All File Changes

v503_preview2 to v503_base (2026-08-24 to 2026-08-31) v503

• build/kent-core/README.md
  • lines changed 1, context: html, text, full: html, text
    ec1a4ee046073ffbd5fcf929a6bc33ea514171a2 Thu Aug 27 14:00:52 2026 -0700
    Fixing an outdated cse server reference to point to soe, no ticket
• confs/hgwbeta.hg.conf
  • lines changed 1, context: html, text, full: html, text
    aceb6e9fb2694e5c5bd8c2518767a04fa8c0a300 Sun Aug 30 01:11:16 2026 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 8, context: html, text, full: html, text
    aceb6e9fb2694e5c5bd8c2518767a04fa8c0a300 Sun Aug 30 01:11:16 2026 -0700
    Installing updated hg.conf files from UCSC servers
• docs/hubs/facetedComposite.md
  • lines changed 432, context: html, text, full: html, text
    047ccb47a7fc8dd0d1aaa461fc170ebc34305bb7 Mon Aug 24 15:33:38 2026 -0700
    Add Faceted Composite Tracks doc page covering trackDb settings and metadata file, refs #36320
• docs/index.md
  • lines changed 3, context: html, text, full: html, text
    c59bd36405b9130e30e25de6d37911298154322e Mon Aug 24 15:38:35 2026 -0700
    Replace the goldenPath faceted composite help page with the new docs page and link it, refs #36320
• docs/staticPage.html
  • lines changed 63, context: html, text, full: html, text
    dad2b237d480ba64706fbb6c63d092b2738a2413 Mon Aug 24 15:33:38 2026 -0700
    Add ### headings as indented TOC sub-items and fix docs sidebar highlighting, refs #36320
• docs/staticPage.lua
  • lines changed 10, context: html, text, full: html, text
    dad2b237d480ba64706fbb6c63d092b2738a2413 Mon Aug 24 15:33:38 2026 -0700
    Add ### headings as indented TOC sub-items and fix docs sidebar highlighting, refs #36320
• src/hg/cirm/cdw/httpsGatewayConfig/README.txt
  • lines changed 5, context: html, text, full: html, text
    72ab5ade9fcc72e242d987bb84c92df08ba7601b Thu Aug 27 11:10:59 2026 -0700
    CIRM: remove references to the retired cirmdcm.soe.ucsc.edu host, refs #38191 cirmdcm.soe.ucsc.edu was the private server CESCG labs used to reach their prepublication data. It is retired, no longer answers on port 80 or 443, and is not being replaced. - cirmBasics.html: drop the "private server" paragraph from the Accounts section, adjust the heading and table of contents to match, and unlink the dead URL in the commented-out video block. - cirmStuff.js: drop the cirmdcm and cirm-01 clauses from isSecureSite(). cirm-01 was the same machine internally. hgwdev and sspsygene are unaffected. - gateway/htdocs/README: remove the dead login-for-testing URL and stop using the retired host as an example. proxy-host.conf is kept: it is the Apache config that stood the gateway up and the README beside it is the recipe that installs it. That README now says up front that the host is retired. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/cirm/gateway/htdocs/README
  • lines changed 4, context: html, text, full: html, text
    72ab5ade9fcc72e242d987bb84c92df08ba7601b Thu Aug 27 11:10:59 2026 -0700
    CIRM: remove references to the retired cirmdcm.soe.ucsc.edu host, refs #38191 cirmdcm.soe.ucsc.edu was the private server CESCG labs used to reach their prepublication data. It is retired, no longer answers on port 80 or 443, and is not being replaced. - cirmBasics.html: drop the "private server" paragraph from the Accounts section, adjust the heading and table of contents to match, and unlink the dead URL in the commented-out video block. - cirmStuff.js: drop the cirmdcm and cirm-01 clauses from isSecureSite(). cirm-01 was the same machine internally. hgwdev and sspsygene are unaffected. - gateway/htdocs/README: remove the dead login-for-testing URL and stop using the retired host as an example. proxy-host.conf is kept: it is the Apache config that stood the gateway up and the README beside it is the recipe that installs it. That README now says up front that the host is retired. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/cirm/gateway/htdocs/help/cirmBasics.html
  • lines changed 8, context: html, text, full: html, text
    72ab5ade9fcc72e242d987bb84c92df08ba7601b Thu Aug 27 11:10:59 2026 -0700
    CIRM: remove references to the retired cirmdcm.soe.ucsc.edu host, refs #38191 cirmdcm.soe.ucsc.edu was the private server CESCG labs used to reach their prepublication data. It is retired, no longer answers on port 80 or 443, and is not being replaced. - cirmBasics.html: drop the "private server" paragraph from the Accounts section, adjust the heading and table of contents to match, and unlink the dead URL in the commented-out video block. - cirmStuff.js: drop the cirmdcm and cirm-01 clauses from isSecureSite(). cirm-01 was the same machine internally. hgwdev and sspsygene are unaffected. - gateway/htdocs/README: remove the dead login-for-testing URL and stop using the retired host as an example. proxy-host.conf is kept: it is the Apache config that stood the gateway up and the README beside it is the recipe that installs it. That README now says up front that the host is retired. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/cirm/gateway/js/cirmStuff.js
  • lines changed 3, context: html, text, full: html, text
    72ab5ade9fcc72e242d987bb84c92df08ba7601b Thu Aug 27 11:10:59 2026 -0700
    CIRM: remove references to the retired cirmdcm.soe.ucsc.edu host, refs #38191 cirmdcm.soe.ucsc.edu was the private server CESCG labs used to reach their prepublication data. It is retired, no longer answers on port 80 or 443, and is not being replaced. - cirmBasics.html: drop the "private server" paragraph from the Accounts section, adjust the heading and table of contents to match, and unlink the dead URL in the commented-out video block. - cirmStuff.js: drop the cirmdcm and cirm-01 clauses from isSecureSite(). cirm-01 was the same machine internally. hgwdev and sspsygene are unaffected. - gateway/htdocs/README: remove the dead login-for-testing URL and stop using the retired host as an example. proxy-host.conf is kept: it is the Apache config that stood the gateway up and the README beside it is the recipe that installs it. That README now says up front that the host is retired. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/hgBlat/hgBlat.c
  • lines changed 1, context: html, text, full: html, text
    83858083785a6b2b1f3c05f93e818e5a89318692 Tue Aug 25 01:42:34 2026 -0700
    hgSession: show cytoBand and gene/locus annotations for each saved session; date-only Created/Last used columns with full timestamp on hover. Factor locusName lookup into reusable hLocusName/hLocusNameExpand in hdb.c and reuse from hgBlat. refs #38157 The Assembly column now shows band, gene/locus name and Mbp position (separated by whitespace, normal text size). hLocusNameExpand centralizes the ex:/in:/ig: and | to - expansion that hgBlat's results page did inline.
  • lines changed 13, context: html, text, full: html, text
    5a3be3af33b76d69d1fc98ee76b9a37f96e96fc7 Wed Aug 26 00:36:52 2026 -0700
    Add opt-in per-phase request timing to the new hgBlat and hgSession pages, shown in a dialog with &measureTiming=1. refs #38157 New reusable perfTimer collector (lib/perfTimer.c) records labeled wall-clock intervals via clock1000() and emits them as JSON; hgBlat and hgSession attach a timing array to their payload when the existing measureTiming cart/CGI var is set. A shared gbShowTimingDialog helper in utils.js renders the server phases plus a client render-time row in a house-style modal, which opens automatically when measureTiming is on. Confirms the position band/locus annotation loop dominates hgSession, and run-BLAT plus locus lookups dominate hgBlat.
  • lines changed 44, context: html, text, full: html, text
    4fd18ab7854e6620576499d1b7f70fd03d9b6f9d Thu Aug 27 09:03:04 2026 -0700
    hgBlat: name a BLAT track after the gene whose exon it hits, and call protein lengths aa #Preview2 week - bugs introduced now will need a build patch to fix topHitLocusLabel() took whatever locusName row hRangeQuery happened to return first, which is bin order and unrelated to the hit. A 400 bp query with 345 bp inside an EGFR exon came back as "400bp chr7:55019001" because the intergenic row upstream sorted first. It now walks all overlapping rows and prefers an exon row over an intron row, breaking ties by how much of the hit each row covers. Protein searches were also labelled "154bp SOD1". Query lengths of a protein search are amino acids, so the track name, its description and the results page (length and the coverage mouseover) now say "aa" for those. refs #38086
• src/hg/hgConvert/hgConvert.c
  • lines changed 4, context: html, text, full: html, text
    d0942d5563ca2fdd0170c4730bb6bf1ecc8258ea Thu Aug 27 09:16:16 2026 -0700
    quickLift: take out the unused visibility string, refs #38032 trackHubBuild and walkTree never wrote visDy. hgConvert allocated it, passed it down, then reassigned it inside the chain loop, leaking a dyString per chain.
• src/hg/hgFileSearch/hgFileSearch.c
  • lines changed 3, context: html, text, full: html, text
    b03051dec6a7b9d132995e809f378bc3277a987a Thu Aug 27 01:18:06 2026 -0700
    escape search terms and uploaded sequence names (XSS), refs #38057 #Preview2 week - bugs introduced now will need a build patch to fix #Preview2 week - bugs introduced now will need a build patch to fix Follow-up to the QA review of dbd10edb43b. hgFileSearch and hgTracks track search: the name/description/simple search boxes echoed the search term into a value attribute unescaped. The earlier pass escaped the hgFileSearch simple box only, which sits inside a USE_TABS block that is not compiled. hgPhyloPlace: uploaded sequence names are echoed in the QC failure messages from vcfFromFasta, in the subtree summary table, in the placement and mutation-path headings, in the subtree download links and in the no-reference-match list. All now go through htmlEncode. hgLiftOver: the failure file was read back while its FILE* was still open and unflushed, so the "Failed input regions" block always came out empty. Close mapped and unmapped right after liftOver writes them.
• src/hg/hgGene/gencodeSection.c
  • lines changed 1, context: html, text, full: html, text
    6a8e756b47341a5584f5c3fca4031401fe507020 Mon Aug 24 11:21:22 2026 -0700
    Updating GeneCards links to their new URL format per their request, also fixes dead cardsearch.pl links on RefSeq and denovoDb click pages. refs #38171
• src/hg/hgGene/hgGeneData/Human/links.ra
  • lines changed 1, context: html, text, full: html, text
    6a8e756b47341a5584f5c3fca4031401fe507020 Mon Aug 24 11:21:22 2026 -0700
    Updating GeneCards links to their new URL format per their request, also fixes dead cardsearch.pl links on RefSeq and denovoDb click pages. refs #38171
• src/hg/hgGene/hgGeneData/Mouse/links.ra
  • lines changed 1, context: html, text, full: html, text
    6a8e756b47341a5584f5c3fca4031401fe507020 Mon Aug 24 11:21:22 2026 -0700
    Updating GeneCards links to their new URL format per their request, also fixes dead cardsearch.pl links on RefSeq and denovoDb click pages. refs #38171
• src/hg/hgGeneGraph/hgGeneGraph
  • lines changed 1, context: html, text, full: html, text
    6a8e756b47341a5584f5c3fca4031401fe507020 Mon Aug 24 11:21:22 2026 -0700
    Updating GeneCards links to their new URL format per their request, also fixes dead cardsearch.pl links on RefSeq and denovoDb click pages. refs #38171
• src/hg/hgLiftOver/hgLiftOver.c
  • lines changed 6, context: html, text, full: html, text
    b03051dec6a7b9d132995e809f378bc3277a987a Thu Aug 27 01:18:06 2026 -0700
    escape search terms and uploaded sequence names (XSS), refs #38057 #Preview2 week - bugs introduced now will need a build patch to fix #Preview2 week - bugs introduced now will need a build patch to fix Follow-up to the QA review of dbd10edb43b. hgFileSearch and hgTracks track search: the name/description/simple search boxes echoed the search term into a value attribute unescaped. The earlier pass escaped the hgFileSearch simple box only, which sits inside a USE_TABS block that is not compiled. hgPhyloPlace: uploaded sequence names are echoed in the QC failure messages from vcfFromFasta, in the subtree summary table, in the placement and mutation-path headings, in the subtree download links and in the no-reference-match list. All now go through htmlEncode. hgLiftOver: the failure file was read back while its FILE* was still open and unflushed, so the "Failed input regions" block always came out empty. Close mapped and unmapped right after liftOver writes them.
