByRange, filterLimits, filterValues, filterType, filterText, filterLabel) now work on INFO fields, plus ID and QUAL. The field list and types come from the VCF header; the bigBed filter code is reused, bigBed behavior unchanged, refs #37617
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    c9d17a52b6b5663c7175b01f801d23198b675f7e Fri Sep 25 12:03:55 2026 -0700
    Revert all bigBed-filters for VCF changes, as Chris did that earlier already. This reverts commit 2521d696f5073ce8cee3f59f423f161fdb77d550.
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    da43847aab52991e91bfec700b16038710710038 Sat Sep 26 21:56:05 2026 -0700
    VCF tracks: new trackDb setting excludeFilterValues, a comma-separated list of FILTER values that are hidden by default; they show up pre-checked in the existing Exclude variants with these FILTER values list, refs #38424
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    d19b85083618569a8b3400a8d17a3d2028ef223d Tue Sep 29 15:38:31 2026 -0700
    The itemRgb doc said a color setting "in the same stanza" loses to an explicit itemRgb on, which is narrower than bedItemRgb() behaves: both settings go through trackDbSetting(), which walks the parent chain, and the two lookups are independent, so a parent's itemRgb on beats a color set on the child itself. Reworded that and the matching colorFields sentence, and added the changes.html row this should have had. Caught by CR of 64adf565f28. refs #36212
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    38fc33c4bbf6c8b960af709cb17a2467d6b6cac2 Tue Sep 29 15:40:59 2026 -0700
    The description page variables section claimed shell and awk examples were safe from substitution, which is wrong twice over: parseVarNameMaybe accepts a bare $db as readily as ${db}, so an example using $db or $track as its own shell variable gets the value put in, and $$ still collapses to a single $. Say that instead, and document $$ as the way to write a literal dollar. The section also renders on trackDbDoc.html, which is the native trackDb doc, where "other trackDb settings are not available" is false, so it is now scoped to a hub's description page. Caught in code review of 8d05f42. refs #38283
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    2353ec21c6649e1de33b43bd1b3b304603ac71f1 Thu Oct 1 15:31:50 2026 -0700
    Document how to set the order of the bars on a barChart track, refs #37619 Adds a "Setting the order of the bars" section to the barChart format page. It explains that the order is a property of the data file rather than of the display, that barChartBars, barChartCategoryUrl, barChartColors and the barChartStatsUrl rows are all positional and have to move together, and then gives three recipes: barChartReorder on a barChart file, the same wrapped in bigBedToBed and bedToBigBed for a bigBarChart, and expMatrixToBarchartBed --groupOrderFile for anyone who is still at the matrix stage and can get the order right the first time. The barChartBars entry in trackDbLibrary.shtml gains a line saying the labels are positional, with a link to the new section. Also corrects the bedToBigBed command in Example 4 to pass -sort. expMatrixToBarchartBed writes its rows in item-name order, since it joins on name, so bedToBigBed rejects the file as unsorted as soon as the two orders disagree. The example has always worked on the three-row file we host, whose rows happen to be in position order already, and fails on real data. Checked the claims against the code rather than against the existing prose: barChartTrack.c walks expScores and the category list in step at increasing x with no sort anywhere, createCategs numbers the categories in label order, facetedTableSelectOffsets hands back the stats row index as the expScores offset, and getSampleValsFromFile matches samples to categories by name, which is why the matrix and sample files need no changes. Every command and both example orderings were run against the files already published under goldenPath/help/examples/barChart. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 7, context: html, text, full: html, text
    6aca098fdf7765a7122271fdcc18d5ddfe468edc Sun Oct 4 09:59:09 2026 -0700
    trackDb docs: maxItems now also sets the VCF record limit of vcfTabix tracks, refs #37306
• src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.yaml
  • lines changed 7, context: html, text, full: html, text
    d19b85083618569a8b3400a8d17a3d2028ef223d Tue Sep 29 15:38:31 2026 -0700
    The itemRgb doc said a color setting "in the same stanza" loses to an explicit itemRgb on, which is narrower than bedItemRgb() behaves: both settings go through trackDbSetting(), which walks the parent chain, and the two lookups are independent, so a parent's itemRgb on beats a color set on the child itself. Reworded that and the matching colorFields sentence, and added the changes.html row this should have had. Caught by CR of 64adf565f28. refs #36212
  • lines changed 28, context: html, text, full: html, text
    38fc33c4bbf6c8b960af709cb17a2467d6b6cac2 Tue Sep 29 15:40:59 2026 -0700
    The description page variables section claimed shell and awk examples were safe from substitution, which is wrong twice over: parseVarNameMaybe accepts a bare $db as readily as ${db}, so an example using $db or $track as its own shell variable gets the value put in, and $$ still collapses to a single $. Say that instead, and document $$ as the way to write a literal dollar. The section also renders on trackDbDoc.html, which is the native trackDb doc, where "other trackDb settings are not available" is false, so it is now scoped to a hub's description page. Caught in code review of 8d05f42. refs #38283
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 58, context: html, text, full: html, text
    79b493d56edd2ffdafebdd20bc69528b3bdfee0a Mon Sep 28 15:54:54 2026 -0700
    News announcement for the redesigned BLAT search and results pages, with the matching indexNews.html item. The entry carries two anchors: #100726 for the usual date form and #newBLAT, which the blatNewFormNewsUrl hg.conf setting on the BLAT banner points at. The banner announces the switch to the new pages on October 28. refs #37996
• src/hg/htdocs/inc/dataApi.html
  • lines changed 42, context: html, text, full: html, text
    1225a489c7de73798ed0051d2141d876a3969486 Sat Sep 26 18:55:01 2026 -0700
    remove orphaned inc/dataApi.html, superseded by goldenPath/help/api.html, refs #37641
• src/hg/htdocs/inc/hgSearch.html
  • lines changed 6, context: html, text, full: html, text
    33a544e0b5f35f7e629290d4d0e74d56b1279f39 Fri Sep 25 13:41:13 2026 -0700
    hgSearch: fix sidebar collapsing when a result has a long unbroken match string, refs #38285
• src/hg/htdocs/index.html
  • lines changed 2, context: html, text, full: html, text
    dbc8dc013509561c1a9612491c0c84358c1db182 Tue Sep 29 17:26:25 2026 -0700
    Home page and contacts page search box did nothing when the text matched a position regex (chr1:1000000-1001000, BED-style, single base): searchBarClick only navigated in the non-position branch, after the hgSearch getChromName lookup. Now a position goes straight to hgTracks, as hgSearch.js already does. Broken since 258a0a679dd. refs #38449
• src/hg/htdocs/indexNews.html
  • lines changed 11, context: html, text, full: html, text
    79b493d56edd2ffdafebdd20bc69528b3bdfee0a Mon Sep 28 15:54:54 2026 -0700
    News announcement for the redesigned BLAT search and results pages, with the matching indexNews.html item. The entry carries two anchors: #100726 for the usual date form and #newBLAT, which the blatNewFormNewsUrl hg.conf setting on the BLAT banner points at. The banner announces the switch to the new pages on October 28. refs #37996
• src/hg/hubApi/apiUtils.c
  • lines changed 4, context: html, text, full: html, text
    d6c216fa6a01dbd47ae3a8848d0b6456adf31a4b Mon Sep 21 17:31:58 2026 -0700
    hubApi: serve bigNarrowPeak tracks, refs #38395 initSupportedTypes() advertises bigNarrowPeak but allowedBigBedType() left it out, so bigFileOpen() returned NULL for a type the API says it supports. Three endpoints were affected: /getData/track and /list/schema reported the bigDataUrl as missing although the file was there, and /list/chromosomes killed the CGI, because bigFileChromInfoOutput() passed the null bbi straight to bbiChromList(). Add bigNarrowPeak to allowedBigBedType(), guard the null in bigFileChromInfoOutput() so a future divergence between the two lists is a 415 rather than a crash, and note in each list that they have to agree. Adds a bigNarrowPeak test to the supportedTypes group covering all three endpoints.
• src/hg/hubApi/blat.c
  • lines changed 1, context: html, text, full: html, text
    7a501bfcc6b8f658a1a3c2b3dfce70a5915243cb Fri Oct 2 15:09:30 2026 -0700
    Updating the /blat missing API key error message in hubApi from "My Track Hubs" to "Track Hubs" to match the My Data menu, refs #37858
• src/hg/hubApi/hubApi.c
  • lines changed 4, context: html, text, full: html, text
    d6c216fa6a01dbd47ae3a8848d0b6456adf31a4b Mon Sep 21 17:31:58 2026 -0700
    hubApi: serve bigNarrowPeak tracks, refs #38395 initSupportedTypes() advertises bigNarrowPeak but allowedBigBedType() left it out, so bigFileOpen() returned NULL for a type the API says it supports. Three endpoints were affected: /getData/track and /list/schema reported the bigDataUrl as missing although the file was there, and /list/chromosomes killed the CGI, because bigFileChromInfoOutput() passed the null bbi straight to bbiChromList(). Add bigNarrowPeak to allowedBigBedType(), guard the null in bigFileChromInfoOutput() so a future divergence between the two lists is a 415 rather than a crash, and note in each list that they have to agree. Adds a bigNarrowPeak test to the supportedTypes group covering all three endpoints.
• src/hg/hubApi/list.c
  • lines changed 2, context: html, text, full: html, text
    d6c216fa6a01dbd47ae3a8848d0b6456adf31a4b Mon Sep 21 17:31:58 2026 -0700
    hubApi: serve bigNarrowPeak tracks, refs #38395 initSupportedTypes() advertises bigNarrowPeak but allowedBigBedType() left it out, so bigFileOpen() returned NULL for a type the API says it supports. Three endpoints were affected: /getData/track and /list/schema reported the bigDataUrl as missing although the file was there, and /list/chromosomes killed the CGI, because bigFileChromInfoOutput() passed the null bbi straight to bbiChromList(). Add bigNarrowPeak to allowedBigBedType(), guard the null in bigFileChromInfoOutput() so a future divergence between the two lists is a 415 rather than a crash, and note in each list that they have to agree. Adds a bigNarrowPeak test to the supportedTypes group covering all three endpoints.
• src/hg/hubApi/tests/expected/bigNarrowPeak.gz
  • lines changed 0, context: html, text, full: html, text
    d6c216fa6a01dbd47ae3a8848d0b6456adf31a4b Mon Sep 21 17:31:58 2026 -0700
    hubApi: serve bigNarrowPeak tracks, refs #38395 initSupportedTypes() advertises bigNarrowPeak but allowedBigBedType() left it out, so bigFileOpen() returned NULL for a type the API says it supports. Three endpoints were affected: /getData/track and /list/schema reported the bigDataUrl as missing although the file was there, and /list/chromosomes killed the CGI, because bigFileChromInfoOutput() passed the null bbi straight to bbiChromList(). Add bigNarrowPeak to allowedBigBedType(), guard the null in bigFileChromInfoOutput() so a future divergence between the two lists is a 415 rather than a crash, and note in each list that they have to agree. Adds a bigNarrowPeak test to the supportedTypes group covering all three endpoints.
  • lines changed 0, context: html, text, full: html, text
    49a1fd197eb0605976bbbe11b949ee425d6dad8a Thu Oct 1 09:48:50 2026 -0700
    Updating hubApi bigNarrowPeak expected output to match the onlyVisibility to visibility change on fiberSeqCompendium_PM00001_peaks in commit ab234fe6290, No RM
• src/hg/hubApi/tests/expected/schema06.gz
  • lines changed 0, context: html, text, full: html, text
    a95e200266087402974f1b02831259d43009b085 Tue Sep 29 10:30:22 2026 -0700
    Updating hubApi schema06 expected output to include the colorFields setting added to crispr10K in commit cf9cfcd463d, No RM
• src/hg/hubApi/tests/makefile
  • lines changed 2, context: html, text, full: html, text
    8adac4bab4fa18bf3cdea99b0da545272cf5652c Mon Sep 21 10:37:40 2026 -0700
    Stripping the \r character from the hubApi err37/err38 test output due to the header printing fix in commit cb99f0b11bd, No RM Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
  • lines changed 14, context: html, text, full: html, text
    d6c216fa6a01dbd47ae3a8848d0b6456adf31a4b Mon Sep 21 17:31:58 2026 -0700
    hubApi: serve bigNarrowPeak tracks, refs #38395 initSupportedTypes() advertises bigNarrowPeak but allowedBigBedType() left it out, so bigFileOpen() returned NULL for a type the API says it supports. Three endpoints were affected: /getData/track and /list/schema reported the bigDataUrl as missing although the file was there, and /list/chromosomes killed the CGI, because bigFileChromInfoOutput() passed the null bbi straight to bbiChromList(). Add bigNarrowPeak to allowedBigBedType(), guard the null in bigFileChromInfoOutput() so a future divergence between the two lists is a 415 rather than a crash, and note in each list that they have to agree. Adds a bigNarrowPeak test to the supportedTypes group covering all three endpoints.
• src/hg/inc/asmAlias.h
  • lines changed 3, context: html, text, full: html, text
    124514ebfd25805353a22085ba5bc02c7bb7c159 Thu Oct 1 11:12:10 2026 -0700
    asmAlias: keep a name that has its own active dbDb row instead of swapping it for an alias, refs #38444 Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
• src/hg/inc/bigBedFilter.h
  • lines changed 15, context: html, text, full: html, text
    2521d696f5073ce8cee3f59f423f161fdb77d550 Fri Sep 25 02:48:37 2026 -0700
    VCF tracks: the bigBed trackDb filters (filter.*, filterByRange, filterLimits, filterValues, filterType, filterText, filterLabel) now work on INFO fields, plus ID and QUAL. The field list and types come from the VCF header; the bigBed filter code is reused, bigBed behavior unchanged, refs #37617
  • lines changed 15, context: html, text, full: html, text
    c9d17a52b6b5663c7175b01f801d23198b675f7e Fri Sep 25 12:03:55 2026 -0700
    Revert all bigBed-filters for VCF changes, as Chris did that earlier already. This reverts commit 2521d696f5073ce8cee3f59f423f161fdb77d550.
  • lines changed 18, context: html, text, full: html, text
    de6d2d4e5d0106a57d1ada79e9e36005676c260e Fri Sep 25 12:39:18 2026 -0700
    Add trackDb defined filters, coloring, and mouseovers for vcf tracks, using INFO fields or sub INFO fields, like vep.Consequence, refs #37617, #37618
• src/hg/inc/hubConnect.h
  • lines changed 8, context: html, text, full: html, text
    b3a26a6aff3896d7577be7f42ce94a7d841c91c7 Wed Sep 23 16:41:09 2026 -0700
    hgTrackUi: let a faceted composite load its metadata from any curated hub copy, refs #29344 Each sandbox attaches its own copy of a curated hub like hs1 (/gbdb/hs1/hubs/<curatedHubPrefix>/hub.txt), so a link to another sandbox's copy arrived on other servers with that hub missing from the cart, and the metadata file was refused. Now any copy in the curated directory from dbDb is accepted. A hub that is not in the cart is checked by its URL in hubStatus only, without fetching it.
• src/hg/inc/hui.h
  • lines changed 13, context: html, text, full: html, text
    2521d696f5073ce8cee3f59f423f161fdb77d550 Fri Sep 25 02:48:37 2026 -0700
    VCF tracks: the bigBed trackDb filters (filter.*, filterByRange, filterLimits, filterValues, filterType, filterText, filterLabel) now work on INFO fields, plus ID and QUAL. The field list and types come from the VCF header; the bigBed filter code is reused, bigBed behavior unchanged, refs #37617
  • lines changed 13, context: html, text, full: html, text
    c9d17a52b6b5663c7175b01f801d23198b675f7e Fri Sep 25 12:03:55 2026 -0700
    Revert all bigBed-filters for VCF changes, as Chris did that earlier already. This reverts commit 2521d696f5073ce8cee3f59f423f161fdb77d550.
  • lines changed 9, context: html, text, full: html, text
    de6d2d4e5d0106a57d1ada79e9e36005676c260e Fri Sep 25 12:39:18 2026 -0700
    Add trackDb defined filters, coloring, and mouseovers for vcf tracks, using INFO fields or sub INFO fields, like vep.Consequence, refs #37617, #37618
• src/hg/inc/quickLift.h
  • lines changed 3, context: html, text, full: html, text
    8de67388be9a67cb94ba95615b7643b4ddc385da Thu Sep 24 17:48:19 2026 -0700
    quickLift: give a lifted maf block the reference's own bases, refs #38249 Inside a chain block the two assemblies run in step but need not agree base for base, and the first row of a lifted block still carried the other assembly's letters. The details page showed hg19's base in the human row of a block lifted onto hg38. quickLiftMafs now reads the reference sequence once over the span of the lifted blocks and writes it into that row, leaving the gaps where they are. The lifted blocks are also sorted by position now. On a chain that turns the alignment over they came back last to first, and the details page listed them in that order.
• src/hg/inc/trackHub.h
  • lines changed 4, context: html, text, full: html, text
    beb596d6144e0deb9ce96c5955c71e6d5f4eaec9 Sat Sep 26 13:01:02 2026 -0700
    trackHub: add an hg.conf switch for hub description page handling, refs #38126 hubHtmlSanitizeOn() in trackHub.c reads the hg.conf setting hubHtmlSanitize, default off, and the description page code in lib and cgilib asks it. With the setting off, that code behaves as it did in v503. hubCheck follows the same setting.
• src/hg/inc/vcfUi.h
  • lines changed 6, context: html, text, full: html, text
    2521d696f5073ce8cee3f59f423f161fdb77d550 Fri Sep 25 02:48:37 2026 -0700
    VCF tracks: the bigBed trackDb filters (filter.*, filterByRange, filterLimits, filterValues, filterType, filterText, filterLabel) now work on INFO fields, plus ID and QUAL. The field list and types come from the VCF header; the bigBed filter code is reused, bigBed behavior unchanged, refs #37617
  • lines changed 6, context: html, text, full: html, text
    c9d17a52b6b5663c7175b01f801d23198b675f7e Fri Sep 25 12:03:55 2026 -0700
    Revert all bigBed-filters for VCF changes, as Chris did that earlier already. This reverts commit 2521d696f5073ce8cee3f59f423f161fdb77d550.
  • lines changed 62, context: html, text, full: html, text
    de6d2d4e5d0106a57d1ada79e9e36005676c260e Fri Sep 25 12:39:18 2026 -0700
    Add trackDb defined filters, coloring, and mouseovers for vcf tracks, using INFO fields or sub INFO fields, like vep.Consequence, refs #37617, #37618
• src/hg/js/autocompleteCat.js
  • lines changed 16, context: html, text, full: html, text
    81a04805893ab59c954464ac449abe65da05ac7f Mon Sep 21 16:28:30 2026 -0700
    highlight NCBI "reference" assemblies in the search result and hg.conf gated with hgGateway.showRefBadge=on default is off refs #38401
• src/hg/js/facetedComposite.js
  • lines changed 63, context: html, text, full: html, text
    b5af24c744cd0f5571634a863c34f208bbd0a199 Wed Sep 23 11:15:40 2026 -0700
    hgTrackUi: better error when a faceted composite's metadata file is refused, refs #29344 The 400 error now says which URL was refused and for which track, and that a hub's metaDataUrl or colorSettingsUrl has to point inside the hub's directory. facetedComposite.js now shows that text instead of just "HTTP Status: 400". Also in facetedComposite.js: facet values with a count of zero are hidden, unless they are checked, and there is a new "Clear all filters" button that unchecks all facets and empties the search boxes.
• src/hg/js/hgMyData.js
  • lines changed 20, context: html, text, full: html, text
    1ab5d5566906c050e5bc8ce2bf2a21cf0d08e439 Mon Sep 21 15:23:53 2026 -0700
    Fix hubspace UI race condition on file metadata editing, wait for the hub.txt parse to finish before offering file metadata edit, refs #38398
• src/hg/js/hgSearch.js
  • lines changed 12, context: html, text, full: html, text
    e2c6af507b9d46c00083b9d560f643ee5f74e688 Fri Sep 25 13:11:31 2026 -0700
    hgSearch: fix JS error clicking MANE search result links, refs #38285
• src/hg/js/hgTracks.js
  • lines changed 7, context: html, text, full: html, text
    2cdae04ddc1e46cdfc2e5e8cf479cbbbb616ad10 Tue Sep 22 15:55:10 2026 -0700
    htmlSanitize tooltips before printing them into the page, refs #38226
  • lines changed 530, context: html, text, full: html, text
    18125243f8a0d219285fe081ed3f1eb8cd558ff2 Sat Sep 26 17:59:16 2026 -0700
    hgTracks: GenBank as a fourth format in the "Download Current Track Data" dialog The file holds the DNA of the region in view plus the selected track items as a GenBank feature table, so a region opens in the sequence editors people already use: SnapGene, Benchling, ApE and the rest. Blocks become join() locations, thickStart..thickEnd a CDS for the types that really carry a gene model, and an item running off the edge of the view gets the partial markers. Written in javascript beside the existing JSON/CSV/TSV converters, because the dialog is entirely client side: it adds one getData/sequence call to the getData/track call it already makes. Behind showGenbankDownload in hg.conf, default off, registered as a release gate in hgConfCatalog.py. Wiggle-type tracks have no GenBank equivalent and are greyed out while the format is selected, and the region is capped at 100 Mbp because the web browser has to build the whole file in memory. The dialog itself is reworked at the same time, for every format: the output format comes first, then the file name, the track list and the check-all buttons; it uses the page's font size and normal-height buttons instead of jquery-ui's smaller ones; and the position sits on its own line with the strand the Reverse button is showing. hgTracks.c adds organism and scientificName to jsonForClient, which the GenBank header needs. refs #38433
  • lines changed 19, context: html, text, full: html, text
    8845ab537236d54abbc2b6815ea80de681ac21ef Sat Sep 26 22:08:34 2026 -0700
    hgTracks: one track-data download at a time, a second click used to leave a timer nothing could stop The download dialog polls a 200ms timer while it waits on the api and keeps that timer id in one field. The Download button stays live while a request is in flight, so a second click started a second timer and overwrote the id of the first. Nothing could stop the first one after that: it went on firing every 200ms once the data had been handed over and cleared, finding nothing to build a file from each time, which since the GenBank output landed means an alert box five times a second until the page is reloaded. startDownload now returns if a download is already running, and the three places that stop the timer go through stopWaiting(), which forgets the id as well as clearing it, so the next download can start and a failed request does not wedge the dialog. refs #38433
  • lines changed 58, context: html, text, full: html, text
    6743564c0d16d85e588d5a9d80097e4690b91666 Tue Sep 29 15:37:43 2026 -0700
    hgTracks: tell the user when a track download is incomplete or still being prepared, and put the GenBank size limit under hg.conf Four things in the "Download Current Track Data" dialog, all of them about a download that quietly does the wrong thing. The api stops at a limit on how many items it will return and says so with maxItemsLimit in the reply, which the dialog ignored. Worse, a truncated reply carries two extra top level fields, maxItemsLimit and dataDownloadUrl, and the CSV/TSV converter took every top level field it did not recognise for a track: the string one was iterated one character per row, and the conversion threw before writing anything. A truncated CSV or TSV download therefore produced no file and no message at all. A track's value is always the array of its rows, so that is now the test for what is a track, rather than a list of field names that the api will keep outgrowing. All formats now say plainly that the file is incomplete, and the GenBank file carries the same warning in its COMMENT block, where it outlives the dialog. Nothing showed that anything was happening between the click and the browser's download, which is one second for two tracks and four for twenty, on a 20 kb region. The Download button now goes disabled with a line beside it while the file is prepared. It is in the button pane rather than the dialog body because the body scrolls once the track list is long. The GenBank region limit drops from 100 Mbp to 25 Mbp. 50 Mbp of chr1 with 24 tracks answers with 340 MB of track json and 50 MB of sequence, which the web browser parses, copies into the file text and copies again into the Blob, so the tab needs several times the region in memory. The limit is now the hg.conf setting maxGenbankRegion, registered in hgConfCatalog.py as a knob: the ceiling belongs to the machine and its users. It is read only when showGenbankDownload is on, and a value that is not a positive number falls back to the default rather than aborting the CGI. refs #38433
  • lines changed 8, context: html, text, full: html, text
    0cfbb0ae0beabd4e52ccad30dd876d4d42795cba Tue Sep 29 23:32:19 2026 -0700
    hgTracks: html-encode the values the track download dialog builds into its markup The dialog assembles its html by string concatenation, and several of the values that go in are not written by the code: the track names and short labels come from trackDb, which for a hub means from the hub, the assembly name can carry a hub's own naming, and the region line is whatever the position box holds. They now go through htmlEncode() from utils.js, the shared helper, which covers both element text and single-quoted attribute values, so a label or a name comes out as the text it is meant to be. refs #38226
• src/hg/js/utils.js
  • lines changed 2, context: html, text, full: html, text
    2cdae04ddc1e46cdfc2e5e8cf479cbbbb616ad10 Tue Sep 22 15:55:10 2026 -0700
    htmlSanitize tooltips before printing them into the page, refs #38226
  • lines changed 1, context: html, text, full: html, text
    3f7bd2d5d5d8c71665acbd21926a2333afe2c674 Wed Sep 23 11:20:20 2026 -0700
    Fix one last tooltip encoding spot after nightly code review, refs #38226
• src/hg/lib/asmAlias.c
  • lines changed 6, context: html, text, full: html, text
    124514ebfd25805353a22085ba5bc02c7bb7c159 Thu Oct 1 11:12:10 2026 -0700
    asmAlias: keep a name that has its own active dbDb row instead of swapping it for an alias, refs #38444 Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
• src/hg/lib/cart.c
  • lines changed 7, context: html, text, full: html, text
    8c0ef9e7b8633c0994cdaf8030d9c49c8b402016 Sat Sep 26 21:53:54 2026 -0700
    cart/hgSession: fix the session-load notice to always name the session actually loaded
  • lines changed 4, context: html, text, full: html, text
    3607635bd5f7e1f690f7a93ef30e9530387f817b Tue Sep 29 10:58:30 2026 -0700
    cart: keep hgPcrResult_imgOrd, the PCR track's place after a drag, refs #38442 The check on hgPcrResult_<db> matches the hgPcrResult_ prefix, and hgPcrResult is also the name of the track that shows the result. So when a user dragged any track, the cart dropped hgPcrResult_imgOrd on the next load, and the PCR track went back to the bottom of the image on every zoom or scroll. Exclude that name exactly, the way hgPcrResult_targetStyle is already excluded.
  • lines changed 7, context: html, text, full: html, text
    758f5d57800f3a5eb3fdd49260bcefbc1435bb91 Mon Oct 5 08:14:28 2026 -0700
    cartLoadUserSessionExt: copy the session owner and name before the cart is cleared, so the session-load notice names the loaded session, refs #38472
• src/hg/lib/customFactory.c
  • lines changed 5, context: html, text, full: html, text
    beb596d6144e0deb9ce96c5955c71e6d5f4eaec9 Sat Sep 26 13:01:02 2026 -0700
    trackHub: add an hg.conf switch for hub description page handling, refs #38126 hubHtmlSanitizeOn() in trackHub.c reads the hg.conf setting hubHtmlSanitize, default off, and the description page code in lib and cgilib asks it. With the setting off, that code behaves as it did in v503. hubCheck follows the same setting.
• src/hg/lib/customTrack.c
  • lines changed 2, context: html, text, full: html, text
    beb596d6144e0deb9ce96c5955c71e6d5f4eaec9 Sat Sep 26 13:01:02 2026 -0700
    trackHub: add an hg.conf switch for hub description page handling, refs #38126 hubHtmlSanitizeOn() in trackHub.c reads the hg.conf setting hubHtmlSanitize, default off, and the description page code in lib and cgilib asks it. With the setting off, that code behaves as it did in v503. hubCheck follows the same setting.
• src/hg/lib/geoMirror.c
  • lines changed 70, context: html, text, full: html, text
    b450839c514656467470338eaae47003e344b522 Sat Sep 26 21:52:53 2026 -0700
    geoMirror: send peer sync payload as a POST body, and pin the certificate check for it
• src/hg/lib/hVarSubst.c
  • lines changed 5, context: html, text, full: html, text
    4a642d5f4c2a3102d5c2620af754d876146d7c24 Sat Sep 26 21:53:49 2026 -0700
    trackHub: restrict a hub genome's organism/description to a plain display-label character set
  • lines changed 31, context: html, text, full: html, text
    8f1e82cfa7e46ca358c97ea135bf20cf0bbf6026 Sun Oct 4 10:49:13 2026 -0700
    hVarSubst/trackHub: encode a hub genome's organism/date text instead of rejecting it The earlier character-exclusion check could reject a hub whose organism or freeze/date label uses ordinary punctuation that has every right to be there. Replace it with a narrow %-encode of the two characters that mattered for where this text gets substituted, applied at render time; everything else passes through unchanged, refs #38399
• src/hg/lib/hdb.c
  • lines changed 2, context: html, text, full: html, text
    a0dde9c4583f3f1b7e31fd079b89ef4cc9b71cfd Mon Sep 21 17:22:33 2026 -0700
    also recognize hut:/gbdb/genark as genark hubs from dbDb refs #38361
  • lines changed 13, context: html, text, full: html, text
    1a9c722ad341c178dc418034e51a1d015507db9b Fri Oct 2 20:23:47 2026 -0700
    Let superTracks nest inside superTracks. refs #38460 A superTrack given a parent used to pass tdbQuery -check -strict and then be dropped at load, with no warning: the browser reported the outer folder as not found. Seven places each looked exactly one level up the parent chain, which is what trackDb.h means by "Folders are superTracks. Currently only one level deep". trackDbSuperMarkup skipped any track that was itself a superTrack when resolving parent, so the link was never made rFindTrack looked "to the sky" one level, so the outer super could not be found by name addChildRefsToParents only walked tdbList, which excludes superTracks, so an inner super never reached its parent's children list findSuperTrack matched tdb->parent->track only, so hgTrackUi could not find the outer folder of a hub assembly flatten rescued the immediate super parent only, so the outer one was never written to the table polishSupers polished the immediate parent only, so the outer super reached the write with a NULL shortLabel and segfaulted groupTrackListAddSuper made a track for one super above a member setSuperTrackHasVisibleMembers marked one level visible Each now walks the chain. The group list still shows only the outermost folder, since superTrack members are not listed there; the inner folders appear on its page with their own controls, as members always have. Walking the chain makes a parent loop fatal where it used to be harmless, so trackDbSuperMarkup now checks that the supertracks form a tree once every link is set, and breaks a loop at the supertrack that closes it, naming that track. Verified by planting a loop: before, hgTrackDb spun in trackDbSetting and had to be killed; now it warns and loads. The same hazard in composite parents is untouched and filed as #38471. Regression: trackDb built with this and with the released hgTrackDb is byte-identical on mm39 (20377 rows) and, on a tree with no nesting, on hg38 (55629) and hs1 (782). With a nested trackDb the only difference on hg38 is the one rescued container row. hgTracks on hg38 renders the same 32 rows and the same 10 supertrack controls as dev, and the wgEncodeReg member list is unchanged. Note for whoever deploys this: trackDbToTxt also has to be rebuilt. It writes the curated hub trackDb.txt from the table, and a released one emits a member whose parent stanza is missing, which breaks the hub.
  • lines changed 13, context: html, text, full: html, text
    314d1a9a41231220ae79fc971758da141c21f233 Fri Oct 2 21:36:10 2026 -0700
    Revert the superTrack nesting fix on master; it lives on superTrackNesting. refs #38460 Taken off master with its only consumer, the TSS trackDb change reverted in the previous commit. It is a library change every CGI links, in trackDbCustom.c, hdb.c, hubConnect.c and hgTracks.c, and nothing on master needs it until the TSS tracks nest again. Kept on the superTrackNesting branch with its regression evidence. Note for whoever lands it: trackDbToTxt has to be rebuilt too, or the curated hub it writes names a parent stanza it did not emit.
  • lines changed 13, context: html, text, full: html, text
    93a3129444064c4d19b4cb49e24b6de4bd0e06a6 Fri Oct 2 21:41:15 2026 -0700
    Restore the superTrack nesting fix. refs #38460 Taking this off master was over-cautious. It is wanted on its own: #38460 is a real bug, a superTrack given a parent passes tdbQuery -check -strict and is then silently dropped at load, and the fix should get into a release rather than wait on a trackDb change that uses it. Nothing on master nests yet, and the fix is behaviour-identical where nothing does: trackDb built with it and with the released hgTrackDb is byte-identical on hg38, hs1 and mm39, and hgTracks renders the same rows and supertrack controls as dev. The TSS trackDb change that uses this stays reverted, on superTrackNesting, until this ships. Whoever releases it: trackDbToTxt has to be rebuilt too, or the curated hub it writes names a parent stanza it did not emit.
• src/hg/lib/hgFind.c
  • lines changed 5, context: html, text, full: html, text
    beb596d6144e0deb9ce96c5955c71e6d5f4eaec9 Sat Sep 26 13:01:02 2026 -0700
    trackHub: add an hg.conf switch for hub description page handling, refs #38126 hubHtmlSanitizeOn() in trackHub.c reads the hg.conf setting hubHtmlSanitize, default off, and the description page code in lib and cgilib asks it. With the setting off, that code behaves as it did in v503. hubCheck follows the same setting.
• src/hg/lib/hubConnect.c
  • lines changed 73, context: html, text, full: html, text
    b3a26a6aff3896d7577be7f42ce94a7d841c91c7 Wed Sep 23 16:41:09 2026 -0700
    hgTrackUi: let a faceted composite load its metadata from any curated hub copy, refs #29344 Each sandbox attaches its own copy of a curated hub like hs1 (/gbdb/hs1/hubs/<curatedHubPrefix>/hub.txt), so a link to another sandbox's copy arrived on other servers with that hub missing from the cart, and the metadata file was refused. Now any copy in the curated directory from dbDb is accepted. A hub that is not in the cart is checked by its URL in hubStatus only, without fetching it.
  • lines changed 12, context: html, text, full: html, text
    1a9c722ad341c178dc418034e51a1d015507db9b Fri Oct 2 20:23:47 2026 -0700
    Let superTracks nest inside superTracks. refs #38460 A superTrack given a parent used to pass tdbQuery -check -strict and then be dropped at load, with no warning: the browser reported the outer folder as not found. Seven places each looked exactly one level up the parent chain, which is what trackDb.h means by "Folders are superTracks. Currently only one level deep". trackDbSuperMarkup skipped any track that was itself a superTrack when resolving parent, so the link was never made rFindTrack looked "to the sky" one level, so the outer super could not be found by name addChildRefsToParents only walked tdbList, which excludes superTracks, so an inner super never reached its parent's children list findSuperTrack matched tdb->parent->track only, so hgTrackUi could not find the outer folder of a hub assembly flatten rescued the immediate super parent only, so the outer one was never written to the table polishSupers polished the immediate parent only, so the outer super reached the write with a NULL shortLabel and segfaulted groupTrackListAddSuper made a track for one super above a member setSuperTrackHasVisibleMembers marked one level visible Each now walks the chain. The group list still shows only the outermost folder, since superTrack members are not listed there; the inner folders appear on its page with their own controls, as members always have. Walking the chain makes a parent loop fatal where it used to be harmless, so trackDbSuperMarkup now checks that the supertracks form a tree once every link is set, and breaks a loop at the supertrack that closes it, naming that track. Verified by planting a loop: before, hgTrackDb spun in trackDbSetting and had to be killed; now it warns and loads. The same hazard in composite parents is untouched and filed as #38471. Regression: trackDb built with this and with the released hgTrackDb is byte-identical on mm39 (20377 rows) and, on a tree with no nesting, on hg38 (55629) and hs1 (782). With a nested trackDb the only difference on hg38 is the one rescued container row. hgTracks on hg38 renders the same 32 rows and the same 10 supertrack controls as dev, and the wgEncodeReg member list is unchanged. Note for whoever deploys this: trackDbToTxt also has to be rebuilt. It writes the curated hub trackDb.txt from the table, and a released one emits a member whose parent stanza is missing, which breaks the hub.
  • lines changed 12, context: html, text, full: html, text
    314d1a9a41231220ae79fc971758da141c21f233 Fri Oct 2 21:36:10 2026 -0700
    Revert the superTrack nesting fix on master; it lives on superTrackNesting. refs #38460 Taken off master with its only consumer, the TSS trackDb change reverted in the previous commit. It is a library change every CGI links, in trackDbCustom.c, hdb.c, hubConnect.c and hgTracks.c, and nothing on master needs it until the TSS tracks nest again. Kept on the superTrackNesting branch with its regression evidence. Note for whoever lands it: trackDbToTxt has to be rebuilt too, or the curated hub it writes names a parent stanza it did not emit.
  • lines changed 12, context: html, text, full: html, text
    93a3129444064c4d19b4cb49e24b6de4bd0e06a6 Fri Oct 2 21:41:15 2026 -0700
    Restore the superTrack nesting fix. refs #38460 Taking this off master was over-cautious. It is wanted on its own: #38460 is a real bug, a superTrack given a parent passes tdbQuery -check -strict and is then silently dropped at load, and the fix should get into a release rather than wait on a trackDb change that uses it. Nothing on master nests yet, and the fix is behaviour-identical where nothing does: trackDb built with it and with the released hgTrackDb is byte-identical on hg38, hs1 and mm39, and hgTracks renders the same rows and supertrack controls as dev. The TSS trackDb change that uses this stays reverted, on superTrackNesting, until this ships. Whoever releases it: trackDbToTxt has to be rebuilt too, or the curated hub it writes names a parent stanza it did not emit.
• src/hg/lib/hui.c
  • lines changed 84, context: html, text, full: html, text
    2521d696f5073ce8cee3f59f423f161fdb77d550 Fri Sep 25 02:48:37 2026 -0700
    VCF tracks: the bigBed trackDb filters (filter.*, filterByRange, filterLimits, filterValues, filterType, filterText, filterLabel) now work on INFO fields, plus ID and QUAL. The field list and types come from the VCF header; the bigBed filter code is reused, bigBed behavior unchanged, refs #37617
  • lines changed 84, context: html, text, full: html, text
    c9d17a52b6b5663c7175b01f801d23198b675f7e Fri Sep 25 12:03:55 2026 -0700
    Revert all bigBed-filters for VCF changes, as Chris did that earlier already. This reverts commit 2521d696f5073ce8cee3f59f423f161fdb77d550.
  • lines changed 26, context: html, text, full: html, text
    de6d2d4e5d0106a57d1ada79e9e36005676c260e Fri Sep 25 12:39:18 2026 -0700
    Add trackDb defined filters, coloring, and mouseovers for vcf tracks, using INFO fields or sub INFO fields, like vep.Consequence, refs #37617, #37618
  • lines changed 6, context: html, text, full: html, text
    bd6026f91fd94fe919fd1b815d27668759021196 Fri Sep 25 13:10:55 2026 -0700
    Fix vcf filter code after merging with master, refs #37617
• src/hg/lib/quickLift.c
  • lines changed 53, context: html, text, full: html, text
    896eb991fff50f44f18811a05171e36fa111163d Thu Sep 24 17:13:20 2026 -0700
    quickLift: leave empty blocks out of a protein alignment before lifting it, refs #38249 The UniProt bigPsl files store block sizes in bases, and pslFromBigPsl divides them by three, so a block shorter than a codon loads with size 0. pslTransMap rejects such an alignment and aborts, which replaced the whole lifted SwissProt track with a BUG message. About one alignment in eight has a block like this. quickLiftPsl now lifts a copy with the empty blocks removed. quickLiftTester has a new case in the shape of Q96ME1-2.
  • lines changed 49, context: html, text, full: html, text
    8de67388be9a67cb94ba95615b7643b4ddc385da Thu Sep 24 17:48:19 2026 -0700
    quickLift: give a lifted maf block the reference's own bases, refs #38249 Inside a chain block the two assemblies run in step but need not agree base for base, and the first row of a lifted block still carried the other assembly's letters. The details page showed hg19's base in the human row of a block lifted onto hg38. quickLiftMafs now reads the reference sequence once over the span of the lifted blocks and writes it into that row, leaving the gaps where they are. The lifted blocks are also sorted by position now. On a chain that turns the alignment over they came back last to first, and the details page listed them in that order.
  • lines changed 4, context: html, text, full: html, text
    565ac9d3328f0be9631e61787e82c4768e96a963 Sun Oct 4 10:46:30 2026 -0700
    quickLift: note that pslWithoutEmptyBlocks is dead code since #38300, refs #38249
• src/hg/lib/tests/cartPcrVarTester.c
  • lines changed 74, context: html, text, full: html, text
    da449b4fe2039f200a2f93d5209c48fe98c0a534 Tue Sep 29 10:58:30 2026 -0700
    cartPcrVarTester: which hgPcrResult_ cart variables survive a cart load, refs #38442 Feeds hgPcrResult_ variables through cartParseOverHash() and says which are kept. With the cart.c fix backed out it shows hgPcrResult_imgOrd dropped and nothing else changes. Registry row and catalog note added.
• src/hg/lib/tests/expected/cartPcrVarTest
  • lines changed 13, context: html, text, full: html, text
    da449b4fe2039f200a2f93d5209c48fe98c0a534 Tue Sep 29 10:58:30 2026 -0700
    cartPcrVarTester: which hgPcrResult_ cart variables survive a cart load, refs #38442 Feeds hgPcrResult_ variables through cartParseOverHash() and says which are kept. With the cart.c fix backed out it shows hgPcrResult_imgOrd dropped and nothing else changes. Registry row and catalog note added.
• src/hg/lib/tests/expected/mallocTopPadTest
  • lines changed 1, context: html, text, full: html, text
    384180e37487b4818cf7a98ca43479dda0bb282d Wed Sep 30 18:11:33 2026 -0700
    backupParseTest, mallocTopPadTest: the off run sets its gate off by name, refs #38185, #38225 Each off conf only included ~/.hg.conf. A developer whose conf chain reaches one that sets the gated variable got the gate on in both runs, and the test failed.
• src/hg/lib/tests/expected/pgSnpManyAllelesTest
  • lines changed 9, context: html, text, full: html, text
    99eb74885ff5bce42cadafee93274df7039dcab5 Sat Sep 26 17:34:11 2026 -0700
    unit tests for four v503 tickets, refs #38391, #37262, #38120, #38107, #38125, #38154 cgiDecodeTest prints what malformed and cut-short %hh escapes decode to, and checks that cgiDecode never reads past the length it is given. udcDotsTest prints the cache directory udc makes for remote URLs with "." and ".." in them, including the ones that must abort. pngWriteTest writes a memGfx image as a PNG, reads it back with libpng, compares every pixel, and checks the row filter of every row. pgSnpManyAllelesTester builds per-allele counts from a VCF record with 150 ALT alleles. Each test fails with its fix backed out, except that zlib-ng was not swapped out for #38125. The test registry gets a row for each ticket.
• src/hg/lib/tests/expected/quickLiftTest
  • lines changed 9, context: html, text, full: html, text
    896eb991fff50f44f18811a05171e36fa111163d Thu Sep 24 17:13:20 2026 -0700
    quickLift: leave empty blocks out of a protein alignment before lifting it, refs #38249 The UniProt bigPsl files store block sizes in bases, and pslFromBigPsl divides them by three, so a block shorter than a codon loads with size 0. pslTransMap rejects such an alignment and aborts, which replaced the whole lifted SwissProt track with a BUG message. About one alignment in eight has a block like this. quickLiftPsl now lifts a copy with the empty blocks removed. quickLiftTester has a new case in the shape of Q96ME1-2.
• src/hg/lib/tests/expected/trackHubSkipHubNameTest
  • lines changed 18, context: html, text, full: html, text
    284ccd608f06ac8c0222b56011aaf22bc7889d77 Sat Sep 26 12:12:04 2026 -0700
    hg/lib tests: VCF INFO filters and colors, and trackHubSkipHubName on names with no second underscore, refs #37617, #37618, #38414 vcfInfoFilterTester reads a five-line VCF and builds each filter and color map from a hand-made trackDb and cart: filter.*, filterText.* and filterValues.* on INFO fields and on vep sub-fields, colorByInfo with the first-declared value winning, and the warning for each setting the VCF header cannot support. trackHubSkipHubNameTester checks where the returned pointer lands before reading through it.
• src/hg/lib/tests/expected/vcfInfoFilterTest
  • lines changed 117, context: html, text, full: html, text
    284ccd608f06ac8c0222b56011aaf22bc7889d77 Sat Sep 26 12:12:04 2026 -0700
    hg/lib tests: VCF INFO filters and colors, and trackHubSkipHubName on names with no second underscore, refs #37617, #37618, #38414 vcfInfoFilterTester reads a five-line VCF and builds each filter and color map from a hand-made trackDb and cart: filter.*, filterText.* and filterValues.* on INFO fields and on vep sub-fields, colorByInfo with the first-declared value winning, and the warning for each setting the VCF header cannot support. trackHubSkipHubNameTester checks where the returned pointer lands before reading through it.
• src/hg/lib/tests/input/pgSnpManyAlleles/test.vcf
  • lines changed 8, context: html, text, full: html, text
    99eb74885ff5bce42cadafee93274df7039dcab5 Sat Sep 26 17:34:11 2026 -0700
    unit tests for four v503 tickets, refs #38391, #37262, #38120, #38107, #38125, #38154 cgiDecodeTest prints what malformed and cut-short %hh escapes decode to, and checks that cgiDecode never reads past the length it is given. udcDotsTest prints the cache directory udc makes for remote URLs with "." and ".." in them, including the ones that must abort. pngWriteTest writes a memGfx image as a PNG, reads it back with libpng, compares every pixel, and checks the row filter of every row. pgSnpManyAllelesTester builds per-allele counts from a VCF record with 150 ALT alleles. Each test fails with its fix backed out, except that zlib-ng was not swapped out for #38125. The test registry gets a row for each ticket.
• src/hg/lib/tests/input/vcfInfoFilter/test.vcf
  • lines changed 14, context: html, text, full: html, text
    284ccd608f06ac8c0222b56011aaf22bc7889d77 Sat Sep 26 12:12:04 2026 -0700
    hg/lib tests: VCF INFO filters and colors, and trackHubSkipHubName on names with no second underscore, refs #37617, #37618, #38414 vcfInfoFilterTester reads a five-line VCF and builds each filter and color map from a hand-made trackDb and cart: filter.*, filterText.* and filterValues.* on INFO fields and on vep sub-fields, colorByInfo with the first-declared value winning, and the warning for each setting the VCF header cannot support. trackHubSkipHubNameTester checks where the returned pointer lands before reading through it.
• src/hg/lib/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    a4caffa71aa9775117f5da25038d5ca5dadcd47a Mon Sep 21 14:29:12 2026 -0700
    tests: name trashDirTester once in the hg/lib/tests all: target 859bc749b05 added the line twice. make no-ops the second one, so nothing was broken, but the list should name it once. Found in code review. refs #38303, refs #37623, refs #38391
  • lines changed 4, context: html, text, full: html, text
    0855c081b7178591b4d1548ec822ce4ea329ec37 Mon Sep 21 14:29:21 2026 -0700
    tests: stop a comment dropping four testers out of hg/lib/tests all: The all: target listed annoGratorTester on a commented line in the middle of the list. The line above it ends in a backslash, so make joins the two lines and the "#" then comments out the rest of the joined line. The continuations carry that comment to the end, so binTest, customTrackTester, hgvsTester and sqlCheck were never built by "make all". True since b30a73b6c5f in 2021. make test still built all four, because customTrackTest:, hgvsTest: and binTest: each name their binary as a prerequisite. Only a bare "make all" in this directory skipped them. Moved the commented line below the list. All ten testers now build and make test still passes. refs #38391
  • lines changed 6, context: html, text, full: html, text
    1f5a5224a1eae411c945406c4e1adb2d5b18ebcb Tue Sep 22 10:46:35 2026 -0700
    genarkLiftOverTest: set genarkLiftOver in the test's own conf, refs #38328 genarkLiftOverDbs returns NULL before it looks at anything when genarkLiftOver is not set, so the test read as "0 back" on every line and went red on an hg.conf that does not have the option. The build account's conf does not have it. The test now writes its own conf and sets the option, the same way geoMirrorSelfTest sets browser.node.
  • lines changed 14, context: html, text, full: html, text
    284ccd608f06ac8c0222b56011aaf22bc7889d77 Sat Sep 26 12:12:04 2026 -0700
    hg/lib tests: VCF INFO filters and colors, and trackHubSkipHubName on names with no second underscore, refs #37617, #37618, #38414 vcfInfoFilterTester reads a five-line VCF and builds each filter and color map from a hand-made trackDb and cart: filter.*, filterText.* and filterValues.* on INFO fields and on vep sub-fields, colorByInfo with the first-declared value winning, and the warning for each setting the VCF header cannot support. trackHubSkipHubNameTester checks where the returned pointer lands before reading through it.
  • lines changed 8, context: html, text, full: html, text
    99eb74885ff5bce42cadafee93274df7039dcab5 Sat Sep 26 17:34:11 2026 -0700
    unit tests for four v503 tickets, refs #38391, #37262, #38120, #38107, #38125, #38154 cgiDecodeTest prints what malformed and cut-short %hh escapes decode to, and checks that cgiDecode never reads past the length it is given. udcDotsTest prints the cache directory udc makes for remote URLs with "." and ".." in them, including the ones that must abort. pngWriteTest writes a memGfx image as a PNG, reads it back with libpng, compares every pixel, and checks the row filter of every row. pgSnpManyAllelesTester builds per-allele counts from a VCF record with 150 ALT alleles. Each test fails with its fix backed out, except that zlib-ng was not swapped out for #38125. The test registry gets a row for each ticket.
  • lines changed 8, context: html, text, full: html, text
    da449b4fe2039f200a2f93d5209c48fe98c0a534 Tue Sep 29 10:58:30 2026 -0700
    cartPcrVarTester: which hgPcrResult_ cart variables survive a cart load, refs #38442 Feeds hgPcrResult_ variables through cartParseOverHash() and says which are kept. With the cart.c fix backed out it shows hgPcrResult_imgOrd dropped and nothing else changes. Registry row and catalog note added.
  • lines changed 2, context: html, text, full: html, text
    384180e37487b4818cf7a98ca43479dda0bb282d Wed Sep 30 18:11:33 2026 -0700
    backupParseTest, mallocTopPadTest: the off run sets its gate off by name, refs #38185, #38225 Each off conf only included ~/.hg.conf. A developer whose conf chain reaches one that sets the gated variable got the gate on in both runs, and the test failed.
• src/hg/lib/tests/pgSnpManyAllelesTester.c
  • lines changed 60, context: html, text, full: html, text
    99eb74885ff5bce42cadafee93274df7039dcab5 Sat Sep 26 17:34:11 2026 -0700
    unit tests for four v503 tickets, refs #38391, #37262, #38120, #38107, #38125, #38154 cgiDecodeTest prints what malformed and cut-short %hh escapes decode to, and checks that cgiDecode never reads past the length it is given. udcDotsTest prints the cache directory udc makes for remote URLs with "." and ".." in them, including the ones that must abort. pngWriteTest writes a memGfx image as a PNG, reads it back with libpng, compares every pixel, and checks the row filter of every row. pgSnpManyAllelesTester builds per-allele counts from a VCF record with 150 ALT alleles. Each test fails with its fix backed out, except that zlib-ng was not swapped out for #38125. The test registry gets a row for each ticket.
• src/hg/lib/tests/quickLiftTester.c
  • lines changed 25, context: html, text, full: html, text
    896eb991fff50f44f18811a05171e36fa111163d Thu Sep 24 17:13:20 2026 -0700
    quickLift: leave empty blocks out of a protein alignment before lifting it, refs #38249 The UniProt bigPsl files store block sizes in bases, and pslFromBigPsl divides them by three, so a block shorter than a codon loads with size 0. pslTransMap rejects such an alignment and aborts, which replaced the whole lifted SwissProt track with a BUG message. About one alignment in eight has a block like this. quickLiftPsl now lifts a copy with the empty blocks removed. quickLiftTester has a new case in the shape of Q96ME1-2.
• src/hg/lib/tests/trackHubSkipHubNameTester.c
  • lines changed 56, context: html, text, full: html, text
    284ccd608f06ac8c0222b56011aaf22bc7889d77 Sat Sep 26 12:12:04 2026 -0700
    hg/lib tests: VCF INFO filters and colors, and trackHubSkipHubName on names with no second underscore, refs #37617, #37618, #38414 vcfInfoFilterTester reads a five-line VCF and builds each filter and color map from a hand-made trackDb and cart: filter.*, filterText.* and filterValues.* on INFO fields and on vep sub-fields, colorByInfo with the first-declared value winning, and the warning for each setting the VCF header cannot support. trackHubSkipHubNameTester checks where the returned pointer lands before reading through it.
• src/hg/lib/tests/vcfInfoFilterTester.c
  • lines changed 219, context: html, text, full: html, text
    284ccd608f06ac8c0222b56011aaf22bc7889d77 Sat Sep 26 12:12:04 2026 -0700
    hg/lib tests: VCF INFO filters and colors, and trackHubSkipHubName on names with no second underscore, refs #37617, #37618, #38414 vcfInfoFilterTester reads a five-line VCF and builds each filter and color map from a hand-made trackDb and cart: filter.*, filterText.* and filterValues.* on INFO fields and on vep sub-fields, colorByInfo with the first-declared value winning, and the warning for each setting the VCF header cannot support. trackHubSkipHubNameTester checks where the returned pointer lands before reading through it.
• src/hg/lib/trackDbCustom.c
  • lines changed 33, context: html, text, full: html, text
    1a9c722ad341c178dc418034e51a1d015507db9b Fri Oct 2 20:23:47 2026 -0700
    Let superTracks nest inside superTracks. refs #38460 A superTrack given a parent used to pass tdbQuery -check -strict and then be dropped at load, with no warning: the browser reported the outer folder as not found. Seven places each looked exactly one level up the parent chain, which is what trackDb.h means by "Folders are superTracks. Currently only one level deep". trackDbSuperMarkup skipped any track that was itself a superTrack when resolving parent, so the link was never made rFindTrack looked "to the sky" one level, so the outer super could not be found by name addChildRefsToParents only walked tdbList, which excludes superTracks, so an inner super never reached its parent's children list findSuperTrack matched tdb->parent->track only, so hgTrackUi could not find the outer folder of a hub assembly flatten rescued the immediate super parent only, so the outer one was never written to the table polishSupers polished the immediate parent only, so the outer super reached the write with a NULL shortLabel and segfaulted groupTrackListAddSuper made a track for one super above a member setSuperTrackHasVisibleMembers marked one level visible Each now walks the chain. The group list still shows only the outermost folder, since superTrack members are not listed there; the inner folders appear on its page with their own controls, as members always have. Walking the chain makes a parent loop fatal where it used to be harmless, so trackDbSuperMarkup now checks that the supertracks form a tree once every link is set, and breaks a loop at the supertrack that closes it, naming that track. Verified by planting a loop: before, hgTrackDb spun in trackDbSetting and had to be killed; now it warns and loads. The same hazard in composite parents is untouched and filed as #38471. Regression: trackDb built with this and with the released hgTrackDb is byte-identical on mm39 (20377 rows) and, on a tree with no nesting, on hg38 (55629) and hs1 (782). With a nested trackDb the only difference on hg38 is the one rescued container row. hgTracks on hg38 renders the same 32 rows and the same 10 supertrack controls as dev, and the wgEncodeReg member list is unchanged. Note for whoever deploys this: trackDbToTxt also has to be rebuilt. It writes the curated hub trackDb.txt from the table, and a released one emits a member whose parent stanza is missing, which breaks the hub.
  • lines changed 33, context: html, text, full: html, text
    314d1a9a41231220ae79fc971758da141c21f233 Fri Oct 2 21:36:10 2026 -0700
    Revert the superTrack nesting fix on master; it lives on superTrackNesting. refs #38460 Taken off master with its only consumer, the TSS trackDb change reverted in the previous commit. It is a library change every CGI links, in trackDbCustom.c, hdb.c, hubConnect.c and hgTracks.c, and nothing on master needs it until the TSS tracks nest again. Kept on the superTrackNesting branch with its regression evidence. Note for whoever lands it: trackDbToTxt has to be rebuilt too, or the curated hub it writes names a parent stanza it did not emit.
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    93a3129444064c4d19b4cb49e24b6de4bd0e06a6 Fri Oct 2 21:41:15 2026 -0700
    Restore the superTrack nesting fix. refs #38460 Taking this off master was over-cautious. It is wanted on its own: #38460 is a real bug, a superTrack given a parent passes tdbQuery -check -strict and is then silently dropped at load, and the fix should get into a release rather than wait on a trackDb change that uses it. Nothing on master nests yet, and the fix is behaviour-identical where nothing does: trackDb built with it and with the released hgTrackDb is byte-identical on hg38, hs1 and mm39, and hgTracks renders the same rows and supertrack controls as dev. The TSS trackDb change that uses this stays reverted, on superTrackNesting, until this ships. Whoever releases it: trackDbToTxt has to be rebuilt too, or the curated hub it writes names a parent stanza it did not emit.
• src/hg/lib/trackHub.c
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    0325ff9542311af737bd2eadd9b105d863c79574 Tue Sep 22 10:58:54 2026 -0700
    Make trackHubSkipHubName not return invalid pointers on bad input names, refs #38414
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    05c7e605c01e595561c32690eb44a7512041e540 Wed Sep 23 09:34:08 2026 -0700
    hubCheck: reject a bigBed type line that declares fewer than three fields, refs #36940 hgc already stops on "type bigBed 1" or "type bigBed 2", but hubCheck passed both, so a hub author only found out when a user clicked an item. Check the declared count against the minimum of three next to the existing check against the file's field count. A bare "type bigBed" does not reach this code and is unchanged. Adds a fieldCountTooFew test with bigBed 1 and bigBed 2 tracks.
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    beb596d6144e0deb9ce96c5955c71e6d5f4eaec9 Sat Sep 26 13:01:02 2026 -0700
    trackHub: add an hg.conf switch for hub description page handling, refs #38126 hubHtmlSanitizeOn() in trackHub.c reads the hg.conf setting hubHtmlSanitize, default off, and the description page code in lib and cgilib asks it. With the setting off, that code behaves as it did in v503. hubCheck follows the same setting.
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    4a642d5f4c2a3102d5c2620af754d876146d7c24 Sat Sep 26 21:53:49 2026 -0700
    trackHub: restrict a hub genome's organism/description to a plain display-label character set
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    dba11b63364870388011d5f04c6563ed440eb2a1 Thu Sep 24 13:49:56 2026 -0700
    quickLift: a container set back to show no longer stays hidden on the target, refs #38198 When hgTracks arrives from a lift (hideTracks), it read a quickLifted superTrack's state from the cart. It copied the source's bare cart value, such as wgEncodeReg4, to hub_NNN_wgEncodeReg4 and then removed the bare one. That had two effects. A container hidden before one lift kept the stored hide after every later lift. This happened because hgTracks prunes a container value that equals its default, so a container set back to show left nothing to carry over. Visiting the target also deleted the source's own setting. The cart read was added for #37535, when the lifted stanza still ended with the source's "superTrack on hide". #37969 removed that line, so the stanza is now correct. On a lift the stanza decides again: any hub_ value for the container is dropped, and the source's value is left alone. Also write "visibility show" for the container rather than "visibility hide". walkTree passed "tvShow" to hTvFromString, which does not know that string and returns hide. With this change, a container hidden on the source keeps its earlier stanza on the target, the same as a hidden track.
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    8f1e82cfa7e46ca358c97ea135bf20cf0bbf6026 Sun Oct 4 10:49:13 2026 -0700
    hVarSubst/trackHub: encode a hub genome's organism/date text instead of rejecting it The earlier character-exclusion check could reject a hub whose organism or freeze/date label uses ordinary punctuation that has every right to be there. Replace it with a narrow %-encode of the two characters that mattered for where this text gets substituted, applied at render time; everything else passes through unchanged, refs #38399
• src/hg/lib/vcfUi.c
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    2521d696f5073ce8cee3f59f423f161fdb77d550 Fri Sep 25 02:48:37 2026 -0700
    VCF tracks: the bigBed trackDb filters (filter.*, filterByRange, filterLimits, filterValues, filterType, filterText, filterLabel) now work on INFO fields, plus ID and QUAL. The field list and types come from the VCF header; the bigBed filter code is reused, bigBed behavior unchanged, refs #37617
  • lines changed 67, context: html, text, full: html, text
    c9d17a52b6b5663c7175b01f801d23198b675f7e Fri Sep 25 12:03:55 2026 -0700
    Revert all bigBed-filters for VCF changes, as Chris did that earlier already. This reverts commit 2521d696f5073ce8cee3f59f423f161fdb77d550.
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    de6d2d4e5d0106a57d1ada79e9e36005676c260e Fri Sep 25 12:39:18 2026 -0700
    Add trackDb defined filters, coloring, and mouseovers for vcf tracks, using INFO fields or sub INFO fields, like vep.Consequence, refs #37617, #37618
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    da43847aab52991e91bfec700b16038710710038 Sat Sep 26 21:56:05 2026 -0700
    VCF tracks: new trackDb setting excludeFilterValues, a comma-separated list of FILTER values that are hidden by default; they show up pre-checked in the existing Exclude variants with these FILTER values list, refs #38424
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
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    b19feb943205afd4ef3915f13476613f2562f773 Sun Oct 4 14:35:46 2026 -0700
    continue VGP update refs #29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
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    59b419bcf74bc81e7de2f4227db3db79432e7898 Mon Sep 21 18:23:24 2026 -0700
    VGP update refs #29545
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    8046b546777ffbd1c1745e081bd419901b7d2efd Sun Sep 27 09:08:33 2026 -0700
    continuing VGP update refs #39545
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    dd43de4966296736e36a57a5921f3902e665d27a Sun Sep 27 22:43:02 2026 -0700
    VGP update refs #29545
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    b19feb943205afd4ef3915f13476613f2562f773 Sun Oct 4 14:35:46 2026 -0700
    continue VGP update refs #29545
• src/hg/makeDb/doc/ce11/gpnStar.txt
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    53ab3f1e293a91ddf71ec7568f4a6ff827bcd278 Fri Oct 2 13:52:36 2026 -0700
    Native GPN-Star track (Ye, Benegas et al., Nature 2026) on hg38, mm39, galGal6, dm6 and ce11, from the authors' Hugging Face hub. Each model is a multiWig sequence logo plus a four-allele -LLR composite using negateValues. The three hg38 models (V/M/P) sit in predictionScoresSuper via human/gpnStar.ra with /gbdb/$D bigDataUrls so -strict drops them on other human assemblies; the other four get a standalone gpnStar superTrack. The authors' bigWigs come from pyBigWig, whose bwAddIntervalSpanSteps writes the last section of each run 6 bases too long (pyBigWig #166) and makes bigWigAverageOverBed and bigWigCorrelate abort, so gpnStarRebuild.sh re-encodes them with wigToBigWig and gpnStarVerify.sh checks every per-base value is unchanged. Entropy scores and the GenArk-only Arabidopsis set are left out, and pennantIcon still has #TBD placeholders for the newsarch anchor and date. refs #38451
• src/hg/makeDb/doc/contrib/hprc2annot/hprc2annot.txt
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    32048e16a50722894cf28d9b7b4b050302e38c75 Wed Sep 30 17:54:58 2026 -0700
    Spell the acronym PCLAI, not pcLAI. refs #35415 The authors write it PCLAI throughout: the upstream README at AI-sandbox/hprc-pclai uses PCLAI 18 times and pcLAI never, under the title "Point Cloud Local Ancestry Inference (PCLAI)". We had pcLAI in 517 places, across the track labels, both description pages, the makedocs, the build scripts and the autoSql. hprcPclai.ra holds 467 of those, in shortLabel, longLabel, dataVersion and comments. It is generated, so the fix went into hprcPclaiMakeTrackDb.py and the file was rebuilt; every line of the resulting diff differs only by the rename. Track names, file names and the lowercase pclai in URLs and data file names are untouched. None of them contained the string pcLAI, and renaming the tracks would break saved sessions for no user-visible gain.
