All File Changes

v498_base to v499_preview (2026-05-11 to 2026-05-18) v499

• .gitignore
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    9b1d1612efa7f321c5d3c500ce799c804c977135 Tue May 12 14:23:51 2026 -0700
    Add to .gitignore update LICENSE to remove htslib just note old htslib directory, not require removal
• .gitmodules
  • lines changed 3, context: html, text, full: html, text
    cc2c8b0181212e97d22db24fc67394f4c634656e Fri Apr 24 20:19:55 2026 -0700
    added htslib submodule
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    2ee9d8c7beac3731a5e835e14921ac4e4cae4f81 Sat Apr 25 11:24:01 2026 -0700
    Moved htslib to submodules/htslib. Removed use of local static shared libraries for libcurl, as UCSC copy is outdated. Add a script that is run to check for htslib submodules being initialized and do the initialization. It also checks for stale src/htslib files
• LICENSE
  • lines changed 8, context: html, text, full: html, text
    9b1d1612efa7f321c5d3c500ce799c804c977135 Tue May 12 14:23:51 2026 -0700
    Add to .gitignore update LICENSE to remove htslib just note old htslib directory, not require removal
• confs/hgwdev.hg.conf
  • lines changed 4, context: html, text, full: html, text
    a63ab731936f5d59015097ac4c46631b10839d26 Sun May 17 01:11:14 2026 -0700
    Installing updated hg.conf files from UCSC servers
• docs/browserSlideDecks.md
  • lines changed 33, context: html, text, full: html, text
    c0de63cd3138fe9fae00a2c57f87a83fd2e236c6 Wed May 13 14:16:41 2026 -0700
    Adding new page for stashing/embedding Genome Browser slide decks, refs #37292
• src/hg/cgilib/search.c
  • lines changed 1, context: html, text, full: html, text
    27f7309bec43391b3ee5370a6b6b3fb0be1e579f Wed May 13 23:33:54 2026 -0700
    Fixing an issue where a select and its parent td had the same name, so options in track search and file search were getting false counts of 0 applied. refs #37556
• src/hg/encode3/validateFiles/validateFiles.c
  • lines changed 1, context: html, text, full: html, text
    3a1b00734b0c19737b48b171decfeb6b9edd27aa Wed May 6 18:16:34 2026 -0700
    Fix issue with new htslib and access to tabix VCF header. Permanently enable tests that would have found this problem. They were disable by a non-extent USE_TABIX make vaiable.
• src/hg/hgCollection/hgCollection.c
  • lines changed 1, context: html, text, full: html, text
    347a829a0b6a74252991d638a3aa5616197a8069 Wed May 13 13:35:17 2026 -0700
    fix broken anchor link typo error
• src/hg/hgCustom/hgCustom.c
  • lines changed 2, context: html, text, full: html, text
    e7264355c83a0d0875b372b7ad26162adb363f6c Tue May 12 13:20:28 2026 -0700
    myVariants v1 follow-ups: CT edit gate, anon-user button gate, hgc duplicate link, item-name synthesis from ref/alt or HGVS, refs #33808
  • lines changed 20, context: html, text, full: html, text
    d7dd4f55e28699bb783563b8bece5bf23f392995 Wed May 13 11:07:57 2026 -0700
    Adds hg.conf myVariantsDataDir for writing ctfiles outside trash/, per-db short/long label rename on hgTrackUi, and a shared removal helper so the hgTrackUi remove button, hgTracks trash icon, and hgCustom checkbox all function the same, refs #33808
  • lines changed 5, context: html, text, full: html, text
    80ab15c036bf35894b59df383c03c51cbeff30be Thu May 14 10:29:53 2026 -0700
    Stop myVariants from clobbering regular custom tracks by giving it its own cart variable (mvCtfile_<db>) instead of overloading ctfile_<db>, refs #37553
• src/hg/hgTables/bam.c
  • lines changed 7, context: html, text, full: html, text
    1ff2e18ba5e50dd2d1becd3cd6a25343578c10b8 Tue Apr 21 14:09:04 2026 -0700
    rework of htslib/UDC integration to use htslib hfile driver mechanism
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 1, context: html, text, full: html, text
    ebfaebfd8dd3cdd58fd6f8261ef3fc4f84f9c0c6 Tue May 12 05:48:51 2026 -0700
    tiny change to link name on hgTrackUi page, tested with Andrea Tanzer and she did not understand what "Track Collection" could mean.
  • lines changed 28, context: html, text, full: html, text
    d121edc0bd2809f1d6de6185a497e6a288958479 Tue May 12 09:18:29 2026 -0700
    hgConvert quickLift: skip pre-lifted tracks, append-and-merge hub file, per-track remove UI, refs #37535 In hgConvert / trackHubBuild: - Skip tracks that already came from a quickLift hub (quickLiftUrl / quickLifted setting) so they don't get re-lifted to a new destination. - Append new track stanzas to an existing per-source hub file instead of overwriting it; new stanzas get priorities after the existing max; duplicate track names are skipped. Also avoids re-emitting a parent supertrack that's already in the file. New public quickLiftHubRemoveTrack(cart, sourceDb, trackName) in trackHub.c rewrites the per-source hub file with the named stanza removed plus all descendant stanzas (parent reference cascade, transitive). hgTrackUi: adds a "Remove from QuickLift" link next to "Duplicate track" for any tdb carrying a quickLiftDb setting. The link hits hgTrackUi_op=quickLiftRemove which calls quickLiftHubRemoveTrack, hides the track in the cart, and 302s to hgTracks. The op argument cart var is qlSourceDb (renamed from quickLiftSourceDb to avoid colliding with the quickLift.* prefix used elsewhere; values cloned out of the cart hash before cartRemove so the helper doesn't see freed strings). hgTracks: adds a small "x" icon (printQuickLiftDelIcon) on tracks in a quickLift group, suppressed on the synthetic bigQuickLiftChain track. JS onQuickLiftDelIconClick fires the same hgTrackUi_op endpoint via synchronous XHR and removes every TD whose icon matches the deleted data-track, so the row goes away in both the QuickLift group and the Visible Tracks group. hubConnect cart handling fixes shaken out by the above: - hubConnectRemakeTrackHubVar's cart-var prefix is now "quickLift." (with the trailing dot) instead of "quickLift", so unrelated keys like qlSourceDb no longer get parsed as hubId/db and crash cart loading on every CGI. Also skips entries whose hubStatus lookup returned NULL. - hubConnectStatusListFromCart no longer calls removeQuickListReference when the current db isn't the lift's destination. A side trip to another assembly between two lifts to the same destination was deleting the earlier attachment's cart var; just skip attaching this load and leave the cart alone so the lift survives the round trip. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • lines changed 5, context: html, text, full: html, text
    a5d8b47d899910abc483c0f15c7d47b4d119683f Tue May 12 10:43:30 2026 -0700
    Fetching supporting files was breaking when a broken hub was attached; switching to hubFromIdNoAbort. refs #36320
  • lines changed 2, context: html, text, full: html, text
    3d006a7244d91a9d72260986a5741a5aa65787dc Tue May 12 15:01:28 2026 -0700
    Widen 'jump to position' dialog after creating a myVariants item via hgvs. Remove 'update custom track' button from hgTrackUi for myVariants tracks. Fix item clicks not working after item name update in last commit, refs #33808
  • lines changed 19, context: html, text, full: html, text
    d7dd4f55e28699bb783563b8bece5bf23f392995 Wed May 13 11:07:57 2026 -0700
    Adds hg.conf myVariantsDataDir for writing ctfiles outside trash/, per-db short/long label rename on hgTrackUi, and a shared removal helper so the hgTrackUi remove button, hgTracks trash icon, and hgCustom checkbox all function the same, refs #33808
  • lines changed 1, context: html, text, full: html, text
    80ab15c036bf35894b59df383c03c51cbeff30be Thu May 14 10:29:53 2026 -0700
    Stop myVariants from clobbering regular custom tracks by giving it its own cart variable (mvCtfile_<db>) instead of overloading ctfile_<db>, refs #37553
• src/hg/hgTracks/bamTrack.c
  • lines changed 5, context: html, text, full: html, text
    1ff2e18ba5e50dd2d1becd3cd6a25343578c10b8 Tue Apr 21 14:09:04 2026 -0700
    rework of htslib/UDC integration to use htslib hfile driver mechanism
• src/hg/hgTracks/hgTracks.c
  • lines changed 25, context: html, text, full: html, text
    d121edc0bd2809f1d6de6185a497e6a288958479 Tue May 12 09:18:29 2026 -0700
    hgConvert quickLift: skip pre-lifted tracks, append-and-merge hub file, per-track remove UI, refs #37535 In hgConvert / trackHubBuild: - Skip tracks that already came from a quickLift hub (quickLiftUrl / quickLifted setting) so they don't get re-lifted to a new destination. - Append new track stanzas to an existing per-source hub file instead of overwriting it; new stanzas get priorities after the existing max; duplicate track names are skipped. Also avoids re-emitting a parent supertrack that's already in the file. New public quickLiftHubRemoveTrack(cart, sourceDb, trackName) in trackHub.c rewrites the per-source hub file with the named stanza removed plus all descendant stanzas (parent reference cascade, transitive). hgTrackUi: adds a "Remove from QuickLift" link next to "Duplicate track" for any tdb carrying a quickLiftDb setting. The link hits hgTrackUi_op=quickLiftRemove which calls quickLiftHubRemoveTrack, hides the track in the cart, and 302s to hgTracks. The op argument cart var is qlSourceDb (renamed from quickLiftSourceDb to avoid colliding with the quickLift.* prefix used elsewhere; values cloned out of the cart hash before cartRemove so the helper doesn't see freed strings). hgTracks: adds a small "x" icon (printQuickLiftDelIcon) on tracks in a quickLift group, suppressed on the synthetic bigQuickLiftChain track. JS onQuickLiftDelIconClick fires the same hgTrackUi_op endpoint via synchronous XHR and removes every TD whose icon matches the deleted data-track, so the row goes away in both the QuickLift group and the Visible Tracks group. hubConnect cart handling fixes shaken out by the above: - hubConnectRemakeTrackHubVar's cart-var prefix is now "quickLift." (with the trailing dot) instead of "quickLift", so unrelated keys like qlSourceDb no longer get parsed as hubId/db and crash cart loading on every CGI. Also skips entries whose hubStatus lookup returned NULL. - hubConnectStatusListFromCart no longer calls removeQuickListReference when the current db isn't the lift's destination. A side trip to another assembly between two lifts to the same destination was deleting the earlier attachment's cart var; just skip attaching this load and leave the cart alone so the lift survives the round trip. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    e7264355c83a0d0875b372b7ad26162adb363f6c Tue May 12 13:20:28 2026 -0700
    myVariants v1 follow-ups: CT edit gate, anon-user button gate, hgc duplicate link, item-name synthesis from ref/alt or HGVS, refs #33808
  • lines changed 1, context: html, text, full: html, text
    630eb30bc3695afcf73a19be6e3bc9a2829b365f Wed May 13 13:04:37 2026 -0700
    Make myVariants items bed12+ rather than bed9+, refs #33808
  • lines changed 7, context: html, text, full: html, text
    80ab15c036bf35894b59df383c03c51cbeff30be Thu May 14 10:29:53 2026 -0700
    Stop myVariants from clobbering regular custom tracks by giving it its own cart variable (mvCtfile_<db>) instead of overloading ctfile_<db>, refs #37553
• src/hg/hgTracks/myVariantsTrack.c
  • lines changed 7, context: html, text, full: html, text
    17fe5238421ff301f2b7360c96db92104e405094 Tue May 12 12:09:08 2026 -0700
    myVariants fixes: widen drag-select dialog a bit to fit the new button, save only the actual variant position, not the variant plus padding position when making a variant out of an hgvs term, refs #33808
  • lines changed 141, context: html, text, full: html, text
    e7264355c83a0d0875b372b7ad26162adb363f6c Tue May 12 13:20:28 2026 -0700
    myVariants v1 follow-ups: CT edit gate, anon-user button gate, hgc duplicate link, item-name synthesis from ref/alt or HGVS, refs #33808
  • lines changed 13, context: html, text, full: html, text
    3d006a7244d91a9d72260986a5741a5aa65787dc Tue May 12 15:01:28 2026 -0700
    Widen 'jump to position' dialog after creating a myVariants item via hgvs. Remove 'update custom track' button from hgTrackUi for myVariants tracks. Fix item clicks not working after item name update in last commit, refs #33808
  • lines changed 209, context: html, text, full: html, text
    630eb30bc3695afcf73a19be6e3bc9a2829b365f Wed May 13 13:04:37 2026 -0700
    Make myVariants items bed12+ rather than bed9+, refs #33808
  • lines changed 6, context: html, text, full: html, text
    80ab15c036bf35894b59df383c03c51cbeff30be Thu May 14 10:29:53 2026 -0700
    Stop myVariants from clobbering regular custom tracks by giving it its own cart variable (mvCtfile_<db>) instead of overloading ctfile_<db>, refs #37553
• src/hg/hgTracks/simpleTracks.c
  • lines changed 3, context: html, text, full: html, text
    9a22e50608d95a5fdb8c3d8c09ee35db8fa129ea Wed May 13 17:04:28 2026 -0700
    Moving the length of the Exon/Intron to the other Exon/Intron line. Adding a space between the length and bp, refs #37439
• src/hg/hgc/ccdsClick.c
  • lines changed 18, context: html, text, full: html, text
    fabf13fff3e3abaf7ef83c69a8c60d0142c288a1 Fri May 15 12:05:59 2026 -0700
    fix two remaining quickLift issues on UCSC RefSeq item detail page: CCDS link routes to source assembly (with coords lifted back) so the ccdsGene handler doesn't try to open the hub-virtual db, and Get Genomic Sequence Near Gene now reads sequence from the destination assembly at the lifted exon coordinates refs #36125
• src/hg/hgc/ccdsClick.h
  • lines changed 1, context: html, text, full: html, text
    fabf13fff3e3abaf7ef83c69a8c60d0142c288a1 Fri May 15 12:05:59 2026 -0700
    fix two remaining quickLift issues on UCSC RefSeq item detail page: CCDS link routes to source assembly (with coords lifted back) so the ccdsGene handler doesn't try to open the hub-virtual db, and Get Genomic Sequence Near Gene now reads sequence from the destination assembly at the lifted exon coordinates refs #36125
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    e7264355c83a0d0875b372b7ad26162adb363f6c Tue May 12 13:20:28 2026 -0700
    myVariants v1 follow-ups: CT edit gate, anon-user button gate, hgc duplicate link, item-name synthesis from ref/alt or HGVS, refs #33808
  • lines changed 42, context: html, text, full: html, text
    fabf13fff3e3abaf7ef83c69a8c60d0142c288a1 Fri May 15 12:05:59 2026 -0700
    fix two remaining quickLift issues on UCSC RefSeq item detail page: CCDS link routes to source assembly (with coords lifted back) so the ccdsGene handler doesn't try to open the hub-virtual db, and Get Genomic Sequence Near Gene now reads sequence from the destination assembly at the lifted exon coordinates refs #36125
  • lines changed 11, context: html, text, full: html, text
    037038e736a88de87b00e5a384b29f45e831419f Fri May 15 14:29:07 2026 -0700
    fix Mysql "Commands out of sync" error on OMIM Genes (omimGene2) detail page prGRShortRefGene runs its own queries on the supplied connection, so calling it mid-iteration of an outer sqlMustGetResult loop on the same conn produced "Commands out of sync; you can't run this command now". Slurp the gene names into an slName list, free the outer result, then iterate, refs #37565
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    1b10a8e2ba4238d3045d8511faf2d7a105b13941 Mon May 18 09:57:49 2026 -0700
    free sqlConnection at end of printOmimGene2Details, refs #37571 Per Chris's review on #37571: the conn allocated at the top of the function was never freed.
• src/hg/hgc/myVariantsClick.c
  • lines changed 70, context: html, text, full: html, text
    630eb30bc3695afcf73a19be6e3bc9a2829b365f Wed May 13 13:04:37 2026 -0700
    Make myVariants items bed12+ rather than bed9+, refs #33808
• src/hg/htdocs/goldenPath/help/facetedComposite.html
  • lines changed 20, context: html, text, full: html, text
    9bafde23616aa7e9d0afd993e507ef63103b1b17 Wed May 13 01:54:22 2026 -0700
    Minor docs update for faceted composites, refs #36320
• src/hg/htdocs/goldenPath/help/trackDb/changes.html
  • lines changed 9, context: html, text, full: html, text
    b3ef92d687a2a170eab7758ff6b197e229675eee Fri May 8 13:23:17 2026 -0700
    add filterPriority and highlightPriority trackDb settings, refs #29223 New filterPriority.<fieldName> setting controls the display order of filter controls on the track configuration page. Lower values display first; filters without an explicit priority sort after those that have one. A companion highlightPriority.<fieldName> setting orders highlight controls the same way. A single priority entry covers all filter styles on the field (filter.*, filterText.*, filterValues.*). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 6, context: html, text, full: html, text
    b3ef92d687a2a170eab7758ff6b197e229675eee Fri May 8 13:23:17 2026 -0700
    add filterPriority and highlightPriority trackDb settings, refs #29223 New filterPriority.<fieldName> setting controls the display order of filter controls on the track configuration page. Lower values display first; filters without an explicit priority sort after those that have one. A companion highlightPriority.<fieldName> setting orders highlight controls the same way. A single priority entry covers all filter styles on the field (filter.*, filterText.*, filterValues.*). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 5, context: html, text, full: html, text
    b3ef92d687a2a170eab7758ff6b197e229675eee Fri May 8 13:23:17 2026 -0700
    add filterPriority and highlightPriority trackDb settings, refs #29223 New filterPriority.<fieldName> setting controls the display order of filter controls on the track configuration page. Lower values display first; filters without an explicit priority sort after those that have one. A companion highlightPriority.<fieldName> setting orders highlight controls the same way. A single priority entry covers all filter styles on the field (filter.*, filterText.*, filterValues.*). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 33, context: html, text, full: html, text
    b3ef92d687a2a170eab7758ff6b197e229675eee Fri May 8 13:23:17 2026 -0700
    add filterPriority and highlightPriority trackDb settings, refs #29223 New filterPriority.<fieldName> setting controls the display order of filter controls on the track configuration page. Lower values display first; filters without an explicit priority sort after those that have one. A companion highlightPriority.<fieldName> setting orders highlight controls the same way. A single priority entry covers all filter styles on the field (filter.*, filterText.*, filterValues.*). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/inc/hgMyData.html
  • lines changed 10, context: html, text, full: html, text
    2c8a873e7286d797e88549d5a2825f0ea6fe3f04 Fri May 15 15:07:52 2026 -0700
    HubSpace now allows tracks hubs to be defined via hub.txt+genomes.txt+trackDb.txt files, refs Baihe email and #37566
• src/hg/htdocs/liftRequest.html
  • lines changed 11, context: html, text, full: html, text
    19e534539738dc80225bff27bda1f1835dc5b3d3 Mon May 11 15:09:10 2026 -0700
    rate limit the lifrt requests to "liftDailyLimi" setting from hg.conf refs #31811
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    e07b87b45f9293c3f45337303886450c390b2585 Tue May 12 13:10:56 2026 -0700
    protect against duplicated pending entries in the ottoRequest table refs #31811
• src/hg/htdocs/style/HGStyle.css
  • lines changed 7, context: html, text, full: html, text
    d121edc0bd2809f1d6de6185a497e6a288958479 Tue May 12 09:18:29 2026 -0700
    hgConvert quickLift: skip pre-lifted tracks, append-and-merge hub file, per-track remove UI, refs #37535 In hgConvert / trackHubBuild: - Skip tracks that already came from a quickLift hub (quickLiftUrl / quickLifted setting) so they don't get re-lifted to a new destination. - Append new track stanzas to an existing per-source hub file instead of overwriting it; new stanzas get priorities after the existing max; duplicate track names are skipped. Also avoids re-emitting a parent supertrack that's already in the file. New public quickLiftHubRemoveTrack(cart, sourceDb, trackName) in trackHub.c rewrites the per-source hub file with the named stanza removed plus all descendant stanzas (parent reference cascade, transitive). hgTrackUi: adds a "Remove from QuickLift" link next to "Duplicate track" for any tdb carrying a quickLiftDb setting. The link hits hgTrackUi_op=quickLiftRemove which calls quickLiftHubRemoveTrack, hides the track in the cart, and 302s to hgTracks. The op argument cart var is qlSourceDb (renamed from quickLiftSourceDb to avoid colliding with the quickLift.* prefix used elsewhere; values cloned out of the cart hash before cartRemove so the helper doesn't see freed strings). hgTracks: adds a small "x" icon (printQuickLiftDelIcon) on tracks in a quickLift group, suppressed on the synthetic bigQuickLiftChain track. JS onQuickLiftDelIconClick fires the same hgTrackUi_op endpoint via synchronous XHR and removes every TD whose icon matches the deleted data-track, so the row goes away in both the QuickLift group and the Visible Tracks group. hubConnect cart handling fixes shaken out by the above: - hubConnectRemakeTrackHubVar's cart-var prefix is now "quickLift." (with the trailing dot) instead of "quickLift", so unrelated keys like qlSourceDb no longer get parsed as hubId/db and crash cart loading on every CGI. Also skips entries whose hubStatus lookup returned NULL. - hubConnectStatusListFromCart no longer calls removeQuickListReference when the current db isn't the lift's destination. A side trip to another assembly between two lifts to the same destination was deleting the earlier attachment's cart var; just skip attaching this load and leave the cart alone so the lift survives the round trip. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/style/liftRequest.css
  • lines changed 20, context: html, text, full: html, text
    a3b8a28c0a5fe9cd632f43784209a80f42607333 Tue May 12 13:18:19 2026 -0700
    protect against duplicated pending entries in the ottoRequest table refs #31811
• src/hg/hubApi/dataApi.h
  • lines changed 2, context: html, text, full: html, text
    e07b87b45f9293c3f45337303886450c390b2585 Tue May 12 13:10:56 2026 -0700
    protect against duplicated pending entries in the ottoRequest table refs #31811
• src/hg/hubApi/liftOver.c
  • lines changed 40, context: html, text, full: html, text
    19e534539738dc80225bff27bda1f1835dc5b3d3 Mon May 11 15:09:10 2026 -0700
    rate limit the lifrt requests to "liftDailyLimi" setting from hg.conf refs #31811
  • lines changed 58, context: html, text, full: html, text
    e07b87b45f9293c3f45337303886450c390b2585 Tue May 12 13:10:56 2026 -0700
    protect against duplicated pending entries in the ottoRequest table refs #31811
• src/hg/inc/bigBedFilter.h
  • lines changed 7, context: html, text, full: html, text
    b3ef92d687a2a170eab7758ff6b197e229675eee Fri May 8 13:23:17 2026 -0700
    add filterPriority and highlightPriority trackDb settings, refs #29223 New filterPriority.<fieldName> setting controls the display order of filter controls on the track configuration page. Lower values display first; filters without an explicit priority sort after those that have one. A companion highlightPriority.<fieldName> setting orders highlight controls the same way. A single priority entry covers all filter styles on the field (filter.*, filterText.*, filterValues.*). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/inc/cart.h
  • lines changed 3, context: html, text, full: html, text
    9927343536614f63516f107aa859b495abf402d1 Mon May 18 09:58:41 2026 -0700
    Reducing bot abuse by restricting the number of IP addresses we'll accept the same hguid from in a short timeframe before requiring a captcha re-up (if captcha is enabled). refs #37494
• src/hg/inc/hgFind.h
  • lines changed 5, context: html, text, full: html, text
    17fe5238421ff301f2b7360c96db92104e405094 Tue May 12 12:09:08 2026 -0700
    myVariants fixes: widen drag-select dialog a bit to fit the new button, save only the actual variant position, not the variant plus padding position when making a variant out of an hgvs term, refs #33808
• src/hg/inc/myVariants.h
  • lines changed 6, context: html, text, full: html, text
    e7264355c83a0d0875b372b7ad26162adb363f6c Tue May 12 13:20:28 2026 -0700
    myVariants v1 follow-ups: CT edit gate, anon-user button gate, hgc duplicate link, item-name synthesis from ref/alt or HGVS, refs #33808
  • lines changed 16, context: html, text, full: html, text
    d7dd4f55e28699bb783563b8bece5bf23f392995 Wed May 13 11:07:57 2026 -0700
    Adds hg.conf myVariantsDataDir for writing ctfiles outside trash/, per-db short/long label rename on hgTrackUi, and a shared removal helper so the hgTrackUi remove button, hgTracks trash icon, and hgCustom checkbox all function the same, refs #33808
  • lines changed 4, context: html, text, full: html, text
    630eb30bc3695afcf73a19be6e3bc9a2829b365f Wed May 13 13:04:37 2026 -0700
    Make myVariants items bed12+ rather than bed9+, refs #33808
  • lines changed 5, context: html, text, full: html, text
    80ab15c036bf35894b59df383c03c51cbeff30be Thu May 14 10:29:53 2026 -0700