• src/hg/hgLogin/hgLogin.c
  • lines changed 68, context: html, text, full: html, text
    75593a4e317eac40b781c83718961f0eb7f84f3a Thu Aug 27 06:32:34 2026 -0700
    Blue bar login and logout now return to the page they were clicked on #Preview2 week - bugs introduced now will need a build patch to fix The Login link in the blue bar sent everyone to the My Sessions page after they signed in, and the Sign out and account links in the logged-in dialog did the same, so a visitor reading a help page or looking at an item details page lost their place. Only hgTracks was handled, as a special case. Adds wikiLinkEncodeCurrentPageReturnUrl(), which builds a returnto for the page the CGI is currently serving, including its query string, since the track and item parameters of pages like hgTrackUi and hgc are not all kept in the cart. hgTracks keeps its old behaviour of returning to hgTracks?hgsid=, because its state is in the cart and its query string can hold a one-shot zoom or drag. hgMenubar does the same for the static pages it is included into, using the page path from the SSI environment. The two checks hgLogin runs on an incoming returnto (URL shape, and the optional login.approvedReturn host list) move to wikiLink.c so that the CGIs building a link apply the same rules before writing it. A URL hgLogin would refuse now becomes an ordinary login link instead of an error page: an over-long or oddly-quoted query string costs the query string, and a host that login.approvedReturn does not cover falls back to the old My Sessions target. Note that with login.approvedReturn set, static-page returns need the bare host added to the list. Also converts the fixed 2 kB buffers in the wikiLink URL builders to dyStrings, since a cgi-encoded return URL can nearly triple in length and safef would have aborted. refs #38192
  • lines changed 13, context: html, text, full: html, text
    304aeae270067c5854358e2c4475ea34419dfec7 Thu Aug 27 17:59:26 2026 -0700
    Updating hgLogin's buttons, form labels, and two error messages to sentence case matching the Track QA Guidelines wiki page, refs #37929
  • lines changed 1, context: html, text, full: html, text
    b6d6aa7d68b7a1e9a1ad74508f2fc25b68f72e50 Fri Aug 28 11:15:39 2026 -0700
    Updating hgLogin's account activation error message to plain language, refs #37929
  • lines changed 14, context: html, text, full: html, text
    1147e5e78e17c3c47d7e625fe4d80f8f3f88b48b Fri Aug 28 13:16:15 2026 -0700
    Updating hgLogin's "choose a username" page to inform that a new account is created, refs #37929
• src/hg/hgLogin/hgLogin.h
  • lines changed 1, context: html, text, full: html, text
    75593a4e317eac40b781c83718961f0eb7f84f3a Thu Aug 27 06:32:34 2026 -0700
    Blue bar login and logout now return to the page they were clicked on #Preview2 week - bugs introduced now will need a build patch to fix The Login link in the blue bar sent everyone to the My Sessions page after they signed in, and the Sign out and account links in the logged-in dialog did the same, so a visitor reading a help page or looking at an item details page lost their place. Only hgTracks was handled, as a special case. Adds wikiLinkEncodeCurrentPageReturnUrl(), which builds a returnto for the page the CGI is currently serving, including its query string, since the track and item parameters of pages like hgTrackUi and hgc are not all kept in the cart. hgTracks keeps its old behaviour of returning to hgTracks?hgsid=, because its state is in the cart and its query string can hold a one-shot zoom or drag. hgMenubar does the same for the static pages it is included into, using the page path from the SSI environment. The two checks hgLogin runs on an incoming returnto (URL shape, and the optional login.approvedReturn host list) move to wikiLink.c so that the CGIs building a link apply the same rules before writing it. A URL hgLogin would refuse now becomes an ordinary login link instead of an error page: an over-long or oddly-quoted query string costs the query string, and a host that login.approvedReturn does not cover falls back to the old My Sessions target. Note that with login.approvedReturn set, static-page returns need the bare host added to the list. Also converts the fixed 2 kB buffers in the wikiLink URL builders to dyStrings, since a cgi-encoded return URL can nearly triple in length and safef would have aborted. refs #38192
• src/hg/hgMenubar/hgMenubar.c
  • lines changed 31, context: html, text, full: html, text
    75593a4e317eac40b781c83718961f0eb7f84f3a Thu Aug 27 06:32:34 2026 -0700
    Blue bar login and logout now return to the page they were clicked on #Preview2 week - bugs introduced now will need a build patch to fix The Login link in the blue bar sent everyone to the My Sessions page after they signed in, and the Sign out and account links in the logged-in dialog did the same, so a visitor reading a help page or looking at an item details page lost their place. Only hgTracks was handled, as a special case. Adds wikiLinkEncodeCurrentPageReturnUrl(), which builds a returnto for the page the CGI is currently serving, including its query string, since the track and item parameters of pages like hgTrackUi and hgc are not all kept in the cart. hgTracks keeps its old behaviour of returning to hgTracks?hgsid=, because its state is in the cart and its query string can hold a one-shot zoom or drag. hgMenubar does the same for the static pages it is included into, using the page path from the SSI environment. The two checks hgLogin runs on an incoming returnto (URL shape, and the optional login.approvedReturn host list) move to wikiLink.c so that the CGIs building a link apply the same rules before writing it. A URL hgLogin would refuse now becomes an ordinary login link instead of an error page: an over-long or oddly-quoted query string costs the query string, and a host that login.approvedReturn does not cover falls back to the old My Sessions target. Note that with login.approvedReturn set, static-page returns need the bare host added to the list. Also converts the fixed 2 kB buffers in the wikiLink URL builders to dyStrings, since a cgi-encoded return URL can nearly triple in length and safef would have aborted. refs #38192
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 11, context: html, text, full: html, text
    b03051dec6a7b9d132995e809f378bc3277a987a Thu Aug 27 01:18:06 2026 -0700
    escape search terms and uploaded sequence names (XSS), refs #38057 #Preview2 week - bugs introduced now will need a build patch to fix #Preview2 week - bugs introduced now will need a build patch to fix Follow-up to the QA review of dbd10edb43b. hgFileSearch and hgTracks track search: the name/description/simple search boxes echoed the search term into a value attribute unescaped. The earlier pass escaped the hgFileSearch simple box only, which sits inside a USE_TABS block that is not compiled. hgPhyloPlace: uploaded sequence names are echoed in the QC failure messages from vcfFromFasta, in the subtree summary table, in the placement and mutation-path headings, in the subtree download links and in the no-reference-match list. All now go through htmlEncode. hgLiftOver: the failure file was read back while its FILE* was still open and unflushed, so the "Failed input regions" block always came out empty. Close mapped and unmapped right after liftOver writes them.
  • lines changed 2, context: html, text, full: html, text
    e8f2f6e391ee65e96e0a99e9a840f55db59bdb60 Fri Jun 5 15:34:13 2026 -0700
    Fixing more bugs found by Claude when Chris ran it.
  • lines changed 1, context: html, text, full: html, text
    56fec2823d2419eb9395bed6f2b56dec2c1daceb Fri Aug 28 02:02:18 2026 -0700
    Escape nodeName in variantPathPrint (XSS), found by automated code review htmlEncode vpn->nodeName before printing in variantPathPrint() to close XSS gap. The node name can be a user-uploaded sample ID (FASTA/VCF), making this a reachable vulnerability of the same class the parent commit closes in other spots.
• src/hg/hgSession/hgSession.c
  • lines changed 85, context: html, text, full: html, text
    83858083785a6b2b1f3c05f93e818e5a89318692 Tue Aug 25 01:42:34 2026 -0700
    hgSession: show cytoBand and gene/locus annotations for each saved session; date-only Created/Last used columns with full timestamp on hover. Factor locusName lookup into reusable hLocusName/hLocusNameExpand in hdb.c and reuse from hgBlat. refs #38157 The Assembly column now shows band, gene/locus name and Mbp position (separated by whitespace, normal text size). hLocusNameExpand centralizes the ex:/in:/ig: and | to - expansion that hgBlat's results page did inline.
  • lines changed 12, context: html, text, full: html, text
    5a3be3af33b76d69d1fc98ee76b9a37f96e96fc7 Wed Aug 26 00:36:52 2026 -0700
    Add opt-in per-phase request timing to the new hgBlat and hgSession pages, shown in a dialog with &measureTiming=1. refs #38157 New reusable perfTimer collector (lib/perfTimer.c) records labeled wall-clock intervals via clock1000() and emits them as JSON; hgBlat and hgSession attach a timing array to their payload when the existing measureTiming cart/CGI var is set. A shared gbShowTimingDialog helper in utils.js renders the server phases plus a client render-time row in a house-style modal, which opens automatically when measureTiming is on. Confirms the position band/locus annotation loop dominates hgSession, and run-BLAT plus locus lookups dominate hgBlat.
  • lines changed 19, context: html, text, full: html, text
    3f97b357c5967755f1e5c914663ce9c7cc385e70 Wed Aug 26 03:01:34 2026 -0700
    Share a link: create the session only when the user asks, and copy in one click Opening the top-right "Share a link" dialog used to save a session right away, so just looking at the dialog left an unused link in the user's session list. The dialog now explains what the link is and offers one "Create link & copy" button that saves the session and copies the URL in a single step. The random name for a machine-generated session is now made client-side and sent with the request, so there is one convention in one place: a leading underscore (kept verbatim by the short-link encoder, so /s/<user>/_XXXXXXXX stays clean) plus eight URL-safe characters. hgSession.c no longer auto-names; a logged-in save with no name is an error, which is what the callers already guarantee. refs #10138
  • lines changed 19, context: html, text, full: html, text
    5872e3a9d5f3d2916bbf10f359011b9d04fc3b93 Wed Aug 26 03:18:39 2026 -0700
    Revert "Share a link: create the session only when the user asks, and copy in one click" This reverts commit 3f97b357c59. The change was work in progress and was committed by mistake; web.c still has the matching data-shortlink part uncommitted, so this half does not stand on its own. The genark syncFtp commit that went out with it is fine and stays.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 50, context: html, text, full: html, text
    f04f1b9af06c823602c5e0ecd3b8c2059d7704d3 Thu Aug 27 14:42:31 2026 -0700
    Faceted composites now have a max display mode setting instead of a full override of child track visibilities, with accompanying support for the onlyVisibility setting. We also now include a filter block (applied to appropriate child tracks) when those settings are in place. refs #37662
  • lines changed 2, context: html, text, full: html, text
    90b8f880be12956b899d973bc565bffdc9b7ce89 Fri Aug 28 08:27:13 2026 -0700
    Moving sort comment on the faceted composite UI, and ading a 'hide subtracks', refs #36320
• src/hg/hgTracks/hgTracks.c
  • lines changed 32, context: html, text, full: html, text
    f04f1b9af06c823602c5e0ecd3b8c2059d7704d3 Thu Aug 27 14:42:31 2026 -0700
    Faceted composites now have a max display mode setting instead of a full override of child track visibilities, with accompanying support for the onlyVisibility setting. We also now include a filter block (applied to appropriate child tracks) when those settings are in place. refs #37662
• src/hg/hgTracks/searchTracks.c
  • lines changed 3, context: html, text, full: html, text
    b03051dec6a7b9d132995e809f378bc3277a987a Thu Aug 27 01:18:06 2026 -0700
    escape search terms and uploaded sequence names (XSS), refs #38057 #Preview2 week - bugs introduced now will need a build patch to fix #Preview2 week - bugs introduced now will need a build patch to fix Follow-up to the QA review of dbd10edb43b. hgFileSearch and hgTracks track search: the name/description/simple search boxes echoed the search term into a value attribute unescaped. The earlier pass escaped the hgFileSearch simple box only, which sits inside a USE_TABS block that is not compiled. hgPhyloPlace: uploaded sequence names are echoed in the QC failure messages from vcfFromFasta, in the subtree summary table, in the placement and mutation-path headings, in the subtree download links and in the no-reference-match list. All now go through htmlEncode. hgLiftOver: the failure file was read back while its FILE* was still open and unflushed, so the "Failed input regions" block always came out empty. Close mapped and unmapped right after liftOver writes them.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 8, context: html, text, full: html, text
    f04f1b9af06c823602c5e0ecd3b8c2059d7704d3 Thu Aug 27 14:42:31 2026 -0700
    Faceted composites now have a max display mode setting instead of a full override of child track visibilities, with accompanying support for the onlyVisibility setting. We also now include a filter block (applied to appropriate child tracks) when those settings are in place. refs #37662
• src/hg/hgc/gencodeClick.c
  • lines changed 1, context: html, text, full: html, text
    6a8e756b47341a5584f5c3fca4031401fe507020 Mon Aug 24 11:21:22 2026 -0700
    Updating GeneCards links to their new URL format per their request, also fixes dead cardsearch.pl links on RefSeq and denovoDb click pages. refs #38171
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    6a8e756b47341a5584f5c3fca4031401fe507020 Mon Aug 24 11:21:22 2026 -0700
    Updating GeneCards links to their new URL format per their request, also fixes dead cardsearch.pl links on RefSeq and denovoDb click pages. refs #38171
• src/hg/htdocs/goldenPath/help/facetedComposite.html
  • lines changed 428, context: html, text, full: html, text
    c59bd36405b9130e30e25de6d37911298154322e Mon Aug 24 15:38:35 2026 -0700
    Replace the goldenPath faceted composite help page with the new docs page and link it, refs #36320
• src/hg/htdocs/goldenPath/help/trackDb/makefile
  • lines changed 7, context: html, text, full: html, text
    b866c1b2c352000ecb5f5a3fdaccd2b613c1b22f Tue Aug 25 12:28:05 2026 -0700
    Generate machine-readable trackDb settings from the help docs, refs #37959 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 12, context: html, text, full: html, text
    f04f1b9af06c823602c5e0ecd3b8c2059d7704d3 Thu Aug 27 14:42:31 2026 -0700
    Faceted composites now have a max display mode setting instead of a full override of child track visibilities, with accompanying support for the onlyVisibility setting. We also now include a filter block (applied to appropriate child tracks) when those settings are in place. refs #37662
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 3, context: html, text, full: html, text
    f04f1b9af06c823602c5e0ecd3b8c2059d7704d3 Thu Aug 27 14:42:31 2026 -0700
    Faceted composites now have a max display mode setting instead of a full override of child track visibilities, with accompanying support for the onlyVisibility setting. We also now include a filter block (applied to appropriate child tracks) when those settings are in place. refs #37662
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 1, context: html, text, full: html, text
    c59bd36405b9130e30e25de6d37911298154322e Mon Aug 24 15:38:35 2026 -0700
    Replace the goldenPath faceted composite help page with the new docs page and link it, refs #36320
  • lines changed 1, context: html, text, full: html, text
    b866c1b2c352000ecb5f5a3fdaccd2b613c1b22f Tue Aug 25 12:28:05 2026 -0700
    Generate machine-readable trackDb settings from the help docs, refs #37959 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 5, context: html, text, full: html, text
    e3c1ec4c7bcd63fc192134ffcb6b7db49f9da729 Tue Aug 25 14:04:10 2026 -0700
    Replace vague here links in the trackDb library with link text naming each destination page. No RM.