• src/hg/makeDb/doc/dm6/gpnStar.txt
  • lines changed 51, context: html, text, full: html, text
    53ab3f1e293a91ddf71ec7568f4a6ff827bcd278 Fri Oct 2 13:52:36 2026 -0700
    Native GPN-Star track (Ye, Benegas et al., Nature 2026) on hg38, mm39, galGal6, dm6 and ce11, from the authors' Hugging Face hub. Each model is a multiWig sequence logo plus a four-allele -LLR composite using negateValues. The three hg38 models (V/M/P) sit in predictionScoresSuper via human/gpnStar.ra with /gbdb/$D bigDataUrls so -strict drops them on other human assemblies; the other four get a standalone gpnStar superTrack. The authors' bigWigs come from pyBigWig, whose bwAddIntervalSpanSteps writes the last section of each run 6 bases too long (pyBigWig #166) and makes bigWigAverageOverBed and bigWigCorrelate abort, so gpnStarRebuild.sh re-encodes them with wigToBigWig and gpnStarVerify.sh checks every per-base value is unchanged. Entropy scores and the GenArk-only Arabidopsis set are left out, and pennantIcon still has #TBD placeholders for the newsarch anchor and date. refs #38451
• src/hg/makeDb/doc/enigma.txt
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    116aaf68aa340197a2a63856a90f533909e15f92 Fri Oct 2 14:25:53 2026 -0700
    BRCAmlaZanti.py: match ENIGMA PP4/BP5 variants by normalized genomic allele instead of HGVS name, so the 297 variants the source papers spell differently (c.4574_4575del vs Li's c.4574_4575delAA, Zanti's ins for a dup, del15) become one item with their LRs multiplied, as Finja Hennig asked. Every item is now drawn the way the ClinVar track draws it (deleted bases shifted left, 2 bp flank for ins/dup), names drop spelled-out bases, LRs are written with 5 significant figures, and the Zanti <CNV> row is dropped. Zanti rows are keyed from their own VCF columns because hgvsToVcf mis-converts intronic insertions (#38469), and the pre-Zanti input now comes from archive/v1.1 since /gbdb BRCAmfa.bb is this script's own output. The hgvsToVcf FILTER and del/dup count checks were added after a Claude review. refs #38467
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
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    a483ae438425d48eab80887eab161c20b97af775 Mon Sep 21 17:59:40 2026 -0700
    GCF_049306965.2 should also display its name GRCz12tu in the menus refs #38361
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    8046b546777ffbd1c1745e081bd419901b7d2efd Sun Sep 27 09:08:33 2026 -0700
    continuing VGP update refs #39545
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    dd43de4966296736e36a57a5921f3902e665d27a Sun Sep 27 22:43:02 2026 -0700
    VGP update refs #29545
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    b19feb943205afd4ef3915f13476613f2562f773 Sun Oct 4 14:35:46 2026 -0700
    continue VGP update refs #29545
• src/hg/makeDb/doc/galGal6/gpnStar.txt
  • lines changed 51, context: html, text, full: html, text
    53ab3f1e293a91ddf71ec7568f4a6ff827bcd278 Fri Oct 2 13:52:36 2026 -0700
    Native GPN-Star track (Ye, Benegas et al., Nature 2026) on hg38, mm39, galGal6, dm6 and ce11, from the authors' Hugging Face hub. Each model is a multiWig sequence logo plus a four-allele -LLR composite using negateValues. The three hg38 models (V/M/P) sit in predictionScoresSuper via human/gpnStar.ra with /gbdb/$D bigDataUrls so -strict drops them on other human assemblies; the other four get a standalone gpnStar superTrack. The authors' bigWigs come from pyBigWig, whose bwAddIntervalSpanSteps writes the last section of each run 6 bases too long (pyBigWig #166) and makes bigWigAverageOverBed and bigWigCorrelate abort, so gpnStarRebuild.sh re-encodes them with wigToBigWig and gpnStarVerify.sh checks every per-base value is unchanged. Entropy scores and the GenArk-only Arabidopsis set are left out, and pennantIcon still has #TBD placeholders for the newsarch anchor and date. refs #38451
• src/hg/makeDb/doc/hg19.txt
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    7e87cadb469b4e0eb4fb7f973154357cfe7fc345 Mon Sep 21 15:56:18 2026 -0700
    QA fixes for the mei (Mobile Insertions) track collection. refs #37524 Fix two data bugs found during QA and rebuild the affected bigBeds. meiEul1dbToBed.py looked up samples and individuals by name, but euL1db joins on 1-based row numbers, so neither join ever matched and the individual count, tissues, clinical conditions and populations were empty on all 8,991 insertions while the contributing-samples table printed row numbers. Both loaders now key on the row number, the table prints the sample name, and the adjacent population filter is case-insensitive so it actually drops "unknown". meiHgsvc3CsvToBed.py took alt[1:] on every record, which dropped the first base of the element on the 96 GRCh38 and 111 T2T-CHM13 records where PALMER2 is the only caller and ALT carries no anchor base; it now prefers INFO SEQ, which always matches SVLEN. Correct seven statements on the description pages against their sources: the HGSVC3 single-caller split was attributed to PALMER rather than L1ME-AID, its orthogonal concordance was 90.8% rather than 92.5%, euL1db was credited with aligning the L1HS consensus when the paper says it was processed from our RepeatMasker track, DeepMEI's network was described as a classifier rather than a genotyper and given the wrong training set, euL1db listed two detection methods absent from the data, and HMEID contradicted itself on the MELT ASSESS cutoff. Also: the SweGen bigDataUrl now points at _swegen.bb so the restricted callset is kept off the download server; the container page no longer claims the whole collection is long-read, lists the two euL1db subtracks, scopes its display conventions to the subtracks they describe, and cites all six papers; dead and wrong track links are repointed and pinned to a db; $db replaces hardcoded hg38 in paths on pages that serve three assemblies; the euL1db labels no longer carry hg38 counts and a lift note that made no sense on hg19; all six subtracks gain a dataVersion; the euL1db filter ranges match the data; and five autoSql field descriptions match what the files contain. Document the gbdb symlinks and the QA changes in doc/hg38/mei.txt, correct the HMEID bedToBigBed type there, and add an hg19.txt pointer since hg19 carries the two euL1db subtracks.
• src/hg/makeDb/doc/hg38/episignatures.txt
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    752cb1161a3dc006932fd3ba179c9b2fbe449c8d Fri Sep 25 14:27:43 2026 -0700
    Updating the episignatures makedoc for the semicolon filter labels and adding a recount command for the opposite-direction sites count, refs #38112
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    9e51fd38996566e7a6cc29dd67f2e05fa429ca3c Mon Sep 28 14:30:05 2026 -0700
    hg38 episignatures: hide epigenCentral bigBed from hgdownload Lou asked for downloads off for this track. tableBrowser off already covers Table Browser/Data Integrator/REST API, but the bigBed itself was still reachable on hgdownload. Prefix the gbdb filename with "_", same convention used for the restricted varFreqs subtracks, which hgdownload's rsync excludes. methaDory.bb is unaffected. refs #38112
• src/hg/makeDb/doc/hg38/fiberSeq.txt
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    10f0f6d5160a96867ecf534e1b9d138df7d9b796 Mon Sep 28 16:17:46 2026 -0700
    Fiber-seq: hide the container by default, and split the five GM lines out into a Rare disease sample class. Max asked for superTrack on rather than on show, since the track covers much the same ground as ENCODE DNase and does not earn a slot in everyone's default hg38 view. The five lymphoblastoid lines GM25455, GM25456, GM27730, GM28570 and GM28572 had been filed as Common Cell Line; Andrew Stergachis says they are rare disease cases consented to broad genomic data sharing and the first of a batch the lab intends to keep adding, so SAMPLE_CLASS_COLORS gains a third entry and the facet now reads 20 HPRC, 16 Common Cell Line, 5 Rare disease sample. refs #36210
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    0ba660768822e93ed43e9a717f580c525094caf8 Mon Sep 28 16:42:18 2026 -0700
    Fiber-seq: sentence case for the Common cell line sample class, which was Title Cased because that is how Mitchell wrote it in the mail that gave us the classification rule. The other two values were already right, and tadsEncode's organ facet is the precedent (Adrenal gland, Bone marrow). The swatch table on the description page had been saying "Common cell line" in its prose all along, so the filter label and the text explaining it now agree. fiberSeq.ra is untouched: the class only lives in the metadata TSV and the colors JSON, both read at runtime, so no trackDb reload is needed. Caught by Lou. refs #36210
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    ab234fe62907c81b702a63f5a73d40500a40916f Tue Sep 29 16:12:28 2026 -0700
    Fiber-seq: give the FIRE peak subtracks "visibility dense" instead of "onlyVisibility dense", so their mouseOver can actually be seen. onlyVisibility pins a faceted child rather than defaulting it: tdbVisLimitedByAncestors() in hg/lib/hui.c overwrites the computed visibility with the pinned mode, so a request for pack or full was discarded even from the URL, and the dropdown offered only hide and dense. Since no bigBed-like track draws per-item map boxes in dense, the mouseOver on all 41 peak stanzas was dead config and fiberSeqCompendium.html was promising a hover nobody could reach. Measured at ACTB with the map_data image map: pinned, a forced pack still computed to dense with 0 FIRE tooltips; defaulted, pack and full compute correctly and carry 8. Peaks still come up dense, which is what Andrew asked for in July. The signal types keep onlyVisibility, where pinning to full costs nothing because a bigWig draws the same at pack and full, and that is verified here too: acc, cpg and hap stay at full whatever is requested, and the container stays hidden on a fresh cart. Also fixes two makeDoc slips, the facet notes naming the script's dict keys rather than the column headings writeMetadata() emits, and the opening summary still saying accessibility and CpG "both became faceted composites" when they were merged into one 235 lines later. Caught by Claude review of 156d289 and 5179d7f. refs #38407
• src/hg/makeDb/doc/hg38/gpnStar.txt
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    53ab3f1e293a91ddf71ec7568f4a6ff827bcd278 Fri Oct 2 13:52:36 2026 -0700
    Native GPN-Star track (Ye, Benegas et al., Nature 2026) on hg38, mm39, galGal6, dm6 and ce11, from the authors' Hugging Face hub. Each model is a multiWig sequence logo plus a four-allele -LLR composite using negateValues. The three hg38 models (V/M/P) sit in predictionScoresSuper via human/gpnStar.ra with /gbdb/$D bigDataUrls so -strict drops them on other human assemblies; the other four get a standalone gpnStar superTrack. The authors' bigWigs come from pyBigWig, whose bwAddIntervalSpanSteps writes the last section of each run 6 bases too long (pyBigWig #166) and makes bigWigAverageOverBed and bigWigCorrelate abort, so gpnStarRebuild.sh re-encodes them with wigToBigWig and gpnStarVerify.sh checks every per-base value is unchanged. Entropy scores and the GenArk-only Arabidopsis set are left out, and pennantIcon still has #TBD placeholders for the newsarch anchor and date. refs #38451
• src/hg/makeDb/doc/hg38/hprcPclai.txt
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    32048e16a50722894cf28d9b7b4b050302e38c75 Wed Sep 30 17:54:58 2026 -0700
    Spell the acronym PCLAI, not pcLAI. refs #35415 The authors write it PCLAI throughout: the upstream README at AI-sandbox/hprc-pclai uses PCLAI 18 times and pcLAI never, under the title "Point Cloud Local Ancestry Inference (PCLAI)". We had pcLAI in 517 places, across the track labels, both description pages, the makedocs, the build scripts and the autoSql. hprcPclai.ra holds 467 of those, in shortLabel, longLabel, dataVersion and comments. It is generated, so the fix went into hprcPclaiMakeTrackDb.py and the file was rebuilt; every line of the resulting diff differs only by the rename. Track names, file names and the lowercase pclai in URLs and data file names are untouched. None of them contained the string pcLAI, and renaming the tracks would break saved sessions for no user-visible gain.
• src/hg/makeDb/doc/hg38/mavemd.txt
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    824df26b6320b692d629566c5a10b15004da82ce Tue Sep 29 16:09:00 2026 -0700
    addProteinSequence in mavemdLib translates each transcript's CDS from hg38.2bit so makeMaveMdVariants can check every projected codon against the reference residue its own HGVS term asserts; the existing comparison against MaveDB's genomic mapping only reaches the 3% of projected items that carry both terms, because 18 of the 40 protein accessions have no genomic-route variants at all. 39 of 40 accessions match at 0.000%; NP_689629.2 (FKRP) has 99 nonsense terms numbered one codon downstream of their own reference residue, which still reach mavemdVar through MaveDB's genomic mapping but are dropped from mavemdMap, which places columns from the protein term and has no fallback. The haplotype test now also reads hgvs_nt, since PTEN 00000054-a-1 states 1,236 haplotypes as c.[1207G>T;1209C>T] with no protein term and they were counted as rejected submissions, making both figures in the makeDoc wrong. assayLine runs the heatmap legend through asciiText because bedField turns the en dash in three MaveDB titles into &#8211; and the legend is drawn as raster text; clinGenId links to by_canonicalid rather than /allele, which serves JSON to a browser, matching human/civic.ra; the generated filter fragment no longer emits the blank line after each group that the makeDoc itself warns ends a stanza; and runBuild.sh tails the log on failure instead of dying silently under set -e. Also reworded the grey legend entry, which said no threshold was reached in either direction but covers 6,656 normal and 145 abnormal items, alphabetized the references, and fixed stale counts in the makeDoc. Caught by Claude review of 29af14b, fcf788d and 97c7de5. refs #38407 refs #37800
• src/hg/makeDb/doc/hg38/mei.txt
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    7e87cadb469b4e0eb4fb7f973154357cfe7fc345 Mon Sep 21 15:56:18 2026 -0700
    QA fixes for the mei (Mobile Insertions) track collection. refs #37524 Fix two data bugs found during QA and rebuild the affected bigBeds. meiEul1dbToBed.py looked up samples and individuals by name, but euL1db joins on 1-based row numbers, so neither join ever matched and the individual count, tissues, clinical conditions and populations were empty on all 8,991 insertions while the contributing-samples table printed row numbers. Both loaders now key on the row number, the table prints the sample name, and the adjacent population filter is case-insensitive so it actually drops "unknown". meiHgsvc3CsvToBed.py took alt[1:] on every record, which dropped the first base of the element on the 96 GRCh38 and 111 T2T-CHM13 records where PALMER2 is the only caller and ALT carries no anchor base; it now prefers INFO SEQ, which always matches SVLEN. Correct seven statements on the description pages against their sources: the HGSVC3 single-caller split was attributed to PALMER rather than L1ME-AID, its orthogonal concordance was 90.8% rather than 92.5%, euL1db was credited with aligning the L1HS consensus when the paper says it was processed from our RepeatMasker track, DeepMEI's network was described as a classifier rather than a genotyper and given the wrong training set, euL1db listed two detection methods absent from the data, and HMEID contradicted itself on the MELT ASSESS cutoff. Also: the SweGen bigDataUrl now points at _swegen.bb so the restricted callset is kept off the download server; the container page no longer claims the whole collection is long-read, lists the two euL1db subtracks, scopes its display conventions to the subtracks they describe, and cites all six papers; dead and wrong track links are repointed and pinned to a db; $db replaces hardcoded hg38 in paths on pages that serve three assemblies; the euL1db labels no longer carry hg38 counts and a lift note that made no sense on hg19; all six subtracks gain a dataVersion; the euL1db filter ranges match the data; and five autoSql field descriptions match what the files contain. Document the gbdb symlinks and the QA changes in doc/hg38/mei.txt, correct the HMEID bedToBigBed type there, and add an hg19.txt pointer since hg19 carries the two euL1db subtracks.
• src/hg/makeDb/doc/hg38/problematic.txt
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    b197e1670a076b65838fd91b869a4ec1c3096c0f Wed Sep 23 16:08:08 2026 -0700
    Add Panmask Difficult 151b, the inverse of Panmask Easy 151b, for the Problematic Regions RTS Panmask marks easy regions under a "Problematic Regions" container, which Anna flagged as confusing. Rather than change the released Panmask Easy track, add a second track with the complement regions, built with featureBits (excluding assembly gaps and restricted to the 24 chromosomes Panmask itself covers). Checked the source first: Zenodo record 16755940 is still v1.4, same version already in use, MD5 verified. New track is alpha only for QA to pick up. refs #38375
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    2ae817bcd648f2a3184bb4b118840e65749fea2d Thu Sep 24 04:15:20 2026 -0700
    problematic.txt/html: reconcile Panmask Easy/Difficult coverage to 87.8%/12.2%, one decimal place, refs #38375
• src/hg/makeDb/doc/hg38/tad.txt
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    b7b9978c92a2376d6d9ef4f0a4974cb8167295f8 Wed Sep 30 14:17:50 2026 -0700
    Updating the TAD tracks from the qa-track SKILL.md pass (hg19, hg38, mm10, mm39): shortLabel fixes for cut-off and duplicate ENCODE and 3DGB subtracks, lowercase biosamples in ENCODE longLabels, " bnd" dropped from Schmitt shortLabels, 3DGB subtracks set to pack with three mm10/mm39 defaults turned on, allButtonPair removed so the Schmitt matrix shows, and McArthur item labels hidden. Merged identical description pages into human/ and mouse/, plus description page cleanups (regenerated References, removed the "How to use these tracks" section, ENCODE pages now say 112 of 117 biosamples use Arrowhead). Also updated the ENCODE metadata columns and organ example in the hg38 makedoc. refs #21599
• src/hg/makeDb/doc/hg38/transcriptionStart.txt
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    acf20930c5cdfa1e352826a702ad8f36344178c4 Thu Sep 24 21:16:13 2026 -0700
    Fixes from an independent review of the TSS tracks. refs #35528 The Data Access sections told users to pass the composite name to the API, which returns HTTP 400. The API serves one bigWig at a time, so both pages now name a single strand of one cell line, verified to return 200. encode4ProCap.html claimed the kent tree held the manifest of which ENCODE files went into each track, and it did not. Commit that manifest as proCapNetEncodeFiles.tsv and name it on the page. It matters because proCapNetEncodeMeta resolves each experiment's default analysis at run time, so re-running it after an ENCODE reprocessing can pick different files. Cite Shah et al. for the ENCODE 4 nascent transcriptome survey the six PRO-cap experiments come from. Sagar Shah was credited by name with no reference. The hg38 makedoc called the 164268582 dropped bases "the N regions", but gap on the primary chromosomes is 150610728. The extra 13.7 Mb is sequence flanking each gap, dropped because most of its 2114 bp window was unresolved.
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    66fafe88184bb3a8a45a50026f4d6c7fbbc24109 Tue Sep 29 10:12:53 2026 -0700
    Rebuild the TSS tracks as traditional composites, for wiggle control. refs #35528 A faceted composite is routed to facetedCompositeUi(), which returns before cfgByCfgType(), so it never draws the wiggle controls: no data view scaling, no viewing range, no windowing function, no track height. Signal tracks need those, so proCapNet and encode4ProCap are now traditional composites. They stay separate composites under the TSS container. The multiWig strand overlays survive the change. The old comment here claimed a multiWig under a plain composite "is flattened away and never drawn"; that is wrong for drawing, which #36320 fixed. Only the hgTrackUi subtrack list flattens, because compositeUiSubtracks() walks to leaves, so the overlays get no inline config block and are configured from their own pages. Raised as #38441. The matrix has to be declared over the leaves, since that is the level hgTrackDb checks: declaring it on the containers fails -strict with "has groups not defined in parent". So a strand is a matrix cell, and the containers carry no subGroups. Sample class survives as a filterComposite dimension, replacing the facet. configurable on gives each subtrack its own config namespace. Drop the faceted machinery: the metadata table, the color file, the constants feeding them and the gbdbDir argument, 39 lines. The metadata.tsv and colors.json already written under /gbdb are now unreferenced and can be deleted. Put the ENCODE accession in each subtrack longLabel, and add a linked table of them to both description pages. A longLabel cannot carry a link, since printSubtrackTableBody() htmlEncodes it, hence the table. The label wording is shortened to keep the longest at 74 characters.
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    bdf448295c10bee74b6baa773f6733ce33171996 Thu Oct 1 20:56:37 2026 -0700
    Store the ProCapNet minus strand negated, and fix group autoscale. refs #35528 Two of the three problems Jairo found on the composite. The negate control did not work on ProCapNet. Its minus-strand files held positive values and were flipped at display time with trackDb negateValues. The composite's control sets one shared value, which replaced the per-track setting and sent both strands the same way, with no route back to the default short of a cart reset. encode4ProCap was fine because ENCODE publishes its minus strand negative already. So put the sign in the data: proCapNetPredToFixedStep gains --negate, proCapNetPredBuild passes it for the minus strand, and negateValues is gone from the stanzas. The twelve existing files were rewritten rather than rebuilt, since the downloads had been deleted; each was checked against its original for identical nBasesCovered, a mirrored value range and exactly negated values. The originals are kept in previousPred, about 197 GB, until QA is done. Group autoscale on the composite did nothing, which was my error: the multiWig containers and the contribution leaves each carried autoScale on, and the child setting wins. The wiggle settings now live only on the composite. The third, an empty row when both strands of a cell line are deselected, is #38441 and is not fixed here. Note in both makedocs and in the generator that this arrangement only partly works and is expected to become a superTrack of multiWig overlays: under a composite, hgTrackUi lists leaves rather than containers, so an overlay gets no inline config block and leaves an empty row when deselected.
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    1c32191759769c28cf763342f5e405420add0170 Thu Oct 1 21:20:54 2026 -0700
    Make the TSS tracks superTracks of multiWig overlays. refs #35528 The composite held the multiWig overlays as children, which drew correctly but left two faults, both from hgTrackUi listing descendant leaves rather than containers: an overlay got no configuration block of its own, and hiding both strands of a cell line left an empty row where the overlay had been. That is #38441. As superTrack members the overlays are tracks in their own right. Each gets a full configuration page, including overlay method and negate values, and hiding one hides the whole overlay. Verified: hiding proCapNet_K562_pred removes the row and leaves the other five. Two top-level superTracks, PRO-cap and ProCapNet, rather than one transcriptionStart folder holding both. superTracks do not nest. A superTrack given a parent passes tdbQuery -check -strict and is then dropped at load, since trackDbSuperMarkup refuses to set a parent on a superTrack and hgTrackDb only writes a superTrack that some track names as its parent. Filed as #38460, with the test case; transcriptionStart.html stays in the tree unused in case it is fixed. What this costs: the subtrack matrix and the sample class filter, which a superTrack does not offer. Each overlay now carries its own wiggle settings and its own html, neither being inherited from a container any more.
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    d0ddd717713f275dc2f567c9b6d733fd3f55bd90 Fri Oct 2 21:27:25 2026 -0700
    Put PRO-cap and ProCapNet inside a Transcription Initiation folder. refs #35528 The two data sources were top-level superTracks because a superTrack could not be a member of another one. #38460 fixes that, so they now sit inside a transcriptionStart superTrack, which is what the collection was meant to be. The container is written before either of its children, and both children before any of their members: tdbQuery -strict rejects a file in which another track comes between a superTrack and one of its children. This depends on the #38460 build. A plain make here with the installed binaries produces a half-built state, since hgTrackDb drops the container from the table and trackDbToTxt then writes an hs1 curated hub whose member names a parent stanza that is not there. Both makedocs say so.
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    e314363411293556f33418abe8923ad1e8bc496a Fri Oct 2 21:36:04 2026 -0700
    Revert the TSS nesting on master; it lives on superTrackNesting. refs #35528 Putting PRO-cap and ProCapNet inside a transcriptionStart superTrack needs the nesting fix in #38460, which is not released. These tracks were released in 3bee9e40921, so on beta and the RR hgTrackDb would drop the container and trackDbToTxt would write an hs1 curated hub whose members name a parent stanza that is not there. The work is on the superTrackNesting branch and can come back once #38460 ships.
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    1e8f4a189b1ad69e1cc4d60177b74ab1fd249da9 Fri Oct 2 22:22:36 2026 -0700
    Record that previousPred has been deleted. refs #35528 367 GB of un-negated minus-strand predictions, kept while the negated files went through QA. Deleting them loses nothing recoverable: negation is its own inverse, so an original comes back by running proCapNetPredToFixedStep --negate over the file now in pred/.
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    0c42aea56b751a2b4a58feb225a9659819a90994 Sat Oct 3 06:22:01 2026 -0700
    Nest the TSS tracks on alpha only, leaving the release as it is. refs #35528 PRO-cap and ProCapNet sit inside a transcriptionStart superTrack on alpha. That needs #38460, which is on master but not in a release, and these tracks are already released, so each source is written twice with complementary release tags: the nested copy alpha, the flat copy beta,public. hgTrackDb takes the copy whose release matches and rejects two whose releases overlap. Verified that beta and public are untouched: a public build from this file is byte-identical to a public build from the released flat tree, same md5 over tableName, shortLabel, type, visibility, priority and settings. tdbQuery -check -strict passes on all three releases, and an alpha build has the container with both members parented while beta and public have neither. Drop the release tags and the flat copies once #38460 ships. The makedocs also record that the alpha build needs hgTrackDb and trackDbToTxt in /cluster/bin/x86_64 to carry the #38460 fix. make alpha does not install there, BINDIR defaults to ~/bin/$MACHTYPE, so they were put in by hand and the weekly utils build will overwrite them.
• src/hg/makeDb/doc/hg38/varFreqs.txt
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    7aa59c8f6afbda4c2157d3990b2bbc48a39cac63 Fri Sep 25 02:48:31 2026 -0700
    varFreqs: add SFARI SPARK 45k WGS subtracks. sfariSparkWgs45k is built from the release's AF table (AN estimated, singletons dropped); sfariSparkWgs45kAsd is built from the genotype pVCFs with ASD/non-ASD counts, for now only the DSCAM locus while the genome-wide parasol run finishes, refs #38424
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    f03f56cd3c795a6fba2b8419662a9a2c5d49f69a Sat Sep 26 14:16:17 2026 -0700
    sfariSparkWgs45kAsd: now genome-wide (518M variants from the 45,178 genotype pVCFs, run on parasol); per-allele INFO fields declared Number=1 so the VCF track filters accept them, doc page no longer says DSCAM only, refs #38424
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    a5c699a7301156154700f51a20ae571bc6987051 Sat Sep 26 17:53:41 2026 -0700
    varFreqs: remove the AF-table-based sfariSparkWgs45k subtrack, superseded by the genotype-based sfariSparkWgs45kAsd; drop its scripts, the DSCAM demo script and their makeDoc sections, refs #38424
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    442e433a90b25deb87f10e6cf1b7b608bb0a6d67 Sat Sep 26 21:56:06 2026 -0700
    sfariSparkWgs45kAsd: flag 25M insertions of non-human (oral bacteria) sequence as FILTER NonHumanIns and hide them by default; add SFARI SPARK 45k WGS to the combined tracks without those insertions and relabel the 12k pilot as SFARI SPARK iWGS v1.1 Pilot, refs #38424
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    66c51e29423da24a7144c7ba99a4cc2ebc96b32c Mon Sep 28 13:54:36 2026 -0700
    varFreqs: combined tracks rebuilt with SFARI SPARK 45k WGS (without its NonHumanIns insertions); add its filter blocks, affected label now ~150,000 individuals, refs #38424
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    9cedfa38c14068c79dec89f76c606ee22b3f931a Wed Sep 30 15:02:37 2026 -0700
    phasedVars: new subtrack hgdp1kSnv, a 17GB version of the 3.5TB gnomAD HGDP+1000G genotype VCF with only SNVs with AC>5 and only GT, so haplotype clustering can be shown up to 5Mbp, refs #37306
• src/hg/makeDb/doc/hs1/t2t-supplied.txt
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    360607541994aa88b49fc241c34bd964a1db7b50 Tue Sep 29 15:07:07 2026 -0700
    Rebuild the hs1 sgdpCopyNumber track as a faceted composite, so its 319 samples are picked from a searchable metadata table rather than 319 checkboxes; the same bigBeds are pointed at by the same /gbdb paths, so no data changed. Subtracks are renamed from <region>_<population>_<libId>_wssd to sgdpCopyNumber_<libId> because a faceted composite requires the parent name plus the primaryKey value, and dataTypes is deliberately unset: with it hgTrackUi parses the data element only as far as the first underscore and would truncate LP6005441-DNA_A01 to LP6005441-DNA. The per-subtrack 'visibility dense' lines are gone because a faceted composite honors a child's own display mode where a classic composite ignores it, so keeping them would pin every sample to dense and remove the per-item click that the copy number is read from. Sample attributes come from the Reich lab SGDP tables and 317 of the 319 join; sgdpCopyNumberBuild.py takes its sample list from the checked-in sgdpCopyNumberSamples.tsv rather than from trackDb, because at release the generated stanzas replace sgdpCopyNumber.trackDb.ra and the legacy region prefix that the two unmatched samples depend on disappears with them. Alpha gets the new file and beta/public keep the old one until the metadata and color files are on the RR, without which the picker renders empty. sgdpCopyNumber_subset, which turns out to be the first 29 samples in plate order rather than any curated set, is not in the alpha version; whether it is retired for good is still open on the ticket. Faceted composite suggested by Gerardo, and the cross-sandbox metadata fetch that this track turned up was fixed by Max in b3a26a6aff3. refs #29344
• src/hg/makeDb/doc/hs1/transcriptionStart.txt
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    66fafe88184bb3a8a45a50026f4d6c7fbbc24109 Tue Sep 29 10:12:53 2026 -0700
    Rebuild the TSS tracks as traditional composites, for wiggle control. refs #35528 A faceted composite is routed to facetedCompositeUi(), which returns before cfgByCfgType(), so it never draws the wiggle controls: no data view scaling, no viewing range, no windowing function, no track height. Signal tracks need those, so proCapNet and encode4ProCap are now traditional composites. They stay separate composites under the TSS container. The multiWig strand overlays survive the change. The old comment here claimed a multiWig under a plain composite "is flattened away and never drawn"; that is wrong for drawing, which #36320 fixed. Only the hgTrackUi subtrack list flattens, because compositeUiSubtracks() walks to leaves, so the overlays get no inline config block and are configured from their own pages. Raised as #38441. The matrix has to be declared over the leaves, since that is the level hgTrackDb checks: declaring it on the containers fails -strict with "has groups not defined in parent". So a strand is a matrix cell, and the containers carry no subGroups. Sample class survives as a filterComposite dimension, replacing the facet. configurable on gives each subtrack its own config namespace. Drop the faceted machinery: the metadata table, the color file, the constants feeding them and the gbdbDir argument, 39 lines. The metadata.tsv and colors.json already written under /gbdb are now unreferenced and can be deleted. Put the ENCODE accession in each subtrack longLabel, and add a linked table of them to both description pages. A longLabel cannot carry a link, since printSubtrackTableBody() htmlEncodes it, hence the table. The label wording is shortened to keep the longest at 74 characters.
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    bdf448295c10bee74b6baa773f6733ce33171996 Thu Oct 1 20:56:37 2026 -0700
    Store the ProCapNet minus strand negated, and fix group autoscale. refs #35528 Two of the three problems Jairo found on the composite. The negate control did not work on ProCapNet. Its minus-strand files held positive values and were flipped at display time with trackDb negateValues. The composite's control sets one shared value, which replaced the per-track setting and sent both strands the same way, with no route back to the default short of a cart reset. encode4ProCap was fine because ENCODE publishes its minus strand negative already. So put the sign in the data: proCapNetPredToFixedStep gains --negate, proCapNetPredBuild passes it for the minus strand, and negateValues is gone from the stanzas. The twelve existing files were rewritten rather than rebuilt, since the downloads had been deleted; each was checked against its original for identical nBasesCovered, a mirrored value range and exactly negated values. The originals are kept in previousPred, about 197 GB, until QA is done. Group autoscale on the composite did nothing, which was my error: the multiWig containers and the contribution leaves each carried autoScale on, and the child setting wins. The wiggle settings now live only on the composite. The third, an empty row when both strands of a cell line are deselected, is #38441 and is not fixed here. Note in both makedocs and in the generator that this arrangement only partly works and is expected to become a superTrack of multiWig overlays: under a composite, hgTrackUi lists leaves rather than containers, so an overlay gets no inline config block and leaves an empty row when deselected.
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    1c32191759769c28cf763342f5e405420add0170 Thu Oct 1 21:20:54 2026 -0700
    Make the TSS tracks superTracks of multiWig overlays. refs #35528 The composite held the multiWig overlays as children, which drew correctly but left two faults, both from hgTrackUi listing descendant leaves rather than containers: an overlay got no configuration block of its own, and hiding both strands of a cell line left an empty row where the overlay had been. That is #38441. As superTrack members the overlays are tracks in their own right. Each gets a full configuration page, including overlay method and negate values, and hiding one hides the whole overlay. Verified: hiding proCapNet_K562_pred removes the row and leaves the other five. Two top-level superTracks, PRO-cap and ProCapNet, rather than one transcriptionStart folder holding both. superTracks do not nest. A superTrack given a parent passes tdbQuery -check -strict and is then dropped at load, since trackDbSuperMarkup refuses to set a parent on a superTrack and hgTrackDb only writes a superTrack that some track names as its parent. Filed as #38460, with the test case; transcriptionStart.html stays in the tree unused in case it is fixed. What this costs: the subtrack matrix and the sample class filter, which a superTrack does not offer. Each overlay now carries its own wiggle settings and its own html, neither being inherited from a container any more.
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    d0ddd717713f275dc2f567c9b6d733fd3f55bd90 Fri Oct 2 21:27:25 2026 -0700
    Put PRO-cap and ProCapNet inside a Transcription Initiation folder. refs #35528 The two data sources were top-level superTracks because a superTrack could not be a member of another one. #38460 fixes that, so they now sit inside a transcriptionStart superTrack, which is what the collection was meant to be. The container is written before either of its children, and both children before any of their members: tdbQuery -strict rejects a file in which another track comes between a superTrack and one of its children. This depends on the #38460 build. A plain make here with the installed binaries produces a half-built state, since hgTrackDb drops the container from the table and trackDbToTxt then writes an hs1 curated hub whose member names a parent stanza that is not there. Both makedocs say so.
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    e314363411293556f33418abe8923ad1e8bc496a Fri Oct 2 21:36:04 2026 -0700
    Revert the TSS nesting on master; it lives on superTrackNesting. refs #35528 Putting PRO-cap and ProCapNet inside a transcriptionStart superTrack needs the nesting fix in #38460, which is not released. These tracks were released in 3bee9e40921, so on beta and the RR hgTrackDb would drop the container and trackDbToTxt would write an hs1 curated hub whose members name a parent stanza that is not there. The work is on the superTrackNesting branch and can come back once #38460 ships.
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    1e8f4a189b1ad69e1cc4d60177b74ab1fd249da9 Fri Oct 2 22:22:36 2026 -0700
    Record that previousPred has been deleted. refs #35528 367 GB of un-negated minus-strand predictions, kept while the negated files went through QA. Deleting them loses nothing recoverable: negation is its own inverse, so an original comes back by running proCapNetPredToFixedStep --negate over the file now in pred/.
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    0c42aea56b751a2b4a58feb225a9659819a90994 Sat Oct 3 06:22:01 2026 -0700
    Nest the TSS tracks on alpha only, leaving the release as it is. refs #35528 PRO-cap and ProCapNet sit inside a transcriptionStart superTrack on alpha. That needs #38460, which is on master but not in a release, and these tracks are already released, so each source is written twice with complementary release tags: the nested copy alpha, the flat copy beta,public. hgTrackDb takes the copy whose release matches and rejects two whose releases overlap. Verified that beta and public are untouched: a public build from this file is byte-identical to a public build from the released flat tree, same md5 over tableName, shortLabel, type, visibility, priority and settings. tdbQuery -check -strict passes on all three releases, and an alpha build has the container with both members parented while beta and public have neither. Drop the release tags and the flat copies once #38460 ships. The makedocs also record that the alpha build needs hgTrackDb and trackDbToTxt in /cluster/bin/x86_64 to carry the #38460 fix. make alpha does not install there, BINDIR defaults to ~/bin/$MACHTYPE, so they were put in by hand and the weekly utils build will overwrite them.
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
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    59b419bcf74bc81e7de2f4227db3db79432e7898 Mon Sep 21 18:23:24 2026 -0700
    VGP update refs #29545
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    b19feb943205afd4ef3915f13476613f2562f773 Sun Oct 4 14:35:46 2026 -0700
    continue VGP update refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
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    8046b546777ffbd1c1745e081bd419901b7d2efd Sun Sep 27 09:08:33 2026 -0700
    continuing VGP update refs #39545
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    b19feb943205afd4ef3915f13476613f2562f773 Sun Oct 4 14:35:46 2026 -0700
    continue VGP update refs #29545
• src/hg/makeDb/doc/mm39/gpnStar.txt
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    53ab3f1e293a91ddf71ec7568f4a6ff827bcd278 Fri Oct 2 13:52:36 2026 -0700
    Native GPN-Star track (Ye, Benegas et al., Nature 2026) on hg38, mm39, galGal6, dm6 and ce11, from the authors' Hugging Face hub. Each model is a multiWig sequence logo plus a four-allele -LLR composite using negateValues. The three hg38 models (V/M/P) sit in predictionScoresSuper via human/gpnStar.ra with /gbdb/$D bigDataUrls so -strict drops them on other human assemblies; the other four get a standalone gpnStar superTrack. The authors' bigWigs come from pyBigWig, whose bwAddIntervalSpanSteps writes the last section of each run 6 bases too long (pyBigWig #166) and makes bigWigAverageOverBed and bigWigCorrelate abort, so gpnStarRebuild.sh re-encodes them with wigToBigWig and gpnStarVerify.sh checks every per-base value is unchanged. Entropy scores and the GenArk-only Arabidopsis set are left out, and pennantIcon still has #TBD placeholders for the newsarch anchor and date. refs #38451
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
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    8046b546777ffbd1c1745e081bd419901b7d2efd Sun Sep 27 09:08:33 2026 -0700
    continuing VGP update refs #39545
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
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    59b419bcf74bc81e7de2f4227db3db79432e7898 Mon Sep 21 18:23:24 2026 -0700
    VGP update refs #29545
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    e964722613c1b0f9ab40c3a6870ba6d8060f523f Sun Sep 27 09:25:53 2026 -0700
    VGP update refs #29545
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    b19feb943205afd4ef3915f13476613f2562f773 Sun Oct 4 14:35:46 2026 -0700
    continue VGP update refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv
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    5696aa327678ae46e826978431f0655af289062d Sun Sep 27 22:41:38 2026 -0700
    NCBI name changing refs #29545
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
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    1a9c722ad341c178dc418034e51a1d015507db9b Fri Oct 2 20:23:47 2026 -0700
    Let superTracks nest inside superTracks. refs #38460 A superTrack given a parent used to pass tdbQuery -check -strict and then be dropped at load, with no warning: the browser reported the outer folder as not found. Seven places each looked exactly one level up the parent chain, which is what trackDb.h means by "Folders are superTracks. Currently only one level deep". trackDbSuperMarkup skipped any track that was itself a superTrack when resolving parent, so the link was never made rFindTrack looked "to the sky" one level, so the outer super could not be found by name addChildRefsToParents only walked tdbList, which excludes superTracks, so an inner super never reached its parent's children list findSuperTrack matched tdb->parent->track only, so hgTrackUi could not find the outer folder of a hub assembly flatten rescued the immediate super parent only, so the outer one was never written to the table polishSupers polished the immediate parent only, so the outer super reached the write with a NULL shortLabel and segfaulted groupTrackListAddSuper made a track for one super above a member setSuperTrackHasVisibleMembers marked one level visible Each now walks the chain. The group list still shows only the outermost folder, since superTrack members are not listed there; the inner folders appear on its page with their own controls, as members always have. Walking the chain makes a parent loop fatal where it used to be harmless, so trackDbSuperMarkup now checks that the supertracks form a tree once every link is set, and breaks a loop at the supertrack that closes it, naming that track. Verified by planting a loop: before, hgTrackDb spun in trackDbSetting and had to be killed; now it warns and loads. The same hazard in composite parents is untouched and filed as #38471. Regression: trackDb built with this and with the released hgTrackDb is byte-identical on mm39 (20377 rows) and, on a tree with no nesting, on hg38 (55629) and hs1 (782). With a nested trackDb the only difference on hg38 is the one rescued container row. hgTracks on hg38 renders the same 32 rows and the same 10 supertrack controls as dev, and the wgEncodeReg member list is unchanged. Note for whoever deploys this: trackDbToTxt also has to be rebuilt. It writes the curated hub trackDb.txt from the table, and a released one emits a member whose parent stanza is missing, which breaks the hub.
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    314d1a9a41231220ae79fc971758da141c21f233 Fri Oct 2 21:36:10 2026 -0700
    Revert the superTrack nesting fix on master; it lives on superTrackNesting. refs #38460 Taken off master with its only consumer, the TSS trackDb change reverted in the previous commit. It is a library change every CGI links, in trackDbCustom.c, hdb.c, hubConnect.c and hgTracks.c, and nothing on master needs it until the TSS tracks nest again. Kept on the superTrackNesting branch with its regression evidence. Note for whoever lands it: trackDbToTxt has to be rebuilt too, or the curated hub it writes names a parent stanza it did not emit.
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    93a3129444064c4d19b4cb49e24b6de4bd0e06a6 Fri Oct 2 21:41:15 2026 -0700
    Restore the superTrack nesting fix. refs #38460 Taking this off master was over-cautious. It is wanted on its own: #38460 is a real bug, a superTrack given a parent passes tdbQuery -check -strict and is then silently dropped at load, and the fix should get into a release rather than wait on a trackDb change that uses it. Nothing on master nests yet, and the fix is behaviour-identical where nothing does: trackDb built with it and with the released hgTrackDb is byte-identical on hg38, hs1 and mm39, and hgTracks renders the same rows and supertrack controls as dev. The TSS trackDb change that uses this stays reverted, on superTrackNesting, until this ships. Whoever releases it: trackDbToTxt has to be rebuilt too, or the curated hub it writes names a parent stanza it did not emit.
• src/hg/makeDb/outside/proCapNet/proCapNetEncodeFiles.tsv
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    acf20930c5cdfa1e352826a702ad8f36344178c4 Thu Sep 24 21:16:13 2026 -0700
    Fixes from an independent review of the TSS tracks. refs #35528 The Data Access sections told users to pass the composite name to the API, which returns HTTP 400. The API serves one bigWig at a time, so both pages now name a single strand of one cell line, verified to return 200. encode4ProCap.html claimed the kent tree held the manifest of which ENCODE files went into each track, and it did not. Commit that manifest as proCapNetEncodeFiles.tsv and name it on the page. It matters because proCapNetEncodeMeta resolves each experiment's default analysis at run time, so re-running it after an ENCODE reprocessing can pick different files. Cite Shah et al. for the ENCODE 4 nascent transcriptome survey the six PRO-cap experiments come from. Sagar Shah was credited by name with no reference. The hg38 makedoc called the 164268582 dropped bases "the N regions", but gap on the primary chromosomes is 150610728. The extra 13.7 Mb is sequence flanking each gap, dropped because most of its 2114 bp window was unresolved.
• src/hg/makeDb/outside/proCapNet/proCapNetPredBuild
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    bdf448295c10bee74b6baa773f6733ce33171996 Thu Oct 1 20:56:37 2026 -0700
    Store the ProCapNet minus strand negated, and fix group autoscale. refs #35528 Two of the three problems Jairo found on the composite. The negate control did not work on ProCapNet. Its minus-strand files held positive values and were flipped at display time with trackDb negateValues. The composite's control sets one shared value, which replaced the per-track setting and sent both strands the same way, with no route back to the default short of a cart reset. encode4ProCap was fine because ENCODE publishes its minus strand negative already. So put the sign in the data: proCapNetPredToFixedStep gains --negate, proCapNetPredBuild passes it for the minus strand, and negateValues is gone from the stanzas. The twelve existing files were rewritten rather than rebuilt, since the downloads had been deleted; each was checked against its original for identical nBasesCovered, a mirrored value range and exactly negated values. The originals are kept in previousPred, about 197 GB, until QA is done. Group autoscale on the composite did nothing, which was my error: the multiWig containers and the contribution leaves each carried autoScale on, and the child setting wins. The wiggle settings now live only on the composite. The third, an empty row when both strands of a cell line are deselected, is #38441 and is not fixed here. Note in both makedocs and in the generator that this arrangement only partly works and is expected to become a superTrack of multiWig overlays: under a composite, hgTrackUi lists leaves rather than containers, so an overlay gets no inline config block and leaves an empty row when deselected.
• src/hg/makeDb/outside/proCapNet/proCapNetPredToFixedStep
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    bdf448295c10bee74b6baa773f6733ce33171996 Thu Oct 1 20:56:37 2026 -0700
    Store the ProCapNet minus strand negated, and fix group autoscale. refs #35528 Two of the three problems Jairo found on the composite. The negate control did not work on ProCapNet. Its minus-strand files held positive values and were flipped at display time with trackDb negateValues. The composite's control sets one shared value, which replaced the per-track setting and sent both strands the same way, with no route back to the default short of a cart reset. encode4ProCap was fine because ENCODE publishes its minus strand negative already. So put the sign in the data: proCapNetPredToFixedStep gains --negate, proCapNetPredBuild passes it for the minus strand, and negateValues is gone from the stanzas. The twelve existing files were rewritten rather than rebuilt, since the downloads had been deleted; each was checked against its original for identical nBasesCovered, a mirrored value range and exactly negated values. The originals are kept in previousPred, about 197 GB, until QA is done. Group autoscale on the composite did nothing, which was my error: the multiWig containers and the contribution leaves each carried autoScale on, and the child setting wins. The wiggle settings now live only on the composite. The third, an empty row when both strands of a cell line are deselected, is #38441 and is not fixed here. Note in both makedocs and in the generator that this arrangement only partly works and is expected to become a superTrack of multiWig overlays: under a composite, hgTrackUi lists leaves rather than containers, so an overlay gets no inline config block and leaves an empty row when deselected.
• src/hg/makeDb/outside/proCapNet/proCapNetTrackDb
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    5e83632c91c1c536880da1e364a41467856135bd Tue Sep 22 11:02:32 2026 -0700
    Rename the TSS container and trim the ProCapNet description. refs #35528 Both labels on the transcriptionStart container are now "Transcription Initiation (TSS)". Changed in proCapNetTrackDb and the two transcriptionStart.ra files regenerated from it, since they are generated and carry a do-not-edit header. Dropped the Processing at UCSC section from the ProCapNet page. How the files reached UCSC is not something a browser user needs; the makeDoc already records it, including the NaN bases dropped from the hg38 predictions. Replaced the Kundaje lab server link with the ENCODE portal. The six ENCODE records are BPNet-model annotations holding the trained model, contribution scores and predicted signal over a selected region set. The genome-wide predictions in this track are roughly fifty times larger than the ENCODE predicted-signal files and are not part of that release, so the page says so rather than naming ENCODE as their source. Claude-Session: https://claude.ai/code/session_01LAB6jWshLvB7eNXQKWVuW5
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    b8a77f50143d1cc2a474fe9a56fe7c362183a07f Fri Sep 25 17:35:01 2026 -0700
    Making the shortLabel sentence case. Updating the shortlabel for the subtracks to say 'Predicted' or 'Contributed', refs #35528
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    717ce54a6012dedd51b0100c643a7a252a16fabb Fri Sep 25 17:46:20 2026 -0700
    Adding windowingFuction maximum to trackDb and the script that generates the trackDb file. refs #35528
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    49de9e93e4417083feb23522a71e3960595828a3 Fri Sep 25 22:46:28 2026 -0700
    ProCapNet label and facet color fixes from QA. refs #35528 The composite longLabel named the sequence-contribution scores, which only exist on hg38, so it was wrong on hs1. Use "ProCapNet predicted PRO-cap" on both assemblies; the scores are described on the track description page. The Sample class swatches reused two colors from the cell-line palette, so a track's color could be read as its class: A673 is a cancer line and drew in #0072B2, which was the Non-cancer swatch. Sample class is a binary facet and does not need a hue, so use black and gray, outside the Okabe-Ito palette. Say in the description that the contribution scores cover about 1% of the genome, so the limit is visible before the display conventions section.
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    31e95f0d1dd4ca08feba9b081a356527bd4b45e6 Sat Sep 26 20:36:20 2026 -0700
    Drop the hand-built Files column from the TSS faceted tables. refs #35528 UCSC will generate the download links in the faceted table, so the Files column each composite built for itself is redundant. Remove downloadCell, the Files header and cell, the Files entry in subtrackUrls, and the DOWNLOAD constant that only fed them. The table is now Tissue, Sample class, Experiment, Cell line on all three composites. writeMetadata no longer needs db or track; the metadata files it writes are byte-identical. Lead each Data Access section with the link to the hgdownload directory, since that is now the way to a single file, and keep the naming convention beside it. Drop the paragraph describing the Files column.
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    66fafe88184bb3a8a45a50026f4d6c7fbbc24109 Tue Sep 29 10:12:53 2026 -0700
    Rebuild the TSS tracks as traditional composites, for wiggle control. refs #35528 A faceted composite is routed to facetedCompositeUi(), which returns before cfgByCfgType(), so it never draws the wiggle controls: no data view scaling, no viewing range, no windowing function, no track height. Signal tracks need those, so proCapNet and encode4ProCap are now traditional composites. They stay separate composites under the TSS container. The multiWig strand overlays survive the change. The old comment here claimed a multiWig under a plain composite "is flattened away and never drawn"; that is wrong for drawing, which #36320 fixed. Only the hgTrackUi subtrack list flattens, because compositeUiSubtracks() walks to leaves, so the overlays get no inline config block and are configured from their own pages. Raised as #38441. The matrix has to be declared over the leaves, since that is the level hgTrackDb checks: declaring it on the containers fails -strict with "has groups not defined in parent". So a strand is a matrix cell, and the containers carry no subGroups. Sample class survives as a filterComposite dimension, replacing the facet. configurable on gives each subtrack its own config namespace. Drop the faceted machinery: the metadata table, the color file, the constants feeding them and the gbdbDir argument, 39 lines. The metadata.tsv and colors.json already written under /gbdb are now unreferenced and can be deleted. Put the ENCODE accession in each subtrack longLabel, and add a linked table of them to both description pages. A longLabel cannot carry a link, since printSubtrackTableBody() htmlEncodes it, hence the table. The label wording is shortened to keep the longest at 74 characters.
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    bdf448295c10bee74b6baa773f6733ce33171996 Thu Oct 1 20:56:37 2026 -0700
    Store the ProCapNet minus strand negated, and fix group autoscale. refs #35528 Two of the three problems Jairo found on the composite. The negate control did not work on ProCapNet. Its minus-strand files held positive values and were flipped at display time with trackDb negateValues. The composite's control sets one shared value, which replaced the per-track setting and sent both strands the same way, with no route back to the default short of a cart reset. encode4ProCap was fine because ENCODE publishes its minus strand negative already. So put the sign in the data: proCapNetPredToFixedStep gains --negate, proCapNetPredBuild passes it for the minus strand, and negateValues is gone from the stanzas. The twelve existing files were rewritten rather than rebuilt, since the downloads had been deleted; each was checked against its original for identical nBasesCovered, a mirrored value range and exactly negated values. The originals are kept in previousPred, about 197 GB, until QA is done. Group autoscale on the composite did nothing, which was my error: the multiWig containers and the contribution leaves each carried autoScale on, and the child setting wins. The wiggle settings now live only on the composite. The third, an empty row when both strands of a cell line are deselected, is #38441 and is not fixed here. Note in both makedocs and in the generator that this arrangement only partly works and is expected to become a superTrack of multiWig overlays: under a composite, hgTrackUi lists leaves rather than containers, so an overlay gets no inline config block and leaves an empty row when deselected.
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    1c32191759769c28cf763342f5e405420add0170 Thu Oct 1 21:20:54 2026 -0700
    Make the TSS tracks superTracks of multiWig overlays. refs #35528 The composite held the multiWig overlays as children, which drew correctly but left two faults, both from hgTrackUi listing descendant leaves rather than containers: an overlay got no configuration block of its own, and hiding both strands of a cell line left an empty row where the overlay had been. That is #38441. As superTrack members the overlays are tracks in their own right. Each gets a full configuration page, including overlay method and negate values, and hiding one hides the whole overlay. Verified: hiding proCapNet_K562_pred removes the row and leaves the other five. Two top-level superTracks, PRO-cap and ProCapNet, rather than one transcriptionStart folder holding both. superTracks do not nest. A superTrack given a parent passes tdbQuery -check -strict and is then dropped at load, since trackDbSuperMarkup refuses to set a parent on a superTrack and hgTrackDb only writes a superTrack that some track names as its parent. Filed as #38460, with the test case; transcriptionStart.html stays in the tree unused in case it is fixed. What this costs: the subtrack matrix and the sample class filter, which a superTrack does not offer. Each overlay now carries its own wiggle settings and its own html, neither being inherited from a container any more.
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    0ca316803a93c570fc7614479afd322194f17217 Fri Oct 2 06:53:26 2026 -0700
    Drop priority from the two TSS superTrack stanzas. refs #35528 The folders take whatever position the group gives them. The member tracks keep their own priorities, which order each overlay within its folder.
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    d0ddd717713f275dc2f567c9b6d733fd3f55bd90 Fri Oct 2 21:27:25 2026 -0700
    Put PRO-cap and ProCapNet inside a Transcription Initiation folder. refs #35528 The two data sources were top-level superTracks because a superTrack could not be a member of another one. #38460 fixes that, so they now sit inside a transcriptionStart superTrack, which is what the collection was meant to be. The container is written before either of its children, and both children before any of their members: tdbQuery -strict rejects a file in which another track comes between a superTrack and one of its children. This depends on the #38460 build. A plain make here with the installed binaries produces a half-built state, since hgTrackDb drops the container from the table and trackDbToTxt then writes an hs1 curated hub whose member names a parent stanza that is not there. Both makedocs say so.
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    e314363411293556f33418abe8923ad1e8bc496a Fri Oct 2 21:36:04 2026 -0700
    Revert the TSS nesting on master; it lives on superTrackNesting. refs #35528 Putting PRO-cap and ProCapNet inside a transcriptionStart superTrack needs the nesting fix in #38460, which is not released. These tracks were released in 3bee9e40921, so on beta and the RR hgTrackDb would drop the container and trackDbToTxt would write an hs1 curated hub whose members name a parent stanza that is not there. The work is on the superTrackNesting branch and can come back once #38460 ships.
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    0c42aea56b751a2b4a58feb225a9659819a90994 Sat Oct 3 06:22:01 2026 -0700
    Nest the TSS tracks on alpha only, leaving the release as it is. refs #35528 PRO-cap and ProCapNet sit inside a transcriptionStart superTrack on alpha. That needs #38460, which is on master but not in a release, and these tracks are already released, so each source is written twice with complementary release tags: the nested copy alpha, the flat copy beta,public. hgTrackDb takes the copy whose release matches and rejects two whose releases overlap. Verified that beta and public are untouched: a public build from this file is byte-identical to a public build from the released flat tree, same md5 over tableName, shortLabel, type, visibility, priority and settings. tdbQuery -check -strict passes on all three releases, and an alpha build has the container with both members parented while beta and public have neither. Drop the release tags and the flat copies once #38460 ships. The makedocs also record that the alpha build needs hgTrackDb and trackDbToTxt in /cluster/bin/x86_64 to carry the #38460 fix. make alpha does not install there, BINDIR defaults to ~/bin/$MACHTYPE, so they were put in by hand and the weekly utils build will overwrite them.
• src/hg/makeDb/scripts/enigma/BRCAmlaZanti.py
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    116aaf68aa340197a2a63856a90f533909e15f92 Fri Oct 2 14:25:53 2026 -0700
    BRCAmlaZanti.py: match ENIGMA PP4/BP5 variants by normalized genomic allele instead of HGVS name, so the 297 variants the source papers spell differently (c.4574_4575del vs Li's c.4574_4575delAA, Zanti's ins for a dup, del15) become one item with their LRs multiplied, as Finja Hennig asked. Every item is now drawn the way the ClinVar track draws it (deleted bases shifted left, 2 bp flank for ins/dup), names drop spelled-out bases, LRs are written with 5 significant figures, and the Zanti <CNV> row is dropped. Zanti rows are keyed from their own VCF columns because hgvsToVcf mis-converts intronic insertions (#38469), and the pre-Zanti input now comes from archive/v1.1 since /gbdb BRCAmfa.bb is this script's own output. The hgvsToVcf FILTER and del/dup count checks were added after a Claude review. refs #38467
• src/hg/makeDb/scripts/episignatures/epigenCentralToBed.py
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    94ca641d99a7745058c8df8a3c38309898cb5973 Fri Sep 25 13:49:11 2026 -0700
    Updating the script that generates the ra file for EpiCentral so it uses semicolons instead removing the commas outright. refs #38112
• src/hg/makeDb/scripts/fiberSeq/fiberSeqSamples.tsv
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    10f0f6d5160a96867ecf534e1b9d138df7d9b796 Mon Sep 28 16:17:46 2026 -0700
    Fiber-seq: hide the container by default, and split the five GM lines out into a Rare disease sample class. Max asked for superTrack on rather than on show, since the track covers much the same ground as ENCODE DNase and does not earn a slot in everyone's default hg38 view. The five lymphoblastoid lines GM25455, GM25456, GM27730, GM28570 and GM28572 had been filed as Common Cell Line; Andrew Stergachis says they are rare disease cases consented to broad genomic data sharing and the first of a batch the lab intends to keep adding, so SAMPLE_CLASS_COLORS gains a third entry and the facet now reads 20 HPRC, 16 Common Cell Line, 5 Rare disease sample. refs #36210
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    0ba660768822e93ed43e9a717f580c525094caf8 Mon Sep 28 16:42:18 2026 -0700
    Fiber-seq: sentence case for the Common cell line sample class, which was Title Cased because that is how Mitchell wrote it in the mail that gave us the classification rule. The other two values were already right, and tadsEncode's organ facet is the precedent (Adrenal gland, Bone marrow). The swatch table on the description page had been saying "Common cell line" in its prose all along, so the filter label and the text explaining it now agree. fiberSeq.ra is untouched: the class only lives in the metadata TSV and the colors JSON, both read at runtime, so no trackDb reload is needed. Caught by Lou. refs #36210
• src/hg/makeDb/scripts/fiberSeq/fiberSeqTrackDb.py
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    10f0f6d5160a96867ecf534e1b9d138df7d9b796 Mon Sep 28 16:17:46 2026 -0700
    Fiber-seq: hide the container by default, and split the five GM lines out into a Rare disease sample class. Max asked for superTrack on rather than on show, since the track covers much the same ground as ENCODE DNase and does not earn a slot in everyone's default hg38 view. The five lymphoblastoid lines GM25455, GM25456, GM27730, GM28570 and GM28572 had been filed as Common Cell Line; Andrew Stergachis says they are rare disease cases consented to broad genomic data sharing and the first of a batch the lab intends to keep adding, so SAMPLE_CLASS_COLORS gains a third entry and the facet now reads 20 HPRC, 16 Common Cell Line, 5 Rare disease sample. refs #36210
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    e1d9e18ef2ac6813136d012f9817ddc50ca5bad9 Mon Sep 28 16:27:37 2026 -0700
    Fiber-seq: spell out the accessibility track's shortLabel as "Fiber-seq Accessible" rather than "Fiber-seq Acc". Twenty characters, which is exactly leftLabelWidthDefaultChars, so it fills the left label without clipping; checked in a render at ACTB. refs #36210
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    0ba660768822e93ed43e9a717f580c525094caf8 Mon Sep 28 16:42:18 2026 -0700
    Fiber-seq: sentence case for the Common cell line sample class, which was Title Cased because that is how Mitchell wrote it in the mail that gave us the classification rule. The other two values were already right, and tadsEncode's organ facet is the precedent (Adrenal gland, Bone marrow). The swatch table on the description page had been saying "Common cell line" in its prose all along, so the filter label and the text explaining it now agree. fiberSeq.ra is untouched: the class only lives in the metadata TSV and the colors JSON, both read at runtime, so no trackDb reload is needed. Caught by Lou. refs #36210
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    54f465e316441236c128491e53c0e5464c0e672c Tue Sep 29 11:40:49 2026 -0700
    Fiber-seq: bring the fiberSeqTrackDb.py docstrings back in line with the three-value sampleClass, and stop the Compendium intro from keeping a running tally of where the lymphoblastoid lines came from. readSamples still said the five GM lines were common cell lines and writeMetadata still said there were two classes, both a few lines from the SAMPLE_CLASS_COLORS entry that added the third. writeMetadata also still had "Common Cell Line" in the old Title Case, which yesterday's rename missed because the string is wrapped across two source lines and a line oriented sed cannot see it; worth remembering for the next rename. The intro sentence had grown a breakdown that did not add up, 20 HPRC plus 5 rare disease against 27 lymphoblastoid lines, leaving GM12878 and HG002 unaccounted; it now points at the Sample class filter instead of counting, since the lab has said more rare disease samples are coming and the tally would go stale again. While in there, the claim that accession order keeps each class together is softened to what the data actually does: the common cell lines fall in two runs either side of the HPRC block. Generated output is unchanged; the .ra, the metadata TSV and the colors JSON all regenerate byte identical. Caught by Claude review of 10f0f6d516. refs #36210
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    ab234fe62907c81b702a63f5a73d40500a40916f Tue Sep 29 16:12:28 2026 -0700
    Fiber-seq: give the FIRE peak subtracks "visibility dense" instead of "onlyVisibility dense", so their mouseOver can actually be seen. onlyVisibility pins a faceted child rather than defaulting it: tdbVisLimitedByAncestors() in hg/lib/hui.c overwrites the computed visibility with the pinned mode, so a request for pack or full was discarded even from the URL, and the dropdown offered only hide and dense. Since no bigBed-like track draws per-item map boxes in dense, the mouseOver on all 41 peak stanzas was dead config and fiberSeqCompendium.html was promising a hover nobody could reach. Measured at ACTB with the map_data image map: pinned, a forced pack still computed to dense with 0 FIRE tooltips; defaulted, pack and full compute correctly and carry 8. Peaks still come up dense, which is what Andrew asked for in July. The signal types keep onlyVisibility, where pinning to full costs nothing because a bigWig draws the same at pack and full, and that is verified here too: acc, cpg and hap stay at full whatever is requested, and the container stays hidden on a fresh cart. Also fixes two makeDoc slips, the facet notes naming the script's dict keys rather than the column headings writeMetadata() emits, and the opening summary still saying accessibility and CpG "both became faceted composites" when they were merged into one 235 lines later. Caught by Claude review of 156d289 and 5179d7f. refs #38407
• src/hg/makeDb/scripts/gnomadV4.1.1/downloadGnomadV4.1.1.sh
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    f20626542200362afacab9387842e1f5bb50c87c Fri Sep 25 12:43:42 2026 -0700
    Experimental gnomAD v4.1.1 VCF track for hg38, refs #37617
• src/hg/makeDb/scripts/gnomadV4.1.1/loadGnomadV4.1.1ChromTables.sh
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    f20626542200362afacab9387842e1f5bb50c87c Fri Sep 25 12:43:42 2026 -0700
    Experimental gnomAD v4.1.1 VCF track for hg38, refs #37617
• src/hg/makeDb/scripts/gpnStar/gpnStarCheckSections.py
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    53ab3f1e293a91ddf71ec7568f4a6ff827bcd278 Fri Oct 2 13:52:36 2026 -0700
    Native GPN-Star track (Ye, Benegas et al., Nature 2026) on hg38, mm39, galGal6, dm6 and ce11, from the authors' Hugging Face hub. Each model is a multiWig sequence logo plus a four-allele -LLR composite using negateValues. The three hg38 models (V/M/P) sit in predictionScoresSuper via human/gpnStar.ra with /gbdb/$D bigDataUrls so -strict drops them on other human assemblies; the other four get a standalone gpnStar superTrack. The authors' bigWigs come from pyBigWig, whose bwAddIntervalSpanSteps writes the last section of each run 6 bases too long (pyBigWig #166) and makes bigWigAverageOverBed and bigWigCorrelate abort, so gpnStarRebuild.sh re-encodes them with wigToBigWig and gpnStarVerify.sh checks every per-base value is unchanged. Entropy scores and the GenArk-only Arabidopsis set are left out, and pennantIcon still has #TBD placeholders for the newsarch anchor and date. refs #38451
• src/hg/makeDb/scripts/gpnStar/gpnStarCoordCheck.py
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    53ab3f1e293a91ddf71ec7568f4a6ff827bcd278 Fri Oct 2 13:52:36 2026 -0700
    Native GPN-Star track (Ye, Benegas et al., Nature 2026) on hg38, mm39, galGal6, dm6 and ce11, from the authors' Hugging Face hub. Each model is a multiWig sequence logo plus a four-allele -LLR composite using negateValues. The three hg38 models (V/M/P) sit in predictionScoresSuper via human/gpnStar.ra with /gbdb/$D bigDataUrls so -strict drops them on other human assemblies; the other four get a standalone gpnStar superTrack. The authors' bigWigs come from pyBigWig, whose bwAddIntervalSpanSteps writes the last section of each run 6 bases too long (pyBigWig #166) and makes bigWigAverageOverBed and bigWigCorrelate abort, so gpnStarRebuild.sh re-encodes them with wigToBigWig and gpnStarVerify.sh checks every per-base value is unchanged. Entropy scores and the GenArk-only Arabidopsis set are left out, and pennantIcon still has #TBD placeholders for the newsarch anchor and date. refs #38451
• src/hg/makeDb/scripts/gpnStar/gpnStarMirror.py
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    53ab3f1e293a91ddf71ec7568f4a6ff827bcd278 Fri Oct 2 13:52:36 2026 -0700
    Native GPN-Star track (Ye, Benegas et al., Nature 2026) on hg38, mm39, galGal6, dm6 and ce11, from the authors' Hugging Face hub. Each model is a multiWig sequence logo plus a four-allele -LLR composite using negateValues. The three hg38 models (V/M/P) sit in predictionScoresSuper via human/gpnStar.ra with /gbdb/$D bigDataUrls so -strict drops them on other human assemblies; the other four get a standalone gpnStar superTrack. The authors' bigWigs come from pyBigWig, whose bwAddIntervalSpanSteps writes the last section of each run 6 bases too long (pyBigWig #166) and makes bigWigAverageOverBed and bigWigCorrelate abort, so gpnStarRebuild.sh re-encodes them with wigToBigWig and gpnStarVerify.sh checks every per-base value is unchanged. Entropy scores and the GenArk-only Arabidopsis set are left out, and pennantIcon still has #TBD placeholders for the newsarch anchor and date. refs #38451
• src/hg/makeDb/scripts/gpnStar/gpnStarRebuild.sh
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    53ab3f1e293a91ddf71ec7568f4a6ff827bcd278 Fri Oct 2 13:52:36 2026 -0700
    Native GPN-Star track (Ye, Benegas et al., Nature 2026) on hg38, mm39, galGal6, dm6 and ce11, from the authors' Hugging Face hub. Each model is a multiWig sequence logo plus a four-allele -LLR composite using negateValues. The three hg38 models (V/M/P) sit in predictionScoresSuper via human/gpnStar.ra with /gbdb/$D bigDataUrls so -strict drops them on other human assemblies; the other four get a standalone gpnStar superTrack. The authors' bigWigs come from pyBigWig, whose bwAddIntervalSpanSteps writes the last section of each run 6 bases too long (pyBigWig #166) and makes bigWigAverageOverBed and bigWigCorrelate abort, so gpnStarRebuild.sh re-encodes them with wigToBigWig and gpnStarVerify.sh checks every per-base value is unchanged. Entropy scores and the GenArk-only Arabidopsis set are left out, and pennantIcon still has #TBD placeholders for the newsarch anchor and date. refs #38451
• src/hg/makeDb/scripts/gpnStar/gpnStarVerify.sh
  • lines changed 24, context: html, text, full: html, text
    53ab3f1e293a91ddf71ec7568f4a6ff827bcd278 Fri Oct 2 13:52:36 2026 -0700
    Native GPN-Star track (Ye, Benegas et al., Nature 2026) on hg38, mm39, galGal6, dm6 and ce11, from the authors' Hugging Face hub. Each model is a multiWig sequence logo plus a four-allele -LLR composite using negateValues. The three hg38 models (V/M/P) sit in predictionScoresSuper via human/gpnStar.ra with /gbdb/$D bigDataUrls so -strict drops them on other human assemblies; the other four get a standalone gpnStar superTrack. The authors' bigWigs come from pyBigWig, whose bwAddIntervalSpanSteps writes the last section of each run 6 bases too long (pyBigWig #166) and makes bigWigAverageOverBed and bigWigCorrelate abort, so gpnStarRebuild.sh re-encodes them with wigToBigWig and gpnStarVerify.sh checks every per-base value is unchanged. Entropy scores and the GenArk-only Arabidopsis set are left out, and pennantIcon still has #TBD placeholders for the newsarch anchor and date. refs #38451
• src/hg/makeDb/scripts/hprc2annot/hprc2annotBuild.sh
  • lines changed 1, context: html, text, full: html, text
    32048e16a50722894cf28d9b7b4b050302e38c75 Wed Sep 30 17:54:58 2026 -0700
    Spell the acronym PCLAI, not pcLAI. refs #35415 The authors write it PCLAI throughout: the upstream README at AI-sandbox/hprc-pclai uses PCLAI 18 times and pcLAI never, under the title "Point Cloud Local Ancestry Inference (PCLAI)". We had pcLAI in 517 places, across the track labels, both description pages, the makedocs, the build scripts and the autoSql. hprcPclai.ra holds 467 of those, in shortLabel, longLabel, dataVersion and comments. It is generated, so the fix went into hprcPclaiMakeTrackDb.py and the file was rebuilt; every line of the resulting diff differs only by the rename. Track names, file names and the lowercase pclai in URLs and data file names are untouched. None of them contained the string pcLAI, and renaming the tracks would break saved sessions for no user-visible gain.