    Stop myVariants from clobbering regular custom tracks by giving it its own cart variable (mvCtfile_<db>) instead of overloading ctfile_<db>, refs #37553
• src/hg/inc/quickLift.h
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    d121edc0bd2809f1d6de6185a497e6a288958479 Tue May 12 09:18:29 2026 -0700
    hgConvert quickLift: skip pre-lifted tracks, append-and-merge hub file, per-track remove UI, refs #37535 In hgConvert / trackHubBuild: - Skip tracks that already came from a quickLift hub (quickLiftUrl / quickLifted setting) so they don't get re-lifted to a new destination. - Append new track stanzas to an existing per-source hub file instead of overwriting it; new stanzas get priorities after the existing max; duplicate track names are skipped. Also avoids re-emitting a parent supertrack that's already in the file. New public quickLiftHubRemoveTrack(cart, sourceDb, trackName) in trackHub.c rewrites the per-source hub file with the named stanza removed plus all descendant stanzas (parent reference cascade, transitive). hgTrackUi: adds a "Remove from QuickLift" link next to "Duplicate track" for any tdb carrying a quickLiftDb setting. The link hits hgTrackUi_op=quickLiftRemove which calls quickLiftHubRemoveTrack, hides the track in the cart, and 302s to hgTracks. The op argument cart var is qlSourceDb (renamed from quickLiftSourceDb to avoid colliding with the quickLift.* prefix used elsewhere; values cloned out of the cart hash before cartRemove so the helper doesn't see freed strings). hgTracks: adds a small "x" icon (printQuickLiftDelIcon) on tracks in a quickLift group, suppressed on the synthetic bigQuickLiftChain track. JS onQuickLiftDelIconClick fires the same hgTrackUi_op endpoint via synchronous XHR and removes every TD whose icon matches the deleted data-track, so the row goes away in both the QuickLift group and the Visible Tracks group. hubConnect cart handling fixes shaken out by the above: - hubConnectRemakeTrackHubVar's cart-var prefix is now "quickLift." (with the trailing dot) instead of "quickLift", so unrelated keys like qlSourceDb no longer get parsed as hubId/db and crash cart loading on every CGI. Also skips entries whose hubStatus lookup returned NULL. - hubConnectStatusListFromCart no longer calls removeQuickListReference when the current db isn't the lift's destination. A side trip to another assembly between two lifts to the same destination was deleting the earlier attachment's cart var; just skip attaching this load and leave the cart alone so the lift survives the round trip. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/js/hgMyData.js
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    2c8a873e7286d797e88549d5a2825f0ea6fe3f04 Fri May 15 15:07:52 2026 -0700
    HubSpace now allows tracks hubs to be defined via hub.txt+genomes.txt+trackDb.txt files, refs Baihe email and #37566
• src/hg/js/hgTracks.js
  • lines changed 26, context: html, text, full: html, text
    d121edc0bd2809f1d6de6185a497e6a288958479 Tue May 12 09:18:29 2026 -0700
    hgConvert quickLift: skip pre-lifted tracks, append-and-merge hub file, per-track remove UI, refs #37535 In hgConvert / trackHubBuild: - Skip tracks that already came from a quickLift hub (quickLiftUrl / quickLifted setting) so they don't get re-lifted to a new destination. - Append new track stanzas to an existing per-source hub file instead of overwriting it; new stanzas get priorities after the existing max; duplicate track names are skipped. Also avoids re-emitting a parent supertrack that's already in the file. New public quickLiftHubRemoveTrack(cart, sourceDb, trackName) in trackHub.c rewrites the per-source hub file with the named stanza removed plus all descendant stanzas (parent reference cascade, transitive). hgTrackUi: adds a "Remove from QuickLift" link next to "Duplicate track" for any tdb carrying a quickLiftDb setting. The link hits hgTrackUi_op=quickLiftRemove which calls quickLiftHubRemoveTrack, hides the track in the cart, and 302s to hgTracks. The op argument cart var is qlSourceDb (renamed from quickLiftSourceDb to avoid colliding with the quickLift.* prefix used elsewhere; values cloned out of the cart hash before cartRemove so the helper doesn't see freed strings). hgTracks: adds a small "x" icon (printQuickLiftDelIcon) on tracks in a quickLift group, suppressed on the synthetic bigQuickLiftChain track. JS onQuickLiftDelIconClick fires the same hgTrackUi_op endpoint via synchronous XHR and removes every TD whose icon matches the deleted data-track, so the row goes away in both the QuickLift group and the Visible Tracks group. hubConnect cart handling fixes shaken out by the above: - hubConnectRemakeTrackHubVar's cart-var prefix is now "quickLift." (with the trailing dot) instead of "quickLift", so unrelated keys like qlSourceDb no longer get parsed as hubId/db and crash cart loading on every CGI. Also skips entries whose hubStatus lookup returned NULL. - hubConnectStatusListFromCart no longer calls removeQuickListReference when the current db isn't the lift's destination. A side trip to another assembly between two lifts to the same destination was deleting the earlier attachment's cart var; just skip attaching this load and leave the cart alone so the lift survives the round trip. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    17fe5238421ff301f2b7360c96db92104e405094 Tue May 12 12:09:08 2026 -0700
    myVariants fixes: widen drag-select dialog a bit to fit the new button, save only the actual variant position, not the variant plus padding position when making a variant out of an hgvs term, refs #33808
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    e7264355c83a0d0875b372b7ad26162adb363f6c Tue May 12 13:20:28 2026 -0700
    myVariants v1 follow-ups: CT edit gate, anon-user button gate, hgc duplicate link, item-name synthesis from ref/alt or HGVS, refs #33808
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    3d006a7244d91a9d72260986a5741a5aa65787dc Tue May 12 15:01:28 2026 -0700
    Widen 'jump to position' dialog after creating a myVariants item via hgvs. Remove 'update custom track' button from hgTrackUi for myVariants tracks. Fix item clicks not working after item name update in last commit, refs #33808
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    630eb30bc3695afcf73a19be6e3bc9a2829b365f Wed May 13 13:04:37 2026 -0700
    Make myVariants items bed12+ rather than bed9+, refs #33808
• src/hg/js/liftRequest.js
  • lines changed 24, context: html, text, full: html, text
    19e534539738dc80225bff27bda1f1835dc5b3d3 Mon May 11 15:09:10 2026 -0700
    rate limit the lifrt requests to "liftDailyLimi" setting from hg.conf refs #31811
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    e07b87b45f9293c3f45337303886450c390b2585 Tue May 12 13:10:56 2026 -0700
    protect against duplicated pending entries in the ottoRequest table refs #31811
• src/hg/js/makefile
  • lines changed 2, context: html, text, full: html, text
    630eb30bc3695afcf73a19be6e3bc9a2829b365f Wed May 13 13:04:37 2026 -0700
    Make myVariants items bed12+ rather than bed9+, refs #33808
• src/hg/js/myVariantsBlocks.js
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    630eb30bc3695afcf73a19be6e3bc9a2829b365f Wed May 13 13:04:37 2026 -0700
    Make myVariants items bed12+ rather than bed9+, refs #33808
• src/hg/js/utils.js
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    59982d783b66d2be7d73ef89ab1b6d741a257f7e Mon May 11 10:12:37 2026 -0700
    Remove dead code block pointed out in nightly code review
• src/hg/lib/botDelay.c
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    9927343536614f63516f107aa859b495abf402d1 Mon May 18 09:58:41 2026 -0700
    Reducing bot abuse by restricting the number of IP addresses we'll accept the same hguid from in a short timeframe before requiring a captcha re-up (if captcha is enabled). refs #37494
• src/hg/lib/cart.c
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    061f2211a2955946e5a15ca6109bf2c667c842ee Fri May 15 08:19:51 2026 -0700
    clear stale lastPosition when cart db changes so QuickLift/hgGateway hops don't trigger a spurious "Unable to resolve lastPosition" banner on the destination assembly refs #37562
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    9927343536614f63516f107aa859b495abf402d1 Mon May 18 09:58:41 2026 -0700
    Reducing bot abuse by restricting the number of IP addresses we'll accept the same hguid from in a short timeframe before requiring a captcha re-up (if captcha is enabled). refs #37494
• src/hg/lib/customTrack.c
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    d7dd4f55e28699bb783563b8bece5bf23f392995 Wed May 13 11:07:57 2026 -0700
    Adds hg.conf myVariantsDataDir for writing ctfiles outside trash/, per-db short/long label rename on hgTrackUi, and a shared removal helper so the hgTrackUi remove button, hgTracks trash icon, and hgCustom checkbox all function the same, refs #33808
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    80ab15c036bf35894b59df383c03c51cbeff30be Thu May 14 10:29:53 2026 -0700
    Stop myVariants from clobbering regular custom tracks by giving it its own cart variable (mvCtfile_<db>) instead of overloading ctfile_<db>, refs #37553
• src/hg/lib/genePred.c
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    dec7900a42fb984be16142c1f090c71cbe09ff05 Thu May 14 17:41:48 2026 -0700
    fix genePred.c not to crash if there are no exon frames when flipping strands refs #36370
• src/hg/lib/hgFind.c
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    17fe5238421ff301f2b7360c96db92104e405094 Tue May 12 12:09:08 2026 -0700
    myVariants fixes: widen drag-select dialog a bit to fit the new button, save only the actual variant position, not the variant plus padding position when making a variant out of an hgvs term, refs #33808
• src/hg/lib/hubConnect.c
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    d121edc0bd2809f1d6de6185a497e6a288958479 Tue May 12 09:18:29 2026 -0700
    hgConvert quickLift: skip pre-lifted tracks, append-and-merge hub file, per-track remove UI, refs #37535 In hgConvert / trackHubBuild: - Skip tracks that already came from a quickLift hub (quickLiftUrl / quickLifted setting) so they don't get re-lifted to a new destination. - Append new track stanzas to an existing per-source hub file instead of overwriting it; new stanzas get priorities after the existing max; duplicate track names are skipped. Also avoids re-emitting a parent supertrack that's already in the file. New public quickLiftHubRemoveTrack(cart, sourceDb, trackName) in trackHub.c rewrites the per-source hub file with the named stanza removed plus all descendant stanzas (parent reference cascade, transitive). hgTrackUi: adds a "Remove from QuickLift" link next to "Duplicate track" for any tdb carrying a quickLiftDb setting. The link hits hgTrackUi_op=quickLiftRemove which calls quickLiftHubRemoveTrack, hides the track in the cart, and 302s to hgTracks. The op argument cart var is qlSourceDb (renamed from quickLiftSourceDb to avoid colliding with the quickLift.* prefix used elsewhere; values cloned out of the cart hash before cartRemove so the helper doesn't see freed strings). hgTracks: adds a small "x" icon (printQuickLiftDelIcon) on tracks in a quickLift group, suppressed on the synthetic bigQuickLiftChain track. JS onQuickLiftDelIconClick fires the same hgTrackUi_op endpoint via synchronous XHR and removes every TD whose icon matches the deleted data-track, so the row goes away in both the QuickLift group and the Visible Tracks group. hubConnect cart handling fixes shaken out by the above: - hubConnectRemakeTrackHubVar's cart-var prefix is now "quickLift." (with the trailing dot) instead of "quickLift", so unrelated keys like qlSourceDb no longer get parsed as hubId/db and crash cart loading on every CGI. Also skips entries whose hubStatus lookup returned NULL. - hubConnectStatusListFromCart no longer calls removeQuickListReference when the current db isn't the lift's destination. A side trip to another assembly between two lifts to the same destination was deleting the earlier attachment's cart var; just skip attaching this load and leave the cart alone so the lift survives the round trip. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/lib/hui.c
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    b3ef92d687a2a170eab7758ff6b197e229675eee Fri May 8 13:23:17 2026 -0700
    add filterPriority and highlightPriority trackDb settings, refs #29223 New filterPriority.<fieldName> setting controls the display order of filter controls on the track configuration page. Lower values display first; filters without an explicit priority sort after those that have one. A companion highlightPriority.<fieldName> setting orders highlight controls the same way. A single priority entry covers all filter styles on the field (filter.*, filterText.*, filterValues.*). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/lib/myVariants.as
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    630eb30bc3695afcf73a19be6e3bc9a2829b365f Wed May 13 13:04:37 2026 -0700
    Make myVariants items bed12+ rather than bed9+, refs #33808
• src/hg/lib/myVariants.c
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    00590f0f1b1b91a318f0d76308bc513a83dc2ad7 Tue May 12 11:26:52 2026 -0700
    Move myVariants tables from myisam to innodb, refs #33808
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    e7264355c83a0d0875b372b7ad26162adb363f6c Tue May 12 13:20:28 2026 -0700
    myVariants v1 follow-ups: CT edit gate, anon-user button gate, hgc duplicate link, item-name synthesis from ref/alt or HGVS, refs #33808
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    d7dd4f55e28699bb783563b8bece5bf23f392995 Wed May 13 11:07:57 2026 -0700
    Adds hg.conf myVariantsDataDir for writing ctfiles outside trash/, per-db short/long label rename on hgTrackUi, and a shared removal helper so the hgTrackUi remove button, hgTracks trash icon, and hgCustom checkbox all function the same, refs #33808
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    630eb30bc3695afcf73a19be6e3bc9a2829b365f Wed May 13 13:04:37 2026 -0700
    Make myVariants items bed12+ rather than bed9+, refs #33808
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    80ab15c036bf35894b59df383c03c51cbeff30be Thu May 14 10:29:53 2026 -0700
    Stop myVariants from clobbering regular custom tracks by giving it its own cart variable (mvCtfile_<db>) instead of overloading ctfile_<db>, refs #37553
• src/hg/lib/myVariants.sql
  • lines changed 1, context: html, text, full: html, text
    00590f0f1b1b91a318f0d76308bc513a83dc2ad7 Tue May 12 11:26:52 2026 -0700
    Move myVariants tables from myisam to innodb, refs #33808
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    630eb30bc3695afcf73a19be6e3bc9a2829b365f Wed May 13 13:04:37 2026 -0700
    Make myVariants items bed12+ rather than bed9+, refs #33808
• src/hg/lib/myVariantsShare.sql
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    00590f0f1b1b91a318f0d76308bc513a83dc2ad7 Tue May 12 11:26:52 2026 -0700
    Move myVariants tables from myisam to innodb, refs #33808
• src/hg/lib/quickLift.c
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    a8d453018226a38dc8bc7fce5891a2e064116029 Tue May 12 10:24:39 2026 -0700
    quickLift: fix hgTracks OOM with multiple lifted bigBed-style tracks, refs #37536 In quickLiftGetIntervals (src/hg/lib/quickLift.c) the first chainList from chainLoadIdRangeHub was reassigned without being freed, leaking the chain heads and their full cBlock lists for every quickLifted track in the window. And the second-pass padding used maxGap * 2 with no upper bound, so a single long item in the source data file (gencodeV49 has genes up to ~800 kb) could pull in chains -- and their dense cBlock lists -- covering many megabases. Free the first chainList, and cap the padding at 1 Mb. On the failing mm10 chr4:148,273,516-148,627,317 session with the hg38 hub_190793 quickLift attached, the request went from OOM at 11+ GB RSS (truncated 6 kb response, 80+ s) to a complete 1.7 MB response in ~1.6 s at ~430 MB RSS. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/lib/trackDb.c
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    b3ef92d687a2a170eab7758ff6b197e229675eee Fri May 8 13:23:17 2026 -0700
    add filterPriority and highlightPriority trackDb settings, refs #29223 New filterPriority.<fieldName> setting controls the display order of filter controls on the track configuration page. Lower values display first; filters without an explicit priority sort after those that have one. A companion highlightPriority.<fieldName> setting orders highlight controls the same way. A single priority entry covers all filter styles on the field (filter.*, filterText.*, filterValues.*). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/lib/trackDbCache.c
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    349adcd7c26d73b53ec1865a4fd14c60b74f9386 Wed May 13 09:18:36 2026 -0700
    trackDbCache: CACHE_TRACK_DB_DIR env var override; add trackDbCacheBench, refs #37551 trackDbCacheOn() in src/hg/lib/trackDbCache.c now reads CACHE_TRACK_DB_DIR from the environment ahead of the cacheTrackDbDir hg.conf setting. When the env var is set its value wins, including the empty string (which disables the cache). This lets a benchmark harness switch caching on and off per hgTracks invocation without editing hg.conf. trackDbCacheBench (src/utils/qa/trackDbCacheBench/) drives hgTracks through cached and uncached runs, with warmups and per-iteration median/min/max timings, and an --evict-cache option that uses posix_fadvise(DONTNEED) to drop cache files from the OS page cache between iterations so disk-backed cache directories can be compared to /dev/shm. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/lib/trackHub.c
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    d121edc0bd2809f1d6de6185a497e6a288958479 Tue May 12 09:18:29 2026 -0700
    hgConvert quickLift: skip pre-lifted tracks, append-and-merge hub file, per-track remove UI, refs #37535 In hgConvert / trackHubBuild: - Skip tracks that already came from a quickLift hub (quickLiftUrl / quickLifted setting) so they don't get re-lifted to a new destination. - Append new track stanzas to an existing per-source hub file instead of overwriting it; new stanzas get priorities after the existing max; duplicate track names are skipped. Also avoids re-emitting a parent supertrack that's already in the file. New public quickLiftHubRemoveTrack(cart, sourceDb, trackName) in trackHub.c rewrites the per-source hub file with the named stanza removed plus all descendant stanzas (parent reference cascade, transitive). hgTrackUi: adds a "Remove from QuickLift" link next to "Duplicate track" for any tdb carrying a quickLiftDb setting. The link hits hgTrackUi_op=quickLiftRemove which calls quickLiftHubRemoveTrack, hides the track in the cart, and 302s to hgTracks. The op argument cart var is qlSourceDb (renamed from quickLiftSourceDb to avoid colliding with the quickLift.* prefix used elsewhere; values cloned out of the cart hash before cartRemove so the helper doesn't see freed strings). hgTracks: adds a small "x" icon (printQuickLiftDelIcon) on tracks in a quickLift group, suppressed on the synthetic bigQuickLiftChain track. JS onQuickLiftDelIconClick fires the same hgTrackUi_op endpoint via synchronous XHR and removes every TD whose icon matches the deleted data-track, so the row goes away in both the QuickLift group and the Visible Tracks group. hubConnect cart handling fixes shaken out by the above: - hubConnectRemakeTrackHubVar's cart-var prefix is now "quickLift." (with the trailing dot) instead of "quickLift", so unrelated keys like qlSourceDb no longer get parsed as hubId/db and crash cart loading on every CGI. Also skips entries whose hubStatus lookup returned NULL. - hubConnectStatusListFromCart no longer calls removeQuickListReference when the current db isn't the lift's destination. A side trip to another assembly between two lifts to the same destination was deleting the earlier attachment's cart var; just skip attaching this load and leave the cart alone so the lift survives the round trip. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/lib/userdata.c
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    2c8a873e7286d797e88549d5a2825f0ea6fe3f04 Fri May 15 15:07:52 2026 -0700
    HubSpace now allows tracks hubs to be defined via hub.txt+genomes.txt+trackDb.txt files, refs Baihe email and #37566
• src/hg/liftRequest/liftRequest.c
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    6469e916f4e7cd2797e63f1e0943bb2b65764632 Mon May 18 09:59:47 2026 -0700
    empty shell to build out for a liftRequest CGI refs #31811
• src/hg/liftRequest/makefile
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    6469e916f4e7cd2797e63f1e0943bb2b65764632 Mon May 18 09:59:47 2026 -0700
    empty shell to build out for a liftRequest CGI refs #31811
• src/hg/makeDb/doc/hg38/encode4.regulation.txt
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    9c0f52be6be34a120bd16008b57fc60728bd63bd Thu May 14 14:48:03 2026 -0700
    Update ENCODE4 Regulation makedocs with note 141 QA follow-ups (H3K27ac color, metadata Organ casing, longLabel species prefix). refs #34923
• src/hg/makeDb/doc/hg38/mei.txt
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    0c1e751423b38dd741875d4cdcc6ffb5d4c4a135 Tue May 12 07:51:34 2026 -0700
    mei: add DeepMEI 1000G subtrack on hg38 91,617 MEIs (68,282 Alu, 16,891 L1, 6,444 SVA) called by DeepMEI on the 3,202 high-coverage 1000 Genomes samples. Same 1-bp anchor convention and Okabe-Ito colors as meiHgsvc3. DeepMEI's symbolic ALT carries no inserted sequence or insertion length, so the bigBed schema is a subset of meiHgsvc3 (no svLen, callerCount, validation flags, insertSeq). Also fixes the INS-svLen:carrierCount label format note in meiHgsvc3.html. refs #37524
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    4f8f8773bec66a9e993e9897e0b032c6e97dead8 Fri May 15 10:12:29 2026 -0700
    mei: add HMEID, SweGen, and euL1db subtracks Three new MEI catalogues under the existing mei superTrack: meiHmeid (hg38) 36,699 MELT MEIs from HMEID v1.1 (NyuWa+1KGP, 5,675 individuals, Niu et al. 2022, PMID 35212372). Site-level VCF; per-cohort and per-1KGP super- population AC/AN/AF; SVTYPE Alu/L1/SVA/HERVK. meiSwegen (hg38 lifted) 18,090 MELT MEIs from the SweGen 1,000-sample Swedish cohort (Ameur 2017, PMID 28832569; Gardner 2017, PMID 28855259). Built on hg19, liftOver to hg38 (10 unmapped). tableBrowser off per SweGen distribution terms. meiEul1db (hg19+hg38) 8,988 curated L1-HS insertion polymorphisms (MRIPs) from euL1db v1.00 (Mir 2015, PMID 25352549), aggregating 142,495 sample-level SRIPs across 32 published studies. Coloured by lineage (germline/somatic/mixed). Built on hg19, liftOver to hg38 (3 unmapped). Helman2014 used numeric chrom names (23=X, 24=Y) which are renamed during the build. meiEul1dbRef (hg19+hg38) 1,540 reference-genome L1-HS copies catalogued by euL1db (companion to meiEul1db). Single shared mei.ra (in human/) uses $D substitution so each stanza serves both assemblies where applicable. refs #37524
• src/hg/makeDb/doc/hg38/mpra.txt
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    d069df7855eb648b5b53c51ef5218fe2e4a1d087 Wed May 13 12:48:53 2026 -0700
    mpraVarDb script rebuild: standardize NA, fix upstream typos, add pvalue note. refs #37359 Build-script changes (mpravardbToBed.py + mpravardb.as): - sanitize_text() now normalizes "None"/"NA"/"N/A"/"null"/"NULL"/"nan" to empty string. Removes 55,108 stale sentinels: 53,144 disease= "None" eQTL rows, 1,964 disease="NA" Kircher rows, 44 ref/alt=NA Myint rows. - Literal-replacement table for three upstream typos: "30 UTR" -> "3'UTR" (26,546 Schuster description rows), "Familial hypercholesterol emia" -> "Familial hypercholesterolemia" (2,176 Kircher disease rows), "Alchol use disorder" -> "Alcohol use disorder" (88 Rao disease rows). - fmt_mo() renders NaN floats as "NA" in mouseOver helper fields; 30,921 rows that previously showed literal "nan" now read "NA". - Tightened name+rsid handling: treat a value as an rsID only if it starts with "rs". 2,088 hg19-coord-style names like "1_1403972_CG" are reformatted to "chr<X>:<hg38pos>:<ref>><alt>" and the rsid field cleared to "" so the dbSNP linkout doesn't fire on a bogus value. - Removed the 250-char truncation that cut Griesemer descriptions mid-sentence; mpravardb.as switched description and mpraStudy from "string" to "lstring" to admit the full upstream text. Description page (mpraVarDb.html): - Added a "Note (pending upstream fix)" paragraph in Methods explaining the 5,092 rows with pvalue > 1 (test statistic mislabeled in the pvalue field by upstream curators for Mouri 2022 and Tewhey 2016). Bracketed by an HTML comment "TEMP: remove once Tao Wang fixes..." for future cleanup when the next snapshot lands. bigBed rebuilt; itemCount 239,028 preserved. Pre-rebuild backup: /hive/data/genomes/hg38/bed/mpra/mpravardb/mpravardb.bb.pre-2026-05-14-backup Makedoc updated with the QA-2 build-script rebuild section.