  • lines changed 60, context: html, text, full: html, text
    f04f1b9af06c823602c5e0ecd3b8c2059d7704d3 Thu Aug 27 14:42:31 2026 -0700
    Faceted composites now have a max display mode setting instead of a full override of child track visibilities, with accompanying support for the onlyVisibility setting. We also now include a filter block (applied to appropriate child tracks) when those settings are in place. refs #37662
• src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.json
  • lines changed 3601, context: html, text, full: html, text
    b866c1b2c352000ecb5f5a3fdaccd2b613c1b22f Tue Aug 25 12:28:05 2026 -0700
    Generate machine-readable trackDb settings from the help docs, refs #37959 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 15, context: html, text, full: html, text
    f04f1b9af06c823602c5e0ecd3b8c2059d7704d3 Thu Aug 27 14:42:31 2026 -0700
    Faceted composites now have a max display mode setting instead of a full override of child track visibilities, with accompanying support for the onlyVisibility setting. We also now include a filter block (applied to appropriate child tracks) when those settings are in place. refs #37662
• src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.yaml
  • lines changed 4687, context: html, text, full: html, text
    b866c1b2c352000ecb5f5a3fdaccd2b613c1b22f Tue Aug 25 12:28:05 2026 -0700
    Generate machine-readable trackDb settings from the help docs, refs #37959 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 37, context: html, text, full: html, text
    f04f1b9af06c823602c5e0ecd3b8c2059d7704d3 Thu Aug 27 14:42:31 2026 -0700
    Faceted composites now have a max display mode setting instead of a full override of child track visibilities, with accompanying support for the onlyVisibility setting. We also now include a filter block (applied to appropriate child tracks) when those settings are in place. refs #37662
• src/hg/htdocs/goldenPath/help/trackDb/trackDbSettingsGen.py
  • lines changed 301, context: html, text, full: html, text
    b866c1b2c352000ecb5f5a3fdaccd2b613c1b22f Tue Aug 25 12:28:05 2026 -0700
    Generate machine-readable trackDb settings from the help docs, refs #37959 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 50, context: html, text, full: html, text
    cf87c27669523cb325d1d2d52e11e6f18d24504e Wed Aug 26 18:36:04 2026 -0700
    Announcing the gnomAD v4.1.1 and MPC tracks. Adding pennantIcons to the new and updated tracks. refs #38166 refs #37351 refs #37478
  • lines changed 1, context: html, text, full: html, text
    9227df124b0a433a7b05eb5367ba33589998dcc0 Wed Aug 26 20:18:16 2026 -0700
    Fixing a misspelled name in the gnomAD v4.1.1 announcement credits: Caitlin Samocha to Kaitlin Samocha. refs #38166
  • lines changed 2, context: html, text, full: html, text
    2740c034d0cb877c9bd055c5a897fa458d458bfa Wed Aug 26 20:38:59 2026 -0700
    Defining the MPC acronym per Bob's feedback, and pluralizing "track" to "tracks", in the gnomAD v4.1.1 announcement. refs #38166
  • lines changed 1, context: html, text, full: html, text
    02d76e6afae0e40826dc8eeff4272544841036c3 Thu Aug 27 00:54:50 2026 -0700
    Fixing "exomes and genomes variants" to "exome and genome variants" in the gnomAD v4.1.1 announcement image caption. refs #38166
  • lines changed 120, context: html, text, full: html, text
    1f5afdd131d8f41f9dead82d52cb5a723e443437 Fri Aug 28 15:25:59 2026 -0700
    Announcing the EVE and popEVE tracks for hg38, refs #37791 #37763
• src/hg/htdocs/images/newsArchImages/eve.png
  • lines changed 0, context: html, text, full: html, text
    1f5afdd131d8f41f9dead82d52cb5a723e443437 Fri Aug 28 15:25:59 2026 -0700
    Announcing the EVE and popEVE tracks for hg38, refs #37791 #37763
• src/hg/htdocs/images/newsArchImages/gnomadV4.1.1_MPC.png
  • lines changed 0, context: html, text, full: html, text
    cf87c27669523cb325d1d2d52e11e6f18d24504e Wed Aug 26 18:36:04 2026 -0700
    Announcing the gnomAD v4.1.1 and MPC tracks. Adding pennantIcons to the new and updated tracks. refs #38166 refs #37351 refs #37478
• src/hg/htdocs/images/newsArchImages/popEve.png
  • lines changed 0, context: html, text, full: html, text
    1f5afdd131d8f41f9dead82d52cb5a723e443437 Fri Aug 28 15:25:59 2026 -0700
    Announcing the EVE and popEVE tracks for hg38, refs #37791 #37763
• src/hg/htdocs/indexNews.html
  • lines changed 13, context: html, text, full: html, text
    cf87c27669523cb325d1d2d52e11e6f18d24504e Wed Aug 26 18:36:04 2026 -0700
    Announcing the gnomAD v4.1.1 and MPC tracks. Adding pennantIcons to the new and updated tracks. refs #38166 refs #37351 refs #37478
  • lines changed 12, context: html, text, full: html, text
    1f5afdd131d8f41f9dead82d52cb5a723e443437 Fri Aug 28 15:25:59 2026 -0700
    Announcing the EVE and popEVE tracks for hg38, refs #37791 #37763
• src/hg/htdocs/staticStyle/gbStatic.css
  • lines changed 6, context: html, text, full: html, text
    dad2b237d480ba64706fbb6c63d092b2738a2413 Mon Aug 24 15:33:38 2026 -0700
    Add ### headings as indented TOC sub-items and fix docs sidebar highlighting, refs #36320
• src/hg/htdocs/style/facetedComposite.css
  • lines changed 12, context: html, text, full: html, text
    90b8f880be12956b899d973bc565bffdc9b7ce89 Fri Aug 28 08:27:13 2026 -0700
    Moving sort comment on the faceted composite UI, and ading a 'hide subtracks', refs #36320
• src/hg/htdocs/style/gbModern.css
  • lines changed 13, context: html, text, full: html, text
    5a3be3af33b76d69d1fc98ee76b9a37f96e96fc7 Wed Aug 26 00:36:52 2026 -0700
    Add opt-in per-phase request timing to the new hgBlat and hgSession pages, shown in a dialog with &measureTiming=1. refs #38157 New reusable perfTimer collector (lib/perfTimer.c) records labeled wall-clock intervals via clock1000() and emits them as JSON; hgBlat and hgSession attach a timing array to their payload when the existing measureTiming cart/CGI var is set. A shared gbShowTimingDialog helper in utils.js renders the server phases plus a client render-time row in a house-style modal, which opens automatically when measureTiming is on. Confirms the position band/locus annotation loop dominates hgSession, and run-BLAT plus locus lookups dominate hgBlat.
• src/hg/htdocs/style/hgSession.css
  • lines changed 3, context: html, text, full: html, text
    83858083785a6b2b1f3c05f93e818e5a89318692 Tue Aug 25 01:42:34 2026 -0700
    hgSession: show cytoBand and gene/locus annotations for each saved session; date-only Created/Last used columns with full timestamp on hover. Factor locusName lookup into reusable hLocusName/hLocusNameExpand in hdb.c and reuse from hgBlat. refs #38157 The Assembly column now shows band, gene/locus name and Mbp position (separated by whitespace, normal text size). hLocusNameExpand centralizes the ex:/in:/ig: and | to - expansion that hgBlat's results page did inline.
  • lines changed 1, context: html, text, full: html, text
    0ff5f19b29ae3b3da4096e1ed1a4b49a4215c8a3 Wed Aug 26 01:53:57 2026 -0700
    hgSession: enlarge the action-row icons (13->17px) so the save/trash glyphs are easier to read
• src/hg/inc/hdb.h
  • lines changed 8, context: html, text, full: html, text
    83858083785a6b2b1f3c05f93e818e5a89318692 Tue Aug 25 01:42:34 2026 -0700
    hgSession: show cytoBand and gene/locus annotations for each saved session; date-only Created/Last used columns with full timestamp on hover. Factor locusName lookup into reusable hLocusName/hLocusNameExpand in hdb.c and reuse from hgBlat. refs #38157 The Assembly column now shows band, gene/locus name and Mbp position (separated by whitespace, normal text size). hLocusNameExpand centralizes the ex:/in:/ig: and | to - expansion that hgBlat's results page did inline.
• src/hg/inc/hui.h
  • lines changed 4, context: html, text, full: html, text
    f04f1b9af06c823602c5e0ecd3b8c2059d7704d3 Thu Aug 27 14:42:31 2026 -0700
    Faceted composites now have a max display mode setting instead of a full override of child track visibilities, with accompanying support for the onlyVisibility setting. We also now include a filter block (applied to appropriate child tracks) when those settings are in place. refs #37662
  • lines changed 4, context: html, text, full: html, text
    90b8f880be12956b899d973bc565bffdc9b7ce89 Fri Aug 28 08:27:13 2026 -0700
    Moving sort comment on the faceted composite UI, and ading a 'hide subtracks', refs #36320
• src/hg/inc/trackDb.h
  • lines changed 4, context: html, text, full: html, text
    f04f1b9af06c823602c5e0ecd3b8c2059d7704d3 Thu Aug 27 14:42:31 2026 -0700
    Faceted composites now have a max display mode setting instead of a full override of child track visibilities, with accompanying support for the onlyVisibility setting. We also now include a filter block (applied to appropriate child tracks) when those settings are in place. refs #37662
• src/hg/inc/trackHub.h
  • lines changed 1, context: html, text, full: html, text
    d0942d5563ca2fdd0170c4730bb6bf1ecc8258ea Thu Aug 27 09:16:16 2026 -0700
    quickLift: take out the unused visibility string, refs #38032 trackHubBuild and walkTree never wrote visDy. hgConvert allocated it, passed it down, then reassigned it inside the chain loop, leaking a dyString per chain.
• src/hg/inc/wikiLink.h
  • lines changed 26, context: html, text, full: html, text
    75593a4e317eac40b781c83718961f0eb7f84f3a Thu Aug 27 06:32:34 2026 -0700
    Blue bar login and logout now return to the page they were clicked on #Preview2 week - bugs introduced now will need a build patch to fix The Login link in the blue bar sent everyone to the My Sessions page after they signed in, and the Sign out and account links in the logged-in dialog did the same, so a visitor reading a help page or looking at an item details page lost their place. Only hgTracks was handled, as a special case. Adds wikiLinkEncodeCurrentPageReturnUrl(), which builds a returnto for the page the CGI is currently serving, including its query string, since the track and item parameters of pages like hgTrackUi and hgc are not all kept in the cart. hgTracks keeps its old behaviour of returning to hgTracks?hgsid=, because its state is in the cart and its query string can hold a one-shot zoom or drag. hgMenubar does the same for the static pages it is included into, using the page path from the SSI environment. The two checks hgLogin runs on an incoming returnto (URL shape, and the optional login.approvedReturn host list) move to wikiLink.c so that the CGIs building a link apply the same rules before writing it. A URL hgLogin would refuse now becomes an ordinary login link instead of an error page: an over-long or oddly-quoted query string costs the query string, and a host that login.approvedReturn does not cover falls back to the old My Sessions target. Note that with login.approvedReturn set, static-page returns need the bare host added to the list. Also converts the fixed 2 kB buffers in the wikiLink URL builders to dyStrings, since a cgi-encoded return URL can nearly triple in length and safef would have aborted. refs #38192
• src/hg/js/facetedComposite.js
  • lines changed 7, context: html, text, full: html, text
    f04f1b9af06c823602c5e0ecd3b8c2059d7704d3 Thu Aug 27 14:42:31 2026 -0700
    Faceted composites now have a max display mode setting instead of a full override of child track visibilities, with accompanying support for the onlyVisibility setting. We also now include a filter block (applied to appropriate child tracks) when those settings are in place. refs #37662
  • lines changed 4, context: html, text, full: html, text
    90b8f880be12956b899d973bc565bffdc9b7ce89 Fri Aug 28 08:27:13 2026 -0700
    Moving sort comment on the faceted composite UI, and ading a 'hide subtracks', refs #36320
• src/hg/js/hgBlat.js
  • lines changed 27, context: html, text, full: html, text
    5a3be3af33b76d69d1fc98ee76b9a37f96e96fc7 Wed Aug 26 00:36:52 2026 -0700
    Add opt-in per-phase request timing to the new hgBlat and hgSession pages, shown in a dialog with &measureTiming=1. refs #38157 New reusable perfTimer collector (lib/perfTimer.c) records labeled wall-clock intervals via clock1000() and emits them as JSON; hgBlat and hgSession attach a timing array to their payload when the existing measureTiming cart/CGI var is set. A shared gbShowTimingDialog helper in utils.js renders the server phases plus a client render-time row in a house-style modal, which opens automatically when measureTiming is on. Confirms the position band/locus annotation loop dominates hgSession, and run-BLAT plus locus lookups dominate hgBlat.