• src/hg/makeDb/scripts/hprc2annot/hprc2annotMakePclaiRefPanel.py
  • lines changed 3, context: html, text, full: html, text
    32048e16a50722894cf28d9b7b4b050302e38c75 Wed Sep 30 17:54:58 2026 -0700
    Spell the acronym PCLAI, not pcLAI. refs #35415 The authors write it PCLAI throughout: the upstream README at AI-sandbox/hprc-pclai uses PCLAI 18 times and pcLAI never, under the title "Point Cloud Local Ancestry Inference (PCLAI)". We had pcLAI in 517 places, across the track labels, both description pages, the makedocs, the build scripts and the autoSql. hprcPclai.ra holds 467 of those, in shortLabel, longLabel, dataVersion and comments. It is generated, so the fix went into hprcPclaiMakeTrackDb.py and the file was rebuilt; every line of the resulting diff differs only by the rename. Track names, file names and the lowercase pclai in URLs and data file names are untouched. None of them contained the string pcLAI, and renaming the tracks would break saved sessions for no user-visible gain.
• src/hg/makeDb/scripts/hprc2annot/pclai.as
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    32048e16a50722894cf28d9b7b4b050302e38c75 Wed Sep 30 17:54:58 2026 -0700
    Spell the acronym PCLAI, not pcLAI. refs #35415 The authors write it PCLAI throughout: the upstream README at AI-sandbox/hprc-pclai uses PCLAI 18 times and pcLAI never, under the title "Point Cloud Local Ancestry Inference (PCLAI)". We had pcLAI in 517 places, across the track labels, both description pages, the makedocs, the build scripts and the autoSql. hprcPclai.ra holds 467 of those, in shortLabel, longLabel, dataVersion and comments. It is generated, so the fix went into hprcPclaiMakeTrackDb.py and the file was rebuilt; every line of the resulting diff differs only by the rename. Track names, file names and the lowercase pclai in URLs and data file names are untouched. None of them contained the string pcLAI, and renaming the tracks would break saved sessions for no user-visible gain.
• src/hg/makeDb/scripts/hprcPclai/hprcPclai.as
  • lines changed 2, context: html, text, full: html, text
    32048e16a50722894cf28d9b7b4b050302e38c75 Wed Sep 30 17:54:58 2026 -0700
    Spell the acronym PCLAI, not pcLAI. refs #35415 The authors write it PCLAI throughout: the upstream README at AI-sandbox/hprc-pclai uses PCLAI 18 times and pcLAI never, under the title "Point Cloud Local Ancestry Inference (PCLAI)". We had pcLAI in 517 places, across the track labels, both description pages, the makedocs, the build scripts and the autoSql. hprcPclai.ra holds 467 of those, in shortLabel, longLabel, dataVersion and comments. It is generated, so the fix went into hprcPclaiMakeTrackDb.py and the file was rebuilt; every line of the resulting diff differs only by the rename. Track names, file names and the lowercase pclai in URLs and data file names are untouched. None of them contained the string pcLAI, and renaming the tracks would break saved sessions for no user-visible gain.
• src/hg/makeDb/scripts/hprcPclai/hprcPclaiDownload.sh
  • lines changed 1, context: html, text, full: html, text
    32048e16a50722894cf28d9b7b4b050302e38c75 Wed Sep 30 17:54:58 2026 -0700
    Spell the acronym PCLAI, not pcLAI. refs #35415 The authors write it PCLAI throughout: the upstream README at AI-sandbox/hprc-pclai uses PCLAI 18 times and pcLAI never, under the title "Point Cloud Local Ancestry Inference (PCLAI)". We had pcLAI in 517 places, across the track labels, both description pages, the makedocs, the build scripts and the autoSql. hprcPclai.ra holds 467 of those, in shortLabel, longLabel, dataVersion and comments. It is generated, so the fix went into hprcPclaiMakeTrackDb.py and the file was rebuilt; every line of the resulting diff differs only by the rename. Track names, file names and the lowercase pclai in URLs and data file names are untouched. None of them contained the string pcLAI, and renaming the tracks would break saved sessions for no user-visible gain.
• src/hg/makeDb/scripts/hprcPclai/hprcPclaiMakeBb.sh
  • lines changed 1, context: html, text, full: html, text
    32048e16a50722894cf28d9b7b4b050302e38c75 Wed Sep 30 17:54:58 2026 -0700
    Spell the acronym PCLAI, not pcLAI. refs #35415 The authors write it PCLAI throughout: the upstream README at AI-sandbox/hprc-pclai uses PCLAI 18 times and pcLAI never, under the title "Point Cloud Local Ancestry Inference (PCLAI)". We had pcLAI in 517 places, across the track labels, both description pages, the makedocs, the build scripts and the autoSql. hprcPclai.ra holds 467 of those, in shortLabel, longLabel, dataVersion and comments. It is generated, so the fix went into hprcPclaiMakeTrackDb.py and the file was rebuilt; every line of the resulting diff differs only by the rename. Track names, file names and the lowercase pclai in URLs and data file names are untouched. None of them contained the string pcLAI, and renaming the tracks would break saved sessions for no user-visible gain.
• src/hg/makeDb/scripts/hprcPclai/hprcPclaiMakeTrackDb.py
  • lines changed 7, context: html, text, full: html, text
    32048e16a50722894cf28d9b7b4b050302e38c75 Wed Sep 30 17:54:58 2026 -0700
    Spell the acronym PCLAI, not pcLAI. refs #35415 The authors write it PCLAI throughout: the upstream README at AI-sandbox/hprc-pclai uses PCLAI 18 times and pcLAI never, under the title "Point Cloud Local Ancestry Inference (PCLAI)". We had pcLAI in 517 places, across the track labels, both description pages, the makedocs, the build scripts and the autoSql. hprcPclai.ra holds 467 of those, in shortLabel, longLabel, dataVersion and comments. It is generated, so the fix went into hprcPclaiMakeTrackDb.py and the file was rebuilt; every line of the resulting diff differs only by the rename. Track names, file names and the lowercase pclai in URLs and data file names are untouched. None of them contained the string pcLAI, and renaming the tracks would break saved sessions for no user-visible gain.
• src/hg/makeDb/scripts/mavemd/makeMaveMdHeatmap.py
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    824df26b6320b692d629566c5a10b15004da82ce Tue Sep 29 16:09:00 2026 -0700
    addProteinSequence in mavemdLib translates each transcript's CDS from hg38.2bit so makeMaveMdVariants can check every projected codon against the reference residue its own HGVS term asserts; the existing comparison against MaveDB's genomic mapping only reaches the 3% of projected items that carry both terms, because 18 of the 40 protein accessions have no genomic-route variants at all. 39 of 40 accessions match at 0.000%; NP_689629.2 (FKRP) has 99 nonsense terms numbered one codon downstream of their own reference residue, which still reach mavemdVar through MaveDB's genomic mapping but are dropped from mavemdMap, which places columns from the protein term and has no fallback. The haplotype test now also reads hgvs_nt, since PTEN 00000054-a-1 states 1,236 haplotypes as c.[1207G>T;1209C>T] with no protein term and they were counted as rejected submissions, making both figures in the makeDoc wrong. assayLine runs the heatmap legend through asciiText because bedField turns the en dash in three MaveDB titles into &#8211; and the legend is drawn as raster text; clinGenId links to by_canonicalid rather than /allele, which serves JSON to a browser, matching human/civic.ra; the generated filter fragment no longer emits the blank line after each group that the makeDoc itself warns ends a stanza; and runBuild.sh tails the log on failure instead of dying silently under set -e. Also reworded the grey legend entry, which said no threshold was reached in either direction but covers 6,656 normal and 145 abnormal items, alphabetized the references, and fixed stale counts in the makeDoc. Caught by Claude review of 29af14b, fcf788d and 97c7de5. refs #38407 refs #37800
• src/hg/makeDb/scripts/mavemd/makeMaveMdVariants.py
  • lines changed 69, context: html, text, full: html, text
    824df26b6320b692d629566c5a10b15004da82ce Tue Sep 29 16:09:00 2026 -0700
    addProteinSequence in mavemdLib translates each transcript's CDS from hg38.2bit so makeMaveMdVariants can check every projected codon against the reference residue its own HGVS term asserts; the existing comparison against MaveDB's genomic mapping only reaches the 3% of projected items that carry both terms, because 18 of the 40 protein accessions have no genomic-route variants at all. 39 of 40 accessions match at 0.000%; NP_689629.2 (FKRP) has 99 nonsense terms numbered one codon downstream of their own reference residue, which still reach mavemdVar through MaveDB's genomic mapping but are dropped from mavemdMap, which places columns from the protein term and has no fallback. The haplotype test now also reads hgvs_nt, since PTEN 00000054-a-1 states 1,236 haplotypes as c.[1207G>T;1209C>T] with no protein term and they were counted as rejected submissions, making both figures in the makeDoc wrong. assayLine runs the heatmap legend through asciiText because bedField turns the en dash in three MaveDB titles into &#8211; and the legend is drawn as raster text; clinGenId links to by_canonicalid rather than /allele, which serves JSON to a browser, matching human/civic.ra; the generated filter fragment no longer emits the blank line after each group that the makeDoc itself warns ends a stanza; and runBuild.sh tails the log on failure instead of dying silently under set -e. Also reworded the grey legend entry, which said no threshold was reached in either direction but covers 6,656 normal and 145 abnormal items, alphabetized the references, and fixed stale counts in the makeDoc. Caught by Claude review of 29af14b, fcf788d and 97c7de5. refs #38407 refs #37800
• src/hg/makeDb/scripts/mavemd/mavemdLib.py
  • lines changed 113, context: html, text, full: html, text
    824df26b6320b692d629566c5a10b15004da82ce Tue Sep 29 16:09:00 2026 -0700
    addProteinSequence in mavemdLib translates each transcript's CDS from hg38.2bit so makeMaveMdVariants can check every projected codon against the reference residue its own HGVS term asserts; the existing comparison against MaveDB's genomic mapping only reaches the 3% of projected items that carry both terms, because 18 of the 40 protein accessions have no genomic-route variants at all. 39 of 40 accessions match at 0.000%; NP_689629.2 (FKRP) has 99 nonsense terms numbered one codon downstream of their own reference residue, which still reach mavemdVar through MaveDB's genomic mapping but are dropped from mavemdMap, which places columns from the protein term and has no fallback. The haplotype test now also reads hgvs_nt, since PTEN 00000054-a-1 states 1,236 haplotypes as c.[1207G>T;1209C>T] with no protein term and they were counted as rejected submissions, making both figures in the makeDoc wrong. assayLine runs the heatmap legend through asciiText because bedField turns the en dash in three MaveDB titles into &#8211; and the legend is drawn as raster text; clinGenId links to by_canonicalid rather than /allele, which serves JSON to a browser, matching human/civic.ra; the generated filter fragment no longer emits the blank line after each group that the makeDoc itself warns ends a stanza; and runBuild.sh tails the log on failure instead of dying silently under set -e. Also reworded the grey legend entry, which said no threshold was reached in either direction but covers 6,656 normal and 145 abnormal items, alphabetized the references, and fixed stale counts in the makeDoc. Caught by Claude review of 29af14b, fcf788d and 97c7de5. refs #38407 refs #37800
• src/hg/makeDb/scripts/mavemd/runBuild.sh
  • lines changed 6, context: html, text, full: html, text
    824df26b6320b692d629566c5a10b15004da82ce Tue Sep 29 16:09:00 2026 -0700
    addProteinSequence in mavemdLib translates each transcript's CDS from hg38.2bit so makeMaveMdVariants can check every projected codon against the reference residue its own HGVS term asserts; the existing comparison against MaveDB's genomic mapping only reaches the 3% of projected items that carry both terms, because 18 of the 40 protein accessions have no genomic-route variants at all. 39 of 40 accessions match at 0.000%; NP_689629.2 (FKRP) has 99 nonsense terms numbered one codon downstream of their own reference residue, which still reach mavemdVar through MaveDB's genomic mapping but are dropped from mavemdMap, which places columns from the protein term and has no fallback. The haplotype test now also reads hgvs_nt, since PTEN 00000054-a-1 states 1,236 haplotypes as c.[1207G>T;1209C>T] with no protein term and they were counted as rejected submissions, making both figures in the makeDoc wrong. assayLine runs the heatmap legend through asciiText because bedField turns the en dash in three MaveDB titles into &#8211; and the legend is drawn as raster text; clinGenId links to by_canonicalid rather than /allele, which serves JSON to a browser, matching human/civic.ra; the generated filter fragment no longer emits the blank line after each group that the makeDoc itself warns ends a stanza; and runBuild.sh tails the log on failure instead of dying silently under set -e. Also reworded the grey legend entry, which said no threshold was reached in either direction but covers 6,656 normal and 145 abnormal items, alphabetized the references, and fixed stale counts in the makeDoc. Caught by Claude review of 29af14b, fcf788d and 97c7de5. refs #38407 refs #37800
• src/hg/makeDb/scripts/mei/meiDeepmei1kg.as
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    7e87cadb469b4e0eb4fb7f973154357cfe7fc345 Mon Sep 21 15:56:18 2026 -0700
    QA fixes for the mei (Mobile Insertions) track collection. refs #37524 Fix two data bugs found during QA and rebuild the affected bigBeds. meiEul1dbToBed.py looked up samples and individuals by name, but euL1db joins on 1-based row numbers, so neither join ever matched and the individual count, tissues, clinical conditions and populations were empty on all 8,991 insertions while the contributing-samples table printed row numbers. Both loaders now key on the row number, the table prints the sample name, and the adjacent population filter is case-insensitive so it actually drops "unknown". meiHgsvc3CsvToBed.py took alt[1:] on every record, which dropped the first base of the element on the 96 GRCh38 and 111 T2T-CHM13 records where PALMER2 is the only caller and ALT carries no anchor base; it now prefers INFO SEQ, which always matches SVLEN. Correct seven statements on the description pages against their sources: the HGSVC3 single-caller split was attributed to PALMER rather than L1ME-AID, its orthogonal concordance was 90.8% rather than 92.5%, euL1db was credited with aligning the L1HS consensus when the paper says it was processed from our RepeatMasker track, DeepMEI's network was described as a classifier rather than a genotyper and given the wrong training set, euL1db listed two detection methods absent from the data, and HMEID contradicted itself on the MELT ASSESS cutoff. Also: the SweGen bigDataUrl now points at _swegen.bb so the restricted callset is kept off the download server; the container page no longer claims the whole collection is long-read, lists the two euL1db subtracks, scopes its display conventions to the subtracks they describe, and cites all six papers; dead and wrong track links are repointed and pinned to a db; $db replaces hardcoded hg38 in paths on pages that serve three assemblies; the euL1db labels no longer carry hg38 counts and a lift note that made no sense on hg19; all six subtracks gain a dataVersion; the euL1db filter ranges match the data; and five autoSql field descriptions match what the files contain. Document the gbdb symlinks and the QA changes in doc/hg38/mei.txt, correct the HMEID bedToBigBed type there, and add an hg19.txt pointer since hg19 carries the two euL1db subtracks.
• src/hg/makeDb/scripts/mei/meiEul1db.as
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    7e87cadb469b4e0eb4fb7f973154357cfe7fc345 Mon Sep 21 15:56:18 2026 -0700
    QA fixes for the mei (Mobile Insertions) track collection. refs #37524 Fix two data bugs found during QA and rebuild the affected bigBeds. meiEul1dbToBed.py looked up samples and individuals by name, but euL1db joins on 1-based row numbers, so neither join ever matched and the individual count, tissues, clinical conditions and populations were empty on all 8,991 insertions while the contributing-samples table printed row numbers. Both loaders now key on the row number, the table prints the sample name, and the adjacent population filter is case-insensitive so it actually drops "unknown". meiHgsvc3CsvToBed.py took alt[1:] on every record, which dropped the first base of the element on the 96 GRCh38 and 111 T2T-CHM13 records where PALMER2 is the only caller and ALT carries no anchor base; it now prefers INFO SEQ, which always matches SVLEN. Correct seven statements on the description pages against their sources: the HGSVC3 single-caller split was attributed to PALMER rather than L1ME-AID, its orthogonal concordance was 90.8% rather than 92.5%, euL1db was credited with aligning the L1HS consensus when the paper says it was processed from our RepeatMasker track, DeepMEI's network was described as a classifier rather than a genotyper and given the wrong training set, euL1db listed two detection methods absent from the data, and HMEID contradicted itself on the MELT ASSESS cutoff. Also: the SweGen bigDataUrl now points at _swegen.bb so the restricted callset is kept off the download server; the container page no longer claims the whole collection is long-read, lists the two euL1db subtracks, scopes its display conventions to the subtracks they describe, and cites all six papers; dead and wrong track links are repointed and pinned to a db; $db replaces hardcoded hg38 in paths on pages that serve three assemblies; the euL1db labels no longer carry hg38 counts and a lift note that made no sense on hg19; all six subtracks gain a dataVersion; the euL1db filter ranges match the data; and five autoSql field descriptions match what the files contain. Document the gbdb symlinks and the QA changes in doc/hg38/mei.txt, correct the HMEID bedToBigBed type there, and add an hg19.txt pointer since hg19 carries the two euL1db subtracks.
• src/hg/makeDb/scripts/mei/meiEul1dbRef.as
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    7e87cadb469b4e0eb4fb7f973154357cfe7fc345 Mon Sep 21 15:56:18 2026 -0700
    QA fixes for the mei (Mobile Insertions) track collection. refs #37524 Fix two data bugs found during QA and rebuild the affected bigBeds. meiEul1dbToBed.py looked up samples and individuals by name, but euL1db joins on 1-based row numbers, so neither join ever matched and the individual count, tissues, clinical conditions and populations were empty on all 8,991 insertions while the contributing-samples table printed row numbers. Both loaders now key on the row number, the table prints the sample name, and the adjacent population filter is case-insensitive so it actually drops "unknown". meiHgsvc3CsvToBed.py took alt[1:] on every record, which dropped the first base of the element on the 96 GRCh38 and 111 T2T-CHM13 records where PALMER2 is the only caller and ALT carries no anchor base; it now prefers INFO SEQ, which always matches SVLEN. Correct seven statements on the description pages against their sources: the HGSVC3 single-caller split was attributed to PALMER rather than L1ME-AID, its orthogonal concordance was 90.8% rather than 92.5%, euL1db was credited with aligning the L1HS consensus when the paper says it was processed from our RepeatMasker track, DeepMEI's network was described as a classifier rather than a genotyper and given the wrong training set, euL1db listed two detection methods absent from the data, and HMEID contradicted itself on the MELT ASSESS cutoff. Also: the SweGen bigDataUrl now points at _swegen.bb so the restricted callset is kept off the download server; the container page no longer claims the whole collection is long-read, lists the two euL1db subtracks, scopes its display conventions to the subtracks they describe, and cites all six papers; dead and wrong track links are repointed and pinned to a db; $db replaces hardcoded hg38 in paths on pages that serve three assemblies; the euL1db labels no longer carry hg38 counts and a lift note that made no sense on hg19; all six subtracks gain a dataVersion; the euL1db filter ranges match the data; and five autoSql field descriptions match what the files contain. Document the gbdb symlinks and the QA changes in doc/hg38/mei.txt, correct the HMEID bedToBigBed type there, and add an hg19.txt pointer since hg19 carries the two euL1db subtracks.
• src/hg/makeDb/scripts/mei/meiEul1dbToBed.py
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    7e87cadb469b4e0eb4fb7f973154357cfe7fc345 Mon Sep 21 15:56:18 2026 -0700
    QA fixes for the mei (Mobile Insertions) track collection. refs #37524 Fix two data bugs found during QA and rebuild the affected bigBeds. meiEul1dbToBed.py looked up samples and individuals by name, but euL1db joins on 1-based row numbers, so neither join ever matched and the individual count, tissues, clinical conditions and populations were empty on all 8,991 insertions while the contributing-samples table printed row numbers. Both loaders now key on the row number, the table prints the sample name, and the adjacent population filter is case-insensitive so it actually drops "unknown". meiHgsvc3CsvToBed.py took alt[1:] on every record, which dropped the first base of the element on the 96 GRCh38 and 111 T2T-CHM13 records where PALMER2 is the only caller and ALT carries no anchor base; it now prefers INFO SEQ, which always matches SVLEN. Correct seven statements on the description pages against their sources: the HGSVC3 single-caller split was attributed to PALMER rather than L1ME-AID, its orthogonal concordance was 90.8% rather than 92.5%, euL1db was credited with aligning the L1HS consensus when the paper says it was processed from our RepeatMasker track, DeepMEI's network was described as a classifier rather than a genotyper and given the wrong training set, euL1db listed two detection methods absent from the data, and HMEID contradicted itself on the MELT ASSESS cutoff. Also: the SweGen bigDataUrl now points at _swegen.bb so the restricted callset is kept off the download server; the container page no longer claims the whole collection is long-read, lists the two euL1db subtracks, scopes its display conventions to the subtracks they describe, and cites all six papers; dead and wrong track links are repointed and pinned to a db; $db replaces hardcoded hg38 in paths on pages that serve three assemblies; the euL1db labels no longer carry hg38 counts and a lift note that made no sense on hg19; all six subtracks gain a dataVersion; the euL1db filter ranges match the data; and five autoSql field descriptions match what the files contain. Document the gbdb symlinks and the QA changes in doc/hg38/mei.txt, correct the HMEID bedToBigBed type there, and add an hg19.txt pointer since hg19 carries the two euL1db subtracks.
• src/hg/makeDb/scripts/mei/meiHgsvc3.as
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    7e87cadb469b4e0eb4fb7f973154357cfe7fc345 Mon Sep 21 15:56:18 2026 -0700
    QA fixes for the mei (Mobile Insertions) track collection. refs #37524 Fix two data bugs found during QA and rebuild the affected bigBeds. meiEul1dbToBed.py looked up samples and individuals by name, but euL1db joins on 1-based row numbers, so neither join ever matched and the individual count, tissues, clinical conditions and populations were empty on all 8,991 insertions while the contributing-samples table printed row numbers. Both loaders now key on the row number, the table prints the sample name, and the adjacent population filter is case-insensitive so it actually drops "unknown". meiHgsvc3CsvToBed.py took alt[1:] on every record, which dropped the first base of the element on the 96 GRCh38 and 111 T2T-CHM13 records where PALMER2 is the only caller and ALT carries no anchor base; it now prefers INFO SEQ, which always matches SVLEN. Correct seven statements on the description pages against their sources: the HGSVC3 single-caller split was attributed to PALMER rather than L1ME-AID, its orthogonal concordance was 90.8% rather than 92.5%, euL1db was credited with aligning the L1HS consensus when the paper says it was processed from our RepeatMasker track, DeepMEI's network was described as a classifier rather than a genotyper and given the wrong training set, euL1db listed two detection methods absent from the data, and HMEID contradicted itself on the MELT ASSESS cutoff. Also: the SweGen bigDataUrl now points at _swegen.bb so the restricted callset is kept off the download server; the container page no longer claims the whole collection is long-read, lists the two euL1db subtracks, scopes its display conventions to the subtracks they describe, and cites all six papers; dead and wrong track links are repointed and pinned to a db; $db replaces hardcoded hg38 in paths on pages that serve three assemblies; the euL1db labels no longer carry hg38 counts and a lift note that made no sense on hg19; all six subtracks gain a dataVersion; the euL1db filter ranges match the data; and five autoSql field descriptions match what the files contain. Document the gbdb symlinks and the QA changes in doc/hg38/mei.txt, correct the HMEID bedToBigBed type there, and add an hg19.txt pointer since hg19 carries the two euL1db subtracks.
• src/hg/makeDb/scripts/mei/meiHgsvc3CsvToBed.py
  • lines changed 9, context: html, text, full: html, text
    7e87cadb469b4e0eb4fb7f973154357cfe7fc345 Mon Sep 21 15:56:18 2026 -0700
    QA fixes for the mei (Mobile Insertions) track collection. refs #37524 Fix two data bugs found during QA and rebuild the affected bigBeds. meiEul1dbToBed.py looked up samples and individuals by name, but euL1db joins on 1-based row numbers, so neither join ever matched and the individual count, tissues, clinical conditions and populations were empty on all 8,991 insertions while the contributing-samples table printed row numbers. Both loaders now key on the row number, the table prints the sample name, and the adjacent population filter is case-insensitive so it actually drops "unknown". meiHgsvc3CsvToBed.py took alt[1:] on every record, which dropped the first base of the element on the 96 GRCh38 and 111 T2T-CHM13 records where PALMER2 is the only caller and ALT carries no anchor base; it now prefers INFO SEQ, which always matches SVLEN. Correct seven statements on the description pages against their sources: the HGSVC3 single-caller split was attributed to PALMER rather than L1ME-AID, its orthogonal concordance was 90.8% rather than 92.5%, euL1db was credited with aligning the L1HS consensus when the paper says it was processed from our RepeatMasker track, DeepMEI's network was described as a classifier rather than a genotyper and given the wrong training set, euL1db listed two detection methods absent from the data, and HMEID contradicted itself on the MELT ASSESS cutoff. Also: the SweGen bigDataUrl now points at _swegen.bb so the restricted callset is kept off the download server; the container page no longer claims the whole collection is long-read, lists the two euL1db subtracks, scopes its display conventions to the subtracks they describe, and cites all six papers; dead and wrong track links are repointed and pinned to a db; $db replaces hardcoded hg38 in paths on pages that serve three assemblies; the euL1db labels no longer carry hg38 counts and a lift note that made no sense on hg19; all six subtracks gain a dataVersion; the euL1db filter ranges match the data; and five autoSql field descriptions match what the files contain. Document the gbdb symlinks and the QA changes in doc/hg38/mei.txt, correct the HMEID bedToBigBed type there, and add an hg19.txt pointer since hg19 carries the two euL1db subtracks.
  • lines changed 3, context: html, text, full: html, text
    e461209cf1fd3758d63641915cd91ca9c8ab3020 Thu Sep 24 17:00:10 2026 -0700
    Remove tool output accidentally left in the mei description page, per CR. refs #37524 getTrackReferences writes its diagnostics to stdout rather than stderr, so six "Failed to fetch complete links from NCBI" lines ended up in the References section of mei.html and rendered as visible text on the track description page. NCBI is still not answering, so rather than rerun the tool the references are now assembled from the citation blocks already present on the six subtrack pages. That also restores the publisher links for every paper, which the failed lookups had degraded to bare PubMed URLs. Also make the INFO SEQ guard in meiHgsvc3CsvToBed.py require a usable string, so an empty SEQ= value would fall back to the ALT-derived sequence instead of silently producing an empty one. No record in either callset carries an empty SEQ today and the rebuilt output is byte-identical.
• src/hg/makeDb/scripts/mei/meiHmeid.as
  • lines changed 1, context: html, text, full: html, text
    7e87cadb469b4e0eb4fb7f973154357cfe7fc345 Mon Sep 21 15:56:18 2026 -0700
    QA fixes for the mei (Mobile Insertions) track collection. refs #37524 Fix two data bugs found during QA and rebuild the affected bigBeds. meiEul1dbToBed.py looked up samples and individuals by name, but euL1db joins on 1-based row numbers, so neither join ever matched and the individual count, tissues, clinical conditions and populations were empty on all 8,991 insertions while the contributing-samples table printed row numbers. Both loaders now key on the row number, the table prints the sample name, and the adjacent population filter is case-insensitive so it actually drops "unknown". meiHgsvc3CsvToBed.py took alt[1:] on every record, which dropped the first base of the element on the 96 GRCh38 and 111 T2T-CHM13 records where PALMER2 is the only caller and ALT carries no anchor base; it now prefers INFO SEQ, which always matches SVLEN. Correct seven statements on the description pages against their sources: the HGSVC3 single-caller split was attributed to PALMER rather than L1ME-AID, its orthogonal concordance was 90.8% rather than 92.5%, euL1db was credited with aligning the L1HS consensus when the paper says it was processed from our RepeatMasker track, DeepMEI's network was described as a classifier rather than a genotyper and given the wrong training set, euL1db listed two detection methods absent from the data, and HMEID contradicted itself on the MELT ASSESS cutoff. Also: the SweGen bigDataUrl now points at _swegen.bb so the restricted callset is kept off the download server; the container page no longer claims the whole collection is long-read, lists the two euL1db subtracks, scopes its display conventions to the subtracks they describe, and cites all six papers; dead and wrong track links are repointed and pinned to a db; $db replaces hardcoded hg38 in paths on pages that serve three assemblies; the euL1db labels no longer carry hg38 counts and a lift note that made no sense on hg19; all six subtracks gain a dataVersion; the euL1db filter ranges match the data; and five autoSql field descriptions match what the files contain. Document the gbdb symlinks and the QA changes in doc/hg38/mei.txt, correct the HMEID bedToBigBed type there, and add an hg19.txt pointer since hg19 carries the two euL1db subtracks.
• src/hg/makeDb/scripts/sgdpCopyNumber/sgdpCopyNumberBuild.py
  • lines changed 408, context: html, text, full: html, text
    360607541994aa88b49fc241c34bd964a1db7b50 Tue Sep 29 15:07:07 2026 -0700
    Rebuild the hs1 sgdpCopyNumber track as a faceted composite, so its 319 samples are picked from a searchable metadata table rather than 319 checkboxes; the same bigBeds are pointed at by the same /gbdb paths, so no data changed. Subtracks are renamed from <region>_<population>_<libId>_wssd to sgdpCopyNumber_<libId> because a faceted composite requires the parent name plus the primaryKey value, and dataTypes is deliberately unset: with it hgTrackUi parses the data element only as far as the first underscore and would truncate LP6005441-DNA_A01 to LP6005441-DNA. The per-subtrack 'visibility dense' lines are gone because a faceted composite honors a child's own display mode where a classic composite ignores it, so keeping them would pin every sample to dense and remove the per-item click that the copy number is read from. Sample attributes come from the Reich lab SGDP tables and 317 of the 319 join; sgdpCopyNumberBuild.py takes its sample list from the checked-in sgdpCopyNumberSamples.tsv rather than from trackDb, because at release the generated stanzas replace sgdpCopyNumber.trackDb.ra and the legacy region prefix that the two unmatched samples depend on disappears with them. Alpha gets the new file and beta/public keep the old one until the metadata and color files are on the RR, without which the picker renders empty. sgdpCopyNumber_subset, which turns out to be the first 29 samples in plate order rather than any curated set, is not in the alpha version; whether it is retired for good is still open on the ticket. Faceted composite suggested by Gerardo, and the cross-sandbox metadata fetch that this track turned up was fixed by Max in b3a26a6aff3. refs #29344
• src/hg/makeDb/scripts/sgdpCopyNumber/sgdpCopyNumberFetchMeta.sh
  • lines changed 30, context: html, text, full: html, text
    360607541994aa88b49fc241c34bd964a1db7b50 Tue Sep 29 15:07:07 2026 -0700
    Rebuild the hs1 sgdpCopyNumber track as a faceted composite, so its 319 samples are picked from a searchable metadata table rather than 319 checkboxes; the same bigBeds are pointed at by the same /gbdb paths, so no data changed. Subtracks are renamed from <region>_<population>_<libId>_wssd to sgdpCopyNumber_<libId> because a faceted composite requires the parent name plus the primaryKey value, and dataTypes is deliberately unset: with it hgTrackUi parses the data element only as far as the first underscore and would truncate LP6005441-DNA_A01 to LP6005441-DNA. The per-subtrack 'visibility dense' lines are gone because a faceted composite honors a child's own display mode where a classic composite ignores it, so keeping them would pin every sample to dense and remove the per-item click that the copy number is read from. Sample attributes come from the Reich lab SGDP tables and 317 of the 319 join; sgdpCopyNumberBuild.py takes its sample list from the checked-in sgdpCopyNumberSamples.tsv rather than from trackDb, because at release the generated stanzas replace sgdpCopyNumber.trackDb.ra and the legacy region prefix that the two unmatched samples depend on disappears with them. Alpha gets the new file and beta/public keep the old one until the metadata and color files are on the RR, without which the picker renders empty. sgdpCopyNumber_subset, which turns out to be the first 29 samples in plate order rather than any curated set, is not in the alpha version; whether it is retired for good is still open on the ticket. Faceted composite suggested by Gerardo, and the cross-sandbox metadata fetch that this track turned up was fixed by Max in b3a26a6aff3. refs #29344
• src/hg/makeDb/scripts/sgdpCopyNumber/sgdpCopyNumberSamples.tsv
  • lines changed 325, context: html, text, full: html, text
    360607541994aa88b49fc241c34bd964a1db7b50 Tue Sep 29 15:07:07 2026 -0700
    Rebuild the hs1 sgdpCopyNumber track as a faceted composite, so its 319 samples are picked from a searchable metadata table rather than 319 checkboxes; the same bigBeds are pointed at by the same /gbdb paths, so no data changed. Subtracks are renamed from <region>_<population>_<libId>_wssd to sgdpCopyNumber_<libId> because a faceted composite requires the parent name plus the primaryKey value, and dataTypes is deliberately unset: with it hgTrackUi parses the data element only as far as the first underscore and would truncate LP6005441-DNA_A01 to LP6005441-DNA. The per-subtrack 'visibility dense' lines are gone because a faceted composite honors a child's own display mode where a classic composite ignores it, so keeping them would pin every sample to dense and remove the per-item click that the copy number is read from. Sample attributes come from the Reich lab SGDP tables and 317 of the 319 join; sgdpCopyNumberBuild.py takes its sample list from the checked-in sgdpCopyNumberSamples.tsv rather than from trackDb, because at release the generated stanzas replace sgdpCopyNumber.trackDb.ra and the legacy region prefix that the two unmatched samples depend on disappears with them. Alpha gets the new file and beta/public keep the old one until the metadata and color files are on the RR, without which the picker renders empty. sgdpCopyNumber_subset, which turns out to be the first 29 samples in plate order rather than any curated set, is not in the alpha version; whether it is retired for good is still open on the ticket. Faceted composite suggested by Gerardo, and the cross-sandbox metadata fetch that this track turned up was fixed by Max in b3a26a6aff3. refs #29344
• src/hg/makeDb/scripts/varFreqs/databases.tsv
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    442e433a90b25deb87f10e6cf1b7b608bb0a6d67 Sat Sep 26 21:56:06 2026 -0700
    sfariSparkWgs45kAsd: flag 25M insertions of non-human (oral bacteria) sequence as FILTER NonHumanIns and hide them by default; add SFARI SPARK 45k WGS to the combined tracks without those insertions and relabel the 12k pilot as SFARI SPARK iWGS v1.1 Pilot, refs #38424
• src/hg/makeDb/scripts/varFreqs/hgdp1kCommonSnvs.sh
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    9cedfa38c14068c79dec89f76c606ee22b3f931a Wed Sep 30 15:02:37 2026 -0700
    phasedVars: new subtrack hgdp1kSnv, a 17GB version of the 3.5TB gnomAD HGDP+1000G genotype VCF with only SNVs with AC>5 and only GT, so haplotype clustering can be shown up to 5Mbp, refs #37306
• src/hg/makeDb/scripts/varFreqs/populations.tsv
  • lines changed 2, context: html, text, full: html, text
    442e433a90b25deb87f10e6cf1b7b608bb0a6d67 Sat Sep 26 21:56:06 2026 -0700
    sfariSparkWgs45kAsd: flag 25M insertions of non-human (oral bacteria) sequence as FILTER NonHumanIns and hide them by default; add SFARI SPARK 45k WGS to the combined tracks without those insertions and relabel the 12k pilot as SFARI SPARK iWGS v1.1 Pilot, refs #38424
• src/hg/makeDb/scripts/varFreqs/sparkWgs45kFlagNonHumanIns.sh
  • lines changed 66, context: html, text, full: html, text
    442e433a90b25deb87f10e6cf1b7b608bb0a6d67 Sat Sep 26 21:56:06 2026 -0700
    sfariSparkWgs45kAsd: flag 25M insertions of non-human (oral bacteria) sequence as FILTER NonHumanIns and hide them by default; add SFARI SPARK 45k WGS to the combined tracks without those insertions and relabel the 12k pilot as SFARI SPARK iWGS v1.1 Pilot, refs #38424
• src/hg/makeDb/scripts/varFreqs/sparkWgs45kNonHumanIns.py
  • lines changed 100, context: html, text, full: html, text
    442e433a90b25deb87f10e6cf1b7b608bb0a6d67 Sat Sep 26 21:56:06 2026 -0700
    sfariSparkWgs45kAsd: flag 25M insertions of non-human (oral bacteria) sequence as FILTER NonHumanIns and hide them by default; add SFARI SPARK 45k WGS to the combined tracks without those insertions and relabel the 12k pilot as SFARI SPARK iWGS v1.1 Pilot, refs #38424
• src/hg/makeDb/scripts/varFreqs/sparkWgs45kPvcfJobs.sh
  • lines changed 29, context: html, text, full: html, text
    7aa59c8f6afbda4c2157d3990b2bbc48a39cac63 Fri Sep 25 02:48:31 2026 -0700
    varFreqs: add SFARI SPARK 45k WGS subtracks. sfariSparkWgs45k is built from the release's AF table (AN estimated, singletons dropped); sfariSparkWgs45kAsd is built from the genotype pVCFs with ASD/non-ASD counts, for now only the DSCAM locus while the genome-wide parasol run finishes, refs #38424
• src/hg/makeDb/scripts/varFreqs/sparkWgs45kPvcfMerge.sh
  • lines changed 24, context: html, text, full: html, text
    7aa59c8f6afbda4c2157d3990b2bbc48a39cac63 Fri Sep 25 02:48:31 2026 -0700
    varFreqs: add SFARI SPARK 45k WGS subtracks. sfariSparkWgs45k is built from the release's AF table (AN estimated, singletons dropped); sfariSparkWgs45kAsd is built from the genotype pVCFs with ASD/non-ASD counts, for now only the DSCAM locus while the genome-wide parasol run finishes, refs #38424
• src/hg/makeDb/scripts/varFreqs/sparkWgs45kPvcfRange.sh
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    7aa59c8f6afbda4c2157d3990b2bbc48a39cac63 Fri Sep 25 02:48:31 2026 -0700
    varFreqs: add SFARI SPARK 45k WGS subtracks. sfariSparkWgs45k is built from the release's AF table (AN estimated, singletons dropped); sfariSparkWgs45kAsd is built from the genotype pVCFs with ASD/non-ASD counts, for now only the DSCAM locus while the genome-wide parasol run finishes, refs #38424
  • lines changed 36, context: html, text, full: html, text
    a5c699a7301156154700f51a20ae571bc6987051 Sat Sep 26 17:53:41 2026 -0700
    varFreqs: remove the AF-table-based sfariSparkWgs45k subtrack, superseded by the genotype-based sfariSparkWgs45kAsd; drop its scripts, the DSCAM demo script and their makeDoc sections, refs #38424
• src/hg/makeDb/scripts/varFreqs/sparkWgs45kPvcfSlice.py
  • lines changed 190, context: html, text, full: html, text
    7aa59c8f6afbda4c2157d3990b2bbc48a39cac63 Fri Sep 25 02:48:31 2026 -0700
    varFreqs: add SFARI SPARK 45k WGS subtracks. sfariSparkWgs45k is built from the release's AF table (AN estimated, singletons dropped); sfariSparkWgs45kAsd is built from the genotype pVCFs with ASD/non-ASD counts, for now only the DSCAM locus while the genome-wide parasol run finishes, refs #38424
• src/hg/makeDb/scripts/varFreqs/sparkWgs45kPvcfToSites.sh
  • lines changed 69, context: html, text, full: html, text
    7aa59c8f6afbda4c2157d3990b2bbc48a39cac63 Fri Sep 25 02:48:31 2026 -0700
    varFreqs: add SFARI SPARK 45k WGS subtracks. sfariSparkWgs45k is built from the release's AF table (AN estimated, singletons dropped); sfariSparkWgs45kAsd is built from the genotype pVCFs with ASD/non-ASD counts, for now only the DSCAM locus while the genome-wide parasol run finishes, refs #38424
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    f03f56cd3c795a6fba2b8419662a9a2c5d49f69a Sat Sep 26 14:16:17 2026 -0700
    sfariSparkWgs45kAsd: now genome-wide (518M variants from the 45,178 genotype pVCFs, run on parasol); per-allele INFO fields declared Number=1 so the VCF track filters accept them, doc page no longer says DSCAM only, refs #38424
• src/hg/makeDb/scripts/varFreqs/sparkWgs45kToVcf.py
  • lines changed 93, context: html, text, full: html, text
    7aa59c8f6afbda4c2157d3990b2bbc48a39cac63 Fri Sep 25 02:48:31 2026 -0700
    varFreqs: add SFARI SPARK 45k WGS subtracks. sfariSparkWgs45k is built from the release's AF table (AN estimated, singletons dropped); sfariSparkWgs45kAsd is built from the genotype pVCFs with ASD/non-ASD counts, for now only the DSCAM locus while the genome-wide parasol run finishes, refs #38424
  • lines changed 93, context: html, text, full: html, text
    a5c699a7301156154700f51a20ae571bc6987051 Sat Sep 26 17:53:41 2026 -0700
    varFreqs: remove the AF-table-based sfariSparkWgs45k subtrack, superseded by the genotype-based sfariSparkWgs45kAsd; drop its scripts, the DSCAM demo script and their makeDoc sections, refs #38424
• src/hg/makeDb/scripts/varFreqs/sparkWgs45kToVcf.sh
  • lines changed 41, context: html, text, full: html, text
    7aa59c8f6afbda4c2157d3990b2bbc48a39cac63 Fri Sep 25 02:48:31 2026 -0700
    varFreqs: add SFARI SPARK 45k WGS subtracks. sfariSparkWgs45k is built from the release's AF table (AN estimated, singletons dropped); sfariSparkWgs45kAsd is built from the genotype pVCFs with ASD/non-ASD counts, for now only the DSCAM locus while the genome-wide parasol run finishes, refs #38424
  • lines changed 41, context: html, text, full: html, text
    a5c699a7301156154700f51a20ae571bc6987051 Sat Sep 26 17:53:41 2026 -0700
    varFreqs: remove the AF-table-based sfariSparkWgs45k subtrack, superseded by the genotype-based sfariSparkWgs45kAsd; drop its scripts, the DSCAM demo script and their makeDoc sections, refs #38424
• src/hg/makeDb/trackDb/bacteria/staAur2/cons369way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/birds/geoFor1/cons7way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/bushbaby/otoGar3/cons3way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/cat/felCat3/multiz4way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/cat/felCat3/phastConsElements4way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/cat/felCat4/cons6way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/chicken/galGal2/multiz7way.html
  • lines changed 27, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/chicken/galGal2/phastConsElements7way.html
  • lines changed 9, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/chicken/galGal3/multiz7way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/chicken/galGal3/phastConsElements7way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/chicken/galGal6/cons77way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/chicken/galGal6/gpnStar.html
  • lines changed 150, context: html, text, full: html, text
    53ab3f1e293a91ddf71ec7568f4a6ff827bcd278 Fri Oct 2 13:52:36 2026 -0700
    Native GPN-Star track (Ye, Benegas et al., Nature 2026) on hg38, mm39, galGal6, dm6 and ce11, from the authors' Hugging Face hub. Each model is a multiWig sequence logo plus a four-allele -LLR composite using negateValues. The three hg38 models (V/M/P) sit in predictionScoresSuper via human/gpnStar.ra with /gbdb/$D bigDataUrls so -strict drops them on other human assemblies; the other four get a standalone gpnStar superTrack. The authors' bigWigs come from pyBigWig, whose bwAddIntervalSpanSteps writes the last section of each run 6 bases too long (pyBigWig #166) and makes bigWigAverageOverBed and bigWigCorrelate abort, so gpnStarRebuild.sh re-encodes them with wigToBigWig and gpnStarVerify.sh checks every per-base value is unchanged. Entropy scores and the GenArk-only Arabidopsis set are left out, and pennantIcon still has #TBD placeholders for the newsarch anchor and date. refs #38451
• src/hg/makeDb/trackDb/chicken/galGal6/gpnStar.ra
  • lines changed 125, context: html, text, full: html, text
    53ab3f1e293a91ddf71ec7568f4a6ff827bcd278 Fri Oct 2 13:52:36 2026 -0700
    Native GPN-Star track (Ye, Benegas et al., Nature 2026) on hg38, mm39, galGal6, dm6 and ce11, from the authors' Hugging Face hub. Each model is a multiWig sequence logo plus a four-allele -LLR composite using negateValues. The three hg38 models (V/M/P) sit in predictionScoresSuper via human/gpnStar.ra with /gbdb/$D bigDataUrls so -strict drops them on other human assemblies; the other four get a standalone gpnStar superTrack. The authors' bigWigs come from pyBigWig, whose bwAddIntervalSpanSteps writes the last section of each run 6 bases too long (pyBigWig #166) and makes bigWigAverageOverBed and bigWigCorrelate abort, so gpnStarRebuild.sh re-encodes them with wigToBigWig and gpnStarVerify.sh checks every per-base value is unchanged. Entropy scores and the GenArk-only Arabidopsis set are left out, and pennantIcon still has #TBD placeholders for the newsarch anchor and date. refs #38451
• src/hg/makeDb/trackDb/chicken/galGal6/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    53ab3f1e293a91ddf71ec7568f4a6ff827bcd278 Fri Oct 2 13:52:36 2026 -0700
    Native GPN-Star track (Ye, Benegas et al., Nature 2026) on hg38, mm39, galGal6, dm6 and ce11, from the authors' Hugging Face hub. Each model is a multiWig sequence logo plus a four-allele -LLR composite using negateValues. The three hg38 models (V/M/P) sit in predictionScoresSuper via human/gpnStar.ra with /gbdb/$D bigDataUrls so -strict drops them on other human assemblies; the other four get a standalone gpnStar superTrack. The authors' bigWigs come from pyBigWig, whose bwAddIntervalSpanSteps writes the last section of each run 6 bases too long (pyBigWig #166) and makes bigWigAverageOverBed and bigWigCorrelate abort, so gpnStarRebuild.sh re-encodes them with wigToBigWig and gpnStarVerify.sh checks every per-base value is unchanged. Entropy scores and the GenArk-only Arabidopsis set are left out, and pennantIcon still has #TBD placeholders for the newsarch anchor and date. refs #38451
• src/hg/makeDb/trackDb/chimp/panTro2/multiz8way.html
  • lines changed 12, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/chimp/panTro3/cons12way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/cow/bosTau4/multiz5way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/cow/bosTau4/phastConsElements5way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/criGri/regenCho1/cons7way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/crispr10K.ra
  • lines changed 1, context: html, text, full: html, text
    cf9cfcd463d40a868f8ee73dead17ff8071dce2f Fri Sep 25 03:00:20 2026 -0700
    CRISPR tracks: expose colorFields dropdown to color guides by off-target specificity (MIT score) or by Moreno-Mateos efficiency, as alternatives to the default Doench/Fusi-based itemRgb color. The bigBed already carries these as the _specColor and _crisprScanColor extra fields; no data rebuild needed.
• src/hg/makeDb/trackDb/crisprAll.ra
  • lines changed 1, context: html, text, full: html, text
    cf9cfcd463d40a868f8ee73dead17ff8071dce2f Fri Sep 25 03:00:20 2026 -0700
    CRISPR tracks: expose colorFields dropdown to color guides by off-target specificity (MIT score) or by Moreno-Mateos efficiency, as alternatives to the default Doench/Fusi-based itemRgb color. The bigBed already carries these as the _specColor and _crisprScanColor extra fields; no data rebuild needed.
• src/hg/makeDb/trackDb/dog/canFam2/multiz4way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/dog/canFam2/phastConsElements4way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/drosophila/dm2/multiz15way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/drosophila/dm2/multiz9way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/drosophila/dm2/phastConsElements15way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/drosophila/dm2/phastConsElements9way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/drosophila/dm3/multiz15way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/drosophila/dm3/phastConsElements15way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/drosophila/dm6/cons124way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/drosophila/dm6/cons27way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/drosophila/dm6/gpnStar.html
  • lines changed 150, context: html, text, full: html, text
    53ab3f1e293a91ddf71ec7568f4a6ff827bcd278 Fri Oct 2 13:52:36 2026 -0700
    Native GPN-Star track (Ye, Benegas et al., Nature 2026) on hg38, mm39, galGal6, dm6 and ce11, from the authors' Hugging Face hub. Each model is a multiWig sequence logo plus a four-allele -LLR composite using negateValues. The three hg38 models (V/M/P) sit in predictionScoresSuper via human/gpnStar.ra with /gbdb/$D bigDataUrls so -strict drops them on other human assemblies; the other four get a standalone gpnStar superTrack. The authors' bigWigs come from pyBigWig, whose bwAddIntervalSpanSteps writes the last section of each run 6 bases too long (pyBigWig #166) and makes bigWigAverageOverBed and bigWigCorrelate abort, so gpnStarRebuild.sh re-encodes them with wigToBigWig and gpnStarVerify.sh checks every per-base value is unchanged. Entropy scores and the GenArk-only Arabidopsis set are left out, and pennantIcon still has #TBD placeholders for the newsarch anchor and date. refs #38451
• src/hg/makeDb/trackDb/drosophila/dm6/gpnStar.ra
  • lines changed 125, context: html, text, full: html, text
    53ab3f1e293a91ddf71ec7568f4a6ff827bcd278 Fri Oct 2 13:52:36 2026 -0700
    Native GPN-Star track (Ye, Benegas et al., Nature 2026) on hg38, mm39, galGal6, dm6 and ce11, from the authors' Hugging Face hub. Each model is a multiWig sequence logo plus a four-allele -LLR composite using negateValues. The three hg38 models (V/M/P) sit in predictionScoresSuper via human/gpnStar.ra with /gbdb/$D bigDataUrls so -strict drops them on other human assemblies; the other four get a standalone gpnStar superTrack. The authors' bigWigs come from pyBigWig, whose bwAddIntervalSpanSteps writes the last section of each run 6 bases too long (pyBigWig #166) and makes bigWigAverageOverBed and bigWigCorrelate abort, so gpnStarRebuild.sh re-encodes them with wigToBigWig and gpnStarVerify.sh checks every per-base value is unchanged. Entropy scores and the GenArk-only Arabidopsis set are left out, and pennantIcon still has #TBD placeholders for the newsarch anchor and date. refs #38451
• src/hg/makeDb/trackDb/drosophila/dm6/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    53ab3f1e293a91ddf71ec7568f4a6ff827bcd278 Fri Oct 2 13:52:36 2026 -0700
    Native GPN-Star track (Ye, Benegas et al., Nature 2026) on hg38, mm39, galGal6, dm6 and ce11, from the authors' Hugging Face hub. Each model is a multiWig sequence logo plus a four-allele -LLR composite using negateValues. The three hg38 models (V/M/P) sit in predictionScoresSuper via human/gpnStar.ra with /gbdb/$D bigDataUrls so -strict drops them on other human assemblies; the other four get a standalone gpnStar superTrack. The authors' bigWigs come from pyBigWig, whose bwAddIntervalSpanSteps writes the last section of each run 6 bases too long (pyBigWig #166) and makes bigWigAverageOverBed and bigWigCorrelate abort, so gpnStarRebuild.sh re-encodes them with wigToBigWig and gpnStarVerify.sh checks every per-base value is unchanged. Entropy scores and the GenArk-only Arabidopsis set are left out, and pennantIcon still has #TBD placeholders for the newsarch anchor and date. refs #38451
• src/hg/makeDb/trackDb/ebola/bunEbo1/cons160way.html
  • lines changed 12, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/ebola/eboVir2/cons49way.html
  • lines changed 12, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/ebola/eboVir3/cons160way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/ebola/resEbo1/cons160way.html
  • lines changed 12, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/ebola/sudEbo1/cons160way.html
  • lines changed 12, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/ebola/taiEbo1/cons160way.html
  • lines changed 12, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/ebola/zaiEbo1/cons160way.html
  • lines changed 12, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/fugu/fr2/multiz5way.html
  • lines changed 27, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/fugu/fr2/phastConsElements5way.html
  • lines changed 9, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/fugu/fr3/cons8way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/galVar/galVar1/cons4way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/galVar/galVar1/cons5way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/galVar/galVar1/cons6way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/gorilla/gorGor3/cons11way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/guineaPig/cavPor3/cons5way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/guineaPig/cavPor3/cons6way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/horse/equCab2/multiz6way.html
  • lines changed 12, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/horse/equCab2/phastConsElements6way.html
  • lines changed 9, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/chainNetVertebrate.ra
  • lines changed 1, context: html, text, full: html, text
    1a2f5a5b07855da8d191c0b9358c945d6abe9f74 Mon Sep 28 15:17:28 2026 -0700
    trackDb: fix the netThaSir1 chain table and drop missing hg18 pgSnp prediction tables, refs #37424 The hg38 netThaSir1 stanza was copied from netAnoCar1 and kept its type line, so hgc looked for chainAnoCar1 and every click failed. It now names thaSir1 and chainThaSir1. The hg18 pgKb1Comb, pgNb1, pgMd8, pgTk1 and pgAbtSolid tracks named SIFT and PolyPhen tables that exist only on hgwdev and were never released. The details page warned on every click on beta and the RR. The two settings are removed.
• src/hg/makeDb/trackDb/human/chm13/html/GCA_009914755.4_T2T-CHM13v2.0.hgLiftOver.html
  • lines changed 2, context: html, text, full: html, text
    733c551e32c88c02773c20af61169100edfb446a Sun Sep 27 16:00:39 2026 -0700
    CHM13 liftOver examples: point at public hs1 instead of a genome-test hub id, refs #37641
• src/hg/makeDb/trackDb/human/encode4ProCap.html
  • lines changed 4, context: html, text, full: html, text
    0f951bfc96241a7362d1512ceecf59a02682a839 Thu Sep 24 20:40:52 2026 -0700
    Description page fixes from a QA pre-pass on the TSS tracks. refs #35528 Encode the non-ASCII character in the Avsec reference on proCapNet.html. getTrackReferences emits raw UTF-8, which the browser does not transcode. Use $db rather than a hardcoded hg38 in the proCapNet download-server link and the bigWigToBedGraph example. One page serves both assemblies, so an hs1 reader was being pointed at hg38 files. Add a Source subsection to proCapNet.html linking the makedoc, the build scripts, the trackDb file and the upstream kundajelab/ProCapNet repository. These links went missing when the Processing at UCSC section was dropped; the prose stays dropped. Drop the cross-links between the two track pages. Track names are prefixed hub_<id>_ on hs1, which is a curated hub, and the id is machine-specific, so a bare-name link cannot work there. Each page now states which assemblies the data is available on instead, naming both GRCh38/hg38 and T2T-CHM13/hs1. Bold the two UI control names on the proCapNet display conventions section.
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    acf20930c5cdfa1e352826a702ad8f36344178c4 Thu Sep 24 21:16:13 2026 -0700
    Fixes from an independent review of the TSS tracks. refs #35528 The Data Access sections told users to pass the composite name to the API, which returns HTTP 400. The API serves one bigWig at a time, so both pages now name a single strand of one cell line, verified to return 200. encode4ProCap.html claimed the kent tree held the manifest of which ENCODE files went into each track, and it did not. Commit that manifest as proCapNetEncodeFiles.tsv and name it on the page. It matters because proCapNetEncodeMeta resolves each experiment's default analysis at run time, so re-running it after an ENCODE reprocessing can pick different files. Cite Shah et al. for the ENCODE 4 nascent transcriptome survey the six PRO-cap experiments come from. Sagar Shah was credited by name with no reference. The hg38 makedoc called the 164268582 dropped bases "the N regions", but gap on the primary chromosomes is 150610728. The extra 13.7 Mb is sequence flanking each gap, dropped because most of its 2114 bp window was unresolved.
  • lines changed 53, context: html, text, full: html, text
    38ccb38771eddfec3230ab3494fb12e11e7cb4ac Fri Sep 25 17:52:32 2026 -0700
    Putting references in alphabetical order. Adding years to citations. Not using the word 'here' and using the actual location/noun. refs #35528
  • lines changed 40, context: html, text, full: html, text
    af96452e1c6ccf783697cead2630de1ca4e91635 Sat Sep 26 06:42:20 2026 -0700
    Put the primary citation first again on the TSS track pages. refs #35528 Alphabetical order buried the paper each track is actually built on: Cochran et al. for ProCapNet, behind Avsec, and Shah et al. for the ENCODE 4 PRO-cap experiments, behind Kwak and Luo. Lead with the primary paper and leave the rest in the order they stood. Reordering only. The years and DOIs added in 38ccb38771e are unchanged.
  • lines changed 27, context: html, text, full: html, text
    40264d0668926b51da94d2ca038dc7349dfc3405 Sat Sep 26 07:59:34 2026 -0700
    Shorten the Methods sections on the two TSS data pages. refs #35528 Both read like a paper's methods section rather than a track description: 43 lines over four subsections on proCapNet, 35 on encode4ProCap. Cut each to three paragraphs, what the model or assay is, how the files we serve were produced, and where the build is recorded. The subsection headings go with it. Kept every fact a user of the track needs: the window and stride, the MANE Select limit on the contribution scores, the unresolved-sequence handling on hg38, the replicate summing, the six ENCODE accessions and the file manifest. Dropped the detail that belongs to the papers, such as the DeepSHAP scalarization and the loss weighting. The container page keeps no Methods section, which is correct for a page that only points at the two data pages.
  • lines changed 24, context: html, text, full: html, text
    31e95f0d1dd4ca08feba9b081a356527bd4b45e6 Sat Sep 26 20:36:20 2026 -0700
    Drop the hand-built Files column from the TSS faceted tables. refs #35528 UCSC will generate the download links in the faceted table, so the Files column each composite built for itself is redundant. Remove downloadCell, the Files header and cell, the Files entry in subtrackUrls, and the DOWNLOAD constant that only fed them. The table is now Tissue, Sample class, Experiment, Cell line on all three composites. writeMetadata no longer needs db or track; the metadata files it writes are byte-identical. Lead each Data Access section with the link to the hgdownload directory, since that is now the way to a single file, and keep the naming convention beside it. Drop the paragraph describing the Files column.
  • lines changed 4, context: html, text, full: html, text
    fe4c75c272ca27de55c0b42396c47f2b00637a4a Mon Sep 28 16:36:20 2026 -0700
    Linking the encode4ProCap trackDb.ra, saying why PRO-cap and contribution scores are hg38 only on the container page, and limiting the ProCapNet prediction claim to the primary chromosomes, refs #35528
  • lines changed 20, context: html, text, full: html, text
    66fafe88184bb3a8a45a50026f4d6c7fbbc24109 Tue Sep 29 10:12:53 2026 -0700
    Rebuild the TSS tracks as traditional composites, for wiggle control. refs #35528 A faceted composite is routed to facetedCompositeUi(), which returns before cfgByCfgType(), so it never draws the wiggle controls: no data view scaling, no viewing range, no windowing function, no track height. Signal tracks need those, so proCapNet and encode4ProCap are now traditional composites. They stay separate composites under the TSS container. The multiWig strand overlays survive the change. The old comment here claimed a multiWig under a plain composite "is flattened away and never drawn"; that is wrong for drawing, which #36320 fixed. Only the hgTrackUi subtrack list flattens, because compositeUiSubtracks() walks to leaves, so the overlays get no inline config block and are configured from their own pages. Raised as #38441. The matrix has to be declared over the leaves, since that is the level hgTrackDb checks: declaring it on the containers fails -strict with "has groups not defined in parent". So a strand is a matrix cell, and the containers carry no subGroups. Sample class survives as a filterComposite dimension, replacing the facet. configurable on gives each subtrack its own config namespace. Drop the faceted machinery: the metadata table, the color file, the constants feeding them and the gbdbDir argument, 39 lines. The metadata.tsv and colors.json already written under /gbdb are now unreferenced and can be deleted. Put the ENCODE accession in each subtrack longLabel, and add a linked table of them to both description pages. A longLabel cannot carry a link, since printSubtrackTableBody() htmlEncodes it, hence the table. The label wording is shortened to keep the longest at 74 characters.
  • lines changed 3, context: html, text, full: html, text
    9f6962c173c405e481da17794d67107e7f8e73a9 Fri Oct 2 16:05:31 2026 -0700
    Replacing the subtrack matrix and Sample class filter paragraph on the PRO-cap and ProCapNet description pages with the track collection layout from Mark's change, and noting that ProCapNet minus strand files store negative values, refs #35528
• src/hg/makeDb/trackDb/human/gpnStar.html
  • lines changed 163, context: html, text, full: html, text
    53ab3f1e293a91ddf71ec7568f4a6ff827bcd278 Fri Oct 2 13:52:36 2026 -0700
    Native GPN-Star track (Ye, Benegas et al., Nature 2026) on hg38, mm39, galGal6, dm6 and ce11, from the authors' Hugging Face hub. Each model is a multiWig sequence logo plus a four-allele -LLR composite using negateValues. The three hg38 models (V/M/P) sit in predictionScoresSuper via human/gpnStar.ra with /gbdb/$D bigDataUrls so -strict drops them on other human assemblies; the other four get a standalone gpnStar superTrack. The authors' bigWigs come from pyBigWig, whose bwAddIntervalSpanSteps writes the last section of each run 6 bases too long (pyBigWig #166) and makes bigWigAverageOverBed and bigWigCorrelate abort, so gpnStarRebuild.sh re-encodes them with wigToBigWig and gpnStarVerify.sh checks every per-base value is unchanged. Entropy scores and the GenArk-only Arabidopsis set are left out, and pennantIcon still has #TBD placeholders for the newsarch anchor and date. refs #38451
• src/hg/makeDb/trackDb/human/gpnStar.ra
  • lines changed 357, context: html, text, full: html, text
    53ab3f1e293a91ddf71ec7568f4a6ff827bcd278 Fri Oct 2 13:52:36 2026 -0700
    Native GPN-Star track (Ye, Benegas et al., Nature 2026) on hg38, mm39, galGal6, dm6 and ce11, from the authors' Hugging Face hub. Each model is a multiWig sequence logo plus a four-allele -LLR composite using negateValues. The three hg38 models (V/M/P) sit in predictionScoresSuper via human/gpnStar.ra with /gbdb/$D bigDataUrls so -strict drops them on other human assemblies; the other four get a standalone gpnStar superTrack. The authors' bigWigs come from pyBigWig, whose bwAddIntervalSpanSteps writes the last section of each run 6 bases too long (pyBigWig #166) and makes bigWigAverageOverBed and bigWigCorrelate abort, so gpnStarRebuild.sh re-encodes them with wigToBigWig and gpnStarVerify.sh checks every per-base value is unchanged. Entropy scores and the GenArk-only Arabidopsis set are left out, and pennantIcon still has #TBD placeholders for the newsarch anchor and date. refs #38451
• src/hg/makeDb/trackDb/human/hg17/multiz17way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg17/multiz8way.html
  • lines changed 27, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg17/phastConsElements17way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg18/cons44way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg18/multiz17way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg18/multiz28way.html
  • lines changed 31, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg18/multizPrimate.html
  • lines changed 10, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg18/phastConsElements17way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg18/phyloPCons28way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg18/phyloPConsLs44way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 21, context: html, text, full: html, text
    1a2f5a5b07855da8d191c0b9358c945d6abe9f74 Mon Sep 28 15:17:28 2026 -0700
    trackDb: fix the netThaSir1 chain table and drop missing hg18 pgSnp prediction tables, refs #37424 The hg38 netThaSir1 stanza was copied from netAnoCar1 and kept its type line, so hgc looked for chainAnoCar1 and every click failed. It now names thaSir1 and chainThaSir1. The hg18 pgKb1Comb, pgNb1, pgMd8, pgTk1 and pgAbtSolid tracks named SIFT and PolyPhen tables that exist only on hgwdev and were never released. The details page warned on every click on beta and the RR. The two settings are removed.