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    be4ae656ffd6994f4d5de689ffe4117861441181 Wed May 13 19:18:41 2026 -0700
    Note pre-existing hg19-pos-in-name observation in mpravardb makedoc. refs #37359 Surfaced during sandbox validation of the 2026-05-14 script rebuild. For ~73k non-rs rows the chr:pos:ref>alt name carries the original hg19 pos because csv_to_bed builds the name before liftOver runs. Display is unaffected; only relevant if a user copies the name field expecting hg38 coordinates. Documented for whenever a future rebuild gets the post-Step-2 name-rewrite fix folded in.
• src/hg/makeDb/doc/hg38/ncOrfs.txt
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    e390536dad43cc58b7f27f31ffc1df699c7dee03 Tue May 12 06:57:32 2026 -0700
    ncOrfs: Kozak strength coloring, codon display, and uORF intron recovery Each ORF in every ncOrfs subtrack now carries three new annotation fields: startCodon, kozakStrength, and kozakTE (Noderer 2014 TE / 100). Features are colored by kozakTE on a 5-bin gradient (blue<0.5, teal, green, orange, red>=0.8), with purple for non-ATG starts and grey for contexts that could not be retrieved. The colors are wired in colorByKozak.py (COLOR_BINS / GREY / PURPLE). thickStart and thickEnd now span the whole ORF and the trackDb stanzas enable baseColorUseCds=given + baseColorDefault=genomicCodons so codon shading is on by default. Filters added for startCodon, kozakStrength, kozakTE on every subtrack. The bed12 GENCODE Phase II tracks (primary / comprehensive) and the metamorf bedORFtable are now converted to bigGenePred so codon display works on them. The OpenProt "kozak" field is renamed to "kozakMotif" in the new .as so the mouseOver's $kozakStrength substitution is not eaten greedily as $kozak + "Strength". utrAnnotUorfs ships as bed9+1 with no exon/intron structure. A new addIntrons.py preprocessor matches each uORF against the other ncORF tracks by exact (chrom, start, end, strand) and copies the block structure of any donor with introns; the contributing database names go in a new intronsSource field (also exposed as a filter). 6,508 of 44,435 uORFs (14.6%) picked up introns, mostly from MetamORF; the rest stay single-block (intronsSource=none). The Noderer 2014 TE table (PMC4299517 / PMID 25170020) is cached in the repo so the build is reproducible without network access. Reference: Noderer WL et al. Quantitative analysis of mammalian translation initiation sites by FACS-seq. Mol Syst Biol. 2014;10:748. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/doc/hg38/nmd.txt
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    7bec995472122739bf0f076de2603708059c65ce Wed May 13 17:23:37 2026 -0700
    Adding NMDetective-AI subtracks (bigWig + bigBed) under the NMD Escape superTrack. refs #33737 Two new subtracks slotted between NMD Escape RefSeq and NMDetective-A (priorities 1.7 and 1.8): - nmdDetectiveAi - position-averaged predictions (bigWig) - nmdDetectiveAiBed - per-stop-gain predictions, one item per (transcript, codon, mutant codon), with diverging Okabe-Ito coloring and a pre-rendered mouseover Predictions are from Veiner et al. (bioRxiv 10.64898/2026.03.24.714003), covering MANE Select transcripts at Gencode v46. Verdict bins in the bigBed mouseover use the GMM-derived thresholds reported in the paper's Methods (-0.17 / +0.43), not symmetric +/- 0.3. Description page covers the +0.5 / -0.5 anchor convention, threshold derivation, and the pre-print status.
• src/hg/makeDb/doc/hg38/varFreqs.txt
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    9a49afb16653363a70d8e4d205513008b7b08df5 Wed May 13 06:18:42 2026 -0700
    varFreqs: add UK Biobank subtrack from Neale Lab Round 2 imputed-v3 variant manifest (13.7M variants, 361k white British samples). TSV → VCF conversion + CrossMap hg19→hg38, refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    3d9187d264d00ee8e681521bc2c942ee2527d4f1 Wed May 13 07:33:38 2026 -0700
    varFreqs: add WBBC (Westlake BioBank for Chinese) subtrack from the Phase I v20210103 release: 4,480 WGS samples, 78.6M variants, per-region frequencies for the 4 Han Chinese geographic subgroups (North/Central/South/Lingnan). databases.tsv + populations.tsv updated for the next varFreqsAll rebuild. refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    4f8f8773bec66a9e993e9897e0b032c6e97dead8 Fri May 15 10:12:29 2026 -0700
    mei: add HMEID, SweGen, and euL1db subtracks Three new MEI catalogues under the existing mei superTrack: meiHmeid (hg38) 36,699 MELT MEIs from HMEID v1.1 (NyuWa+1KGP, 5,675 individuals, Niu et al. 2022, PMID 35212372). Site-level VCF; per-cohort and per-1KGP super- population AC/AN/AF; SVTYPE Alu/L1/SVA/HERVK. meiSwegen (hg38 lifted) 18,090 MELT MEIs from the SweGen 1,000-sample Swedish cohort (Ameur 2017, PMID 28832569; Gardner 2017, PMID 28855259). Built on hg19, liftOver to hg38 (10 unmapped). tableBrowser off per SweGen distribution terms. meiEul1db (hg19+hg38) 8,988 curated L1-HS insertion polymorphisms (MRIPs) from euL1db v1.00 (Mir 2015, PMID 25352549), aggregating 142,495 sample-level SRIPs across 32 published studies. Coloured by lineage (germline/somatic/mixed). Built on hg19, liftOver to hg38 (3 unmapped). Helman2014 used numeric chrom names (23=X, 24=Y) which are renamed during the build. meiEul1dbRef (hg19+hg38) 1,540 reference-genome L1-HS copies catalogued by euL1db (companion to meiEul1db). Single shared mei.ra (in human/) uses $D substitution so each stanza serves both assemblies where applicable. refs #37524
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    99ae46aca64e768875e6cbb2a232a0648bea5344 Fri May 15 10:13:21 2026 -0700
    varFreqs: prefix non-downloadable /gbdb subdirs with "_" so hgdownload rsync skips them; update bigDataUrl paths and Data Access wording on description pages for topmed, allofus, sfariSparkExomes/sfariSparkWgs, and mxbFreq. Combined varFreqsAll.bb moved into _all/. refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    89491842e0ec6b2250aa6f6dc2c83c294930e6d6 Sun May 17 14:38:40 2026 -0700
    Add ChinaMAP phase 1 variant frequencies subtrack on hg38 ChinaMAP (Cao et al. 2020, Cell Res, PMID 32355288) is a deep-WGS cohort of 10,588 Chinese individuals across 27 provinces and 8 ethnic groups, with 147.4 M autosomal variants (136.7 M SNPs + 10.7 M short indels). The released VCF is already on GRCh38 with chr-prefixed chromosomes and ships AC/AF/AN plus matched 1KGP_* INFO fields, so it is served directly via vcfTabix. The ChinaMAP Limitations on Use prohibit redistribution, so the gbdb directory is _chinamap (hidden from hgdownload) and the trackDb stanza has tableBrowser off. Registered in scripts/varFreqs/databases.tsv so the next varFreqsAll combined rebuild picks it up; filter UI is deliberately not added yet (WBBC/TPMI precedent). , refs #36642
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    0a5389e8b81efa99e932f5e9e2424b27ce1af095 Sun May 17 14:53:57 2026 -0700
    varFreqs: add GenomeIndia subtrack (9,768 WGS, 83 endogamous Indian populations, Bhattacharyya 2025) and wire into databases.tsv for the next varFreqsAll rebuild. TSV->VCF conversion synthesizes AC=round(AF*AN) with AN=19536 since the upstream release only ships AF, refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/doc/hs1/mucins.txt
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    99db113e49bd1dd42a3040eaed1e61188a117ecf Wed May 13 05:44:18 2026 -0700
    mucins: new locus-specific mucin VNTR/non-VNTR exon track on hs1 (alpha) Adds a new 'Locus-specific' container in the genes group with two bigGenePred subtracks (mucinsVntr, mucinsNonVntr) derived from Plender et al. 2024 supplementary table 2. The .ra and HTML files live under trackDb/human/ so future locus-specific tracks can share them; hs1 picks them up via include ../mucins.ra alpha. refs #37540
• src/hg/makeDb/doc/mm10.encode4.regulation.txt
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    9c0f52be6be34a120bd16008b57fc60728bd63bd Thu May 14 14:48:03 2026 -0700
    Update ENCODE4 Regulation makedocs with note 141 QA follow-ups (H3K27ac color, metadata Organ casing, longLabel species prefix). refs #34923
• src/hg/makeDb/doc/mm10.txt
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    85b50d205c9a3dec2daf25805e3cf3a929b19a05 Wed May 13 10:57:25 2026 -0700
    Updating the mouseDevTimecourse superTrack per author requests: Renamed shortLabel and longLabel. Made the superTrack on by default with only M21 TPM visible. Added a priority setting. Reordered tissues in .facets files (documented in makedocs). refs #37001
• src/hg/makeDb/doc/mm39/mouseDevTimecourse.txt
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    85b50d205c9a3dec2daf25805e3cf3a929b19a05 Wed May 13 10:57:25 2026 -0700
    Updating the mouseDevTimecourse superTrack per author requests: Renamed shortLabel and longLabel. Made the superTrack on by default with only M21 TPM visible. Added a priority setting. Reordered tissues in .facets files (documented in makedocs). refs #37001
• src/hg/makeDb/doc/vgp577way/mkHtml.pl
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    9b6653339725825ef07c07651fd3003ac1fd88b6 Fri May 15 12:49:43 2026 -0700
    adding in html description page refs #31811
• src/hg/makeDb/doc/vgp577way/mkTdb.sh
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    9b6653339725825ef07c07651fd3003ac1fd88b6 Fri May 15 12:49:43 2026 -0700
    adding in html description page refs #31811
• src/hg/makeDb/doc/vgp577way/vgp577way.pl
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    9b6653339725825ef07c07651fd3003ac1fd88b6 Fri May 15 12:49:43 2026 -0700
    adding in html description page refs #31811
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
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    b949789517a3c519ff77d0763d2175497599d62e Thu May 14 10:51:36 2026 -0700
    fixup the H5N1 name per user bug report
• src/hg/makeDb/scripts/mei/meiDeepmei1kg.as
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    0c1e751423b38dd741875d4cdcc6ffb5d4c4a135 Tue May 12 07:51:34 2026 -0700
    mei: add DeepMEI 1000G subtrack on hg38 91,617 MEIs (68,282 Alu, 16,891 L1, 6,444 SVA) called by DeepMEI on the 3,202 high-coverage 1000 Genomes samples. Same 1-bp anchor convention and Okabe-Ito colors as meiHgsvc3. DeepMEI's symbolic ALT carries no inserted sequence or insertion length, so the bigBed schema is a subset of meiHgsvc3 (no svLen, callerCount, validation flags, insertSeq). Also fixes the INS-svLen:carrierCount label format note in meiHgsvc3.html. refs #37524
• src/hg/makeDb/scripts/mei/meiDeepmei1kgVcfToBed.py
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    0c1e751423b38dd741875d4cdcc6ffb5d4c4a135 Tue May 12 07:51:34 2026 -0700
    mei: add DeepMEI 1000G subtrack on hg38 91,617 MEIs (68,282 Alu, 16,891 L1, 6,444 SVA) called by DeepMEI on the 3,202 high-coverage 1000 Genomes samples. Same 1-bp anchor convention and Okabe-Ito colors as meiHgsvc3. DeepMEI's symbolic ALT carries no inserted sequence or insertion length, so the bigBed schema is a subset of meiHgsvc3 (no svLen, callerCount, validation flags, insertSeq). Also fixes the INS-svLen:carrierCount label format note in meiHgsvc3.html. refs #37524
• src/hg/makeDb/scripts/mei/meiEul1db.as
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    4f8f8773bec66a9e993e9897e0b032c6e97dead8 Fri May 15 10:12:29 2026 -0700
    mei: add HMEID, SweGen, and euL1db subtracks Three new MEI catalogues under the existing mei superTrack: meiHmeid (hg38) 36,699 MELT MEIs from HMEID v1.1 (NyuWa+1KGP, 5,675 individuals, Niu et al. 2022, PMID 35212372). Site-level VCF; per-cohort and per-1KGP super- population AC/AN/AF; SVTYPE Alu/L1/SVA/HERVK. meiSwegen (hg38 lifted) 18,090 MELT MEIs from the SweGen 1,000-sample Swedish cohort (Ameur 2017, PMID 28832569; Gardner 2017, PMID 28855259). Built on hg19, liftOver to hg38 (10 unmapped). tableBrowser off per SweGen distribution terms. meiEul1db (hg19+hg38) 8,988 curated L1-HS insertion polymorphisms (MRIPs) from euL1db v1.00 (Mir 2015, PMID 25352549), aggregating 142,495 sample-level SRIPs across 32 published studies. Coloured by lineage (germline/somatic/mixed). Built on hg19, liftOver to hg38 (3 unmapped). Helman2014 used numeric chrom names (23=X, 24=Y) which are renamed during the build. meiEul1dbRef (hg19+hg38) 1,540 reference-genome L1-HS copies catalogued by euL1db (companion to meiEul1db). Single shared mei.ra (in human/) uses $D substitution so each stanza serves both assemblies where applicable. refs #37524
• src/hg/makeDb/scripts/mei/meiEul1dbRef.as
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    4f8f8773bec66a9e993e9897e0b032c6e97dead8 Fri May 15 10:12:29 2026 -0700
    mei: add HMEID, SweGen, and euL1db subtracks Three new MEI catalogues under the existing mei superTrack: meiHmeid (hg38) 36,699 MELT MEIs from HMEID v1.1 (NyuWa+1KGP, 5,675 individuals, Niu et al. 2022, PMID 35212372). Site-level VCF; per-cohort and per-1KGP super- population AC/AN/AF; SVTYPE Alu/L1/SVA/HERVK. meiSwegen (hg38 lifted) 18,090 MELT MEIs from the SweGen 1,000-sample Swedish cohort (Ameur 2017, PMID 28832569; Gardner 2017, PMID 28855259). Built on hg19, liftOver to hg38 (10 unmapped). tableBrowser off per SweGen distribution terms. meiEul1db (hg19+hg38) 8,988 curated L1-HS insertion polymorphisms (MRIPs) from euL1db v1.00 (Mir 2015, PMID 25352549), aggregating 142,495 sample-level SRIPs across 32 published studies. Coloured by lineage (germline/somatic/mixed). Built on hg19, liftOver to hg38 (3 unmapped). Helman2014 used numeric chrom names (23=X, 24=Y) which are renamed during the build. meiEul1dbRef (hg19+hg38) 1,540 reference-genome L1-HS copies catalogued by euL1db (companion to meiEul1db). Single shared mei.ra (in human/) uses $D substitution so each stanza serves both assemblies where applicable. refs #37524
• src/hg/makeDb/scripts/mei/meiEul1dbRefToBed.py
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    4f8f8773bec66a9e993e9897e0b032c6e97dead8 Fri May 15 10:12:29 2026 -0700
    mei: add HMEID, SweGen, and euL1db subtracks Three new MEI catalogues under the existing mei superTrack: meiHmeid (hg38) 36,699 MELT MEIs from HMEID v1.1 (NyuWa+1KGP, 5,675 individuals, Niu et al. 2022, PMID 35212372). Site-level VCF; per-cohort and per-1KGP super- population AC/AN/AF; SVTYPE Alu/L1/SVA/HERVK. meiSwegen (hg38 lifted) 18,090 MELT MEIs from the SweGen 1,000-sample Swedish cohort (Ameur 2017, PMID 28832569; Gardner 2017, PMID 28855259). Built on hg19, liftOver to hg38 (10 unmapped). tableBrowser off per SweGen distribution terms. meiEul1db (hg19+hg38) 8,988 curated L1-HS insertion polymorphisms (MRIPs) from euL1db v1.00 (Mir 2015, PMID 25352549), aggregating 142,495 sample-level SRIPs across 32 published studies. Coloured by lineage (germline/somatic/mixed). Built on hg19, liftOver to hg38 (3 unmapped). Helman2014 used numeric chrom names (23=X, 24=Y) which are renamed during the build. meiEul1dbRef (hg19+hg38) 1,540 reference-genome L1-HS copies catalogued by euL1db (companion to meiEul1db). Single shared mei.ra (in human/) uses $D substitution so each stanza serves both assemblies where applicable. refs #37524
• src/hg/makeDb/scripts/mei/meiEul1dbToBed.py
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    4f8f8773bec66a9e993e9897e0b032c6e97dead8 Fri May 15 10:12:29 2026 -0700
    mei: add HMEID, SweGen, and euL1db subtracks Three new MEI catalogues under the existing mei superTrack: meiHmeid (hg38) 36,699 MELT MEIs from HMEID v1.1 (NyuWa+1KGP, 5,675 individuals, Niu et al. 2022, PMID 35212372). Site-level VCF; per-cohort and per-1KGP super- population AC/AN/AF; SVTYPE Alu/L1/SVA/HERVK. meiSwegen (hg38 lifted) 18,090 MELT MEIs from the SweGen 1,000-sample Swedish cohort (Ameur 2017, PMID 28832569; Gardner 2017, PMID 28855259). Built on hg19, liftOver to hg38 (10 unmapped). tableBrowser off per SweGen distribution terms. meiEul1db (hg19+hg38) 8,988 curated L1-HS insertion polymorphisms (MRIPs) from euL1db v1.00 (Mir 2015, PMID 25352549), aggregating 142,495 sample-level SRIPs across 32 published studies. Coloured by lineage (germline/somatic/mixed). Built on hg19, liftOver to hg38 (3 unmapped). Helman2014 used numeric chrom names (23=X, 24=Y) which are renamed during the build. meiEul1dbRef (hg19+hg38) 1,540 reference-genome L1-HS copies catalogued by euL1db (companion to meiEul1db). Single shared mei.ra (in human/) uses $D substitution so each stanza serves both assemblies where applicable. refs #37524
• src/hg/makeDb/scripts/mei/meiHmeid.as
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    4f8f8773bec66a9e993e9897e0b032c6e97dead8 Fri May 15 10:12:29 2026 -0700
    mei: add HMEID, SweGen, and euL1db subtracks Three new MEI catalogues under the existing mei superTrack: meiHmeid (hg38) 36,699 MELT MEIs from HMEID v1.1 (NyuWa+1KGP, 5,675 individuals, Niu et al. 2022, PMID 35212372). Site-level VCF; per-cohort and per-1KGP super- population AC/AN/AF; SVTYPE Alu/L1/SVA/HERVK. meiSwegen (hg38 lifted) 18,090 MELT MEIs from the SweGen 1,000-sample Swedish cohort (Ameur 2017, PMID 28832569; Gardner 2017, PMID 28855259). Built on hg19, liftOver to hg38 (10 unmapped). tableBrowser off per SweGen distribution terms. meiEul1db (hg19+hg38) 8,988 curated L1-HS insertion polymorphisms (MRIPs) from euL1db v1.00 (Mir 2015, PMID 25352549), aggregating 142,495 sample-level SRIPs across 32 published studies. Coloured by lineage (germline/somatic/mixed). Built on hg19, liftOver to hg38 (3 unmapped). Helman2014 used numeric chrom names (23=X, 24=Y) which are renamed during the build. meiEul1dbRef (hg19+hg38) 1,540 reference-genome L1-HS copies catalogued by euL1db (companion to meiEul1db). Single shared mei.ra (in human/) uses $D substitution so each stanza serves both assemblies where applicable. refs #37524
• src/hg/makeDb/scripts/mei/meiHmeidVcfToBed.py
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    4f8f8773bec66a9e993e9897e0b032c6e97dead8 Fri May 15 10:12:29 2026 -0700
    mei: add HMEID, SweGen, and euL1db subtracks Three new MEI catalogues under the existing mei superTrack: meiHmeid (hg38) 36,699 MELT MEIs from HMEID v1.1 (NyuWa+1KGP, 5,675 individuals, Niu et al. 2022, PMID 35212372). Site-level VCF; per-cohort and per-1KGP super- population AC/AN/AF; SVTYPE Alu/L1/SVA/HERVK. meiSwegen (hg38 lifted) 18,090 MELT MEIs from the SweGen 1,000-sample Swedish cohort (Ameur 2017, PMID 28832569; Gardner 2017, PMID 28855259). Built on hg19, liftOver to hg38 (10 unmapped). tableBrowser off per SweGen distribution terms. meiEul1db (hg19+hg38) 8,988 curated L1-HS insertion polymorphisms (MRIPs) from euL1db v1.00 (Mir 2015, PMID 25352549), aggregating 142,495 sample-level SRIPs across 32 published studies. Coloured by lineage (germline/somatic/mixed). Built on hg19, liftOver to hg38 (3 unmapped). Helman2014 used numeric chrom names (23=X, 24=Y) which are renamed during the build. meiEul1dbRef (hg19+hg38) 1,540 reference-genome L1-HS copies catalogued by euL1db (companion to meiEul1db). Single shared mei.ra (in human/) uses $D substitution so each stanza serves both assemblies where applicable. refs #37524
• src/hg/makeDb/scripts/mei/meiSwegen.as
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    4f8f8773bec66a9e993e9897e0b032c6e97dead8 Fri May 15 10:12:29 2026 -0700
    mei: add HMEID, SweGen, and euL1db subtracks Three new MEI catalogues under the existing mei superTrack: meiHmeid (hg38) 36,699 MELT MEIs from HMEID v1.1 (NyuWa+1KGP, 5,675 individuals, Niu et al. 2022, PMID 35212372). Site-level VCF; per-cohort and per-1KGP super- population AC/AN/AF; SVTYPE Alu/L1/SVA/HERVK. meiSwegen (hg38 lifted) 18,090 MELT MEIs from the SweGen 1,000-sample Swedish cohort (Ameur 2017, PMID 28832569; Gardner 2017, PMID 28855259). Built on hg19, liftOver to hg38 (10 unmapped). tableBrowser off per SweGen distribution terms. meiEul1db (hg19+hg38) 8,988 curated L1-HS insertion polymorphisms (MRIPs) from euL1db v1.00 (Mir 2015, PMID 25352549), aggregating 142,495 sample-level SRIPs across 32 published studies. Coloured by lineage (germline/somatic/mixed). Built on hg19, liftOver to hg38 (3 unmapped). Helman2014 used numeric chrom names (23=X, 24=Y) which are renamed during the build. meiEul1dbRef (hg19+hg38) 1,540 reference-genome L1-HS copies catalogued by euL1db (companion to meiEul1db). Single shared mei.ra (in human/) uses $D substitution so each stanza serves both assemblies where applicable. refs #37524
• src/hg/makeDb/scripts/mei/meiSwegenVcfToBed.py
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    4f8f8773bec66a9e993e9897e0b032c6e97dead8 Fri May 15 10:12:29 2026 -0700
    mei: add HMEID, SweGen, and euL1db subtracks Three new MEI catalogues under the existing mei superTrack: meiHmeid (hg38) 36,699 MELT MEIs from HMEID v1.1 (NyuWa+1KGP, 5,675 individuals, Niu et al. 2022, PMID 35212372). Site-level VCF; per-cohort and per-1KGP super- population AC/AN/AF; SVTYPE Alu/L1/SVA/HERVK. meiSwegen (hg38 lifted) 18,090 MELT MEIs from the SweGen 1,000-sample Swedish cohort (Ameur 2017, PMID 28832569; Gardner 2017, PMID 28855259). Built on hg19, liftOver to hg38 (10 unmapped). tableBrowser off per SweGen distribution terms. meiEul1db (hg19+hg38) 8,988 curated L1-HS insertion polymorphisms (MRIPs) from euL1db v1.00 (Mir 2015, PMID 25352549), aggregating 142,495 sample-level SRIPs across 32 published studies. Coloured by lineage (germline/somatic/mixed). Built on hg19, liftOver to hg38 (3 unmapped). Helman2014 used numeric chrom names (23=X, 24=Y) which are renamed during the build. meiEul1dbRef (hg19+hg38) 1,540 reference-genome L1-HS copies catalogued by euL1db (companion to meiEul1db). Single shared mei.ra (in human/) uses $D substitution so each stanza serves both assemblies where applicable. refs #37524
• src/hg/makeDb/scripts/mpravardb/mpravardb.as
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    d069df7855eb648b5b53c51ef5218fe2e4a1d087 Wed May 13 12:48:53 2026 -0700
    mpraVarDb script rebuild: standardize NA, fix upstream typos, add pvalue note. refs #37359 Build-script changes (mpravardbToBed.py + mpravardb.as): - sanitize_text() now normalizes "None"/"NA"/"N/A"/"null"/"NULL"/"nan" to empty string. Removes 55,108 stale sentinels: 53,144 disease= "None" eQTL rows, 1,964 disease="NA" Kircher rows, 44 ref/alt=NA Myint rows. - Literal-replacement table for three upstream typos: "30 UTR" -> "3'UTR" (26,546 Schuster description rows), "Familial hypercholesterol emia" -> "Familial hypercholesterolemia" (2,176 Kircher disease rows), "Alchol use disorder" -> "Alcohol use disorder" (88 Rao disease rows). - fmt_mo() renders NaN floats as "NA" in mouseOver helper fields; 30,921 rows that previously showed literal "nan" now read "NA". - Tightened name+rsid handling: treat a value as an rsID only if it starts with "rs". 2,088 hg19-coord-style names like "1_1403972_CG" are reformatted to "chr<X>:<hg38pos>:<ref>><alt>" and the rsid field cleared to "" so the dbSNP linkout doesn't fire on a bogus value. - Removed the 250-char truncation that cut Griesemer descriptions mid-sentence; mpravardb.as switched description and mpraStudy from "string" to "lstring" to admit the full upstream text. Description page (mpraVarDb.html): - Added a "Note (pending upstream fix)" paragraph in Methods explaining the 5,092 rows with pvalue > 1 (test statistic mislabeled in the pvalue field by upstream curators for Mouri 2022 and Tewhey 2016). Bracketed by an HTML comment "TEMP: remove once Tao Wang fixes..." for future cleanup when the next snapshot lands. bigBed rebuilt; itemCount 239,028 preserved. Pre-rebuild backup: /hive/data/genomes/hg38/bed/mpra/mpravardb/mpravardb.bb.pre-2026-05-14-backup Makedoc updated with the QA-2 build-script rebuild section.