  • lines changed 29, context: html, text, full: html, text
    b1ea00a1ea5559c4f27b00da2f90493bd8a3a88e Wed Aug 26 00:57:26 2026 -0700
    hgBlat: reorder the search-form checkboxes to Keep results, Show rearrangements, No min. score, Search many genomes. refs #37893
  • lines changed 8, context: html, text, full: html, text
    4fd18ab7854e6620576499d1b7f70fd03d9b6f9d Thu Aug 27 09:03:04 2026 -0700
    hgBlat: name a BLAT track after the gene whose exon it hits, and call protein lengths aa #Preview2 week - bugs introduced now will need a build patch to fix topHitLocusLabel() took whatever locusName row hRangeQuery happened to return first, which is bin order and unrelated to the hit. A 400 bp query with 345 bp inside an EGFR exon came back as "400bp chr7:55019001" because the intergenic row upstream sorted first. It now walks all overlapping rows and prefers an exon row over an intron row, breaking ties by how much of the hit each row covers. Protein searches were also labelled "154bp SOD1". Query lengths of a protein search are amino acids, so the track name, its description and the results page (length and the coverage mouseover) now say "aa" for those. refs #38086
• src/hg/js/hgPhyloPlace.js
  • lines changed 1, context: html, text, full: html, text
    e8f2f6e391ee65e96e0a99e9a840f55db59bdb60 Fri Jun 5 15:34:13 2026 -0700
    Fixing more bugs found by Claude when Chris ran it.
• src/hg/js/hgSession.js
  • lines changed 5, context: html, text, full: html, text
    0108f1eb54fdce9856131873059928583be0bacb Mon Aug 24 03:58:09 2026 -0700
    hgSession: add a Last used column to the sessions table. refs #38157
  • lines changed 23, context: html, text, full: html, text
    83858083785a6b2b1f3c05f93e818e5a89318692 Tue Aug 25 01:42:34 2026 -0700
    hgSession: show cytoBand and gene/locus annotations for each saved session; date-only Created/Last used columns with full timestamp on hover. Factor locusName lookup into reusable hLocusName/hLocusNameExpand in hdb.c and reuse from hgBlat. refs #38157 The Assembly column now shows band, gene/locus name and Mbp position (separated by whitespace, normal text size). hLocusNameExpand centralizes the ex:/in:/ig: and | to - expansion that hgBlat's results page did inline.
  • lines changed 25, context: html, text, full: html, text
    5a3be3af33b76d69d1fc98ee76b9a37f96e96fc7 Wed Aug 26 00:36:52 2026 -0700
    Add opt-in per-phase request timing to the new hgBlat and hgSession pages, shown in a dialog with &measureTiming=1. refs #38157 New reusable perfTimer collector (lib/perfTimer.c) records labeled wall-clock intervals via clock1000() and emits them as JSON; hgBlat and hgSession attach a timing array to their payload when the existing measureTiming cart/CGI var is set. A shared gbShowTimingDialog helper in utils.js renders the server phases plus a client render-time row in a house-style modal, which opens automatically when measureTiming is on. Confirms the position band/locus annotation loop dominates hgSession, and run-BLAT plus locus lookups dominate hgBlat.
  • lines changed 9, context: html, text, full: html, text
    b7951c4e839a7fcb1d761084ba1fba8a06089049 Wed Aug 26 01:52:20 2026 -0700
    hgSession: use the outline floppy-disk icon for Overwrite, easier to recognize as save
  • lines changed 6, context: html, text, full: html, text
    3f97b357c5967755f1e5c914663ce9c7cc385e70 Wed Aug 26 03:01:34 2026 -0700
    Share a link: create the session only when the user asks, and copy in one click Opening the top-right "Share a link" dialog used to save a session right away, so just looking at the dialog left an unused link in the user's session list. The dialog now explains what the link is and offers one "Create link & copy" button that saves the session and copies the URL in a single step. The random name for a machine-generated session is now made client-side and sent with the request, so there is one convention in one place: a leading underscore (kept verbatim by the short-link encoder, so /s/<user>/_XXXXXXXX stays clean) plus eight URL-safe characters. hgSession.c no longer auto-names; a logged-in save with no name is an error, which is what the callers already guarantee. refs #10138
  • lines changed 6, context: html, text, full: html, text
    5872e3a9d5f3d2916bbf10f359011b9d04fc3b93 Wed Aug 26 03:18:39 2026 -0700
    Revert "Share a link: create the session only when the user asks, and copy in one click" This reverts commit 3f97b357c59. The change was work in progress and was committed by mistake; web.c still has the matching data-shortlink part uncommitted, so this half does not stand on its own. The genark syncFtp commit that went out with it is fine and stays.
• src/hg/js/hgTracks.js
  • lines changed 13, context: html, text, full: html, text
    e5cddda75c01e4bc890d381eb4b95713c96cea1c Tue Aug 25 10:08:37 2026 -0700
    Remove track from visible tracks group on hiding the track, refs #38035
  • lines changed 14, context: html, text, full: html, text
    e782dd6b9d73b9e138d57e3ad213bb6402b3802d Wed Aug 26 02:52:41 2026 -0700
    hgTracks: deleting a custom track now clears it from the Visible Tracks list too A visible custom track is listed twice under the image, once in its own group and once in the Visible Tracks group. Both the right-click Delete Custom Track item and the trash icon left the other copy behind until the page was reloaded. Remove every track-list cell that carries the track's delete icon, in deleteCustomTrack() so both paths get it. refs #38087
• src/hg/js/topLinks.js
  • lines changed 49, context: html, text, full: html, text
    3f97b357c5967755f1e5c914663ce9c7cc385e70 Wed Aug 26 03:01:34 2026 -0700
    Share a link: create the session only when the user asks, and copy in one click Opening the top-right "Share a link" dialog used to save a session right away, so just looking at the dialog left an unused link in the user's session list. The dialog now explains what the link is and offers one "Create link & copy" button that saves the session and copies the URL in a single step. The random name for a machine-generated session is now made client-side and sent with the request, so there is one convention in one place: a leading underscore (kept verbatim by the short-link encoder, so /s/<user>/_XXXXXXXX stays clean) plus eight URL-safe characters. hgSession.c no longer auto-names; a logged-in save with no name is an error, which is what the callers already guarantee. refs #10138
  • lines changed 49, context: html, text, full: html, text
    5872e3a9d5f3d2916bbf10f359011b9d04fc3b93 Wed Aug 26 03:18:39 2026 -0700
    Revert "Share a link: create the session only when the user asks, and copy in one click" This reverts commit 3f97b357c59. The change was work in progress and was committed by mistake; web.c still has the matching data-shortlink part uncommitted, so this half does not stand on its own. The genark syncFtp commit that went out with it is fine and stays.
  • lines changed 1, context: html, text, full: html, text
    90908c5b29e3ea47dc5b3088d46a60b6ba09eefb Sun Aug 30 13:41:37 2026 -0700
    Updating the My Track Hubs link in the account popup to go to Connected Hubs instead of Hub Upload. refs #36267
• src/hg/js/utils.js
  • lines changed 78, context: html, text, full: html, text
    5a3be3af33b76d69d1fc98ee76b9a37f96e96fc7 Wed Aug 26 00:36:52 2026 -0700
    Add opt-in per-phase request timing to the new hgBlat and hgSession pages, shown in a dialog with &measureTiming=1. refs #38157 New reusable perfTimer collector (lib/perfTimer.c) records labeled wall-clock intervals via clock1000() and emits them as JSON; hgBlat and hgSession attach a timing array to their payload when the existing measureTiming cart/CGI var is set. A shared gbShowTimingDialog helper in utils.js renders the server phases plus a client render-time row in a house-style modal, which opens automatically when measureTiming is on. Confirms the position band/locus annotation loop dominates hgSession, and run-BLAT plus locus lookups dominate hgBlat.
• src/hg/lib/cart.c
  • lines changed 7, context: html, text, full: html, text
    f04f1b9af06c823602c5e0ecd3b8c2059d7704d3 Thu Aug 27 14:42:31 2026 -0700
    Faceted composites now have a max display mode setting instead of a full override of child track visibilities, with accompanying support for the onlyVisibility setting. We also now include a filter block (applied to appropriate child tracks) when those settings are in place. refs #37662
• src/hg/lib/hdb.c
  • lines changed 40, context: html, text, full: html, text
    83858083785a6b2b1f3c05f93e818e5a89318692 Tue Aug 25 01:42:34 2026 -0700
    hgSession: show cytoBand and gene/locus annotations for each saved session; date-only Created/Last used columns with full timestamp on hover. Factor locusName lookup into reusable hLocusName/hLocusNameExpand in hdb.c and reuse from hgBlat. refs #38157 The Assembly column now shows band, gene/locus name and Mbp position (separated by whitespace, normal text size). hLocusNameExpand centralizes the ex:/in:/ig: and | to - expansion that hgBlat's results page did inline.
• src/hg/lib/hui.c
  • lines changed 62, context: html, text, full: html, text
    f04f1b9af06c823602c5e0ecd3b8c2059d7704d3 Thu Aug 27 14:42:31 2026 -0700
    Faceted composites now have a max display mode setting instead of a full override of child track visibilities, with accompanying support for the onlyVisibility setting. We also now include a filter block (applied to appropriate child tracks) when those settings are in place. refs #37662
  • lines changed 43, context: html, text, full: html, text
    90b8f880be12956b899d973bc565bffdc9b7ce89 Fri Aug 28 08:27:13 2026 -0700
    Moving sort comment on the faceted composite UI, and ading a 'hide subtracks', refs #36320
• src/hg/lib/trackDbCustom.c
  • lines changed 9, context: html, text, full: html, text
    f04f1b9af06c823602c5e0ecd3b8c2059d7704d3 Thu Aug 27 14:42:31 2026 -0700
    Faceted composites now have a max display mode setting instead of a full override of child track visibilities, with accompanying support for the onlyVisibility setting. We also now include a filter block (applied to appropriate child tracks) when those settings are in place. refs #37662
• src/hg/lib/trackHub.c
  • lines changed 3, context: html, text, full: html, text
    d0942d5563ca2fdd0170c4730bb6bf1ecc8258ea Thu Aug 27 09:16:16 2026 -0700
    quickLift: take out the unused visibility string, refs #38032 trackHubBuild and walkTree never wrote visDy. hgConvert allocated it, passed it down, then reassigned it inside the chain loop, leaking a dyString per chain.