• src/hg/makeDb/trackDb/human/hg19/cons100way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg19/cons46way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg19/tad.ra
  • lines changed 25, context: html, text, full: html, text
    b7b9978c92a2376d6d9ef4f0a4974cb8167295f8 Wed Sep 30 14:17:50 2026 -0700
    Updating the TAD tracks from the qa-track SKILL.md pass (hg19, hg38, mm10, mm39): shortLabel fixes for cut-off and duplicate ENCODE and 3DGB subtracks, lowercase biosamples in ENCODE longLabels, " bnd" dropped from Schmitt shortLabels, 3DGB subtracks set to pack with three mm10/mm39 defaults turned on, allButtonPair removed so the Schmitt matrix shows, and McArthur item labels hidden. Merged identical description pages into human/ and mouse/, plus description page cleanups (regenerated References, removed the "How to use these tracks" section, ENCODE pages now say 112 of 117 biosamples use Arrowhead). Also updated the ENCODE metadata columns and organ example in the hg38 makedoc. refs #21599
• src/hg/makeDb/trackDb/human/hg19/tads.html
  • lines changed 45, context: html, text, full: html, text
    b7b9978c92a2376d6d9ef4f0a4974cb8167295f8 Wed Sep 30 14:17:50 2026 -0700
    Updating the TAD tracks from the qa-track SKILL.md pass (hg19, hg38, mm10, mm39): shortLabel fixes for cut-off and duplicate ENCODE and 3DGB subtracks, lowercase biosamples in ENCODE longLabels, " bnd" dropped from Schmitt shortLabels, 3DGB subtracks set to pack with three mm10/mm39 defaults turned on, allButtonPair removed so the Schmitt matrix shows, and McArthur item labels hidden. Merged identical description pages into human/ and mouse/, plus description page cleanups (regenerated References, removed the "How to use these tracks" section, ENCODE pages now say 112 of 117 biosamples use Arrowhead). Also updated the ENCODE metadata columns and organ example in the hg38 makedoc. refs #21599
• src/hg/makeDb/trackDb/human/hg19/tadsMcArthur.html
  • lines changed 62, context: html, text, full: html, text
    b7b9978c92a2376d6d9ef4f0a4974cb8167295f8 Wed Sep 30 14:17:50 2026 -0700
    Updating the TAD tracks from the qa-track SKILL.md pass (hg19, hg38, mm10, mm39): shortLabel fixes for cut-off and duplicate ENCODE and 3DGB subtracks, lowercase biosamples in ENCODE longLabels, " bnd" dropped from Schmitt shortLabels, 3DGB subtracks set to pack with three mm10/mm39 defaults turned on, allButtonPair removed so the Schmitt matrix shows, and McArthur item labels hidden. Merged identical description pages into human/ and mouse/, plus description page cleanups (regenerated References, removed the "How to use these tracks" section, ENCODE pages now say 112 of 117 biosamples use Arrowhead). Also updated the ENCODE metadata columns and organ example in the hg38 makedoc. refs #21599
• src/hg/makeDb/trackDb/human/hg19/tadsSchmitt.html
  • lines changed 44, context: html, text, full: html, text
    b7b9978c92a2376d6d9ef4f0a4974cb8167295f8 Wed Sep 30 14:17:50 2026 -0700
    Updating the TAD tracks from the qa-track SKILL.md pass (hg19, hg38, mm10, mm39): shortLabel fixes for cut-off and duplicate ENCODE and 3DGB subtracks, lowercase biosamples in ENCODE longLabels, " bnd" dropped from Schmitt shortLabels, 3DGB subtracks set to pack with three mm10/mm39 defaults turned on, allButtonPair removed so the Schmitt matrix shows, and McArthur item labels hidden. Merged identical description pages into human/ and mouse/, plus description page cleanups (regenerated References, removed the "How to use these tracks" section, ENCODE pages now say 112 of 117 biosamples use Arrowhead). Also updated the ENCODE metadata columns and organ example in the hg38 makedoc. refs #21599
• src/hg/makeDb/trackDb/human/hg38/cons100way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/cons17way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/cons20way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/cons241way.html
  • lines changed 34, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 5, context: html, text, full: html, text
    b9c41cec68f33aec1a64d8cc709af9afc15155fa Fri Sep 25 22:49:03 2026 -0700
    hg38 cons241way: point the phyloP tree model text at the directory, refs #34803 The link went to phyloP241way/hg38.phyloP241way.mod, which does not exist and never has under that name. The models live in cactus241way/phyloP241way, and there are three of them rather than one: a general model and separate chrX and chrY models. Link the directory and say so. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/cons27way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/cons30way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/cons470way.html
  • lines changed 45, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/cons5way.html
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    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/cons7way.html
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    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/epigenCentral.html
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    70ec78b7ef15cc060932b5b8dd436fd34bcbdaf1 Fri Sep 25 13:31:22 2026 -0700
    Adding a paragraph about a filtering issue that happens when there is a tie in the absolute max value. refs #38112
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    b0f7c3b8ed633f460990b271070d2c72a4d05ba1 Fri Sep 25 14:55:45 2026 -0700
    Adding GitHub links for the makedoc, scripts, and trackDb to the EpigenCentral page, crediting Max, adding the Turinsky DOI, and using serial commas, refs #38112
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    10be0991b45bc01981e68f72a660adbbcc999f77 Fri Sep 25 15:53:33 2026 -0700
    Updating the filter paragraph on the track description page. Updating the defaultLabels since searching for a CpG ID would result in not showing that ID, refs #38112
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    682284bfd2b229728cbef4ecf79e8b5481953327 Sun Oct 4 05:55:37 2026 -0700
    hg38 epigenCentral: description wording from the EpigenCentral reviewers (available on, direction filter, classification models, drop Dup7 NA note, credits)
• src/hg/makeDb/trackDb/human/hg38/episignatures.html
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    b9529a41ea64f905aced9a54e8eb527c4ad490cf Fri Sep 25 14:59:00 2026 -0700
    Adding more missing commas, refs #38112
• src/hg/makeDb/trackDb/human/hg38/episignatures.ra
  • lines changed 1, context: html, text, full: html, text
    b6ba7ab70c14692cd2cad15a17fb9b605f0efe1e Fri Sep 25 13:13:09 2026 -0700
    Updating the longLabel to sentence case, refs #38112 #38371
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    1aca3edb987bc90a17be6a22efad5446d4e42029 Fri Sep 25 13:44:48 2026 -0700
    Updating the packmode labels to show the episignature instead of the CpG ID. Adding semicolons to the filters so it matches the MethaDory track, refs #38371
  • lines changed 1, context: html, text, full: html, text
    10be0991b45bc01981e68f72a660adbbcc999f77 Fri Sep 25 15:53:33 2026 -0700
    Updating the filter paragraph on the track description page. Updating the defaultLabels since searching for a CpG ID would result in not showing that ID, refs #38112
  • lines changed 1, context: html, text, full: html, text
    9e51fd38996566e7a6cc29dd67f2e05fa429ca3c Mon Sep 28 14:30:05 2026 -0700
    hg38 episignatures: hide epigenCentral bigBed from hgdownload Lou asked for downloads off for this track. tableBrowser off already covers Table Browser/Data Integrator/REST API, but the bigBed itself was still reachable on hgdownload. Prefix the gbdb filename with "_", same convention used for the restricted varFreqs subtracks, which hgdownload's rsync excludes. methaDory.bb is unaffected. refs #38112
• src/hg/makeDb/trackDb/human/hg38/fiberSeq.html
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    10f0f6d5160a96867ecf534e1b9d138df7d9b796 Mon Sep 28 16:17:46 2026 -0700
    Fiber-seq: hide the container by default, and split the five GM lines out into a Rare disease sample class. Max asked for superTrack on rather than on show, since the track covers much the same ground as ENCODE DNase and does not earn a slot in everyone's default hg38 view. The five lymphoblastoid lines GM25455, GM25456, GM27730, GM28570 and GM28572 had been filed as Common Cell Line; Andrew Stergachis says they are rare disease cases consented to broad genomic data sharing and the first of a batch the lab intends to keep adding, so SAMPLE_CLASS_COLORS gains a third entry and the facet now reads 20 HPRC, 16 Common Cell Line, 5 Rare disease sample. refs #36210
• src/hg/makeDb/trackDb/human/hg38/fiberSeq.ra
  • lines changed 1, context: html, text, full: html, text
    10f0f6d5160a96867ecf534e1b9d138df7d9b796 Mon Sep 28 16:17:46 2026 -0700
    Fiber-seq: hide the container by default, and split the five GM lines out into a Rare disease sample class. Max asked for superTrack on rather than on show, since the track covers much the same ground as ENCODE DNase and does not earn a slot in everyone's default hg38 view. The five lymphoblastoid lines GM25455, GM25456, GM27730, GM28570 and GM28572 had been filed as Common Cell Line; Andrew Stergachis says they are rare disease cases consented to broad genomic data sharing and the first of a batch the lab intends to keep adding, so SAMPLE_CLASS_COLORS gains a third entry and the facet now reads 20 HPRC, 16 Common Cell Line, 5 Rare disease sample. refs #36210
  • lines changed 1, context: html, text, full: html, text
    e1d9e18ef2ac6813136d012f9817ddc50ca5bad9 Mon Sep 28 16:27:37 2026 -0700
    Fiber-seq: spell out the accessibility track's shortLabel as "Fiber-seq Accessible" rather than "Fiber-seq Acc". Twenty characters, which is exactly leftLabelWidthDefaultChars, so it fills the left label without clipping; checked in a render at ACTB. refs #36210
  • lines changed 41, context: html, text, full: html, text
    ab234fe62907c81b702a63f5a73d40500a40916f Tue Sep 29 16:12:28 2026 -0700
    Fiber-seq: give the FIRE peak subtracks "visibility dense" instead of "onlyVisibility dense", so their mouseOver can actually be seen. onlyVisibility pins a faceted child rather than defaulting it: tdbVisLimitedByAncestors() in hg/lib/hui.c overwrites the computed visibility with the pinned mode, so a request for pack or full was discarded even from the URL, and the dropdown offered only hide and dense. Since no bigBed-like track draws per-item map boxes in dense, the mouseOver on all 41 peak stanzas was dead config and fiberSeqCompendium.html was promising a hover nobody could reach. Measured at ACTB with the map_data image map: pinned, a forced pack still computed to dense with 0 FIRE tooltips; defaulted, pack and full compute correctly and carry 8. Peaks still come up dense, which is what Andrew asked for in July. The signal types keep onlyVisibility, where pinning to full costs nothing because a bigWig draws the same at pack and full, and that is verified here too: acc, cpg and hap stay at full whatever is requested, and the container stays hidden on a fresh cart. Also fixes two makeDoc slips, the facet notes naming the script's dict keys rather than the column headings writeMetadata() emits, and the opening summary still saying accessibility and CpG "both became faceted composites" when they were merged into one 235 lines later. Caught by Claude review of 156d289 and 5179d7f. refs #38407
• src/hg/makeDb/trackDb/human/hg38/fiberSeqAcc.html
  • lines changed 1, context: html, text, full: html, text
    0b41a0f1e7f66e0bce33b879275a93ccb9d8f976 Mon Sep 28 16:33:18 2026 -0700
    Fiber-seq description pages: bold the six data type names in the Compendium Description, and drop three passages that explained our own rendering rather than the data. The sample table no longer opens by justifying itself with how many checkboxes 41 samples times six data types would need; the difference track now says each position is colored by the most stringent threshold it meets, instead of describing the order the four signals are painted in; and the peak paragraph no longer explains that dense mode has no per-item hover. "Container name" and "subtracks" become "collection name" and "FIRE peaks", per the rule against exposing internal container terms, and the API paragraph points at the Table Browser for the peaks rather than only saying they are unavailable. Per Lou's review. refs #36210
• src/hg/makeDb/trackDb/human/hg38/fiberSeqCompendium.html
  • lines changed 11, context: html, text, full: html, text
    10f0f6d5160a96867ecf534e1b9d138df7d9b796 Mon Sep 28 16:17:46 2026 -0700
    Fiber-seq: hide the container by default, and split the five GM lines out into a Rare disease sample class. Max asked for superTrack on rather than on show, since the track covers much the same ground as ENCODE DNase and does not earn a slot in everyone's default hg38 view. The five lymphoblastoid lines GM25455, GM25456, GM27730, GM28570 and GM28572 had been filed as Common Cell Line; Andrew Stergachis says they are rare disease cases consented to broad genomic data sharing and the first of a batch the lab intends to keep adding, so SAMPLE_CLASS_COLORS gains a third entry and the facet now reads 20 HPRC, 16 Common Cell Line, 5 Rare disease sample. refs #36210
  • lines changed 27, context: html, text, full: html, text
    0b41a0f1e7f66e0bce33b879275a93ccb9d8f976 Mon Sep 28 16:33:18 2026 -0700
    Fiber-seq description pages: bold the six data type names in the Compendium Description, and drop three passages that explained our own rendering rather than the data. The sample table no longer opens by justifying itself with how many checkboxes 41 samples times six data types would need; the difference track now says each position is colored by the most stringent threshold it meets, instead of describing the order the four signals are painted in; and the peak paragraph no longer explains that dense mode has no per-item hover. "Container name" and "subtracks" become "collection name" and "FIRE peaks", per the rule against exposing internal container terms, and the API paragraph points at the Table Browser for the peaks rather than only saying they are unavailable. Per Lou's review. refs #36210
  • lines changed 3, context: html, text, full: html, text
    54f465e316441236c128491e53c0e5464c0e672c Tue Sep 29 11:40:49 2026 -0700
    Fiber-seq: bring the fiberSeqTrackDb.py docstrings back in line with the three-value sampleClass, and stop the Compendium intro from keeping a running tally of where the lymphoblastoid lines came from. readSamples still said the five GM lines were common cell lines and writeMetadata still said there were two classes, both a few lines from the SAMPLE_CLASS_COLORS entry that added the third. writeMetadata also still had "Common Cell Line" in the old Title Case, which yesterday's rename missed because the string is wrapped across two source lines and a line oriented sed cannot see it; worth remembering for the next rename. The intro sentence had grown a breakdown that did not add up, 20 HPRC plus 5 rare disease against 27 lymphoblastoid lines, leaving GM12878 and HG002 unaccounted; it now points at the Sample class filter instead of counting, since the lab has said more rare disease samples are coming and the tally would go stale again. While in there, the claim that accession order keeps each class together is softened to what the data actually does: the common cell lines fall in two runs either side of the HPRC block. Generated output is unchanged; the .ra, the metadata TSV and the colors JSON all regenerate byte identical. Caught by Claude review of 10f0f6d516. refs #36210
• src/hg/makeDb/trackDb/human/hg38/fiveUltraUorfs.html
  • lines changed 50, context: html, text, full: html, text
    1995fb5512978d502812e7693d5d487bea61f507 Wed Sep 23 15:26:14 2026 -0700
    Updating the ncOrfs description pages: Restructuring gencNcOrfs.html's Description and Display Conventions sections and cleaning up wording. Updating the Description section of fiveUltraUorfs.html. Updating ncOrfs.html's GENCODE and 5ULTRA sections to match their subtrack pages and trimming the GENCODE summary. Minor updates to ncOrfs.ra. Refs #37649
• src/hg/makeDb/trackDb/human/hg38/gencNcOrfs.html
  • lines changed 100, context: html, text, full: html, text
    1995fb5512978d502812e7693d5d487bea61f507 Wed Sep 23 15:26:14 2026 -0700
    Updating the ncOrfs description pages: Restructuring gencNcOrfs.html's Description and Display Conventions sections and cleaning up wording. Updating the Description section of fiveUltraUorfs.html. Updating ncOrfs.html's GENCODE and 5ULTRA sections to match their subtrack pages and trimming the GENCODE summary. Minor updates to ncOrfs.ra. Refs #37649
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 1, context: html, text, full: html, text
    f20626542200362afacab9387842e1f5bb50c87c Fri Sep 25 12:43:42 2026 -0700
    Experimental gnomAD v4.1.1 VCF track for hg38, refs #37617
• src/hg/makeDb/trackDb/human/hg38/gnomadV4.1.1.ra
  • lines changed 26, context: html, text, full: html, text
    f20626542200362afacab9387842e1f5bb50c87c Fri Sep 25 12:43:42 2026 -0700
    Experimental gnomAD v4.1.1 VCF track for hg38, refs #37617
• src/hg/makeDb/trackDb/human/hg38/hg38.GCA_040939475.2.chainNet.ra
  • lines changed 49, context: html, text, full: html, text
    1c0a16d8c4d5ad60b5bd5f0fe6470bdd4c5f3f58 Wed Sep 23 16:26:39 2026 -0700
    chainNet trackDb for hg38 GCA_040939475.2, otto liftOver
• src/hg/makeDb/trackDb/human/hg38/hg38.GCF_002880755.1.chainNet.ra
  • lines changed 49, context: html, text, full: html, text
    5b1a5a9767296bfeb7c1a1d08fc9c6677e7ca032 Fri Sep 25 02:32:27 2026 -0700
    chainNet trackDb for hg38 GCF_002880755.1, otto liftOver
• src/hg/makeDb/trackDb/human/hg38/hprcPclai.html
  • lines changed 7, context: html, text, full: html, text
    32048e16a50722894cf28d9b7b4b050302e38c75 Wed Sep 30 17:54:58 2026 -0700
    Spell the acronym PCLAI, not pcLAI. refs #35415 The authors write it PCLAI throughout: the upstream README at AI-sandbox/hprc-pclai uses PCLAI 18 times and pcLAI never, under the title "Point Cloud Local Ancestry Inference (PCLAI)". We had pcLAI in 517 places, across the track labels, both description pages, the makedocs, the build scripts and the autoSql. hprcPclai.ra holds 467 of those, in shortLabel, longLabel, dataVersion and comments. It is generated, so the fix went into hprcPclaiMakeTrackDb.py and the file was rebuilt; every line of the resulting diff differs only by the rename. Track names, file names and the lowercase pclai in URLs and data file names are untouched. None of them contained the string pcLAI, and renaming the tracks would break saved sessions for no user-visible gain.
• src/hg/makeDb/trackDb/human/hg38/hprcPclai.ra
  • lines changed 467, context: html, text, full: html, text
    32048e16a50722894cf28d9b7b4b050302e38c75 Wed Sep 30 17:54:58 2026 -0700
    Spell the acronym PCLAI, not pcLAI. refs #35415 The authors write it PCLAI throughout: the upstream README at AI-sandbox/hprc-pclai uses PCLAI 18 times and pcLAI never, under the title "Point Cloud Local Ancestry Inference (PCLAI)". We had pcLAI in 517 places, across the track labels, both description pages, the makedocs, the build scripts and the autoSql. hprcPclai.ra holds 467 of those, in shortLabel, longLabel, dataVersion and comments. It is generated, so the fix went into hprcPclaiMakeTrackDb.py and the file was rebuilt; every line of the resulting diff differs only by the rename. Track names, file names and the lowercase pclai in URLs and data file names are untouched. None of them contained the string pcLAI, and renaming the tracks would break saved sessions for no user-visible gain.
• src/hg/makeDb/trackDb/human/hg38/mavemd.html
  • lines changed 42, context: html, text, full: html, text
    824df26b6320b692d629566c5a10b15004da82ce Tue Sep 29 16:09:00 2026 -0700
    addProteinSequence in mavemdLib translates each transcript's CDS from hg38.2bit so makeMaveMdVariants can check every projected codon against the reference residue its own HGVS term asserts; the existing comparison against MaveDB's genomic mapping only reaches the 3% of projected items that carry both terms, because 18 of the 40 protein accessions have no genomic-route variants at all. 39 of 40 accessions match at 0.000%; NP_689629.2 (FKRP) has 99 nonsense terms numbered one codon downstream of their own reference residue, which still reach mavemdVar through MaveDB's genomic mapping but are dropped from mavemdMap, which places columns from the protein term and has no fallback. The haplotype test now also reads hgvs_nt, since PTEN 00000054-a-1 states 1,236 haplotypes as c.[1207G>T;1209C>T] with no protein term and they were counted as rejected submissions, making both figures in the makeDoc wrong. assayLine runs the heatmap legend through asciiText because bedField turns the en dash in three MaveDB titles into &#8211; and the legend is drawn as raster text; clinGenId links to by_canonicalid rather than /allele, which serves JSON to a browser, matching human/civic.ra; the generated filter fragment no longer emits the blank line after each group that the makeDoc itself warns ends a stanza; and runBuild.sh tails the log on failure instead of dying silently under set -e. Also reworded the grey legend entry, which said no threshold was reached in either direction but covers 6,656 normal and 145 abnormal items, alphabetized the references, and fixed stale counts in the makeDoc. Caught by Claude review of 29af14b, fcf788d and 97c7de5. refs #38407 refs #37800
• src/hg/makeDb/trackDb/human/hg38/mavemd.ra
  • lines changed 1, context: html, text, full: html, text
    824df26b6320b692d629566c5a10b15004da82ce Tue Sep 29 16:09:00 2026 -0700
    addProteinSequence in mavemdLib translates each transcript's CDS from hg38.2bit so makeMaveMdVariants can check every projected codon against the reference residue its own HGVS term asserts; the existing comparison against MaveDB's genomic mapping only reaches the 3% of projected items that carry both terms, because 18 of the 40 protein accessions have no genomic-route variants at all. 39 of 40 accessions match at 0.000%; NP_689629.2 (FKRP) has 99 nonsense terms numbered one codon downstream of their own reference residue, which still reach mavemdVar through MaveDB's genomic mapping but are dropped from mavemdMap, which places columns from the protein term and has no fallback. The haplotype test now also reads hgvs_nt, since PTEN 00000054-a-1 states 1,236 haplotypes as c.[1207G>T;1209C>T] with no protein term and they were counted as rejected submissions, making both figures in the makeDoc wrong. assayLine runs the heatmap legend through asciiText because bedField turns the en dash in three MaveDB titles into &#8211; and the legend is drawn as raster text; clinGenId links to by_canonicalid rather than /allele, which serves JSON to a browser, matching human/civic.ra; the generated filter fragment no longer emits the blank line after each group that the makeDoc itself warns ends a stanza; and runBuild.sh tails the log on failure instead of dying silently under set -e. Also reworded the grey legend entry, which said no threshold was reached in either direction but covers 6,656 normal and 145 abnormal items, alphabetized the references, and fixed stale counts in the makeDoc. Caught by Claude review of 29af14b, fcf788d and 97c7de5. refs #38407 refs #37800
• src/hg/makeDb/trackDb/human/hg38/mavemdMap.html
  • lines changed 44, context: html, text, full: html, text
    824df26b6320b692d629566c5a10b15004da82ce Tue Sep 29 16:09:00 2026 -0700
    addProteinSequence in mavemdLib translates each transcript's CDS from hg38.2bit so makeMaveMdVariants can check every projected codon against the reference residue its own HGVS term asserts; the existing comparison against MaveDB's genomic mapping only reaches the 3% of projected items that carry both terms, because 18 of the 40 protein accessions have no genomic-route variants at all. 39 of 40 accessions match at 0.000%; NP_689629.2 (FKRP) has 99 nonsense terms numbered one codon downstream of their own reference residue, which still reach mavemdVar through MaveDB's genomic mapping but are dropped from mavemdMap, which places columns from the protein term and has no fallback. The haplotype test now also reads hgvs_nt, since PTEN 00000054-a-1 states 1,236 haplotypes as c.[1207G>T;1209C>T] with no protein term and they were counted as rejected submissions, making both figures in the makeDoc wrong. assayLine runs the heatmap legend through asciiText because bedField turns the en dash in three MaveDB titles into &#8211; and the legend is drawn as raster text; clinGenId links to by_canonicalid rather than /allele, which serves JSON to a browser, matching human/civic.ra; the generated filter fragment no longer emits the blank line after each group that the makeDoc itself warns ends a stanza; and runBuild.sh tails the log on failure instead of dying silently under set -e. Also reworded the grey legend entry, which said no threshold was reached in either direction but covers 6,656 normal and 145 abnormal items, alphabetized the references, and fixed stale counts in the makeDoc. Caught by Claude review of 29af14b, fcf788d and 97c7de5. refs #38407 refs #37800
• src/hg/makeDb/trackDb/human/hg38/mavemdVar.html
  • lines changed 45, context: html, text, full: html, text
    824df26b6320b692d629566c5a10b15004da82ce Tue Sep 29 16:09:00 2026 -0700
    addProteinSequence in mavemdLib translates each transcript's CDS from hg38.2bit so makeMaveMdVariants can check every projected codon against the reference residue its own HGVS term asserts; the existing comparison against MaveDB's genomic mapping only reaches the 3% of projected items that carry both terms, because 18 of the 40 protein accessions have no genomic-route variants at all. 39 of 40 accessions match at 0.000%; NP_689629.2 (FKRP) has 99 nonsense terms numbered one codon downstream of their own reference residue, which still reach mavemdVar through MaveDB's genomic mapping but are dropped from mavemdMap, which places columns from the protein term and has no fallback. The haplotype test now also reads hgvs_nt, since PTEN 00000054-a-1 states 1,236 haplotypes as c.[1207G>T;1209C>T] with no protein term and they were counted as rejected submissions, making both figures in the makeDoc wrong. assayLine runs the heatmap legend through asciiText because bedField turns the en dash in three MaveDB titles into &#8211; and the legend is drawn as raster text; clinGenId links to by_canonicalid rather than /allele, which serves JSON to a browser, matching human/civic.ra; the generated filter fragment no longer emits the blank line after each group that the makeDoc itself warns ends a stanza; and runBuild.sh tails the log on failure instead of dying silently under set -e. Also reworded the grey legend entry, which said no threshold was reached in either direction but covers 6,656 normal and 145 abnormal items, alphabetized the references, and fixed stale counts in the makeDoc. Caught by Claude review of 29af14b, fcf788d and 97c7de5. refs #38407 refs #37800
• src/hg/makeDb/trackDb/human/hg38/miniMapChains.ra
  • lines changed 72, context: html, text, full: html, text
    6c02c046a1f2a5d9462db2dc26dfe46369d3c3cf Wed Sep 30 15:51:43 2026 -0700
    shown miniMap2 hs1 alignment and swapped from hs1 refs #34360
• src/hg/makeDb/trackDb/human/hg38/mpra.ra
  • lines changed 1, context: html, text, full: html, text
    f4d967492fedb59d2e528cf196e35c1da248ae96 Fri Oct 2 07:15:47 2026 -0700
    Quarterly pennant cleanup: removing New/Updated pennantIcons released before July 2026 (strVar, nmd, promoterAi, primateAi, mpra, varaico). No RM.
• src/hg/makeDb/trackDb/human/hg38/ncOrfs.html
  • lines changed 56, context: html, text, full: html, text
    1995fb5512978d502812e7693d5d487bea61f507 Wed Sep 23 15:26:14 2026 -0700
    Updating the ncOrfs description pages: Restructuring gencNcOrfs.html's Description and Display Conventions sections and cleaning up wording. Updating the Description section of fiveUltraUorfs.html. Updating ncOrfs.html's GENCODE and 5ULTRA sections to match their subtrack pages and trimming the GENCODE summary. Minor updates to ncOrfs.ra. Refs #37649
• src/hg/makeDb/trackDb/human/hg38/ncOrfs.ra
  • lines changed 3, context: html, text, full: html, text
    1995fb5512978d502812e7693d5d487bea61f507 Wed Sep 23 15:26:14 2026 -0700
    Updating the ncOrfs description pages: Restructuring gencNcOrfs.html's Description and Display Conventions sections and cleaning up wording. Updating the Description section of fiveUltraUorfs.html. Updating ncOrfs.html's GENCODE and 5ULTRA sections to match their subtrack pages and trimming the GENCODE summary. Minor updates to ncOrfs.ra. Refs #37649
• src/hg/makeDb/trackDb/human/hg38/nmd.ra
  • lines changed 1, context: html, text, full: html, text
    f4d967492fedb59d2e528cf196e35c1da248ae96 Fri Oct 2 07:15:47 2026 -0700
    Quarterly pennant cleanup: removing New/Updated pennantIcons released before July 2026 (strVar, nmd, promoterAi, primateAi, mpra, varaico). No RM.
• src/hg/makeDb/trackDb/human/hg38/problematic.html
  • lines changed 10, context: html, text, full: html, text
    b197e1670a076b65838fd91b869a4ec1c3096c0f Wed Sep 23 16:08:08 2026 -0700
    Add Panmask Difficult 151b, the inverse of Panmask Easy 151b, for the Problematic Regions RTS Panmask marks easy regions under a "Problematic Regions" container, which Anna flagged as confusing. Rather than change the released Panmask Easy track, add a second track with the complement regions, built with featureBits (excluding assembly gaps and restricted to the 24 chromosomes Panmask itself covers). Checked the source first: Zenodo record 16755940 is still v1.4, same version already in use, MD5 verified. New track is alpha only for QA to pick up. refs #38375
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    1bab8758e7a5fe01120847c7fa68de71d1aa709e Wed Sep 23 16:16:44 2026 -0700
    commenting out a docs piece before release
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    2ae817bcd648f2a3184bb4b118840e65749fea2d Thu Sep 24 04:15:20 2026 -0700
    problematic.txt/html: reconcile Panmask Easy/Difficult coverage to 87.8%/12.2%, one decimal place, refs #38375
• src/hg/makeDb/trackDb/human/hg38/problematic.ra
  • lines changed 11, context: html, text, full: html, text
    b197e1670a076b65838fd91b869a4ec1c3096c0f Wed Sep 23 16:08:08 2026 -0700
    Add Panmask Difficult 151b, the inverse of Panmask Easy 151b, for the Problematic Regions RTS Panmask marks easy regions under a "Problematic Regions" container, which Anna flagged as confusing. Rather than change the released Panmask Easy track, add a second track with the complement regions, built with featureBits (excluding assembly gaps and restricted to the 24 chromosomes Panmask itself covers). Checked the source first: Zenodo record 16755940 is still v1.4, same version already in use, MD5 verified. New track is alpha only for QA to pick up. refs #38375
  • lines changed 2, context: html, text, full: html, text
    537820f946a4a16341ed8f68c477a89d8c11ce62 Wed Sep 23 16:20:49 2026 -0700
    docs
• src/hg/makeDb/trackDb/human/hg38/strVar.ra
  • lines changed 1, context: html, text, full: html, text
    f4d967492fedb59d2e528cf196e35c1da248ae96 Fri Oct 2 07:15:47 2026 -0700
    Quarterly pennant cleanup: removing New/Updated pennantIcons released before July 2026 (strVar, nmd, promoterAi, primateAi, mpra, varaico). No RM.
• src/hg/makeDb/trackDb/human/hg38/tad.ra
  • lines changed 25, context: html, text, full: html, text
    b7b9978c92a2376d6d9ef4f0a4974cb8167295f8 Wed Sep 30 14:17:50 2026 -0700
    Updating the TAD tracks from the qa-track SKILL.md pass (hg19, hg38, mm10, mm39): shortLabel fixes for cut-off and duplicate ENCODE and 3DGB subtracks, lowercase biosamples in ENCODE longLabels, " bnd" dropped from Schmitt shortLabels, 3DGB subtracks set to pack with three mm10/mm39 defaults turned on, allButtonPair removed so the Schmitt matrix shows, and McArthur item labels hidden. Merged identical description pages into human/ and mouse/, plus description page cleanups (regenerated References, removed the "How to use these tracks" section, ENCODE pages now say 112 of 117 biosamples use Arrowhead). Also updated the ENCODE metadata columns and organ example in the hg38 makedoc. refs #21599
• src/hg/makeDb/trackDb/human/hg38/tads.html
  • lines changed 80, context: html, text, full: html, text
    b7b9978c92a2376d6d9ef4f0a4974cb8167295f8 Wed Sep 30 14:17:50 2026 -0700
    Updating the TAD tracks from the qa-track SKILL.md pass (hg19, hg38, mm10, mm39): shortLabel fixes for cut-off and duplicate ENCODE and 3DGB subtracks, lowercase biosamples in ENCODE longLabels, " bnd" dropped from Schmitt shortLabels, 3DGB subtracks set to pack with three mm10/mm39 defaults turned on, allButtonPair removed so the Schmitt matrix shows, and McArthur item labels hidden. Merged identical description pages into human/ and mouse/, plus description page cleanups (regenerated References, removed the "How to use these tracks" section, ENCODE pages now say 112 of 117 biosamples use Arrowhead). Also updated the ENCODE metadata columns and organ example in the hg38 makedoc. refs #21599
• src/hg/makeDb/trackDb/human/hg38/tads3dgb.html
  • lines changed 34, context: html, text, full: html, text
    b7b9978c92a2376d6d9ef4f0a4974cb8167295f8 Wed Sep 30 14:17:50 2026 -0700
    Updating the TAD tracks from the qa-track SKILL.md pass (hg19, hg38, mm10, mm39): shortLabel fixes for cut-off and duplicate ENCODE and 3DGB subtracks, lowercase biosamples in ENCODE longLabels, " bnd" dropped from Schmitt shortLabels, 3DGB subtracks set to pack with three mm10/mm39 defaults turned on, allButtonPair removed so the Schmitt matrix shows, and McArthur item labels hidden. Merged identical description pages into human/ and mouse/, plus description page cleanups (regenerated References, removed the "How to use these tracks" section, ENCODE pages now say 112 of 117 biosamples use Arrowhead). Also updated the ENCODE metadata columns and organ example in the hg38 makedoc. refs #21599
• src/hg/makeDb/trackDb/human/hg38/tads3dgb.ra
  • lines changed 506, context: html, text, full: html, text
    b7b9978c92a2376d6d9ef4f0a4974cb8167295f8 Wed Sep 30 14:17:50 2026 -0700
    Updating the TAD tracks from the qa-track SKILL.md pass (hg19, hg38, mm10, mm39): shortLabel fixes for cut-off and duplicate ENCODE and 3DGB subtracks, lowercase biosamples in ENCODE longLabels, " bnd" dropped from Schmitt shortLabels, 3DGB subtracks set to pack with three mm10/mm39 defaults turned on, allButtonPair removed so the Schmitt matrix shows, and McArthur item labels hidden. Merged identical description pages into human/ and mouse/, plus description page cleanups (regenerated References, removed the "How to use these tracks" section, ENCODE pages now say 112 of 117 biosamples use Arrowhead). Also updated the ENCODE metadata columns and organ example in the hg38 makedoc. refs #21599
• src/hg/makeDb/trackDb/human/hg38/tadsDixon.html
  • lines changed 44, context: html, text, full: html, text
    b7b9978c92a2376d6d9ef4f0a4974cb8167295f8 Wed Sep 30 14:17:50 2026 -0700
    Updating the TAD tracks from the qa-track SKILL.md pass (hg19, hg38, mm10, mm39): shortLabel fixes for cut-off and duplicate ENCODE and 3DGB subtracks, lowercase biosamples in ENCODE longLabels, " bnd" dropped from Schmitt shortLabels, 3DGB subtracks set to pack with three mm10/mm39 defaults turned on, allButtonPair removed so the Schmitt matrix shows, and McArthur item labels hidden. Merged identical description pages into human/ and mouse/, plus description page cleanups (regenerated References, removed the "How to use these tracks" section, ENCODE pages now say 112 of 117 biosamples use Arrowhead). Also updated the ENCODE metadata columns and organ example in the hg38 makedoc. refs #21599
• src/hg/makeDb/trackDb/human/hg38/tadsEncode.html
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    b7b9978c92a2376d6d9ef4f0a4974cb8167295f8 Wed Sep 30 14:17:50 2026 -0700
    Updating the TAD tracks from the qa-track SKILL.md pass (hg19, hg38, mm10, mm39): shortLabel fixes for cut-off and duplicate ENCODE and 3DGB subtracks, lowercase biosamples in ENCODE longLabels, " bnd" dropped from Schmitt shortLabels, 3DGB subtracks set to pack with three mm10/mm39 defaults turned on, allButtonPair removed so the Schmitt matrix shows, and McArthur item labels hidden. Merged identical description pages into human/ and mouse/, plus description page cleanups (regenerated References, removed the "How to use these tracks" section, ENCODE pages now say 112 of 117 biosamples use Arrowhead). Also updated the ENCODE metadata columns and organ example in the hg38 makedoc. refs #21599
• src/hg/makeDb/trackDb/human/hg38/tadsEncode.ra
  • lines changed 86, context: html, text, full: html, text
    b7b9978c92a2376d6d9ef4f0a4974cb8167295f8 Wed Sep 30 14:17:50 2026 -0700
    Updating the TAD tracks from the qa-track SKILL.md pass (hg19, hg38, mm10, mm39): shortLabel fixes for cut-off and duplicate ENCODE and 3DGB subtracks, lowercase biosamples in ENCODE longLabels, " bnd" dropped from Schmitt shortLabels, 3DGB subtracks set to pack with three mm10/mm39 defaults turned on, allButtonPair removed so the Schmitt matrix shows, and McArthur item labels hidden. Merged identical description pages into human/ and mouse/, plus description page cleanups (regenerated References, removed the "How to use these tracks" section, ENCODE pages now say 112 of 117 biosamples use Arrowhead). Also updated the ENCODE metadata columns and organ example in the hg38 makedoc. refs #21599
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    1c0a16d8c4d5ad60b5bd5f0fe6470bdd4c5f3f58 Wed Sep 23 16:26:39 2026 -0700
    chainNet trackDb for hg38 GCA_040939475.2, otto liftOver
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    5b1a5a9767296bfeb7c1a1d08fc9c6677e7ca032 Fri Sep 25 02:32:27 2026 -0700
    chainNet trackDb for hg38 GCF_002880755.1, otto liftOver
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    f9a684a437d33c33690cf6ffc91faf155d9d5121 Fri Sep 25 15:57:57 2026 -0700
    Staging the Episignatures track on hgwbeta, refs #38112 and #38371
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    ce7133b45942cf33b8bf074af8b3fd6952381f95 Tue Sep 29 16:50:33 2026 -0700
    Staging the STR track on beta for hg38, hg19, and hs1, refs #38268
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    6c02c046a1f2a5d9462db2dc26dfe46369d3c3cf Wed Sep 30 15:51:43 2026 -0700
    shown miniMap2 hs1 alignment and swapped from hs1 refs #34360
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    3bee9e40921231f206014d66a54c6af7581bd4b7 Fri Oct 2 16:54:40 2026 -0700
    Releasing the ProCapNet tracks, refs #35528
• src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra
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    5e83632c91c1c536880da1e364a41467856135bd Tue Sep 22 11:02:32 2026 -0700
    Rename the TSS container and trim the ProCapNet description. refs #35528 Both labels on the transcriptionStart container are now "Transcription Initiation (TSS)". Changed in proCapNetTrackDb and the two transcriptionStart.ra files regenerated from it, since they are generated and carry a do-not-edit header. Dropped the Processing at UCSC section from the ProCapNet page. How the files reached UCSC is not something a browser user needs; the makeDoc already records it, including the NaN bases dropped from the hg38 predictions. Replaced the Kundaje lab server link with the ENCODE portal. The six ENCODE records are BPNet-model annotations holding the trained model, contribution scores and predicted signal over a selected region set. The genome-wide predictions in this track are roughly fifty times larger than the ENCODE predicted-signal files and are not part of that release, so the page says so rather than naming ENCODE as their source. Claude-Session: https://claude.ai/code/session_01LAB6jWshLvB7eNXQKWVuW5
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    b8a77f50143d1cc2a474fe9a56fe7c362183a07f Fri Sep 25 17:35:01 2026 -0700
    Making the shortLabel sentence case. Updating the shortlabel for the subtracks to say 'Predicted' or 'Contributed', refs #35528
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    717ce54a6012dedd51b0100c643a7a252a16fabb Fri Sep 25 17:46:20 2026 -0700
    Adding windowingFuction maximum to trackDb and the script that generates the trackDb file. refs #35528
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    49de9e93e4417083feb23522a71e3960595828a3 Fri Sep 25 22:46:28 2026 -0700
    ProCapNet label and facet color fixes from QA. refs #35528 The composite longLabel named the sequence-contribution scores, which only exist on hg38, so it was wrong on hs1. Use "ProCapNet predicted PRO-cap" on both assemblies; the scores are described on the track description page. The Sample class swatches reused two colors from the cell-line palette, so a track's color could be read as its class: A673 is a cancer line and drew in #0072B2, which was the Non-cancer swatch. Sample class is a binary facet and does not need a hue, so use black and gray, outside the Okabe-Ito palette. Say in the description that the contribution scores cover about 1% of the genome, so the limit is visible before the display conventions section.
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    31e95f0d1dd4ca08feba9b081a356527bd4b45e6 Sat Sep 26 20:36:20 2026 -0700
    Drop the hand-built Files column from the TSS faceted tables. refs #35528 UCSC will generate the download links in the faceted table, so the Files column each composite built for itself is redundant. Remove downloadCell, the Files header and cell, the Files entry in subtrackUrls, and the DOWNLOAD constant that only fed them. The table is now Tissue, Sample class, Experiment, Cell line on all three composites. writeMetadata no longer needs db or track; the metadata files it writes are byte-identical. Lead each Data Access section with the link to the hgdownload directory, since that is now the way to a single file, and keep the naming convention beside it. Drop the paragraph describing the Files column.
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    66fafe88184bb3a8a45a50026f4d6c7fbbc24109 Tue Sep 29 10:12:53 2026 -0700
    Rebuild the TSS tracks as traditional composites, for wiggle control. refs #35528 A faceted composite is routed to facetedCompositeUi(), which returns before cfgByCfgType(), so it never draws the wiggle controls: no data view scaling, no viewing range, no windowing function, no track height. Signal tracks need those, so proCapNet and encode4ProCap are now traditional composites. They stay separate composites under the TSS container. The multiWig strand overlays survive the change. The old comment here claimed a multiWig under a plain composite "is flattened away and never drawn"; that is wrong for drawing, which #36320 fixed. Only the hgTrackUi subtrack list flattens, because compositeUiSubtracks() walks to leaves, so the overlays get no inline config block and are configured from their own pages. Raised as #38441. The matrix has to be declared over the leaves, since that is the level hgTrackDb checks: declaring it on the containers fails -strict with "has groups not defined in parent". So a strand is a matrix cell, and the containers carry no subGroups. Sample class survives as a filterComposite dimension, replacing the facet. configurable on gives each subtrack its own config namespace. Drop the faceted machinery: the metadata table, the color file, the constants feeding them and the gbdbDir argument, 39 lines. The metadata.tsv and colors.json already written under /gbdb are now unreferenced and can be deleted. Put the ENCODE accession in each subtrack longLabel, and add a linked table of them to both description pages. A longLabel cannot carry a link, since printSubtrackTableBody() htmlEncodes it, hence the table. The label wording is shortened to keep the longest at 74 characters.
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    bdf448295c10bee74b6baa773f6733ce33171996 Thu Oct 1 20:56:37 2026 -0700
    Store the ProCapNet minus strand negated, and fix group autoscale. refs #35528 Two of the three problems Jairo found on the composite. The negate control did not work on ProCapNet. Its minus-strand files held positive values and were flipped at display time with trackDb negateValues. The composite's control sets one shared value, which replaced the per-track setting and sent both strands the same way, with no route back to the default short of a cart reset. encode4ProCap was fine because ENCODE publishes its minus strand negative already. So put the sign in the data: proCapNetPredToFixedStep gains --negate, proCapNetPredBuild passes it for the minus strand, and negateValues is gone from the stanzas. The twelve existing files were rewritten rather than rebuilt, since the downloads had been deleted; each was checked against its original for identical nBasesCovered, a mirrored value range and exactly negated values. The originals are kept in previousPred, about 197 GB, until QA is done. Group autoscale on the composite did nothing, which was my error: the multiWig containers and the contribution leaves each carried autoScale on, and the child setting wins. The wiggle settings now live only on the composite. The third, an empty row when both strands of a cell line are deselected, is #38441 and is not fixed here. Note in both makedocs and in the generator that this arrangement only partly works and is expected to become a superTrack of multiWig overlays: under a composite, hgTrackUi lists leaves rather than containers, so an overlay gets no inline config block and leaves an empty row when deselected.
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    1c32191759769c28cf763342f5e405420add0170 Thu Oct 1 21:20:54 2026 -0700
    Make the TSS tracks superTracks of multiWig overlays. refs #35528 The composite held the multiWig overlays as children, which drew correctly but left two faults, both from hgTrackUi listing descendant leaves rather than containers: an overlay got no configuration block of its own, and hiding both strands of a cell line left an empty row where the overlay had been. That is #38441. As superTrack members the overlays are tracks in their own right. Each gets a full configuration page, including overlay method and negate values, and hiding one hides the whole overlay. Verified: hiding proCapNet_K562_pred removes the row and leaves the other five. Two top-level superTracks, PRO-cap and ProCapNet, rather than one transcriptionStart folder holding both. superTracks do not nest. A superTrack given a parent passes tdbQuery -check -strict and is then dropped at load, since trackDbSuperMarkup refuses to set a parent on a superTrack and hgTrackDb only writes a superTrack that some track names as its parent. Filed as #38460, with the test case; transcriptionStart.html stays in the tree unused in case it is fixed. What this costs: the subtrack matrix and the sample class filter, which a superTrack does not offer. Each overlay now carries its own wiggle settings and its own html, neither being inherited from a container any more.
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    0ca316803a93c570fc7614479afd322194f17217 Fri Oct 2 06:53:26 2026 -0700
    Drop priority from the two TSS superTrack stanzas. refs #35528 The folders take whatever position the group gives them. The member tracks keep their own priorities, which order each overlay within its folder.
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    d0ddd717713f275dc2f567c9b6d733fd3f55bd90 Fri Oct 2 21:27:25 2026 -0700
    Put PRO-cap and ProCapNet inside a Transcription Initiation folder. refs #35528 The two data sources were top-level superTracks because a superTrack could not be a member of another one. #38460 fixes that, so they now sit inside a transcriptionStart superTrack, which is what the collection was meant to be. The container is written before either of its children, and both children before any of their members: tdbQuery -strict rejects a file in which another track comes between a superTrack and one of its children. This depends on the #38460 build. A plain make here with the installed binaries produces a half-built state, since hgTrackDb drops the container from the table and trackDbToTxt then writes an hs1 curated hub whose member names a parent stanza that is not there. Both makedocs say so.
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    e314363411293556f33418abe8923ad1e8bc496a Fri Oct 2 21:36:04 2026 -0700
    Revert the TSS nesting on master; it lives on superTrackNesting. refs #35528 Putting PRO-cap and ProCapNet inside a transcriptionStart superTrack needs the nesting fix in #38460, which is not released. These tracks were released in 3bee9e40921, so on beta and the RR hgTrackDb would drop the container and trackDbToTxt would write an hs1 curated hub whose members name a parent stanza that is not there. The work is on the superTrackNesting branch and can come back once #38460 ships.
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    0c42aea56b751a2b4a58feb225a9659819a90994 Sat Oct 3 06:22:01 2026 -0700
    Nest the TSS tracks on alpha only, leaving the release as it is. refs #35528 PRO-cap and ProCapNet sit inside a transcriptionStart superTrack on alpha. That needs #38460, which is on master but not in a release, and these tracks are already released, so each source is written twice with complementary release tags: the nested copy alpha, the flat copy beta,public. hgTrackDb takes the copy whose release matches and rejects two whose releases overlap. Verified that beta and public are untouched: a public build from this file is byte-identical to a public build from the released flat tree, same md5 over tableName, shortLabel, type, visibility, priority and settings. tdbQuery -check -strict passes on all three releases, and an alpha build has the container with both members parented while beta and public have neither. Drop the release tags and the flat copies once #38460 ships. The makedocs also record that the alpha build needs hgTrackDb and trackDbToTxt in /cluster/bin/x86_64 to carry the #38460 fix. make alpha does not install there, BINDIR defaults to ~/bin/$MACHTYPE, so they were put in by hand and the weekly utils build will overwrite them.
• src/hg/makeDb/trackDb/human/hs1/chainLiftOverHg38.ra
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    ad6dd2177ad20bea9e32563ee76a1c598bccb6d5 Tue Sep 29 23:22:17 2026 -0700
    adding hg38 liftOver chain from lastz refs #34360
• src/hg/makeDb/trackDb/human/hs1/crispr.ra
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    cf9cfcd463d40a868f8ee73dead17ff8071dce2f Fri Sep 25 03:00:20 2026 -0700
    CRISPR tracks: expose colorFields dropdown to color guides by off-target specificity (MIT score) or by Moreno-Mateos efficiency, as alternatives to the default Doench/Fusi-based itemRgb color. The bigBed already carries these as the _specColor and _crisprScanColor extra fields; no data rebuild needed.
• src/hg/makeDb/trackDb/human/hs1/html/sgdpCopyNumber.html
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    360607541994aa88b49fc241c34bd964a1db7b50 Tue Sep 29 15:07:07 2026 -0700
    Rebuild the hs1 sgdpCopyNumber track as a faceted composite, so its 319 samples are picked from a searchable metadata table rather than 319 checkboxes; the same bigBeds are pointed at by the same /gbdb paths, so no data changed. Subtracks are renamed from <region>_<population>_<libId>_wssd to sgdpCopyNumber_<libId> because a faceted composite requires the parent name plus the primaryKey value, and dataTypes is deliberately unset: with it hgTrackUi parses the data element only as far as the first underscore and would truncate LP6005441-DNA_A01 to LP6005441-DNA. The per-subtrack 'visibility dense' lines are gone because a faceted composite honors a child's own display mode where a classic composite ignores it, so keeping them would pin every sample to dense and remove the per-item click that the copy number is read from. Sample attributes come from the Reich lab SGDP tables and 317 of the 319 join; sgdpCopyNumberBuild.py takes its sample list from the checked-in sgdpCopyNumberSamples.tsv rather than from trackDb, because at release the generated stanzas replace sgdpCopyNumber.trackDb.ra and the legacy region prefix that the two unmatched samples depend on disappears with them. Alpha gets the new file and beta/public keep the old one until the metadata and color files are on the RR, without which the picker renders empty. sgdpCopyNumber_subset, which turns out to be the first 29 samples in plate order rather than any curated set, is not in the alpha version; whether it is retired for good is still open on the ticket. Faceted composite suggested by Gerardo, and the cross-sandbox metadata fetch that this track turned up was fixed by Max in b3a26a6aff3. refs #29344
• src/hg/makeDb/trackDb/human/hs1/humanChainNet.trackDb.ra
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    ad6dd2177ad20bea9e32563ee76a1c598bccb6d5 Tue Sep 29 23:22:17 2026 -0700
    adding hg38 liftOver chain from lastz refs #34360
• src/hg/makeDb/trackDb/human/hs1/miniMapChains.ra
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    bfe895921db1a915cbd21cc0e70c09d1c159e32b Tue Sep 29 23:06:22 2026 -0700
    showing minimap2 chains to hg38 refs #34360
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    ad6dd2177ad20bea9e32563ee76a1c598bccb6d5 Tue Sep 29 23:22:17 2026 -0700
    adding hg38 liftOver chain from lastz refs #34360
• src/hg/makeDb/trackDb/human/hs1/sgdpCopyNumber.alpha.trackDb.ra
  • lines changed 2895, context: html, text, full: html, text
    360607541994aa88b49fc241c34bd964a1db7b50 Tue Sep 29 15:07:07 2026 -0700
    Rebuild the hs1 sgdpCopyNumber track as a faceted composite, so its 319 samples are picked from a searchable metadata table rather than 319 checkboxes; the same bigBeds are pointed at by the same /gbdb paths, so no data changed. Subtracks are renamed from <region>_<population>_<libId>_wssd to sgdpCopyNumber_<libId> because a faceted composite requires the parent name plus the primaryKey value, and dataTypes is deliberately unset: with it hgTrackUi parses the data element only as far as the first underscore and would truncate LP6005441-DNA_A01 to LP6005441-DNA. The per-subtrack 'visibility dense' lines are gone because a faceted composite honors a child's own display mode where a classic composite ignores it, so keeping them would pin every sample to dense and remove the per-item click that the copy number is read from. Sample attributes come from the Reich lab SGDP tables and 317 of the 319 join; sgdpCopyNumberBuild.py takes its sample list from the checked-in sgdpCopyNumberSamples.tsv rather than from trackDb, because at release the generated stanzas replace sgdpCopyNumber.trackDb.ra and the legacy region prefix that the two unmatched samples depend on disappears with them. Alpha gets the new file and beta/public keep the old one until the metadata and color files are on the RR, without which the picker renders empty. sgdpCopyNumber_subset, which turns out to be the first 29 samples in plate order rather than any curated set, is not in the alpha version; whether it is retired for good is still open on the ticket. Faceted composite suggested by Gerardo, and the cross-sandbox metadata fetch that this track turned up was fixed by Max in b3a26a6aff3. refs #29344
• src/hg/makeDb/trackDb/human/hs1/t2t-supplied.trackDb.ra
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    360607541994aa88b49fc241c34bd964a1db7b50 Tue Sep 29 15:07:07 2026 -0700
    Rebuild the hs1 sgdpCopyNumber track as a faceted composite, so its 319 samples are picked from a searchable metadata table rather than 319 checkboxes; the same bigBeds are pointed at by the same /gbdb paths, so no data changed. Subtracks are renamed from <region>_<population>_<libId>_wssd to sgdpCopyNumber_<libId> because a faceted composite requires the parent name plus the primaryKey value, and dataTypes is deliberately unset: with it hgTrackUi parses the data element only as far as the first underscore and would truncate LP6005441-DNA_A01 to LP6005441-DNA. The per-subtrack 'visibility dense' lines are gone because a faceted composite honors a child's own display mode where a classic composite ignores it, so keeping them would pin every sample to dense and remove the per-item click that the copy number is read from. Sample attributes come from the Reich lab SGDP tables and 317 of the 319 join; sgdpCopyNumberBuild.py takes its sample list from the checked-in sgdpCopyNumberSamples.tsv rather than from trackDb, because at release the generated stanzas replace sgdpCopyNumber.trackDb.ra and the legacy region prefix that the two unmatched samples depend on disappears with them. Alpha gets the new file and beta/public keep the old one until the metadata and color files are on the RR, without which the picker renders empty. sgdpCopyNumber_subset, which turns out to be the first 29 samples in plate order rather than any curated set, is not in the alpha version; whether it is retired for good is still open on the ticket. Faceted composite suggested by Gerardo, and the cross-sandbox metadata fetch that this track turned up was fixed by Max in b3a26a6aff3. refs #29344
• src/hg/makeDb/trackDb/human/hs1/trackDb.ra
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    bfe895921db1a915cbd21cc0e70c09d1c159e32b Tue Sep 29 23:06:22 2026 -0700
    showing minimap2 chains to hg38 refs #34360
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    3bee9e40921231f206014d66a54c6af7581bd4b7 Fri Oct 2 16:54:40 2026 -0700
    Releasing the ProCapNet tracks, refs #35528
• src/hg/makeDb/trackDb/human/hs1/transcriptionStart.ra
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    5e83632c91c1c536880da1e364a41467856135bd Tue Sep 22 11:02:32 2026 -0700
    Rename the TSS container and trim the ProCapNet description. refs #35528 Both labels on the transcriptionStart container are now "Transcription Initiation (TSS)". Changed in proCapNetTrackDb and the two transcriptionStart.ra files regenerated from it, since they are generated and carry a do-not-edit header. Dropped the Processing at UCSC section from the ProCapNet page. How the files reached UCSC is not something a browser user needs; the makeDoc already records it, including the NaN bases dropped from the hg38 predictions. Replaced the Kundaje lab server link with the ENCODE portal. The six ENCODE records are BPNet-model annotations holding the trained model, contribution scores and predicted signal over a selected region set. The genome-wide predictions in this track are roughly fifty times larger than the ENCODE predicted-signal files and are not part of that release, so the page says so rather than naming ENCODE as their source. Claude-Session: https://claude.ai/code/session_01LAB6jWshLvB7eNXQKWVuW5
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    b8a77f50143d1cc2a474fe9a56fe7c362183a07f Fri Sep 25 17:35:01 2026 -0700
    Making the shortLabel sentence case. Updating the shortlabel for the subtracks to say 'Predicted' or 'Contributed', refs #35528
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    717ce54a6012dedd51b0100c643a7a252a16fabb Fri Sep 25 17:46:20 2026 -0700
    Adding windowingFuction maximum to trackDb and the script that generates the trackDb file. refs #35528
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    49de9e93e4417083feb23522a71e3960595828a3 Fri Sep 25 22:46:28 2026 -0700
    ProCapNet label and facet color fixes from QA. refs #35528 The composite longLabel named the sequence-contribution scores, which only exist on hg38, so it was wrong on hs1. Use "ProCapNet predicted PRO-cap" on both assemblies; the scores are described on the track description page. The Sample class swatches reused two colors from the cell-line palette, so a track's color could be read as its class: A673 is a cancer line and drew in #0072B2, which was the Non-cancer swatch. Sample class is a binary facet and does not need a hue, so use black and gray, outside the Okabe-Ito palette. Say in the description that the contribution scores cover about 1% of the genome, so the limit is visible before the display conventions section.
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    31e95f0d1dd4ca08feba9b081a356527bd4b45e6 Sat Sep 26 20:36:20 2026 -0700
    Drop the hand-built Files column from the TSS faceted tables. refs #35528 UCSC will generate the download links in the faceted table, so the Files column each composite built for itself is redundant. Remove downloadCell, the Files header and cell, the Files entry in subtrackUrls, and the DOWNLOAD constant that only fed them. The table is now Tissue, Sample class, Experiment, Cell line on all three composites. writeMetadata no longer needs db or track; the metadata files it writes are byte-identical. Lead each Data Access section with the link to the hgdownload directory, since that is now the way to a single file, and keep the naming convention beside it. Drop the paragraph describing the Files column.
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    66fafe88184bb3a8a45a50026f4d6c7fbbc24109 Tue Sep 29 10:12:53 2026 -0700
    Rebuild the TSS tracks as traditional composites, for wiggle control. refs #35528 A faceted composite is routed to facetedCompositeUi(), which returns before cfgByCfgType(), so it never draws the wiggle controls: no data view scaling, no viewing range, no windowing function, no track height. Signal tracks need those, so proCapNet and encode4ProCap are now traditional composites. They stay separate composites under the TSS container. The multiWig strand overlays survive the change. The old comment here claimed a multiWig under a plain composite "is flattened away and never drawn"; that is wrong for drawing, which #36320 fixed. Only the hgTrackUi subtrack list flattens, because compositeUiSubtracks() walks to leaves, so the overlays get no inline config block and are configured from their own pages. Raised as #38441. The matrix has to be declared over the leaves, since that is the level hgTrackDb checks: declaring it on the containers fails -strict with "has groups not defined in parent". So a strand is a matrix cell, and the containers carry no subGroups. Sample class survives as a filterComposite dimension, replacing the facet. configurable on gives each subtrack its own config namespace. Drop the faceted machinery: the metadata table, the color file, the constants feeding them and the gbdbDir argument, 39 lines. The metadata.tsv and colors.json already written under /gbdb are now unreferenced and can be deleted. Put the ENCODE accession in each subtrack longLabel, and add a linked table of them to both description pages. A longLabel cannot carry a link, since printSubtrackTableBody() htmlEncodes it, hence the table. The label wording is shortened to keep the longest at 74 characters.
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    bdf448295c10bee74b6baa773f6733ce33171996 Thu Oct 1 20:56:37 2026 -0700
    Store the ProCapNet minus strand negated, and fix group autoscale. refs #35528 Two of the three problems Jairo found on the composite. The negate control did not work on ProCapNet. Its minus-strand files held positive values and were flipped at display time with trackDb negateValues. The composite's control sets one shared value, which replaced the per-track setting and sent both strands the same way, with no route back to the default short of a cart reset. encode4ProCap was fine because ENCODE publishes its minus strand negative already. So put the sign in the data: proCapNetPredToFixedStep gains --negate, proCapNetPredBuild passes it for the minus strand, and negateValues is gone from the stanzas. The twelve existing files were rewritten rather than rebuilt, since the downloads had been deleted; each was checked against its original for identical nBasesCovered, a mirrored value range and exactly negated values. The originals are kept in previousPred, about 197 GB, until QA is done. Group autoscale on the composite did nothing, which was my error: the multiWig containers and the contribution leaves each carried autoScale on, and the child setting wins. The wiggle settings now live only on the composite. The third, an empty row when both strands of a cell line are deselected, is #38441 and is not fixed here. Note in both makedocs and in the generator that this arrangement only partly works and is expected to become a superTrack of multiWig overlays: under a composite, hgTrackUi lists leaves rather than containers, so an overlay gets no inline config block and leaves an empty row when deselected.
  • lines changed 81, context: html, text, full: html, text
    1c32191759769c28cf763342f5e405420add0170 Thu Oct 1 21:20:54 2026 -0700
    Make the TSS tracks superTracks of multiWig overlays. refs #35528 The composite held the multiWig overlays as children, which drew correctly but left two faults, both from hgTrackUi listing descendant leaves rather than containers: an overlay got no configuration block of its own, and hiding both strands of a cell line left an empty row where the overlay had been. That is #38441. As superTrack members the overlays are tracks in their own right. Each gets a full configuration page, including overlay method and negate values, and hiding one hides the whole overlay. Verified: hiding proCapNet_K562_pred removes the row and leaves the other five. Two top-level superTracks, PRO-cap and ProCapNet, rather than one transcriptionStart folder holding both. superTracks do not nest. A superTrack given a parent passes tdbQuery -check -strict and is then dropped at load, since trackDbSuperMarkup refuses to set a parent on a superTrack and hgTrackDb only writes a superTrack that some track names as its parent. Filed as #38460, with the test case; transcriptionStart.html stays in the tree unused in case it is fixed. What this costs: the subtrack matrix and the sample class filter, which a superTrack does not offer. Each overlay now carries its own wiggle settings and its own html, neither being inherited from a container any more.
  • lines changed 1, context: html, text, full: html, text
    0ca316803a93c570fc7614479afd322194f17217 Fri Oct 2 06:53:26 2026 -0700
    Drop priority from the two TSS superTrack stanzas. refs #35528 The folders take whatever position the group gives them. The member tracks keep their own priorities, which order each overlay within its folder.
  • lines changed 7, context: html, text, full: html, text
    d0ddd717713f275dc2f567c9b6d733fd3f55bd90 Fri Oct 2 21:27:25 2026 -0700
    Put PRO-cap and ProCapNet inside a Transcription Initiation folder. refs #35528 The two data sources were top-level superTracks because a superTrack could not be a member of another one. #38460 fixes that, so they now sit inside a transcriptionStart superTrack, which is what the collection was meant to be. The container is written before either of its children, and both children before any of their members: tdbQuery -strict rejects a file in which another track comes between a superTrack and one of its children. This depends on the #38460 build. A plain make here with the installed binaries produces a half-built state, since hgTrackDb drops the container from the table and trackDbToTxt then writes an hs1 curated hub whose member names a parent stanza that is not there. Both makedocs say so.
  • lines changed 7, context: html, text, full: html, text
    e314363411293556f33418abe8923ad1e8bc496a Fri Oct 2 21:36:04 2026 -0700
    Revert the TSS nesting on master; it lives on superTrackNesting. refs #35528 Putting PRO-cap and ProCapNet inside a transcriptionStart superTrack needs the nesting fix in #38460, which is not released. These tracks were released in 3bee9e40921, so on beta and the RR hgTrackDb would drop the container and trackDbToTxt would write an hs1 curated hub whose members name a parent stanza that is not there. The work is on the superTrackNesting branch and can come back once #38460 ships.
  • lines changed 16, context: html, text, full: html, text
    0c42aea56b751a2b4a58feb225a9659819a90994 Sat Oct 3 06:22:01 2026 -0700
    Nest the TSS tracks on alpha only, leaving the release as it is. refs #35528 PRO-cap and ProCapNet sit inside a transcriptionStart superTrack on alpha. That needs #38460, which is on master but not in a release, and these tracks are already released, so each source is written twice with complementary release tags: the nested copy alpha, the flat copy beta,public. hgTrackDb takes the copy whose release matches and rejects two whose releases overlap. Verified that beta and public are untouched: a public build from this file is byte-identical to a public build from the released flat tree, same md5 over tableName, shortLabel, type, visibility, priority and settings. tdbQuery -check -strict passes on all three releases, and an alpha build has the container with both members parented while beta and public have neither. Drop the release tags and the flat copies once #38460 ships. The makedocs also record that the alpha build needs hgTrackDb and trackDbToTxt in /cluster/bin/x86_64 to carry the #38460 fix. make alpha does not install there, BINDIR defaults to ~/bin/$MACHTYPE, so they were put in by hand and the weekly utils build will overwrite them.
• src/hg/makeDb/trackDb/human/mei.html
  • lines changed 101, context: html, text, full: html, text
    7e87cadb469b4e0eb4fb7f973154357cfe7fc345 Mon Sep 21 15:56:18 2026 -0700
    QA fixes for the mei (Mobile Insertions) track collection. refs #37524 Fix two data bugs found during QA and rebuild the affected bigBeds. meiEul1dbToBed.py looked up samples and individuals by name, but euL1db joins on 1-based row numbers, so neither join ever matched and the individual count, tissues, clinical conditions and populations were empty on all 8,991 insertions while the contributing-samples table printed row numbers. Both loaders now key on the row number, the table prints the sample name, and the adjacent population filter is case-insensitive so it actually drops "unknown". meiHgsvc3CsvToBed.py took alt[1:] on every record, which dropped the first base of the element on the 96 GRCh38 and 111 T2T-CHM13 records where PALMER2 is the only caller and ALT carries no anchor base; it now prefers INFO SEQ, which always matches SVLEN. Correct seven statements on the description pages against their sources: the HGSVC3 single-caller split was attributed to PALMER rather than L1ME-AID, its orthogonal concordance was 90.8% rather than 92.5%, euL1db was credited with aligning the L1HS consensus when the paper says it was processed from our RepeatMasker track, DeepMEI's network was described as a classifier rather than a genotyper and given the wrong training set, euL1db listed two detection methods absent from the data, and HMEID contradicted itself on the MELT ASSESS cutoff. Also: the SweGen bigDataUrl now points at _swegen.bb so the restricted callset is kept off the download server; the container page no longer claims the whole collection is long-read, lists the two euL1db subtracks, scopes its display conventions to the subtracks they describe, and cites all six papers; dead and wrong track links are repointed and pinned to a db; $db replaces hardcoded hg38 in paths on pages that serve three assemblies; the euL1db labels no longer carry hg38 counts and a lift note that made no sense on hg19; all six subtracks gain a dataVersion; the euL1db filter ranges match the data; and five autoSql field descriptions match what the files contain. Document the gbdb symlinks and the QA changes in doc/hg38/mei.txt, correct the HMEID bedToBigBed type there, and add an hg19.txt pointer since hg19 carries the two euL1db subtracks.
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    e461209cf1fd3758d63641915cd91ca9c8ab3020 Thu Sep 24 17:00:10 2026 -0700
    Remove tool output accidentally left in the mei description page, per CR. refs #37524 getTrackReferences writes its diagnostics to stdout rather than stderr, so six "Failed to fetch complete links from NCBI" lines ended up in the References section of mei.html and rendered as visible text on the track description page. NCBI is still not answering, so rather than rerun the tool the references are now assembled from the citation blocks already present on the six subtrack pages. That also restores the publisher links for every paper, which the failed lookups had degraded to bare PubMed URLs. Also make the INFO SEQ guard in meiHgsvc3CsvToBed.py require a usable string, so an empty SEQ= value would fall back to the ALT-derived sequence instead of silently producing an empty one. No record in either callset carries an empty SEQ today and the rebuilt output is byte-identical.