• src/hg/makeDb/scripts/mpravardb/mpravardbToBed.py
  • lines changed 50, context: html, text, full: html, text
    d069df7855eb648b5b53c51ef5218fe2e4a1d087 Wed May 13 12:48:53 2026 -0700
    mpraVarDb script rebuild: standardize NA, fix upstream typos, add pvalue note. refs #37359 Build-script changes (mpravardbToBed.py + mpravardb.as): - sanitize_text() now normalizes "None"/"NA"/"N/A"/"null"/"NULL"/"nan" to empty string. Removes 55,108 stale sentinels: 53,144 disease= "None" eQTL rows, 1,964 disease="NA" Kircher rows, 44 ref/alt=NA Myint rows. - Literal-replacement table for three upstream typos: "30 UTR" -> "3'UTR" (26,546 Schuster description rows), "Familial hypercholesterol emia" -> "Familial hypercholesterolemia" (2,176 Kircher disease rows), "Alchol use disorder" -> "Alcohol use disorder" (88 Rao disease rows). - fmt_mo() renders NaN floats as "NA" in mouseOver helper fields; 30,921 rows that previously showed literal "nan" now read "NA". - Tightened name+rsid handling: treat a value as an rsID only if it starts with "rs". 2,088 hg19-coord-style names like "1_1403972_CG" are reformatted to "chr<X>:<hg38pos>:<ref>><alt>" and the rsid field cleared to "" so the dbSNP linkout doesn't fire on a bogus value. - Removed the 250-char truncation that cut Griesemer descriptions mid-sentence; mpravardb.as switched description and mpraStudy from "string" to "lstring" to admit the full upstream text. Description page (mpraVarDb.html): - Added a "Note (pending upstream fix)" paragraph in Methods explaining the 5,092 rows with pvalue > 1 (test statistic mislabeled in the pvalue field by upstream curators for Mouri 2022 and Tewhey 2016). Bracketed by an HTML comment "TEMP: remove once Tao Wang fixes..." for future cleanup when the next snapshot lands. bigBed rebuilt; itemCount 239,028 preserved. Pre-rebuild backup: /hive/data/genomes/hg38/bed/mpra/mpravardb/mpravardb.bb.pre-2026-05-14-backup Makedoc updated with the QA-2 build-script rebuild section.
• src/hg/makeDb/scripts/mucins/mucinsToBigGenePred.py
  • lines changed 106, context: html, text, full: html, text
    99db113e49bd1dd42a3040eaed1e61188a117ecf Wed May 13 05:44:18 2026 -0700
    mucins: new locus-specific mucin VNTR/non-VNTR exon track on hs1 (alpha) Adds a new 'Locus-specific' container in the genes group with two bigGenePred subtracks (mucinsVntr, mucinsNonVntr) derived from Plender et al. 2024 supplementary table 2. The .ra and HTML files live under trackDb/human/ so future locus-specific tracks can share them; hs1 picks them up via include ../mucins.ra alpha. refs #37540
• src/hg/makeDb/scripts/ncOrfs/addIntrons.py
  • lines changed 133, context: html, text, full: html, text
    e390536dad43cc58b7f27f31ffc1df699c7dee03 Tue May 12 06:57:32 2026 -0700
    ncOrfs: Kozak strength coloring, codon display, and uORF intron recovery Each ORF in every ncOrfs subtrack now carries three new annotation fields: startCodon, kozakStrength, and kozakTE (Noderer 2014 TE / 100). Features are colored by kozakTE on a 5-bin gradient (blue<0.5, teal, green, orange, red>=0.8), with purple for non-ATG starts and grey for contexts that could not be retrieved. The colors are wired in colorByKozak.py (COLOR_BINS / GREY / PURPLE). thickStart and thickEnd now span the whole ORF and the trackDb stanzas enable baseColorUseCds=given + baseColorDefault=genomicCodons so codon shading is on by default. Filters added for startCodon, kozakStrength, kozakTE on every subtrack. The bed12 GENCODE Phase II tracks (primary / comprehensive) and the metamorf bedORFtable are now converted to bigGenePred so codon display works on them. The OpenProt "kozak" field is renamed to "kozakMotif" in the new .as so the mouseOver's $kozakStrength substitution is not eaten greedily as $kozak + "Strength". utrAnnotUorfs ships as bed9+1 with no exon/intron structure. A new addIntrons.py preprocessor matches each uORF against the other ncORF tracks by exact (chrom, start, end, strand) and copies the block structure of any donor with introns; the contributing database names go in a new intronsSource field (also exposed as a filter). 6,508 of 44,435 uORFs (14.6%) picked up introns, mostly from MetamORF; the rest stay single-block (intronsSource=none). The Noderer 2014 TE table (PMC4299517 / PMID 25170020) is cached in the repo so the build is reproducible without network access. Reference: Noderer WL et al. Quantitative analysis of mammalian translation initiation sites by FACS-seq. Mol Syst Biol. 2014;10:748. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/ncOrfs/colorByKozak.py
  • lines changed 480, context: html, text, full: html, text
    e390536dad43cc58b7f27f31ffc1df699c7dee03 Tue May 12 06:57:32 2026 -0700
    ncOrfs: Kozak strength coloring, codon display, and uORF intron recovery Each ORF in every ncOrfs subtrack now carries three new annotation fields: startCodon, kozakStrength, and kozakTE (Noderer 2014 TE / 100). Features are colored by kozakTE on a 5-bin gradient (blue<0.5, teal, green, orange, red>=0.8), with purple for non-ATG starts and grey for contexts that could not be retrieved. The colors are wired in colorByKozak.py (COLOR_BINS / GREY / PURPLE). thickStart and thickEnd now span the whole ORF and the trackDb stanzas enable baseColorUseCds=given + baseColorDefault=genomicCodons so codon shading is on by default. Filters added for startCodon, kozakStrength, kozakTE on every subtrack. The bed12 GENCODE Phase II tracks (primary / comprehensive) and the metamorf bedORFtable are now converted to bigGenePred so codon display works on them. The OpenProt "kozak" field is renamed to "kozakMotif" in the new .as so the mouseOver's $kozakStrength substitution is not eaten greedily as $kozak + "Strength". utrAnnotUorfs ships as bed9+1 with no exon/intron structure. A new addIntrons.py preprocessor matches each uORF against the other ncORF tracks by exact (chrom, start, end, strand) and copies the block structure of any donor with introns; the contributing database names go in a new intronsSource field (also exposed as a filter). 6,508 of 44,435 uORFs (14.6%) picked up introns, mostly from MetamORF; the rest stay single-block (intronsSource=none). The Noderer 2014 TE table (PMC4299517 / PMID 25170020) is cached in the repo so the build is reproducible without network access. Reference: Noderer WL et al. Quantitative analysis of mammalian translation initiation sites by FACS-seq. Mol Syst Biol. 2014;10:748. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/ncOrfs/gencNcOrf.as
  • lines changed 33, context: html, text, full: html, text
    e390536dad43cc58b7f27f31ffc1df699c7dee03 Tue May 12 06:57:32 2026 -0700
    ncOrfs: Kozak strength coloring, codon display, and uORF intron recovery Each ORF in every ncOrfs subtrack now carries three new annotation fields: startCodon, kozakStrength, and kozakTE (Noderer 2014 TE / 100). Features are colored by kozakTE on a 5-bin gradient (blue<0.5, teal, green, orange, red>=0.8), with purple for non-ATG starts and grey for contexts that could not be retrieved. The colors are wired in colorByKozak.py (COLOR_BINS / GREY / PURPLE). thickStart and thickEnd now span the whole ORF and the trackDb stanzas enable baseColorUseCds=given + baseColorDefault=genomicCodons so codon shading is on by default. Filters added for startCodon, kozakStrength, kozakTE on every subtrack. The bed12 GENCODE Phase II tracks (primary / comprehensive) and the metamorf bedORFtable are now converted to bigGenePred so codon display works on them. The OpenProt "kozak" field is renamed to "kozakMotif" in the new .as so the mouseOver's $kozakStrength substitution is not eaten greedily as $kozak + "Strength". utrAnnotUorfs ships as bed9+1 with no exon/intron structure. A new addIntrons.py preprocessor matches each uORF against the other ncORF tracks by exact (chrom, start, end, strand) and copies the block structure of any donor with introns; the contributing database names go in a new intronsSource field (also exposed as a filter). 6,508 of 44,435 uORFs (14.6%) picked up introns, mostly from MetamORF; the rest stay single-block (intronsSource=none). The Noderer 2014 TE table (PMC4299517 / PMID 25170020) is cached in the repo so the build is reproducible without network access. Reference: Noderer WL et al. Quantitative analysis of mammalian translation initiation sites by FACS-seq. Mol Syst Biol. 2014;10:748. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/ncOrfs/gencNcOrfPhase2.as
  • lines changed 27, context: html, text, full: html, text
    e390536dad43cc58b7f27f31ffc1df699c7dee03 Tue May 12 06:57:32 2026 -0700
    ncOrfs: Kozak strength coloring, codon display, and uORF intron recovery Each ORF in every ncOrfs subtrack now carries three new annotation fields: startCodon, kozakStrength, and kozakTE (Noderer 2014 TE / 100). Features are colored by kozakTE on a 5-bin gradient (blue<0.5, teal, green, orange, red>=0.8), with purple for non-ATG starts and grey for contexts that could not be retrieved. The colors are wired in colorByKozak.py (COLOR_BINS / GREY / PURPLE). thickStart and thickEnd now span the whole ORF and the trackDb stanzas enable baseColorUseCds=given + baseColorDefault=genomicCodons so codon shading is on by default. Filters added for startCodon, kozakStrength, kozakTE on every subtrack. The bed12 GENCODE Phase II tracks (primary / comprehensive) and the metamorf bedORFtable are now converted to bigGenePred so codon display works on them. The OpenProt "kozak" field is renamed to "kozakMotif" in the new .as so the mouseOver's $kozakStrength substitution is not eaten greedily as $kozak + "Strength". utrAnnotUorfs ships as bed9+1 with no exon/intron structure. A new addIntrons.py preprocessor matches each uORF against the other ncORF tracks by exact (chrom, start, end, strand) and copies the block structure of any donor with introns; the contributing database names go in a new intronsSource field (also exposed as a filter). 6,508 of 44,435 uORFs (14.6%) picked up introns, mostly from MetamORF; the rest stay single-block (intronsSource=none). The Noderer 2014 TE table (PMC4299517 / PMID 25170020) is cached in the repo so the build is reproducible without network access. Reference: Noderer WL et al. Quantitative analysis of mammalian translation initiation sites by FACS-seq. Mol Syst Biol. 2014;10:748. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/ncOrfs/metamorf.as
  • lines changed 32, context: html, text, full: html, text
    e390536dad43cc58b7f27f31ffc1df699c7dee03 Tue May 12 06:57:32 2026 -0700
    ncOrfs: Kozak strength coloring, codon display, and uORF intron recovery Each ORF in every ncOrfs subtrack now carries three new annotation fields: startCodon, kozakStrength, and kozakTE (Noderer 2014 TE / 100). Features are colored by kozakTE on a 5-bin gradient (blue<0.5, teal, green, orange, red>=0.8), with purple for non-ATG starts and grey for contexts that could not be retrieved. The colors are wired in colorByKozak.py (COLOR_BINS / GREY / PURPLE). thickStart and thickEnd now span the whole ORF and the trackDb stanzas enable baseColorUseCds=given + baseColorDefault=genomicCodons so codon shading is on by default. Filters added for startCodon, kozakStrength, kozakTE on every subtrack. The bed12 GENCODE Phase II tracks (primary / comprehensive) and the metamorf bedORFtable are now converted to bigGenePred so codon display works on them. The OpenProt "kozak" field is renamed to "kozakMotif" in the new .as so the mouseOver's $kozakStrength substitution is not eaten greedily as $kozak + "Strength". utrAnnotUorfs ships as bed9+1 with no exon/intron structure. A new addIntrons.py preprocessor matches each uORF against the other ncORF tracks by exact (chrom, start, end, strand) and copies the block structure of any donor with introns; the contributing database names go in a new intronsSource field (also exposed as a filter). 6,508 of 44,435 uORFs (14.6%) picked up introns, mostly from MetamORF; the rest stay single-block (intronsSource=none). The Noderer 2014 TE table (PMC4299517 / PMID 25170020) is cached in the repo so the build is reproducible without network access. Reference: Noderer WL et al. Quantitative analysis of mammalian translation initiation sites by FACS-seq. Mol Syst Biol. 2014;10:748. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/ncOrfs/nuorfdb.as
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    e390536dad43cc58b7f27f31ffc1df699c7dee03 Tue May 12 06:57:32 2026 -0700
    ncOrfs: Kozak strength coloring, codon display, and uORF intron recovery Each ORF in every ncOrfs subtrack now carries three new annotation fields: startCodon, kozakStrength, and kozakTE (Noderer 2014 TE / 100). Features are colored by kozakTE on a 5-bin gradient (blue<0.5, teal, green, orange, red>=0.8), with purple for non-ATG starts and grey for contexts that could not be retrieved. The colors are wired in colorByKozak.py (COLOR_BINS / GREY / PURPLE). thickStart and thickEnd now span the whole ORF and the trackDb stanzas enable baseColorUseCds=given + baseColorDefault=genomicCodons so codon shading is on by default. Filters added for startCodon, kozakStrength, kozakTE on every subtrack. The bed12 GENCODE Phase II tracks (primary / comprehensive) and the metamorf bedORFtable are now converted to bigGenePred so codon display works on them. The OpenProt "kozak" field is renamed to "kozakMotif" in the new .as so the mouseOver's $kozakStrength substitution is not eaten greedily as $kozak + "Strength". utrAnnotUorfs ships as bed9+1 with no exon/intron structure. A new addIntrons.py preprocessor matches each uORF against the other ncORF tracks by exact (chrom, start, end, strand) and copies the block structure of any donor with introns; the contributing database names go in a new intronsSource field (also exposed as a filter). 6,508 of 44,435 uORFs (14.6%) picked up introns, mostly from MetamORF; the rest stay single-block (intronsSource=none). The Noderer 2014 TE table (PMC4299517 / PMID 25170020) is cached in the repo so the build is reproducible without network access. Reference: Noderer WL et al. Quantitative analysis of mammalian translation initiation sites by FACS-seq. Mol Syst Biol. 2014;10:748. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/ncOrfs/openprot.as
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    e390536dad43cc58b7f27f31ffc1df699c7dee03 Tue May 12 06:57:32 2026 -0700
    ncOrfs: Kozak strength coloring, codon display, and uORF intron recovery Each ORF in every ncOrfs subtrack now carries three new annotation fields: startCodon, kozakStrength, and kozakTE (Noderer 2014 TE / 100). Features are colored by kozakTE on a 5-bin gradient (blue<0.5, teal, green, orange, red>=0.8), with purple for non-ATG starts and grey for contexts that could not be retrieved. The colors are wired in colorByKozak.py (COLOR_BINS / GREY / PURPLE). thickStart and thickEnd now span the whole ORF and the trackDb stanzas enable baseColorUseCds=given + baseColorDefault=genomicCodons so codon shading is on by default. Filters added for startCodon, kozakStrength, kozakTE on every subtrack. The bed12 GENCODE Phase II tracks (primary / comprehensive) and the metamorf bedORFtable are now converted to bigGenePred so codon display works on them. The OpenProt "kozak" field is renamed to "kozakMotif" in the new .as so the mouseOver's $kozakStrength substitution is not eaten greedily as $kozak + "Strength". utrAnnotUorfs ships as bed9+1 with no exon/intron structure. A new addIntrons.py preprocessor matches each uORF against the other ncORF tracks by exact (chrom, start, end, strand) and copies the block structure of any donor with introns; the contributing database names go in a new intronsSource field (also exposed as a filter). 6,508 of 44,435 uORFs (14.6%) picked up introns, mostly from MetamORF; the rest stay single-block (intronsSource=none). The Noderer 2014 TE table (PMC4299517 / PMID 25170020) is cached in the repo so the build is reproducible without network access. Reference: Noderer WL et al. Quantitative analysis of mammalian translation initiation sites by FACS-seq. Mol Syst Biol. 2014;10:748. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/ncOrfs/run_kozak.sh
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    e390536dad43cc58b7f27f31ffc1df699c7dee03 Tue May 12 06:57:32 2026 -0700
    ncOrfs: Kozak strength coloring, codon display, and uORF intron recovery Each ORF in every ncOrfs subtrack now carries three new annotation fields: startCodon, kozakStrength, and kozakTE (Noderer 2014 TE / 100). Features are colored by kozakTE on a 5-bin gradient (blue<0.5, teal, green, orange, red>=0.8), with purple for non-ATG starts and grey for contexts that could not be retrieved. The colors are wired in colorByKozak.py (COLOR_BINS / GREY / PURPLE). thickStart and thickEnd now span the whole ORF and the trackDb stanzas enable baseColorUseCds=given + baseColorDefault=genomicCodons so codon shading is on by default. Filters added for startCodon, kozakStrength, kozakTE on every subtrack. The bed12 GENCODE Phase II tracks (primary / comprehensive) and the metamorf bedORFtable are now converted to bigGenePred so codon display works on them. The OpenProt "kozak" field is renamed to "kozakMotif" in the new .as so the mouseOver's $kozakStrength substitution is not eaten greedily as $kozak + "Strength". utrAnnotUorfs ships as bed9+1 with no exon/intron structure. A new addIntrons.py preprocessor matches each uORF against the other ncORF tracks by exact (chrom, start, end, strand) and copies the block structure of any donor with introns; the contributing database names go in a new intronsSource field (also exposed as a filter). 6,508 of 44,435 uORFs (14.6%) picked up introns, mostly from MetamORF; the rest stay single-block (intronsSource=none). The Noderer 2014 TE table (PMC4299517 / PMID 25170020) is cached in the repo so the build is reproducible without network access. Reference: Noderer WL et al. Quantitative analysis of mammalian translation initiation sites by FACS-seq. Mol Syst Biol. 2014;10:748. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/ncOrfs/translational_efficiency.txt
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    e390536dad43cc58b7f27f31ffc1df699c7dee03 Tue May 12 06:57:32 2026 -0700
    ncOrfs: Kozak strength coloring, codon display, and uORF intron recovery Each ORF in every ncOrfs subtrack now carries three new annotation fields: startCodon, kozakStrength, and kozakTE (Noderer 2014 TE / 100). Features are colored by kozakTE on a 5-bin gradient (blue<0.5, teal, green, orange, red>=0.8), with purple for non-ATG starts and grey for contexts that could not be retrieved. The colors are wired in colorByKozak.py (COLOR_BINS / GREY / PURPLE). thickStart and thickEnd now span the whole ORF and the trackDb stanzas enable baseColorUseCds=given + baseColorDefault=genomicCodons so codon shading is on by default. Filters added for startCodon, kozakStrength, kozakTE on every subtrack. The bed12 GENCODE Phase II tracks (primary / comprehensive) and the metamorf bedORFtable are now converted to bigGenePred so codon display works on them. The OpenProt "kozak" field is renamed to "kozakMotif" in the new .as so the mouseOver's $kozakStrength substitution is not eaten greedily as $kozak + "Strength". utrAnnotUorfs ships as bed9+1 with no exon/intron structure. A new addIntrons.py preprocessor matches each uORF against the other ncORF tracks by exact (chrom, start, end, strand) and copies the block structure of any donor with introns; the contributing database names go in a new intronsSource field (also exposed as a filter). 6,508 of 44,435 uORFs (14.6%) picked up introns, mostly from MetamORF; the rest stay single-block (intronsSource=none). The Noderer 2014 TE table (PMC4299517 / PMID 25170020) is cached in the repo so the build is reproducible without network access. Reference: Noderer WL et al. Quantitative analysis of mammalian translation initiation sites by FACS-seq. Mol Syst Biol. 2014;10:748. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/ncOrfs/utrAnnotUorfs.as
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    e390536dad43cc58b7f27f31ffc1df699c7dee03 Tue May 12 06:57:32 2026 -0700
    ncOrfs: Kozak strength coloring, codon display, and uORF intron recovery Each ORF in every ncOrfs subtrack now carries three new annotation fields: startCodon, kozakStrength, and kozakTE (Noderer 2014 TE / 100). Features are colored by kozakTE on a 5-bin gradient (blue<0.5, teal, green, orange, red>=0.8), with purple for non-ATG starts and grey for contexts that could not be retrieved. The colors are wired in colorByKozak.py (COLOR_BINS / GREY / PURPLE). thickStart and thickEnd now span the whole ORF and the trackDb stanzas enable baseColorUseCds=given + baseColorDefault=genomicCodons so codon shading is on by default. Filters added for startCodon, kozakStrength, kozakTE on every subtrack. The bed12 GENCODE Phase II tracks (primary / comprehensive) and the metamorf bedORFtable are now converted to bigGenePred so codon display works on them. The OpenProt "kozak" field is renamed to "kozakMotif" in the new .as so the mouseOver's $kozakStrength substitution is not eaten greedily as $kozak + "Strength". utrAnnotUorfs ships as bed9+1 with no exon/intron structure. A new addIntrons.py preprocessor matches each uORF against the other ncORF tracks by exact (chrom, start, end, strand) and copies the block structure of any donor with introns; the contributing database names go in a new intronsSource field (also exposed as a filter). 6,508 of 44,435 uORFs (14.6%) picked up introns, mostly from MetamORF; the rest stay single-block (intronsSource=none). The Noderer 2014 TE table (PMC4299517 / PMID 25170020) is cached in the repo so the build is reproducible without network access. Reference: Noderer WL et al. Quantitative analysis of mammalian translation initiation sites by FACS-seq. Mol Syst Biol. 2014;10:748. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/nmd/nmdDetectAi/makeBigBed.py
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    7bec995472122739bf0f076de2603708059c65ce Wed May 13 17:23:37 2026 -0700
    Adding NMDetective-AI subtracks (bigWig + bigBed) under the NMD Escape superTrack. refs #33737 Two new subtracks slotted between NMD Escape RefSeq and NMDetective-A (priorities 1.7 and 1.8): - nmdDetectiveAi - position-averaged predictions (bigWig) - nmdDetectiveAiBed - per-stop-gain predictions, one item per (transcript, codon, mutant codon), with diverging Okabe-Ito coloring and a pre-rendered mouseover Predictions are from Veiner et al. (bioRxiv 10.64898/2026.03.24.714003), covering MANE Select transcripts at Gencode v46. Verdict bins in the bigBed mouseover use the GMM-derived thresholds reported in the paper's Methods (-0.17 / +0.43), not symmetric +/- 0.3. Description page covers the +0.5 / -0.5 anchor convention, threshold derivation, and the pre-print status.