• src/hg/lib/web.c
  • lines changed 23, context: html, text, full: html, text
    75593a4e317eac40b781c83718961f0eb7f84f3a Thu Aug 27 06:32:34 2026 -0700
    Blue bar login and logout now return to the page they were clicked on #Preview2 week - bugs introduced now will need a build patch to fix The Login link in the blue bar sent everyone to the My Sessions page after they signed in, and the Sign out and account links in the logged-in dialog did the same, so a visitor reading a help page or looking at an item details page lost their place. Only hgTracks was handled, as a special case. Adds wikiLinkEncodeCurrentPageReturnUrl(), which builds a returnto for the page the CGI is currently serving, including its query string, since the track and item parameters of pages like hgTrackUi and hgc are not all kept in the cart. hgTracks keeps its old behaviour of returning to hgTracks?hgsid=, because its state is in the cart and its query string can hold a one-shot zoom or drag. hgMenubar does the same for the static pages it is included into, using the page path from the SSI environment. The two checks hgLogin runs on an incoming returnto (URL shape, and the optional login.approvedReturn host list) move to wikiLink.c so that the CGIs building a link apply the same rules before writing it. A URL hgLogin would refuse now becomes an ordinary login link instead of an error page: an over-long or oddly-quoted query string costs the query string, and a host that login.approvedReturn does not cover falls back to the old My Sessions target. Note that with login.approvedReturn set, static-page returns need the bare host added to the list. Also converts the fixed 2 kB buffers in the wikiLink URL builders to dyStrings, since a cgi-encoded return URL can nearly triple in length and safef would have aborted. refs #38192
• src/hg/lib/wikiLink.c
  • lines changed 193, context: html, text, full: html, text
    75593a4e317eac40b781c83718961f0eb7f84f3a Thu Aug 27 06:32:34 2026 -0700
    Blue bar login and logout now return to the page they were clicked on #Preview2 week - bugs introduced now will need a build patch to fix The Login link in the blue bar sent everyone to the My Sessions page after they signed in, and the Sign out and account links in the logged-in dialog did the same, so a visitor reading a help page or looking at an item details page lost their place. Only hgTracks was handled, as a special case. Adds wikiLinkEncodeCurrentPageReturnUrl(), which builds a returnto for the page the CGI is currently serving, including its query string, since the track and item parameters of pages like hgTrackUi and hgc are not all kept in the cart. hgTracks keeps its old behaviour of returning to hgTracks?hgsid=, because its state is in the cart and its query string can hold a one-shot zoom or drag. hgMenubar does the same for the static pages it is included into, using the page path from the SSI environment. The two checks hgLogin runs on an incoming returnto (URL shape, and the optional login.approvedReturn host list) move to wikiLink.c so that the CGIs building a link apply the same rules before writing it. A URL hgLogin would refuse now becomes an ordinary login link instead of an error page: an over-long or oddly-quoted query string costs the query string, and a host that login.approvedReturn does not cover falls back to the old My Sessions target. Note that with login.approvedReturn set, static-page returns need the bare host added to the list. Also converts the fixed 2 kB buffers in the wikiLink URL builders to dyStrings, since a cgi-encoded return URL can nearly triple in length and safef would have aborted. refs #38192
• src/hg/makeDb/doc/archaeaAsmHub/archaea.orderList.tsv
  • lines changed 163, context: html, text, full: html, text
    45470fd5cae828c4a2bf3d03f163791574d8a908 Mon Aug 24 20:35:27 2026 -0700
    RefSeq and VGP updates refs @29545
  • lines changed 2, context: html, text, full: html, text
    ea2d262f5f16f49380500fdf3a6758c14faf409b Tue Aug 25 20:01:33 2026 -0700
    adding two per user request refs @29545
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 198, context: html, text, full: html, text
    45470fd5cae828c4a2bf3d03f163791574d8a908 Mon Aug 24 20:35:27 2026 -0700
    RefSeq and VGP updates refs @29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 11, context: html, text, full: html, text
    45470fd5cae828c4a2bf3d03f163791574d8a908 Mon Aug 24 20:35:27 2026 -0700
    RefSeq and VGP updates refs @29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 29, context: html, text, full: html, text
    45470fd5cae828c4a2bf3d03f163791574d8a908 Mon Aug 24 20:35:27 2026 -0700
    RefSeq and VGP updates refs @29545
• src/hg/makeDb/doc/hg38/ncbiRefSeq.txt
  • lines changed 18, context: html, text, full: html, text
    219f66fde04ded54d6992855d1fef738aa5b6a6f Thu Aug 27 17:12:34 2026 -0700
    Give the RefSeq Historical subtrack its own dataVersion, refs #35766 The Historical track inherited the composite's dataVersion file, which tracks the current RefSeq annotation release, so the track advertised RS_2025_08 while its data is RS_2024_08. This affected three places: the long label in the browser image (simpleTracks.c appends the version for any track whose name starts with ncbiRef), the track settings page, and the details pages. A subtrack may carry its own dataVersion; trackDbSetting reads the local value first and only climbs to the parent when there isn't one. Same pattern already used by clinGenHaplo and the nmdEsc* subtracks. Also adds the version file step to the makedoc, and a reminder to the weekly notifier mail so the next refresh doesn't leave it stale again. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/doc/hg38/singleCellSignalsPeaks.txt
  • lines changed 36, context: html, text, full: html, text
    8bb883ed32e24a1007bf9f97ee1793a46bf47bd0 Thu Aug 27 10:00:43 2026 -0700
    singleCellSignalsPeaks: classify the SEA-AD and Allen tracks, add BrainVar stages 72 hg38 SEA-AD and 89 mm10 allen-basal-ganglia tracks had lost their broad cell class and were drawing in dataset colours instead of the shared palette; both assemblies are now 0 unclassified. Fix is in the hub build (cellBrowser ucsc/allTracksHub). Adds an "Other glia" class, since "Other" was doing four unrelated jobs. BrainVar goes 4 -> 13 hg38 subtracks with the new stage-split pseudobulk. Scaling moves to "autoScale group" on the composite so selected subtracks share one scale, and every bigWig now carries a data range -- without one the 13 BrainVar tracks drew as flat lines against hgTracks' built-in 0:127. Description pages and makeDocs updated, including removing the stale claim that SEA-AD is coloured by its own subclass palette. refs #37914, refs #37820 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 8, context: html, text, full: html, text
    550a0e2666bcce27181a0cb0eab32ed261e444f6 Thu Aug 27 14:56:42 2026 -0700
    singleCellSignalsPeaks: color the Cell class facet checkboxes, refs #37820, refs #37914 The faceted UI already draws a color swatch beside each checkbox of any facet named in a colorSettingsUrl JSON, and the track already colors its subtracks by broad cell class from celltype-palette.tsv. Publish that palette so the selector shows the same colors: copySingleCellSignalsPeaksFiles.py now writes <bed>/singleCellSignalsPeaks_colors.json alongside the facet metadata, and the composite header names it. Rendered from the one shared palette, so a class is the same color in the checkbox list, in the drawn tracks, and on both assemblies. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 50, context: html, text, full: html, text
    3aac3982aa2b300c100086920451b2dc98a7f2b9 Fri Aug 28 14:49:32 2026 -0700
    singleCellSignalsPeaks: drop 5 superseded hg38 subtracks, alphabetize the references, refs #37820 The hg38 .ra is regenerated from the hub build, 934 -> 929 subtracks: - the 4 combined-stage BrainVar gene-activity tracks, superseded by the prenatal/postnatal pair of the same cell type, so every remaining BrainVar track now carries a life stage - neuro-degen-atac/peaks.bb, superseded by peaks.v2.bb (that dataset's hub.txt comments the peaks.bb bigDataUrl out and serves v2). The two collided on one track id and shipped as two indistinguishable "All cell types, peaks" tracks; with the collision gone the survivor is named ..._peaks and its label loses the "(peaks)" disambiguator. The exclusion itself lives in the hub build's new exclude_track_paths denylist (cellBrowser ucsc/allTracksHub/hub_config.json), not in a hand edit here, so the next regeneration cannot put the tracks back. Facet metadata was refreshed to match: .ra and metadata are 1:1 at 929. Subtrack priorities renumber because they are per-class sequence counters and the dropped BrainVar tracks were first in their classes. Both description pages now list their references alphabetically by first author (hg38 9 refs, mm10 7); no reference text changed. makeDoc: new section 1b documents the denylist and what is currently on it, and the counts are brought up to date. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 128, context: html, text, full: html, text
    45470fd5cae828c4a2bf3d03f163791574d8a908 Mon Aug 24 20:35:27 2026 -0700
    RefSeq and VGP updates refs @29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 76, context: html, text, full: html, text
    45470fd5cae828c4a2bf3d03f163791574d8a908 Mon Aug 24 20:35:27 2026 -0700
    RefSeq and VGP updates refs @29545
• src/hg/makeDb/doc/mm10/singleCellSignalsPeaks.txt
  • lines changed 87, context: html, text, full: html, text
    8bb883ed32e24a1007bf9f97ee1793a46bf47bd0 Thu Aug 27 10:00:43 2026 -0700
    singleCellSignalsPeaks: classify the SEA-AD and Allen tracks, add BrainVar stages 72 hg38 SEA-AD and 89 mm10 allen-basal-ganglia tracks had lost their broad cell class and were drawing in dataset colours instead of the shared palette; both assemblies are now 0 unclassified. Fix is in the hub build (cellBrowser ucsc/allTracksHub). Adds an "Other glia" class, since "Other" was doing four unrelated jobs. BrainVar goes 4 -> 13 hg38 subtracks with the new stage-split pseudobulk. Scaling moves to "autoScale group" on the composite so selected subtracks share one scale, and every bigWig now carries a data range -- without one the 13 BrainVar tracks drew as flat lines against hgTracks' built-in 0:127. Description pages and makeDocs updated, including removing the stale claim that SEA-AD is coloured by its own subclass palette. refs #37914, refs #37820 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 12, context: html, text, full: html, text
    550a0e2666bcce27181a0cb0eab32ed261e444f6 Thu Aug 27 14:56:42 2026 -0700
    singleCellSignalsPeaks: color the Cell class facet checkboxes, refs #37820, refs #37914 The faceted UI already draws a color swatch beside each checkbox of any facet named in a colorSettingsUrl JSON, and the track already colors its subtracks by broad cell class from celltype-palette.tsv. Publish that palette so the selector shows the same colors: copySingleCellSignalsPeaksFiles.py now writes <bed>/singleCellSignalsPeaks_colors.json alongside the facet metadata, and the composite header names it. Rendered from the one shared palette, so a class is the same color in the checkbox list, in the drawn tracks, and on both assemblies. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 5, context: html, text, full: html, text
    05e212467751884f63353f671cf97c3f83f7a8a8 Fri Aug 28 14:47:20 2026 -0700
    singleCellSignalsPeaks mm10 makeDoc: correct the autoScale subtrack counts, refs #37914 Matches the corrected DROP_KEYS note in the hub build (cellBrowser ucsc/allTracksHub/build_stanzas.py): 475 subtracks corpus-wide (402 hg38, 73 mm10) inherited `autoScale group` from their source hubs, and a further 677 (184 hg38, 493 mm10) carried `autoScale on`, so build_stanzas drops autoScale for all 1152. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 6, context: html, text, full: html, text
    45470fd5cae828c4a2bf3d03f163791574d8a908 Mon Aug 24 20:35:27 2026 -0700
    RefSeq and VGP updates refs @29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    45470fd5cae828c4a2bf3d03f163791574d8a908 Mon Aug 24 20:35:27 2026 -0700
    RefSeq and VGP updates refs @29545
  • lines changed 12, context: html, text, full: html, text
    38021c2708cee8f71dec0a53d46bd10ad220fee5 Tue Aug 25 14:46:10 2026 -0700
    correct English name for Pan paniscus is bonobo refs #29545
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 27, context: html, text, full: html, text
    45470fd5cae828c4a2bf3d03f163791574d8a908 Mon Aug 24 20:35:27 2026 -0700
    RefSeq and VGP updates refs @29545
• src/hg/makeDb/scripts/singleCellSignalsPeaks/build_celltype_crosswalks.py
  • lines changed 8, context: html, text, full: html, text
    8bb883ed32e24a1007bf9f97ee1793a46bf47bd0 Thu Aug 27 10:00:43 2026 -0700
    singleCellSignalsPeaks: classify the SEA-AD and Allen tracks, add BrainVar stages 72 hg38 SEA-AD and 89 mm10 allen-basal-ganglia tracks had lost their broad cell class and were drawing in dataset colours instead of the shared palette; both assemblies are now 0 unclassified. Fix is in the hub build (cellBrowser ucsc/allTracksHub). Adds an "Other glia" class, since "Other" was doing four unrelated jobs. BrainVar goes 4 -> 13 hg38 subtracks with the new stage-split pseudobulk. Scaling moves to "autoScale group" on the composite so selected subtracks share one scale, and every bigWig now carries a data range -- without one the 13 BrainVar tracks drew as flat lines against hgTracks' built-in 0:127. Description pages and makeDocs updated, including removing the stale claim that SEA-AD is coloured by its own subclass palette. refs #37914, refs #37820 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/singleCellSignalsPeaks/celltype-crosswalks/celltype-class.tsv
  • lines changed 9, context: html, text, full: html, text
    8bb883ed32e24a1007bf9f97ee1793a46bf47bd0 Thu Aug 27 10:00:43 2026 -0700
    singleCellSignalsPeaks: classify the SEA-AD and Allen tracks, add BrainVar stages 72 hg38 SEA-AD and 89 mm10 allen-basal-ganglia tracks had lost their broad cell class and were drawing in dataset colours instead of the shared palette; both assemblies are now 0 unclassified. Fix is in the hub build (cellBrowser ucsc/allTracksHub). Adds an "Other glia" class, since "Other" was doing four unrelated jobs. BrainVar goes 4 -> 13 hg38 subtracks with the new stage-split pseudobulk. Scaling moves to "autoScale group" on the composite so selected subtracks share one scale, and every bigWig now carries a data range -- without one the 13 BrainVar tracks drew as flat lines against hgTracks' built-in 0:127. Description pages and makeDocs updated, including removing the stale claim that SEA-AD is coloured by its own subclass palette. refs #37914, refs #37820 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/singleCellSignalsPeaks/celltype-crosswalks/celltype-palette.tsv
  • lines changed 1, context: html, text, full: html, text
    8bb883ed32e24a1007bf9f97ee1793a46bf47bd0 Thu Aug 27 10:00:43 2026 -0700
    singleCellSignalsPeaks: classify the SEA-AD and Allen tracks, add BrainVar stages 72 hg38 SEA-AD and 89 mm10 allen-basal-ganglia tracks had lost their broad cell class and were drawing in dataset colours instead of the shared palette; both assemblies are now 0 unclassified. Fix is in the hub build (cellBrowser ucsc/allTracksHub). Adds an "Other glia" class, since "Other" was doing four unrelated jobs. BrainVar goes 4 -> 13 hg38 subtracks with the new stage-split pseudobulk. Scaling moves to "autoScale group" on the composite so selected subtracks share one scale, and every bigWig now carries a data range -- without one the 13 BrainVar tracks drew as flat lines against hgTracks' built-in 0:127. Description pages and makeDocs updated, including removing the stale claim that SEA-AD is coloured by its own subclass palette. refs #37914, refs #37820 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/singleCellSignalsPeaks/celltype-crosswalks/paper-decodes/hg38_ct_class.tsv
  • lines changed 1, context: html, text, full: html, text
    8bb883ed32e24a1007bf9f97ee1793a46bf47bd0 Thu Aug 27 10:00:43 2026 -0700
    singleCellSignalsPeaks: classify the SEA-AD and Allen tracks, add BrainVar stages 72 hg38 SEA-AD and 89 mm10 allen-basal-ganglia tracks had lost their broad cell class and were drawing in dataset colours instead of the shared palette; both assemblies are now 0 unclassified. Fix is in the hub build (cellBrowser ucsc/allTracksHub). Adds an "Other glia" class, since "Other" was doing four unrelated jobs. BrainVar goes 4 -> 13 hg38 subtracks with the new stage-split pseudobulk. Scaling moves to "autoScale group" on the composite so selected subtracks share one scale, and every bigWig now carries a data range -- without one the 13 BrainVar tracks drew as flat lines against hgTracks' built-in 0:127. Description pages and makeDocs updated, including removing the stale claim that SEA-AD is coloured by its own subclass palette. refs #37914, refs #37820 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/singleCellSignalsPeaks/copySingleCellSignalsPeaksFiles.py
  • lines changed 72, context: html, text, full: html, text
    550a0e2666bcce27181a0cb0eab32ed261e444f6 Thu Aug 27 14:56:42 2026 -0700
    singleCellSignalsPeaks: color the Cell class facet checkboxes, refs #37820, refs #37914 The faceted UI already draws a color swatch beside each checkbox of any facet named in a colorSettingsUrl JSON, and the track already colors its subtracks by broad cell class from celltype-palette.tsv. Publish that palette so the selector shows the same colors: copySingleCellSignalsPeaksFiles.py now writes <bed>/singleCellSignalsPeaks_colors.json alongside the facet metadata, and the composite header names it. Rendered from the one shared palette, so a class is the same color in the checkbox list, in the drawn tracks, and on both assemblies. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/singleCellSignalsPeaks/makeSingleCellSignalsPeaksRa.py
  • lines changed 8, context: html, text, full: html, text
    8bb883ed32e24a1007bf9f97ee1793a46bf47bd0 Thu Aug 27 10:00:43 2026 -0700
    singleCellSignalsPeaks: classify the SEA-AD and Allen tracks, add BrainVar stages 72 hg38 SEA-AD and 89 mm10 allen-basal-ganglia tracks had lost their broad cell class and were drawing in dataset colours instead of the shared palette; both assemblies are now 0 unclassified. Fix is in the hub build (cellBrowser ucsc/allTracksHub). Adds an "Other glia" class, since "Other" was doing four unrelated jobs. BrainVar goes 4 -> 13 hg38 subtracks with the new stage-split pseudobulk. Scaling moves to "autoScale group" on the composite so selected subtracks share one scale, and every bigWig now carries a data range -- without one the 13 BrainVar tracks drew as flat lines against hgTracks' built-in 0:127. Description pages and makeDocs updated, including removing the stale claim that SEA-AD is coloured by its own subclass palette. refs #37914, refs #37820 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 5, context: html, text, full: html, text
    550a0e2666bcce27181a0cb0eab32ed261e444f6 Thu Aug 27 14:56:42 2026 -0700
    singleCellSignalsPeaks: color the Cell class facet checkboxes, refs #37820, refs #37914 The faceted UI already draws a color swatch beside each checkbox of any facet named in a colorSettingsUrl JSON, and the track already colors its subtracks by broad cell class from celltype-palette.tsv. Publish that palette so the selector shows the same colors: copySingleCellSignalsPeaksFiles.py now writes <bed>/singleCellSignalsPeaks_colors.json alongside the facet metadata, and the composite header names it. Rendered from the one shared palette, so a class is the same color in the checkbox list, in the drawn tracks, and on both assemblies. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/tp53/tp53Flossies.py
  • lines changed 10, context: html, text, full: html, text
    87f5ac2d9279932b8d45b75e9c7d30fdd062a5b7 Mon Aug 24 18:21:40 2026 -0700
    Fixes from nightly CR: guard FLOSSIES carrier count, drop dead variable. refs #37399 refs #38139 Hardening on the FLOSSIES carrier-count fix, per nightly code review: - Add a consistency guard: carriers are summed from the per-population het and hom counts, and the build now raises if sum(pop_hets)+sum(pop_homs) does not equal allele_count. In this export the two are identical (allele_count is het+hom, not the usual het+2*hom), so this catches a future re-fetch that renames pop_hets/pop_homs or switches to standard allele-count semantics, instead of silently zeroing carriers and mis-tiering every coding variant. Verified the identity holds for all 118 current records. - Remove the now-dead hom (hom_count) local, left over from the old allele_count - hom_count formula. No output change (FLOSSIES bigBed is byte-identical; tiers unchanged).