• src/hg/makeDb/trackDb/human/mei.ra
  • lines changed 16, context: html, text, full: html, text
    7e87cadb469b4e0eb4fb7f973154357cfe7fc345 Mon Sep 21 15:56:18 2026 -0700
    QA fixes for the mei (Mobile Insertions) track collection. refs #37524 Fix two data bugs found during QA and rebuild the affected bigBeds. meiEul1dbToBed.py looked up samples and individuals by name, but euL1db joins on 1-based row numbers, so neither join ever matched and the individual count, tissues, clinical conditions and populations were empty on all 8,991 insertions while the contributing-samples table printed row numbers. Both loaders now key on the row number, the table prints the sample name, and the adjacent population filter is case-insensitive so it actually drops "unknown". meiHgsvc3CsvToBed.py took alt[1:] on every record, which dropped the first base of the element on the 96 GRCh38 and 111 T2T-CHM13 records where PALMER2 is the only caller and ALT carries no anchor base; it now prefers INFO SEQ, which always matches SVLEN. Correct seven statements on the description pages against their sources: the HGSVC3 single-caller split was attributed to PALMER rather than L1ME-AID, its orthogonal concordance was 90.8% rather than 92.5%, euL1db was credited with aligning the L1HS consensus when the paper says it was processed from our RepeatMasker track, DeepMEI's network was described as a classifier rather than a genotyper and given the wrong training set, euL1db listed two detection methods absent from the data, and HMEID contradicted itself on the MELT ASSESS cutoff. Also: the SweGen bigDataUrl now points at _swegen.bb so the restricted callset is kept off the download server; the container page no longer claims the whole collection is long-read, lists the two euL1db subtracks, scopes its display conventions to the subtracks they describe, and cites all six papers; dead and wrong track links are repointed and pinned to a db; $db replaces hardcoded hg38 in paths on pages that serve three assemblies; the euL1db labels no longer carry hg38 counts and a lift note that made no sense on hg19; all six subtracks gain a dataVersion; the euL1db filter ranges match the data; and five autoSql field descriptions match what the files contain. Document the gbdb symlinks and the QA changes in doc/hg38/mei.txt, correct the HMEID bedToBigBed type there, and add an hg19.txt pointer since hg19 carries the two euL1db subtracks.
  • lines changed 2, context: html, text, full: html, text
    8e55bcac3b1cf604a3cebbb7eaf4aac109449f76 Tue Sep 22 06:13:02 2026 -0700
    changing track name, refs #37524
• src/hg/makeDb/trackDb/human/meiDeepmei1kg.html
  • lines changed 33, context: html, text, full: html, text
    7e87cadb469b4e0eb4fb7f973154357cfe7fc345 Mon Sep 21 15:56:18 2026 -0700
    QA fixes for the mei (Mobile Insertions) track collection. refs #37524 Fix two data bugs found during QA and rebuild the affected bigBeds. meiEul1dbToBed.py looked up samples and individuals by name, but euL1db joins on 1-based row numbers, so neither join ever matched and the individual count, tissues, clinical conditions and populations were empty on all 8,991 insertions while the contributing-samples table printed row numbers. Both loaders now key on the row number, the table prints the sample name, and the adjacent population filter is case-insensitive so it actually drops "unknown". meiHgsvc3CsvToBed.py took alt[1:] on every record, which dropped the first base of the element on the 96 GRCh38 and 111 T2T-CHM13 records where PALMER2 is the only caller and ALT carries no anchor base; it now prefers INFO SEQ, which always matches SVLEN. Correct seven statements on the description pages against their sources: the HGSVC3 single-caller split was attributed to PALMER rather than L1ME-AID, its orthogonal concordance was 90.8% rather than 92.5%, euL1db was credited with aligning the L1HS consensus when the paper says it was processed from our RepeatMasker track, DeepMEI's network was described as a classifier rather than a genotyper and given the wrong training set, euL1db listed two detection methods absent from the data, and HMEID contradicted itself on the MELT ASSESS cutoff. Also: the SweGen bigDataUrl now points at _swegen.bb so the restricted callset is kept off the download server; the container page no longer claims the whole collection is long-read, lists the two euL1db subtracks, scopes its display conventions to the subtracks they describe, and cites all six papers; dead and wrong track links are repointed and pinned to a db; $db replaces hardcoded hg38 in paths on pages that serve three assemblies; the euL1db labels no longer carry hg38 counts and a lift note that made no sense on hg19; all six subtracks gain a dataVersion; the euL1db filter ranges match the data; and five autoSql field descriptions match what the files contain. Document the gbdb symlinks and the QA changes in doc/hg38/mei.txt, correct the HMEID bedToBigBed type there, and add an hg19.txt pointer since hg19 carries the two euL1db subtracks.
• src/hg/makeDb/trackDb/human/meiEul1db.html
  • lines changed 15, context: html, text, full: html, text
    7e87cadb469b4e0eb4fb7f973154357cfe7fc345 Mon Sep 21 15:56:18 2026 -0700
    QA fixes for the mei (Mobile Insertions) track collection. refs #37524 Fix two data bugs found during QA and rebuild the affected bigBeds. meiEul1dbToBed.py looked up samples and individuals by name, but euL1db joins on 1-based row numbers, so neither join ever matched and the individual count, tissues, clinical conditions and populations were empty on all 8,991 insertions while the contributing-samples table printed row numbers. Both loaders now key on the row number, the table prints the sample name, and the adjacent population filter is case-insensitive so it actually drops "unknown". meiHgsvc3CsvToBed.py took alt[1:] on every record, which dropped the first base of the element on the 96 GRCh38 and 111 T2T-CHM13 records where PALMER2 is the only caller and ALT carries no anchor base; it now prefers INFO SEQ, which always matches SVLEN. Correct seven statements on the description pages against their sources: the HGSVC3 single-caller split was attributed to PALMER rather than L1ME-AID, its orthogonal concordance was 90.8% rather than 92.5%, euL1db was credited with aligning the L1HS consensus when the paper says it was processed from our RepeatMasker track, DeepMEI's network was described as a classifier rather than a genotyper and given the wrong training set, euL1db listed two detection methods absent from the data, and HMEID contradicted itself on the MELT ASSESS cutoff. Also: the SweGen bigDataUrl now points at _swegen.bb so the restricted callset is kept off the download server; the container page no longer claims the whole collection is long-read, lists the two euL1db subtracks, scopes its display conventions to the subtracks they describe, and cites all six papers; dead and wrong track links are repointed and pinned to a db; $db replaces hardcoded hg38 in paths on pages that serve three assemblies; the euL1db labels no longer carry hg38 counts and a lift note that made no sense on hg19; all six subtracks gain a dataVersion; the euL1db filter ranges match the data; and five autoSql field descriptions match what the files contain. Document the gbdb symlinks and the QA changes in doc/hg38/mei.txt, correct the HMEID bedToBigBed type there, and add an hg19.txt pointer since hg19 carries the two euL1db subtracks.
• src/hg/makeDb/trackDb/human/meiEul1dbRef.html
  • lines changed 13, context: html, text, full: html, text
    7e87cadb469b4e0eb4fb7f973154357cfe7fc345 Mon Sep 21 15:56:18 2026 -0700
    QA fixes for the mei (Mobile Insertions) track collection. refs #37524 Fix two data bugs found during QA and rebuild the affected bigBeds. meiEul1dbToBed.py looked up samples and individuals by name, but euL1db joins on 1-based row numbers, so neither join ever matched and the individual count, tissues, clinical conditions and populations were empty on all 8,991 insertions while the contributing-samples table printed row numbers. Both loaders now key on the row number, the table prints the sample name, and the adjacent population filter is case-insensitive so it actually drops "unknown". meiHgsvc3CsvToBed.py took alt[1:] on every record, which dropped the first base of the element on the 96 GRCh38 and 111 T2T-CHM13 records where PALMER2 is the only caller and ALT carries no anchor base; it now prefers INFO SEQ, which always matches SVLEN. Correct seven statements on the description pages against their sources: the HGSVC3 single-caller split was attributed to PALMER rather than L1ME-AID, its orthogonal concordance was 90.8% rather than 92.5%, euL1db was credited with aligning the L1HS consensus when the paper says it was processed from our RepeatMasker track, DeepMEI's network was described as a classifier rather than a genotyper and given the wrong training set, euL1db listed two detection methods absent from the data, and HMEID contradicted itself on the MELT ASSESS cutoff. Also: the SweGen bigDataUrl now points at _swegen.bb so the restricted callset is kept off the download server; the container page no longer claims the whole collection is long-read, lists the two euL1db subtracks, scopes its display conventions to the subtracks they describe, and cites all six papers; dead and wrong track links are repointed and pinned to a db; $db replaces hardcoded hg38 in paths on pages that serve three assemblies; the euL1db labels no longer carry hg38 counts and a lift note that made no sense on hg19; all six subtracks gain a dataVersion; the euL1db filter ranges match the data; and five autoSql field descriptions match what the files contain. Document the gbdb symlinks and the QA changes in doc/hg38/mei.txt, correct the HMEID bedToBigBed type there, and add an hg19.txt pointer since hg19 carries the two euL1db subtracks.
• src/hg/makeDb/trackDb/human/meiHgsvc3.html
  • lines changed 14, context: html, text, full: html, text
    7e87cadb469b4e0eb4fb7f973154357cfe7fc345 Mon Sep 21 15:56:18 2026 -0700
    QA fixes for the mei (Mobile Insertions) track collection. refs #37524 Fix two data bugs found during QA and rebuild the affected bigBeds. meiEul1dbToBed.py looked up samples and individuals by name, but euL1db joins on 1-based row numbers, so neither join ever matched and the individual count, tissues, clinical conditions and populations were empty on all 8,991 insertions while the contributing-samples table printed row numbers. Both loaders now key on the row number, the table prints the sample name, and the adjacent population filter is case-insensitive so it actually drops "unknown". meiHgsvc3CsvToBed.py took alt[1:] on every record, which dropped the first base of the element on the 96 GRCh38 and 111 T2T-CHM13 records where PALMER2 is the only caller and ALT carries no anchor base; it now prefers INFO SEQ, which always matches SVLEN. Correct seven statements on the description pages against their sources: the HGSVC3 single-caller split was attributed to PALMER rather than L1ME-AID, its orthogonal concordance was 90.8% rather than 92.5%, euL1db was credited with aligning the L1HS consensus when the paper says it was processed from our RepeatMasker track, DeepMEI's network was described as a classifier rather than a genotyper and given the wrong training set, euL1db listed two detection methods absent from the data, and HMEID contradicted itself on the MELT ASSESS cutoff. Also: the SweGen bigDataUrl now points at _swegen.bb so the restricted callset is kept off the download server; the container page no longer claims the whole collection is long-read, lists the two euL1db subtracks, scopes its display conventions to the subtracks they describe, and cites all six papers; dead and wrong track links are repointed and pinned to a db; $db replaces hardcoded hg38 in paths on pages that serve three assemblies; the euL1db labels no longer carry hg38 counts and a lift note that made no sense on hg19; all six subtracks gain a dataVersion; the euL1db filter ranges match the data; and five autoSql field descriptions match what the files contain. Document the gbdb symlinks and the QA changes in doc/hg38/mei.txt, correct the HMEID bedToBigBed type there, and add an hg19.txt pointer since hg19 carries the two euL1db subtracks.
• src/hg/makeDb/trackDb/human/meiHmeid.html
  • lines changed 10, context: html, text, full: html, text
    7e87cadb469b4e0eb4fb7f973154357cfe7fc345 Mon Sep 21 15:56:18 2026 -0700
    QA fixes for the mei (Mobile Insertions) track collection. refs #37524 Fix two data bugs found during QA and rebuild the affected bigBeds. meiEul1dbToBed.py looked up samples and individuals by name, but euL1db joins on 1-based row numbers, so neither join ever matched and the individual count, tissues, clinical conditions and populations were empty on all 8,991 insertions while the contributing-samples table printed row numbers. Both loaders now key on the row number, the table prints the sample name, and the adjacent population filter is case-insensitive so it actually drops "unknown". meiHgsvc3CsvToBed.py took alt[1:] on every record, which dropped the first base of the element on the 96 GRCh38 and 111 T2T-CHM13 records where PALMER2 is the only caller and ALT carries no anchor base; it now prefers INFO SEQ, which always matches SVLEN. Correct seven statements on the description pages against their sources: the HGSVC3 single-caller split was attributed to PALMER rather than L1ME-AID, its orthogonal concordance was 90.8% rather than 92.5%, euL1db was credited with aligning the L1HS consensus when the paper says it was processed from our RepeatMasker track, DeepMEI's network was described as a classifier rather than a genotyper and given the wrong training set, euL1db listed two detection methods absent from the data, and HMEID contradicted itself on the MELT ASSESS cutoff. Also: the SweGen bigDataUrl now points at _swegen.bb so the restricted callset is kept off the download server; the container page no longer claims the whole collection is long-read, lists the two euL1db subtracks, scopes its display conventions to the subtracks they describe, and cites all six papers; dead and wrong track links are repointed and pinned to a db; $db replaces hardcoded hg38 in paths on pages that serve three assemblies; the euL1db labels no longer carry hg38 counts and a lift note that made no sense on hg19; all six subtracks gain a dataVersion; the euL1db filter ranges match the data; and five autoSql field descriptions match what the files contain. Document the gbdb symlinks and the QA changes in doc/hg38/mei.txt, correct the HMEID bedToBigBed type there, and add an hg19.txt pointer since hg19 carries the two euL1db subtracks.
• src/hg/makeDb/trackDb/human/meiSwegen.html
  • lines changed 14, context: html, text, full: html, text
    7e87cadb469b4e0eb4fb7f973154357cfe7fc345 Mon Sep 21 15:56:18 2026 -0700
    QA fixes for the mei (Mobile Insertions) track collection. refs #37524 Fix two data bugs found during QA and rebuild the affected bigBeds. meiEul1dbToBed.py looked up samples and individuals by name, but euL1db joins on 1-based row numbers, so neither join ever matched and the individual count, tissues, clinical conditions and populations were empty on all 8,991 insertions while the contributing-samples table printed row numbers. Both loaders now key on the row number, the table prints the sample name, and the adjacent population filter is case-insensitive so it actually drops "unknown". meiHgsvc3CsvToBed.py took alt[1:] on every record, which dropped the first base of the element on the 96 GRCh38 and 111 T2T-CHM13 records where PALMER2 is the only caller and ALT carries no anchor base; it now prefers INFO SEQ, which always matches SVLEN. Correct seven statements on the description pages against their sources: the HGSVC3 single-caller split was attributed to PALMER rather than L1ME-AID, its orthogonal concordance was 90.8% rather than 92.5%, euL1db was credited with aligning the L1HS consensus when the paper says it was processed from our RepeatMasker track, DeepMEI's network was described as a classifier rather than a genotyper and given the wrong training set, euL1db listed two detection methods absent from the data, and HMEID contradicted itself on the MELT ASSESS cutoff. Also: the SweGen bigDataUrl now points at _swegen.bb so the restricted callset is kept off the download server; the container page no longer claims the whole collection is long-read, lists the two euL1db subtracks, scopes its display conventions to the subtracks they describe, and cites all six papers; dead and wrong track links are repointed and pinned to a db; $db replaces hardcoded hg38 in paths on pages that serve three assemblies; the euL1db labels no longer carry hg38 counts and a lift note that made no sense on hg19; all six subtracks gain a dataVersion; the euL1db filter ranges match the data; and five autoSql field descriptions match what the files contain. Document the gbdb symlinks and the QA changes in doc/hg38/mei.txt, correct the HMEID bedToBigBed type there, and add an hg19.txt pointer since hg19 carries the two euL1db subtracks.
• src/hg/makeDb/trackDb/human/phasedVars.html
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    9cedfa38c14068c79dec89f76c606ee22b3f931a Wed Sep 30 15:02:37 2026 -0700
    phasedVars: new subtrack hgdp1kSnv, a 17GB version of the 3.5TB gnomAD HGDP+1000G genotype VCF with only SNVs with AC>5 and only GT, so haplotype clustering can be shown up to 5Mbp, refs #37306
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    85320722a5537e851769a87a141b2094aa145847 Mon Oct 5 01:29:25 2026 -0700
    phasedVars.html: comment out the hgdp1kSnv methods paragraph until that subtrack is released, refs #37306
• src/hg/makeDb/trackDb/human/phasedVars.ra
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    9cedfa38c14068c79dec89f76c606ee22b3f931a Wed Sep 30 15:02:37 2026 -0700
    phasedVars: new subtrack hgdp1kSnv, a 17GB version of the 3.5TB gnomAD HGDP+1000G genotype VCF with only SNVs with AC>5 and only GT, so haplotype clustering can be shown up to 5Mbp, refs #37306
• src/hg/makeDb/trackDb/human/predictionScoresSuper.html
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    53ab3f1e293a91ddf71ec7568f4a6ff827bcd278 Fri Oct 2 13:52:36 2026 -0700
    Native GPN-Star track (Ye, Benegas et al., Nature 2026) on hg38, mm39, galGal6, dm6 and ce11, from the authors' Hugging Face hub. Each model is a multiWig sequence logo plus a four-allele -LLR composite using negateValues. The three hg38 models (V/M/P) sit in predictionScoresSuper via human/gpnStar.ra with /gbdb/$D bigDataUrls so -strict drops them on other human assemblies; the other four get a standalone gpnStar superTrack. The authors' bigWigs come from pyBigWig, whose bwAddIntervalSpanSteps writes the last section of each run 6 bases too long (pyBigWig #166) and makes bigWigAverageOverBed and bigWigCorrelate abort, so gpnStarRebuild.sh re-encodes them with wigToBigWig and gpnStarVerify.sh checks every per-base value is unchanged. Entropy scores and the GenArk-only Arabidopsis set are left out, and pennantIcon still has #TBD placeholders for the newsarch anchor and date. refs #38451
• src/hg/makeDb/trackDb/human/predictionScoresSuper.ra
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    53ab3f1e293a91ddf71ec7568f4a6ff827bcd278 Fri Oct 2 13:52:36 2026 -0700
    Native GPN-Star track (Ye, Benegas et al., Nature 2026) on hg38, mm39, galGal6, dm6 and ce11, from the authors' Hugging Face hub. Each model is a multiWig sequence logo plus a four-allele -LLR composite using negateValues. The three hg38 models (V/M/P) sit in predictionScoresSuper via human/gpnStar.ra with /gbdb/$D bigDataUrls so -strict drops them on other human assemblies; the other four get a standalone gpnStar superTrack. The authors' bigWigs come from pyBigWig, whose bwAddIntervalSpanSteps writes the last section of each run 6 bases too long (pyBigWig #166) and makes bigWigAverageOverBed and bigWigCorrelate abort, so gpnStarRebuild.sh re-encodes them with wigToBigWig and gpnStarVerify.sh checks every per-base value is unchanged. Entropy scores and the GenArk-only Arabidopsis set are left out, and pennantIcon still has #TBD placeholders for the newsarch anchor and date. refs #38451
• src/hg/makeDb/trackDb/human/primateAi.ra
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    f4d967492fedb59d2e528cf196e35c1da248ae96 Fri Oct 2 07:15:47 2026 -0700
    Quarterly pennant cleanup: removing New/Updated pennantIcons released before July 2026 (strVar, nmd, promoterAi, primateAi, mpra, varaico). No RM.
• src/hg/makeDb/trackDb/human/proCapNet.html
  • lines changed 27, context: html, text, full: html, text
    5e83632c91c1c536880da1e364a41467856135bd Tue Sep 22 11:02:32 2026 -0700
    Rename the TSS container and trim the ProCapNet description. refs #35528 Both labels on the transcriptionStart container are now "Transcription Initiation (TSS)". Changed in proCapNetTrackDb and the two transcriptionStart.ra files regenerated from it, since they are generated and carry a do-not-edit header. Dropped the Processing at UCSC section from the ProCapNet page. How the files reached UCSC is not something a browser user needs; the makeDoc already records it, including the NaN bases dropped from the hg38 predictions. Replaced the Kundaje lab server link with the ENCODE portal. The six ENCODE records are BPNet-model annotations holding the trained model, contribution scores and predicted signal over a selected region set. The genome-wide predictions in this track are roughly fifty times larger than the ENCODE predicted-signal files and are not part of that release, so the page says so rather than naming ENCODE as their source. Claude-Session: https://claude.ai/code/session_01LAB6jWshLvB7eNXQKWVuW5
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    0f951bfc96241a7362d1512ceecf59a02682a839 Thu Sep 24 20:40:52 2026 -0700
    Description page fixes from a QA pre-pass on the TSS tracks. refs #35528 Encode the non-ASCII character in the Avsec reference on proCapNet.html. getTrackReferences emits raw UTF-8, which the browser does not transcode. Use $db rather than a hardcoded hg38 in the proCapNet download-server link and the bigWigToBedGraph example. One page serves both assemblies, so an hs1 reader was being pointed at hg38 files. Add a Source subsection to proCapNet.html linking the makedoc, the build scripts, the trackDb file and the upstream kundajelab/ProCapNet repository. These links went missing when the Processing at UCSC section was dropped; the prose stays dropped. Drop the cross-links between the two track pages. Track names are prefixed hub_<id>_ on hs1, which is a curated hub, and the id is machine-specific, so a bare-name link cannot work there. Each page now states which assemblies the data is available on instead, naming both GRCh38/hg38 and T2T-CHM13/hs1. Bold the two UI control names on the proCapNet display conventions section.
  • lines changed 2, context: html, text, full: html, text
    79073841f4c544426db6c1f805af94844cabef23 Thu Sep 24 20:46:08 2026 -0700
    Say why the ProCapNet contribution scores are hg38 only. refs #35528 The page gave the reason as "that is the assembly they were computed against", which restates the fact rather than explaining it. The scores are computed at MANE Select transcription start sites and MANE is not defined for T2T-CHM13.
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    acf20930c5cdfa1e352826a702ad8f36344178c4 Thu Sep 24 21:16:13 2026 -0700
    Fixes from an independent review of the TSS tracks. refs #35528 The Data Access sections told users to pass the composite name to the API, which returns HTTP 400. The API serves one bigWig at a time, so both pages now name a single strand of one cell line, verified to return 200. encode4ProCap.html claimed the kent tree held the manifest of which ENCODE files went into each track, and it did not. Commit that manifest as proCapNetEncodeFiles.tsv and name it on the page. It matters because proCapNetEncodeMeta resolves each experiment's default analysis at run time, so re-running it after an ENCODE reprocessing can pick different files. Cite Shah et al. for the ENCODE 4 nascent transcriptome survey the six PRO-cap experiments come from. Sagar Shah was credited by name with no reference. The hg38 makedoc called the 164268582 dropped bases "the N regions", but gap on the primary chromosomes is 150610728. The extra 13.7 Mb is sequence flanking each gap, dropped because most of its 2114 bp window was unresolved.
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    38ccb38771eddfec3230ab3494fb12e11e7cb4ac Fri Sep 25 17:52:32 2026 -0700
    Putting references in alphabetical order. Adding years to citations. Not using the word 'here' and using the actual location/noun. refs #35528
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    49de9e93e4417083feb23522a71e3960595828a3 Fri Sep 25 22:46:28 2026 -0700
    ProCapNet label and facet color fixes from QA. refs #35528 The composite longLabel named the sequence-contribution scores, which only exist on hg38, so it was wrong on hs1. Use "ProCapNet predicted PRO-cap" on both assemblies; the scores are described on the track description page. The Sample class swatches reused two colors from the cell-line palette, so a track's color could be read as its class: A673 is a cancer line and drew in #0072B2, which was the Non-cancer swatch. Sample class is a binary facet and does not need a hue, so use black and gray, outside the Okabe-Ito palette. Say in the description that the contribution scores cover about 1% of the genome, so the limit is visible before the display conventions section.
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    af96452e1c6ccf783697cead2630de1ca4e91635 Sat Sep 26 06:42:20 2026 -0700
    Put the primary citation first again on the TSS track pages. refs #35528 Alphabetical order buried the paper each track is actually built on: Cochran et al. for ProCapNet, behind Avsec, and Shah et al. for the ENCODE 4 PRO-cap experiments, behind Kwak and Luo. Lead with the primary paper and leave the rest in the order they stood. Reordering only. The years and DOIs added in 38ccb38771e are unchanged.
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    40264d0668926b51da94d2ca038dc7349dfc3405 Sat Sep 26 07:59:34 2026 -0700
    Shorten the Methods sections on the two TSS data pages. refs #35528 Both read like a paper's methods section rather than a track description: 43 lines over four subsections on proCapNet, 35 on encode4ProCap. Cut each to three paragraphs, what the model or assay is, how the files we serve were produced, and where the build is recorded. The subsection headings go with it. Kept every fact a user of the track needs: the window and stride, the MANE Select limit on the contribution scores, the unresolved-sequence handling on hg38, the replicate summing, the six ENCODE accessions and the file manifest. Dropped the detail that belongs to the papers, such as the DeepSHAP scalarization and the loss weighting. The container page keeps no Methods section, which is correct for a page that only points at the two data pages.
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    31e95f0d1dd4ca08feba9b081a356527bd4b45e6 Sat Sep 26 20:36:20 2026 -0700
    Drop the hand-built Files column from the TSS faceted tables. refs #35528 UCSC will generate the download links in the faceted table, so the Files column each composite built for itself is redundant. Remove downloadCell, the Files header and cell, the Files entry in subtrackUrls, and the DOWNLOAD constant that only fed them. The table is now Tissue, Sample class, Experiment, Cell line on all three composites. writeMetadata no longer needs db or track; the metadata files it writes are byte-identical. Lead each Data Access section with the link to the hgdownload directory, since that is now the way to a single file, and keep the naming convention beside it. Drop the paragraph describing the Files column.
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    fe4c75c272ca27de55c0b42396c47f2b00637a4a Mon Sep 28 16:36:20 2026 -0700
    Linking the encode4ProCap trackDb.ra, saying why PRO-cap and contribution scores are hg38 only on the container page, and limiting the ProCapNet prediction claim to the primary chromosomes, refs #35528
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    66fafe88184bb3a8a45a50026f4d6c7fbbc24109 Tue Sep 29 10:12:53 2026 -0700
    Rebuild the TSS tracks as traditional composites, for wiggle control. refs #35528 A faceted composite is routed to facetedCompositeUi(), which returns before cfgByCfgType(), so it never draws the wiggle controls: no data view scaling, no viewing range, no windowing function, no track height. Signal tracks need those, so proCapNet and encode4ProCap are now traditional composites. They stay separate composites under the TSS container. The multiWig strand overlays survive the change. The old comment here claimed a multiWig under a plain composite "is flattened away and never drawn"; that is wrong for drawing, which #36320 fixed. Only the hgTrackUi subtrack list flattens, because compositeUiSubtracks() walks to leaves, so the overlays get no inline config block and are configured from their own pages. Raised as #38441. The matrix has to be declared over the leaves, since that is the level hgTrackDb checks: declaring it on the containers fails -strict with "has groups not defined in parent". So a strand is a matrix cell, and the containers carry no subGroups. Sample class survives as a filterComposite dimension, replacing the facet. configurable on gives each subtrack its own config namespace. Drop the faceted machinery: the metadata table, the color file, the constants feeding them and the gbdbDir argument, 39 lines. The metadata.tsv and colors.json already written under /gbdb are now unreferenced and can be deleted. Put the ENCODE accession in each subtrack longLabel, and add a linked table of them to both description pages. A longLabel cannot carry a link, since printSubtrackTableBody() htmlEncodes it, hence the table. The label wording is shortened to keep the longest at 74 characters.
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    624943dde3397629da2a91d62e83efe7df98d065 Thu Oct 1 16:30:28 2026 -0700
    Pointing the ProCapNet description to the ENCODE Model column of the accession table instead of the removed Experiment column from the bigCompositeUI, refs #35528
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    9f6962c173c405e481da17794d67107e7f8e73a9 Fri Oct 2 16:05:31 2026 -0700
    Replacing the subtrack matrix and Sample class filter paragraph on the PRO-cap and ProCapNet description pages with the track collection layout from Mark's change, and noting that ProCapNet minus strand files store negative values, refs #35528
• src/hg/makeDb/trackDb/human/promoterAi.ra
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    f4d967492fedb59d2e528cf196e35c1da248ae96 Fri Oct 2 07:15:47 2026 -0700
    Quarterly pennant cleanup: removing New/Updated pennantIcons released before July 2026 (strVar, nmd, promoterAi, primateAi, mpra, varaico). No RM.
• src/hg/makeDb/trackDb/human/sfariSparkExomes.html
  • lines changed 59, context: html, text, full: html, text
    7aa59c8f6afbda4c2157d3990b2bbc48a39cac63 Fri Sep 25 02:48:31 2026 -0700
    varFreqs: add SFARI SPARK 45k WGS subtracks. sfariSparkWgs45k is built from the release's AF table (AN estimated, singletons dropped); sfariSparkWgs45kAsd is built from the genotype pVCFs with ASD/non-ASD counts, for now only the DSCAM locus while the genome-wide parasol run finishes, refs #38424
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    f03f56cd3c795a6fba2b8419662a9a2c5d49f69a Sat Sep 26 14:16:17 2026 -0700
    sfariSparkWgs45kAsd: now genome-wide (518M variants from the 45,178 genotype pVCFs, run on parasol); per-allele INFO fields declared Number=1 so the VCF track filters accept them, doc page no longer says DSCAM only, refs #38424
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    a5c699a7301156154700f51a20ae571bc6987051 Sat Sep 26 17:53:41 2026 -0700
    varFreqs: remove the AF-table-based sfariSparkWgs45k subtrack, superseded by the genotype-based sfariSparkWgs45kAsd; drop its scripts, the DSCAM demo script and their makeDoc sections, refs #38424
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    442e433a90b25deb87f10e6cf1b7b608bb0a6d67 Sat Sep 26 21:56:06 2026 -0700
    sfariSparkWgs45kAsd: flag 25M insertions of non-human (oral bacteria) sequence as FILTER NonHumanIns and hide them by default; add SFARI SPARK 45k WGS to the combined tracks without those insertions and relabel the 12k pilot as SFARI SPARK iWGS v1.1 Pilot, refs #38424
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    d8d88eb7e5c8e6df478626e5b88ee7c923c43995 Sun Oct 4 09:48:15 2026 -0700
    sfariSparkExomes.html: SFARI will realign and re-call the 45k WGS release (alt-aware alignment problem), the track will be updated then, refs #38424
• src/hg/makeDb/trackDb/human/strVarNew.ra
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    f4d967492fedb59d2e528cf196e35c1da248ae96 Fri Oct 2 07:15:47 2026 -0700
    Quarterly pennant cleanup: removing New/Updated pennantIcons released before July 2026 (strVar, nmd, promoterAi, primateAi, mpra, varaico). No RM.
• src/hg/makeDb/trackDb/human/tadsDixon.html
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    b7b9978c92a2376d6d9ef4f0a4974cb8167295f8 Wed Sep 30 14:17:50 2026 -0700
    Updating the TAD tracks from the qa-track SKILL.md pass (hg19, hg38, mm10, mm39): shortLabel fixes for cut-off and duplicate ENCODE and 3DGB subtracks, lowercase biosamples in ENCODE longLabels, " bnd" dropped from Schmitt shortLabels, 3DGB subtracks set to pack with three mm10/mm39 defaults turned on, allButtonPair removed so the Schmitt matrix shows, and McArthur item labels hidden. Merged identical description pages into human/ and mouse/, plus description page cleanups (regenerated References, removed the "How to use these tracks" section, ENCODE pages now say 112 of 117 biosamples use Arrowhead). Also updated the ENCODE metadata columns and organ example in the hg38 makedoc. refs #21599
• src/hg/makeDb/trackDb/human/tadsMcArthur.html
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    b7b9978c92a2376d6d9ef4f0a4974cb8167295f8 Wed Sep 30 14:17:50 2026 -0700
    Updating the TAD tracks from the qa-track SKILL.md pass (hg19, hg38, mm10, mm39): shortLabel fixes for cut-off and duplicate ENCODE and 3DGB subtracks, lowercase biosamples in ENCODE longLabels, " bnd" dropped from Schmitt shortLabels, 3DGB subtracks set to pack with three mm10/mm39 defaults turned on, allButtonPair removed so the Schmitt matrix shows, and McArthur item labels hidden. Merged identical description pages into human/ and mouse/, plus description page cleanups (regenerated References, removed the "How to use these tracks" section, ENCODE pages now say 112 of 117 biosamples use Arrowhead). Also updated the ENCODE metadata columns and organ example in the hg38 makedoc. refs #21599
• src/hg/makeDb/trackDb/human/tadsSchmitt.html
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    b7b9978c92a2376d6d9ef4f0a4974cb8167295f8 Wed Sep 30 14:17:50 2026 -0700
    Updating the TAD tracks from the qa-track SKILL.md pass (hg19, hg38, mm10, mm39): shortLabel fixes for cut-off and duplicate ENCODE and 3DGB subtracks, lowercase biosamples in ENCODE longLabels, " bnd" dropped from Schmitt shortLabels, 3DGB subtracks set to pack with three mm10/mm39 defaults turned on, allButtonPair removed so the Schmitt matrix shows, and McArthur item labels hidden. Merged identical description pages into human/ and mouse/, plus description page cleanups (regenerated References, removed the "How to use these tracks" section, ENCODE pages now say 112 of 117 biosamples use Arrowhead). Also updated the ENCODE metadata columns and organ example in the hg38 makedoc. refs #21599
• src/hg/makeDb/trackDb/human/trackDb.ra
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    ce7133b45942cf33b8bf074af8b3fd6952381f95 Tue Sep 29 16:50:33 2026 -0700
    Staging the STR track on beta for hg38, hg19, and hs1, refs #38268
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    f4d967492fedb59d2e528cf196e35c1da248ae96 Fri Oct 2 07:15:47 2026 -0700
    Quarterly pennant cleanup: removing New/Updated pennantIcons released before July 2026 (strVar, nmd, promoterAi, primateAi, mpra, varaico). No RM.
• src/hg/makeDb/trackDb/human/transcriptionStart.html
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    0f951bfc96241a7362d1512ceecf59a02682a839 Thu Sep 24 20:40:52 2026 -0700
    Description page fixes from a QA pre-pass on the TSS tracks. refs #35528 Encode the non-ASCII character in the Avsec reference on proCapNet.html. getTrackReferences emits raw UTF-8, which the browser does not transcode. Use $db rather than a hardcoded hg38 in the proCapNet download-server link and the bigWigToBedGraph example. One page serves both assemblies, so an hs1 reader was being pointed at hg38 files. Add a Source subsection to proCapNet.html linking the makedoc, the build scripts, the trackDb file and the upstream kundajelab/ProCapNet repository. These links went missing when the Processing at UCSC section was dropped; the prose stays dropped. Drop the cross-links between the two track pages. Track names are prefixed hub_<id>_ on hs1, which is a curated hub, and the id is machine-specific, so a bare-name link cannot work there. Each page now states which assemblies the data is available on instead, naming both GRCh38/hg38 and T2T-CHM13/hs1. Bold the two UI control names on the proCapNet display conventions section.
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    fe4c75c272ca27de55c0b42396c47f2b00637a4a Mon Sep 28 16:36:20 2026 -0700
    Linking the encode4ProCap trackDb.ra, saying why PRO-cap and contribution scores are hg38 only on the container page, and limiting the ProCapNet prediction claim to the primary chromosomes, refs #35528
• src/hg/makeDb/trackDb/human/varFreqs.html
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    cd80acf5ecf157dedd8be818d5a684f6334b8b61 Sat Sep 26 18:19:43 2026 -0700
    varFreqs: add SFARI SPARK 45k WGS to the summary table; the old 12,519-genome SPARK WGS subtrack is now labeled SFARI SPARK iWGS v1.1 Pilot, refs #38424
• src/hg/makeDb/trackDb/human/varFreqs.ra
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    7aa59c8f6afbda4c2157d3990b2bbc48a39cac63 Fri Sep 25 02:48:31 2026 -0700
    varFreqs: add SFARI SPARK 45k WGS subtracks. sfariSparkWgs45k is built from the release's AF table (AN estimated, singletons dropped); sfariSparkWgs45kAsd is built from the genotype pVCFs with ASD/non-ASD counts, for now only the DSCAM locus while the genome-wide parasol run finishes, refs #38424
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    f03f56cd3c795a6fba2b8419662a9a2c5d49f69a Sat Sep 26 14:16:17 2026 -0700
    sfariSparkWgs45kAsd: now genome-wide (518M variants from the 45,178 genotype pVCFs, run on parasol); per-allele INFO fields declared Number=1 so the VCF track filters accept them, doc page no longer says DSCAM only, refs #38424
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    a5c699a7301156154700f51a20ae571bc6987051 Sat Sep 26 17:53:41 2026 -0700
    varFreqs: remove the AF-table-based sfariSparkWgs45k subtrack, superseded by the genotype-based sfariSparkWgs45kAsd; drop its scripts, the DSCAM demo script and their makeDoc sections, refs #38424
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    cd80acf5ecf157dedd8be818d5a684f6334b8b61 Sat Sep 26 18:19:43 2026 -0700
    varFreqs: add SFARI SPARK 45k WGS to the summary table; the old 12,519-genome SPARK WGS subtrack is now labeled SFARI SPARK iWGS v1.1 Pilot, refs #38424
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    442e433a90b25deb87f10e6cf1b7b608bb0a6d67 Sat Sep 26 21:56:06 2026 -0700
    sfariSparkWgs45kAsd: flag 25M insertions of non-human (oral bacteria) sequence as FILTER NonHumanIns and hide them by default; add SFARI SPARK 45k WGS to the combined tracks without those insertions and relabel the 12k pilot as SFARI SPARK iWGS v1.1 Pilot, refs #38424
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    66c51e29423da24a7144c7ba99a4cc2ebc96b32c Mon Sep 28 13:54:36 2026 -0700
    varFreqs: combined tracks rebuilt with SFARI SPARK 45k WGS (without its NonHumanIns insertions); add its filter blocks, affected label now ~150,000 individuals, refs #38424
• src/hg/makeDb/trackDb/human/varFreqsAffected.html
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    442e433a90b25deb87f10e6cf1b7b608bb0a6d67 Sat Sep 26 21:56:06 2026 -0700
    sfariSparkWgs45kAsd: flag 25M insertions of non-human (oral bacteria) sequence as FILTER NonHumanIns and hide them by default; add SFARI SPARK 45k WGS to the combined tracks without those insertions and relabel the 12k pilot as SFARI SPARK iWGS v1.1 Pilot, refs #38424
• src/hg/makeDb/trackDb/human/varFreqsBackground.html
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    442e433a90b25deb87f10e6cf1b7b608bb0a6d67 Sat Sep 26 21:56:06 2026 -0700
    sfariSparkWgs45kAsd: flag 25M insertions of non-human (oral bacteria) sequence as FILTER NonHumanIns and hide them by default; add SFARI SPARK 45k WGS to the combined tracks without those insertions and relabel the 12k pilot as SFARI SPARK iWGS v1.1 Pilot, refs #38424
• src/hg/makeDb/trackDb/lamprey/petMar1/multiz6way.html
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    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/lamprey/petMar1/phastConsElements6way.html
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    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/lamprey/petMar2/cons7way.html
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    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/lancelet/braFlo1/multiz5way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/lancelet/braFlo1/phastConsElements5way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/lizard/anoCar2/cons7way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/marmoset/calJac1/multiz9way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/marmoset/calJac1/phastConsElements9way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/marmoset/calJac3/cons13way.html
  • lines changed 40, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/medaka/oryLat1/multiz5way.html
  • lines changed 12, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/medaka/oryLat1/phastConsElements5way.html
  • lines changed 9, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/medaka/oryLat2/multiz5way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/medaka/oryLat2/phastConsElements5way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/cons60way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/tads3dgb.html
  • lines changed 66, context: html, text, full: html, text
    b7b9978c92a2376d6d9ef4f0a4974cb8167295f8 Wed Sep 30 14:17:50 2026 -0700
    Updating the TAD tracks from the qa-track SKILL.md pass (hg19, hg38, mm10, mm39): shortLabel fixes for cut-off and duplicate ENCODE and 3DGB subtracks, lowercase biosamples in ENCODE longLabels, " bnd" dropped from Schmitt shortLabels, 3DGB subtracks set to pack with three mm10/mm39 defaults turned on, allButtonPair removed so the Schmitt matrix shows, and McArthur item labels hidden. Merged identical description pages into human/ and mouse/, plus description page cleanups (regenerated References, removed the "How to use these tracks" section, ENCODE pages now say 112 of 117 biosamples use Arrowhead). Also updated the ENCODE metadata columns and organ example in the hg38 makedoc. refs #21599
• src/hg/makeDb/trackDb/mouse/mm10/tads3dgb.ra
  • lines changed 33, context: html, text, full: html, text
    b7b9978c92a2376d6d9ef4f0a4974cb8167295f8 Wed Sep 30 14:17:50 2026 -0700
    Updating the TAD tracks from the qa-track SKILL.md pass (hg19, hg38, mm10, mm39): shortLabel fixes for cut-off and duplicate ENCODE and 3DGB subtracks, lowercase biosamples in ENCODE longLabels, " bnd" dropped from Schmitt shortLabels, 3DGB subtracks set to pack with three mm10/mm39 defaults turned on, allButtonPair removed so the Schmitt matrix shows, and McArthur item labels hidden. Merged identical description pages into human/ and mouse/, plus description page cleanups (regenerated References, removed the "How to use these tracks" section, ENCODE pages now say 112 of 117 biosamples use Arrowhead). Also updated the ENCODE metadata columns and organ example in the hg38 makedoc. refs #21599
• src/hg/makeDb/trackDb/mouse/mm10/tadsEncode.html
  • lines changed 68, context: html, text, full: html, text
    b7b9978c92a2376d6d9ef4f0a4974cb8167295f8 Wed Sep 30 14:17:50 2026 -0700
    Updating the TAD tracks from the qa-track SKILL.md pass (hg19, hg38, mm10, mm39): shortLabel fixes for cut-off and duplicate ENCODE and 3DGB subtracks, lowercase biosamples in ENCODE longLabels, " bnd" dropped from Schmitt shortLabels, 3DGB subtracks set to pack with three mm10/mm39 defaults turned on, allButtonPair removed so the Schmitt matrix shows, and McArthur item labels hidden. Merged identical description pages into human/ and mouse/, plus description page cleanups (regenerated References, removed the "How to use these tracks" section, ENCODE pages now say 112 of 117 biosamples use Arrowhead). Also updated the ENCODE metadata columns and organ example in the hg38 makedoc. refs #21599
• src/hg/makeDb/trackDb/mouse/mm10/tadsEncode.ra
  • lines changed 9, context: html, text, full: html, text
    b7b9978c92a2376d6d9ef4f0a4974cb8167295f8 Wed Sep 30 14:17:50 2026 -0700
    Updating the TAD tracks from the qa-track SKILL.md pass (hg19, hg38, mm10, mm39): shortLabel fixes for cut-off and duplicate ENCODE and 3DGB subtracks, lowercase biosamples in ENCODE longLabels, " bnd" dropped from Schmitt shortLabels, 3DGB subtracks set to pack with three mm10/mm39 defaults turned on, allButtonPair removed so the Schmitt matrix shows, and McArthur item labels hidden. Merged identical description pages into human/ and mouse/, plus description page cleanups (regenerated References, removed the "How to use these tracks" section, ENCODE pages now say 112 of 117 biosamples use Arrowhead). Also updated the ENCODE metadata columns and organ example in the hg38 makedoc. refs #21599
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    983d1e972217fb20781724d2cec9dfaec6fa96af Mon Sep 21 17:48:17 2026 -0700
    Removing the release tags for the cactus mouse strains track, refs #38308
• src/hg/makeDb/trackDb/mouse/mm39/cons35way.html
  • lines changed 25, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm39/gpnStar.html
  • lines changed 150, context: html, text, full: html, text
    53ab3f1e293a91ddf71ec7568f4a6ff827bcd278 Fri Oct 2 13:52:36 2026 -0700
    Native GPN-Star track (Ye, Benegas et al., Nature 2026) on hg38, mm39, galGal6, dm6 and ce11, from the authors' Hugging Face hub. Each model is a multiWig sequence logo plus a four-allele -LLR composite using negateValues. The three hg38 models (V/M/P) sit in predictionScoresSuper via human/gpnStar.ra with /gbdb/$D bigDataUrls so -strict drops them on other human assemblies; the other four get a standalone gpnStar superTrack. The authors' bigWigs come from pyBigWig, whose bwAddIntervalSpanSteps writes the last section of each run 6 bases too long (pyBigWig #166) and makes bigWigAverageOverBed and bigWigCorrelate abort, so gpnStarRebuild.sh re-encodes them with wigToBigWig and gpnStarVerify.sh checks every per-base value is unchanged. Entropy scores and the GenArk-only Arabidopsis set are left out, and pennantIcon still has #TBD placeholders for the newsarch anchor and date. refs #38451
• src/hg/makeDb/trackDb/mouse/mm39/gpnStar.ra
  • lines changed 125, context: html, text, full: html, text
    53ab3f1e293a91ddf71ec7568f4a6ff827bcd278 Fri Oct 2 13:52:36 2026 -0700
    Native GPN-Star track (Ye, Benegas et al., Nature 2026) on hg38, mm39, galGal6, dm6 and ce11, from the authors' Hugging Face hub. Each model is a multiWig sequence logo plus a four-allele -LLR composite using negateValues. The three hg38 models (V/M/P) sit in predictionScoresSuper via human/gpnStar.ra with /gbdb/$D bigDataUrls so -strict drops them on other human assemblies; the other four get a standalone gpnStar superTrack. The authors' bigWigs come from pyBigWig, whose bwAddIntervalSpanSteps writes the last section of each run 6 bases too long (pyBigWig #166) and makes bigWigAverageOverBed and bigWigCorrelate abort, so gpnStarRebuild.sh re-encodes them with wigToBigWig and gpnStarVerify.sh checks every per-base value is unchanged. Entropy scores and the GenArk-only Arabidopsis set are left out, and pennantIcon still has #TBD placeholders for the newsarch anchor and date. refs #38451
• src/hg/makeDb/trackDb/mouse/mm39/tads.html
  • lines changed 94, context: html, text, full: html, text
    b7b9978c92a2376d6d9ef4f0a4974cb8167295f8 Wed Sep 30 14:17:50 2026 -0700
    Updating the TAD tracks from the qa-track SKILL.md pass (hg19, hg38, mm10, mm39): shortLabel fixes for cut-off and duplicate ENCODE and 3DGB subtracks, lowercase biosamples in ENCODE longLabels, " bnd" dropped from Schmitt shortLabels, 3DGB subtracks set to pack with three mm10/mm39 defaults turned on, allButtonPair removed so the Schmitt matrix shows, and McArthur item labels hidden. Merged identical description pages into human/ and mouse/, plus description page cleanups (regenerated References, removed the "How to use these tracks" section, ENCODE pages now say 112 of 117 biosamples use Arrowhead). Also updated the ENCODE metadata columns and organ example in the hg38 makedoc. refs #21599
• src/hg/makeDb/trackDb/mouse/mm39/tads3dgb.ra
  • lines changed 33, context: html, text, full: html, text
    b7b9978c92a2376d6d9ef4f0a4974cb8167295f8 Wed Sep 30 14:17:50 2026 -0700
    Updating the TAD tracks from the qa-track SKILL.md pass (hg19, hg38, mm10, mm39): shortLabel fixes for cut-off and duplicate ENCODE and 3DGB subtracks, lowercase biosamples in ENCODE longLabels, " bnd" dropped from Schmitt shortLabels, 3DGB subtracks set to pack with three mm10/mm39 defaults turned on, allButtonPair removed so the Schmitt matrix shows, and McArthur item labels hidden. Merged identical description pages into human/ and mouse/, plus description page cleanups (regenerated References, removed the "How to use these tracks" section, ENCODE pages now say 112 of 117 biosamples use Arrowhead). Also updated the ENCODE metadata columns and organ example in the hg38 makedoc. refs #21599
• src/hg/makeDb/trackDb/mouse/mm39/tadsDixon.html
  • lines changed 46, context: html, text, full: html, text
    b7b9978c92a2376d6d9ef4f0a4974cb8167295f8 Wed Sep 30 14:17:50 2026 -0700
    Updating the TAD tracks from the qa-track SKILL.md pass (hg19, hg38, mm10, mm39): shortLabel fixes for cut-off and duplicate ENCODE and 3DGB subtracks, lowercase biosamples in ENCODE longLabels, " bnd" dropped from Schmitt shortLabels, 3DGB subtracks set to pack with three mm10/mm39 defaults turned on, allButtonPair removed so the Schmitt matrix shows, and McArthur item labels hidden. Merged identical description pages into human/ and mouse/, plus description page cleanups (regenerated References, removed the "How to use these tracks" section, ENCODE pages now say 112 of 117 biosamples use Arrowhead). Also updated the ENCODE metadata columns and organ example in the hg38 makedoc. refs #21599
• src/hg/makeDb/trackDb/mouse/mm39/tadsEncode.ra
  • lines changed 9, context: html, text, full: html, text
    b7b9978c92a2376d6d9ef4f0a4974cb8167295f8 Wed Sep 30 14:17:50 2026 -0700
    Updating the TAD tracks from the qa-track SKILL.md pass (hg19, hg38, mm10, mm39): shortLabel fixes for cut-off and duplicate ENCODE and 3DGB subtracks, lowercase biosamples in ENCODE longLabels, " bnd" dropped from Schmitt shortLabels, 3DGB subtracks set to pack with three mm10/mm39 defaults turned on, allButtonPair removed so the Schmitt matrix shows, and McArthur item labels hidden. Merged identical description pages into human/ and mouse/, plus description page cleanups (regenerated References, removed the "How to use these tracks" section, ENCODE pages now say 112 of 117 biosamples use Arrowhead). Also updated the ENCODE metadata columns and organ example in the hg38 makedoc. refs #21599
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    53ab3f1e293a91ddf71ec7568f4a6ff827bcd278 Fri Oct 2 13:52:36 2026 -0700
    Native GPN-Star track (Ye, Benegas et al., Nature 2026) on hg38, mm39, galGal6, dm6 and ce11, from the authors' Hugging Face hub. Each model is a multiWig sequence logo plus a four-allele -LLR composite using negateValues. The three hg38 models (V/M/P) sit in predictionScoresSuper via human/gpnStar.ra with /gbdb/$D bigDataUrls so -strict drops them on other human assemblies; the other four get a standalone gpnStar superTrack. The authors' bigWigs come from pyBigWig, whose bwAddIntervalSpanSteps writes the last section of each run 6 bases too long (pyBigWig #166) and makes bigWigAverageOverBed and bigWigCorrelate abort, so gpnStarRebuild.sh re-encodes them with wigToBigWig and gpnStarVerify.sh checks every per-base value is unchanged. Entropy scores and the GenArk-only Arabidopsis set are left out, and pennantIcon still has #TBD placeholders for the newsarch anchor and date. refs #38451
• src/hg/makeDb/trackDb/mouse/mm5/multiz5way.html
  • lines changed 27, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm6/multiz10way.html
  • lines changed 27, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm7/multiz17way.html
  • lines changed 27, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm8/multiz17way.html
  • lines changed 27, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm9/cons30way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm9/multiz30way.html
  • lines changed 31, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/phastConsElements17way.html
  • lines changed 8, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/tads.html
  • lines changed 37, context: html, text, full: html, text
    b7b9978c92a2376d6d9ef4f0a4974cb8167295f8 Wed Sep 30 14:17:50 2026 -0700
    Updating the TAD tracks from the qa-track SKILL.md pass (hg19, hg38, mm10, mm39): shortLabel fixes for cut-off and duplicate ENCODE and 3DGB subtracks, lowercase biosamples in ENCODE longLabels, " bnd" dropped from Schmitt shortLabels, 3DGB subtracks set to pack with three mm10/mm39 defaults turned on, allButtonPair removed so the Schmitt matrix shows, and McArthur item labels hidden. Merged identical description pages into human/ and mouse/, plus description page cleanups (regenerated References, removed the "How to use these tracks" section, ENCODE pages now say 112 of 117 biosamples use Arrowhead). Also updated the ENCODE metadata columns and organ example in the hg38 makedoc. refs #21599
• src/hg/makeDb/trackDb/mouse/tads3dgb.html
  • lines changed 18, context: html, text, full: html, text
    b7b9978c92a2376d6d9ef4f0a4974cb8167295f8 Wed Sep 30 14:17:50 2026 -0700
    Updating the TAD tracks from the qa-track SKILL.md pass (hg19, hg38, mm10, mm39): shortLabel fixes for cut-off and duplicate ENCODE and 3DGB subtracks, lowercase biosamples in ENCODE longLabels, " bnd" dropped from Schmitt shortLabels, 3DGB subtracks set to pack with three mm10/mm39 defaults turned on, allButtonPair removed so the Schmitt matrix shows, and McArthur item labels hidden. Merged identical description pages into human/ and mouse/, plus description page cleanups (regenerated References, removed the "How to use these tracks" section, ENCODE pages now say 112 of 117 biosamples use Arrowhead). Also updated the ENCODE metadata columns and organ example in the hg38 makedoc. refs #21599
• src/hg/makeDb/trackDb/mouse/tadsDixon.html
  • lines changed 9, context: html, text, full: html, text
    b7b9978c92a2376d6d9ef4f0a4974cb8167295f8 Wed Sep 30 14:17:50 2026 -0700
    Updating the TAD tracks from the qa-track SKILL.md pass (hg19, hg38, mm10, mm39): shortLabel fixes for cut-off and duplicate ENCODE and 3DGB subtracks, lowercase biosamples in ENCODE longLabels, " bnd" dropped from Schmitt shortLabels, 3DGB subtracks set to pack with three mm10/mm39 defaults turned on, allButtonPair removed so the Schmitt matrix shows, and McArthur item labels hidden. Merged identical description pages into human/ and mouse/, plus description page cleanups (regenerated References, removed the "How to use these tracks" section, ENCODE pages now say 112 of 117 biosamples use Arrowhead). Also updated the ENCODE metadata columns and organ example in the hg38 makedoc. refs #21599
• src/hg/makeDb/trackDb/mouse/tadsEncode.html
  • lines changed 33, context: html, text, full: html, text
    b7b9978c92a2376d6d9ef4f0a4974cb8167295f8 Wed Sep 30 14:17:50 2026 -0700
    Updating the TAD tracks from the qa-track SKILL.md pass (hg19, hg38, mm10, mm39): shortLabel fixes for cut-off and duplicate ENCODE and 3DGB subtracks, lowercase biosamples in ENCODE longLabels, " bnd" dropped from Schmitt shortLabels, 3DGB subtracks set to pack with three mm10/mm39 defaults turned on, allButtonPair removed so the Schmitt matrix shows, and McArthur item labels hidden. Merged identical description pages into human/ and mouse/, plus description page cleanups (regenerated References, removed the "How to use these tracks" section, ENCODE pages now say 112 of 117 biosamples use Arrowhead). Also updated the ENCODE metadata columns and organ example in the hg38 makedoc. refs #21599
• src/hg/makeDb/trackDb/mouseLemur/micMur3/cons3way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/opossum/monDom4/multiz7way.html
  • lines changed 27, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/opossum/monDom4/phastConsElements7way.html
  • lines changed 9, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/opossum/monDom5/multiz9way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/opossum/multiz5way.html
  • lines changed 12, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/orangutan/ponAbe2/multiz8way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/orangutan/ponAbe2/phastConsElements8way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/phastConsElements.html
  • lines changed 8, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/platypus/ornAna1/multiz6way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/platypus/ornAna1/phastConsElements6way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/rat/regenRn1/cons7way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/rat/rn4/multiz9way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/rat/rn4/phastConsElements9way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/rat/rn5/cons13way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/rat/rn6/cons20way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/relatedTracks.ra
  • lines changed 4, context: html, text, full: html, text
    cf3a4c948a0285f6e0ba711688679c904b07e178 Fri Sep 25 14:40:33 2026 -0700
    Adding related tracks for the EpiCentral track, refs #38112
  • lines changed 4, context: html, text, full: html, text
    f3020b17f2fcd376aca99d97d778c11625c0927f Fri Sep 25 17:49:08 2026 -0700
    Relating different TSS and promoter tracks, refs #35528
  • lines changed 18, context: html, text, full: html, text
    53ab3f1e293a91ddf71ec7568f4a6ff827bcd278 Fri Oct 2 13:52:36 2026 -0700
    Native GPN-Star track (Ye, Benegas et al., Nature 2026) on hg38, mm39, galGal6, dm6 and ce11, from the authors' Hugging Face hub. Each model is a multiWig sequence logo plus a four-allele -LLR composite using negateValues. The three hg38 models (V/M/P) sit in predictionScoresSuper via human/gpnStar.ra with /gbdb/$D bigDataUrls so -strict drops them on other human assemblies; the other four get a standalone gpnStar superTrack. The authors' bigWigs come from pyBigWig, whose bwAddIntervalSpanSteps writes the last section of each run 6 bases too long (pyBigWig #166) and makes bigWigAverageOverBed and bigWigCorrelate abort, so gpnStarRebuild.sh re-encodes them with wigToBigWig and gpnStarVerify.sh checks every per-base value is unchanged. Entropy scores and the GenArk-only Arabidopsis set are left out, and pennantIcon still has #TBD placeholders for the newsarch anchor and date. refs #38451
• src/hg/makeDb/trackDb/rhesus/rheMac2/multiz5waySyn.html
  • lines changed 12, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/sacCer/multizYeast.html
  • lines changed 27, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/sacCer/sacCer2/multiz7way.html
  • lines changed 37, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/sacCer/sacCer3/multiz7way.html
  • lines changed 38, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/stickleback/gasAcu1/multiz8way.html
  • lines changed 27, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/stickleback/gasAcu1/phastConsElements8way.html
  • lines changed 9, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 5, context: html, text, full: html, text
    2521d696f5073ce8cee3f59f423f161fdb77d550 Fri Sep 25 02:48:37 2026 -0700
    VCF tracks: the bigBed trackDb filters (filter.*, filterByRange, filterLimits, filterValues, filterType, filterText, filterLabel) now work on INFO fields, plus ID and QUAL. The field list and types come from the VCF header; the bigBed filter code is reused, bigBed behavior unchanged, refs #37617
  • lines changed 5, context: html, text, full: html, text
    c9d17a52b6b5663c7175b01f801d23198b675f7e Fri Sep 25 12:03:55 2026 -0700
    Revert all bigBed-filters for VCF changes, as Chris did that earlier already. This reverts commit 2521d696f5073ce8cee3f59f423f161fdb77d550.
  • lines changed 2, context: html, text, full: html, text
    f20626542200362afacab9387842e1f5bb50c87c Fri Sep 25 12:43:42 2026 -0700
    Experimental gnomAD v4.1.1 VCF track for hg38, refs #37617
  • lines changed 1, context: html, text, full: html, text
    da43847aab52991e91bfec700b16038710710038 Sat Sep 26 21:56:05 2026 -0700
    VCF tracks: new trackDb setting excludeFilterValues, a comma-separated list of FILTER values that are hidden by default; they show up pre-checked in the existing Exclude variants with these FILTER values list, refs #38424
  • lines changed 1, context: html, text, full: html, text
    280bb44983d29e071e862ede483aececbf22d482 Mon Sep 28 09:53:56 2026 -0700
    Remove vcfPhasedTrio type from colorByInfo tag as it is currently unsupported for now, refs daily code review email
• src/hg/makeDb/trackDb/tarsier/tarSyr2/cons17way.html
  • lines changed 39, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/tarsier/tarSyr2/cons20way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    cf9cfcd463d40a868f8ee73dead17ff8071dce2f Fri Sep 25 03:00:20 2026 -0700
    CRISPR tracks: expose colorFields dropdown to color guides by off-target specificity (MIT score) or by Moreno-Mateos efficiency, as alternatives to the default Doench/Fusi-based itemRgb color. The bigBed already carries these as the _specColor and _crisprScanColor extra fields; no data rebuild needed.
• src/hg/makeDb/trackDb/treeShrew/tupChi1/cons4way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/treeShrew/tupChi1/cons5way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/virus/wuhCor1/cons119way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/virus/wuhCor1/cons44way.html
  • lines changed 48, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/worm/ce10/cons7way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/worm/ce10/cons9way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/worm/ce11/cons135way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/worm/ce11/cons26way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/worm/ce11/gpnStar.html
  • lines changed 150, context: html, text, full: html, text
    53ab3f1e293a91ddf71ec7568f4a6ff827bcd278 Fri Oct 2 13:52:36 2026 -0700
    Native GPN-Star track (Ye, Benegas et al., Nature 2026) on hg38, mm39, galGal6, dm6 and ce11, from the authors' Hugging Face hub. Each model is a multiWig sequence logo plus a four-allele -LLR composite using negateValues. The three hg38 models (V/M/P) sit in predictionScoresSuper via human/gpnStar.ra with /gbdb/$D bigDataUrls so -strict drops them on other human assemblies; the other four get a standalone gpnStar superTrack. The authors' bigWigs come from pyBigWig, whose bwAddIntervalSpanSteps writes the last section of each run 6 bases too long (pyBigWig #166) and makes bigWigAverageOverBed and bigWigCorrelate abort, so gpnStarRebuild.sh re-encodes them with wigToBigWig and gpnStarVerify.sh checks every per-base value is unchanged. Entropy scores and the GenArk-only Arabidopsis set are left out, and pennantIcon still has #TBD placeholders for the newsarch anchor and date. refs #38451
• src/hg/makeDb/trackDb/worm/ce11/gpnStar.ra
  • lines changed 125, context: html, text, full: html, text
    53ab3f1e293a91ddf71ec7568f4a6ff827bcd278 Fri Oct 2 13:52:36 2026 -0700
    Native GPN-Star track (Ye, Benegas et al., Nature 2026) on hg38, mm39, galGal6, dm6 and ce11, from the authors' Hugging Face hub. Each model is a multiWig sequence logo plus a four-allele -LLR composite using negateValues. The three hg38 models (V/M/P) sit in predictionScoresSuper via human/gpnStar.ra with /gbdb/$D bigDataUrls so -strict drops them on other human assemblies; the other four get a standalone gpnStar superTrack. The authors' bigWigs come from pyBigWig, whose bwAddIntervalSpanSteps writes the last section of each run 6 bases too long (pyBigWig #166) and makes bigWigAverageOverBed and bigWigCorrelate abort, so gpnStarRebuild.sh re-encodes them with wigToBigWig and gpnStarVerify.sh checks every per-base value is unchanged. Entropy scores and the GenArk-only Arabidopsis set are left out, and pennantIcon still has #TBD placeholders for the newsarch anchor and date. refs #38451
• src/hg/makeDb/trackDb/worm/ce11/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    53ab3f1e293a91ddf71ec7568f4a6ff827bcd278 Fri Oct 2 13:52:36 2026 -0700
    Native GPN-Star track (Ye, Benegas et al., Nature 2026) on hg38, mm39, galGal6, dm6 and ce11, from the authors' Hugging Face hub. Each model is a multiWig sequence logo plus a four-allele -LLR composite using negateValues. The three hg38 models (V/M/P) sit in predictionScoresSuper via human/gpnStar.ra with /gbdb/$D bigDataUrls so -strict drops them on other human assemblies; the other four get a standalone gpnStar superTrack. The authors' bigWigs come from pyBigWig, whose bwAddIntervalSpanSteps writes the last section of each run 6 bases too long (pyBigWig #166) and makes bigWigAverageOverBed and bigWigCorrelate abort, so gpnStarRebuild.sh re-encodes them with wigToBigWig and gpnStarVerify.sh checks every per-base value is unchanged. Entropy scores and the GenArk-only Arabidopsis set are left out, and pennantIcon still has #TBD placeholders for the newsarch anchor and date. refs #38451
• src/hg/makeDb/trackDb/worm/ce4/multiz5way.html
  • lines changed 27, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/worm/ce4/phastConsElements5way.html
  • lines changed 9, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/worm/ce6/multiz6way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/worm/ce6/phastConsElements6way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/worm/ce9/cons10way.html
  • lines changed 41, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/xenTro/xenTro1/multiz5way.html
  • lines changed 27, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/xenTro/xenTro2/multiz7way.html
  • lines changed 29, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/xenTro/xenTro2/phastConsElements7way.html
  • lines changed 16, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/xenTro/xenTro3/cons9way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/xenTro/xenTro9/cons11way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/zebrafish/danRer10/cons12way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/zebrafish/danRer11/danRer11.GCF_049306965.2.chainNet.ra
  • lines changed 49, context: html, text, full: html, text
    a8cddaa41b8aba592873f48a24b15229c052bfbd Tue Sep 22 05:08:06 2026 -0700
    chainNet trackDb for danRer11 GCF_049306965.2, otto liftOver
• src/hg/makeDb/trackDb/zebrafish/danRer11/danRer11.GCF_052040795.1.chainNet.ra
  • lines changed 49, context: html, text, full: html, text
    efaa2288304bd000222111bb024c336d8c56929a Tue Sep 22 03:35:40 2026 -0700
    chainNet trackDb for danRer11 GCF_052040795.1, otto liftOver
• src/hg/makeDb/trackDb/zebrafish/danRer11/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    efaa2288304bd000222111bb024c336d8c56929a Tue Sep 22 03:35:40 2026 -0700
    chainNet trackDb for danRer11 GCF_052040795.1, otto liftOver
  • lines changed 1, context: html, text, full: html, text
    a8cddaa41b8aba592873f48a24b15229c052bfbd Tue Sep 22 05:08:06 2026 -0700
    chainNet trackDb for danRer11 GCF_049306965.2, otto liftOver
• src/hg/makeDb/trackDb/zebrafish/danRer2/multiz6way.html
  • lines changed 27, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/zebrafish/danRer3/multiz5way.html
  • lines changed 27, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/zebrafish/danRer4/multiz7way.html
  • lines changed 27, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/zebrafish/danRer6/multiz6way.html
  • lines changed 37, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/zebrafish/danRer7/cons8way.html
  • lines changed 42, context: html, text, full: html, text
    97805fb2ceb73357aa78aa94107148dc355d4e1c Tue Sep 22 08:36:22 2026 -0700
    Conservation tracks: give the description pages a real Data Access section, refs #34803 The hgdownload link block on these pages had no header, and on 18 of them it sat above the Description, which is where it got overlooked. Move it into an <h2>Data Access</h2> in the usual place, after Methods and before Credits, and add pointers to the Table Browser, the Data Integrator and the REST API, plus the maf* and bigWig* command line tools. 134 pages: 55 had a download block that was moved and labeled, 56 get a list built from hgdownload directories that were checked to exist, 21 have no download directory of their own and so get the Table Browser and API pointers only, and 2 already had a Data Access section that was reworked. Existing download lists are unchanged apart from http -> https and an added target="_blank". Wording follows what each track actually holds, so the alignment-only pages do not claim conservation scores and the Data Integrator is only mentioned where it can really be used, since it does not handle MAF. Also corrects one link: hg18 cons44way pointed at multiz44way/maf, which redirects; it is now multiz44way/maf/. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c8e8fc540646df02203db3233f927e10fc7630d2 Wed Sep 23 15:55:37 2026 -0700
    Conservation track descriptions: stop wrapping the download list in a <p>, refs #34803 A <ul> is not allowed inside a <p>, so the </p> that followed each download list was parsed as an implicit empty paragraph and thrown away. Close the paragraph after the lead-in sentence instead, and leave the list at the same level as the other paragraphs. 113 pages, one moved </p> each. Nothing renders differently; HTML Tidy goes from 226 warnings on these sections to none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makefile
  • lines changed 1, context: html, text, full: html, text
    722e46a2cca739fb7abe042315e8ca3c5e55f8f5 Wed Sep 23 14:25:15 2026 -0700
    Run the hg/utils tests from make test, and fix the two that had gone red, no redmine make test never reached hg/utils. hg/makefile only descends into an app that has a tests/makefile, and hg/utils has none, so the hubCheck, vcfToHgvs and other hg/utils tests were skipped without a message. Added utils to TEST_DIRS. hubCheck stopped warning about a track with no description page after 1258d7f65e7. A track with no page now keeps the empty string that trackDbCustom.c sets, and hubCheck tested for NULL. It now uses isEmpty(). badType gained a real error when 571aecdf42c stopped dropping tracks, and its expected output was never updated. vcfToHgvs stopLoss reads the live hg38 ncbiRefSeq tables, which now have 32 more transcripts and NM_153819.2.