• src/hg/makeDb/scripts/nmd/nmdDetectAi/nmdDetectAi.as
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    7bec995472122739bf0f076de2603708059c65ce Wed May 13 17:23:37 2026 -0700
    Adding NMDetective-AI subtracks (bigWig + bigBed) under the NMD Escape superTrack. refs #33737 Two new subtracks slotted between NMD Escape RefSeq and NMDetective-A (priorities 1.7 and 1.8): - nmdDetectiveAi - position-averaged predictions (bigWig) - nmdDetectiveAiBed - per-stop-gain predictions, one item per (transcript, codon, mutant codon), with diverging Okabe-Ito coloring and a pre-rendered mouseover Predictions are from Veiner et al. (bioRxiv 10.64898/2026.03.24.714003), covering MANE Select transcripts at Gencode v46. Verdict bins in the bigBed mouseover use the GMM-derived thresholds reported in the paper's Methods (-0.17 / +0.43), not symmetric +/- 0.3. Description page covers the +0.5 / -0.5 anchor convention, threshold derivation, and the pre-print status.
• src/hg/makeDb/scripts/varFreqs/databases.tsv
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    3d9187d264d00ee8e681521bc2c942ee2527d4f1 Wed May 13 07:33:38 2026 -0700
    varFreqs: add WBBC (Westlake BioBank for Chinese) subtrack from the Phase I v20210103 release: 4,480 WGS samples, 78.6M variants, per-region frequencies for the 4 Han Chinese geographic subgroups (North/Central/South/Lingnan). databases.tsv + populations.tsv updated for the next varFreqsAll rebuild. refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    89491842e0ec6b2250aa6f6dc2c83c294930e6d6 Sun May 17 14:38:40 2026 -0700
    Add ChinaMAP phase 1 variant frequencies subtrack on hg38 ChinaMAP (Cao et al. 2020, Cell Res, PMID 32355288) is a deep-WGS cohort of 10,588 Chinese individuals across 27 provinces and 8 ethnic groups, with 147.4 M autosomal variants (136.7 M SNPs + 10.7 M short indels). The released VCF is already on GRCh38 with chr-prefixed chromosomes and ships AC/AF/AN plus matched 1KGP_* INFO fields, so it is served directly via vcfTabix. The ChinaMAP Limitations on Use prohibit redistribution, so the gbdb directory is _chinamap (hidden from hgdownload) and the trackDb stanza has tableBrowser off. Registered in scripts/varFreqs/databases.tsv so the next varFreqsAll combined rebuild picks it up; filter UI is deliberately not added yet (WBBC/TPMI precedent). , refs #36642
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    0a5389e8b81efa99e932f5e9e2424b27ce1af095 Sun May 17 14:53:57 2026 -0700
    varFreqs: add GenomeIndia subtrack (9,768 WGS, 83 endogamous Indian populations, Bhattacharyya 2025) and wire into databases.tsv for the next varFreqsAll rebuild. TSV->VCF conversion synthesizes AC=round(AF*AN) with AN=19536 since the upstream release only ships AF, refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/varFreqs/genomeindiaToVcf.py
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    0a5389e8b81efa99e932f5e9e2424b27ce1af095 Sun May 17 14:53:57 2026 -0700
    varFreqs: add GenomeIndia subtrack (9,768 WGS, 83 endogamous Indian populations, Bhattacharyya 2025) and wire into databases.tsv for the next varFreqsAll rebuild. TSV->VCF conversion synthesizes AC=round(AF*AN) with AN=19536 since the upstream release only ships AF, refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/varFreqs/populations.tsv
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    3d9187d264d00ee8e681521bc2c942ee2527d4f1 Wed May 13 07:33:38 2026 -0700
    varFreqs: add WBBC (Westlake BioBank for Chinese) subtrack from the Phase I v20210103 release: 4,480 WGS samples, 78.6M variants, per-region frequencies for the 4 Han Chinese geographic subgroups (North/Central/South/Lingnan). databases.tsv + populations.tsv updated for the next varFreqsAll rebuild. refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/varFreqs/ukbbToVcf.py
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    9a49afb16653363a70d8e4d205513008b7b08df5 Wed May 13 06:18:42 2026 -0700
    varFreqs: add UK Biobank subtrack from Neale Lab Round 2 imputed-v3 variant manifest (13.7M variants, 361k white British samples). TSV → VCF conversion + CrossMap hg19→hg38, refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/varFreqs/wbbcFix.py
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    3d9187d264d00ee8e681521bc2c942ee2527d4f1 Wed May 13 07:33:38 2026 -0700
    varFreqs: add WBBC (Westlake BioBank for Chinese) subtrack from the Phase I v20210103 release: 4,480 WGS samples, 78.6M variants, per-region frequencies for the 4 Han Chinese geographic subgroups (North/Central/South/Lingnan). databases.tsv + populations.tsv updated for the next varFreqsAll rebuild. refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/cpgIsland.html
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    75640104127592366faa7478485e5a88f8144a0b Thu May 14 08:44:10 2026 -0700
    fixing Miklem -> Micklem, refs #37539
• src/hg/makeDb/trackDb/cpgIslandExt.html
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    75640104127592366faa7478485e5a88f8144a0b Thu May 14 08:44:10 2026 -0700
    fixing Miklem -> Micklem, refs #37539
• src/hg/makeDb/trackDb/cpgIslandSuper.html
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    75640104127592366faa7478485e5a88f8144a0b Thu May 14 08:44:10 2026 -0700
    fixing Miklem -> Micklem, refs #37539
• src/hg/makeDb/trackDb/human/allofus.html
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    99ae46aca64e768875e6cbb2a232a0648bea5344 Fri May 15 10:13:21 2026 -0700
    varFreqs: prefix non-downloadable /gbdb subdirs with "_" so hgdownload rsync skips them; update bigDataUrl paths and Data Access wording on description pages for topmed, allofus, sfariSparkExomes/sfariSparkWgs, and mxbFreq. Combined varFreqsAll.bb moved into _all/. refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/chinamap.html
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    89491842e0ec6b2250aa6f6dc2c83c294930e6d6 Sun May 17 14:38:40 2026 -0700
    Add ChinaMAP phase 1 variant frequencies subtrack on hg38 ChinaMAP (Cao et al. 2020, Cell Res, PMID 32355288) is a deep-WGS cohort of 10,588 Chinese individuals across 27 provinces and 8 ethnic groups, with 147.4 M autosomal variants (136.7 M SNPs + 10.7 M short indels). The released VCF is already on GRCh38 with chr-prefixed chromosomes and ships AC/AF/AN plus matched 1KGP_* INFO fields, so it is served directly via vcfTabix. The ChinaMAP Limitations on Use prohibit redistribution, so the gbdb directory is _chinamap (hidden from hgdownload) and the trackDb stanza has tableBrowser off. Registered in scripts/varFreqs/databases.tsv so the next varFreqsAll combined rebuild picks it up; filter UI is deliberately not added yet (WBBC/TPMI precedent). , refs #36642
• src/hg/makeDb/trackDb/human/genomeindia.html
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    0a5389e8b81efa99e932f5e9e2424b27ce1af095 Sun May 17 14:53:57 2026 -0700
    varFreqs: add GenomeIndia subtrack (9,768 WGS, 83 endogamous Indian populations, Bhattacharyya 2025) and wire into databases.tsv for the next varFreqsAll rebuild. TSV->VCF conversion synthesizes AC=round(AF*AN) with AN=19536 since the upstream release only ships AF, refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/gencNcOrfs.html
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    0e8db317577ae12e12f630a202284356580a0855 Tue May 12 16:51:33 2026 -0700
    Adding documentation about the Kozak display conventions. Fixing the references section found by Claude, refs #35101
• src/hg/makeDb/trackDb/human/hg38/metamorf.html
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    e0f6831ec83b8ded192579901d76dfff561d0500 Tue May 12 07:15:28 2026 -0700
    ncOrfs: point subtrack docs at the .kozak.bb files The trackDb stanzas now serve the Kozak-colored .kozak.bb files; update the example bigBedToBed download URLs on the four subtrack doc pages so they match what is actually published. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    0e8db317577ae12e12f630a202284356580a0855 Tue May 12 16:51:33 2026 -0700
    Adding documentation about the Kozak display conventions. Fixing the references section found by Claude, refs #35101
• src/hg/makeDb/trackDb/human/hg38/mpraVarDb.html
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    d069df7855eb648b5b53c51ef5218fe2e4a1d087 Wed May 13 12:48:53 2026 -0700
    mpraVarDb script rebuild: standardize NA, fix upstream typos, add pvalue note. refs #37359 Build-script changes (mpravardbToBed.py + mpravardb.as): - sanitize_text() now normalizes "None"/"NA"/"N/A"/"null"/"NULL"/"nan" to empty string. Removes 55,108 stale sentinels: 53,144 disease= "None" eQTL rows, 1,964 disease="NA" Kircher rows, 44 ref/alt=NA Myint rows. - Literal-replacement table for three upstream typos: "30 UTR" -> "3'UTR" (26,546 Schuster description rows), "Familial hypercholesterol emia" -> "Familial hypercholesterolemia" (2,176 Kircher disease rows), "Alchol use disorder" -> "Alcohol use disorder" (88 Rao disease rows). - fmt_mo() renders NaN floats as "NA" in mouseOver helper fields; 30,921 rows that previously showed literal "nan" now read "NA". - Tightened name+rsid handling: treat a value as an rsID only if it starts with "rs". 2,088 hg19-coord-style names like "1_1403972_CG" are reformatted to "chr<X>:<hg38pos>:<ref>><alt>" and the rsid field cleared to "" so the dbSNP linkout doesn't fire on a bogus value. - Removed the 250-char truncation that cut Griesemer descriptions mid-sentence; mpravardb.as switched description and mpraStudy from "string" to "lstring" to admit the full upstream text. Description page (mpraVarDb.html): - Added a "Note (pending upstream fix)" paragraph in Methods explaining the 5,092 rows with pvalue > 1 (test statistic mislabeled in the pvalue field by upstream curators for Mouri 2022 and Tewhey 2016). Bracketed by an HTML comment "TEMP: remove once Tao Wang fixes..." for future cleanup when the next snapshot lands. bigBed rebuilt; itemCount 239,028 preserved. Pre-rebuild backup: /hive/data/genomes/hg38/bed/mpra/mpravardb/mpravardb.bb.pre-2026-05-14-backup Makedoc updated with the QA-2 build-script rebuild section.
• src/hg/makeDb/trackDb/human/hg38/ncOrfs.html
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    e390536dad43cc58b7f27f31ffc1df699c7dee03 Tue May 12 06:57:32 2026 -0700
    ncOrfs: Kozak strength coloring, codon display, and uORF intron recovery Each ORF in every ncOrfs subtrack now carries three new annotation fields: startCodon, kozakStrength, and kozakTE (Noderer 2014 TE / 100). Features are colored by kozakTE on a 5-bin gradient (blue<0.5, teal, green, orange, red>=0.8), with purple for non-ATG starts and grey for contexts that could not be retrieved. The colors are wired in colorByKozak.py (COLOR_BINS / GREY / PURPLE). thickStart and thickEnd now span the whole ORF and the trackDb stanzas enable baseColorUseCds=given + baseColorDefault=genomicCodons so codon shading is on by default. Filters added for startCodon, kozakStrength, kozakTE on every subtrack. The bed12 GENCODE Phase II tracks (primary / comprehensive) and the metamorf bedORFtable are now converted to bigGenePred so codon display works on them. The OpenProt "kozak" field is renamed to "kozakMotif" in the new .as so the mouseOver's $kozakStrength substitution is not eaten greedily as $kozak + "Strength". utrAnnotUorfs ships as bed9+1 with no exon/intron structure. A new addIntrons.py preprocessor matches each uORF against the other ncORF tracks by exact (chrom, start, end, strand) and copies the block structure of any donor with introns; the contributing database names go in a new intronsSource field (also exposed as a filter). 6,508 of 44,435 uORFs (14.6%) picked up introns, mostly from MetamORF; the rest stay single-block (intronsSource=none). The Noderer 2014 TE table (PMC4299517 / PMID 25170020) is cached in the repo so the build is reproducible without network access. Reference: Noderer WL et al. Quantitative analysis of mammalian translation initiation sites by FACS-seq. Mol Syst Biol. 2014;10:748. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    6771720648a87e9780015cd45f03f4eb24406eb6 Tue May 12 07:24:57 2026 -0700
    ncOrfs: document the Kozak annotation scripts and credit VuTR Add a paragraph to the supertrack html describing the colorByKozak.py / addIntrons.py scripts and the per-track autoSql files, with links to the kent source tree and the makedoc. The Kozak strength logic is a Python port of the routines in the VuTR pipeline (Whiffin lab); credit them. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    0e8db317577ae12e12f630a202284356580a0855 Tue May 12 16:51:33 2026 -0700
    Adding documentation about the Kozak display conventions. Fixing the references section found by Claude, refs #35101
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    7d78f921ec9565ca90aa5ea868a1a5cf43bc6c3e Wed May 13 15:13:57 2026 -0700
    Fixing row count typo (off by 1), refs #35101
• src/hg/makeDb/trackDb/human/hg38/ncOrfs.ra
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    e390536dad43cc58b7f27f31ffc1df699c7dee03 Tue May 12 06:57:32 2026 -0700
    ncOrfs: Kozak strength coloring, codon display, and uORF intron recovery Each ORF in every ncOrfs subtrack now carries three new annotation fields: startCodon, kozakStrength, and kozakTE (Noderer 2014 TE / 100). Features are colored by kozakTE on a 5-bin gradient (blue<0.5, teal, green, orange, red>=0.8), with purple for non-ATG starts and grey for contexts that could not be retrieved. The colors are wired in colorByKozak.py (COLOR_BINS / GREY / PURPLE). thickStart and thickEnd now span the whole ORF and the trackDb stanzas enable baseColorUseCds=given + baseColorDefault=genomicCodons so codon shading is on by default. Filters added for startCodon, kozakStrength, kozakTE on every subtrack. The bed12 GENCODE Phase II tracks (primary / comprehensive) and the metamorf bedORFtable are now converted to bigGenePred so codon display works on them. The OpenProt "kozak" field is renamed to "kozakMotif" in the new .as so the mouseOver's $kozakStrength substitution is not eaten greedily as $kozak + "Strength". utrAnnotUorfs ships as bed9+1 with no exon/intron structure. A new addIntrons.py preprocessor matches each uORF against the other ncORF tracks by exact (chrom, start, end, strand) and copies the block structure of any donor with introns; the contributing database names go in a new intronsSource field (also exposed as a filter). 6,508 of 44,435 uORFs (14.6%) picked up introns, mostly from MetamORF; the rest stay single-block (intronsSource=none). The Noderer 2014 TE table (PMC4299517 / PMID 25170020) is cached in the repo so the build is reproducible without network access. Reference: Noderer WL et al. Quantitative analysis of mammalian translation initiation sites by FACS-seq. Mol Syst Biol. 2014;10:748. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    f2d54453461ea7e7e6ef2477fc449410e5d4461a Tue May 12 10:22:36 2026 -0700
    Fixing the type for the tracks since there are no extra fields. Updating the mouseOver, refs #35101
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    d9a5c6aced28abadab3aedb645c7b96c2f7c834f Tue May 12 16:30:08 2026 -0700
    Updating the filters for the ncORFs track, refs #35101
• src/hg/makeDb/trackDb/human/hg38/nmd.html
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    7bec995472122739bf0f076de2603708059c65ce Wed May 13 17:23:37 2026 -0700
    Adding NMDetective-AI subtracks (bigWig + bigBed) under the NMD Escape superTrack. refs #33737 Two new subtracks slotted between NMD Escape RefSeq and NMDetective-A (priorities 1.7 and 1.8): - nmdDetectiveAi - position-averaged predictions (bigWig) - nmdDetectiveAiBed - per-stop-gain predictions, one item per (transcript, codon, mutant codon), with diverging Okabe-Ito coloring and a pre-rendered mouseover Predictions are from Veiner et al. (bioRxiv 10.64898/2026.03.24.714003), covering MANE Select transcripts at Gencode v46. Verdict bins in the bigBed mouseover use the GMM-derived thresholds reported in the paper's Methods (-0.17 / +0.43), not symmetric +/- 0.3. Description page covers the +0.5 / -0.5 anchor convention, threshold derivation, and the pre-print status.
• src/hg/makeDb/trackDb/human/hg38/nmd.ra
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    7bec995472122739bf0f076de2603708059c65ce Wed May 13 17:23:37 2026 -0700
    Adding NMDetective-AI subtracks (bigWig + bigBed) under the NMD Escape superTrack. refs #33737 Two new subtracks slotted between NMD Escape RefSeq and NMDetective-A (priorities 1.7 and 1.8): - nmdDetectiveAi - position-averaged predictions (bigWig) - nmdDetectiveAiBed - per-stop-gain predictions, one item per (transcript, codon, mutant codon), with diverging Okabe-Ito coloring and a pre-rendered mouseover Predictions are from Veiner et al. (bioRxiv 10.64898/2026.03.24.714003), covering MANE Select transcripts at Gencode v46. Verdict bins in the bigBed mouseover use the GMM-derived thresholds reported in the paper's Methods (-0.17 / +0.43), not symmetric +/- 0.3. Description page covers the +0.5 / -0.5 anchor convention, threshold derivation, and the pre-print status.
• src/hg/makeDb/trackDb/human/hg38/nmdDetectiveAi.html
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    7bec995472122739bf0f076de2603708059c65ce Wed May 13 17:23:37 2026 -0700
    Adding NMDetective-AI subtracks (bigWig + bigBed) under the NMD Escape superTrack. refs #33737 Two new subtracks slotted between NMD Escape RefSeq and NMDetective-A (priorities 1.7 and 1.8): - nmdDetectiveAi - position-averaged predictions (bigWig) - nmdDetectiveAiBed - per-stop-gain predictions, one item per (transcript, codon, mutant codon), with diverging Okabe-Ito coloring and a pre-rendered mouseover Predictions are from Veiner et al. (bioRxiv 10.64898/2026.03.24.714003), covering MANE Select transcripts at Gencode v46. Verdict bins in the bigBed mouseover use the GMM-derived thresholds reported in the paper's Methods (-0.17 / +0.43), not symmetric +/- 0.3. Description page covers the +0.5 / -0.5 anchor convention, threshold derivation, and the pre-print status.