• src/hg/makeDb/trackDb/apis/apiMel2/dnaMethylation.html
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/apis/apiMel2/mb2_apiMel2_colors.json
  • lines changed 24, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/apis/apiMel2/mb2_apiMel2_metadata.tsv
  • lines changed 211, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/apis/apiMel2/methbase2.ra
  • lines changed 7993, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/apis/apiMel2/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
  • lines changed 1, context: html, text, full: html, text
    53dff34f95bdea27e7747c8bcecb03a7ae45bdfd Thu Aug 27 14:58:41 2026 -0700
    Whoops, ensuring the MethBase2 stuff is set to alpha, and doesn't escape before review. refs #36320
• src/hg/makeDb/trackDb/buildTrix
  • lines changed 39, context: html, text, full: html, text
    0b36c1276f7fd41e8ba9ad53bbdb20c1d438913d Tue Aug 25 12:08:14 2026 -0700
    trackDb: build the trix once per database, and run the beta make in parallel, refs #35489 The trackDb make for a final build takes about 18 minutes. It is not one slow step. It is 348 per-database chains of short processes and network round trips, run strictly one after another. Two changes. First, stop building the same trix twice. The beta recipe called buildTrix once for hgwbeta and again for hgwdev, with identical inputs and only the destination differing. buildTrix now takes -alsoTo=machine:path, so the index is built once and sent to both places. It also assembles the files in a temporary directory under their final names, so each destination takes one rsync instead of one per file. That takes the trix step from ten ssh connections per database down to two, and it no longer leaves .offsets files behind in the trackDb directory. Second, run the make in parallel. The header comment warning against this was out of date. hgTrackDb and hgFindSpec put their temporary files in TMPDIR under process-unique names, and every other file and table a recipe writes is already named after its database, so the per-database chains do not collide. Two makes at once are still unsafe, because they share table names, and the comment now says that instead. makeStrictBeta.csh passes -O -j 8. Set TRACKDB_MAKE_JOBS to change the job count. Going much above 8 wants ssh connection sharing first, or hgwbeta's sshd starts refusing connections. Measured over all 348 databases, with the output compared line by line against a serial run each time: 321 seconds today, 194 with the tdbQuery fix alone, 81 with -j 8 alone, and 39 with both. The -j 8 figure lands on the hg38 chain, which is why the tdbQuery fix matters more than its share of the total suggests.
  • lines changed 5, context: html, text, full: html, text
    adca1531bedb1f883c7f46f37bfcf690858050c2 Wed Aug 26 08:15:31 2026 -0700
    trackDb: rsync the trix files by name, not the directory they sit in, refs #35489 The beta make died on the first database with: rsync: [generator] failed to set times on "/data/trix/.": Operation not permitted (1) rsync error: some files/attrs were not transferred (code 23) My change yesterday replaced five per-file rsyncs with one rsync of the temporary directory. A trailing slash on the source means "the contents of this directory", but rsync still puts the directory itself in the file list. So -a gets applied to the destination directory too, and rsync tries to give /data/trix the temporary directory's timestamp. The build user does not own /data/trix, the utime call fails, and rsync exits 23. strace shows the extra call the file list form never makes: dir source: utimensat(AT_FDCWD, ".", [... 2019-09-09 ...]) = 0 file list: no call on "." The -alsoTo destination on hgwdev would have failed the same way, since the build user does not own /hive/data/inside/trix either. Name the five files as arguments, the way the code did before. That is still one rsync and one ssh connection per destination, so the speedup stays.
• src/hg/makeDb/trackDb/calMil/calMil1/dnaMethylation.html
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/calMil/calMil1/mb2_calMil1_colors.json
  • lines changed 5, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/calMil/calMil1/mb2_calMil1_metadata.tsv
  • lines changed 2, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/calMil/calMil1/methbase2.ra
  • lines changed 51, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/calMil/calMil1/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
  • lines changed 1, context: html, text, full: html, text
    53dff34f95bdea27e7747c8bcecb03a7ae45bdfd Thu Aug 27 14:58:41 2026 -0700
    Whoops, ensuring the MethBase2 stuff is set to alpha, and doesn't escape before review. refs #36320
• src/hg/makeDb/trackDb/cat/felCat9/dnaMethylation.html
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/cat/felCat9/mb2_felCat9_colors.json
  • lines changed 6, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/cat/felCat9/mb2_felCat9_metadata.tsv
  • lines changed 10, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/cat/felCat9/methbase2.ra
  • lines changed 355, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/cat/felCat9/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
  • lines changed 1, context: html, text, full: html, text
    53dff34f95bdea27e7747c8bcecb03a7ae45bdfd Thu Aug 27 14:58:41 2026 -0700
    Whoops, ensuring the MethBase2 stuff is set to alpha, and doesn't escape before review. refs #36320
• src/hg/makeDb/trackDb/chicken/galGal6/dnaMethylation.html
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/chicken/galGal6/mb2_galGal6_colors.json
  • lines changed 24, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/chicken/galGal6/mb2_galGal6_metadata.tsv
  • lines changed 284, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/chicken/galGal6/methbase2.ra
  • lines changed 10757, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/chicken/galGal6/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
  • lines changed 1, context: html, text, full: html, text
    53dff34f95bdea27e7747c8bcecb03a7ae45bdfd Thu Aug 27 14:58:41 2026 -0700
    Whoops, ensuring the MethBase2 stuff is set to alpha, and doesn't escape before review. refs #36320
• src/hg/makeDb/trackDb/chimp/panTro6/dnaMethylation.html
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/chimp/panTro6/mb2_panTro6_colors.json
  • lines changed 16, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/chimp/panTro6/mb2_panTro6_metadata.tsv
  • lines changed 60, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/chimp/panTro6/methbase2.ra
  • lines changed 2255, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/chimp/panTro6/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
  • lines changed 1, context: html, text, full: html, text
    53dff34f95bdea27e7747c8bcecb03a7ae45bdfd Thu Aug 27 14:58:41 2026 -0700
    Whoops, ensuring the MethBase2 stuff is set to alpha, and doesn't escape before review. refs #36320
• src/hg/makeDb/trackDb/cow/bosTau9/dnaMethylation.html
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/cow/bosTau9/mb2_bosTau9_colors.json
  • lines changed 24, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/cow/bosTau9/mb2_bosTau9_metadata.tsv
  • lines changed 589, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/cow/bosTau9/methbase2.ra
  • lines changed 22217, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/cow/bosTau9/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
  • lines changed 1, context: html, text, full: html, text
    53dff34f95bdea27e7747c8bcecb03a7ae45bdfd Thu Aug 27 14:58:41 2026 -0700
    Whoops, ensuring the MethBase2 stuff is set to alpha, and doesn't escape before review. refs #36320
• src/hg/makeDb/trackDb/dog/canFam6/dnaMethylation.html
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/dog/canFam6/mb2_canFam6_colors.json
  • lines changed 16, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/dog/canFam6/mb2_canFam6_metadata.tsv
  • lines changed 146, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/dog/canFam6/methbase2.ra
  • lines changed 5523, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/dog/canFam6/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
  • lines changed 1, context: html, text, full: html, text
    53dff34f95bdea27e7747c8bcecb03a7ae45bdfd Thu Aug 27 14:58:41 2026 -0700
    Whoops, ensuring the MethBase2 stuff is set to alpha, and doesn't escape before review. refs #36320
• src/hg/makeDb/trackDb/dolphin/turTru2/dnaMethylation.html
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/dolphin/turTru2/mb2_turTru2_colors.json
  • lines changed 5, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/dolphin/turTru2/mb2_turTru2_metadata.tsv
  • lines changed 2, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/dolphin/turTru2/methbase2.ra
  • lines changed 51, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/dolphin/turTru2/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
  • lines changed 1, context: html, text, full: html, text
    53dff34f95bdea27e7747c8bcecb03a7ae45bdfd Thu Aug 27 14:58:41 2026 -0700
    Whoops, ensuring the MethBase2 stuff is set to alpha, and doesn't escape before review. refs #36320
• src/hg/makeDb/trackDb/fugu/fr3/dnaMethylation.html
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/fugu/fr3/mb2_fr3_colors.json
  • lines changed 15, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/fugu/fr3/mb2_fr3_metadata.tsv
  • lines changed 16, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/fugu/fr3/methbase2.ra
  • lines changed 583, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/fugu/fr3/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
  • lines changed 1, context: html, text, full: html, text
    53dff34f95bdea27e7747c8bcecb03a7ae45bdfd Thu Aug 27 14:58:41 2026 -0700
    Whoops, ensuring the MethBase2 stuff is set to alpha, and doesn't escape before review. refs #36320
• src/hg/makeDb/trackDb/gibbon/nomLeu3/dnaMethylation.html
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/gibbon/nomLeu3/mb2_nomLeu3_colors.json
  • lines changed 5, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/gibbon/nomLeu3/mb2_nomLeu3_metadata.tsv
  • lines changed 2, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/gibbon/nomLeu3/methbase2.ra
  • lines changed 51, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/gibbon/nomLeu3/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
  • lines changed 1, context: html, text, full: html, text
    53dff34f95bdea27e7747c8bcecb03a7ae45bdfd Thu Aug 27 14:58:41 2026 -0700
    Whoops, ensuring the MethBase2 stuff is set to alpha, and doesn't escape before review. refs #36320
• src/hg/makeDb/trackDb/gorilla/gorGor6/dnaMethylation.html
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/gorilla/gorGor6/mb2_gorGor6_colors.json
  • lines changed 7, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/gorilla/gorGor6/mb2_gorGor6_metadata.tsv
  • lines changed 7, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/gorilla/gorGor6/methbase2.ra
  • lines changed 241, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/gorilla/gorGor6/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
  • lines changed 1, context: html, text, full: html, text
    53dff34f95bdea27e7747c8bcecb03a7ae45bdfd Thu Aug 27 14:58:41 2026 -0700
    Whoops, ensuring the MethBase2 stuff is set to alpha, and doesn't escape before review. refs #36320
• src/hg/makeDb/trackDb/horse/equCab3/dnaMethylation.html
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/horse/equCab3/mb2_equCab3_colors.json
  • lines changed 7, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/horse/equCab3/mb2_equCab3_metadata.tsv
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/horse/equCab3/methbase2.ra
  • lines changed 127, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/horse/equCab3/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
  • lines changed 1, context: html, text, full: html, text
    53dff34f95bdea27e7747c8bcecb03a7ae45bdfd Thu Aug 27 14:58:41 2026 -0700
    Whoops, ensuring the MethBase2 stuff is set to alpha, and doesn't escape before review. refs #36320
• src/hg/makeDb/trackDb/human/eve.ra
  • lines changed 1, context: html, text, full: html, text
    1f5afdd131d8f41f9dead82d52cb5a723e443437 Fri Aug 28 15:25:59 2026 -0700
    Announcing the EVE and popEVE tracks for hg38, refs #37791 #37763
• src/hg/makeDb/trackDb/human/genCC.ra
  • lines changed 1, context: html, text, full: html, text
    6a8e756b47341a5584f5c3fca4031401fe507020 Mon Aug 24 11:21:22 2026 -0700
    Updating GeneCards links to their new URL format per their request, also fixes dead cardsearch.pl links on RefSeq and denovoDb click pages. refs #38171
• src/hg/makeDb/trackDb/human/hg19/denovoDb.ra
  • lines changed 2, context: html, text, full: html, text
    6a8e756b47341a5584f5c3fca4031401fe507020 Mon Aug 24 11:21:22 2026 -0700
    Updating GeneCards links to their new URL format per their request, also fixes dead cardsearch.pl links on RefSeq and denovoDb click pages. refs #38171
• src/hg/makeDb/trackDb/human/hg38/gnomad.constraint.alpha.ra
  • lines changed 1, context: html, text, full: html, text
    8ddc3930661eeb43c7483f7e3f43f189100d6d86 Mon Aug 24 23:49:57 2026 -0700
    Updating release tags to beta for the gnomAD v4.1.1 tracks and updating the Transcript Missense v4.1.1 mouseOver, refs #37351
• src/hg/makeDb/trackDb/human/hg38/gnomad.constraint.public.ra
  • lines changed 178, context: html, text, full: html, text
    1524ca6f78d40d477144943e182b6ab616c6216e Wed Aug 26 16:50:17 2026 -0700
    Releasing the gnomAD v4.1.1 tracks. Removed the release tags from the gnomadVariantsV4.1 v4.1.1 stanza, deleted the old v4.1 stanza, and merged gnomad.constraint.alpha.ra/gnomad.constraint.public.ra into gnomad.constraint.ra. refs #37351
• src/hg/makeDb/trackDb/human/hg38/gnomad.constraint.ra
  • lines changed 0, context: html, text, full: html, text
    1524ca6f78d40d477144943e182b6ab616c6216e Wed Aug 26 16:50:17 2026 -0700
    Releasing the gnomAD v4.1.1 tracks. Removed the release tags from the gnomadVariantsV4.1 v4.1.1 stanza, deleted the old v4.1 stanza, and merged gnomad.constraint.alpha.ra/gnomad.constraint.public.ra into gnomad.constraint.ra. refs #37351
  • lines changed 3, context: html, text, full: html, text
    cf87c27669523cb325d1d2d52e11e6f18d24504e Wed Aug 26 18:36:04 2026 -0700
    Announcing the gnomAD v4.1.1 and MPC tracks. Adding pennantIcons to the new and updated tracks. refs #38166 refs #37351 refs #37478
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 8, context: html, text, full: html, text
    8ddc3930661eeb43c7483f7e3f43f189100d6d86 Mon Aug 24 23:49:57 2026 -0700
    Updating release tags to beta for the gnomAD v4.1.1 tracks and updating the Transcript Missense v4.1.1 mouseOver, refs #37351