• src/hg/oneShot/pngLevelBench/README
  • lines changed 67, context: html, text, full: html, text
    385cb594dbd4ff14124a64816d0a649458bff44d Wed Sep 2 12:15:29 2026 -0700
    pngLevelBench: measure what each png compression level costs and saves, refs #38109 The compression level decision needs two numbers per level: the bytes the track image grows by, and the encode time it saves. A reader gains from a lower level only above B/S, which is a speed, so the two numbers turn each level into one break-even link speed to compare against the reader throughput the log reader reports. The encode matches lib/pngwrite.c exactly, RGBA with the row filter pinned to UP, and nothing is written to disk, so the time is the encode alone. The check that makes an offline measurement stand for what the CGI does is -check: at level 6, which is what libpng's default resolves to, this has to reproduce the file hgTracks wrote, byte for byte. It does, for every image tried. Also here are the three scripts around it: picking a traffic weighted corpus of real hgTracks URLs out of an access log, rendering them against a parked hgTracks, and aggregating the result into per level bytes, ms and break-even speed. The README gives the order they run in and the one known weakness, that a replayed URL renders the trackDb default track set rather than the reader's own.
  • lines changed 18, context: html, text, full: html, text
    9b9dc9590258144d7b7f17d1ecafb674d2d86956 Wed Sep 2 13:26:40 2026 -0700
    pngLevelBench: sweep the row filter as well as the level, refs #38109 The filter and the level interact, and #38107 picked the filter at the default level only, so measuring one with the other pinned answers half a question. pngLevelBench now takes -filters and -baseFilter, its -tab output carries a filter column, and everything is compared against the pair the browser ships, up at level 6. levelReport.py reads the new column and still accepts rows written before it existed. Two scripts around it grew what a second, larger corpus needed. pickUrls.py takes --seed and --exclude, so a later sample does not repeat an earlier one. render.sh takes its arguments rather than a hardcoded directory, and renders several at once; six in parallel is about seven a second against a ticket sandbox, against one every eight seconds one at a time, and it changes nothing that is measured, since the encode is timed offline afterwards.
• src/hg/oneShot/pngLevelBench/levelReport.py
  • lines changed 128, context: html, text, full: html, text
    385cb594dbd4ff14124a64816d0a649458bff44d Wed Sep 2 12:15:29 2026 -0700
    pngLevelBench: measure what each png compression level costs and saves, refs #38109 The compression level decision needs two numbers per level: the bytes the track image grows by, and the encode time it saves. A reader gains from a lower level only above B/S, which is a speed, so the two numbers turn each level into one break-even link speed to compare against the reader throughput the log reader reports. The encode matches lib/pngwrite.c exactly, RGBA with the row filter pinned to UP, and nothing is written to disk, so the time is the encode alone. The check that makes an offline measurement stand for what the CGI does is -check: at level 6, which is what libpng's default resolves to, this has to reproduce the file hgTracks wrote, byte for byte. It does, for every image tried. Also here are the three scripts around it: picking a traffic weighted corpus of real hgTracks URLs out of an access log, rendering them against a parked hgTracks, and aggregating the result into per level bytes, ms and break-even speed. The README gives the order they run in and the one known weakness, that a replayed URL renders the trackDb default track set rather than the reader's own.
  • lines changed 114, context: html, text, full: html, text
    9b9dc9590258144d7b7f17d1ecafb674d2d86956 Wed Sep 2 13:26:40 2026 -0700
    pngLevelBench: sweep the row filter as well as the level, refs #38109 The filter and the level interact, and #38107 picked the filter at the default level only, so measuring one with the other pinned answers half a question. pngLevelBench now takes -filters and -baseFilter, its -tab output carries a filter column, and everything is compared against the pair the browser ships, up at level 6. levelReport.py reads the new column and still accepts rows written before it existed. Two scripts around it grew what a second, larger corpus needed. pickUrls.py takes --seed and --exclude, so a later sample does not repeat an earlier one. render.sh takes its arguments rather than a hardcoded directory, and renders several at once; six in parallel is about seven a second against a ticket sandbox, against one every eight seconds one at a time, and it changes nothing that is measured, since the encode is timed offline afterwards.
• src/hg/oneShot/pngLevelBench/makefile
  • lines changed 19, context: html, text, full: html, text
    385cb594dbd4ff14124a64816d0a649458bff44d Wed Sep 2 12:15:29 2026 -0700
    pngLevelBench: measure what each png compression level costs and saves, refs #38109 The compression level decision needs two numbers per level: the bytes the track image grows by, and the encode time it saves. A reader gains from a lower level only above B/S, which is a speed, so the two numbers turn each level into one break-even link speed to compare against the reader throughput the log reader reports. The encode matches lib/pngwrite.c exactly, RGBA with the row filter pinned to UP, and nothing is written to disk, so the time is the encode alone. The check that makes an offline measurement stand for what the CGI does is -check: at level 6, which is what libpng's default resolves to, this has to reproduce the file hgTracks wrote, byte for byte. It does, for every image tried. Also here are the three scripts around it: picking a traffic weighted corpus of real hgTracks URLs out of an access log, rendering them against a parked hgTracks, and aggregating the result into per level bytes, ms and break-even speed. The README gives the order they run in and the one known weakness, that a replayed URL renders the trackDb default track set rather than the reader's own.
• src/hg/oneShot/pngLevelBench/pickUrls.py
  • lines changed 79, context: html, text, full: html, text
    385cb594dbd4ff14124a64816d0a649458bff44d Wed Sep 2 12:15:29 2026 -0700
    pngLevelBench: measure what each png compression level costs and saves, refs #38109 The compression level decision needs two numbers per level: the bytes the track image grows by, and the encode time it saves. A reader gains from a lower level only above B/S, which is a speed, so the two numbers turn each level into one break-even link speed to compare against the reader throughput the log reader reports. The encode matches lib/pngwrite.c exactly, RGBA with the row filter pinned to UP, and nothing is written to disk, so the time is the encode alone. The check that makes an offline measurement stand for what the CGI does is -check: at level 6, which is what libpng's default resolves to, this has to reproduce the file hgTracks wrote, byte for byte. It does, for every image tried. Also here are the three scripts around it: picking a traffic weighted corpus of real hgTracks URLs out of an access log, rendering them against a parked hgTracks, and aggregating the result into per level bytes, ms and break-even speed. The README gives the order they run in and the one known weakness, that a replayed URL renders the trackDb default track set rather than the reader's own.
  • lines changed 20, context: html, text, full: html, text
    9b9dc9590258144d7b7f17d1ecafb674d2d86956 Wed Sep 2 13:26:40 2026 -0700
    pngLevelBench: sweep the row filter as well as the level, refs #38109 The filter and the level interact, and #38107 picked the filter at the default level only, so measuring one with the other pinned answers half a question. pngLevelBench now takes -filters and -baseFilter, its -tab output carries a filter column, and everything is compared against the pair the browser ships, up at level 6. levelReport.py reads the new column and still accepts rows written before it existed. Two scripts around it grew what a second, larger corpus needed. pickUrls.py takes --seed and --exclude, so a later sample does not repeat an earlier one. render.sh takes its arguments rather than a hardcoded directory, and renders several at once; six in parallel is about seven a second against a ticket sandbox, against one every eight seconds one at a time, and it changes nothing that is measured, since the encode is timed offline afterwards.
• src/hg/oneShot/pngLevelBench/pngLevelBench.c
  • lines changed 280, context: html, text, full: html, text
    385cb594dbd4ff14124a64816d0a649458bff44d Wed Sep 2 12:15:29 2026 -0700
    pngLevelBench: measure what each png compression level costs and saves, refs #38109 The compression level decision needs two numbers per level: the bytes the track image grows by, and the encode time it saves. A reader gains from a lower level only above B/S, which is a speed, so the two numbers turn each level into one break-even link speed to compare against the reader throughput the log reader reports. The encode matches lib/pngwrite.c exactly, RGBA with the row filter pinned to UP, and nothing is written to disk, so the time is the encode alone. The check that makes an offline measurement stand for what the CGI does is -check: at level 6, which is what libpng's default resolves to, this has to reproduce the file hgTracks wrote, byte for byte. It does, for every image tried. Also here are the three scripts around it: picking a traffic weighted corpus of real hgTracks URLs out of an access log, rendering them against a parked hgTracks, and aggregating the result into per level bytes, ms and break-even speed. The README gives the order they run in and the one known weakness, that a replayed URL renders the trackDb default track set rather than the reader's own.
  • lines changed 162, context: html, text, full: html, text
    9b9dc9590258144d7b7f17d1ecafb674d2d86956 Wed Sep 2 13:26:40 2026 -0700
    pngLevelBench: sweep the row filter as well as the level, refs #38109 The filter and the level interact, and #38107 picked the filter at the default level only, so measuring one with the other pinned answers half a question. pngLevelBench now takes -filters and -baseFilter, its -tab output carries a filter column, and everything is compared against the pair the browser ships, up at level 6. levelReport.py reads the new column and still accepts rows written before it existed. Two scripts around it grew what a second, larger corpus needed. pickUrls.py takes --seed and --exclude, so a later sample does not repeat an earlier one. render.sh takes its arguments rather than a hardcoded directory, and renders several at once; six in parallel is about seven a second against a ticket sandbox, against one every eight seconds one at a time, and it changes nothing that is measured, since the encode is timed offline afterwards.
• src/hg/oneShot/pngLevelBench/render.sh
  • lines changed 15, context: html, text, full: html, text
    385cb594dbd4ff14124a64816d0a649458bff44d Wed Sep 2 12:15:29 2026 -0700
    pngLevelBench: measure what each png compression level costs and saves, refs #38109 The compression level decision needs two numbers per level: the bytes the track image grows by, and the encode time it saves. A reader gains from a lower level only above B/S, which is a speed, so the two numbers turn each level into one break-even link speed to compare against the reader throughput the log reader reports. The encode matches lib/pngwrite.c exactly, RGBA with the row filter pinned to UP, and nothing is written to disk, so the time is the encode alone. The check that makes an offline measurement stand for what the CGI does is -check: at level 6, which is what libpng's default resolves to, this has to reproduce the file hgTracks wrote, byte for byte. It does, for every image tried. Also here are the three scripts around it: picking a traffic weighted corpus of real hgTracks URLs out of an access log, rendering them against a parked hgTracks, and aggregating the result into per level bytes, ms and break-even speed. The README gives the order they run in and the one known weakness, that a replayed URL renders the trackDb default track set rather than the reader's own.
  • lines changed 31, context: html, text, full: html, text
    9b9dc9590258144d7b7f17d1ecafb674d2d86956 Wed Sep 2 13:26:40 2026 -0700
    pngLevelBench: sweep the row filter as well as the level, refs #38109 The filter and the level interact, and #38107 picked the filter at the default level only, so measuring one with the other pinned answers half a question. pngLevelBench now takes -filters and -baseFilter, its -tab output carries a filter column, and everything is compared against the pair the browser ships, up at level 6. levelReport.py reads the new column and still accepts rows written before it existed. Two scripts around it grew what a second, larger corpus needed. pickUrls.py takes --seed and --exclude, so a later sample does not repeat an earlier one. render.sh takes its arguments rather than a hardcoded directory, and renders several at once; six in parallel is about seven a second against a ticket sandbox, against one every eight seconds one at a time, and it changes nothing that is measured, since the encode is timed offline afterwards.
• src/hg/utils/automation/AsmHub.pm
  • lines changed 37, context: html, text, full: html, text
    6dcfa7d1962d9e9dbfa5cbe651b6e301101287ef Fri Sep 25 12:51:58 2026 -0700
    beginning to get a miniMap2 process in place refs #34360
  • lines changed 20, context: html, text, full: html, text
    1c41dff03108b4818777b9c9914e81c72555163f Tue Sep 29 12:28:41 2026 -0700
    miniMap2 now with swap option refs #34360
• src/hg/utils/automation/AssemblyDivergence.pm
  • lines changed 194, context: html, text, full: html, text
    6dcfa7d1962d9e9dbfa5cbe651b6e301101287ef Fri Sep 25 12:51:58 2026 -0700
    beginning to get a miniMap2 process in place refs #34360
  • lines changed 93, context: html, text, full: html, text
    1c0824920cd06057c2e7c02d9cb7ecc153a99d5e Fri Sep 25 14:00:59 2026 -0700
    please no ssh from cluster nodes back to hgwdev to run hgsql commands refs #34360
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    be5cbe094825357e026912debc79944cc15bacde Sun Sep 27 12:58:52 2026 -0700
    claude review fixing bugs better safety on database assembly mash sketch archive refs #34360
• src/hg/utils/automation/HgAutomate.pm
  • lines changed 18, context: html, text, full: html, text
    6dcfa7d1962d9e9dbfa5cbe651b6e301101287ef Fri Sep 25 12:51:58 2026 -0700
    beginning to get a miniMap2 process in place refs #34360
  • lines changed 18, context: html, text, full: html, text
    1c0824920cd06057c2e7c02d9cb7ecc153a99d5e Fri Sep 25 14:00:59 2026 -0700
    please no ssh from cluster nodes back to hgwdev to run hgsql commands refs #34360
• src/hg/utils/automation/aliasTextToBed.pl
  • lines changed 1, context: html, text, full: html, text
    4a6fab6dc819469ff2a299cd310ee19994d7e03a Fri Sep 25 15:08:49 2026 -0700
    allow a T2T name column refs #38110
• src/hg/utils/automation/asmHubMiniMap2ChainNet.pl
  • lines changed 183, context: html, text, full: html, text
    3c1b9cee5a4152b70e2fc10b432082ea89fecae6 Tue Sep 29 15:06:19 2026 -0700
    add trackDb construction for miniMap2 chain tracks refs #34360
  • lines changed 68, context: html, text, full: html, text
    7b14110dc65b6711d7c57fa03594b71b8f93a53e Tue Sep 29 22:49:39 2026 -0700
    add Data Access section to the description pages refs #34360
• src/hg/utils/automation/asmHubMiniMap2ChainNetComposite.pl
  • lines changed 297, context: html, text, full: html, text
    3c1b9cee5a4152b70e2fc10b432082ea89fecae6 Tue Sep 29 15:06:19 2026 -0700
    add trackDb construction for miniMap2 chain tracks refs #34360
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    8149f2d63d04238813b626ab194b45eeaa91e32f Tue Sep 29 15:20:22 2026 -0700
    fixup swap directory recognition refs #34360
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    7b14110dc65b6711d7c57fa03594b71b8f93a53e Tue Sep 29 22:49:39 2026 -0700
    add Data Access section to the description pages refs #34360
• src/hg/utils/automation/asmHubMiniMap2ChainNetTrackDb.pl
  • lines changed 219, context: html, text, full: html, text
    3c1b9cee5a4152b70e2fc10b432082ea89fecae6 Tue Sep 29 15:06:19 2026 -0700
    add trackDb construction for miniMap2 chain tracks refs #34360
  • lines changed 5, context: html, text, full: html, text
    8149f2d63d04238813b626ab194b45eeaa91e32f Tue Sep 29 15:20:22 2026 -0700
    fixup swap directory recognition refs #34360
• src/hg/utils/automation/asmHubMiniMap2ChainNetTrackDb.sh
  • lines changed 167, context: html, text, full: html, text
    3c1b9cee5a4152b70e2fc10b432082ea89fecae6 Tue Sep 29 15:06:19 2026 -0700
    add trackDb construction for miniMap2 chain tracks refs #34360
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    8149f2d63d04238813b626ab194b45eeaa91e32f Tue Sep 29 15:20:22 2026 -0700
    fixup swap directory recognition refs #34360
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 21, context: html, text, full: html, text
    3c1b9cee5a4152b70e2fc10b432082ea89fecae6 Tue Sep 29 15:06:19 2026 -0700
    add trackDb construction for miniMap2 chain tracks refs #34360
  • lines changed 6, context: html, text, full: html, text
    8149f2d63d04238813b626ab194b45eeaa91e32f Tue Sep 29 15:20:22 2026 -0700
    fixup swap directory recognition refs #34360
• src/hg/utils/automation/doAssemblyHub.pl
  • lines changed 44, context: html, text, full: html, text
    e8b649b163d747c026dde4606542fcc024a6943a Sun Sep 27 13:14:54 2026 -0700
    add the mash sketch operation to the GenArk build refs #34360
• src/hg/utils/automation/doMiniMap2.pl
  • lines changed 785, context: html, text, full: html, text
    6dcfa7d1962d9e9dbfa5cbe651b6e301101287ef Fri Sep 25 12:51:58 2026 -0700
    beginning to get a miniMap2 process in place refs #34360
  • lines changed 5, context: html, text, full: html, text
    1c0824920cd06057c2e7c02d9cb7ecc153a99d5e Fri Sep 25 14:00:59 2026 -0700
    please no ssh from cluster nodes back to hgwdev to run hgsql commands refs #34360
  • lines changed 116, context: html, text, full: html, text
    70b908a5c6475d6c2770a3305f9319d88d0cb62e Mon Sep 28 22:31:27 2026 -0700
    readjusting output results and feature bit file locations refs #34360
  • lines changed 216, context: html, text, full: html, text
    cb2aa0e55497911448f0a42bff3b368057847eef Tue Sep 29 11:58:39 2026 -0700
    may have the primary query on target working OK refs #34360
  • lines changed 209, context: html, text, full: html, text
    1c41dff03108b4818777b9c9914e81c72555163f Tue Sep 29 12:28:41 2026 -0700
    miniMap2 now with swap option refs #34360
• src/hg/utils/automation/makefile
  • lines changed 3, context: html, text, full: html, text
    59e735bf19713b82dd5898fbd7b0e34cb5e980af Fri Sep 25 12:58:50 2026 -0700
    OK to place these new functions for miniMap2 and mashDistance into scripts directory #34360
• src/hg/utils/automation/mashDistance.pl
  • lines changed 131, context: html, text, full: html, text
    6dcfa7d1962d9e9dbfa5cbe651b6e301101287ef Fri Sep 25 12:51:58 2026 -0700
    beginning to get a miniMap2 process in place refs #34360
  • lines changed 2, context: html, text, full: html, text
    75f0d8f409975fddfd9c01378b4404d19393ec6b Fri Sep 25 12:53:35 2026 -0700
    beginning to get a miniMap2 process in place refs #34360
  • lines changed 46, context: html, text, full: html, text
    1c0824920cd06057c2e7c02d9cb7ecc153a99d5e Fri Sep 25 14:00:59 2026 -0700
    please no ssh from cluster nodes back to hgwdev to run hgsql commands refs #34360
• src/hg/utils/cartFileVarCatalog/cartFileVarCatalog.py
  • lines changed 3, context: html, text, full: html, text
    da449b4fe2039f200a2f93d5209c48fe98c0a534 Tue Sep 29 10:58:30 2026 -0700
    cartPcrVarTester: which hgPcrResult_ cart variables survive a cart load, refs #38442 Feeds hgPcrResult_ variables through cartParseOverHash() and says which are kept. With the cart.c fix backed out it shows hgPcrResult_imgOrd dropped and nothing else changes. Registry row and catalog note added.
• src/hg/utils/docent/README.md
  • lines changed 9, context: html, text, full: html, text
    6f3f3596f3dc61a8a738717b9701e69a86b5bb0b Mon Sep 21 17:24:33 2026 -0700
    docent: wait: {gone:} for a selector to leave, and rm38257 stops racing itself rm38257 went red in the 2026-09-21 nightly with the #38257 fix still live on genome-test. The script was waiting on the wrong half of the click. hgHubConnect.js switches the tab synchronously inside the click dispatch, while topLinks.js closes the Account popup from a setTimeout(..., 0). So the tab is the half that settles FIRST, and waiting for it returned a tick early: the expect after it read a page that still had the popup on it. Measured with a MutationObserver over the click, the tab goes active at t=43ms and the popup goes on the next task. wait: now also takes {gone: <selector>}, which waits for a selector to leave the DOM, so a script can wait on the vanishing half of an answer. rm38257 uses it. Six runs each way on genome-test, same build, only the script differing: 6 of 6 green with the new wait:, 3 of 6 red with the old one, failing at the same step with the same message the nightly printed. The whole directory is green, 98 of 98. refs #37892, refs #38252
  • lines changed 3, context: html, text, full: html, text
    1fbda5badde574c10884e5339fdda1f5b7495990 Thu Sep 24 13:45:30 2026 -0700
    docent: regression script for the Sessions page Replace keeping who can load it, refs #38311 rm38311 saves a private session from the save card, saves over it with the private box unticked, and checks that the row still has its lock. It passes on hgwbeta (v504) and genome-test, and fails on hgw0 (v503). Docent changes it needed: - a fill: verb, to type into any form field - login: no longer dies when a navigation is still under way during its bad-password check, which is what broke it on ticket parks - a park is driven on its https port, because hgLogin posts its form to https:// on the port it was reached on; the parks' self-signed certificate is accepted on loopback targets only - hgw0 maps to hgcentral, and a park's https port finds its hg.conf
  • lines changed 2, context: html, text, full: html, text
    9bd1a5356bcf1a68ea715e5b0d9c3731203f6d88 Sat Sep 26 12:12:14 2026 -0700
    docent: hubUpload: verb, which drops files into the Hub Upload dashboard, and a value: check in expect: for what a form field holds, refs #37892, #38398 Nothing is uploaded by hubUpload:, so a run leaves nothing on the server. value: exists because a selector cannot read a field that a framework draws: it sets the value property, and [value=...] reads only the attribute.
  • lines changed 4, context: html, text, full: html, text
    9cdd7a15f40c41874620a7d2bc907d77489f7746 Sat Sep 26 17:43:32 2026 -0700
    docent: setVis:, rightClick:, and drag: then: none / dialog: auto, refs #37892, #38035, #38071, #38087 setVis: sets a track's visibility with its own dropdown under the image. The change event fires and the page's handler runs, with no navigation. track: asks for the mode in a URL, so it cannot see what that handler does to the page. rightClick: opens the track right-click menu and picks an entry by its text. An exact match wins over a substring. A miss fails the run and lists the entries on offer. drag: then: none leaves the drag-select dialog open for later click: steps. dialog: auto hands the selection to dragSelect.selectEnd(), so the page decides between the dialog and a straight zoom instead of the verb forcing the dialog on. A track name ending in * now matches a row id by prefix, for custom tracks. shot: also captures an open right-click menu.
• src/hg/utils/docent/docent.js
  • lines changed 16, context: html, text, full: html, text
    6f3f3596f3dc61a8a738717b9701e69a86b5bb0b Mon Sep 21 17:24:33 2026 -0700
    docent: wait: {gone:} for a selector to leave, and rm38257 stops racing itself rm38257 went red in the 2026-09-21 nightly with the #38257 fix still live on genome-test. The script was waiting on the wrong half of the click. hgHubConnect.js switches the tab synchronously inside the click dispatch, while topLinks.js closes the Account popup from a setTimeout(..., 0). So the tab is the half that settles FIRST, and waiting for it returned a tick early: the expect after it read a page that still had the popup on it. Measured with a MutationObserver over the click, the tab goes active at t=43ms and the popup goes on the next task. wait: now also takes {gone: <selector>}, which waits for a selector to leave the DOM, so a script can wait on the vanishing half of an answer. rm38257 uses it. Six runs each way on genome-test, same build, only the script differing: 6 of 6 green with the new wait:, 3 of 6 red with the old one, failing at the same step with the same message the nightly printed. The whole directory is green, 98 of 98. refs #37892, refs #38252
  • lines changed 32, context: html, text, full: html, text
    1fbda5badde574c10884e5339fdda1f5b7495990 Thu Sep 24 13:45:30 2026 -0700
    docent: regression script for the Sessions page Replace keeping who can load it, refs #38311 rm38311 saves a private session from the save card, saves over it with the private box unticked, and checks that the row still has its lock. It passes on hgwbeta (v504) and genome-test, and fails on hgw0 (v503). Docent changes it needed: - a fill: verb, to type into any form field - login: no longer dies when a navigation is still under way during its bad-password check, which is what broke it on ticket parks - a park is driven on its https port, because hgLogin posts its form to https:// on the port it was reached on; the parks' self-signed certificate is accepted on loopback targets only - hgw0 maps to hgcentral, and a park's https port finds its hg.conf
  • lines changed 64, context: html, text, full: html, text
    9bd1a5356bcf1a68ea715e5b0d9c3731203f6d88 Sat Sep 26 12:12:14 2026 -0700
    docent: hubUpload: verb, which drops files into the Hub Upload dashboard, and a value: check in expect: for what a form field holds, refs #37892, #38398 Nothing is uploaded by hubUpload:, so a run leaves nothing on the server. value: exists because a selector cannot read a field that a framework draws: it sets the value property, and [value=...] reads only the attribute.
  • lines changed 135, context: html, text, full: html, text
    9cdd7a15f40c41874620a7d2bc907d77489f7746 Sat Sep 26 17:43:32 2026 -0700
    docent: setVis:, rightClick:, and drag: then: none / dialog: auto, refs #37892, #38035, #38071, #38087 setVis: sets a track's visibility with its own dropdown under the image. The change event fires and the page's handler runs, with no navigation. track: asks for the mode in a URL, so it cannot see what that handler does to the page. rightClick: opens the track right-click menu and picks an entry by its text. An exact match wins over a substring. A miss fails the run and lists the entries on offer. drag: then: none leaves the drag-select dialog open for later click: steps. dialog: auto hands the selection to dragSelect.selectEnd(), so the page decides between the dialog and a straight zoom instead of the verb forcing the dialog on. A track name ending in * now matches a row id by prefix, for custom tracks. shot: also captures an open right-click menu.
  • lines changed 29, context: html, text, full: html, text
    ce29202faf7a2b48e62a6e3f579ba09000d00c0b Sun Sep 27 15:51:36 2026 -0700
    docent: put the server's warning text in a failure message, refs #38252 A run that failed on noText: "Warning/Error", or on a custom track that never loaded, said only that the server complained. The reason was left in the Apache error log. The new serverWarnings() reads the hgTracks warning list and hgCustom's Error/Warning line. A failed expect: and a failed addCustomTrack now print each one as a "server said:" line.
• src/hg/utils/docent/targetConf.js
  • lines changed 4, context: html, text, full: html, text
    1fbda5badde574c10884e5339fdda1f5b7495990 Thu Sep 24 13:45:30 2026 -0700
    docent: regression script for the Sessions page Replace keeping who can load it, refs #38311 rm38311 saves a private session from the save card, saves over it with the private box unticked, and checks that the row still has its lock. It passes on hgwbeta (v504) and genome-test, and fails on hgw0 (v503). Docent changes it needed: - a fill: verb, to type into any form field - login: no longer dies when a navigation is still under way during its bad-password check, which is what broke it on ticket parks - a park is driven on its https port, because hgLogin posts its form to https:// on the port it was reached on; the parks' self-signed certificate is accepted on loopback targets only - hgw0 maps to hgcentral, and a park's https port finds its hg.conf
• src/hg/utils/docent/tests/README.txt
  • lines changed 3, context: html, text, full: html, text
    9bd1a5356bcf1a68ea715e5b0d9c3731203f6d88 Sat Sep 26 12:12:14 2026 -0700
    docent: hubUpload: verb, which drops files into the Hub Upload dashboard, and a value: check in expect: for what a form field holds, refs #37892, #38398 Nothing is uploaded by hubUpload:, so a run leaves nothing on the server. value: exists because a selector cannot read a field that a framework draws: it sets the value property, and [value=...] reads only the attribute.
  • lines changed 6, context: html, text, full: html, text
    9cdd7a15f40c41874620a7d2bc907d77489f7746 Sat Sep 26 17:43:32 2026 -0700
    docent: setVis:, rightClick:, and drag: then: none / dialog: auto, refs #37892, #38035, #38071, #38087 setVis: sets a track's visibility with its own dropdown under the image. The change event fires and the page's handler runs, with no navigation. track: asks for the mode in a URL, so it cannot see what that handler does to the page. rightClick: opens the track right-click menu and picks an entry by its text. An exact match wins over a substring. A miss fails the run and lists the entries on offer. drag: then: none leaves the drag-select dialog open for later click: steps. dialog: auto hands the selection to dragSelect.selectEnd(), so the page decides between the dialog and a straight zoom instead of the verb forcing the dialog on. A track name ending in * now matches a row id by prefix, for custom tracks. shot: also captures an open right-click menu.
• src/hg/utils/docent/tests/regress/README.txt
  • lines changed 21, context: html, text, full: html, text
    966c49bdf93dada183133e06522bfb0152de6168 Wed Sep 23 13:38:34 2026 -0700
    docent: the nightly writes a status page, refs #38252 nightlyStatus.py reads the nightly logs, flips.log and each committed script's proof: lines, and writes one page with a row per script, anchored by its name so a ticket can link to one row. Each row has the current state and the date it has held since, the last 14 days, the strongest proof: level in plain words, and links to the script, the ticket and any before/after picture. Each row also has a link to try it on genome-test and on hgwbeta: the script's steps as far as one URL can rebuild them, with track: steps resolved by DOCENT_DERIVE. Every link is fetched with a fresh cart first, and the page calls it verified only when the fetch draws what the expect: step names. A night is a log written by an --update run, which is what cron does, not a log named _0410: the 09-14 and 09-15 runs started late and a name match dropped them. nightly.sh runs it after the log is complete and adds one line to the mail, the page URL or the error. It changes nothing else about the night's verdict or exit status.
  • lines changed 4, context: html, text, full: html, text
    1fbda5badde574c10884e5339fdda1f5b7495990 Thu Sep 24 13:45:30 2026 -0700
    docent: regression script for the Sessions page Replace keeping who can load it, refs #38311 rm38311 saves a private session from the save card, saves over it with the private box unticked, and checks that the row still has its lock. It passes on hgwbeta (v504) and genome-test, and fails on hgw0 (v503). Docent changes it needed: - a fill: verb, to type into any form field - login: no longer dies when a navigation is still under way during its bad-password check, which is what broke it on ticket parks - a park is driven on its https port, because hgLogin posts its form to https:// on the port it was reached on; the parks' self-signed certificate is accepted on loopback targets only - hgw0 maps to hgcentral, and a park's https port finds its hg.conf
• src/hg/utils/docent/tests/regress/nightly.sh
  • lines changed 14, context: html, text, full: html, text
    966c49bdf93dada183133e06522bfb0152de6168 Wed Sep 23 13:38:34 2026 -0700
    docent: the nightly writes a status page, refs #38252 nightlyStatus.py reads the nightly logs, flips.log and each committed script's proof: lines, and writes one page with a row per script, anchored by its name so a ticket can link to one row. Each row has the current state and the date it has held since, the last 14 days, the strongest proof: level in plain words, and links to the script, the ticket and any before/after picture. Each row also has a link to try it on genome-test and on hgwbeta: the script's steps as far as one URL can rebuild them, with track: steps resolved by DOCENT_DERIVE. Every link is fetched with a fresh cart first, and the page calls it verified only when the fetch draws what the expect: step names. A night is a log written by an --update run, which is what cron does, not a log named _0410: the 09-14 and 09-15 runs started late and a name match dropped them. nightly.sh runs it after the log is complete and adds one line to the mail, the page URL or the error. It changes nothing else about the night's verdict or exit status.
• src/hg/utils/docent/tests/regress/nightlyStatus.py
  • lines changed 435, context: html, text, full: html, text
    966c49bdf93dada183133e06522bfb0152de6168 Wed Sep 23 13:38:34 2026 -0700
    docent: the nightly writes a status page, refs #38252 nightlyStatus.py reads the nightly logs, flips.log and each committed script's proof: lines, and writes one page with a row per script, anchored by its name so a ticket can link to one row. Each row has the current state and the date it has held since, the last 14 days, the strongest proof: level in plain words, and links to the script, the ticket and any before/after picture. Each row also has a link to try it on genome-test and on hgwbeta: the script's steps as far as one URL can rebuild them, with track: steps resolved by DOCENT_DERIVE. Every link is fetched with a fresh cart first, and the page calls it verified only when the fetch draws what the expect: step names. A night is a log written by an --update run, which is what cron does, not a log named _0410: the 09-14 and 09-15 runs started late and a name match dropped them. nightly.sh runs it after the log is complete and adds one line to the mail, the page URL or the error. It changes nothing else about the night's verdict or exit status.
  • lines changed 12, context: html, text, full: html, text
    91008f116877a4ac9de458dec4abb98ca3249dbf Wed Sep 23 17:15:55 2026 -0700
    docent status page: try-it links for sessions loaded by URL, none on hgwbeta for named ones, refs #38252 A named session lives in one machine's hgcentral, so its hgwbeta link only answered "Could not find session"; those rows now offer genome-test alone and say why. A session loaded from a text file by URL works on any server, so a script that loads one now gets a link, with both servers.
• src/hg/utils/docent/tests/regress/rm20824.docent.yaml
  • lines changed 63, context: html, text, full: html, text
    58fa228f2f91ae8c6a5c62109e904f57e1f9a66d Wed Sep 30 11:03:02 2026 -0700
    docent regression scripts for nineteen v504 tickets, and their registry rows Each script watches one v504 fix. Fourteen fail on v503 (ts park 38316) and pass on genome-test (release-ab). rm38313 and rm38393 are sandbox-ab, because no release predates their fix. rm37984, rm38233 and rm38384 are assertion-only; each header says why. The registry now names the script in the docent column for these tickets, and has new rows for #38157 and #38393. #38275 stays unwatched in the table: the script that watches it is rm37389, which is named for another ticket. refs #20824, #27988, #36292, #37595, #37621, #37929, #37984, #38157, #38192, #38197, #38233, #38254, #38264, #38273, #38313, #38323, #38372, #38384, #38393, #38252, #38391 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
• src/hg/utils/docent/tests/regress/rm27988.docent.yaml
  • lines changed 76, context: html, text, full: html, text
    58fa228f2f91ae8c6a5c62109e904f57e1f9a66d Wed Sep 30 11:03:02 2026 -0700
    docent regression scripts for nineteen v504 tickets, and their registry rows Each script watches one v504 fix. Fourteen fail on v503 (ts park 38316) and pass on genome-test (release-ab). rm38313 and rm38393 are sandbox-ab, because no release predates their fix. rm37984, rm38233 and rm38384 are assertion-only; each header says why. The registry now names the script in the docent column for these tickets, and has new rows for #38157 and #38393. #38275 stays unwatched in the table: the script that watches it is rm37389, which is named for another ticket. refs #20824, #27988, #36292, #37595, #37621, #37929, #37984, #38157, #38192, #38197, #38233, #38254, #38264, #38273, #38313, #38323, #38372, #38384, #38393, #38252, #38391 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
• src/hg/utils/docent/tests/regress/rm35580.docent.yaml
  • lines changed 3, context: html, text, full: html, text
    4bf8479a43a493e2899953b7358c9464abbc3959 Wed Sep 23 17:15:55 2026 -0700
    docent: regression scripts load sessions from text files, not from one machine's hgcentral, refs #38252 A named session runs only on the machine whose hgcentral holds it, so hgwbeta and the RR answered "Could not find session". The sessions are now text files in regress/sessionFiles, saved with hgSession's own save to file, and the scripts load them by raw GitHub URL. rm36805, rm35580 and rm36340 pass on genome-test and hgwbeta. rm36340's session held its custom tracks as a customTrash table on genome-test. The track source is a file of its own now, loaded through hgt.customText, without two commented-out tracks whose URLs carry a password. Its first check now asks for a custom track row and the hub's row, and fails when the session file does not load. A lifted session cannot be a file: it names its quickLift hub by a path on the server that made it, and re-pointing it does not work (#38046). rm37388, rm37389 and rm38272 build that lift in steps instead, the GenArk GCA_018466835.2 mitochondrion lifted to hg38, and pass on genome-test and hgwbeta. rm38272 also fails on genome.ucsc.edu (v503) at its settings page, with the bug's own error, so it gains a release-ab proof line.
• src/hg/utils/docent/tests/regress/rm36292.docent.yaml
  • lines changed 95, context: html, text, full: html, text
    58fa228f2f91ae8c6a5c62109e904f57e1f9a66d Wed Sep 30 11:03:02 2026 -0700
    docent regression scripts for nineteen v504 tickets, and their registry rows Each script watches one v504 fix. Fourteen fail on v503 (ts park 38316) and pass on genome-test (release-ab). rm38313 and rm38393 are sandbox-ab, because no release predates their fix. rm37984, rm38233 and rm38384 are assertion-only; each header says why. The registry now names the script in the docent column for these tickets, and has new rows for #38157 and #38393. #38275 stays unwatched in the table: the script that watches it is rm37389, which is named for another ticket. refs #20824, #27988, #36292, #37595, #37621, #37929, #37984, #38157, #38192, #38197, #38233, #38254, #38264, #38273, #38313, #38323, #38372, #38384, #38393, #38252, #38391 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
• src/hg/utils/docent/tests/regress/rm36340.docent.yaml
  • lines changed 14, context: html, text, full: html, text
    4bf8479a43a493e2899953b7358c9464abbc3959 Wed Sep 23 17:15:55 2026 -0700
    docent: regression scripts load sessions from text files, not from one machine's hgcentral, refs #38252 A named session runs only on the machine whose hgcentral holds it, so hgwbeta and the RR answered "Could not find session". The sessions are now text files in regress/sessionFiles, saved with hgSession's own save to file, and the scripts load them by raw GitHub URL. rm36805, rm35580 and rm36340 pass on genome-test and hgwbeta. rm36340's session held its custom tracks as a customTrash table on genome-test. The track source is a file of its own now, loaded through hgt.customText, without two commented-out tracks whose URLs carry a password. Its first check now asks for a custom track row and the hub's row, and fails when the session file does not load. A lifted session cannot be a file: it names its quickLift hub by a path on the server that made it, and re-pointing it does not work (#38046). rm37388, rm37389 and rm38272 build that lift in steps instead, the GenArk GCA_018466835.2 mitochondrion lifted to hg38, and pass on genome-test and hgwbeta. rm38272 also fails on genome.ucsc.edu (v503) at its settings page, with the bug's own error, so it gains a release-ab proof line.
• src/hg/utils/docent/tests/regress/rm36805.docent.yaml
  • lines changed 4, context: html, text, full: html, text
    4bf8479a43a493e2899953b7358c9464abbc3959 Wed Sep 23 17:15:55 2026 -0700
    docent: regression scripts load sessions from text files, not from one machine's hgcentral, refs #38252 A named session runs only on the machine whose hgcentral holds it, so hgwbeta and the RR answered "Could not find session". The sessions are now text files in regress/sessionFiles, saved with hgSession's own save to file, and the scripts load them by raw GitHub URL. rm36805, rm35580 and rm36340 pass on genome-test and hgwbeta. rm36340's session held its custom tracks as a customTrash table on genome-test. The track source is a file of its own now, loaded through hgt.customText, without two commented-out tracks whose URLs carry a password. Its first check now asks for a custom track row and the hub's row, and fails when the session file does not load. A lifted session cannot be a file: it names its quickLift hub by a path on the server that made it, and re-pointing it does not work (#38046). rm37388, rm37389 and rm38272 build that lift in steps instead, the GenArk GCA_018466835.2 mitochondrion lifted to hg38, and pass on genome-test and hgwbeta. rm38272 also fails on genome.ucsc.edu (v503) at its settings page, with the bug's own error, so it gains a release-ab proof line.
• src/hg/utils/docent/tests/regress/rm37388.docent.yaml
  • lines changed 14, context: html, text, full: html, text
    4bf8479a43a493e2899953b7358c9464abbc3959 Wed Sep 23 17:15:55 2026 -0700
    docent: regression scripts load sessions from text files, not from one machine's hgcentral, refs #38252 A named session runs only on the machine whose hgcentral holds it, so hgwbeta and the RR answered "Could not find session". The sessions are now text files in regress/sessionFiles, saved with hgSession's own save to file, and the scripts load them by raw GitHub URL. rm36805, rm35580 and rm36340 pass on genome-test and hgwbeta. rm36340's session held its custom tracks as a customTrash table on genome-test. The track source is a file of its own now, loaded through hgt.customText, without two commented-out tracks whose URLs carry a password. Its first check now asks for a custom track row and the hub's row, and fails when the session file does not load. A lifted session cannot be a file: it names its quickLift hub by a path on the server that made it, and re-pointing it does not work (#38046). rm37388, rm37389 and rm38272 build that lift in steps instead, the GenArk GCA_018466835.2 mitochondrion lifted to hg38, and pass on genome-test and hgwbeta. rm38272 also fails on genome.ucsc.edu (v503) at its settings page, with the bug's own error, so it gains a release-ab proof line.
• src/hg/utils/docent/tests/regress/rm37389.docent.yaml
  • lines changed 13, context: html, text, full: html, text
    4bf8479a43a493e2899953b7358c9464abbc3959 Wed Sep 23 17:15:55 2026 -0700
    docent: regression scripts load sessions from text files, not from one machine's hgcentral, refs #38252 A named session runs only on the machine whose hgcentral holds it, so hgwbeta and the RR answered "Could not find session". The sessions are now text files in regress/sessionFiles, saved with hgSession's own save to file, and the scripts load them by raw GitHub URL. rm36805, rm35580 and rm36340 pass on genome-test and hgwbeta. rm36340's session held its custom tracks as a customTrash table on genome-test. The track source is a file of its own now, loaded through hgt.customText, without two commented-out tracks whose URLs carry a password. Its first check now asks for a custom track row and the hub's row, and fails when the session file does not load. A lifted session cannot be a file: it names its quickLift hub by a path on the server that made it, and re-pointing it does not work (#38046). rm37388, rm37389 and rm38272 build that lift in steps instead, the GenArk GCA_018466835.2 mitochondrion lifted to hg38, and pass on genome-test and hgwbeta. rm38272 also fails on genome.ucsc.edu (v503) at its settings page, with the bug's own error, so it gains a release-ab proof line.
• src/hg/utils/docent/tests/regress/rm37595.docent.yaml
  • lines changed 69, context: html, text, full: html, text
    58fa228f2f91ae8c6a5c62109e904f57e1f9a66d Wed Sep 30 11:03:02 2026 -0700
    docent regression scripts for nineteen v504 tickets, and their registry rows Each script watches one v504 fix. Fourteen fail on v503 (ts park 38316) and pass on genome-test (release-ab). rm38313 and rm38393 are sandbox-ab, because no release predates their fix. rm37984, rm38233 and rm38384 are assertion-only; each header says why. The registry now names the script in the docent column for these tickets, and has new rows for #38157 and #38393. #38275 stays unwatched in the table: the script that watches it is rm37389, which is named for another ticket. refs #20824, #27988, #36292, #37595, #37621, #37929, #37984, #38157, #38192, #38197, #38233, #38254, #38264, #38273, #38313, #38323, #38372, #38384, #38393, #38252, #38391 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
• src/hg/utils/docent/tests/regress/rm37617.docent.yaml
  • lines changed 47, context: html, text, full: html, text
    f3bec731c93f26f8f1984fd727c6ee55ebf99f85 Tue Sep 29 13:00:12 2026 -0700
    docent regression scripts for three v505 tickets, and registry updates, refs #37617, #37618, #38442, #38249, #38252 rm37617 checks that filter.AF on a VCF INFO field hides the variants below the trackDb minimum, and rm37618 that colorByInfo colors each item by its INFO value. Both use a four-variant fixture hub, docentFixtures/rm37617. rm38442 runs the ticket's PCR search, sets the places a drag saves, and checks that the PCR track keeps its place after a zoom. All three fail on hgwbeta (v504) and pass on genome-test. registry.tsv names the three scripts, adds a row for #38387, and raises the #38249 quickLiftTester row to sandbox-ab: backing out either quickLift fix by hand turns the test red.
• src/hg/utils/docent/tests/regress/rm37618.docent.yaml
  • lines changed 35, context: html, text, full: html, text
    f3bec731c93f26f8f1984fd727c6ee55ebf99f85 Tue Sep 29 13:00:12 2026 -0700
    docent regression scripts for three v505 tickets, and registry updates, refs #37617, #37618, #38442, #38249, #38252 rm37617 checks that filter.AF on a VCF INFO field hides the variants below the trackDb minimum, and rm37618 that colorByInfo colors each item by its INFO value. Both use a four-variant fixture hub, docentFixtures/rm37617. rm38442 runs the ticket's PCR search, sets the places a drag saves, and checks that the PCR track keeps its place after a zoom. All three fail on hgwbeta (v504) and pass on genome-test. registry.tsv names the three scripts, adds a row for #38387, and raises the #38249 quickLiftTester row to sandbox-ab: backing out either quickLift fix by hand turns the test red.
• src/hg/utils/docent/tests/regress/rm37621.docent.yaml
  • lines changed 68, context: html, text, full: html, text
    58fa228f2f91ae8c6a5c62109e904f57e1f9a66d Wed Sep 30 11:03:02 2026 -0700
    docent regression scripts for nineteen v504 tickets, and their registry rows Each script watches one v504 fix. Fourteen fail on v503 (ts park 38316) and pass on genome-test (release-ab). rm38313 and rm38393 are sandbox-ab, because no release predates their fix. rm37984, rm38233 and rm38384 are assertion-only; each header says why. The registry now names the script in the docent column for these tickets, and has new rows for #38157 and #38393. #38275 stays unwatched in the table: the script that watches it is rm37389, which is named for another ticket. refs #20824, #27988, #36292, #37595, #37621, #37929, #37984, #38157, #38192, #38197, #38233, #38254, #38264, #38273, #38313, #38323, #38372, #38384, #38393, #38252, #38391 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
• src/hg/utils/docent/tests/regress/rm37929.docent.yaml
  • lines changed 88, context: html, text, full: html, text
    58fa228f2f91ae8c6a5c62109e904f57e1f9a66d Wed Sep 30 11:03:02 2026 -0700
    docent regression scripts for nineteen v504 tickets, and their registry rows Each script watches one v504 fix. Fourteen fail on v503 (ts park 38316) and pass on genome-test (release-ab). rm38313 and rm38393 are sandbox-ab, because no release predates their fix. rm37984, rm38233 and rm38384 are assertion-only; each header says why. The registry now names the script in the docent column for these tickets, and has new rows for #38157 and #38393. #38275 stays unwatched in the table: the script that watches it is rm37389, which is named for another ticket. refs #20824, #27988, #36292, #37595, #37621, #37929, #37984, #38157, #38192, #38197, #38233, #38254, #38264, #38273, #38313, #38323, #38372, #38384, #38393, #38252, #38391 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
• src/hg/utils/docent/tests/regress/rm37972.docent.yaml
  • lines changed 96, context: html, text, full: html, text
    2daf01cbbc39c63db64caccf4a87f20a7f2f5f97 Sat Sep 26 17:43:37 2026 -0700
    docent regression scripts for the v503 tickets, refs #38252, #37972, #37987, #37990, #38027, #38033, #38035, #38039, #38071, #38072, #38082, #38087, #38120, #38154, #38155, #38231 One script per ticket. Each one passes on genome-test. Twelve also fail on a v502_branch build for the reason the script exists, and carry a release-ab proof line. rm38072, rm38120 and rm38231 can never fail on a released build, and their headers say why.
• src/hg/utils/docent/tests/regress/rm37984.docent.yaml
  • lines changed 66, context: html, text, full: html, text
    58fa228f2f91ae8c6a5c62109e904f57e1f9a66d Wed Sep 30 11:03:02 2026 -0700
    docent regression scripts for nineteen v504 tickets, and their registry rows Each script watches one v504 fix. Fourteen fail on v503 (ts park 38316) and pass on genome-test (release-ab). rm38313 and rm38393 are sandbox-ab, because no release predates their fix. rm37984, rm38233 and rm38384 are assertion-only; each header says why. The registry now names the script in the docent column for these tickets, and has new rows for #38157 and #38393. #38275 stays unwatched in the table: the script that watches it is rm37389, which is named for another ticket. refs #20824, #27988, #36292, #37595, #37621, #37929, #37984, #38157, #38192, #38197, #38233, #38254, #38264, #38273, #38313, #38323, #38372, #38384, #38393, #38252, #38391 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
• src/hg/utils/docent/tests/regress/rm37987.docent.yaml
  • lines changed 67, context: html, text, full: html, text
    2daf01cbbc39c63db64caccf4a87f20a7f2f5f97 Sat Sep 26 17:43:37 2026 -0700
    docent regression scripts for the v503 tickets, refs #38252, #37972, #37987, #37990, #38027, #38033, #38035, #38039, #38071, #38072, #38082, #38087, #38120, #38154, #38155, #38231 One script per ticket. Each one passes on genome-test. Twelve also fail on a v502_branch build for the reason the script exists, and carry a release-ab proof line. rm38072, rm38120 and rm38231 can never fail on a released build, and their headers say why.
• src/hg/utils/docent/tests/regress/rm37990.docent.yaml
  • lines changed 47, context: html, text, full: html, text
    2daf01cbbc39c63db64caccf4a87f20a7f2f5f97 Sat Sep 26 17:43:37 2026 -0700
    docent regression scripts for the v503 tickets, refs #38252, #37972, #37987, #37990, #38027, #38033, #38035, #38039, #38071, #38072, #38082, #38087, #38120, #38154, #38155, #38231 One script per ticket. Each one passes on genome-test. Twelve also fail on a v502_branch build for the reason the script exists, and carry a release-ab proof line. rm38072, rm38120 and rm38231 can never fail on a released build, and their headers say why.
• src/hg/utils/docent/tests/regress/rm38011.docent.yaml
  • lines changed 68, context: html, text, full: html, text
    9cc5eeb88ad0d6bea3449fcc1de1fbe54d79dafd Sat Sep 26 17:47:52 2026 -0700
    docent regression scripts for hgLogin and a batch of page fields, refs #38252, #38011, #38057
• src/hg/utils/docent/tests/regress/rm38027.docent.yaml
  • lines changed 32, context: html, text, full: html, text
    2daf01cbbc39c63db64caccf4a87f20a7f2f5f97 Sat Sep 26 17:43:37 2026 -0700
    docent regression scripts for the v503 tickets, refs #38252, #37972, #37987, #37990, #38027, #38033, #38035, #38039, #38071, #38072, #38082, #38087, #38120, #38154, #38155, #38231 One script per ticket. Each one passes on genome-test. Twelve also fail on a v502_branch build for the reason the script exists, and carry a release-ab proof line. rm38072, rm38120 and rm38231 can never fail on a released build, and their headers say why.
• src/hg/utils/docent/tests/regress/rm38033.docent.yaml
  • lines changed 53, context: html, text, full: html, text
    2daf01cbbc39c63db64caccf4a87f20a7f2f5f97 Sat Sep 26 17:43:37 2026 -0700
    docent regression scripts for the v503 tickets, refs #38252, #37972, #37987, #37990, #38027, #38033, #38035, #38039, #38071, #38072, #38082, #38087, #38120, #38154, #38155, #38231 One script per ticket. Each one passes on genome-test. Twelve also fail on a v502_branch build for the reason the script exists, and carry a release-ab proof line. rm38072, rm38120 and rm38231 can never fail on a released build, and their headers say why.
• src/hg/utils/docent/tests/regress/rm38035.docent.yaml
  • lines changed 61, context: html, text, full: html, text
    2daf01cbbc39c63db64caccf4a87f20a7f2f5f97 Sat Sep 26 17:43:37 2026 -0700
    docent regression scripts for the v503 tickets, refs #38252, #37972, #37987, #37990, #38027, #38033, #38035, #38039, #38071, #38072, #38082, #38087, #38120, #38154, #38155, #38231 One script per ticket. Each one passes on genome-test. Twelve also fail on a v502_branch build for the reason the script exists, and carry a release-ab proof line. rm38072, rm38120 and rm38231 can never fail on a released build, and their headers say why.
• src/hg/utils/docent/tests/regress/rm38039.docent.yaml
  • lines changed 38, context: html, text, full: html, text
    2daf01cbbc39c63db64caccf4a87f20a7f2f5f97 Sat Sep 26 17:43:37 2026 -0700
    docent regression scripts for the v503 tickets, refs #38252, #37972, #37987, #37990, #38027, #38033, #38035, #38039, #38071, #38072, #38082, #38087, #38120, #38154, #38155, #38231 One script per ticket. Each one passes on genome-test. Twelve also fail on a v502_branch build for the reason the script exists, and carry a release-ab proof line. rm38072, rm38120 and rm38231 can never fail on a released build, and their headers say why.
• src/hg/utils/docent/tests/regress/rm38057.docent.yaml
  • lines changed 57, context: html, text, full: html, text
    9cc5eeb88ad0d6bea3449fcc1de1fbe54d79dafd Sat Sep 26 17:47:52 2026 -0700
    docent regression scripts for hgLogin and a batch of page fields, refs #38252, #38011, #38057
• src/hg/utils/docent/tests/regress/rm38071.docent.yaml
  • lines changed 51, context: html, text, full: html, text
    2daf01cbbc39c63db64caccf4a87f20a7f2f5f97 Sat Sep 26 17:43:37 2026 -0700
    docent regression scripts for the v503 tickets, refs #38252, #37972, #37987, #37990, #38027, #38033, #38035, #38039, #38071, #38072, #38082, #38087, #38120, #38154, #38155, #38231 One script per ticket. Each one passes on genome-test. Twelve also fail on a v502_branch build for the reason the script exists, and carry a release-ab proof line. rm38072, rm38120 and rm38231 can never fail on a released build, and their headers say why.
• src/hg/utils/docent/tests/regress/rm38072.docent.yaml
  • lines changed 34, context: html, text, full: html, text
    2daf01cbbc39c63db64caccf4a87f20a7f2f5f97 Sat Sep 26 17:43:37 2026 -0700
    docent regression scripts for the v503 tickets, refs #38252, #37972, #37987, #37990, #38027, #38033, #38035, #38039, #38071, #38072, #38082, #38087, #38120, #38154, #38155, #38231 One script per ticket. Each one passes on genome-test. Twelve also fail on a v502_branch build for the reason the script exists, and carry a release-ab proof line. rm38072, rm38120 and rm38231 can never fail on a released build, and their headers say why.
• src/hg/utils/docent/tests/regress/rm38082.docent.yaml
  • lines changed 51, context: html, text, full: html, text
    2daf01cbbc39c63db64caccf4a87f20a7f2f5f97 Sat Sep 26 17:43:37 2026 -0700
    docent regression scripts for the v503 tickets, refs #38252, #37972, #37987, #37990, #38027, #38033, #38035, #38039, #38071, #38072, #38082, #38087, #38120, #38154, #38155, #38231 One script per ticket. Each one passes on genome-test. Twelve also fail on a v502_branch build for the reason the script exists, and carry a release-ab proof line. rm38072, rm38120 and rm38231 can never fail on a released build, and their headers say why.
• src/hg/utils/docent/tests/regress/rm38087.docent.yaml
  • lines changed 88, context: html, text, full: html, text
    2daf01cbbc39c63db64caccf4a87f20a7f2f5f97 Sat Sep 26 17:43:37 2026 -0700
    docent regression scripts for the v503 tickets, refs #38252, #37972, #37987, #37990, #38027, #38033, #38035, #38039, #38071, #38072, #38082, #38087, #38120, #38154, #38155, #38231 One script per ticket. Each one passes on genome-test. Twelve also fail on a v502_branch build for the reason the script exists, and carry a release-ab proof line. rm38072, rm38120 and rm38231 can never fail on a released build, and their headers say why.
• src/hg/utils/docent/tests/regress/rm38120.docent.yaml
  • lines changed 53, context: html, text, full: html, text
    2daf01cbbc39c63db64caccf4a87f20a7f2f5f97 Sat Sep 26 17:43:37 2026 -0700
    docent regression scripts for the v503 tickets, refs #38252, #37972, #37987, #37990, #38027, #38033, #38035, #38039, #38071, #38072, #38082, #38087, #38120, #38154, #38155, #38231 One script per ticket. Each one passes on genome-test. Twelve also fail on a v502_branch build for the reason the script exists, and carry a release-ab proof line. rm38072, rm38120 and rm38231 can never fail on a released build, and their headers say why.
• src/hg/utils/docent/tests/regress/rm38154.docent.yaml
  • lines changed 53, context: html, text, full: html, text
    2daf01cbbc39c63db64caccf4a87f20a7f2f5f97 Sat Sep 26 17:43:37 2026 -0700
    docent regression scripts for the v503 tickets, refs #38252, #37972, #37987, #37990, #38027, #38033, #38035, #38039, #38071, #38072, #38082, #38087, #38120, #38154, #38155, #38231 One script per ticket. Each one passes on genome-test. Twelve also fail on a v502_branch build for the reason the script exists, and carry a release-ab proof line. rm38072, rm38120 and rm38231 can never fail on a released build, and their headers say why.
• src/hg/utils/docent/tests/regress/rm38155.docent.yaml
  • lines changed 68, context: html, text, full: html, text
    2daf01cbbc39c63db64caccf4a87f20a7f2f5f97 Sat Sep 26 17:43:37 2026 -0700
    docent regression scripts for the v503 tickets, refs #38252, #37972, #37987, #37990, #38027, #38033, #38035, #38039, #38071, #38072, #38082, #38087, #38120, #38154, #38155, #38231 One script per ticket. Each one passes on genome-test. Twelve also fail on a v502_branch build for the reason the script exists, and carry a release-ab proof line. rm38072, rm38120 and rm38231 can never fail on a released build, and their headers say why.
• src/hg/utils/docent/tests/regress/rm38157.docent.yaml
  • lines changed 69, context: html, text, full: html, text
    58fa228f2f91ae8c6a5c62109e904f57e1f9a66d Wed Sep 30 11:03:02 2026 -0700
    docent regression scripts for nineteen v504 tickets, and their registry rows Each script watches one v504 fix. Fourteen fail on v503 (ts park 38316) and pass on genome-test (release-ab). rm38313 and rm38393 are sandbox-ab, because no release predates their fix. rm37984, rm38233 and rm38384 are assertion-only; each header says why. The registry now names the script in the docent column for these tickets, and has new rows for #38157 and #38393. #38275 stays unwatched in the table: the script that watches it is rm37389, which is named for another ticket. refs #20824, #27988, #36292, #37595, #37621, #37929, #37984, #38157, #38192, #38197, #38233, #38254, #38264, #38273, #38313, #38323, #38372, #38384, #38393, #38252, #38391 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
• src/hg/utils/docent/tests/regress/rm38192.docent.yaml
  • lines changed 96, context: html, text, full: html, text
    58fa228f2f91ae8c6a5c62109e904f57e1f9a66d Wed Sep 30 11:03:02 2026 -0700
    docent regression scripts for nineteen v504 tickets, and their registry rows Each script watches one v504 fix. Fourteen fail on v503 (ts park 38316) and pass on genome-test (release-ab). rm38313 and rm38393 are sandbox-ab, because no release predates their fix. rm37984, rm38233 and rm38384 are assertion-only; each header says why. The registry now names the script in the docent column for these tickets, and has new rows for #38157 and #38393. #38275 stays unwatched in the table: the script that watches it is rm37389, which is named for another ticket. refs #20824, #27988, #36292, #37595, #37621, #37929, #37984, #38157, #38192, #38197, #38233, #38254, #38264, #38273, #38313, #38323, #38372, #38384, #38393, #38252, #38391 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
• src/hg/utils/docent/tests/regress/rm38197.docent.yaml
  • lines changed 94, context: html, text, full: html, text
    58fa228f2f91ae8c6a5c62109e904f57e1f9a66d Wed Sep 30 11:03:02 2026 -0700
    docent regression scripts for nineteen v504 tickets, and their registry rows Each script watches one v504 fix. Fourteen fail on v503 (ts park 38316) and pass on genome-test (release-ab). rm38313 and rm38393 are sandbox-ab, because no release predates their fix. rm37984, rm38233 and rm38384 are assertion-only; each header says why. The registry now names the script in the docent column for these tickets, and has new rows for #38157 and #38393. #38275 stays unwatched in the table: the script that watches it is rm37389, which is named for another ticket. refs #20824, #27988, #36292, #37595, #37621, #37929, #37984, #38157, #38192, #38197, #38233, #38254, #38264, #38273, #38313, #38323, #38372, #38384, #38393, #38252, #38391 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
• src/hg/utils/docent/tests/regress/rm38198.docent.yaml
  • lines changed 56, context: html, text, full: html, text
    b1d1b8806245f651bfa6c41230c77797c324d16d Mon Sep 28 09:50:59 2026 -0700
    docent rm38198: cover the reopen, a container set back to show stayed hidden on the target, refs #38198 Adds Jairo's three-lift recipe to the existing script: show wgEncodeReg4 with H3K27ac, lift; hide the container, lift; show it again, lift. It checks that H3K27ac is on the target after lift 3, that the source container is still hidden after the lift 2 target visit, and that H3K27ac stays on the target after lift 2. Each check fails on its own on a build without dba11b63364.
  • lines changed 1, context: html, text, full: html, text
    27e27b2c53090276a82fa8a4a8ae89f8db288263 Tue Sep 29 14:13:18 2026 -0700
    docent rm38198 release-ab proof line, and registry rows for #38428 and #38430, refs #38198, #38428, #38430, #38252 rm38198's container reopen section fails on hgwbeta (v504, which lacks dba11b63364) and passes on genome-test. htmlSanitizeTest goes red when the svg allowlist of 7a356d85dba is backed out by hand, so #38428 gets a sandbox-ab row. #38430 gets a page row with no test yet. Both changes sit behind the hubHtmlSanitize gate.
• src/hg/utils/docent/tests/regress/rm38226.docent.yaml
  • lines changed 62, context: html, text, full: html, text
    521a3f76eebab0854aa5c46374356cadddd6ef7d Sat Sep 26 12:12:14 2026 -0700
    docent regression scripts for the hgTracks tooltip text and the Hub Upload file card, refs #38252, #38226, #38398 Both fail on hgwbeta (v504) and pass on genome-test; the proof lines say what each failure was.
• src/hg/utils/docent/tests/regress/rm38231.docent.yaml
  • lines changed 41, context: html, text, full: html, text
    2daf01cbbc39c63db64caccf4a87f20a7f2f5f97 Sat Sep 26 17:43:37 2026 -0700
    docent regression scripts for the v503 tickets, refs #38252, #37972, #37987, #37990, #38027, #38033, #38035, #38039, #38071, #38072, #38082, #38087, #38120, #38154, #38155, #38231 One script per ticket. Each one passes on genome-test. Twelve also fail on a v502_branch build for the reason the script exists, and carry a release-ab proof line. rm38072, rm38120 and rm38231 can never fail on a released build, and their headers say why.
• src/hg/utils/docent/tests/regress/rm38233.docent.yaml
  • lines changed 82, context: html, text, full: html, text
    58fa228f2f91ae8c6a5c62109e904f57e1f9a66d Wed Sep 30 11:03:02 2026 -0700
    docent regression scripts for nineteen v504 tickets, and their registry rows Each script watches one v504 fix. Fourteen fail on v503 (ts park 38316) and pass on genome-test (release-ab). rm38313 and rm38393 are sandbox-ab, because no release predates their fix. rm37984, rm38233 and rm38384 are assertion-only; each header says why. The registry now names the script in the docent column for these tickets, and has new rows for #38157 and #38393. #38275 stays unwatched in the table: the script that watches it is rm37389, which is named for another ticket. refs #20824, #27988, #36292, #37595, #37621, #37929, #37984, #38157, #38192, #38197, #38233, #38254, #38264, #38273, #38313, #38323, #38372, #38384, #38393, #38252, #38391 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
• src/hg/utils/docent/tests/regress/rm38254.docent.yaml
  • lines changed 63, context: html, text, full: html, text
    58fa228f2f91ae8c6a5c62109e904f57e1f9a66d Wed Sep 30 11:03:02 2026 -0700
    docent regression scripts for nineteen v504 tickets, and their registry rows Each script watches one v504 fix. Fourteen fail on v503 (ts park 38316) and pass on genome-test (release-ab). rm38313 and rm38393 are sandbox-ab, because no release predates their fix. rm37984, rm38233 and rm38384 are assertion-only; each header says why. The registry now names the script in the docent column for these tickets, and has new rows for #38157 and #38393. #38275 stays unwatched in the table: the script that watches it is rm37389, which is named for another ticket. refs #20824, #27988, #36292, #37595, #37621, #37929, #37984, #38157, #38192, #38197, #38233, #38254, #38264, #38273, #38313, #38323, #38372, #38384, #38393, #38252, #38391 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
• src/hg/utils/docent/tests/regress/rm38257.docent.yaml
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    6f3f3596f3dc61a8a738717b9701e69a86b5bb0b Mon Sep 21 17:24:33 2026 -0700
    docent: wait: {gone:} for a selector to leave, and rm38257 stops racing itself rm38257 went red in the 2026-09-21 nightly with the #38257 fix still live on genome-test. The script was waiting on the wrong half of the click. hgHubConnect.js switches the tab synchronously inside the click dispatch, while topLinks.js closes the Account popup from a setTimeout(..., 0). So the tab is the half that settles FIRST, and waiting for it returned a tick early: the expect after it read a page that still had the popup on it. Measured with a MutationObserver over the click, the tab goes active at t=43ms and the popup goes on the next task. wait: now also takes {gone: <selector>}, which waits for a selector to leave the DOM, so a script can wait on the vanishing half of an answer. rm38257 uses it. Six runs each way on genome-test, same build, only the script differing: 6 of 6 green with the new wait:, 3 of 6 red with the old one, failing at the same step with the same message the nightly printed. The whole directory is green, 98 of 98. refs #37892, refs #38252
• src/hg/utils/docent/tests/regress/rm38264.docent.yaml
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    58fa228f2f91ae8c6a5c62109e904f57e1f9a66d Wed Sep 30 11:03:02 2026 -0700
    docent regression scripts for nineteen v504 tickets, and their registry rows Each script watches one v504 fix. Fourteen fail on v503 (ts park 38316) and pass on genome-test (release-ab). rm38313 and rm38393 are sandbox-ab, because no release predates their fix. rm37984, rm38233 and rm38384 are assertion-only; each header says why. The registry now names the script in the docent column for these tickets, and has new rows for #38157 and #38393. #38275 stays unwatched in the table: the script that watches it is rm37389, which is named for another ticket. refs #20824, #27988, #36292, #37595, #37621, #37929, #37984, #38157, #38192, #38197, #38233, #38254, #38264, #38273, #38313, #38323, #38372, #38384, #38393, #38252, #38391 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
• src/hg/utils/docent/tests/regress/rm38272.docent.yaml
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    4bf8479a43a493e2899953b7358c9464abbc3959 Wed Sep 23 17:15:55 2026 -0700
    docent: regression scripts load sessions from text files, not from one machine's hgcentral, refs #38252 A named session runs only on the machine whose hgcentral holds it, so hgwbeta and the RR answered "Could not find session". The sessions are now text files in regress/sessionFiles, saved with hgSession's own save to file, and the scripts load them by raw GitHub URL. rm36805, rm35580 and rm36340 pass on genome-test and hgwbeta. rm36340's session held its custom tracks as a customTrash table on genome-test. The track source is a file of its own now, loaded through hgt.customText, without two commented-out tracks whose URLs carry a password. Its first check now asks for a custom track row and the hub's row, and fails when the session file does not load. A lifted session cannot be a file: it names its quickLift hub by a path on the server that made it, and re-pointing it does not work (#38046). rm37388, rm37389 and rm38272 build that lift in steps instead, the GenArk GCA_018466835.2 mitochondrion lifted to hg38, and pass on genome-test and hgwbeta. rm38272 also fails on genome.ucsc.edu (v503) at its settings page, with the bug's own error, so it gains a release-ab proof line.