• src/hg/makeDb/trackDb/human/hg38/nuorfdb.html
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    e0f6831ec83b8ded192579901d76dfff561d0500 Tue May 12 07:15:28 2026 -0700
    ncOrfs: point subtrack docs at the .kozak.bb files The trackDb stanzas now serve the Kozak-colored .kozak.bb files; update the example bigBedToBed download URLs on the four subtrack doc pages so they match what is actually published. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    0e8db317577ae12e12f630a202284356580a0855 Tue May 12 16:51:33 2026 -0700
    Adding documentation about the Kozak display conventions. Fixing the references section found by Claude, refs #35101
• src/hg/makeDb/trackDb/human/hg38/openprot.html
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    e0f6831ec83b8ded192579901d76dfff561d0500 Tue May 12 07:15:28 2026 -0700
    ncOrfs: point subtrack docs at the .kozak.bb files The trackDb stanzas now serve the Kozak-colored .kozak.bb files; update the example bigBedToBed download URLs on the four subtrack doc pages so they match what is actually published. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    0e8db317577ae12e12f630a202284356580a0855 Tue May 12 16:51:33 2026 -0700
    Adding documentation about the Kozak display conventions. Fixing the references section found by Claude, refs #35101
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    5cdfbadbb31400fffdef53c04a3285a63e4fc2cb Fri May 15 10:03:21 2026 -0700
    Silent release of MPRA track, refs #37359
• src/hg/makeDb/trackDb/human/hg38/utrAnnotUorfs.html
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    e0f6831ec83b8ded192579901d76dfff561d0500 Tue May 12 07:15:28 2026 -0700
    ncOrfs: point subtrack docs at the .kozak.bb files The trackDb stanzas now serve the Kozak-colored .kozak.bb files; update the example bigBedToBed download URLs on the four subtrack doc pages so they match what is actually published. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    0e8db317577ae12e12f630a202284356580a0855 Tue May 12 16:51:33 2026 -0700
    Adding documentation about the Kozak display conventions. Fixing the references section found by Claude, refs #35101
• src/hg/makeDb/trackDb/human/hg38/vgp577way.html
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    f3f2f2737fb10c23e74c589ded7a1dae1b6a760b Fri May 15 13:40:09 2026 -0700
    add description page and phyloP track for VGP 577-way refs #31811
• src/hg/makeDb/trackDb/human/hg38/vgp577way.trackDb.ra
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    0f8e1c68f7bd3806bfd5c0fe0005ee9b71ffdc92 Fri May 15 14:06:48 2026 -0700
    add description page and phyloP track for VGP 577-way refs #31811
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.html
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    4467111a88e1be93379b63492fc5c072e1dab930 Wed May 13 20:37:11 2026 -0700
    ENCODE4 Regulation DNase/ATAC/Histone/CTCF (Indiv.) description page cleanup (hg38 and mm10): added Signal/Peak subtrack info, matched filter facet names to hgTrackUi (Assay, Organ, Biosample Type, Data Type, Life Stage), removed first-person Credits. refs #34923
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.ra
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    47519c28b9a21f1ca7ad8881ccd375ff40d7b206 Thu May 14 14:46:13 2026 -0700
    Fix hg38 H3K27ac peak color and strip species prefix from ENCODE4 Regulation bigComposite longLabels. refs #34923 Two QA cleanups from #34923 note 141: - hg38 H3K27ac peak subtracks were colored 255,205,0 (bright #FFCD00, the cCRE classification yellow) while the matching signal subtracks used 181,145,0 (mustard #B59100, the contrast-darkened assay color from /gbdb/hg38/encode4/regulation/epi_colors.json). Changed all 554 peak stanzas in wgEncodeReg4Epigenetics.ra to 181,145,0 so peak + signal match each other and the description-page color legend. mm10 H3K27ac already used 181,145,0 throughout. - Stripped the redundant "Homo sapiens " / "Mus musculus " prefix from the longLabel of every subtrack in the six bigComposite .ra files. 100% of subtracks had the prefix (14,929 total: 6,353 hg38 Epi + 4,964 hg38 TfChip + 1,046 hg38 RnaSeq + 1,178 mm10 Epi + 334 mm10 TfChip + 1,054 mm10 RnaSeq). The species is implicit on a specific assembly and the prefix was pushing biosample descriptions off the visible label width. shortLabels and track names untouched.
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4RnaSeq.ra
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    47519c28b9a21f1ca7ad8881ccd375ff40d7b206 Thu May 14 14:46:13 2026 -0700
    Fix hg38 H3K27ac peak color and strip species prefix from ENCODE4 Regulation bigComposite longLabels. refs #34923 Two QA cleanups from #34923 note 141: - hg38 H3K27ac peak subtracks were colored 255,205,0 (bright #FFCD00, the cCRE classification yellow) while the matching signal subtracks used 181,145,0 (mustard #B59100, the contrast-darkened assay color from /gbdb/hg38/encode4/regulation/epi_colors.json). Changed all 554 peak stanzas in wgEncodeReg4Epigenetics.ra to 181,145,0 so peak + signal match each other and the description-page color legend. mm10 H3K27ac already used 181,145,0 throughout. - Stripped the redundant "Homo sapiens " / "Mus musculus " prefix from the longLabel of every subtrack in the six bigComposite .ra files. 100% of subtracks had the prefix (14,929 total: 6,353 hg38 Epi + 4,964 hg38 TfChip + 1,046 hg38 RnaSeq + 1,178 mm10 Epi + 334 mm10 TfChip + 1,054 mm10 RnaSeq). The species is implicit on a specific assembly and the prefix was pushing biosample descriptions off the visible label width. shortLabels and track names untouched.
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.ra
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    47519c28b9a21f1ca7ad8881ccd375ff40d7b206 Thu May 14 14:46:13 2026 -0700
    Fix hg38 H3K27ac peak color and strip species prefix from ENCODE4 Regulation bigComposite longLabels. refs #34923 Two QA cleanups from #34923 note 141: - hg38 H3K27ac peak subtracks were colored 255,205,0 (bright #FFCD00, the cCRE classification yellow) while the matching signal subtracks used 181,145,0 (mustard #B59100, the contrast-darkened assay color from /gbdb/hg38/encode4/regulation/epi_colors.json). Changed all 554 peak stanzas in wgEncodeReg4Epigenetics.ra to 181,145,0 so peak + signal match each other and the description-page color legend. mm10 H3K27ac already used 181,145,0 throughout. - Stripped the redundant "Homo sapiens " / "Mus musculus " prefix from the longLabel of every subtrack in the six bigComposite .ra files. 100% of subtracks had the prefix (14,929 total: 6,353 hg38 Epi + 4,964 hg38 TfChip + 1,046 hg38 RnaSeq + 1,178 mm10 Epi + 334 mm10 TfChip + 1,054 mm10 RnaSeq). The species is implicit on a specific assembly and the prefix was pushing biosample descriptions off the visible label width. shortLabels and track names untouched.
• src/hg/makeDb/trackDb/human/hs1/trackDb.ra
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    99db113e49bd1dd42a3040eaed1e61188a117ecf Wed May 13 05:44:18 2026 -0700
    mucins: new locus-specific mucin VNTR/non-VNTR exon track on hs1 (alpha) Adds a new 'Locus-specific' container in the genes group with two bigGenePred subtracks (mucinsVntr, mucinsNonVntr) derived from Plender et al. 2024 supplementary table 2. The .ra and HTML files live under trackDb/human/ so future locus-specific tracks can share them; hs1 picks them up via include ../mucins.ra alpha. refs #37540
• src/hg/makeDb/trackDb/human/hs1/vgp577way.html
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    18a9b36bfd20cd33be49311a62bda0a268ea670b Fri May 15 14:02:29 2026 -0700
    add description page and phyloP track for VGP 577-way refs #31811
• src/hg/makeDb/trackDb/human/hs1/vgp577way.trackDb.ra
  • lines changed 28, context: html, text, full: html, text
    18a9b36bfd20cd33be49311a62bda0a268ea670b Fri May 15 14:02:29 2026 -0700
    add description page and phyloP track for VGP 577-way refs #31811
• src/hg/makeDb/trackDb/human/indigenomes.html
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    2f44ab096235810d5d621b7356bc64fbebe82494 Wed May 13 13:02:57 2026 -0700
    varFreqs: fix numeric-claim discrepancies on indigenomes.html and sgdpFreq.html. indigenomes.html: clarify that the deployed VCF is the public release subset (18,016,257 records) of the larger Jain 2021 callset (55.8M variants), and note that the public release is sites-only with a VRT variant-type INFO field and no AC/AF. sgdpFreq.html: update Methods to reflect the deployed file (44,756,737 SNV records, 601,775 multiallelic decomposed); drop the "34.4M SNPs + 2.1M indels" claim; clarify that the Mallick 2016 FermiKit indel callset is not carried in this track. refs #36642
• src/hg/makeDb/trackDb/human/locusSpec.html
  • lines changed 27, context: html, text, full: html, text
    99db113e49bd1dd42a3040eaed1e61188a117ecf Wed May 13 05:44:18 2026 -0700
    mucins: new locus-specific mucin VNTR/non-VNTR exon track on hs1 (alpha) Adds a new 'Locus-specific' container in the genes group with two bigGenePred subtracks (mucinsVntr, mucinsNonVntr) derived from Plender et al. 2024 supplementary table 2. The .ra and HTML files live under trackDb/human/ so future locus-specific tracks can share them; hs1 picks them up via include ../mucins.ra alpha. refs #37540
• src/hg/makeDb/trackDb/human/mei.html
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    0c1e751423b38dd741875d4cdcc6ffb5d4c4a135 Tue May 12 07:51:34 2026 -0700
    mei: add DeepMEI 1000G subtrack on hg38 91,617 MEIs (68,282 Alu, 16,891 L1, 6,444 SVA) called by DeepMEI on the 3,202 high-coverage 1000 Genomes samples. Same 1-bp anchor convention and Okabe-Ito colors as meiHgsvc3. DeepMEI's symbolic ALT carries no inserted sequence or insertion length, so the bigBed schema is a subset of meiHgsvc3 (no svLen, callerCount, validation flags, insertSeq). Also fixes the INS-svLen:carrierCount label format note in meiHgsvc3.html. refs #37524
• src/hg/makeDb/trackDb/human/mei.ra
  • lines changed 20, context: html, text, full: html, text
    0c1e751423b38dd741875d4cdcc6ffb5d4c4a135 Tue May 12 07:51:34 2026 -0700
    mei: add DeepMEI 1000G subtrack on hg38 91,617 MEIs (68,282 Alu, 16,891 L1, 6,444 SVA) called by DeepMEI on the 3,202 high-coverage 1000 Genomes samples. Same 1-bp anchor convention and Okabe-Ito colors as meiHgsvc3. DeepMEI's symbolic ALT carries no inserted sequence or insertion length, so the bigBed schema is a subset of meiHgsvc3 (no svLen, callerCount, validation flags, insertSeq). Also fixes the INS-svLen:carrierCount label format note in meiHgsvc3.html. refs #37524
  • lines changed 104, context: html, text, full: html, text
    4f8f8773bec66a9e993e9897e0b032c6e97dead8 Fri May 15 10:12:29 2026 -0700
    mei: add HMEID, SweGen, and euL1db subtracks Three new MEI catalogues under the existing mei superTrack: meiHmeid (hg38) 36,699 MELT MEIs from HMEID v1.1 (NyuWa+1KGP, 5,675 individuals, Niu et al. 2022, PMID 35212372). Site-level VCF; per-cohort and per-1KGP super- population AC/AN/AF; SVTYPE Alu/L1/SVA/HERVK. meiSwegen (hg38 lifted) 18,090 MELT MEIs from the SweGen 1,000-sample Swedish cohort (Ameur 2017, PMID 28832569; Gardner 2017, PMID 28855259). Built on hg19, liftOver to hg38 (10 unmapped). tableBrowser off per SweGen distribution terms. meiEul1db (hg19+hg38) 8,988 curated L1-HS insertion polymorphisms (MRIPs) from euL1db v1.00 (Mir 2015, PMID 25352549), aggregating 142,495 sample-level SRIPs across 32 published studies. Coloured by lineage (germline/somatic/mixed). Built on hg19, liftOver to hg38 (3 unmapped). Helman2014 used numeric chrom names (23=X, 24=Y) which are renamed during the build. meiEul1dbRef (hg19+hg38) 1,540 reference-genome L1-HS copies catalogued by euL1db (companion to meiEul1db). Single shared mei.ra (in human/) uses $D substitution so each stanza serves both assemblies where applicable. refs #37524
• src/hg/makeDb/trackDb/human/meiDeepmei1kg.html
  • lines changed 141, context: html, text, full: html, text
    0c1e751423b38dd741875d4cdcc6ffb5d4c4a135 Tue May 12 07:51:34 2026 -0700
    mei: add DeepMEI 1000G subtrack on hg38 91,617 MEIs (68,282 Alu, 16,891 L1, 6,444 SVA) called by DeepMEI on the 3,202 high-coverage 1000 Genomes samples. Same 1-bp anchor convention and Okabe-Ito colors as meiHgsvc3. DeepMEI's symbolic ALT carries no inserted sequence or insertion length, so the bigBed schema is a subset of meiHgsvc3 (no svLen, callerCount, validation flags, insertSeq). Also fixes the INS-svLen:carrierCount label format note in meiHgsvc3.html. refs #37524
• src/hg/makeDb/trackDb/human/meiEul1db.html
  • lines changed 122, context: html, text, full: html, text
    4f8f8773bec66a9e993e9897e0b032c6e97dead8 Fri May 15 10:12:29 2026 -0700
    mei: add HMEID, SweGen, and euL1db subtracks Three new MEI catalogues under the existing mei superTrack: meiHmeid (hg38) 36,699 MELT MEIs from HMEID v1.1 (NyuWa+1KGP, 5,675 individuals, Niu et al. 2022, PMID 35212372). Site-level VCF; per-cohort and per-1KGP super- population AC/AN/AF; SVTYPE Alu/L1/SVA/HERVK. meiSwegen (hg38 lifted) 18,090 MELT MEIs from the SweGen 1,000-sample Swedish cohort (Ameur 2017, PMID 28832569; Gardner 2017, PMID 28855259). Built on hg19, liftOver to hg38 (10 unmapped). tableBrowser off per SweGen distribution terms. meiEul1db (hg19+hg38) 8,988 curated L1-HS insertion polymorphisms (MRIPs) from euL1db v1.00 (Mir 2015, PMID 25352549), aggregating 142,495 sample-level SRIPs across 32 published studies. Coloured by lineage (germline/somatic/mixed). Built on hg19, liftOver to hg38 (3 unmapped). Helman2014 used numeric chrom names (23=X, 24=Y) which are renamed during the build. meiEul1dbRef (hg19+hg38) 1,540 reference-genome L1-HS copies catalogued by euL1db (companion to meiEul1db). Single shared mei.ra (in human/) uses $D substitution so each stanza serves both assemblies where applicable. refs #37524
• src/hg/makeDb/trackDb/human/meiEul1dbRef.html
  • lines changed 94, context: html, text, full: html, text
    4f8f8773bec66a9e993e9897e0b032c6e97dead8 Fri May 15 10:12:29 2026 -0700
    mei: add HMEID, SweGen, and euL1db subtracks Three new MEI catalogues under the existing mei superTrack: meiHmeid (hg38) 36,699 MELT MEIs from HMEID v1.1 (NyuWa+1KGP, 5,675 individuals, Niu et al. 2022, PMID 35212372). Site-level VCF; per-cohort and per-1KGP super- population AC/AN/AF; SVTYPE Alu/L1/SVA/HERVK. meiSwegen (hg38 lifted) 18,090 MELT MEIs from the SweGen 1,000-sample Swedish cohort (Ameur 2017, PMID 28832569; Gardner 2017, PMID 28855259). Built on hg19, liftOver to hg38 (10 unmapped). tableBrowser off per SweGen distribution terms. meiEul1db (hg19+hg38) 8,988 curated L1-HS insertion polymorphisms (MRIPs) from euL1db v1.00 (Mir 2015, PMID 25352549), aggregating 142,495 sample-level SRIPs across 32 published studies. Coloured by lineage (germline/somatic/mixed). Built on hg19, liftOver to hg38 (3 unmapped). Helman2014 used numeric chrom names (23=X, 24=Y) which are renamed during the build. meiEul1dbRef (hg19+hg38) 1,540 reference-genome L1-HS copies catalogued by euL1db (companion to meiEul1db). Single shared mei.ra (in human/) uses $D substitution so each stanza serves both assemblies where applicable. refs #37524
• src/hg/makeDb/trackDb/human/meiHgsvc3.html
  • lines changed 1, context: html, text, full: html, text
    0c1e751423b38dd741875d4cdcc6ffb5d4c4a135 Tue May 12 07:51:34 2026 -0700
    mei: add DeepMEI 1000G subtrack on hg38 91,617 MEIs (68,282 Alu, 16,891 L1, 6,444 SVA) called by DeepMEI on the 3,202 high-coverage 1000 Genomes samples. Same 1-bp anchor convention and Okabe-Ito colors as meiHgsvc3. DeepMEI's symbolic ALT carries no inserted sequence or insertion length, so the bigBed schema is a subset of meiHgsvc3 (no svLen, callerCount, validation flags, insertSeq). Also fixes the INS-svLen:carrierCount label format note in meiHgsvc3.html. refs #37524
• src/hg/makeDb/trackDb/human/meiHmeid.html
  • lines changed 151, context: html, text, full: html, text
    4f8f8773bec66a9e993e9897e0b032c6e97dead8 Fri May 15 10:12:29 2026 -0700
    mei: add HMEID, SweGen, and euL1db subtracks Three new MEI catalogues under the existing mei superTrack: meiHmeid (hg38) 36,699 MELT MEIs from HMEID v1.1 (NyuWa+1KGP, 5,675 individuals, Niu et al. 2022, PMID 35212372). Site-level VCF; per-cohort and per-1KGP super- population AC/AN/AF; SVTYPE Alu/L1/SVA/HERVK. meiSwegen (hg38 lifted) 18,090 MELT MEIs from the SweGen 1,000-sample Swedish cohort (Ameur 2017, PMID 28832569; Gardner 2017, PMID 28855259). Built on hg19, liftOver to hg38 (10 unmapped). tableBrowser off per SweGen distribution terms. meiEul1db (hg19+hg38) 8,988 curated L1-HS insertion polymorphisms (MRIPs) from euL1db v1.00 (Mir 2015, PMID 25352549), aggregating 142,495 sample-level SRIPs across 32 published studies. Coloured by lineage (germline/somatic/mixed). Built on hg19, liftOver to hg38 (3 unmapped). Helman2014 used numeric chrom names (23=X, 24=Y) which are renamed during the build. meiEul1dbRef (hg19+hg38) 1,540 reference-genome L1-HS copies catalogued by euL1db (companion to meiEul1db). Single shared mei.ra (in human/) uses $D substitution so each stanza serves both assemblies where applicable. refs #37524
• src/hg/makeDb/trackDb/human/meiSwegen.html
  • lines changed 169, context: html, text, full: html, text
    4f8f8773bec66a9e993e9897e0b032c6e97dead8 Fri May 15 10:12:29 2026 -0700
    mei: add HMEID, SweGen, and euL1db subtracks Three new MEI catalogues under the existing mei superTrack: meiHmeid (hg38) 36,699 MELT MEIs from HMEID v1.1 (NyuWa+1KGP, 5,675 individuals, Niu et al. 2022, PMID 35212372). Site-level VCF; per-cohort and per-1KGP super- population AC/AN/AF; SVTYPE Alu/L1/SVA/HERVK. meiSwegen (hg38 lifted) 18,090 MELT MEIs from the SweGen 1,000-sample Swedish cohort (Ameur 2017, PMID 28832569; Gardner 2017, PMID 28855259). Built on hg19, liftOver to hg38 (10 unmapped). tableBrowser off per SweGen distribution terms. meiEul1db (hg19+hg38) 8,988 curated L1-HS insertion polymorphisms (MRIPs) from euL1db v1.00 (Mir 2015, PMID 25352549), aggregating 142,495 sample-level SRIPs across 32 published studies. Coloured by lineage (germline/somatic/mixed). Built on hg19, liftOver to hg38 (3 unmapped). Helman2014 used numeric chrom names (23=X, 24=Y) which are renamed during the build. meiEul1dbRef (hg19+hg38) 1,540 reference-genome L1-HS copies catalogued by euL1db (companion to meiEul1db). Single shared mei.ra (in human/) uses $D substitution so each stanza serves both assemblies where applicable. refs #37524
• src/hg/makeDb/trackDb/human/mucins.ra
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    99db113e49bd1dd42a3040eaed1e61188a117ecf Wed May 13 05:44:18 2026 -0700
    mucins: new locus-specific mucin VNTR/non-VNTR exon track on hs1 (alpha) Adds a new 'Locus-specific' container in the genes group with two bigGenePred subtracks (mucinsVntr, mucinsNonVntr) derived from Plender et al. 2024 supplementary table 2. The .ra and HTML files live under trackDb/human/ so future locus-specific tracks can share them; hs1 picks them up via include ../mucins.ra alpha. refs #37540
• src/hg/makeDb/trackDb/human/mucinsNonVntr.html
  • lines changed 96, context: html, text, full: html, text
    99db113e49bd1dd42a3040eaed1e61188a117ecf Wed May 13 05:44:18 2026 -0700
    mucins: new locus-specific mucin VNTR/non-VNTR exon track on hs1 (alpha) Adds a new 'Locus-specific' container in the genes group with two bigGenePred subtracks (mucinsVntr, mucinsNonVntr) derived from Plender et al. 2024 supplementary table 2. The .ra and HTML files live under trackDb/human/ so future locus-specific tracks can share them; hs1 picks them up via include ../mucins.ra alpha. refs #37540
• src/hg/makeDb/trackDb/human/mucinsVntr.html
  • lines changed 98, context: html, text, full: html, text
    99db113e49bd1dd42a3040eaed1e61188a117ecf Wed May 13 05:44:18 2026 -0700
    mucins: new locus-specific mucin VNTR/non-VNTR exon track on hs1 (alpha) Adds a new 'Locus-specific' container in the genes group with two bigGenePred subtracks (mucinsVntr, mucinsNonVntr) derived from Plender et al. 2024 supplementary table 2. The .ra and HTML files live under trackDb/human/ so future locus-specific tracks can share them; hs1 picks them up via include ../mucins.ra alpha. refs #37540
• src/hg/makeDb/trackDb/human/mxbFreq.html
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    99ae46aca64e768875e6cbb2a232a0648bea5344 Fri May 15 10:13:21 2026 -0700
    varFreqs: prefix non-downloadable /gbdb subdirs with "_" so hgdownload rsync skips them; update bigDataUrl paths and Data Access wording on description pages for topmed, allofus, sfariSparkExomes/sfariSparkWgs, and mxbFreq. Combined varFreqsAll.bb moved into _all/. refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/sfariSparkExomes.html
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    99ae46aca64e768875e6cbb2a232a0648bea5344 Fri May 15 10:13:21 2026 -0700
    varFreqs: prefix non-downloadable /gbdb subdirs with "_" so hgdownload rsync skips them; update bigDataUrl paths and Data Access wording on description pages for topmed, allofus, sfariSparkExomes/sfariSparkWgs, and mxbFreq. Combined varFreqsAll.bb moved into _all/. refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/sgdpFreq.html
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    2f44ab096235810d5d621b7356bc64fbebe82494 Wed May 13 13:02:57 2026 -0700
    varFreqs: fix numeric-claim discrepancies on indigenomes.html and sgdpFreq.html. indigenomes.html: clarify that the deployed VCF is the public release subset (18,016,257 records) of the larger Jain 2021 callset (55.8M variants), and note that the public release is sites-only with a VRT variant-type INFO field and no AC/AF. sgdpFreq.html: update Methods to reflect the deployed file (44,756,737 SNV records, 601,775 multiallelic decomposed); drop the "34.4M SNPs + 2.1M indels" claim; clarify that the Mallick 2016 FermiKit indel callset is not carried in this track. refs #36642
• src/hg/makeDb/trackDb/human/swefreq.html
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    4f8f8773bec66a9e993e9897e0b032c6e97dead8 Fri May 15 10:12:29 2026 -0700
    mei: add HMEID, SweGen, and euL1db subtracks Three new MEI catalogues under the existing mei superTrack: meiHmeid (hg38) 36,699 MELT MEIs from HMEID v1.1 (NyuWa+1KGP, 5,675 individuals, Niu et al. 2022, PMID 35212372). Site-level VCF; per-cohort and per-1KGP super- population AC/AN/AF; SVTYPE Alu/L1/SVA/HERVK. meiSwegen (hg38 lifted) 18,090 MELT MEIs from the SweGen 1,000-sample Swedish cohort (Ameur 2017, PMID 28832569; Gardner 2017, PMID 28855259). Built on hg19, liftOver to hg38 (10 unmapped). tableBrowser off per SweGen distribution terms. meiEul1db (hg19+hg38) 8,988 curated L1-HS insertion polymorphisms (MRIPs) from euL1db v1.00 (Mir 2015, PMID 25352549), aggregating 142,495 sample-level SRIPs across 32 published studies. Coloured by lineage (germline/somatic/mixed). Built on hg19, liftOver to hg38 (3 unmapped). Helman2014 used numeric chrom names (23=X, 24=Y) which are renamed during the build. meiEul1dbRef (hg19+hg38) 1,540 reference-genome L1-HS copies catalogued by euL1db (companion to meiEul1db). Single shared mei.ra (in human/) uses $D substitution so each stanza serves both assemblies where applicable. refs #37524
• src/hg/makeDb/trackDb/human/topmed.html
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    99ae46aca64e768875e6cbb2a232a0648bea5344 Fri May 15 10:13:21 2026 -0700
    varFreqs: prefix non-downloadable /gbdb subdirs with "_" so hgdownload rsync skips them; update bigDataUrl paths and Data Access wording on description pages for topmed, allofus, sfariSparkExomes/sfariSparkWgs, and mxbFreq. Combined varFreqsAll.bb moved into _all/. refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/ukbb.html
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    9a49afb16653363a70d8e4d205513008b7b08df5 Wed May 13 06:18:42 2026 -0700
    varFreqs: add UK Biobank subtrack from Neale Lab Round 2 imputed-v3 variant manifest (13.7M variants, 361k white British samples). TSV → VCF conversion + CrossMap hg19→hg38, refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/varFreqs.html
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    9a49afb16653363a70d8e4d205513008b7b08df5 Wed May 13 06:18:42 2026 -0700
    varFreqs: add UK Biobank subtrack from Neale Lab Round 2 imputed-v3 variant manifest (13.7M variants, 361k white British samples). TSV → VCF conversion + CrossMap hg19→hg38, refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    3d9187d264d00ee8e681521bc2c942ee2527d4f1 Wed May 13 07:33:38 2026 -0700
    varFreqs: add WBBC (Westlake BioBank for Chinese) subtrack from the Phase I v20210103 release: 4,480 WGS samples, 78.6M variants, per-region frequencies for the 4 Han Chinese geographic subgroups (North/Central/South/Lingnan). databases.tsv + populations.tsv updated for the next varFreqsAll rebuild. refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    89491842e0ec6b2250aa6f6dc2c83c294930e6d6 Sun May 17 14:38:40 2026 -0700
    Add ChinaMAP phase 1 variant frequencies subtrack on hg38 ChinaMAP (Cao et al. 2020, Cell Res, PMID 32355288) is a deep-WGS cohort of 10,588 Chinese individuals across 27 provinces and 8 ethnic groups, with 147.4 M autosomal variants (136.7 M SNPs + 10.7 M short indels). The released VCF is already on GRCh38 with chr-prefixed chromosomes and ships AC/AF/AN plus matched 1KGP_* INFO fields, so it is served directly via vcfTabix. The ChinaMAP Limitations on Use prohibit redistribution, so the gbdb directory is _chinamap (hidden from hgdownload) and the trackDb stanza has tableBrowser off. Registered in scripts/varFreqs/databases.tsv so the next varFreqsAll combined rebuild picks it up; filter UI is deliberately not added yet (WBBC/TPMI precedent). , refs #36642