  • lines changed 86, context: html, text, full: html, text
    9dae2176099f0f0db44ea88b2707fa73b664aa37 Wed Aug 26 17:45:10 2026 -0700
    Completing the release for the gnomAD v4.1.1 tracks: adding a pennantIcon and removing release tags and deleted old v4.1 stanza that were missed by an earlier commit. refs #37351
  • lines changed 1, context: html, text, full: html, text
    cf87c27669523cb325d1d2d52e11e6f18d24504e Wed Aug 26 18:36:04 2026 -0700
    Announcing the gnomAD v4.1.1 and MPC tracks. Adding pennantIcons to the new and updated tracks. refs #38166 refs #37351 refs #37478
• src/hg/makeDb/trackDb/human/hg38/gnomadMpc.ra
  • lines changed 1, context: html, text, full: html, text
    e59cff1f1f78e393e66bd65db33c30b60be835ca Mon Aug 24 23:50:26 2026 -0700
    Updating the gnomadMpc v4.1.1 longLabel, refs #37478
  • lines changed 2, context: html, text, full: html, text
    cf87c27669523cb325d1d2d52e11e6f18d24504e Wed Aug 26 18:36:04 2026 -0700
    Announcing the gnomAD v4.1.1 and MPC tracks. Adding pennantIcons to the new and updated tracks. refs #38166 refs #37351 refs #37478
• src/hg/makeDb/trackDb/human/hg38/hg38.GCF_040939455.1.chainNet.ra
  • lines changed 49, context: html, text, full: html, text
    2207c70df00aea31175fb51b590a16d023467a08 Fri Aug 28 20:55:29 2026 -0700
    chainNet trackDb for hg38 GCF_040939455.1, otto liftOver
• src/hg/makeDb/trackDb/human/hg38/mane.ra
  • lines changed 1, context: html, text, full: html, text
    6a8e756b47341a5584f5c3fca4031401fe507020 Mon Aug 24 11:21:22 2026 -0700
    Updating GeneCards links to their new URL format per their request, also fixes dead cardsearch.pl links on RefSeq and denovoDb click pages. refs #38171
• src/hg/makeDb/trackDb/human/hg38/mb2.ra
  • lines changed 74992, context: html, text, full: html, text
    e091f937cb2d73a65e02eb56d1175db12e77f40c Thu Aug 27 15:00:34 2026 -0700
    Removing older version of MethBase2 development, refs #36320
• src/hg/makeDb/trackDb/human/hg38/mb2_hg38_colors.json
  • lines changed 24, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/human/hg38/mb2_hg38_metadata.tsv
  • lines changed 6512, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/human/hg38/methbase2.ra
  • lines changed 102046, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/human/hg38/methbase2_2.ra
  • lines changed 102565, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/human/hg38/methbase2_3.ra
  • lines changed 41953, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.html
  • lines changed 19, context: html, text, full: html, text
    8bb883ed32e24a1007bf9f97ee1793a46bf47bd0 Thu Aug 27 10:00:43 2026 -0700
    singleCellSignalsPeaks: classify the SEA-AD and Allen tracks, add BrainVar stages 72 hg38 SEA-AD and 89 mm10 allen-basal-ganglia tracks had lost their broad cell class and were drawing in dataset colours instead of the shared palette; both assemblies are now 0 unclassified. Fix is in the hub build (cellBrowser ucsc/allTracksHub). Adds an "Other glia" class, since "Other" was doing four unrelated jobs. BrainVar goes 4 -> 13 hg38 subtracks with the new stage-split pseudobulk. Scaling moves to "autoScale group" on the composite so selected subtracks share one scale, and every bigWig now carries a data range -- without one the 13 BrainVar tracks drew as flat lines against hgTracks' built-in 0:127. Description pages and makeDocs updated, including removing the stale claim that SEA-AD is coloured by its own subclass palette. refs #37914, refs #37820 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 64, context: html, text, full: html, text
    3aac3982aa2b300c100086920451b2dc98a7f2b9 Fri Aug 28 14:49:32 2026 -0700
    singleCellSignalsPeaks: drop 5 superseded hg38 subtracks, alphabetize the references, refs #37820 The hg38 .ra is regenerated from the hub build, 934 -> 929 subtracks: - the 4 combined-stage BrainVar gene-activity tracks, superseded by the prenatal/postnatal pair of the same cell type, so every remaining BrainVar track now carries a life stage - neuro-degen-atac/peaks.bb, superseded by peaks.v2.bb (that dataset's hub.txt comments the peaks.bb bigDataUrl out and serves v2). The two collided on one track id and shipped as two indistinguishable "All cell types, peaks" tracks; with the collision gone the survivor is named ..._peaks and its label loses the "(peaks)" disambiguator. The exclusion itself lives in the hub build's new exclude_track_paths denylist (cellBrowser ucsc/allTracksHub/hub_config.json), not in a hand edit here, so the next regeneration cannot put the tracks back. Facet metadata was refreshed to match: .ra and metadata are 1:1 at 929. Subtrack priorities renumber because they are per-class sequence counters and the dropped BrainVar tracks were first in their classes. Both description pages now list their references alphabetically by first author (hg38 9 refs, mm10 7); no reference text changed. makeDoc: new section 1b documents the denylist and what is currently on it, and the counts are brought up to date. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.ra
  • lines changed 1461, context: html, text, full: html, text
    8bb883ed32e24a1007bf9f97ee1793a46bf47bd0 Thu Aug 27 10:00:43 2026 -0700
    singleCellSignalsPeaks: classify the SEA-AD and Allen tracks, add BrainVar stages 72 hg38 SEA-AD and 89 mm10 allen-basal-ganglia tracks had lost their broad cell class and were drawing in dataset colours instead of the shared palette; both assemblies are now 0 unclassified. Fix is in the hub build (cellBrowser ucsc/allTracksHub). Adds an "Other glia" class, since "Other" was doing four unrelated jobs. BrainVar goes 4 -> 13 hg38 subtracks with the new stage-split pseudobulk. Scaling moves to "autoScale group" on the composite so selected subtracks share one scale, and every bigWig now carries a data range -- without one the 13 BrainVar tracks drew as flat lines against hgTracks' built-in 0:127. Description pages and makeDocs updated, including removing the stale claim that SEA-AD is coloured by its own subclass palette. refs #37914, refs #37820 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 1, context: html, text, full: html, text
    550a0e2666bcce27181a0cb0eab32ed261e444f6 Thu Aug 27 14:56:42 2026 -0700
    singleCellSignalsPeaks: color the Cell class facet checkboxes, refs #37820, refs #37914 The faceted UI already draws a color swatch beside each checkbox of any facet named in a colorSettingsUrl JSON, and the track already colors its subtracks by broad cell class from celltype-palette.tsv. Publish that palette so the selector shows the same colors: copySingleCellSignalsPeaksFiles.py now writes <bed>/singleCellSignalsPeaks_colors.json alongside the facet metadata, and the composite header names it. Rendered from the one shared palette, so a class is the same color in the checkbox list, in the drawn tracks, and on both assemblies. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 10, context: html, text, full: html, text
    6c09237078e2ea2fd7c383babc73a8f3b379202e Thu Aug 27 15:35:40 2026 -0700
    Risk Loci in Alzheimers peak track was duplicated. Removed duplicate. refs #37914
  • lines changed 341, context: html, text, full: html, text
    3aac3982aa2b300c100086920451b2dc98a7f2b9 Fri Aug 28 14:49:32 2026 -0700
    singleCellSignalsPeaks: drop 5 superseded hg38 subtracks, alphabetize the references, refs #37820 The hg38 .ra is regenerated from the hub build, 934 -> 929 subtracks: - the 4 combined-stage BrainVar gene-activity tracks, superseded by the prenatal/postnatal pair of the same cell type, so every remaining BrainVar track now carries a life stage - neuro-degen-atac/peaks.bb, superseded by peaks.v2.bb (that dataset's hub.txt comments the peaks.bb bigDataUrl out and serves v2). The two collided on one track id and shipped as two indistinguishable "All cell types, peaks" tracks; with the collision gone the survivor is named ..._peaks and its label loses the "(peaks)" disambiguator. The exclusion itself lives in the hub build's new exclude_track_paths denylist (cellBrowser ucsc/allTracksHub/hub_config.json), not in a hand edit here, so the next regeneration cannot put the tracks back. Facet metadata was refreshed to match: .ra and metadata are 1:1 at 929. Subtrack priorities renumber because they are per-class sequence counters and the dropped BrainVar tracks were first in their classes. Both description pages now list their references alphabetically by first author (hg38 9 refs, mm10 7); no reference text changed. makeDoc: new section 1b documents the denylist and what is currently on it, and the counts are brought up to date. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    e1f1369eff4f4330846e6ddd7e6cd01c855e871b Wed Aug 26 17:04:14 2026 -0700
    Releasing the gnomAD MPC tracks. Removed the alpha,beta tag from the gnomadMpc.ra include. refs #37478
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
  • lines changed 1, context: html, text, full: html, text
    53dff34f95bdea27e7747c8bcecb03a7ae45bdfd Thu Aug 27 14:58:41 2026 -0700
    Whoops, ensuring the MethBase2 stuff is set to alpha, and doesn't escape before review. refs #36320
  • lines changed 4, context: html, text, full: html, text
    e091f937cb2d73a65e02eb56d1175db12e77f40c Thu Aug 27 15:00:34 2026 -0700
    Removing older version of MethBase2 development, refs #36320
  • lines changed 1, context: html, text, full: html, text
    2207c70df00aea31175fb51b590a16d023467a08 Fri Aug 28 20:55:29 2026 -0700
    chainNet trackDb for hg38 GCF_040939455.1, otto liftOver
• src/hg/makeDb/trackDb/human/hs1/hs1.GCF_000165445.2.chainNet.ra
  • lines changed 49, context: html, text, full: html, text
    c164e63dca84ba536a55eef5c50288869f1c184d Fri Aug 28 20:55:38 2026 -0700
    chainNet trackDb for hs1 GCF_000165445.2, otto liftOver
• src/hg/makeDb/trackDb/human/hs1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    c164e63dca84ba536a55eef5c50288869f1c184d Fri Aug 28 20:55:38 2026 -0700
    chainNet trackDb for hs1 GCF_000165445.2, otto liftOver
• src/hg/makeDb/trackDb/human/popEve.ra
  • lines changed 1, context: html, text, full: html, text
    1f5afdd131d8f41f9dead82d52cb5a723e443437 Fri Aug 28 15:25:59 2026 -0700
    Announcing the EVE and popEVE tracks for hg38, refs #37791 #37763
• src/hg/makeDb/trackDb/human/predictionScoresSuper.ra
  • lines changed 2, context: html, text, full: html, text
    e97d61e4e25c4c10fc6a4b74ede6f10923983618 Thu Aug 27 16:45:31 2026 -0700
    Releasing the EVE and popEVE tracks for hg38, refs #37763 #37791
  • lines changed 1, context: html, text, full: html, text
    1f5afdd131d8f41f9dead82d52cb5a723e443437 Fri Aug 28 15:25:59 2026 -0700
    Announcing the EVE and popEVE tracks for hg38, refs #37791 #37763
• src/hg/makeDb/trackDb/human/trackDb.geneHancer.ra
  • lines changed 4, context: html, text, full: html, text
    6a8e756b47341a5584f5c3fca4031401fe507020 Mon Aug 24 11:21:22 2026 -0700
    Updating GeneCards links to their new URL format per their request, also fixes dead cardsearch.pl links on RefSeq and denovoDb click pages. refs #38171
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    219f66fde04ded54d6992855d1fef738aa5b6a6f Thu Aug 27 17:12:34 2026 -0700
    Give the RefSeq Historical subtrack its own dataVersion, refs #35766 The Historical track inherited the composite's dataVersion file, which tracks the current RefSeq annotation release, so the track advertised RS_2025_08 while its data is RS_2024_08. This affected three places: the long label in the browser image (simpleTracks.c appends the version for any track whose name starts with ncbiRef), the track settings page, and the details pages. A subtrack may carry its own dataVersion; trackDbSetting reads the local value first and only climbs to the parent when there isn't one. Same pattern already used by clinGenHaplo and the nmdEsc* subtracks. Also adds the version file step to the makedoc, and a reminder to the weekly notifier mail so the next refresh doesn't leave it stale again. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/macaca/macFas5/dnaMethylation.html
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/macaca/macFas5/mb2_macFas5_colors.json
  • lines changed 16, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/macaca/macFas5/mb2_macFas5_metadata.tsv
  • lines changed 35, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/macaca/macFas5/methbase2.ra
  • lines changed 1295, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/macaca/macFas5/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
  • lines changed 1, context: html, text, full: html, text
    53dff34f95bdea27e7747c8bcecb03a7ae45bdfd Thu Aug 27 14:58:41 2026 -0700
    Whoops, ensuring the MethBase2 stuff is set to alpha, and doesn't escape before review. refs #36320
• src/hg/makeDb/trackDb/makefile
  • lines changed 12, context: html, text, full: html, text
    0b36c1276f7fd41e8ba9ad53bbdb20c1d438913d Tue Aug 25 12:08:14 2026 -0700
    trackDb: build the trix once per database, and run the beta make in parallel, refs #35489 The trackDb make for a final build takes about 18 minutes. It is not one slow step. It is 348 per-database chains of short processes and network round trips, run strictly one after another. Two changes. First, stop building the same trix twice. The beta recipe called buildTrix once for hgwbeta and again for hgwdev, with identical inputs and only the destination differing. buildTrix now takes -alsoTo=machine:path, so the index is built once and sent to both places. It also assembles the files in a temporary directory under their final names, so each destination takes one rsync instead of one per file. That takes the trix step from ten ssh connections per database down to two, and it no longer leaves .offsets files behind in the trackDb directory. Second, run the make in parallel. The header comment warning against this was out of date. hgTrackDb and hgFindSpec put their temporary files in TMPDIR under process-unique names, and every other file and table a recipe writes is already named after its database, so the per-database chains do not collide. Two makes at once are still unsafe, because they share table names, and the comment now says that instead. makeStrictBeta.csh passes -O -j 8. Set TRACKDB_MAKE_JOBS to change the job count. Going much above 8 wants ssh connection sharing first, or hgwbeta's sshd starts refusing connections. Measured over all 348 databases, with the output compared line by line against a serial run each time: 321 seconds today, 194 with the tdbQuery fix alone, 81 with -j 8 alone, and 39 with both. The -j 8 figure lands on the hg38 chain, which is why the tdbQuery fix matters more than its share of the total suggests.