• src/hg/utils/docent/tests/regress/rm38273.docent.yaml
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    58fa228f2f91ae8c6a5c62109e904f57e1f9a66d Wed Sep 30 11:03:02 2026 -0700
    docent regression scripts for nineteen v504 tickets, and their registry rows Each script watches one v504 fix. Fourteen fail on v503 (ts park 38316) and pass on genome-test (release-ab). rm38313 and rm38393 are sandbox-ab, because no release predates their fix. rm37984, rm38233 and rm38384 are assertion-only; each header says why. The registry now names the script in the docent column for these tickets, and has new rows for #38157 and #38393. #38275 stays unwatched in the table: the script that watches it is rm37389, which is named for another ticket. refs #20824, #27988, #36292, #37595, #37621, #37929, #37984, #38157, #38192, #38197, #38233, #38254, #38264, #38273, #38313, #38323, #38372, #38384, #38393, #38252, #38391 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
• src/hg/utils/docent/tests/regress/rm38279.docent.yaml
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    0d147408e678df6e37e2a7e0a24934b80d0826e4 Wed Sep 30 06:51:55 2026 -0700
    docent rm38279: follow the window-size density note to its new wording, "window too large, zoom in", from 32eec44ad31. The nightly went red at step 2 on the old string. Steps 1 and 2 now check the new string, and the header no longer describes the prefix overlap that the reword removed. refs #38279, #38252
• src/hg/utils/docent/tests/regress/rm38283.docent.yaml
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    bcfcb704e8296f881896ee6197365ae719ea61d6 Wed Sep 23 11:06:11 2026 -0700
    docent: rm38283 finds the container link by its text and a delimiter, refs #38252 #38283 Since 09f26ed9a7d (#38380) the page adds &hgsid= to every cgi-bin link, so the description page's link no longer ends with the track name and the $= check failed. A plain *= would pass without the substitution, because hgc prints its own hgTrackUi and hgTables links that name the composite. So the check now requires the fixture's link text, and "&" or the end of the href after the name. The delimiter matters because _rm38283Super is a prefix of _rm38283SuperKid. Passes on genome-test. Fails at step 5 on the v503 docker image, and fails when either check is pointed at a wrong name or a prefix of the right one.
• src/hg/utils/docent/tests/regress/rm38298.docent.yaml
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    347d7590b576fa145bfd0d73cee612536158ed60 Wed Sep 23 11:06:11 2026 -0700
    docent: rm38298 expects the reworded codon note, refs #38252 #38298 d459a7a421c changed the note from "at this codon" to "before this codon", because the indel lies upstream of the shifted codon. The check now carries the whole new clause, and the header makes the same correction. Passes on genome-test. Fails at step 4 on hgwbeta (v503), which has no note.
• src/hg/utils/docent/tests/regress/rm38311.docent.yaml
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    1fbda5badde574c10884e5339fdda1f5b7495990 Thu Sep 24 13:45:30 2026 -0700
    docent: regression script for the Sessions page Replace keeping who can load it, refs #38311 rm38311 saves a private session from the save card, saves over it with the private box unticked, and checks that the row still has its lock. It passes on hgwbeta (v504) and genome-test, and fails on hgw0 (v503). Docent changes it needed: - a fill: verb, to type into any form field - login: no longer dies when a navigation is still under way during its bad-password check, which is what broke it on ticket parks - a park is driven on its https port, because hgLogin posts its form to https:// on the port it was reached on; the parks' self-signed certificate is accepted on loopback targets only - hgw0 maps to hgcentral, and a park's https port finds its hg.conf
• src/hg/utils/docent/tests/regress/rm38313.docent.yaml
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    58fa228f2f91ae8c6a5c62109e904f57e1f9a66d Wed Sep 30 11:03:02 2026 -0700
    docent regression scripts for nineteen v504 tickets, and their registry rows Each script watches one v504 fix. Fourteen fail on v503 (ts park 38316) and pass on genome-test (release-ab). rm38313 and rm38393 are sandbox-ab, because no release predates their fix. rm37984, rm38233 and rm38384 are assertion-only; each header says why. The registry now names the script in the docent column for these tickets, and has new rows for #38157 and #38393. #38275 stays unwatched in the table: the script that watches it is rm37389, which is named for another ticket. refs #20824, #27988, #36292, #37595, #37621, #37929, #37984, #38157, #38192, #38197, #38233, #38254, #38264, #38273, #38313, #38323, #38372, #38384, #38393, #38252, #38391 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
• src/hg/utils/docent/tests/regress/rm38323.docent.yaml
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    58fa228f2f91ae8c6a5c62109e904f57e1f9a66d Wed Sep 30 11:03:02 2026 -0700
    docent regression scripts for nineteen v504 tickets, and their registry rows Each script watches one v504 fix. Fourteen fail on v503 (ts park 38316) and pass on genome-test (release-ab). rm38313 and rm38393 are sandbox-ab, because no release predates their fix. rm37984, rm38233 and rm38384 are assertion-only; each header says why. The registry now names the script in the docent column for these tickets, and has new rows for #38157 and #38393. #38275 stays unwatched in the table: the script that watches it is rm37389, which is named for another ticket. refs #20824, #27988, #36292, #37595, #37621, #37929, #37984, #38157, #38192, #38197, #38233, #38254, #38264, #38273, #38313, #38323, #38372, #38384, #38393, #38252, #38391 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
• src/hg/utils/docent/tests/regress/rm38372.docent.yaml
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    58fa228f2f91ae8c6a5c62109e904f57e1f9a66d Wed Sep 30 11:03:02 2026 -0700
    docent regression scripts for nineteen v504 tickets, and their registry rows Each script watches one v504 fix. Fourteen fail on v503 (ts park 38316) and pass on genome-test (release-ab). rm38313 and rm38393 are sandbox-ab, because no release predates their fix. rm37984, rm38233 and rm38384 are assertion-only; each header says why. The registry now names the script in the docent column for these tickets, and has new rows for #38157 and #38393. #38275 stays unwatched in the table: the script that watches it is rm37389, which is named for another ticket. refs #20824, #27988, #36292, #37595, #37621, #37929, #37984, #38157, #38192, #38197, #38233, #38254, #38264, #38273, #38313, #38323, #38372, #38384, #38393, #38252, #38391 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
• src/hg/utils/docent/tests/regress/rm38384.docent.yaml
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    58fa228f2f91ae8c6a5c62109e904f57e1f9a66d Wed Sep 30 11:03:02 2026 -0700
    docent regression scripts for nineteen v504 tickets, and their registry rows Each script watches one v504 fix. Fourteen fail on v503 (ts park 38316) and pass on genome-test (release-ab). rm38313 and rm38393 are sandbox-ab, because no release predates their fix. rm37984, rm38233 and rm38384 are assertion-only; each header says why. The registry now names the script in the docent column for these tickets, and has new rows for #38157 and #38393. #38275 stays unwatched in the table: the script that watches it is rm37389, which is named for another ticket. refs #20824, #27988, #36292, #37595, #37621, #37929, #37984, #38157, #38192, #38197, #38233, #38254, #38264, #38273, #38313, #38323, #38372, #38384, #38393, #38252, #38391 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
• src/hg/utils/docent/tests/regress/rm38393.docent.yaml
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    58fa228f2f91ae8c6a5c62109e904f57e1f9a66d Wed Sep 30 11:03:02 2026 -0700
    docent regression scripts for nineteen v504 tickets, and their registry rows Each script watches one v504 fix. Fourteen fail on v503 (ts park 38316) and pass on genome-test (release-ab). rm38313 and rm38393 are sandbox-ab, because no release predates their fix. rm37984, rm38233 and rm38384 are assertion-only; each header says why. The registry now names the script in the docent column for these tickets, and has new rows for #38157 and #38393. #38275 stays unwatched in the table: the script that watches it is rm37389, which is named for another ticket. refs #20824, #27988, #36292, #37595, #37621, #37929, #37984, #38157, #38192, #38197, #38233, #38254, #38264, #38273, #38313, #38323, #38372, #38384, #38393, #38252, #38391 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
• src/hg/utils/docent/tests/regress/rm38398.docent.yaml
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    521a3f76eebab0854aa5c46374356cadddd6ef7d Sat Sep 26 12:12:14 2026 -0700
    docent regression scripts for the hgTracks tooltip text and the Hub Upload file card, refs #38252, #38226, #38398 Both fail on hgwbeta (v504) and pass on genome-test; the proof lines say what each failure was.
• src/hg/utils/docent/tests/regress/rm38428.docent.yaml
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    49e53454d32ce13f5af4ece42112423534102fdd Tue Sep 29 14:30:20 2026 -0700
    docent regression scripts for #38428 and #38430, and the #38387 registry note, refs #38428, #38430, #38387, #38252 rm38428 checks that a hub track's svg color legend survives the description filter and the script inside it does not. rm38430 checks that hgGateway filters a hub assembly's description page. Both need hubHtmlSanitize=on, and both fail on a v504_branch build with the gate on and pass on genome-test. Fixtures in docentFixtures/rm38428 and rm38430. The #38387 registry note records the docker QA instances: kent-tip, built after the fix, runs ft_min_word_len=3 and finds hs1; kent-beta, built before it, runs 4 and does not.
• src/hg/utils/docent/tests/regress/rm38430.docent.yaml
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    49e53454d32ce13f5af4ece42112423534102fdd Tue Sep 29 14:30:20 2026 -0700
    docent regression scripts for #38428 and #38430, and the #38387 registry note, refs #38428, #38430, #38387, #38252 rm38428 checks that a hub track's svg color legend survives the description filter and the script inside it does not. rm38430 checks that hgGateway filters a hub assembly's description page. Both need hubHtmlSanitize=on, and both fail on a v504_branch build with the gate on and pass on genome-test. Fixtures in docentFixtures/rm38428 and rm38430. The #38387 registry note records the docker QA instances: kent-tip, built after the fix, runs ft_min_word_len=3 and finds hs1; kent-beta, built before it, runs 4 and does not.
• src/hg/utils/docent/tests/regress/rm38442.docent.yaml
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    f3bec731c93f26f8f1984fd727c6ee55ebf99f85 Tue Sep 29 13:00:12 2026 -0700
    docent regression scripts for three v505 tickets, and registry updates, refs #37617, #37618, #38442, #38249, #38252 rm37617 checks that filter.AF on a VCF INFO field hides the variants below the trackDb minimum, and rm37618 that colorByInfo colors each item by its INFO value. Both use a four-variant fixture hub, docentFixtures/rm37617. rm38442 runs the ticket's PCR search, sets the places a drag saves, and checks that the PCR track keeps its place after a zoom. All three fail on hgwbeta (v504) and pass on genome-test. registry.tsv names the three scripts, adds a row for #38387, and raises the #38249 quickLiftTester row to sandbox-ab: backing out either quickLift fix by hand turns the test red.
• src/hg/utils/docent/tests/regress/rm38444.docent.yaml
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    bd1a1caa044f8b0e65d4f558831c83c1b8807d2e Sat Oct 3 17:02:05 2026 -0700
    docent rm38444: a db name with its own dbDb row stays that assembly instead of its asmAlias accession, and its registry row, refs #38444, #38252
• src/hg/utils/docent/tests/regress/rm38456.docent.yaml
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    f8a1b70516b4cb68471cf5fda1f25fe5a06e034e Thu Oct 1 07:04:33 2026 -0700
    docent rm38456: the fix reached genome-test, so the script is no longer an xfail, refs #38456 It failed on genome-test at check 1 before 35c5facfb9e arrived and passed there after the same day's make alpha. Renamed from rm38456.xfail.docent.yaml, with a server-flip proof line, and the registry row now names the new file.
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    c8f3ef912f63007961da179e06f2d6d96ea4cf34 Thu Oct 1 08:31:35 2026 -0700
    docent rm38456: name the share checkbox's shadow variable in full, refs #38456
• src/hg/utils/docent/tests/regress/rm38456.xfail.docent.yaml
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    ebf73550fcb8e858388755a7d34541d510209bae Wed Sep 30 17:12:00 2026 -0700
    docent rm38456: a Save request without the share flag or the name, and its registry row, refs #38456 Three checks: a fresh cart with no share flag, a cart that still holds a stored share value while the request has none, and a request with no name. Committed as an xfail until the fix reaches genome-test. Each check was seen to fail on a build without its part of the fix.
• src/hg/utils/docent/tests/regress/rm38462.docent.yaml
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    fb5921dc918983ecc5182b1ef23a9fc64b556114 Fri Oct 2 10:00:42 2026 -0700
    docent rm38462 out of xfail after genome-test built the fix, refs #38462, #38252
• src/hg/utils/docent/tests/regress/rm38462.xfail.docent.yaml
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    fcc4da57b6aa6aabe40dce88cb8b67e4a5508aff Fri Oct 2 09:35:00 2026 -0700
    docent rm38462 xfail script for negateValues whiskers, and its registry row, refs #38462, #38252
• src/hg/utils/docent/tests/regress/sessionFiles/README.txt
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    4bf8479a43a493e2899953b7358c9464abbc3959 Wed Sep 23 17:15:55 2026 -0700
    docent: regression scripts load sessions from text files, not from one machine's hgcentral, refs #38252 A named session runs only on the machine whose hgcentral holds it, so hgwbeta and the RR answered "Could not find session". The sessions are now text files in regress/sessionFiles, saved with hgSession's own save to file, and the scripts load them by raw GitHub URL. rm36805, rm35580 and rm36340 pass on genome-test and hgwbeta. rm36340's session held its custom tracks as a customTrash table on genome-test. The track source is a file of its own now, loaded through hgt.customText, without two commented-out tracks whose URLs carry a password. Its first check now asks for a custom track row and the hub's row, and fails when the session file does not load. A lifted session cannot be a file: it names its quickLift hub by a path on the server that made it, and re-pointing it does not work (#38046). rm37388, rm37389 and rm38272 build that lift in steps instead, the GenArk GCA_018466835.2 mitochondrion lifted to hg38, and pass on genome-test and hgwbeta. rm38272 also fails on genome.ucsc.edu (v503) at its settings page, with the bug's own error, so it gains a release-ab proof line.
• src/hg/utils/docent/tests/regress/sessionFiles/RM_35326_bug.txt
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    4bf8479a43a493e2899953b7358c9464abbc3959 Wed Sep 23 17:15:55 2026 -0700
    docent: regression scripts load sessions from text files, not from one machine's hgcentral, refs #38252 A named session runs only on the machine whose hgcentral holds it, so hgwbeta and the RR answered "Could not find session". The sessions are now text files in regress/sessionFiles, saved with hgSession's own save to file, and the scripts load them by raw GitHub URL. rm36805, rm35580 and rm36340 pass on genome-test and hgwbeta. rm36340's session held its custom tracks as a customTrash table on genome-test. The track source is a file of its own now, loaded through hgt.customText, without two commented-out tracks whose URLs carry a password. Its first check now asks for a custom track row and the hub's row, and fails when the session file does not load. A lifted session cannot be a file: it names its quickLift hub by a path on the server that made it, and re-pointing it does not work (#38046). rm37388, rm37389 and rm38272 build that lift in steps instead, the GenArk GCA_018466835.2 mitochondrion lifted to hg38, and pass on genome-test and hgwbeta. rm38272 also fails on genome.ucsc.edu (v503) at its settings page, with the bug's own error, so it gains a release-ab proof line.
• src/hg/utils/docent/tests/regress/sessionFiles/RM_36805_TOGA_hangs.txt
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    4bf8479a43a493e2899953b7358c9464abbc3959 Wed Sep 23 17:15:55 2026 -0700
    docent: regression scripts load sessions from text files, not from one machine's hgcentral, refs #38252 A named session runs only on the machine whose hgcentral holds it, so hgwbeta and the RR answered "Could not find session". The sessions are now text files in regress/sessionFiles, saved with hgSession's own save to file, and the scripts load them by raw GitHub URL. rm36805, rm35580 and rm36340 pass on genome-test and hgwbeta. rm36340's session held its custom tracks as a customTrash table on genome-test. The track source is a file of its own now, loaded through hgt.customText, without two commented-out tracks whose URLs carry a password. Its first check now asks for a custom track row and the hub's row, and fails when the session file does not load. A lifted session cannot be a file: it names its quickLift hub by a path on the server that made it, and re-pointing it does not work (#38046). rm37388, rm37389 and rm38272 build that lift in steps instead, the GenArk GCA_018466835.2 mitochondrion lifted to hg38, and pass on genome-test and hgwbeta. rm38272 also fails on genome.ucsc.edu (v503) at its settings page, with the bug's own error, so it gains a release-ab proof line.
• src/hg/utils/docent/tests/regress/sessionFiles/quickLift_CT_hub.ct.txt
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    4bf8479a43a493e2899953b7358c9464abbc3959 Wed Sep 23 17:15:55 2026 -0700
    docent: regression scripts load sessions from text files, not from one machine's hgcentral, refs #38252 A named session runs only on the machine whose hgcentral holds it, so hgwbeta and the RR answered "Could not find session". The sessions are now text files in regress/sessionFiles, saved with hgSession's own save to file, and the scripts load them by raw GitHub URL. rm36805, rm35580 and rm36340 pass on genome-test and hgwbeta. rm36340's session held its custom tracks as a customTrash table on genome-test. The track source is a file of its own now, loaded through hgt.customText, without two commented-out tracks whose URLs carry a password. Its first check now asks for a custom track row and the hub's row, and fails when the session file does not load. A lifted session cannot be a file: it names its quickLift hub by a path on the server that made it, and re-pointing it does not work (#38046). rm37388, rm37389 and rm38272 build that lift in steps instead, the GenArk GCA_018466835.2 mitochondrion lifted to hg38, and pass on genome-test and hgwbeta. rm38272 also fails on genome.ucsc.edu (v503) at its settings page, with the bug's own error, so it gains a release-ab proof line.
• src/hg/utils/docent/tests/regress/sessionFiles/quickLift_CT_hub.txt
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    4bf8479a43a493e2899953b7358c9464abbc3959 Wed Sep 23 17:15:55 2026 -0700
    docent: regression scripts load sessions from text files, not from one machine's hgcentral, refs #38252 A named session runs only on the machine whose hgcentral holds it, so hgwbeta and the RR answered "Could not find session". The sessions are now text files in regress/sessionFiles, saved with hgSession's own save to file, and the scripts load them by raw GitHub URL. rm36805, rm35580 and rm36340 pass on genome-test and hgwbeta. rm36340's session held its custom tracks as a customTrash table on genome-test. The track source is a file of its own now, loaded through hgt.customText, without two commented-out tracks whose URLs carry a password. Its first check now asks for a custom track row and the hub's row, and fails when the session file does not load. A lifted session cannot be a file: it names its quickLift hub by a path on the server that made it, and re-pointing it does not work (#38046). rm37388, rm37389 and rm38272 build that lift in steps instead, the GenArk GCA_018466835.2 mitochondrion lifted to hg38, and pass on genome-test and hgwbeta. rm38272 also fails on genome.ucsc.edu (v503) at its settings page, with the bug's own error, so it gains a release-ab proof line.
• src/hg/utils/hgConfCatalog/hgConfAges.json
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    eb4042bf96a8a37ea613e7c0860c6a49d210bc24 Wed Sep 23 09:38:32 2026 -0700
    hgConfCatalog: rebuild the age cache at v504, refs #37925 Built at v503, so gates added since had no date. Rebuilt with harvestHgConf.py --age --refresh after v504_branch was cut.
• src/hg/utils/hgConfCatalog/hgConfCatalog.py
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    4cc508894c798f9c27a347b7801b0215e15cfba7 Tue Sep 22 02:31:08 2026 -0700
    hgConfCatalog: register hgGateway.showRefBadge, refs #37925 Written by nightlyRegister.sh, which records the settings the tree reads that the catalog was missing. Only facts copied off the call site are filled in. No classification is guessed: a new boolean gets no role=, because calling a release gate a knob would hide it from the sunset report for good, and every row lands in the 'Awaiting review' section until somebody reads the call site. hgGateway.showRefBadge hg/hgGateway/hgGateway.c:1102 (38401) wrote 1 row to the 'Awaiting review' section of hgConfCatalog.py; classify it and move it out
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    aeb4691c5f621712c9918e5a6e6a58c8b2de837d Wed Sep 23 09:32:26 2026 -0700
    hgConfCatalog: hgGateway.showRefBadge and denseClick are release gates, refs #37925 Both came in through --auto-register. showRefBadge (#38401) gates the reference badge in the gateway search results; denseClick (#38364) gates per-item map boxes in a dense row, with a trackDb opt-in under it.
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    18125243f8a0d219285fe081ed3f1eb8cd558ff2 Sat Sep 26 17:59:16 2026 -0700
    hgTracks: GenBank as a fourth format in the "Download Current Track Data" dialog The file holds the DNA of the region in view plus the selected track items as a GenBank feature table, so a region opens in the sequence editors people already use: SnapGene, Benchling, ApE and the rest. Blocks become join() locations, thickStart..thickEnd a CDS for the types that really carry a gene model, and an item running off the edge of the view gets the partial markers. Written in javascript beside the existing JSON/CSV/TSV converters, because the dialog is entirely client side: it adds one getData/sequence call to the getData/track call it already makes. Behind showGenbankDownload in hg.conf, default off, registered as a release gate in hgConfCatalog.py. Wiggle-type tracks have no GenBank equivalent and are greyed out while the format is selected, and the region is capped at 100 Mbp because the web browser has to build the whole file in memory. The dialog itself is reworked at the same time, for every format: the output format comes first, then the file name, the track list and the check-all buttons; it uses the page's font size and normal-height buttons instead of jquery-ui's smaller ones; and the position sits on its own line with the strand the Reverse button is showing. hgTracks.c adds organism and scientificName to jsonForClient, which the GenBank header needs. refs #38433
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    0a83d5e5518e414b2745d4429f3770b70d8fc9ac Sat Sep 26 21:59:44 2026 -0700
    hgConfCatalog: update groupDropdown description to match current behavior refs #38434
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    d4e9b27ceb9fe5be2e6c121d7cc74adccf23a7f1 Sun Sep 27 02:30:51 2026 -0700
    hgConfCatalog: register hubHtmlSanitize, refs #37925 Written by nightlyRegister.sh, which records the settings the tree reads that the catalog was missing. Only facts copied off the call site are filled in. No classification is guessed: a new boolean gets no role=, because calling a release gate a knob would hide it from the sunset report for good, and every row lands in the 'Awaiting review' section until somebody reads the call site. hubHtmlSanitize hg/lib/trackHub.c:1013 (38126) wrote 1 row to the 'Awaiting review' section of hgConfCatalog.py; classify it and move it out
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    2bdcf31450f998eff8aaf558eabdae8aa949f3af Mon Sep 28 10:07:57 2026 -0700
    hgConfCatalog: classify hubHtmlSanitize as a release gate, refs #37925 #38126 The nightly auto-register had written the row but left it unclassified, so the reconcile flagged it. It ships off in v504 and is meant to flip on in v505, so it is a gate.
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    6743564c0d16d85e588d5a9d80097e4690b91666 Tue Sep 29 15:37:43 2026 -0700
    hgTracks: tell the user when a track download is incomplete or still being prepared, and put the GenBank size limit under hg.conf Four things in the "Download Current Track Data" dialog, all of them about a download that quietly does the wrong thing. The api stops at a limit on how many items it will return and says so with maxItemsLimit in the reply, which the dialog ignored. Worse, a truncated reply carries two extra top level fields, maxItemsLimit and dataDownloadUrl, and the CSV/TSV converter took every top level field it did not recognise for a track: the string one was iterated one character per row, and the conversion threw before writing anything. A truncated CSV or TSV download therefore produced no file and no message at all. A track's value is always the array of its rows, so that is now the test for what is a track, rather than a list of field names that the api will keep outgrowing. All formats now say plainly that the file is incomplete, and the GenBank file carries the same warning in its COMMENT block, where it outlives the dialog. Nothing showed that anything was happening between the click and the browser's download, which is one second for two tracks and four for twenty, on a 20 kb region. The Download button now goes disabled with a line beside it while the file is prepared. It is in the button pane rather than the dialog body because the body scrolls once the track list is long. The GenBank region limit drops from 100 Mbp to 25 Mbp. 50 Mbp of chr1 with 24 tracks answers with 340 MB of track json and 50 MB of sequence, which the web browser parses, copies into the file text and copies again into the Blob, so the tab needs several times the region in memory. The limit is now the hg.conf setting maxGenbankRegion, registered in hgConfCatalog.py as a knob: the ceiling belongs to the machine and its users. It is read only when showGenbankDownload is on, and a value that is not a positive number falls back to the default rather than aborting the CGI. refs #38433
• src/hg/utils/hgConfCatalog/nightlyRegister.sh
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    7cadd1e0531239dac79b60e741e8ba3221a32cac Wed Sep 23 09:48:31 2026 -0700
    hgConfCatalog: nightlyRegister.sh rebuilds the age cache once a release, refs #37925 Nothing refreshed the committed hgConfAges.json: the wrap-up rebuilds a private copy in the build's logs, so the committed one went stale at every release and new gates showed as 'age unknown'. When CGI_VERSION is newer than the cache, fetch all release branches, rebuild the cache once the new v*_branch exists, and commit it with the catalog.
• src/hg/utils/hubCheck/hubCheck.c
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    722e46a2cca739fb7abe042315e8ca3c5e55f8f5 Wed Sep 23 14:25:15 2026 -0700
    Run the hg/utils tests from make test, and fix the two that had gone red, no redmine make test never reached hg/utils. hg/makefile only descends into an app that has a tests/makefile, and hg/utils has none, so the hubCheck, vcfToHgvs and other hg/utils tests were skipped without a message. Added utils to TEST_DIRS. hubCheck stopped warning about a track with no description page after 1258d7f65e7. A track with no page now keeps the empty string that trackDbCustom.c sets, and hubCheck tested for NULL. It now uses isEmpty(). badType gained a real error when 571aecdf42c stopped dropping tracks, and its expected output was never updated. vcfToHgvs stopLoss reads the live hg38 ncbiRefSeq tables, which now have 32 more transcripts and NM_153819.2.
• src/hg/utils/hubCheck/tests/expected/badType.output.txt
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    722e46a2cca739fb7abe042315e8ca3c5e55f8f5 Wed Sep 23 14:25:15 2026 -0700
    Run the hg/utils tests from make test, and fix the two that had gone red, no redmine make test never reached hg/utils. hg/makefile only descends into an app that has a tests/makefile, and hg/utils has none, so the hubCheck, vcfToHgvs and other hg/utils tests were skipped without a message. Added utils to TEST_DIRS. hubCheck stopped warning about a track with no description page after 1258d7f65e7. A track with no page now keeps the empty string that trackDbCustom.c sets, and hubCheck tested for NULL. It now uses isEmpty(). badType gained a real error when 571aecdf42c stopped dropping tracks, and its expected output was never updated. vcfToHgvs stopLoss reads the live hg38 ncbiRefSeq tables, which now have 32 more transcripts and NM_153819.2.
• src/hg/utils/hubCheck/tests/expected/fieldCountTooFew.output.txt
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    05c7e605c01e595561c32690eb44a7512041e540 Wed Sep 23 09:34:08 2026 -0700
    hubCheck: reject a bigBed type line that declares fewer than three fields, refs #36940 hgc already stops on "type bigBed 1" or "type bigBed 2", but hubCheck passed both, so a hub author only found out when a user clicked an item. Check the declared count against the minimum of three next to the existing check against the file's field count. A bare "type bigBed" does not reach this code and is unchanged. Adds a fieldCountTooFew test with bigBed 1 and bigBed 2 tracks.
• src/hg/utils/hubCheck/tests/input/fieldCountTooFew.txt
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    05c7e605c01e595561c32690eb44a7512041e540 Wed Sep 23 09:34:08 2026 -0700
    hubCheck: reject a bigBed type line that declares fewer than three fields, refs #36940 hgc already stops on "type bigBed 1" or "type bigBed 2", but hubCheck passed both, so a hub author only found out when a user clicked an item. Check the declared count against the minimum of three next to the existing check against the file's field count. A bare "type bigBed" does not reach this code and is unchanged. Adds a fieldCountTooFew test with bigBed 1 and bigBed 2 tracks.
• src/hg/utils/hubCheck/tests/makefile
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    05c7e605c01e595561c32690eb44a7512041e540 Wed Sep 23 09:34:08 2026 -0700
    hubCheck: reject a bigBed type line that declares fewer than three fields, refs #36940 hgc already stops on "type bigBed 1" or "type bigBed 2", but hubCheck passed both, so a hub author only found out when a user clicked an item. Check the declared count against the minimum of three next to the existing check against the file's field count. A bare "type bigBed" does not reach this code and is unchanged. Adds a fieldCountTooFew test with bigBed 1 and bigBed 2 tracks.
• src/hg/utils/otto/genArk/asmAlias/asmAliasUpdate.py
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    2b14cc7d4cd492874f2e2a89e05d5cd720dbe304 Thu Oct 1 15:54:21 2026 -0700
    do not use any alias names if such a name, case insensitive, is already a name in hgcentral.dbDb.name column refs #38444
• src/hg/utils/otto/genArk/ncbiMirror/loadAssemblySummaries.sh
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    2289b2aaf691efca9e98d99681ae28d821012896 Wed Sep 23 16:51:58 2026 -0700
    script used by fetch.sh to load the assembly_summary files into the "genark" database refs #32596
• src/hg/utils/otto/methbase2/makefile
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    ec8d25d5bd0eac0a4f5172603e704106cbf6c66b Sun Oct 4 06:37:38 2026 -0700
    methbase2 otto: ssh to hgdownload as the invoking user, not as qateam, refs #34246
• src/hg/utils/otto/methbase2/methbaseDownload
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    ec8d25d5bd0eac0a4f5172603e704106cbf6c66b Sun Oct 4 06:37:38 2026 -0700
    methbase2 otto: ssh to hgdownload as the invoking user, not as qateam, refs #34246
• src/hg/utils/otto/methbase2/methbaseOtto.sh
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    ec8d25d5bd0eac0a4f5172603e704106cbf6c66b Sun Oct 4 06:37:38 2026 -0700
    methbase2 otto: ssh to hgdownload as the invoking user, not as qateam, refs #34246
• src/hg/utils/otto/ottoMonitor/README
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    3a5d6583ad4aea08655f9e1408baa712c6339cd1 Wed Sep 30 09:47:52 2026 -0700
    ottoMonitor: compare each otto track on hgwdev with genome.ucsc.edu, refs #38101, #38436 A job can run on time while its output never reaches the RR, because the push is a separate root cron that the otto run does not see. DECIPHER rebuilt its track every week from 2022 while decipherAutoPush was commented out, and the monitor called it on time. The monitor now reads the "Data last updated at UCSC" line from hgTrackUi on both hosts. It reports a track whose public copy has stayed behind hgwdev for more than 8 days. It finds the tracks itself, from the /gbdb links into the otto area and the trackDb bigDataUrl that names them. ottoMonitorPublic.tsv lists only the few it cannot find that way, mostly SQL tables. --no-public skips the check.
• src/hg/utils/otto/ottoMonitor/ottoMonitor.py
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    3a5d6583ad4aea08655f9e1408baa712c6339cd1 Wed Sep 30 09:47:52 2026 -0700
    ottoMonitor: compare each otto track on hgwdev with genome.ucsc.edu, refs #38101, #38436 A job can run on time while its output never reaches the RR, because the push is a separate root cron that the otto run does not see. DECIPHER rebuilt its track every week from 2022 while decipherAutoPush was commented out, and the monitor called it on time. The monitor now reads the "Data last updated at UCSC" line from hgTrackUi on both hosts. It reports a track whose public copy has stayed behind hgwdev for more than 8 days. It finds the tracks itself, from the /gbdb links into the otto area and the trackDb bigDataUrl that names them. ottoMonitorPublic.tsv lists only the few it cannot find that way, mostly SQL tables. --no-public skips the check.
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    a945138a550db38e817ea9fe9da16096e0f0ab45 Thu Oct 1 08:31:35 2026 -0700
    ottoMonitor: remember the ticket it files, and add the ottoWatchers people to every ticket, refs #38101, #38436 fileTicket() now returns the new ticket number, and both callers store it, so the "ticket is already open" check works and a failure that persists is not filed again every night. The number is cleared when the job or track is back to ok. A new "# ottoWatchers:" header line in ottoOwners.tsv names people to add as watchers to every ticket.
• src/hg/utils/otto/ottoMonitor/ottoMonitorPublic.tsv
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    3a5d6583ad4aea08655f9e1408baa712c6339cd1 Wed Sep 30 09:47:52 2026 -0700
    ottoMonitor: compare each otto track on hgwdev with genome.ucsc.edu, refs #38101, #38436 A job can run on time while its output never reaches the RR, because the push is a separate root cron that the otto run does not see. DECIPHER rebuilt its track every week from 2022 while decipherAutoPush was commented out, and the monitor called it on time. The monitor now reads the "Data last updated at UCSC" line from hgTrackUi on both hosts. It reports a track whose public copy has stayed behind hgwdev for more than 8 days. It finds the tracks itself, from the /gbdb links into the otto area and the trackDb bigDataUrl that names them. ottoMonitorPublic.tsv lists only the few it cannot find that way, mostly SQL tables. --no-public skips the check.
• src/hg/utils/otto/uniprot/doUniprot
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    90abb8f3321fc8cc0feb99ec196cd692dd55a5b0 Fri Sep 25 14:42:10 2026 -0700
    uniprot otto: size miniprot's memory from the proteins too, and survive a missing NCBI table Twelve taxa died with "[morecore] insufficient memory" inside their reservation. The formula sized the job from the genome alone, on a curve I measured by varying the genome (227, 424 and 811 Mb) while holding the protein set at 125 sequences. That characterised one input and generalised as though it had characterised the function: the real runs align whole proteomes, 78457 sequences for zebrafish, and the alignment work scales with that as well. A 0.46 Gb genome that the genome term put at 8 GB ran out of memory. There is now a term for the protein input and the floor is 16 GB rather than 8. Checked by rerunning the exact job that failed, at the new reservation: it completes and writes a 74 MB GFF. Reserving too much costs queue slots on a cluster that absorbs these jobs easily; reserving too little throws the assembly away after minutes of work. Six more taxa died on a missing ncbi/<taxId>.tsv. Not every organism is in NCBI's gene2refseq, so for some of them that file cannot exist. It is only used to resolve UniProt's Entrez cross-references, and the caller already checks whether it got anything, so a missing table now returns nothing and costs a little filtering accuracy rather than the assembly. Those taxa would also have sent every future run back to re-split 2.4 GB looking for a table that will never appear, so the split now leaves an empty file behind to record that it looked. refs #38300
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    51975d67889e63fbc5fbad0cf1a909ebcca5f25e Sat Sep 26 14:15:10 2026 -0700
    uniprot otto: let a run finish when a few taxa fail, and say where to read about them A run over hundreds of organisms always has a few that cannot be built: one UniProt barely annotates, one NCBI has no gene table for, a genome needing more memory than was reserved. Until now any single one of them aborted the run before the flip, so 24 failures out of 664 taxa kept the other 640 from being published, twice. --allowFailures=N carries on and publishes when no more than N taxa failed, and doUpdate.sh passes 10 unless the caller says otherwise, so the monthly cron is no longer hostage to a handful of awkward organisms. Above the threshold it still aborts and publishes nothing, which is the right answer when something systemic has broken. Nothing is quieter as a result. Every failure is reported with its traceback as before, and now each one also gets its own file under failedTaxa/<taxId>.log holding the taxon, its assemblies, the time and the traceback. lastRun.log is overwritten by the next run and interleaves every taxon, so a failure someone wants to look at a day later was hard to find in it; these files are not overwritten except by another failure of the same taxon. The end-of-run report names each failed taxon with its assemblies and the path to its log, and prints the --dbs argument to retry exactly those. The failure mail from doUpdate.sh lists the log paths too. Checked all three paths: below the threshold the run continues, above it aborts, with no failures nothing changes. Checked that the cron form gets --allowFailures=10, that an explicit --allowFailures wins, and that it does not disturb other arguments. refs #38300
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    6831b39717c5f1b1c4c6e605916396c8b0890f7a Sat Sep 26 17:51:45 2026 -0700
    uniprot otto: a help string cannot mix %default with python formatting The --allowFailures help text ended with a python % substitution while also containing optparse's %default placeholder, so python tried to read %d out of %default and every invocation died before parsing arguments: TypeError: %d format: a real number is required, not str Spell the directory out instead. Checked that no other help string in the file combines the two. refs #38300
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    4decf5fbe82051b2d5aff9cabce3feae9dfafae1 Sat Sep 26 18:48:55 2026 -0700
    uniprot: stop declaring the alignments as amino acid coordinates, and show them properly The bigPsl seqType field describes the coordinates, not the letters stored beside them, and the UniProt query side is in bases: these proteins reach the genome through transcripts, so a query runs three bases to a residue. Declaring amino acids made pslFromBigPsl divide the block sizes by three and leave the query coordinates alone, so every reader got an alignment measured in two units at once. That fed a heap overflow in the alignment page, drew blocks short in hgTracks, and loaded sub-codon blocks as size 0, which aborted pslTransMap and took down the lifted SwissProt track (#38249). pslProtFromNaLike() converts such a psl to one counted in residues. Blocks are trimmed to whole codons, and a residue whose codon straddles an exon junction sits in two places in the genome at once, so it gets no column and the page says how many are missing rather than dropping them silently: 0.9% of residues, though 87% of alignments have at least one. A bigPsl also keeps the reference strand where a psl reads the query strand, so minus-strand items arrived claiming the protein was reversed and were rendered as reverse complemented nucleotide ambiguity codes; pslRc moves them to the convention blat uses, query forward and the strand on the target. Checked on hg38 against the translated genome: 210,416 residues over both strands, 99.86% identical, the remainder real protein-vs-reference variation. All 29 items of a test region render the stored protein at the right residues. Files already published still say amino acid and must keep working until they are rebuilt, so the conversion also requires the blocks to measure the target the way the target is measured; verified that separates the two shapes on 3000 records each way, and that all 29 render without crashing in the old format, where they now say plainly that the coordinates and the sequence do not match. refs #38300
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    8954c29282f84de8f41c183a4cbb2817fbbb87c5 Mon Sep 28 13:53:57 2026 -0700
    uniprot otto: an empty cached mapping means nothing aligned, not a broken file, refs #38300
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    45eb30c0414d20710274af10680660b9d00f04b8 Mon Oct 5 01:23:09 2026 -0700
    uniprot otto: raise miniprot's memory when a job runs out, and skip an assembly with no transcripts Two of the eight taxa that failed the GenArk run died with "[morecore] insufficient memory" inside their reservation, so the sizing was wrong a second time. Measuring says it cannot be sized from the inputs at all: 0.46 Gb of genome with 78457 proteins fits in 16 GB, while 0.86 Gb with 50305 proteins peaks at 43.3 GB. Half the protein and twice the genome needs at least 2.7 times the memory, so no sum of a genome term and a protein term fits both. What drives it is how much alignment work the sequence generates, which the file sizes do not show. So stop predicting. The formula stays as a first guess and the batch is run again with four times the reservation when a job ran out of memory, up to three tries. A batch that failed for any other reason is not retried, so the 2.5 Gb genome that segfaults is still only run once. Checked the detector against both real batches: the one that ran out of memory reads as such, the one that segfaulted does not. para records the raw wait status, so 134 means the abort miniprot makes when malloc fails. The reservation lives in the batch, so freeing it and deleting the state files is what lets para make use a new one; checked that freeBatch does not prompt and that a cleared batch runs again. Three more of the eight had a gene track that produced no transcripts at all. BLAST was pointed at an empty database and all 929 of its jobs crashed, taking the taxon down after a long detour through the cluster. There is nothing to align against, so that assembly is now skipped the way one with no alignments already is. refs #38300
• src/hg/utils/otto/uniprot/doUpdate.sh
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    51975d67889e63fbc5fbad0cf1a909ebcca5f25e Sat Sep 26 14:15:10 2026 -0700
    uniprot otto: let a run finish when a few taxa fail, and say where to read about them A run over hundreds of organisms always has a few that cannot be built: one UniProt barely annotates, one NCBI has no gene table for, a genome needing more memory than was reserved. Until now any single one of them aborted the run before the flip, so 24 failures out of 664 taxa kept the other 640 from being published, twice. --allowFailures=N carries on and publishes when no more than N taxa failed, and doUpdate.sh passes 10 unless the caller says otherwise, so the monthly cron is no longer hostage to a handful of awkward organisms. Above the threshold it still aborts and publishes nothing, which is the right answer when something systemic has broken. Nothing is quieter as a result. Every failure is reported with its traceback as before, and now each one also gets its own file under failedTaxa/<taxId>.log holding the taxon, its assemblies, the time and the traceback. lastRun.log is overwritten by the next run and interleaves every taxon, so a failure someone wants to look at a day later was hard to find in it; these files are not overwritten except by another failure of the same taxon. The end-of-run report names each failed taxon with its assemblies and the path to its log, and prints the --dbs argument to retry exactly those. The failure mail from doUpdate.sh lists the log paths too. Checked all three paths: below the threshold the run continues, above it aborts, with no failures nothing changes. Checked that the cron form gets --allowFailures=10, that an explicit --allowFailures wins, and that it does not disturb other arguments. refs #38300
• src/hg/utils/vcfToHgvs/tests/expected/stopLoss.tab
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    722e46a2cca739fb7abe042315e8ca3c5e55f8f5 Wed Sep 23 14:25:15 2026 -0700
    Run the hg/utils tests from make test, and fix the two that had gone red, no redmine make test never reached hg/utils. hg/makefile only descends into an app that has a tests/makefile, and hg/utils has none, so the hubCheck, vcfToHgvs and other hg/utils tests were skipped without a message. Added utils to TEST_DIRS. hubCheck stopped warning about a track with no description page after 1258d7f65e7. A track with no page now keeps the empty string that trackDbCustom.c sets, and hubCheck tested for NULL. It now uses isEmpty(). badType gained a real error when 571aecdf42c stopped dropping tracks, and its expected output was never updated. vcfToHgvs stopLoss reads the live hg38 ncbiRefSeq tables, which now have 32 more transcripts and NM_153819.2.
• src/inc/htmlPage.h
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    d48a1f1935917a45b20ae782f4a0ab53da13e6a9 Tue Sep 15 12:53:04 2026 -0700
    hgTablesTest: skip an oversized page instead of dying inside the allocator, refs #38359 A dense file-backed track can hand back hundreds of megabytes for a single five-megabyte test region. hg38 hgdp returned 602MB, which took carefulAlloc past its 500MB ceiling, and carefulAlloc exits the process where it stands rather than errAborting, on the grounds that errAbort itself allocates. So the run ended with one line on stderr, nothing in the log, and every table still to come forfeited. The arm in quickSubmit meant to catch exactly this and name the track had never once run. htmlPage now takes an optional ceiling on the response it will read into memory. Past it the fetch frees what it has read and errAborts naming the url, which the robot's errCatch turns back into an ordinary return of no page. The ceiling defaults to none, which leaves hgNearTest, hgBlatTest and htmlCheck exactly as they were. hgTablesTest sets it to 100MB, a fifth of the allocator ceiling: the dyString roughly doubles as it grows and the old buffer is still live while the new one fills, and the parsed page then sits alongside its text. An oversized page is logged and skipped, not counted as an error. A track that answers a 5Mb region with 600MB is one this robot cannot test, which is the same situation the row count screen already catches before submitting; counting it would put a failure in every weekly run and leave the summary as useless a gate as the one that never failed. The log is line buffered now as well. Finding out that a run died partway through is what this robot is for, and a block of buffered lines lost on the way out is part of how the old failure left no trace of which track it was on. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/inc/net.h
  • lines changed 5, context: html, text, full: html, text
    d48a1f1935917a45b20ae782f4a0ab53da13e6a9 Tue Sep 15 12:53:04 2026 -0700
    hgTablesTest: skip an oversized page instead of dying inside the allocator, refs #38359 A dense file-backed track can hand back hundreds of megabytes for a single five-megabyte test region. hg38 hgdp returned 602MB, which took carefulAlloc past its 500MB ceiling, and carefulAlloc exits the process where it stands rather than errAborting, on the grounds that errAbort itself allocates. So the run ended with one line on stderr, nothing in the log, and every table still to come forfeited. The arm in quickSubmit meant to catch exactly this and name the track had never once run. htmlPage now takes an optional ceiling on the response it will read into memory. Past it the fetch frees what it has read and errAborts naming the url, which the robot's errCatch turns back into an ordinary return of no page. The ceiling defaults to none, which leaves hgNearTest, hgBlatTest and htmlCheck exactly as they were. hgTablesTest sets it to 100MB, a fifth of the allocator ceiling: the dyString roughly doubles as it grows and the old buffer is still live while the new one fills, and the parsed page then sits alongside its text. An oversized page is logged and skipped, not counted as an error. A track that answers a 5Mb region with 600MB is one this robot cannot test, which is the same situation the row count screen already catches before submitting; counting it would put a failure in every weekly run and leave the summary as useless a gate as the one that never failed. The log is line buffered now as well. Finding out that a run died partway through is what this robot is for, and a block of buffered lines lost on the way out is part of how the old failure left no trace of which track it was on. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/inc/psl.h
  • lines changed 5, context: html, text, full: html, text
    4decf5fbe82051b2d5aff9cabce3feae9dfafae1 Sat Sep 26 18:48:55 2026 -0700
    uniprot: stop declaring the alignments as amino acid coordinates, and show them properly The bigPsl seqType field describes the coordinates, not the letters stored beside them, and the UniProt query side is in bases: these proteins reach the genome through transcripts, so a query runs three bases to a residue. Declaring amino acids made pslFromBigPsl divide the block sizes by three and leave the query coordinates alone, so every reader got an alignment measured in two units at once. That fed a heap overflow in the alignment page, drew blocks short in hgTracks, and loaded sub-codon blocks as size 0, which aborted pslTransMap and took down the lifted SwissProt track (#38249). pslProtFromNaLike() converts such a psl to one counted in residues. Blocks are trimmed to whole codons, and a residue whose codon straddles an exon junction sits in two places in the genome at once, so it gets no column and the page says how many are missing rather than dropping them silently: 0.9% of residues, though 87% of alignments have at least one. A bigPsl also keeps the reference strand where a psl reads the query strand, so minus-strand items arrived claiming the protein was reversed and were rendered as reverse complemented nucleotide ambiguity codes; pslRc moves them to the convention blat uses, query forward and the strand on the target. Checked on hg38 against the translated genome: 210,416 residues over both strands, 99.86% identical, the remainder real protein-vs-reference variation. All 29 items of a test region render the stored protein at the right residues. Files already published still say amino acid and must keep working until they are rebuilt, so the conversion also requires the blocks to measure the target the way the target is measured; verified that separates the two shapes on 3000 records each way, and that all 29 render without crashing in the old format, where they now say plainly that the coordinates and the sequence do not match. refs #38300
• src/lib/htmlPage.c
  • lines changed 33, context: html, text, full: html, text
    d48a1f1935917a45b20ae782f4a0ab53da13e6a9 Tue Sep 15 12:53:04 2026 -0700
    hgTablesTest: skip an oversized page instead of dying inside the allocator, refs #38359 A dense file-backed track can hand back hundreds of megabytes for a single five-megabyte test region. hg38 hgdp returned 602MB, which took carefulAlloc past its 500MB ceiling, and carefulAlloc exits the process where it stands rather than errAborting, on the grounds that errAbort itself allocates. So the run ended with one line on stderr, nothing in the log, and every table still to come forfeited. The arm in quickSubmit meant to catch exactly this and name the track had never once run. htmlPage now takes an optional ceiling on the response it will read into memory. Past it the fetch frees what it has read and errAborts naming the url, which the robot's errCatch turns back into an ordinary return of no page. The ceiling defaults to none, which leaves hgNearTest, hgBlatTest and htmlCheck exactly as they were. hgTablesTest sets it to 100MB, a fifth of the allocator ceiling: the dyString roughly doubles as it grows and the old buffer is still live while the new one fills, and the parsed page then sits alongside its text. An oversized page is logged and skipped, not counted as an error. A track that answers a 5Mb region with 600MB is one this robot cannot test, which is the same situation the row count screen already catches before submitting; counting it would put a failure in every weekly run and leave the summary as useless a gate as the one that never failed. The log is line buffered now as well. Finding out that a run died partway through is what this robot is for, and a block of buffered lines lost on the way out is part of how the old failure left no trace of which track it was on. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 14, context: html, text, full: html, text
    99e615846246a19fdb5d01fcea5dce49179dd2ba Tue Sep 22 10:52:28 2026 -0700
    htmlPage: parse valueless tag attributes such as SELECTED The attribute name scanner read everything up to the next equals sign, so <OPTION SELECTED value='any'> became a single attribute named "SELECTED value". A lookup for SELECTED then found nothing and the SELECT fell back to its first option. The same happened to CHECKED on a checkbox, and to the src in <script async src=...>. A name now ends at white space as well, with a look-ahead so that spaces around the equals sign still work. This is what put 21 soft errors in every hgNearTest robot run since v495. refs #38413
• src/lib/htmlSanitize.c
  • lines changed 88, context: html, text, full: html, text
    7a356d85dba1647c6d918b315e075da7e31ab7cb Sat Sep 26 12:10:36 2026 -0700
    htmlSanitize: keep simple svg drawings in hub description pages, refs #38428 Description pages that draw small svg shapes, such as a colour legend, came out empty. svg, g, circle, ellipse, rect, line, polyline, polygon and path now come through with their size, position, fill and stroke attributes. Other svg elements are left out. Over the 5390-page hub corpus only the 32 pages that contain an svg change, and no page's text changes.
  • lines changed 173, context: html, text, full: html, text
    3842ba31ab0b697b0d4026b5751da7dac7c84e35 Tue Sep 29 13:49:49 2026 -0700
    htmlSanitize: keep the stdTbl and copyLinkSpan class names, refs #38126 GenArk description pages use these two classes from our own stylesheet and scripts: stdTbl for bordered tables, and copyLinkSpan with data-target for the Copy button next to the share link. They now come through, and data-target gets the same prefix as the id it names. Style values are now read the same way on every pass, so a page that is saved again comes out unchanged. Over the 5390-page hub corpus, 278 pages change, all in class or data-target only, and no page's text changes.
• src/lib/htmshell.c
  • lines changed 12, context: html, text, full: html, text
    0c48fcbee53684d81c83e92973238ad49d8e1f32 Wed Sep 23 11:46:28 2026 -0700
    Fix the html,css,,javascript, and attribute Encode methods to handle null input strings, refs #38226
  • lines changed 2, context: html, text, full: html, text
    ab2c23ac0279b262bbc6ecd601d1da77daefe67d Fri Sep 25 02:48:37 2026 -0700
    htmlTextStripTags and htmlTextStripJavascriptCssAndTags allocated no room for the terminating NUL, so a label without tags got garbage bytes, e.g. in filter tooltips, refs #37617
• src/lib/net.c
  • lines changed 20, context: html, text, full: html, text
    d48a1f1935917a45b20ae782f4a0ab53da13e6a9 Tue Sep 15 12:53:04 2026 -0700
    hgTablesTest: skip an oversized page instead of dying inside the allocator, refs #38359 A dense file-backed track can hand back hundreds of megabytes for a single five-megabyte test region. hg38 hgdp returned 602MB, which took carefulAlloc past its 500MB ceiling, and carefulAlloc exits the process where it stands rather than errAborting, on the grounds that errAbort itself allocates. So the run ended with one line on stderr, nothing in the log, and every table still to come forfeited. The arm in quickSubmit meant to catch exactly this and name the track had never once run. htmlPage now takes an optional ceiling on the response it will read into memory. Past it the fetch frees what it has read and errAborts naming the url, which the robot's errCatch turns back into an ordinary return of no page. The ceiling defaults to none, which leaves hgNearTest, hgBlatTest and htmlCheck exactly as they were. hgTablesTest sets it to 100MB, a fifth of the allocator ceiling: the dyString roughly doubles as it grows and the old buffer is still live while the new one fills, and the parsed page then sits alongside its text. An oversized page is logged and skipped, not counted as an error. A track that answers a 5Mb region with 600MB is one this robot cannot test, which is the same situation the row count screen already catches before submitting; counting it would put a failure in every weekly run and leave the summary as useless a gate as the one that never failed. The log is line buffered now as well. Finding out that a run died partway through is what this robot is for, and a block of buffered lines lost on the way out is part of how the old failure left no trace of which track it was on. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/lib/psl.c
  • lines changed 84, context: html, text, full: html, text
    4decf5fbe82051b2d5aff9cabce3feae9dfafae1 Sat Sep 26 18:48:55 2026 -0700
    uniprot: stop declaring the alignments as amino acid coordinates, and show them properly The bigPsl seqType field describes the coordinates, not the letters stored beside them, and the UniProt query side is in bases: these proteins reach the genome through transcripts, so a query runs three bases to a residue. Declaring amino acids made pslFromBigPsl divide the block sizes by three and leave the query coordinates alone, so every reader got an alignment measured in two units at once. That fed a heap overflow in the alignment page, drew blocks short in hgTracks, and loaded sub-codon blocks as size 0, which aborted pslTransMap and took down the lifted SwissProt track (#38249). pslProtFromNaLike() converts such a psl to one counted in residues. Blocks are trimmed to whole codons, and a residue whose codon straddles an exon junction sits in two places in the genome at once, so it gets no column and the page says how many are missing rather than dropping them silently: 0.9% of residues, though 87% of alignments have at least one. A bigPsl also keeps the reference strand where a psl reads the query strand, so minus-strand items arrived claiming the protein was reversed and were rendered as reverse complemented nucleotide ambiguity codes; pslRc moves them to the convention blat uses, query forward and the strand on the target. Checked on hg38 against the translated genome: 210,416 residues over both strands, 99.86% identical, the remainder real protein-vs-reference variation. All 29 items of a test region render the stored protein at the right residues. Files already published still say amino acid and must keep working until they are rebuilt, so the conversion also requires the blocks to measure the target the way the target is measured; verified that separates the two shapes on 3000 records each way, and that all 29 render without crashing in the old format, where they now say plainly that the coordinates and the sequence do not match. refs #38300
• src/lib/pslShow.c
  • lines changed 43, context: html, text, full: html, text
    72282e5a10d847e7b8fc013b53bcff15e90499e8 Sat Sep 26 18:27:01 2026 -0700
    pslShow: clip alignment blocks to the sequences supplied, a bigPsl with out-of-range query coords could write past the end of the heap buffers
• src/lib/tests/cgiDecodeTest.c
  • lines changed 107, context: html, text, full: html, text
    99eb74885ff5bce42cadafee93274df7039dcab5 Sat Sep 26 17:34:11 2026 -0700
    unit tests for four v503 tickets, refs #38391, #37262, #38120, #38107, #38125, #38154 cgiDecodeTest prints what malformed and cut-short %hh escapes decode to, and checks that cgiDecode never reads past the length it is given. udcDotsTest prints the cache directory udc makes for remote URLs with "." and ".." in them, including the ones that must abort. pngWriteTest writes a memGfx image as a PNG, reads it back with libpng, compares every pixel, and checks the row filter of every row. pgSnpManyAllelesTester builds per-allele counts from a VCF record with 150 ALT alleles. Each test fails with its fix backed out, except that zlib-ng was not swapped out for #38125. The test registry gets a row for each ticket.
• src/lib/tests/expected/cgiDecodeTest
  • lines changed 33, context: html, text, full: html, text
    99eb74885ff5bce42cadafee93274df7039dcab5 Sat Sep 26 17:34:11 2026 -0700
    unit tests for four v503 tickets, refs #38391, #37262, #38120, #38107, #38125, #38154 cgiDecodeTest prints what malformed and cut-short %hh escapes decode to, and checks that cgiDecode never reads past the length it is given. udcDotsTest prints the cache directory udc makes for remote URLs with "." and ".." in them, including the ones that must abort. pngWriteTest writes a memGfx image as a PNG, reads it back with libpng, compares every pixel, and checks the row filter of every row. pgSnpManyAllelesTester builds per-allele counts from a VCF record with 150 ALT alleles. Each test fails with its fix backed out, except that zlib-ng was not swapped out for #38125. The test registry gets a row for each ticket.
• src/lib/tests/expected/htmlEncodeTest
  • lines changed 29, context: html, text, full: html, text
    4e33b15085b7cd23fe95256b9d2e9911751aa598 Sat Sep 26 12:12:04 2026 -0700
    lib tests: htmlEncode and attributeEncode on NULL, and the tag strippers on labels with no tags, refs #38226, #37617 Runs under the careful allocator, whose marker straight after each block makes a missing terminator show up on every run.
• src/lib/tests/expected/htmlSanitizeTest
  • lines changed 28, context: html, text, full: html, text
    7a356d85dba1647c6d918b315e075da7e31ab7cb Sat Sep 26 12:10:36 2026 -0700
    htmlSanitize: keep simple svg drawings in hub description pages, refs #38428 Description pages that draw small svg shapes, such as a colour legend, came out empty. svg, g, circle, ellipse, rect, line, polyline, polygon and path now come through with their size, position, fill and stroke attributes. Other svg elements are left out. Over the 5390-page hub corpus only the 32 pages that contain an svg change, and no page's text changes.
  • lines changed 25, context: html, text, full: html, text
    3842ba31ab0b697b0d4026b5751da7dac7c84e35 Tue Sep 29 13:49:49 2026 -0700
    htmlSanitize: keep the stdTbl and copyLinkSpan class names, refs #38126 GenArk description pages use these two classes from our own stylesheet and scripts: stdTbl for bordered tables, and copyLinkSpan with data-target for the Copy button next to the share link. They now come through, and data-target gets the same prefix as the id it names. Style values are now read the same way on every pass, so a page that is saved again comes out unchanged. Over the 5390-page hub corpus, 278 pages change, all in class or data-target only, and no page's text changes.
• src/lib/tests/expected/netSlurpMaxTest
  • lines changed 19, context: html, text, full: html, text
    a9054011188cb975a65a7d9767096a0ffdceb366 Mon Sep 21 17:34:46 2026 -0700
    netSlurpMaxTest: cover the response size ceiling, refs #38359 The fix this defends changes nothing on any page. Its only caller is the hgTablesTest robot, and the failure it prevents is the process exiting from inside carefulAlloc with nothing written to the log, so a unit test is the only test there can be. Four parts. netSlurpFileMax on a plain file, both sides of the boundary, including a ceiling exactly at the file size, which has to read it. The same calls under pushCarefulMemHandler, where carefulTotalAllocated() says whether the abandoned buffer was really freed: a buffer left behind would stay counted against the ceiling and the cap would buy one oversized page and no more. A matched pair of forked children on a file past the allocator ceiling, one read capped and one not, since exit(1) from inside the allocator cannot be seen any other way. And htmlPageSetMaxSize reaching htmlSlurpWithCookies against a server on the loopback interface, because the ceiling travels through a module-wide static and that wiring can rot with no caller changing. Backed the fix out three ways and watched each go red for its own reason. Removing the size check fails 9 of the 18 assertions. Keeping the check and dropping only the dyStringFree fails 3, and only the three that count allocation. Reverting htmlSlurpWithCookies to a plain netSlurpFile fails 2, and only the two that reach through htmlPage. Recorded as sandbox-ab. The registry row carries "-" for the release: the ticket has no target version.
• src/lib/tests/expected/pngWriteTest
  • lines changed 6, context: html, text, full: html, text
    99eb74885ff5bce42cadafee93274df7039dcab5 Sat Sep 26 17:34:11 2026 -0700
    unit tests for four v503 tickets, refs #38391, #37262, #38120, #38107, #38125, #38154 cgiDecodeTest prints what malformed and cut-short %hh escapes decode to, and checks that cgiDecode never reads past the length it is given. udcDotsTest prints the cache directory udc makes for remote URLs with "." and ".." in them, including the ones that must abort. pngWriteTest writes a memGfx image as a PNG, reads it back with libpng, compares every pixel, and checks the row filter of every row. pgSnpManyAllelesTester builds per-allele counts from a VCF record with 150 ALT alleles. Each test fails with its fix backed out, except that zlib-ng was not swapped out for #38125. The test registry gets a row for each ticket.
• src/lib/tests/expected/udcDotsTest
  • lines changed 26, context: html, text, full: html, text
    99eb74885ff5bce42cadafee93274df7039dcab5 Sat Sep 26 17:34:11 2026 -0700
    unit tests for four v503 tickets, refs #38391, #37262, #38120, #38107, #38125, #38154 cgiDecodeTest prints what malformed and cut-short %hh escapes decode to, and checks that cgiDecode never reads past the length it is given. udcDotsTest prints the cache directory udc makes for remote URLs with "." and ".." in them, including the ones that must abort. pngWriteTest writes a memGfx image as a PNG, reads it back with libpng, compares every pixel, and checks the row filter of every row. pgSnpManyAllelesTester builds per-allele counts from a VCF record with 150 ALT alleles. Each test fails with its fix backed out, except that zlib-ng was not swapped out for #38125. The test registry gets a row for each ticket.
• src/lib/tests/expected/valuelessAttrs.out
  • lines changed 15, context: html, text, full: html, text
    99e615846246a19fdb5d01fcea5dce49179dd2ba Tue Sep 22 10:52:28 2026 -0700
    htmlPage: parse valueless tag attributes such as SELECTED The attribute name scanner read everything up to the next equals sign, so <OPTION SELECTED value='any'> became a single attribute named "SELECTED value". A lookup for SELECTED then found nothing and the SELECT fell back to its first option. The same happened to CHECKED on a checkbox, and to the src in <script async src=...>. A name now ends at white space as well, with a look-ahead so that spaces around the equals sign still work. This is what put 21 soft errors in every hgNearTest robot run since v495. refs #38413
• src/lib/tests/htmlEncodeTest.c
  • lines changed 71, context: html, text, full: html, text
    4e33b15085b7cd23fe95256b9d2e9911751aa598 Sat Sep 26 12:12:04 2026 -0700
    lib tests: htmlEncode and attributeEncode on NULL, and the tag strippers on labels with no tags, refs #38226, #37617 Runs under the careful allocator, whose marker straight after each block makes a missing terminator show up on every run.
• src/lib/tests/htmlSanitizeTest.c
  • lines changed 22, context: html, text, full: html, text
    7a356d85dba1647c6d918b315e075da7e31ab7cb Sat Sep 26 12:10:36 2026 -0700
    htmlSanitize: keep simple svg drawings in hub description pages, refs #38428 Description pages that draw small svg shapes, such as a colour legend, came out empty. svg, g, circle, ellipse, rect, line, polyline, polygon and path now come through with their size, position, fill and stroke attributes. Other svg elements are left out. Over the 5390-page hub corpus only the 32 pages that contain an svg change, and no page's text changes.
  • lines changed 15, context: html, text, full: html, text
    3842ba31ab0b697b0d4026b5751da7dac7c84e35 Tue Sep 29 13:49:49 2026 -0700
    htmlSanitize: keep the stdTbl and copyLinkSpan class names, refs #38126 GenArk description pages use these two classes from our own stylesheet and scripts: stdTbl for bordered tables, and copyLinkSpan with data-target for the Copy button next to the share link. They now come through, and data-target gets the same prefix as the id it names. Style values are now read the same way on every pass, so a page that is saved again comes out unchanged. Over the 5390-page hub corpus, 278 pages change, all in class or data-target only, and no page's text changes.