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    0a5389e8b81efa99e932f5e9e2424b27ce1af095 Sun May 17 14:53:57 2026 -0700
    varFreqs: add GenomeIndia subtrack (9,768 WGS, 83 endogamous Indian populations, Bhattacharyya 2025) and wire into databases.tsv for the next varFreqsAll rebuild. TSV->VCF conversion synthesizes AC=round(AF*AN) with AN=19536 since the upstream release only ships AF, refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    50d82c22527518595fcedf3066db5b3dbe011b88 Sun May 17 15:28:05 2026 -0700
    Add Taiwan TPMI row to varFreqs overview table The TPMI subtrack was added a few days ago but never made it into the Available Datasets table on the varFreqs supertrack description page. , refs #36642
• src/hg/makeDb/trackDb/human/varFreqs.ra
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    9a49afb16653363a70d8e4d205513008b7b08df5 Wed May 13 06:18:42 2026 -0700
    varFreqs: add UK Biobank subtrack from Neale Lab Round 2 imputed-v3 variant manifest (13.7M variants, 361k white British samples). TSV → VCF conversion + CrossMap hg19→hg38, refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • lines changed 10, context: html, text, full: html, text
    3d9187d264d00ee8e681521bc2c942ee2527d4f1 Wed May 13 07:33:38 2026 -0700
    varFreqs: add WBBC (Westlake BioBank for Chinese) subtrack from the Phase I v20210103 release: 4,480 WGS samples, 78.6M variants, per-region frequencies for the 4 Han Chinese geographic subgroups (North/Central/South/Lingnan). databases.tsv + populations.tsv updated for the next varFreqsAll rebuild. refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    459736686ba7726d2e9bfe63757183b4e8153e53 Wed May 13 13:09:18 2026 -0700
    varFreqs: set default visibility to hide on all 26 non-summary subtracks. Leaves varFreqsAll on pack (the summary combined-track stays the default view) and the supertrack on hide. Users opt into individual cohorts via the combined-track filter; enabling the supertrack no longer tries to render 25+ vcfTabix tracks at once. Confirmed by Max. refs #36642
  • lines changed 18, context: html, text, full: html, text
    4f8f8773bec66a9e993e9897e0b032c6e97dead8 Fri May 15 10:12:29 2026 -0700
    mei: add HMEID, SweGen, and euL1db subtracks Three new MEI catalogues under the existing mei superTrack: meiHmeid (hg38) 36,699 MELT MEIs from HMEID v1.1 (NyuWa+1KGP, 5,675 individuals, Niu et al. 2022, PMID 35212372). Site-level VCF; per-cohort and per-1KGP super- population AC/AN/AF; SVTYPE Alu/L1/SVA/HERVK. meiSwegen (hg38 lifted) 18,090 MELT MEIs from the SweGen 1,000-sample Swedish cohort (Ameur 2017, PMID 28832569; Gardner 2017, PMID 28855259). Built on hg19, liftOver to hg38 (10 unmapped). tableBrowser off per SweGen distribution terms. meiEul1db (hg19+hg38) 8,988 curated L1-HS insertion polymorphisms (MRIPs) from euL1db v1.00 (Mir 2015, PMID 25352549), aggregating 142,495 sample-level SRIPs across 32 published studies. Coloured by lineage (germline/somatic/mixed). Built on hg19, liftOver to hg38 (3 unmapped). Helman2014 used numeric chrom names (23=X, 24=Y) which are renamed during the build. meiEul1dbRef (hg19+hg38) 1,540 reference-genome L1-HS copies catalogued by euL1db (companion to meiEul1db). Single shared mei.ra (in human/) uses $D substitution so each stanza serves both assemblies where applicable. refs #37524
  • lines changed 14, context: html, text, full: html, text
    99ae46aca64e768875e6cbb2a232a0648bea5344 Fri May 15 10:13:21 2026 -0700
    varFreqs: prefix non-downloadable /gbdb subdirs with "_" so hgdownload rsync skips them; update bigDataUrl paths and Data Access wording on description pages for topmed, allofus, sfariSparkExomes/sfariSparkWgs, and mxbFreq. Combined varFreqsAll.bb moved into _all/. refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • lines changed 11, context: html, text, full: html, text
    89491842e0ec6b2250aa6f6dc2c83c294930e6d6 Sun May 17 14:38:40 2026 -0700
    Add ChinaMAP phase 1 variant frequencies subtrack on hg38 ChinaMAP (Cao et al. 2020, Cell Res, PMID 32355288) is a deep-WGS cohort of 10,588 Chinese individuals across 27 provinces and 8 ethnic groups, with 147.4 M autosomal variants (136.7 M SNPs + 10.7 M short indels). The released VCF is already on GRCh38 with chr-prefixed chromosomes and ships AC/AF/AN plus matched 1KGP_* INFO fields, so it is served directly via vcfTabix. The ChinaMAP Limitations on Use prohibit redistribution, so the gbdb directory is _chinamap (hidden from hgdownload) and the trackDb stanza has tableBrowser off. Registered in scripts/varFreqs/databases.tsv so the next varFreqsAll combined rebuild picks it up; filter UI is deliberately not added yet (WBBC/TPMI precedent). , refs #36642
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    0a5389e8b81efa99e932f5e9e2424b27ce1af095 Sun May 17 14:53:57 2026 -0700
    varFreqs: add GenomeIndia subtrack (9,768 WGS, 83 endogamous Indian populations, Bhattacharyya 2025) and wire into databases.tsv for the next varFreqsAll rebuild. TSV->VCF conversion synthesizes AC=round(AF*AN) with AN=19536 since the upstream release only ships AF, refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/wbbc.html
  • lines changed 104, context: html, text, full: html, text
    3d9187d264d00ee8e681521bc2c942ee2527d4f1 Wed May 13 07:33:38 2026 -0700
    varFreqs: add WBBC (Westlake BioBank for Chinese) subtrack from the Phase I v20210103 release: 4,480 WGS samples, 78.6M variants, per-region frequencies for the 4 Han Chinese geographic subgroups (North/Central/South/Lingnan). databases.tsv + populations.tsv updated for the next varFreqsAll rebuild. refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.html
  • lines changed 16, context: html, text, full: html, text
    4467111a88e1be93379b63492fc5c072e1dab930 Wed May 13 20:37:11 2026 -0700
    ENCODE4 Regulation DNase/ATAC/Histone/CTCF (Indiv.) description page cleanup (hg38 and mm10): added Signal/Peak subtrack info, matched filter facet names to hgTrackUi (Assay, Organ, Biosample Type, Data Type, Life Stage), removed first-person Credits. refs #34923
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.ra
  • lines changed 1178, context: html, text, full: html, text
    47519c28b9a21f1ca7ad8881ccd375ff40d7b206 Thu May 14 14:46:13 2026 -0700
    Fix hg38 H3K27ac peak color and strip species prefix from ENCODE4 Regulation bigComposite longLabels. refs #34923 Two QA cleanups from #34923 note 141: - hg38 H3K27ac peak subtracks were colored 255,205,0 (bright #FFCD00, the cCRE classification yellow) while the matching signal subtracks used 181,145,0 (mustard #B59100, the contrast-darkened assay color from /gbdb/hg38/encode4/regulation/epi_colors.json). Changed all 554 peak stanzas in wgEncodeReg4Epigenetics.ra to 181,145,0 so peak + signal match each other and the description-page color legend. mm10 H3K27ac already used 181,145,0 throughout. - Stripped the redundant "Homo sapiens " / "Mus musculus " prefix from the longLabel of every subtrack in the six bigComposite .ra files. 100% of subtracks had the prefix (14,929 total: 6,353 hg38 Epi + 4,964 hg38 TfChip + 1,046 hg38 RnaSeq + 1,178 mm10 Epi + 334 mm10 TfChip + 1,054 mm10 RnaSeq). The species is implicit on a specific assembly and the prefix was pushing biosample descriptions off the visible label width. shortLabels and track names untouched.
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegRnaSeq.ra
  • lines changed 1054, context: html, text, full: html, text
    47519c28b9a21f1ca7ad8881ccd375ff40d7b206 Thu May 14 14:46:13 2026 -0700
    Fix hg38 H3K27ac peak color and strip species prefix from ENCODE4 Regulation bigComposite longLabels. refs #34923 Two QA cleanups from #34923 note 141: - hg38 H3K27ac peak subtracks were colored 255,205,0 (bright #FFCD00, the cCRE classification yellow) while the matching signal subtracks used 181,145,0 (mustard #B59100, the contrast-darkened assay color from /gbdb/hg38/encode4/regulation/epi_colors.json). Changed all 554 peak stanzas in wgEncodeReg4Epigenetics.ra to 181,145,0 so peak + signal match each other and the description-page color legend. mm10 H3K27ac already used 181,145,0 throughout. - Stripped the redundant "Homo sapiens " / "Mus musculus " prefix from the longLabel of every subtrack in the six bigComposite .ra files. 100% of subtracks had the prefix (14,929 total: 6,353 hg38 Epi + 4,964 hg38 TfChip + 1,046 hg38 RnaSeq + 1,178 mm10 Epi + 334 mm10 TfChip + 1,054 mm10 RnaSeq). The species is implicit on a specific assembly and the prefix was pushing biosample descriptions off the visible label width. shortLabels and track names untouched.
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.ra
  • lines changed 334, context: html, text, full: html, text
    47519c28b9a21f1ca7ad8881ccd375ff40d7b206 Thu May 14 14:46:13 2026 -0700
    Fix hg38 H3K27ac peak color and strip species prefix from ENCODE4 Regulation bigComposite longLabels. refs #34923 Two QA cleanups from #34923 note 141: - hg38 H3K27ac peak subtracks were colored 255,205,0 (bright #FFCD00, the cCRE classification yellow) while the matching signal subtracks used 181,145,0 (mustard #B59100, the contrast-darkened assay color from /gbdb/hg38/encode4/regulation/epi_colors.json). Changed all 554 peak stanzas in wgEncodeReg4Epigenetics.ra to 181,145,0 so peak + signal match each other and the description-page color legend. mm10 H3K27ac already used 181,145,0 throughout. - Stripped the redundant "Homo sapiens " / "Mus musculus " prefix from the longLabel of every subtrack in the six bigComposite .ra files. 100% of subtracks had the prefix (14,929 total: 6,353 hg38 Epi + 4,964 hg38 TfChip + 1,046 hg38 RnaSeq + 1,178 mm10 Epi + 334 mm10 TfChip + 1,054 mm10 RnaSeq). The species is implicit on a specific assembly and the prefix was pushing biosample descriptions off the visible label width. shortLabels and track names untouched.
• src/hg/makeDb/trackDb/mouse/mm10/mouseDevTimecourse.ra
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    85b50d205c9a3dec2daf25805e3cf3a929b19a05 Wed May 13 10:57:25 2026 -0700
    Updating the mouseDevTimecourse superTrack per author requests: Renamed shortLabel and longLabel. Made the superTrack on by default with only M21 TPM visible. Added a priority setting. Reordered tissues in .facets files (documented in makedocs). refs #37001
• src/hg/makeDb/trackDb/mouse/mm39/mouseDevTimecourse.ra
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    85b50d205c9a3dec2daf25805e3cf3a929b19a05 Wed May 13 10:57:25 2026 -0700
    Updating the mouseDevTimecourse superTrack per author requests: Renamed shortLabel and longLabel. Made the superTrack on by default with only M21 TPM visible. Added a priority setting. Reordered tissues in .facets files (documented in makedocs). refs #37001
• src/hg/makeDb/trackDb/mouse/mm39/vgp577way.html
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    18a9b36bfd20cd33be49311a62bda0a268ea670b Fri May 15 14:02:29 2026 -0700
    add description page and phyloP track for VGP 577-way refs #31811
• src/hg/makeDb/trackDb/tagTypes.tab
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    b3ef92d687a2a170eab7758ff6b197e229675eee Fri May 8 13:23:17 2026 -0700
    add filterPriority and highlightPriority trackDb settings, refs #29223 New filterPriority.<fieldName> setting controls the display order of filter controls on the track configuration page. Lower values display first; filters without an explicit priority sort after those that have one. A companion highlightPriority.<fieldName> setting orders highlight controls the same way. A single priority entry covers all filter styles on the field (filter.*, filterText.*, filterValues.*). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/worm/ce11/trackDb.ra
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    9d843bd7d7d7c373b47631456f5ee0043f6d2cea Mon May 11 12:01:52 2026 -0700
    otto liftOver tracks are commented out so they will not pollute the hgwdev browser refs #31811
• src/hg/makeDb/trackDb/zebrafish/danRer11/trackDb.ra
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    9d843bd7d7d7c373b47631456f5ee0043f6d2cea Mon May 11 12:01:52 2026 -0700
    otto liftOver tracks are commented out so they will not pollute the hgwdev browser refs #31811
• src/hg/utils/gtfToGenePred/gtfToGenePred.c
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    1fc1fed014272d6781d8f98845efae537e808e58 Sat May 16 20:07:30 2026 -0700
    added option to get attribute output from gtfToGenePred in TSV format
• src/hg/utils/gtfToGenePred/tests/expected/impliedStop.info
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    1fc1fed014272d6781d8f98845efae537e808e58 Sat May 16 20:07:30 2026 -0700
    added option to get attribute output from gtfToGenePred in TSV format
• src/hg/utils/gtfToGenePred/tests/makefile
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    1fc1fed014272d6781d8f98845efae537e808e58 Sat May 16 20:07:30 2026 -0700
    added option to get attribute output from gtfToGenePred in TSV format
• src/hg/utils/otto/genarkContrib/genarkContrib.sh
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    6746944c5c6e9318343c8895d908f444179b70bc Tue May 12 12:44:39 2026 -0700
    beginning of script to add contrib tracks to genark assemblies refs #37543
• src/hg/utils/otto/omim/checkOmim.sh
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    d1fb9d605d77792dff66878cf1a8990320861049 Tue May 12 12:57:38 2026 -0700
    Make the OMIM otto fetch surface its wget log on failure and retry patiently. Previously, "set -e" killed the script after a partial wget failure before the "if [ $? -ne 0 ]" branch could run, so the build email showed only "fetching files ..." with no hint that the public omim.org mim2gene.txt URL had returned 403 (Cloudflare). The fetch now retries on 403/408/429/5xx with linear backoff (up to ~13 min of attempts) and prints wget.log into the email when it still gives up. No RM.
• src/hg/utils/otto/userRequests/chainNetTrackDb.pl
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    93026392de53b8abf15a3605b88aa6d7fb0f962d Mon May 11 12:05:53 2026 -0700
    do not need to run "make" in the trackDb since the "include" line is now a comment refs #31811
• src/hg/utils/otto/userRequests/featureBitsSnapshot.py
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    79837f643d9b21431d679ea7216f7e68150b2adf Mon May 11 15:34:40 2026 -0700
    making the ottoRequestView CGI efficient and avoiding repeatedly scanning files to get numbers that are not changing refs #31811
• src/hg/utils/otto/userRequests/ottoBuildGenArkHub.py
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    d95edf23464d1e0768072f9ed96d6d237ff9da83 Thu May 14 10:41:48 2026 -0700
    push script for any GenArk hub update refs #31811
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    c3fc03a88ff8fcd8fffadcdd960693268c2a6f5f Thu May 14 11:43:43 2026 -0700
    correctly use a dedicated clean otto kent source tree for operations in the source tree refs #31811
• src/hg/utils/otto/userRequests/ottoLib.py
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    d95edf23464d1e0768072f9ed96d6d237ff9da83 Thu May 14 10:41:48 2026 -0700
    push script for any GenArk hub update refs #31811
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    c3fc03a88ff8fcd8fffadcdd960693268c2a6f5f Thu May 14 11:43:43 2026 -0700
    correctly use a dedicated clean otto kent source tree for operations in the source tree refs #31811
• src/hg/utils/otto/userRequests/ottoRequestView.cgi
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    5648ce80fa4b2461fd6ef1d2192370896472cf37 Mon May 11 15:11:22 2026 -0700
    correctly recognize previous lastz/chain/net completed by in-house process and go directly to the hgdownload push and improve the efficiency of the web page ottoRequestView CGI refs #31811
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    79837f643d9b21431d679ea7216f7e68150b2adf Mon May 11 15:34:40 2026 -0700
    making the ottoRequestView CGI efficient and avoiding repeatedly scanning files to get numbers that are not changing refs #31811
• src/hg/utils/otto/userRequests/ottoRequestWatch.sh
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    5648ce80fa4b2461fd6ef1d2192370896472cf37 Mon May 11 15:11:22 2026 -0700
    correctly recognize previous lastz/chain/net completed by in-house process and go directly to the hgdownload push and improve the efficiency of the web page ottoRequestView CGI refs #31811
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    79837f643d9b21431d679ea7216f7e68150b2adf Mon May 11 15:34:40 2026 -0700
    making the ottoRequestView CGI efficient and avoiding repeatedly scanning files to get numbers that are not changing refs #31811
• src/hg/utils/rts/hg38/Non_Coding_SNVs_hg38
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    3c24a0d5ece77c493f9def39d135aae37dfbb226 Fri May 15 14:43:02 2026 -0700
    Updating RTS Non_Coding_SNVs_hg38 from abenet's source session via rtsUpdate. Cart version 2 -> 10 with substantial track refresh: clinGen* additions, dbSnp155 family, gnomadStructuralVariants, gnomadConstraint, spliceAI, jaspar2026, gnomadCopyNumberVariants; older entries retired (crispr*, knownGeneV36/V38, rmskHmmer, transMapV4/V6, etc.). refs #32768
• src/hg/utils/rts/rtsUpdate
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    705b694649940189cdb66af57560c97a0cd606f7 Fri May 15 14:42:52 2026 -0700
    Three small rtsUpdate fixes uncovered during first live test on Non_Coding_SNVs_hg38: line-buffer stdout so git diff output interleaves correctly with surrounding prints, replace deprecated datetime.utcnow() with timezone-aware datetime.now(datetime.timezone.utc), and print a trailing newline after confirm() so the post-prompt status message doesn't land on the same line as the prompt. refs #32768
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    87eb0adf61763660f65ec29bacf3d8f138c4b56d Fri May 15 15:11:59 2026 -0700
    Move rtsUpdate's audit log out of the kent tree to ~/.rtsUpdate.log, so it stays as a local audit trail without producing an untracked file (or merge-conflict-prone tracked file) in src/hg/utils/rts/. refs #32768
• src/htslib
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    cc2c8b0181212e97d22db24fc67394f4c634656e Fri Apr 24 20:19:55 2026 -0700
    added htslib submodule
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    012294051c7f9ded1f8392899feebbebd26ead5c Fri Apr 24 22:03:38 2026 -0700
    makefile will initialize htslib submodule if needed
• src/htslib/INSTALL
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/LICENSE
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/Makefile
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/NEWS
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/README
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/bgzf.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/bgzip.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/config.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/config.h.in
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/config.log
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/config.mk
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/config.mk.in
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/config.status
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/configure
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/configure.ac
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/cram/cram.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/cram/cram_codecs.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/cram/cram_codecs.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/cram/cram_decode.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/cram/cram_decode.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/cram/cram_encode.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/cram/cram_encode.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/cram/cram_external.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/cram/cram_index.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/cram/cram_index.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/cram/cram_io.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/cram/cram_io.c.00
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/cram/cram_io.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/cram/cram_samtools.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/cram/cram_samtools.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/cram/cram_stats.c
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• src/htslib/cram/cram_stats.h
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• src/htslib/cram/cram_structs.h
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• src/htslib/cram/files.c
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• src/htslib/cram/mFILE.h
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• src/htslib/cram/misc.h
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• src/htslib/cram/open_trace_file.c
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• src/htslib/test/ce.fa
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/test/faidx.fa
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/test/test-vcf-hdr-in.vcf
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/test/test-vcf-sweep.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/test/test_view.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/test/xx#blank.sam
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• src/htslib/test/xx#minimal.sam
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• src/htslib/test/xx#pair.sam
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• src/htslib/test/xx#rg.sam
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• src/htslib/test/xx#tlen.sam
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• src/htslib/test/xx#tlen2.sam
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• src/htslib/test/xx#triplet.sam
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• src/htslib/test/xx#unsorted.sam
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• src/htslib/test/xx.fa.fai
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• src/htslib/vcf.5
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• src/htslib/vcf.c
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• src/htslib/vcf_sweep.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/vcfutils.c
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• src/inc/bamFile.h
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    1ff2e18ba5e50dd2d1becd3cd6a25343578c10b8 Tue Apr 21 14:09:04 2026 -0700
    rework of htslib/UDC integration to use htslib hfile driver mechanism
• src/inc/common.mk
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    1ff2e18ba5e50dd2d1becd3cd6a25343578c10b8 Tue Apr 21 14:09:04 2026 -0700
    rework of htslib/UDC integration to use htslib hfile driver mechanism
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    2ee9d8c7beac3731a5e835e14921ac4e4cae4f81 Sat Apr 25 11:24:01 2026 -0700
    Moved htslib to submodules/htslib. Removed use of local static shared libraries for libcurl, as UCSC copy is outdated. Add a script that is run to check for htslib submodules being initialized and do the initialization. It also checks for stale src/htslib files
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    683ed1ec1118d21c351579f323fa0f5760c91100 Mon May 18 05:32:11 2026 -0700
    add --llzma for non-hgwdev builds
• src/inc/hfileUdc.h
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    1ff2e18ba5e50dd2d1becd3cd6a25343578c10b8 Tue Apr 21 14:09:04 2026 -0700
    rework of htslib/UDC integration to use htslib hfile driver mechanism
• src/inc/udc.h
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    1ff2e18ba5e50dd2d1becd3cd6a25343578c10b8 Tue Apr 21 14:09:04 2026 -0700
    rework of htslib/UDC integration to use htslib hfile driver mechanism
• src/lib/bamFile.c
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    1ff2e18ba5e50dd2d1becd3cd6a25343578c10b8 Tue Apr 21 14:09:04 2026 -0700
    rework of htslib/UDC integration to use htslib hfile driver mechanism
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    fe875492a7da5c0f64cd9c6d43cd6809478ec2a4 Sat May 9 08:32:48 2026 -0700
    *.bai and *.tbi index files were by-passing UDC and being downloaded to current directory
• src/lib/hfileUdc.c
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    1ff2e18ba5e50dd2d1becd3cd6a25343578c10b8 Tue Apr 21 14:09:04 2026 -0700
    rework of htslib/UDC integration to use htslib hfile driver mechanism
• src/lib/knetUdc.c
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    1ff2e18ba5e50dd2d1becd3cd6a25343578c10b8 Tue Apr 21 14:09:04 2026 -0700
    rework of htslib/UDC integration to use htslib hfile driver mechanism
• src/lib/linefile.c
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    fe875492a7da5c0f64cd9c6d43cd6809478ec2a4 Sat May 9 08:32:48 2026 -0700
    *.bai and *.tbi index files were by-passing UDC and being downloaded to current directory
• src/lib/makefile
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    1ff2e18ba5e50dd2d1becd3cd6a25343578c10b8 Tue Apr 21 14:09:04 2026 -0700
    rework of htslib/UDC integration to use htslib hfile driver mechanism
• src/lib/tests/expected/vcfHeader1kGNoGenotypes.out
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    3a1b00734b0c19737b48b171decfeb6b9edd27aa Wed May 6 18:16:34 2026 -0700
    Fix issue with new htslib and access to tabix VCF header. Permanently enable tests that would have found this problem. They were disable by a non-extent USE_TABIX make vaiable.