• src/lib/tests/httpsFerryLeakTest.c
  • lines changed 76, context: html, text, full: html, text
    31f2090cd11876f61a92260838078077f68a94ee Thu Sep 24 15:32:25 2026 -0700
    Add a test program and wrapper for debugging hung https connections, refs #38366
• src/lib/tests/httpsFerryLeakTest.sh
  • lines changed 60, context: html, text, full: html, text
    31f2090cd11876f61a92260838078077f68a94ee Thu Sep 24 15:32:25 2026 -0700
    Add a test program and wrapper for debugging hung https connections, refs #38366
• src/lib/tests/input/valuelessAttrs.html
  • lines changed 40, context: html, text, full: html, text
    99e615846246a19fdb5d01fcea5dce49179dd2ba Tue Sep 22 10:52:28 2026 -0700
    htmlPage: parse valueless tag attributes such as SELECTED The attribute name scanner read everything up to the next equals sign, so <OPTION SELECTED value='any'> became a single attribute named "SELECTED value". A lookup for SELECTED then found nothing and the SELECT fell back to its first option. The same happened to CHECKED on a checkbox, and to the src in <script async src=...>. A name now ends at white space as well, with a look-ahead so that spaces around the equals sign still work. This is what put 21 soft errors in every hgNearTest robot run since v495. refs #38413
• src/lib/tests/makefile
  • lines changed 8, context: html, text, full: html, text
    a9054011188cb975a65a7d9767096a0ffdceb366 Mon Sep 21 17:34:46 2026 -0700
    netSlurpMaxTest: cover the response size ceiling, refs #38359 The fix this defends changes nothing on any page. Its only caller is the hgTablesTest robot, and the failure it prevents is the process exiting from inside carefulAlloc with nothing written to the log, so a unit test is the only test there can be. Four parts. netSlurpFileMax on a plain file, both sides of the boundary, including a ceiling exactly at the file size, which has to read it. The same calls under pushCarefulMemHandler, where carefulTotalAllocated() says whether the abandoned buffer was really freed: a buffer left behind would stay counted against the ceiling and the cap would buy one oversized page and no more. A matched pair of forked children on a file past the allocator ceiling, one read capped and one not, since exit(1) from inside the allocator cannot be seen any other way. And htmlPageSetMaxSize reaching htmlSlurpWithCookies against a server on the loopback interface, because the ceiling travels through a module-wide static and that wiring can rot with no caller changing. Backed the fix out three ways and watched each go red for its own reason. Removing the size check fails 9 of the 18 assertions. Keeping the check and dropping only the dyStringFree fails 3, and only the three that count allocation. Reverting htmlSlurpWithCookies to a plain netSlurpFile fails 2, and only the two that reach through htmlPage. Recorded as sandbox-ab. The registry row carries "-" for the release: the ticket has no target version.
  • lines changed 2, context: html, text, full: html, text
    99e615846246a19fdb5d01fcea5dce49179dd2ba Tue Sep 22 10:52:28 2026 -0700
    htmlPage: parse valueless tag attributes such as SELECTED The attribute name scanner read everything up to the next equals sign, so <OPTION SELECTED value='any'> became a single attribute named "SELECTED value". A lookup for SELECTED then found nothing and the SELECT fell back to its first option. The same happened to CHECKED on a checkbox, and to the src in <script async src=...>. A name now ends at white space as well, with a look-ahead so that spaces around the equals sign still work. This is what put 21 soft errors in every hgNearTest robot run since v495. refs #38413
  • lines changed 5, context: html, text, full: html, text
    31f2090cd11876f61a92260838078077f68a94ee Thu Sep 24 15:32:25 2026 -0700
    Add a test program and wrapper for debugging hung https connections, refs #38366
  • lines changed 8, context: html, text, full: html, text
    4e33b15085b7cd23fe95256b9d2e9911751aa598 Sat Sep 26 12:12:04 2026 -0700
    lib tests: htmlEncode and attributeEncode on NULL, and the tag strippers on labels with no tags, refs #38226, #37617 Runs under the careful allocator, whose marker straight after each block makes a missing terminator show up on every run.
  • lines changed 21, context: html, text, full: html, text
    99eb74885ff5bce42cadafee93274df7039dcab5 Sat Sep 26 17:34:11 2026 -0700
    unit tests for four v503 tickets, refs #38391, #37262, #38120, #38107, #38125, #38154 cgiDecodeTest prints what malformed and cut-short %hh escapes decode to, and checks that cgiDecode never reads past the length it is given. udcDotsTest prints the cache directory udc makes for remote URLs with "." and ".." in them, including the ones that must abort. pngWriteTest writes a memGfx image as a PNG, reads it back with libpng, compares every pixel, and checks the row filter of every row. pgSnpManyAllelesTester builds per-allele counts from a VCF record with 150 ALT alleles. Each test fails with its fix backed out, except that zlib-ng was not swapped out for #38125. The test registry gets a row for each ticket.
• src/lib/tests/netSlurpMaxTest.c
  • lines changed 362, context: html, text, full: html, text
    a9054011188cb975a65a7d9767096a0ffdceb366 Mon Sep 21 17:34:46 2026 -0700
    netSlurpMaxTest: cover the response size ceiling, refs #38359 The fix this defends changes nothing on any page. Its only caller is the hgTablesTest robot, and the failure it prevents is the process exiting from inside carefulAlloc with nothing written to the log, so a unit test is the only test there can be. Four parts. netSlurpFileMax on a plain file, both sides of the boundary, including a ceiling exactly at the file size, which has to read it. The same calls under pushCarefulMemHandler, where carefulTotalAllocated() says whether the abandoned buffer was really freed: a buffer left behind would stay counted against the ceiling and the cap would buy one oversized page and no more. A matched pair of forked children on a file past the allocator ceiling, one read capped and one not, since exit(1) from inside the allocator cannot be seen any other way. And htmlPageSetMaxSize reaching htmlSlurpWithCookies against a server on the loopback interface, because the ceiling travels through a module-wide static and that wiring can rot with no caller changing. Backed the fix out three ways and watched each go red for its own reason. Removing the size check fails 9 of the 18 assertions. Keeping the check and dropping only the dyStringFree fails 3, and only the three that count allocation. Reverting htmlSlurpWithCookies to a plain netSlurpFile fails 2, and only the two that reach through htmlPage. Recorded as sandbox-ab. The registry row carries "-" for the release: the ticket has no target version.
• src/lib/tests/pngWriteTest.c
  • lines changed 169, context: html, text, full: html, text
    99eb74885ff5bce42cadafee93274df7039dcab5 Sat Sep 26 17:34:11 2026 -0700
    unit tests for four v503 tickets, refs #38391, #37262, #38120, #38107, #38125, #38154 cgiDecodeTest prints what malformed and cut-short %hh escapes decode to, and checks that cgiDecode never reads past the length it is given. udcDotsTest prints the cache directory udc makes for remote URLs with "." and ".." in them, including the ones that must abort. pngWriteTest writes a memGfx image as a PNG, reads it back with libpng, compares every pixel, and checks the row filter of every row. pgSnpManyAllelesTester builds per-allele counts from a VCF record with 150 ALT alleles. Each test fails with its fix backed out, except that zlib-ng was not swapped out for #38125. The test registry gets a row for each ticket.
• src/lib/tests/udcDotsTest.c
  • lines changed 70, context: html, text, full: html, text
    99eb74885ff5bce42cadafee93274df7039dcab5 Sat Sep 26 17:34:11 2026 -0700
    unit tests for four v503 tickets, refs #38391, #37262, #38120, #38107, #38125, #38154 cgiDecodeTest prints what malformed and cut-short %hh escapes decode to, and checks that cgiDecode never reads past the length it is given. udcDotsTest prints the cache directory udc makes for remote URLs with "." and ".." in them, including the ones that must abort. pngWriteTest writes a memGfx image as a PNG, reads it back with libpng, compares every pixel, and checks the row filter of every row. pgSnpManyAllelesTester builds per-allele counts from a VCF record with 150 ALT alleles. Each test fails with its fix backed out, except that zlib-ng was not swapped out for #38125. The test registry gets a row for each ticket.
• src/product/installer/browserSetup.sh
  • lines changed 45, context: html, text, full: html, text
    8f8455798f19c20cfabbf11e16c21f8352a02e9c Sat Sep 19 07:04:47 2026 -0700
    set ft_min_word_len=3 in browserSetup.sh so three-letter assembly names can be found in the assembly search box, refs #38387 The assembly search box asks hubApi for assemblies matching what was typed, and that lookup is a MySQL FULLTEXT search over hgcentral.assemblyList. The table is MyISAM, so ft_min_word_len decides the shortest word that gets into the index. Mariadb defaults to 4, which leaves out every three-letter assembly name, so hs1, rn7 and dm6 could not be found in a mirror or in a released docker image. hgwdev has always run with 3, which is why the same search worked here. updateBlatServers now sets the value, restarts Mariadb and then loads hgcentral.sql. That order matters: the new value is only live after a restart, and the FULLTEXT index is rebuilt by the DROP TABLE, CREATE and INSERT of assemblyList in that dump, so no REPAIR is needed. updateBlatServers is the one place hgcentral is reloaded, reached from mysqlDbSetup on install and from cgiUpdate on both cgiUpdate and update, so one call site covers every path and every OS. An error from the init script is tolerated around the restart. In the docker image Mariadb runs under runit, so a stop shuts the server down, the supervisor starts it again a second later, and the init script reports a failure although the restart worked. The running value is checked afterwards, and a warning names the REPAIR command if it did not take. Tested in a stock container that had ft_min_word_len=4 and no assemblyList table at all. Afterwards hs1, rn7 and dm6 are all found through hubApi/findGenome?browser=mustExist, with hs1 first for a search of hs1.
• src/utils/barChartReorder/barChartReorder
  • lines changed 95, context: html, text, full: html, text
    d87ef2fb8472135b899fd1a89434033d5895217a Thu Oct 1 15:31:26 2026 -0700
    Add barChartReorder, a utility for changing the order of the bars in a barChart track, refs #37619 The bars of a barChart are drawn in the order their values appear in the expScores field, and nothing re-sorts them when the track is drawn, so the order is a property of the data file. Putting the bars in a different order means rewriting that field in every row, which is awkward enough by hand that we have twice done it for a data author instead of explaining it. This has come up on #36998 and #37001. barChartReorder takes the current bar order and the wanted order as two lists of names, rewrites expScores in every row, optionally puts a .categories file into the same order, and prints the barChartBars line for the track. It works on any barChart BED whatever produced it, so unlike the --groupOrderFile option of expMatrixToBarchartBed it does not assume the file was built here from an expression matrix. A bigBarChart is handled by converting it with bigBedToBed and rebuilding it afterwards, which the usage message spells out. It refuses to write a half-correct file: the two orders must name the same bars, every row must hold as many values as there are names, and a .categories file must have a row for each bar. Listed in USER_APP_SCRIPTS so it reaches hgdownload, and in the no-argument branch of mkREADME.sh so the README picks up its usage message rather than the argparse error that -verbose=2 would produce. Its tests are also wired into the test target directly. testAll iterates ALL_APPS, which does not include USER_APP_SCRIPTS, so none of these programs' tests have ever been reachable from "make test" - that is why the suite sitting next to expMatrixToBarchartBed never reported it was broken. The makefile already keeps a short list of directories testAll cannot reach, and this adds two more to it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/barChartReorder/makefile
  • lines changed 11, context: html, text, full: html, text
    d87ef2fb8472135b899fd1a89434033d5895217a Thu Oct 1 15:31:26 2026 -0700
    Add barChartReorder, a utility for changing the order of the bars in a barChart track, refs #37619 The bars of a barChart are drawn in the order their values appear in the expScores field, and nothing re-sorts them when the track is drawn, so the order is a property of the data file. Putting the bars in a different order means rewriting that field in every row, which is awkward enough by hand that we have twice done it for a data author instead of explaining it. This has come up on #36998 and #37001. barChartReorder takes the current bar order and the wanted order as two lists of names, rewrites expScores in every row, optionally puts a .categories file into the same order, and prints the barChartBars line for the track. It works on any barChart BED whatever produced it, so unlike the --groupOrderFile option of expMatrixToBarchartBed it does not assume the file was built here from an expression matrix. A bigBarChart is handled by converting it with bigBedToBed and rebuilding it afterwards, which the usage message spells out. It refuses to write a half-correct file: the two orders must name the same bars, every row must hold as many values as there are names, and a .categories file must have a row for each bar. Listed in USER_APP_SCRIPTS so it reaches hgdownload, and in the no-argument branch of mkREADME.sh so the README picks up its usage message rather than the argparse error that -verbose=2 would produce. Its tests are also wired into the test target directly. testAll iterates ALL_APPS, which does not include USER_APP_SCRIPTS, so none of these programs' tests have ever been reachable from "make test" - that is why the suite sitting next to expMatrixToBarchartBed never reported it was broken. The makefile already keeps a short list of directories testAll cannot reach, and this adds two more to it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/barChartReorder/tests/expected/bars.txt
  • lines changed 1, context: html, text, full: html, text
    d87ef2fb8472135b899fd1a89434033d5895217a Thu Oct 1 15:31:26 2026 -0700
    Add barChartReorder, a utility for changing the order of the bars in a barChart track, refs #37619 The bars of a barChart are drawn in the order their values appear in the expScores field, and nothing re-sorts them when the track is drawn, so the order is a property of the data file. Putting the bars in a different order means rewriting that field in every row, which is awkward enough by hand that we have twice done it for a data author instead of explaining it. This has come up on #36998 and #37001. barChartReorder takes the current bar order and the wanted order as two lists of names, rewrites expScores in every row, optionally puts a .categories file into the same order, and prints the barChartBars line for the track. It works on any barChart BED whatever produced it, so unlike the --groupOrderFile option of expMatrixToBarchartBed it does not assume the file was built here from an expression matrix. A bigBarChart is handled by converting it with bigBedToBed and rebuilding it afterwards, which the usage message spells out. It refuses to write a half-correct file: the two orders must name the same bars, every row must hold as many values as there are names, and a .categories file must have a row for each bar. Listed in USER_APP_SCRIPTS so it reaches hgdownload, and in the no-argument branch of mkREADME.sh so the README picks up its usage message rather than the argparse error that -verbose=2 would produce. Its tests are also wired into the test target directly. testAll iterates ALL_APPS, which does not include USER_APP_SCRIPTS, so none of these programs' tests have ever been reachable from "make test" - that is why the suite sitting next to expMatrixToBarchartBed never reported it was broken. The makefile already keeps a short list of directories testAll cannot reach, and this adds two more to it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/barChartReorder/tests/expected/simple.bed
  • lines changed 2, context: html, text, full: html, text
    d87ef2fb8472135b899fd1a89434033d5895217a Thu Oct 1 15:31:26 2026 -0700
    Add barChartReorder, a utility for changing the order of the bars in a barChart track, refs #37619 The bars of a barChart are drawn in the order their values appear in the expScores field, and nothing re-sorts them when the track is drawn, so the order is a property of the data file. Putting the bars in a different order means rewriting that field in every row, which is awkward enough by hand that we have twice done it for a data author instead of explaining it. This has come up on #36998 and #37001. barChartReorder takes the current bar order and the wanted order as two lists of names, rewrites expScores in every row, optionally puts a .categories file into the same order, and prints the barChartBars line for the track. It works on any barChart BED whatever produced it, so unlike the --groupOrderFile option of expMatrixToBarchartBed it does not assume the file was built here from an expression matrix. A bigBarChart is handled by converting it with bigBedToBed and rebuilding it afterwards, which the usage message spells out. It refuses to write a half-correct file: the two orders must name the same bars, every row must hold as many values as there are names, and a .categories file must have a row for each bar. Listed in USER_APP_SCRIPTS so it reaches hgdownload, and in the no-argument branch of mkREADME.sh so the README picks up its usage message rather than the argparse error that -verbose=2 would produce. Its tests are also wired into the test target directly. testAll iterates ALL_APPS, which does not include USER_APP_SCRIPTS, so none of these programs' tests have ever been reachable from "make test" - that is why the suite sitting next to expMatrixToBarchartBed never reported it was broken. The makefile already keeps a short list of directories testAll cannot reach, and this adds two more to it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/barChartReorder/tests/expected/test.bed
  • lines changed 4, context: html, text, full: html, text
    d87ef2fb8472135b899fd1a89434033d5895217a Thu Oct 1 15:31:26 2026 -0700
    Add barChartReorder, a utility for changing the order of the bars in a barChart track, refs #37619 The bars of a barChart are drawn in the order their values appear in the expScores field, and nothing re-sorts them when the track is drawn, so the order is a property of the data file. Putting the bars in a different order means rewriting that field in every row, which is awkward enough by hand that we have twice done it for a data author instead of explaining it. This has come up on #36998 and #37001. barChartReorder takes the current bar order and the wanted order as two lists of names, rewrites expScores in every row, optionally puts a .categories file into the same order, and prints the barChartBars line for the track. It works on any barChart BED whatever produced it, so unlike the --groupOrderFile option of expMatrixToBarchartBed it does not assume the file was built here from an expression matrix. A bigBarChart is handled by converting it with bigBedToBed and rebuilding it afterwards, which the usage message spells out. It refuses to write a half-correct file: the two orders must name the same bars, every row must hold as many values as there are names, and a .categories file must have a row for each bar. Listed in USER_APP_SCRIPTS so it reaches hgdownload, and in the no-argument branch of mkREADME.sh so the README picks up its usage message rather than the argparse error that -verbose=2 would produce. Its tests are also wired into the test target directly. testAll iterates ALL_APPS, which does not include USER_APP_SCRIPTS, so none of these programs' tests have ever been reachable from "make test" - that is why the suite sitting next to expMatrixToBarchartBed never reported it was broken. The makefile already keeps a short list of directories testAll cannot reach, and this adds two more to it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/barChartReorder/tests/expected/test.categories
  • lines changed 5, context: html, text, full: html, text
    d87ef2fb8472135b899fd1a89434033d5895217a Thu Oct 1 15:31:26 2026 -0700
    Add barChartReorder, a utility for changing the order of the bars in a barChart track, refs #37619 The bars of a barChart are drawn in the order their values appear in the expScores field, and nothing re-sorts them when the track is drawn, so the order is a property of the data file. Putting the bars in a different order means rewriting that field in every row, which is awkward enough by hand that we have twice done it for a data author instead of explaining it. This has come up on #36998 and #37001. barChartReorder takes the current bar order and the wanted order as two lists of names, rewrites expScores in every row, optionally puts a .categories file into the same order, and prints the barChartBars line for the track. It works on any barChart BED whatever produced it, so unlike the --groupOrderFile option of expMatrixToBarchartBed it does not assume the file was built here from an expression matrix. A bigBarChart is handled by converting it with bigBedToBed and rebuilding it afterwards, which the usage message spells out. It refuses to write a half-correct file: the two orders must name the same bars, every row must hold as many values as there are names, and a .categories file must have a row for each bar. Listed in USER_APP_SCRIPTS so it reaches hgdownload, and in the no-argument branch of mkREADME.sh so the README picks up its usage message rather than the argparse error that -verbose=2 would produce. Its tests are also wired into the test target directly. testAll iterates ALL_APPS, which does not include USER_APP_SCRIPTS, so none of these programs' tests have ever been reachable from "make test" - that is why the suite sitting next to expMatrixToBarchartBed never reported it was broken. The makefile already keeps a short list of directories testAll cannot reach, and this adds two more to it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/barChartReorder/tests/in/bad.newOrder
  • lines changed 3, context: html, text, full: html, text
    d87ef2fb8472135b899fd1a89434033d5895217a Thu Oct 1 15:31:26 2026 -0700
    Add barChartReorder, a utility for changing the order of the bars in a barChart track, refs #37619 The bars of a barChart are drawn in the order their values appear in the expScores field, and nothing re-sorts them when the track is drawn, so the order is a property of the data file. Putting the bars in a different order means rewriting that field in every row, which is awkward enough by hand that we have twice done it for a data author instead of explaining it. This has come up on #36998 and #37001. barChartReorder takes the current bar order and the wanted order as two lists of names, rewrites expScores in every row, optionally puts a .categories file into the same order, and prints the barChartBars line for the track. It works on any barChart BED whatever produced it, so unlike the --groupOrderFile option of expMatrixToBarchartBed it does not assume the file was built here from an expression matrix. A bigBarChart is handled by converting it with bigBedToBed and rebuilding it afterwards, which the usage message spells out. It refuses to write a half-correct file: the two orders must name the same bars, every row must hold as many values as there are names, and a .categories file must have a row for each bar. Listed in USER_APP_SCRIPTS so it reaches hgdownload, and in the no-argument branch of mkREADME.sh so the README picks up its usage message rather than the argparse error that -verbose=2 would produce. Its tests are also wired into the test target directly. testAll iterates ALL_APPS, which does not include USER_APP_SCRIPTS, so none of these programs' tests have ever been reachable from "make test" - that is why the suite sitting next to expMatrixToBarchartBed never reported it was broken. The makefile already keeps a short list of directories testAll cannot reach, and this adds two more to it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/barChartReorder/tests/in/short.bed
  • lines changed 1, context: html, text, full: html, text
    d87ef2fb8472135b899fd1a89434033d5895217a Thu Oct 1 15:31:26 2026 -0700
    Add barChartReorder, a utility for changing the order of the bars in a barChart track, refs #37619 The bars of a barChart are drawn in the order their values appear in the expScores field, and nothing re-sorts them when the track is drawn, so the order is a property of the data file. Putting the bars in a different order means rewriting that field in every row, which is awkward enough by hand that we have twice done it for a data author instead of explaining it. This has come up on #36998 and #37001. barChartReorder takes the current bar order and the wanted order as two lists of names, rewrites expScores in every row, optionally puts a .categories file into the same order, and prints the barChartBars line for the track. It works on any barChart BED whatever produced it, so unlike the --groupOrderFile option of expMatrixToBarchartBed it does not assume the file was built here from an expression matrix. A bigBarChart is handled by converting it with bigBedToBed and rebuilding it afterwards, which the usage message spells out. It refuses to write a half-correct file: the two orders must name the same bars, every row must hold as many values as there are names, and a .categories file must have a row for each bar. Listed in USER_APP_SCRIPTS so it reaches hgdownload, and in the no-argument branch of mkREADME.sh so the README picks up its usage message rather than the argparse error that -verbose=2 would produce. Its tests are also wired into the test target directly. testAll iterates ALL_APPS, which does not include USER_APP_SCRIPTS, so none of these programs' tests have ever been reachable from "make test" - that is why the suite sitting next to expMatrixToBarchartBed never reported it was broken. The makefile already keeps a short list of directories testAll cannot reach, and this adds two more to it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/barChartReorder/tests/in/simple.bed
  • lines changed 2, context: html, text, full: html, text
    d87ef2fb8472135b899fd1a89434033d5895217a Thu Oct 1 15:31:26 2026 -0700
    Add barChartReorder, a utility for changing the order of the bars in a barChart track, refs #37619 The bars of a barChart are drawn in the order their values appear in the expScores field, and nothing re-sorts them when the track is drawn, so the order is a property of the data file. Putting the bars in a different order means rewriting that field in every row, which is awkward enough by hand that we have twice done it for a data author instead of explaining it. This has come up on #36998 and #37001. barChartReorder takes the current bar order and the wanted order as two lists of names, rewrites expScores in every row, optionally puts a .categories file into the same order, and prints the barChartBars line for the track. It works on any barChart BED whatever produced it, so unlike the --groupOrderFile option of expMatrixToBarchartBed it does not assume the file was built here from an expression matrix. A bigBarChart is handled by converting it with bigBedToBed and rebuilding it afterwards, which the usage message spells out. It refuses to write a half-correct file: the two orders must name the same bars, every row must hold as many values as there are names, and a .categories file must have a row for each bar. Listed in USER_APP_SCRIPTS so it reaches hgdownload, and in the no-argument branch of mkREADME.sh so the README picks up its usage message rather than the argparse error that -verbose=2 would produce. Its tests are also wired into the test target directly. testAll iterates ALL_APPS, which does not include USER_APP_SCRIPTS, so none of these programs' tests have ever been reachable from "make test" - that is why the suite sitting next to expMatrixToBarchartBed never reported it was broken. The makefile already keeps a short list of directories testAll cannot reach, and this adds two more to it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/barChartReorder/tests/in/test.bed
  • lines changed 4, context: html, text, full: html, text
    d87ef2fb8472135b899fd1a89434033d5895217a Thu Oct 1 15:31:26 2026 -0700
    Add barChartReorder, a utility for changing the order of the bars in a barChart track, refs #37619 The bars of a barChart are drawn in the order their values appear in the expScores field, and nothing re-sorts them when the track is drawn, so the order is a property of the data file. Putting the bars in a different order means rewriting that field in every row, which is awkward enough by hand that we have twice done it for a data author instead of explaining it. This has come up on #36998 and #37001. barChartReorder takes the current bar order and the wanted order as two lists of names, rewrites expScores in every row, optionally puts a .categories file into the same order, and prints the barChartBars line for the track. It works on any barChart BED whatever produced it, so unlike the --groupOrderFile option of expMatrixToBarchartBed it does not assume the file was built here from an expression matrix. A bigBarChart is handled by converting it with bigBedToBed and rebuilding it afterwards, which the usage message spells out. It refuses to write a half-correct file: the two orders must name the same bars, every row must hold as many values as there are names, and a .categories file must have a row for each bar. Listed in USER_APP_SCRIPTS so it reaches hgdownload, and in the no-argument branch of mkREADME.sh so the README picks up its usage message rather than the argparse error that -verbose=2 would produce. Its tests are also wired into the test target directly. testAll iterates ALL_APPS, which does not include USER_APP_SCRIPTS, so none of these programs' tests have ever been reachable from "make test" - that is why the suite sitting next to expMatrixToBarchartBed never reported it was broken. The makefile already keeps a short list of directories testAll cannot reach, and this adds two more to it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/barChartReorder/tests/in/test.categories
  • lines changed 5, context: html, text, full: html, text
    d87ef2fb8472135b899fd1a89434033d5895217a Thu Oct 1 15:31:26 2026 -0700
    Add barChartReorder, a utility for changing the order of the bars in a barChart track, refs #37619 The bars of a barChart are drawn in the order their values appear in the expScores field, and nothing re-sorts them when the track is drawn, so the order is a property of the data file. Putting the bars in a different order means rewriting that field in every row, which is awkward enough by hand that we have twice done it for a data author instead of explaining it. This has come up on #36998 and #37001. barChartReorder takes the current bar order and the wanted order as two lists of names, rewrites expScores in every row, optionally puts a .categories file into the same order, and prints the barChartBars line for the track. It works on any barChart BED whatever produced it, so unlike the --groupOrderFile option of expMatrixToBarchartBed it does not assume the file was built here from an expression matrix. A bigBarChart is handled by converting it with bigBedToBed and rebuilding it afterwards, which the usage message spells out. It refuses to write a half-correct file: the two orders must name the same bars, every row must hold as many values as there are names, and a .categories file must have a row for each bar. Listed in USER_APP_SCRIPTS so it reaches hgdownload, and in the no-argument branch of mkREADME.sh so the README picks up its usage message rather than the argparse error that -verbose=2 would produce. Its tests are also wired into the test target directly. testAll iterates ALL_APPS, which does not include USER_APP_SCRIPTS, so none of these programs' tests have ever been reachable from "make test" - that is why the suite sitting next to expMatrixToBarchartBed never reported it was broken. The makefile already keeps a short list of directories testAll cannot reach, and this adds two more to it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/barChartReorder/tests/in/test.newOrder
  • lines changed 5, context: html, text, full: html, text
    d87ef2fb8472135b899fd1a89434033d5895217a Thu Oct 1 15:31:26 2026 -0700
    Add barChartReorder, a utility for changing the order of the bars in a barChart track, refs #37619 The bars of a barChart are drawn in the order their values appear in the expScores field, and nothing re-sorts them when the track is drawn, so the order is a property of the data file. Putting the bars in a different order means rewriting that field in every row, which is awkward enough by hand that we have twice done it for a data author instead of explaining it. This has come up on #36998 and #37001. barChartReorder takes the current bar order and the wanted order as two lists of names, rewrites expScores in every row, optionally puts a .categories file into the same order, and prints the barChartBars line for the track. It works on any barChart BED whatever produced it, so unlike the --groupOrderFile option of expMatrixToBarchartBed it does not assume the file was built here from an expression matrix. A bigBarChart is handled by converting it with bigBedToBed and rebuilding it afterwards, which the usage message spells out. It refuses to write a half-correct file: the two orders must name the same bars, every row must hold as many values as there are names, and a .categories file must have a row for each bar. Listed in USER_APP_SCRIPTS so it reaches hgdownload, and in the no-argument branch of mkREADME.sh so the README picks up its usage message rather than the argparse error that -verbose=2 would produce. Its tests are also wired into the test target directly. testAll iterates ALL_APPS, which does not include USER_APP_SCRIPTS, so none of these programs' tests have ever been reachable from "make test" - that is why the suite sitting next to expMatrixToBarchartBed never reported it was broken. The makefile already keeps a short list of directories testAll cannot reach, and this adds two more to it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/barChartReorder/tests/in/test.oldOrder
  • lines changed 5, context: html, text, full: html, text
    d87ef2fb8472135b899fd1a89434033d5895217a Thu Oct 1 15:31:26 2026 -0700
    Add barChartReorder, a utility for changing the order of the bars in a barChart track, refs #37619 The bars of a barChart are drawn in the order their values appear in the expScores field, and nothing re-sorts them when the track is drawn, so the order is a property of the data file. Putting the bars in a different order means rewriting that field in every row, which is awkward enough by hand that we have twice done it for a data author instead of explaining it. This has come up on #36998 and #37001. barChartReorder takes the current bar order and the wanted order as two lists of names, rewrites expScores in every row, optionally puts a .categories file into the same order, and prints the barChartBars line for the track. It works on any barChart BED whatever produced it, so unlike the --groupOrderFile option of expMatrixToBarchartBed it does not assume the file was built here from an expression matrix. A bigBarChart is handled by converting it with bigBedToBed and rebuilding it afterwards, which the usage message spells out. It refuses to write a half-correct file: the two orders must name the same bars, every row must hold as many values as there are names, and a .categories file must have a row for each bar. Listed in USER_APP_SCRIPTS so it reaches hgdownload, and in the no-argument branch of mkREADME.sh so the README picks up its usage message rather than the argparse error that -verbose=2 would produce. Its tests are also wired into the test target directly. testAll iterates ALL_APPS, which does not include USER_APP_SCRIPTS, so none of these programs' tests have ever been reachable from "make test" - that is why the suite sitting next to expMatrixToBarchartBed never reported it was broken. The makefile already keeps a short list of directories testAll cannot reach, and this adds two more to it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/barChartReorder/tests/makefile
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    d87ef2fb8472135b899fd1a89434033d5895217a Thu Oct 1 15:31:26 2026 -0700
    Add barChartReorder, a utility for changing the order of the bars in a barChart track, refs #37619 The bars of a barChart are drawn in the order their values appear in the expScores field, and nothing re-sorts them when the track is drawn, so the order is a property of the data file. Putting the bars in a different order means rewriting that field in every row, which is awkward enough by hand that we have twice done it for a data author instead of explaining it. This has come up on #36998 and #37001. barChartReorder takes the current bar order and the wanted order as two lists of names, rewrites expScores in every row, optionally puts a .categories file into the same order, and prints the barChartBars line for the track. It works on any barChart BED whatever produced it, so unlike the --groupOrderFile option of expMatrixToBarchartBed it does not assume the file was built here from an expression matrix. A bigBarChart is handled by converting it with bigBedToBed and rebuilding it afterwards, which the usage message spells out. It refuses to write a half-correct file: the two orders must name the same bars, every row must hold as many values as there are names, and a .categories file must have a row for each bar. Listed in USER_APP_SCRIPTS so it reaches hgdownload, and in the no-argument branch of mkREADME.sh so the README picks up its usage message rather than the argparse error that -verbose=2 would produce. Its tests are also wired into the test target directly. testAll iterates ALL_APPS, which does not include USER_APP_SCRIPTS, so none of these programs' tests have ever been reachable from "make test" - that is why the suite sitting next to expMatrixToBarchartBed never reported it was broken. The makefile already keeps a short list of directories testAll cannot reach, and this adds two more to it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed
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    d2a7668073c78b3ed86ee6e23beebd6dac702640 Thu Oct 1 15:30:45 2026 -0700
    Fix expMatrixToBarchartBed, which has aborted on every run since the python3 port, refs #37619 The port in 9ec8ecc35be left three things behind: - median() and the tpmCutoffs block use / where they index a list. Under python2 those were integer divisions; under python3 they are floats, so both the default median path and --useMean abort with a TypeError. - Every NamedTemporaryFile lost its bufsize=1, but two of them are read by name through os.system while python still holds the buffer. Small inputs came out as a header line with no data rows. Restored the original line-buffered behaviour with an explicit flush before each read. The six tests in tests/ would have caught this on the first run, but nothing reaches them: testAll in src/utils/makefile iterates ALL_APPS, and USER_APP_SCRIPTS is not part of it. They also invoked the bare program name, which PATH resolves to the installed copy rather than the one in the tree, so they were testing the shipped binary. They now run ../expMatrixToBarchartBed. The makefile wiring that makes them run at all comes with barChartReorder. Two columns of the expected output needed regenerating, neither of them because of this fix: - _lineLength is one smaller throughout. bedJoinTabOffset was rewritten in C in 46dc535d3f5 and measures the line without its trailing newline. This is harmless, since hgc reads _dataLen bytes and then chopByWhite's, and the comment in getSampleValsFromFile says so. Confirmed that every offset and length still lands on its own matrix row. - score moves by one 111-wide bucket on rows whose value sits exactly on one of the nine cutoffs. The value reaches an intermediate file through str() and comes back through float(). python2's str() kept 12 significant digits, so such a row compared as strictly less than its own cutoff and fell a bucket; python3 round trips exactly. It affects about six rows whatever the size of the dataset, since there are only nine cutoffs, and never by more than one bucket. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/expMatrixToBarchartBed/tests/allOptions.output
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    d2a7668073c78b3ed86ee6e23beebd6dac702640 Thu Oct 1 15:30:45 2026 -0700
    Fix expMatrixToBarchartBed, which has aborted on every run since the python3 port, refs #37619 The port in 9ec8ecc35be left three things behind: - median() and the tpmCutoffs block use / where they index a list. Under python2 those were integer divisions; under python3 they are floats, so both the default median path and --useMean abort with a TypeError. - Every NamedTemporaryFile lost its bufsize=1, but two of them are read by name through os.system while python still holds the buffer. Small inputs came out as a header line with no data rows. Restored the original line-buffered behaviour with an explicit flush before each read. The six tests in tests/ would have caught this on the first run, but nothing reaches them: testAll in src/utils/makefile iterates ALL_APPS, and USER_APP_SCRIPTS is not part of it. They also invoked the bare program name, which PATH resolves to the installed copy rather than the one in the tree, so they were testing the shipped binary. They now run ../expMatrixToBarchartBed. The makefile wiring that makes them run at all comes with barChartReorder. Two columns of the expected output needed regenerating, neither of them because of this fix: - _lineLength is one smaller throughout. bedJoinTabOffset was rewritten in C in 46dc535d3f5 and measures the line without its trailing newline. This is harmless, since hgc reads _dataLen bytes and then chopByWhite's, and the comment in getSampleValsFromFile says so. Confirmed that every offset and length still lands on its own matrix row. - score moves by one 111-wide bucket on rows whose value sits exactly on one of the nine cutoffs. The value reaches an intermediate file through str() and comes back through float(). python2's str() kept 12 significant digits, so such a row compared as strictly less than its own cutoff and fell a bucket; python3 round trips exactly. It affects about six rows whatever the size of the dataset, since there are only nine cutoffs, and never by more than one bucket. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/expMatrixToBarchartBed/tests/allOptions2.output
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    d2a7668073c78b3ed86ee6e23beebd6dac702640 Thu Oct 1 15:30:45 2026 -0700
    Fix expMatrixToBarchartBed, which has aborted on every run since the python3 port, refs #37619 The port in 9ec8ecc35be left three things behind: - median() and the tpmCutoffs block use / where they index a list. Under python2 those were integer divisions; under python3 they are floats, so both the default median path and --useMean abort with a TypeError. - Every NamedTemporaryFile lost its bufsize=1, but two of them are read by name through os.system while python still holds the buffer. Small inputs came out as a header line with no data rows. Restored the original line-buffered behaviour with an explicit flush before each read. The six tests in tests/ would have caught this on the first run, but nothing reaches them: testAll in src/utils/makefile iterates ALL_APPS, and USER_APP_SCRIPTS is not part of it. They also invoked the bare program name, which PATH resolves to the installed copy rather than the one in the tree, so they were testing the shipped binary. They now run ../expMatrixToBarchartBed. The makefile wiring that makes them run at all comes with barChartReorder. Two columns of the expected output needed regenerating, neither of them because of this fix: - _lineLength is one smaller throughout. bedJoinTabOffset was rewritten in C in 46dc535d3f5 and measures the line without its trailing newline. This is harmless, since hgc reads _dataLen bytes and then chopByWhite's, and the comment in getSampleValsFromFile says so. Confirmed that every offset and length still lands on its own matrix row. - score moves by one 111-wide bucket on rows whose value sits exactly on one of the nine cutoffs. The value reaches an intermediate file through str() and comes back through float(). python2's str() kept 12 significant digits, so such a row compared as strictly less than its own cutoff and fell a bucket; python3 round trips exactly. It affects about six rows whatever the size of the dataset, since there are only nine cutoffs, and never by more than one bucket. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/expMatrixToBarchartBed/tests/extraFields.output
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    d2a7668073c78b3ed86ee6e23beebd6dac702640 Thu Oct 1 15:30:45 2026 -0700
    Fix expMatrixToBarchartBed, which has aborted on every run since the python3 port, refs #37619 The port in 9ec8ecc35be left three things behind: - median() and the tpmCutoffs block use / where they index a list. Under python2 those were integer divisions; under python3 they are floats, so both the default median path and --useMean abort with a TypeError. - Every NamedTemporaryFile lost its bufsize=1, but two of them are read by name through os.system while python still holds the buffer. Small inputs came out as a header line with no data rows. Restored the original line-buffered behaviour with an explicit flush before each read. The six tests in tests/ would have caught this on the first run, but nothing reaches them: testAll in src/utils/makefile iterates ALL_APPS, and USER_APP_SCRIPTS is not part of it. They also invoked the bare program name, which PATH resolves to the installed copy rather than the one in the tree, so they were testing the shipped binary. They now run ../expMatrixToBarchartBed. The makefile wiring that makes them run at all comes with barChartReorder. Two columns of the expected output needed regenerating, neither of them because of this fix: - _lineLength is one smaller throughout. bedJoinTabOffset was rewritten in C in 46dc535d3f5 and measures the line without its trailing newline. This is harmless, since hgc reads _dataLen bytes and then chopByWhite's, and the comment in getSampleValsFromFile says so. Confirmed that every offset and length still lands on its own matrix row. - score moves by one 111-wide bucket on rows whose value sits exactly on one of the nine cutoffs. The value reaches an intermediate file through str() and comes back through float(). python2's str() kept 12 significant digits, so such a row compared as strictly less than its own cutoff and fell a bucket; python3 round trips exactly. It affects about six rows whatever the size of the dataset, since there are only nine cutoffs, and never by more than one bucket. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/expMatrixToBarchartBed/tests/floats.output
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    d2a7668073c78b3ed86ee6e23beebd6dac702640 Thu Oct 1 15:30:45 2026 -0700
    Fix expMatrixToBarchartBed, which has aborted on every run since the python3 port, refs #37619 The port in 9ec8ecc35be left three things behind: - median() and the tpmCutoffs block use / where they index a list. Under python2 those were integer divisions; under python3 they are floats, so both the default median path and --useMean abort with a TypeError. - Every NamedTemporaryFile lost its bufsize=1, but two of them are read by name through os.system while python still holds the buffer. Small inputs came out as a header line with no data rows. Restored the original line-buffered behaviour with an explicit flush before each read. The six tests in tests/ would have caught this on the first run, but nothing reaches them: testAll in src/utils/makefile iterates ALL_APPS, and USER_APP_SCRIPTS is not part of it. They also invoked the bare program name, which PATH resolves to the installed copy rather than the one in the tree, so they were testing the shipped binary. They now run ../expMatrixToBarchartBed. The makefile wiring that makes them run at all comes with barChartReorder. Two columns of the expected output needed regenerating, neither of them because of this fix: - _lineLength is one smaller throughout. bedJoinTabOffset was rewritten in C in 46dc535d3f5 and measures the line without its trailing newline. This is harmless, since hgc reads _dataLen bytes and then chopByWhite's, and the comment in getSampleValsFromFile says so. Confirmed that every offset and length still lands on its own matrix row. - score moves by one 111-wide bucket on rows whose value sits exactly on one of the nine cutoffs. The value reaches an intermediate file through str() and comes back through float(). python2's str() kept 12 significant digits, so such a row compared as strictly less than its own cutoff and fell a bucket; python3 round trips exactly. It affects about six rows whatever the size of the dataset, since there are only nine cutoffs, and never by more than one bucket. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/expMatrixToBarchartBed/tests/makefile
  • lines changed 8, context: html, text, full: html, text
    d2a7668073c78b3ed86ee6e23beebd6dac702640 Thu Oct 1 15:30:45 2026 -0700
    Fix expMatrixToBarchartBed, which has aborted on every run since the python3 port, refs #37619 The port in 9ec8ecc35be left three things behind: - median() and the tpmCutoffs block use / where they index a list. Under python2 those were integer divisions; under python3 they are floats, so both the default median path and --useMean abort with a TypeError. - Every NamedTemporaryFile lost its bufsize=1, but two of them are read by name through os.system while python still holds the buffer. Small inputs came out as a header line with no data rows. Restored the original line-buffered behaviour with an explicit flush before each read. The six tests in tests/ would have caught this on the first run, but nothing reaches them: testAll in src/utils/makefile iterates ALL_APPS, and USER_APP_SCRIPTS is not part of it. They also invoked the bare program name, which PATH resolves to the installed copy rather than the one in the tree, so they were testing the shipped binary. They now run ../expMatrixToBarchartBed. The makefile wiring that makes them run at all comes with barChartReorder. Two columns of the expected output needed regenerating, neither of them because of this fix: - _lineLength is one smaller throughout. bedJoinTabOffset was rewritten in C in 46dc535d3f5 and measures the line without its trailing newline. This is harmless, since hgc reads _dataLen bytes and then chopByWhite's, and the comment in getSampleValsFromFile says so. Confirmed that every offset and length still lands on its own matrix row. - score moves by one 111-wide bucket on rows whose value sits exactly on one of the nine cutoffs. The value reaches an intermediate file through str() and comes back through float(). python2's str() kept 12 significant digits, so such a row compared as strictly less than its own cutoff and fell a bucket; python3 round trips exactly. It affects about six rows whatever the size of the dataset, since there are only nine cutoffs, and never by more than one bucket. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/expMatrixToBarchartBed/tests/test.output
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    d2a7668073c78b3ed86ee6e23beebd6dac702640 Thu Oct 1 15:30:45 2026 -0700
    Fix expMatrixToBarchartBed, which has aborted on every run since the python3 port, refs #37619 The port in 9ec8ecc35be left three things behind: - median() and the tpmCutoffs block use / where they index a list. Under python2 those were integer divisions; under python3 they are floats, so both the default median path and --useMean abort with a TypeError. - Every NamedTemporaryFile lost its bufsize=1, but two of them are read by name through os.system while python still holds the buffer. Small inputs came out as a header line with no data rows. Restored the original line-buffered behaviour with an explicit flush before each read. The six tests in tests/ would have caught this on the first run, but nothing reaches them: testAll in src/utils/makefile iterates ALL_APPS, and USER_APP_SCRIPTS is not part of it. They also invoked the bare program name, which PATH resolves to the installed copy rather than the one in the tree, so they were testing the shipped binary. They now run ../expMatrixToBarchartBed. The makefile wiring that makes them run at all comes with barChartReorder. Two columns of the expected output needed regenerating, neither of them because of this fix: - _lineLength is one smaller throughout. bedJoinTabOffset was rewritten in C in 46dc535d3f5 and measures the line without its trailing newline. This is harmless, since hgc reads _dataLen bytes and then chopByWhite's, and the comment in getSampleValsFromFile says so. Confirmed that every offset and length still lands on its own matrix row. - score moves by one 111-wide bucket on rows whose value sits exactly on one of the nine cutoffs. The value reaches an intermediate file through str() and comes back through float(). python2's str() kept 12 significant digits, so such a row compared as strictly less than its own cutoff and fell a bucket; python3 round trips exactly. It affects about six rows whatever the size of the dataset, since there are only nine cutoffs, and never by more than one bucket. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/expMatrixToBarchartBed/tests/test.output2
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    d2a7668073c78b3ed86ee6e23beebd6dac702640 Thu Oct 1 15:30:45 2026 -0700
    Fix expMatrixToBarchartBed, which has aborted on every run since the python3 port, refs #37619 The port in 9ec8ecc35be left three things behind: - median() and the tpmCutoffs block use / where they index a list. Under python2 those were integer divisions; under python3 they are floats, so both the default median path and --useMean abort with a TypeError. - Every NamedTemporaryFile lost its bufsize=1, but two of them are read by name through os.system while python still holds the buffer. Small inputs came out as a header line with no data rows. Restored the original line-buffered behaviour with an explicit flush before each read. The six tests in tests/ would have caught this on the first run, but nothing reaches them: testAll in src/utils/makefile iterates ALL_APPS, and USER_APP_SCRIPTS is not part of it. They also invoked the bare program name, which PATH resolves to the installed copy rather than the one in the tree, so they were testing the shipped binary. They now run ../expMatrixToBarchartBed. The makefile wiring that makes them run at all comes with barChartReorder. Two columns of the expected output needed regenerating, neither of them because of this fix: - _lineLength is one smaller throughout. bedJoinTabOffset was rewritten in C in 46dc535d3f5 and measures the line without its trailing newline. This is harmless, since hgc reads _dataLen bytes and then chopByWhite's, and the comment in getSampleValsFromFile says so. Confirmed that every offset and length still lands on its own matrix row. - score moves by one 111-wide bucket on rows whose value sits exactly on one of the nine cutoffs. The value reaches an intermediate file through str() and comes back through float(). python2's str() kept 12 significant digits, so such a row compared as strictly less than its own cutoff and fell a bucket; python3 round trips exactly. It affects about six rows whatever the size of the dataset, since there are only nine cutoffs, and never by more than one bucket. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/makefile
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    8331ea06f434b295c7b5383bc1e64f3f4a371387 Thu Sep 24 16:01:29 2026 -0700
    adding pafToPsl to userApps output refs #34360
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    d87ef2fb8472135b899fd1a89434033d5895217a Thu Oct 1 15:31:26 2026 -0700
    Add barChartReorder, a utility for changing the order of the bars in a barChart track, refs #37619 The bars of a barChart are drawn in the order their values appear in the expScores field, and nothing re-sorts them when the track is drawn, so the order is a property of the data file. Putting the bars in a different order means rewriting that field in every row, which is awkward enough by hand that we have twice done it for a data author instead of explaining it. This has come up on #36998 and #37001. barChartReorder takes the current bar order and the wanted order as two lists of names, rewrites expScores in every row, optionally puts a .categories file into the same order, and prints the barChartBars line for the track. It works on any barChart BED whatever produced it, so unlike the --groupOrderFile option of expMatrixToBarchartBed it does not assume the file was built here from an expression matrix. A bigBarChart is handled by converting it with bigBedToBed and rebuilding it afterwards, which the usage message spells out. It refuses to write a half-correct file: the two orders must name the same bars, every row must hold as many values as there are names, and a .categories file must have a row for each bar. Listed in USER_APP_SCRIPTS so it reaches hgdownload, and in the no-argument branch of mkREADME.sh so the README picks up its usage message rather than the argparse error that -verbose=2 would produce. Its tests are also wired into the test target directly. testAll iterates ALL_APPS, which does not include USER_APP_SCRIPTS, so none of these programs' tests have ever been reachable from "make test" - that is why the suite sitting next to expMatrixToBarchartBed never reported it was broken. The makefile already keeps a short list of directories testAll cannot reach, and this adds two more to it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/pafToPsl/makefile
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    b269cf8292be3c573bb92058fbd6a3df5cf385c9 Thu Sep 24 15:44:03 2026 -0700
    translation of Chenxi Zhou code from Gene Myers FASTGA PAFtoPSL.c code to kent C code refs #34360
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    1e49359da6689c022a312353f97af28d161802c3 Thu Sep 24 15:54:15 2026 -0700
    add test target refs #34360
• src/utils/pafToPsl/pafToPsl.c
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    b269cf8292be3c573bb92058fbd6a3df5cf385c9 Thu Sep 24 15:44:03 2026 -0700
    translation of Chenxi Zhou code from Gene Myers FASTGA PAFtoPSL.c code to kent C code refs #34360
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    13324df7d810e3cd1d64d93e8f83de7f7611e473 Fri Sep 25 18:55:52 2026 -0700
    claude found and error in the code and added a test for the bug refs #34360
• src/utils/pafToPsl/tests/expected/hg38ChrMt.psl
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    0137e8b20a8d122324fcaa984c882ade51bd41f1 Thu Sep 24 15:53:48 2026 -0700
    test for pafToPsl command refs #34360
• src/utils/pafToPsl/tests/expected/indelEdges.psl
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    13324df7d810e3cd1d64d93e8f83de7f7611e473 Fri Sep 25 18:55:52 2026 -0700
    claude found and error in the code and added a test for the bug refs #34360
• src/utils/pafToPsl/tests/input/hg38ChrMt.paf
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    0137e8b20a8d122324fcaa984c882ade51bd41f1 Thu Sep 24 15:53:48 2026 -0700
    test for pafToPsl command refs #34360
• src/utils/pafToPsl/tests/input/indelEdges.paf
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    13324df7d810e3cd1d64d93e8f83de7f7611e473 Fri Sep 25 18:55:52 2026 -0700
    claude found and error in the code and added a test for the bug refs #34360
• src/utils/pafToPsl/tests/makefile
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    0137e8b20a8d122324fcaa984c882ade51bd41f1 Thu Sep 24 15:53:48 2026 -0700
    test for pafToPsl command refs #34360
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    d6c5f9d4c46a1be9fc24bc548052232560710faf Fri Sep 25 18:58:33 2026 -0700
    claude found and error in the code and added a test for the bug refs #34360
• src/utils/qa/qaTestScript.py
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    2ec957f2ac313ee21abfb3724042d681f5774eba Thu Sep 24 16:32:50 2026 -0700
    Updating the hgBlat all genomes checkbox locator to work on both the classic and new BLAT pages, No RM
• src/utils/qa/weeklybld/buildEnv.csh
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    affd45994680abc5a5b4fbbeeacda1c0047ec63e Mon Oct 5 10:00:26 2026 -0700
    v505 preview1 (automated)
• src/utils/qa/weeklybld/trackCheckRobot.py
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    27ded228b74091b4d9bf1bccfcc98b11eac32483 Mon Sep 28 15:04:56 2026 -0700
    trackCheckRobot: skip hub-backed assemblies and wait longer for slow pages, refs #37424 The robot lists tracks from each assembly's MySQL trackDb table. Hub-backed assemblies (dbDb nibPath "hub:...") have no such table, so 17 GenArk assemblies failed with "Unknown database" every week. They are now left out. The 30 second timeout was too short for seven tracks that fail every release. The wuhCor1 phylogenetic tree tracks take about 40 seconds in hgTracks. The hg38 470-way and 241-way alignment details pages take 2 to 6 minutes in hgc. hgTracks requests now wait 120 seconds and hgc requests wait 600 seconds.
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    fed2e9c1d310026a998c2212a2e2508670a16373 Mon Sep 28 15:16:04 2026 -0700
    trackCheckRobot: probe faceted subtracks again, keep hub-backed dbs that have tables, show HGERROR text, refs #37424 Since #37662 a subtrack of a faceted composite can no longer override its hidden ancestors, so "<subtrack>=full" after hideAll drew nothing. hg38 fell from 19608 checked tracks to 9927, and mm10 from 8095 to 6182. For those subtracks the robot now sets the parent composite and superTrack to full and adds <subtrack>_sel=1. The other default-selected subtracks draw too, so only hgc links with g=<subtrack> are kept. The hub-backed skip also dropped hs1, rn8 and mpxvRivers. They have a "hub:" nibPath but also a MySQL database, and they were checked before. Only hub-backed assemblies without a database are skipped now. HGERROR lines now include the message from the page, for example "No chainAnoCar1 track in database hg38 for chr7". Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
• src/utils/redmineCli
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    67cf0a3977040d7f607149d36479886e3e9d12a3 Mon Sep 21 17:24:39 2026 -0700
    redmineCli: let a comment say who wrote it. No RM. A comment Claude posts carries a "From Claude:" line, which is wrong when the words are the developer's own and Claude only sent them. The comment subcommand takes --written-by NAME now, and writes "Written by NAME, posted by Claude:" instead. With no NAME it reads the name off the API key. prepend_attribution recognises both lines, so text that already begins with either one is posted unchanged, and a draft file can carry its own header.
• src/utils/testRegistry/README
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    b1a4f0619269b4c813036fc592c97471de310515 Sun Sep 20 17:53:28 2026 -0700
    registry: hold every v504 ticket, including the ones a unit test is wrong for The table held only the tickets that want a unit test, 37 of the release's 66. That cannot answer "how much of v504 is tested", because the 29 it left out are indistinguishable from tickets nobody has looked at: both are absent. So all 66 are here now, and the 29 carry a new why, "page" -- what changed is what a page says or does, so the docent suite is the right test and no unit test is wanted. Each says what changed and where the fix is, so the claim is checkable rather than asserted; "this one does not need a unit test" was a judgement living in one head, and now it is a row somebody can argue with. A page row may not name a unit test, which check enforces. `needed` leaves them out, since they are not waiting for anything. `unwatched` does not: a ticket with no test of any kind is worth seeing whichever kind it should have had, and that list is 19 now rather than 4 -- the four blocked ones plus fifteen that nothing watches and nobody had recorded. refs #38391
• src/utils/testRegistry/registry.tsv
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    e0002dfd343ef6768b23d4ae4e54ed88f2553669 Sun Sep 20 14:39:55 2026 -0700
    registry: three tickets now have docent scripts rm38086, rm38253 and rm38317 landed on #38252 this morning, from this registry's own list of tickets that nothing was watching. Their rows said there was no docent script, which stopped being true. The check written yesterday for exactly this found all three on its first day, by name, without anybody thinking to look. That is what the "-" half of the docent column is for. The unwatched list is four now, not seven. refs #38391, refs #38252
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    b1a4f0619269b4c813036fc592c97471de310515 Sun Sep 20 17:53:28 2026 -0700
    registry: hold every v504 ticket, including the ones a unit test is wrong for The table held only the tickets that want a unit test, 37 of the release's 66. That cannot answer "how much of v504 is tested", because the 29 it left out are indistinguishable from tickets nobody has looked at: both are absent. So all 66 are here now, and the 29 carry a new why, "page" -- what changed is what a page says or does, so the docent suite is the right test and no unit test is wanted. Each says what changed and where the fix is, so the claim is checkable rather than asserted; "this one does not need a unit test" was a judgement living in one head, and now it is a row somebody can argue with. A page row may not name a unit test, which check enforces. `needed` leaves them out, since they are not waiting for anything. `unwatched` does not: a ticket with no test of any kind is worth seeing whichever kind it should have had, and that list is 19 now rather than 4 -- the four blocked ones plus fifteen that nothing watches and nobody had recorded. refs #38391
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    a9054011188cb975a65a7d9767096a0ffdceb366 Mon Sep 21 17:34:46 2026 -0700
    netSlurpMaxTest: cover the response size ceiling, refs #38359 The fix this defends changes nothing on any page. Its only caller is the hgTablesTest robot, and the failure it prevents is the process exiting from inside carefulAlloc with nothing written to the log, so a unit test is the only test there can be. Four parts. netSlurpFileMax on a plain file, both sides of the boundary, including a ceiling exactly at the file size, which has to read it. The same calls under pushCarefulMemHandler, where carefulTotalAllocated() says whether the abandoned buffer was really freed: a buffer left behind would stay counted against the ceiling and the cap would buy one oversized page and no more. A matched pair of forked children on a file past the allocator ceiling, one read capped and one not, since exit(1) from inside the allocator cannot be seen any other way. And htmlPageSetMaxSize reaching htmlSlurpWithCookies against a server on the loopback interface, because the ceiling travels through a module-wide static and that wiring can rot with no caller changing. Backed the fix out three ways and watched each go red for its own reason. Removing the size check fails 9 of the 18 assertions. Keeping the check and dropping only the dyStringFree fails 3, and only the three that count allocation. Reverting htmlSlurpWithCookies to a plain netSlurpFile fails 2, and only the two that reach through htmlPage. Recorded as sandbox-ab. The registry row carries "-" for the release: the ticket has no target version.
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    ac540bf096a2398161cc910bf4fd965541469e06 Fri Sep 25 08:47:53 2026 -0700
    registry: 38311 now has a docent script, fixes the nightly make test rot check, refs #38391
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    4ac2738c397a05c257e089715017f76c619b2634 Sat Sep 26 12:12:14 2026 -0700
    testRegistry: rows for #37617, #37618, #38226, #38398 and #38414, refs #38391
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    99eb74885ff5bce42cadafee93274df7039dcab5 Sat Sep 26 17:34:11 2026 -0700
    unit tests for four v503 tickets, refs #38391, #37262, #38120, #38107, #38125, #38154 cgiDecodeTest prints what malformed and cut-short %hh escapes decode to, and checks that cgiDecode never reads past the length it is given. udcDotsTest prints the cache directory udc makes for remote URLs with "." and ".." in them, including the ones that must abort. pngWriteTest writes a memGfx image as a PNG, reads it back with libpng, compares every pixel, and checks the row filter of every row. pgSnpManyAllelesTester builds per-allele counts from a VCF record with 150 ALT alleles. Each test fails with its fix backed out, except that zlib-ng was not swapped out for #38125. The test registry gets a row for each ticket.
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    d5dd2e676327434c209118ba222b50d1b4ef3b00 Sat Sep 26 17:58:10 2026 -0700
    registry: #38120 and #38154 now have docent scripts, so testRegistry check passes again, refs #38391, #38252
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    da449b4fe2039f200a2f93d5209c48fe98c0a534 Tue Sep 29 10:58:30 2026 -0700
    cartPcrVarTester: which hgPcrResult_ cart variables survive a cart load, refs #38442 Feeds hgPcrResult_ variables through cartParseOverHash() and says which are kept. With the cart.c fix backed out it shows hgPcrResult_imgOrd dropped and nothing else changes. Registry row and catalog note added.
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    f3bec731c93f26f8f1984fd727c6ee55ebf99f85 Tue Sep 29 13:00:12 2026 -0700
    docent regression scripts for three v505 tickets, and registry updates, refs #37617, #37618, #38442, #38249, #38252 rm37617 checks that filter.AF on a VCF INFO field hides the variants below the trackDb minimum, and rm37618 that colorByInfo colors each item by its INFO value. Both use a four-variant fixture hub, docentFixtures/rm37617. rm38442 runs the ticket's PCR search, sets the places a drag saves, and checks that the PCR track keeps its place after a zoom. All three fail on hgwbeta (v504) and pass on genome-test. registry.tsv names the three scripts, adds a row for #38387, and raises the #38249 quickLiftTester row to sandbox-ab: backing out either quickLift fix by hand turns the test red.
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    27e27b2c53090276a82fa8a4a8ae89f8db288263 Tue Sep 29 14:13:18 2026 -0700
    docent rm38198 release-ab proof line, and registry rows for #38428 and #38430, refs #38198, #38428, #38430, #38252 rm38198's container reopen section fails on hgwbeta (v504, which lacks dba11b63364) and passes on genome-test. htmlSanitizeTest goes red when the svg allowlist of 7a356d85dba is backed out by hand, so #38428 gets a sandbox-ab row. #38430 gets a page row with no test yet. Both changes sit behind the hubHtmlSanitize gate.
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    49e53454d32ce13f5af4ece42112423534102fdd Tue Sep 29 14:30:20 2026 -0700
    docent regression scripts for #38428 and #38430, and the #38387 registry note, refs #38428, #38430, #38387, #38252 rm38428 checks that a hub track's svg color legend survives the description filter and the script inside it does not. rm38430 checks that hgGateway filters a hub assembly's description page. Both need hubHtmlSanitize=on, and both fail on a v504_branch build with the gate on and pass on genome-test. Fixtures in docentFixtures/rm38428 and rm38430. The #38387 registry note records the docker QA instances: kent-tip, built after the fix, runs ft_min_word_len=3 and finds hs1; kent-beta, built before it, runs 4 and does not.
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    58fa228f2f91ae8c6a5c62109e904f57e1f9a66d Wed Sep 30 11:03:02 2026 -0700
    docent regression scripts for nineteen v504 tickets, and their registry rows Each script watches one v504 fix. Fourteen fail on v503 (ts park 38316) and pass on genome-test (release-ab). rm38313 and rm38393 are sandbox-ab, because no release predates their fix. rm37984, rm38233 and rm38384 are assertion-only; each header says why. The registry now names the script in the docent column for these tickets, and has new rows for #38157 and #38393. #38275 stays unwatched in the table: the script that watches it is rm37389, which is named for another ticket. refs #20824, #27988, #36292, #37595, #37621, #37929, #37984, #38157, #38192, #38197, #38233, #38254, #38264, #38273, #38313, #38323, #38372, #38384, #38393, #38252, #38391 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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    ebf73550fcb8e858388755a7d34541d510209bae Wed Sep 30 17:12:00 2026 -0700
    docent rm38456: a Save request without the share flag or the name, and its registry row, refs #38456 Three checks: a fresh cart with no share flag, a cart that still holds a stored share value while the request has none, and a request with no name. Committed as an xfail until the fix reaches genome-test. Each check was seen to fail on a build without its part of the fix.
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    f8a1b70516b4cb68471cf5fda1f25fe5a06e034e Thu Oct 1 07:04:33 2026 -0700
    docent rm38456: the fix reached genome-test, so the script is no longer an xfail, refs #38456 It failed on genome-test at check 1 before 35c5facfb9e arrived and passed there after the same day's make alpha. Renamed from rm38456.xfail.docent.yaml, with a server-flip proof line, and the registry row now names the new file.
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    fcc4da57b6aa6aabe40dce88cb8b67e4a5508aff Fri Oct 2 09:35:00 2026 -0700
    docent rm38462 xfail script for negateValues whiskers, and its registry row, refs #38462, #38252
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    fb5921dc918983ecc5182b1ef23a9fc64b556114 Fri Oct 2 10:00:42 2026 -0700
    docent rm38462 out of xfail after genome-test built the fix, refs #38462, #38252
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    bd1a1caa044f8b0e65d4f558831c83c1b8807d2e Sat Oct 3 17:02:05 2026 -0700
    docent rm38444: a db name with its own dbDb row stays that assembly instead of its asmAlias accession, and its registry row, refs #38444, #38252
• src/utils/testRegistry/testRegistry
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    b1a4f0619269b4c813036fc592c97471de310515 Sun Sep 20 17:53:28 2026 -0700
    registry: hold every v504 ticket, including the ones a unit test is wrong for The table held only the tickets that want a unit test, 37 of the release's 66. That cannot answer "how much of v504 is tested", because the 29 it left out are indistinguishable from tickets nobody has looked at: both are absent. So all 66 are here now, and the 29 carry a new why, "page" -- what changed is what a page says or does, so the docent suite is the right test and no unit test is wanted. Each says what changed and where the fix is, so the claim is checkable rather than asserted; "this one does not need a unit test" was a judgement living in one head, and now it is a row somebody can argue with. A page row may not name a unit test, which check enforces. `needed` leaves them out, since they are not waiting for anything. `unwatched` does not: a ticket with no test of any kind is worth seeing whichever kind it should have had, and that list is 19 now rather than 4 -- the four blocked ones plus fifteen that nothing watches and nobody had recorded. refs #38391
• src/utils/testRegistry/tests/expected/check.out
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    b1a4f0619269b4c813036fc592c97471de310515 Sun Sep 20 17:53:28 2026 -0700
    registry: hold every v504 ticket, including the ones a unit test is wrong for The table held only the tickets that want a unit test, 37 of the release's 66. That cannot answer "how much of v504 is tested", because the 29 it left out are indistinguishable from tickets nobody has looked at: both are absent. So all 66 are here now, and the 29 carry a new why, "page" -- what changed is what a page says or does, so the docent suite is the right test and no unit test is wanted. Each says what changed and where the fix is, so the claim is checkable rather than asserted; "this one does not need a unit test" was a judgement living in one head, and now it is a row somebody can argue with. A page row may not name a unit test, which check enforces. `needed` leaves them out, since they are not waiting for anything. `unwatched` does not: a ticket with no test of any kind is worth seeing whichever kind it should have had, and that list is 19 now rather than 4 -- the four blocked ones plus fifteen that nothing watches and nobody had recorded. refs #38391
• src/utils/testRegistry/tests/input/bad.tsv
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    b1a4f0619269b4c813036fc592c97471de310515 Sun Sep 20 17:53:28 2026 -0700
    registry: hold every v504 ticket, including the ones a unit test is wrong for The table held only the tickets that want a unit test, 37 of the release's 66. That cannot answer "how much of v504 is tested", because the 29 it left out are indistinguishable from tickets nobody has looked at: both are absent. So all 66 are here now, and the 29 carry a new why, "page" -- what changed is what a page says or does, so the docent suite is the right test and no unit test is wanted. Each says what changed and where the fix is, so the claim is checkable rather than asserted; "this one does not need a unit test" was a judgement living in one head, and now it is a row somebody can argue with. A page row may not name a unit test, which check enforces. `needed` leaves them out, since they are not waiting for anything. `unwatched` does not: a ticket with no test of any kind is worth seeing whichever kind it should have had, and that list is 19 now rather than 4 -- the four blocked ones plus fifteen that nothing watches and nobody had recorded. refs #38391
• src/utils/userApps/mkREADME.sh
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    d87ef2fb8472135b899fd1a89434033d5895217a Thu Oct 1 15:31:26 2026 -0700
    Add barChartReorder, a utility for changing the order of the bars in a barChart track, refs #37619 The bars of a barChart are drawn in the order their values appear in the expScores field, and nothing re-sorts them when the track is drawn, so the order is a property of the data file. Putting the bars in a different order means rewriting that field in every row, which is awkward enough by hand that we have twice done it for a data author instead of explaining it. This has come up on #36998 and #37001. barChartReorder takes the current bar order and the wanted order as two lists of names, rewrites expScores in every row, optionally puts a .categories file into the same order, and prints the barChartBars line for the track. It works on any barChart BED whatever produced it, so unlike the --groupOrderFile option of expMatrixToBarchartBed it does not assume the file was built here from an expression matrix. A bigBarChart is handled by converting it with bigBedToBed and rebuilding it afterwards, which the usage message spells out. It refuses to write a half-correct file: the two orders must name the same bars, every row must hold as many values as there are names, and a .categories file must have a row for each bar. Listed in USER_APP_SCRIPTS so it reaches hgdownload, and in the no-argument branch of mkREADME.sh so the README picks up its usage message rather than the argparse error that -verbose=2 would produce. Its tests are also wired into the test target directly. testAll iterates ALL_APPS, which does not include USER_APP_SCRIPTS, so none of these programs' tests have ever been reachable from "make test" - that is why the suite sitting next to expMatrixToBarchartBed never reported it was broken. The makefile already keeps a short list of directories testAll cannot reach, and this adds two more to it. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>