• src/lib/tests/expected/vcfHeader1kGWithGenotypes.out
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    3a1b00734b0c19737b48b171decfeb6b9edd27aa Wed May 6 18:16:34 2026 -0700
    Fix issue with new htslib and access to tabix VCF header. Permanently enable tests that would have found this problem. They were disable by a non-extent USE_TABIX make vaiable.
• src/lib/tests/expected/vcfHeaderOldV3.out
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    3a1b00734b0c19737b48b171decfeb6b9edd27aa Wed May 6 18:16:34 2026 -0700
    Fix issue with new htslib and access to tabix VCF header. Permanently enable tests that would have found this problem. They were disable by a non-extent USE_TABIX make vaiable.
• src/lib/tests/makefile
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    3a1b00734b0c19737b48b171decfeb6b9edd27aa Wed May 6 18:16:34 2026 -0700
    Fix issue with new htslib and access to tabix VCF header. Permanently enable tests that would have found this problem. They were disable by a non-extent USE_TABIX make vaiable.
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    c113b6a136531a9793170068d067c49f18df77cd Sat May 9 07:32:42 2026 -0700
    Update htslib to handle initialize order issue. Fix test program build order dependency
• src/lib/tests/tabixFetch.c
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    3a1b00734b0c19737b48b171decfeb6b9edd27aa Wed May 6 18:16:34 2026 -0700
    Fix issue with new htslib and access to tabix VCF header. Permanently enable tests that would have found this problem. They were disable by a non-extent USE_TABIX make vaiable.
• src/lib/tests/vcfParseTest.c
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    3a1b00734b0c19737b48b171decfeb6b9edd27aa Wed May 6 18:16:34 2026 -0700
    Fix issue with new htslib and access to tabix VCF header. Permanently enable tests that would have found this problem. They were disable by a non-extent USE_TABIX make vaiable.
• src/lib/udc.c
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    1ff2e18ba5e50dd2d1becd3cd6a25343578c10b8 Tue Apr 21 14:09:04 2026 -0700
    rework of htslib/UDC integration to use htslib hfile driver mechanism
• src/lib/vcf.c
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    3a1b00734b0c19737b48b171decfeb6b9edd27aa Wed May 6 18:16:34 2026 -0700
    Fix issue with new htslib and access to tabix VCF header. Permanently enable tests that would have found this problem. They were disable by a non-extent USE_TABIX make vaiable.
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    fe875492a7da5c0f64cd9c6d43cd6809478ec2a4 Sat May 9 08:32:48 2026 -0700
    *.bai and *.tbi index files were by-passing UDC and being downloaded to current directory
• src/makefile
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    012294051c7f9ded1f8392899feebbebd26ead5c Fri Apr 24 22:03:38 2026 -0700
    makefile will initialize htslib submodule if needed
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    2ee9d8c7beac3731a5e835e14921ac4e4cae4f81 Sat Apr 25 11:24:01 2026 -0700
    Moved htslib to submodules/htslib. Removed use of local static shared libraries for libcurl, as UCSC copy is outdated. Add a script that is run to check for htslib submodules being initialized and do the initialization. It also checks for stale src/htslib files
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    22c3e40ac360c345ab79f6bd3a51dbde33b2b4cd Tue May 12 14:25:49 2026 -0700
    move submoduleSet to submodule dir
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    5049589b9025e6961a2aab60f629159033141dc2 Tue May 12 14:31:21 2026 -0700
    run topChecks before any topLibs, even if done in parallel
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    2655a0cce4d565ac1c1c54fcf238b49cba2c5d37 Tue May 12 14:50:08 2026 -0700
    try to make sure topCheck runs first
• src/product/installer/browserSetup.sh
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    c75167799dc7d5939b879e49861653c823a81307 Tue May 12 14:16:46 2026 -0700
    fixing browserSetup.sh issue, reported by andy smith, no redmine
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    fa5cb52522742a54651d302464cb5deadfa7b7c7 Mon May 18 02:54:46 2026 -0700
    andy smith noticed that on the most recent ubuntu the mysql datadir was moved. Adding code now to auto-detect the datadir location and running the function after every use of MYSQLDIR. Except for OSX, but OSX without brew is not really supported anymore and needs work anyways. No redmine
• src/submoduleSetup
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    2ee9d8c7beac3731a5e835e14921ac4e4cae4f81 Sat Apr 25 11:24:01 2026 -0700
    Moved htslib to submodules/htslib. Removed use of local static shared libraries for libcurl, as UCSC copy is outdated. Add a script that is run to check for htslib submodules being initialized and do the initialization. It also checks for stale src/htslib files
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    9b1d1612efa7f321c5d3c500ce799c804c977135 Tue May 12 14:23:51 2026 -0700
    Add to .gitignore update LICENSE to remove htslib just note old htslib directory, not require removal
• src/submodules/README.md
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    625a5f2525117ff4c3e5a73ad73c020af9bdd1f5 Wed Apr 29 19:45:37 2026 -0700
    added README for submodules, currently just htslib
• src/submodules/htslib
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    2ee9d8c7beac3731a5e835e14921ac4e4cae4f81 Sat Apr 25 11:24:01 2026 -0700
    Moved htslib to submodules/htslib. Removed use of local static shared libraries for libcurl, as UCSC copy is outdated. Add a script that is run to check for htslib submodules being initialized and do the initialization. It also checks for stale src/htslib files
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    c113b6a136531a9793170068d067c49f18df77cd Sat May 9 07:32:42 2026 -0700
    Update htslib to handle initialize order issue. Fix test program build order dependency
• src/submodules/submoduleSetup
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    22c3e40ac360c345ab79f6bd3a51dbde33b2b4cd Tue May 12 14:25:49 2026 -0700
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• src/userApps/fetchKentSource.sh
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    1fd0ab8b59002435f0da06a8c5f1525db09024dc Thu Apr 30 20:52:15 2026 -0700
    inital conversion of fetchKentSource, can not test until on github
• src/utils/cpgIslandExt/README
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    75640104127592366faa7478485e5a88f8144a0b Thu May 14 08:44:10 2026 -0700
    fixing Miklem -> Micklem, refs #37539
• src/utils/qa/qaTestScript.py
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    298fb768b2cb86fcaf45101db0c7e6d9aea1a5c6 Fri May 15 14:29:27 2026 -0700
    Make HGVS test more reliable by waiting for the track element to appear before clicking, instead of pausing for a fixed 2 seconds. No RM.
• src/utils/qa/quickLiftBench/README.md
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    e5697049b1e077237d1f83c8293e23d62ded0820 Tue May 12 11:40:26 2026 -0700
    quickLiftBench: Mode C reference hub + hub-variant case schema, refs #37445 Adds a synthetic 4-track hub (bigBed native + lifted, bigWig native + lifted) at utils/qa/quickLiftBench/testHub/, regenerated via buildTestHub.sh, and extends the bench schema so a variant can be a mapping (hubUrl + db + position + tracks) in addition to the existing saved-session string. The two new cases mode_c_hs1_bb and mode_c_hs1_bw exercise quickLift on hs1 against an hg38-sourced chain, with both variants rendering at the same hs1 coords so the only difference is whether the chain-remap step runs. First numbers (n=10, hgwdev, chr22:15M-50M, 5000 source features / 34000 bedGraph bins): case native total lifted total parallel-fetch delta mode_c_hs1_bb 1376 ms 1154 ms +900 ms (chain remap) mode_c_hs1_bw 26 ms 27 ms negligible bigBed scales per-feature (~180 us/feature for 5000 hg38 features remapped); bigWig is essentially free. Also moves the regress_quickLift_parallel case from server: sandbox to server: hgwdev now that #37470 has landed on dev. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    d9568e415754516b14bff72b0daf67a0f7f69999 Tue May 12 16:53:34 2026 -0700
    quickLiftBench: add nSweep + posSweep orchestrators and paper Table 1, refs #37445 nSweep.py rebuilds testHub at each (N, BW_STEP) point and runs the bench, tagging every row with N + bw_step so the merged sweep.tsv plots "quickLift overhead vs feature count". buildTestHub.sh now also takes a FEATURE_W env var so the BED12 block model scales down at high N (auto-picked by nSweep so requested N fits the region without overlap). posSweep.py mirrors the orchestrator shape but varies the viewed window on a fixed hub; built-in canonical positions cover 0..5000 in-window features against the default testHub. paper_table1.md collects the headline Mode C cells from the 2026-05-12 N + position sweeps: bigBed quickLift ratio scales 4.3x -> 10.3x with feature count, bigWig stays flat ~5x; sparse windows show near-zero quickLift overhead.
• src/utils/qa/quickLiftBench/cases.yaml
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    e5697049b1e077237d1f83c8293e23d62ded0820 Tue May 12 11:40:26 2026 -0700
    quickLiftBench: Mode C reference hub + hub-variant case schema, refs #37445 Adds a synthetic 4-track hub (bigBed native + lifted, bigWig native + lifted) at utils/qa/quickLiftBench/testHub/, regenerated via buildTestHub.sh, and extends the bench schema so a variant can be a mapping (hubUrl + db + position + tracks) in addition to the existing saved-session string. The two new cases mode_c_hs1_bb and mode_c_hs1_bw exercise quickLift on hs1 against an hg38-sourced chain, with both variants rendering at the same hs1 coords so the only difference is whether the chain-remap step runs. First numbers (n=10, hgwdev, chr22:15M-50M, 5000 source features / 34000 bedGraph bins): case native total lifted total parallel-fetch delta mode_c_hs1_bb 1376 ms 1154 ms +900 ms (chain remap) mode_c_hs1_bw 26 ms 27 ms negligible bigBed scales per-feature (~180 us/feature for 5000 hg38 features remapped); bigWig is essentially free. Also moves the regress_quickLift_parallel case from server: sandbox to server: hgwdev now that #37470 has landed on dev. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    e4b101c93789880b099cdd781ef75ea32002707e Tue May 12 12:13:39 2026 -0700
    quickLiftBench: Mode B cases + split hub.txt into per-genome files, refs #37445 Adds mode_b_bb and mode_b_bw cases: native render on the source assembly (hg38) vs the same source data quickLifted to a different assembly (hs1). Different db per variant; positions chosen to cover approximately the same biological region on chr22. buildTestHub.sh now emits two single-genome useOneFile hubs (hub_hs1.txt + hub_hg38.txt). A single useOneFile hub cannot host multiple genomes -- trackHubGenomeReadRa() in trackHub.c:679 breaks out of the genome-parsing loop at the first `track` line, so any 2nd `genome` block after a track stanza is silently dropped. The Mode C cases are updated to point at hub_hs1.txt. First numbers (n=10, hgwdev, chr22:15M-50M): case native lifted ratio notes mode_b_bb 2746 ms 1682 ms 0.61 hg38 trackDb load dominates native; lifted on hs1 is faster despite the chain remap. mode_b_bw 786 ms 639 ms 0.81 same effect. mode_c_hs1_bb 1830 ms 2071 ms 1.13 ~240 ms remap cost. mode_c_hs1_bw 111 ms 623 ms 5.61 ~510 ms remap cost (cold chain cache). Mode B captures the full cross-assembly cost a user sees; Mode C is the controlled isolation of pure quickLift overhead. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/utils/qa/quickLiftBench/nSweep.py
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    d9568e415754516b14bff72b0daf67a0f7f69999 Tue May 12 16:53:34 2026 -0700
    quickLiftBench: add nSweep + posSweep orchestrators and paper Table 1, refs #37445 nSweep.py rebuilds testHub at each (N, BW_STEP) point and runs the bench, tagging every row with N + bw_step so the merged sweep.tsv plots "quickLift overhead vs feature count". buildTestHub.sh now also takes a FEATURE_W env var so the BED12 block model scales down at high N (auto-picked by nSweep so requested N fits the region without overlap). posSweep.py mirrors the orchestrator shape but varies the viewed window on a fixed hub; built-in canonical positions cover 0..5000 in-window features against the default testHub. paper_table1.md collects the headline Mode C cells from the 2026-05-12 N + position sweeps: bigBed quickLift ratio scales 4.3x -> 10.3x with feature count, bigWig stays flat ~5x; sparse windows show near-zero quickLift overhead.
• src/utils/qa/quickLiftBench/paper_table1.md
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    d9568e415754516b14bff72b0daf67a0f7f69999 Tue May 12 16:53:34 2026 -0700
    quickLiftBench: add nSweep + posSweep orchestrators and paper Table 1, refs #37445 nSweep.py rebuilds testHub at each (N, BW_STEP) point and runs the bench, tagging every row with N + bw_step so the merged sweep.tsv plots "quickLift overhead vs feature count". buildTestHub.sh now also takes a FEATURE_W env var so the BED12 block model scales down at high N (auto-picked by nSweep so requested N fits the region without overlap). posSweep.py mirrors the orchestrator shape but varies the viewed window on a fixed hub; built-in canonical positions cover 0..5000 in-window features against the default testHub. paper_table1.md collects the headline Mode C cells from the 2026-05-12 N + position sweeps: bigBed quickLift ratio scales 4.3x -> 10.3x with feature count, bigWig stays flat ~5x; sparse windows show near-zero quickLift overhead.
• src/utils/qa/quickLiftBench/posSweep.py
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    d9568e415754516b14bff72b0daf67a0f7f69999 Tue May 12 16:53:34 2026 -0700
    quickLiftBench: add nSweep + posSweep orchestrators and paper Table 1, refs #37445 nSweep.py rebuilds testHub at each (N, BW_STEP) point and runs the bench, tagging every row with N + bw_step so the merged sweep.tsv plots "quickLift overhead vs feature count". buildTestHub.sh now also takes a FEATURE_W env var so the BED12 block model scales down at high N (auto-picked by nSweep so requested N fits the region without overlap). posSweep.py mirrors the orchestrator shape but varies the viewed window on a fixed hub; built-in canonical positions cover 0..5000 in-window features against the default testHub. paper_table1.md collects the headline Mode C cells from the 2026-05-12 N + position sweeps: bigBed quickLift ratio scales 4.3x -> 10.3x with feature count, bigWig stays flat ~5x; sparse windows show near-zero quickLift overhead.
• src/utils/qa/quickLiftBench/quickLiftBench.py
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    e5697049b1e077237d1f83c8293e23d62ded0820 Tue May 12 11:40:26 2026 -0700
    quickLiftBench: Mode C reference hub + hub-variant case schema, refs #37445 Adds a synthetic 4-track hub (bigBed native + lifted, bigWig native + lifted) at utils/qa/quickLiftBench/testHub/, regenerated via buildTestHub.sh, and extends the bench schema so a variant can be a mapping (hubUrl + db + position + tracks) in addition to the existing saved-session string. The two new cases mode_c_hs1_bb and mode_c_hs1_bw exercise quickLift on hs1 against an hg38-sourced chain, with both variants rendering at the same hs1 coords so the only difference is whether the chain-remap step runs. First numbers (n=10, hgwdev, chr22:15M-50M, 5000 source features / 34000 bedGraph bins): case native total lifted total parallel-fetch delta mode_c_hs1_bb 1376 ms 1154 ms +900 ms (chain remap) mode_c_hs1_bw 26 ms 27 ms negligible bigBed scales per-feature (~180 us/feature for 5000 hg38 features remapped); bigWig is essentially free. Also moves the regress_quickLift_parallel case from server: sandbox to server: hgwdev now that #37470 has landed on dev. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/utils/qa/quickLiftBench/testHub/buildTestHub.sh
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    e5697049b1e077237d1f83c8293e23d62ded0820 Tue May 12 11:40:26 2026 -0700
    quickLiftBench: Mode C reference hub + hub-variant case schema, refs #37445 Adds a synthetic 4-track hub (bigBed native + lifted, bigWig native + lifted) at utils/qa/quickLiftBench/testHub/, regenerated via buildTestHub.sh, and extends the bench schema so a variant can be a mapping (hubUrl + db + position + tracks) in addition to the existing saved-session string. The two new cases mode_c_hs1_bb and mode_c_hs1_bw exercise quickLift on hs1 against an hg38-sourced chain, with both variants rendering at the same hs1 coords so the only difference is whether the chain-remap step runs. First numbers (n=10, hgwdev, chr22:15M-50M, 5000 source features / 34000 bedGraph bins): case native total lifted total parallel-fetch delta mode_c_hs1_bb 1376 ms 1154 ms +900 ms (chain remap) mode_c_hs1_bw 26 ms 27 ms negligible bigBed scales per-feature (~180 us/feature for 5000 hg38 features remapped); bigWig is essentially free. Also moves the regress_quickLift_parallel case from server: sandbox to server: hgwdev now that #37470 has landed on dev. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    e4b101c93789880b099cdd781ef75ea32002707e Tue May 12 12:13:39 2026 -0700
    quickLiftBench: Mode B cases + split hub.txt into per-genome files, refs #37445 Adds mode_b_bb and mode_b_bw cases: native render on the source assembly (hg38) vs the same source data quickLifted to a different assembly (hs1). Different db per variant; positions chosen to cover approximately the same biological region on chr22. buildTestHub.sh now emits two single-genome useOneFile hubs (hub_hs1.txt + hub_hg38.txt). A single useOneFile hub cannot host multiple genomes -- trackHubGenomeReadRa() in trackHub.c:679 breaks out of the genome-parsing loop at the first `track` line, so any 2nd `genome` block after a track stanza is silently dropped. The Mode C cases are updated to point at hub_hs1.txt. First numbers (n=10, hgwdev, chr22:15M-50M): case native lifted ratio notes mode_b_bb 2746 ms 1682 ms 0.61 hg38 trackDb load dominates native; lifted on hs1 is faster despite the chain remap. mode_b_bw 786 ms 639 ms 0.81 same effect. mode_c_hs1_bb 1830 ms 2071 ms 1.13 ~240 ms remap cost. mode_c_hs1_bw 111 ms 623 ms 5.61 ~510 ms remap cost (cold chain cache). Mode B captures the full cross-assembly cost a user sees; Mode C is the controlled isolation of pure quickLift overhead. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    d9568e415754516b14bff72b0daf67a0f7f69999 Tue May 12 16:53:34 2026 -0700
    quickLiftBench: add nSweep + posSweep orchestrators and paper Table 1, refs #37445 nSweep.py rebuilds testHub at each (N, BW_STEP) point and runs the bench, tagging every row with N + bw_step so the merged sweep.tsv plots "quickLift overhead vs feature count". buildTestHub.sh now also takes a FEATURE_W env var so the BED12 block model scales down at high N (auto-picked by nSweep so requested N fits the region without overlap). posSweep.py mirrors the orchestrator shape but varies the viewed window on a fixed hub; built-in canonical positions cover 0..5000 in-window features against the default testHub. paper_table1.md collects the headline Mode C cells from the 2026-05-12 N + position sweeps: bigBed quickLift ratio scales 4.3x -> 10.3x with feature count, bigWig stays flat ~5x; sparse windows show near-zero quickLift overhead.
• src/utils/qa/trackDbCacheBench/README.md
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    349adcd7c26d73b53ec1865a4fd14c60b74f9386 Wed May 13 09:18:36 2026 -0700
    trackDbCache: CACHE_TRACK_DB_DIR env var override; add trackDbCacheBench, refs #37551 trackDbCacheOn() in src/hg/lib/trackDbCache.c now reads CACHE_TRACK_DB_DIR from the environment ahead of the cacheTrackDbDir hg.conf setting. When the env var is set its value wins, including the empty string (which disables the cache). This lets a benchmark harness switch caching on and off per hgTracks invocation without editing hg.conf. trackDbCacheBench (src/utils/qa/trackDbCacheBench/) drives hgTracks through cached and uncached runs, with warmups and per-iteration median/min/max timings, and an --evict-cache option that uses posix_fadvise(DONTNEED) to drop cache files from the OS page cache between iterations so disk-backed cache directories can be compared to /dev/shm. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/utils/qa/trackDbCacheBench/trackDbCacheBench.py
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    349adcd7c26d73b53ec1865a4fd14c60b74f9386 Wed May 13 09:18:36 2026 -0700
    trackDbCache: CACHE_TRACK_DB_DIR env var override; add trackDbCacheBench, refs #37551 trackDbCacheOn() in src/hg/lib/trackDbCache.c now reads CACHE_TRACK_DB_DIR from the environment ahead of the cacheTrackDbDir hg.conf setting. When the env var is set its value wins, including the empty string (which disables the cache). This lets a benchmark harness switch caching on and off per hgTracks invocation without editing hg.conf. trackDbCacheBench (src/utils/qa/trackDbCacheBench/) drives hgTracks through cached and uncached runs, with warmups and per-iteration median/min/max timings, and an --evict-cache option that uses posix_fadvise(DONTNEED) to drop cache files from the OS page cache between iterations so disk-backed cache directories can be compared to /dev/shm. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

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