• src/hg/makeDb/trackDb/medaka/oryLat2/dnaMethylation.html
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/medaka/oryLat2/mb2_oryLat2_colors.json
  • lines changed 7, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/medaka/oryLat2/mb2_oryLat2_metadata.tsv
  • lines changed 23, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/medaka/oryLat2/methbase2.ra
  • lines changed 849, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/medaka/oryLat2/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
  • lines changed 1, context: html, text, full: html, text
    53dff34f95bdea27e7747c8bcecb03a7ae45bdfd Thu Aug 27 14:58:41 2026 -0700
    Whoops, ensuring the MethBase2 stuff is set to alpha, and doesn't escape before review. refs #36320
• src/hg/makeDb/trackDb/mouse/mm10/singleCellSignalsPeaks.html
  • lines changed 10, context: html, text, full: html, text
    8bb883ed32e24a1007bf9f97ee1793a46bf47bd0 Thu Aug 27 10:00:43 2026 -0700
    singleCellSignalsPeaks: classify the SEA-AD and Allen tracks, add BrainVar stages 72 hg38 SEA-AD and 89 mm10 allen-basal-ganglia tracks had lost their broad cell class and were drawing in dataset colours instead of the shared palette; both assemblies are now 0 unclassified. Fix is in the hub build (cellBrowser ucsc/allTracksHub). Adds an "Other glia" class, since "Other" was doing four unrelated jobs. BrainVar goes 4 -> 13 hg38 subtracks with the new stage-split pseudobulk. Scaling moves to "autoScale group" on the composite so selected subtracks share one scale, and every bigWig now carries a data range -- without one the 13 BrainVar tracks drew as flat lines against hgTracks' built-in 0:127. Description pages and makeDocs updated, including removing the stale claim that SEA-AD is coloured by its own subclass palette. refs #37914, refs #37820 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 87, context: html, text, full: html, text
    3aac3982aa2b300c100086920451b2dc98a7f2b9 Fri Aug 28 14:49:32 2026 -0700
    singleCellSignalsPeaks: drop 5 superseded hg38 subtracks, alphabetize the references, refs #37820 The hg38 .ra is regenerated from the hub build, 934 -> 929 subtracks: - the 4 combined-stage BrainVar gene-activity tracks, superseded by the prenatal/postnatal pair of the same cell type, so every remaining BrainVar track now carries a life stage - neuro-degen-atac/peaks.bb, superseded by peaks.v2.bb (that dataset's hub.txt comments the peaks.bb bigDataUrl out and serves v2). The two collided on one track id and shipped as two indistinguishable "All cell types, peaks" tracks; with the collision gone the survivor is named ..._peaks and its label loses the "(peaks)" disambiguator. The exclusion itself lives in the hub build's new exclude_track_paths denylist (cellBrowser ucsc/allTracksHub/hub_config.json), not in a hand edit here, so the next regeneration cannot put the tracks back. Facet metadata was refreshed to match: .ra and metadata are 1:1 at 929. Subtrack priorities renumber because they are per-class sequence counters and the dropped BrainVar tracks were first in their classes. Both description pages now list their references alphabetically by first author (hg38 9 refs, mm10 7); no reference text changed. makeDoc: new section 1b documents the denylist and what is currently on it, and the counts are brought up to date. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/singleCellSignalsPeaks.ra
  • lines changed 797, context: html, text, full: html, text
    8bb883ed32e24a1007bf9f97ee1793a46bf47bd0 Thu Aug 27 10:00:43 2026 -0700
    singleCellSignalsPeaks: classify the SEA-AD and Allen tracks, add BrainVar stages 72 hg38 SEA-AD and 89 mm10 allen-basal-ganglia tracks had lost their broad cell class and were drawing in dataset colours instead of the shared palette; both assemblies are now 0 unclassified. Fix is in the hub build (cellBrowser ucsc/allTracksHub). Adds an "Other glia" class, since "Other" was doing four unrelated jobs. BrainVar goes 4 -> 13 hg38 subtracks with the new stage-split pseudobulk. Scaling moves to "autoScale group" on the composite so selected subtracks share one scale, and every bigWig now carries a data range -- without one the 13 BrainVar tracks drew as flat lines against hgTracks' built-in 0:127. Description pages and makeDocs updated, including removing the stale claim that SEA-AD is coloured by its own subclass palette. refs #37914, refs #37820 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 1, context: html, text, full: html, text
    550a0e2666bcce27181a0cb0eab32ed261e444f6 Thu Aug 27 14:56:42 2026 -0700
    singleCellSignalsPeaks: color the Cell class facet checkboxes, refs #37820, refs #37914 The faceted UI already draws a color swatch beside each checkbox of any facet named in a colorSettingsUrl JSON, and the track already colors its subtracks by broad cell class from celltype-palette.tsv. Publish that palette so the selector shows the same colors: copySingleCellSignalsPeaksFiles.py now writes <bed>/singleCellSignalsPeaks_colors.json alongside the facet metadata, and the composite header names it. Rendered from the one shared palette, so a class is the same color in the checkbox list, in the drawn tracks, and on both assemblies. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    df4fcc5d86a76fbc325da43d3f1b9b5ab5f6f4eb Mon Aug 24 18:39:38 2026 -0700
    Adding release tags since this track is a new default, refs #37001
  • lines changed 1, context: html, text, full: html, text
    1cf4925201a690fa236b77d604269d6aa739b4af Fri Aug 28 14:06:50 2026 -0700
    Add the alpha,beta release tag to the mm10 signal composite include line. refs #37001 The previous commit tagged mouseDevTimecourse.ra but not developmentTimecourseSignalMm10.ra. On mm10 the superTrack parent and the bigWig composite child live in separate files with separate include lines, so the parent became alpha,beta while the untagged child stayed at all three levels. At public the child outlived its parent, and tdbQuery -strict reported "parent mouseDevTimecourse of developmentTimecourseSignalMm10 release n/a doesn't exist". Note this only shows up at -release=public; a default -strict run is alpha, where the parent still exists, so it looks clean. mm39 was never affected because both its subtracks are inside the one included file.
• src/hg/makeDb/trackDb/mouse/mm39/dnaMethylation.html
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/mouse/mm39/mb2_mm39_colors.json
  • lines changed 24, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/mouse/mm39/mb2_mm39_metadata.tsv
  • lines changed 6648, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/mouse/mm39/methbase2.ra
  • lines changed 103253, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/mouse/mm39/methbase2_2.ra
  • lines changed 102229, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/mouse/mm39/methbase2_3.ra
  • lines changed 45349, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    df4fcc5d86a76fbc325da43d3f1b9b5ab5f6f4eb Mon Aug 24 18:39:38 2026 -0700
    Adding release tags since this track is a new default, refs #37001
  • lines changed 10, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
  • lines changed 1, context: html, text, full: html, text
    53dff34f95bdea27e7747c8bcecb03a7ae45bdfd Thu Aug 27 14:58:41 2026 -0700
    Whoops, ensuring the MethBase2 stuff is set to alpha, and doesn't escape before review. refs #36320
• src/hg/makeDb/trackDb/opossum/monDom5/dnaMethylation.html
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/opossum/monDom5/mb2_monDom5_colors.json
  • lines changed 10, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/opossum/monDom5/mb2_monDom5_metadata.tsv
  • lines changed 45, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/opossum/monDom5/methbase2.ra
  • lines changed 1685, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/opossum/monDom5/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
  • lines changed 1, context: html, text, full: html, text
    53dff34f95bdea27e7747c8bcecb03a7ae45bdfd Thu Aug 27 14:58:41 2026 -0700
    Whoops, ensuring the MethBase2 stuff is set to alpha, and doesn't escape before review. refs #36320
• src/hg/makeDb/trackDb/orangutan/ponAbe3/dnaMethylation.html
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/orangutan/ponAbe3/mb2_ponAbe3_colors.json
  • lines changed 6, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/orangutan/ponAbe3/mb2_ponAbe3_metadata.tsv
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/orangutan/ponAbe3/methbase2.ra
  • lines changed 127, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/orangutan/ponAbe3/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
  • lines changed 1, context: html, text, full: html, text
    53dff34f95bdea27e7747c8bcecb03a7ae45bdfd Thu Aug 27 14:58:41 2026 -0700
    Whoops, ensuring the MethBase2 stuff is set to alpha, and doesn't escape before review. refs #36320
• src/hg/makeDb/trackDb/panda/ailMel1/dnaMethylation.html
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/panda/ailMel1/mb2_ailMel1_colors.json
  • lines changed 6, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/panda/ailMel1/mb2_ailMel1_metadata.tsv
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/panda/ailMel1/methbase2.ra
  • lines changed 127, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/panda/ailMel1/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
  • lines changed 1, context: html, text, full: html, text
    53dff34f95bdea27e7747c8bcecb03a7ae45bdfd Thu Aug 27 14:58:41 2026 -0700
    Whoops, ensuring the MethBase2 stuff is set to alpha, and doesn't escape before review. refs #36320
• src/hg/makeDb/trackDb/pig/susScr11/dnaMethylation.html
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/pig/susScr11/mb2_susScr11_colors.json
  • lines changed 24, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/pig/susScr11/mb2_susScr11_metadata.tsv
  • lines changed 474, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/pig/susScr11/methbase2.ra
  • lines changed 17907, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/pig/susScr11/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
  • lines changed 1, context: html, text, full: html, text
    53dff34f95bdea27e7747c8bcecb03a7ae45bdfd Thu Aug 27 14:58:41 2026 -0700
    Whoops, ensuring the MethBase2 stuff is set to alpha, and doesn't escape before review. refs #36320
• src/hg/makeDb/trackDb/platypus/ornAna2/dnaMethylation.html
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/platypus/ornAna2/mb2_ornAna2_colors.json
  • lines changed 5, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/platypus/ornAna2/mb2_ornAna2_metadata.tsv
  • lines changed 2, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/platypus/ornAna2/methbase2.ra
  • lines changed 51, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/platypus/ornAna2/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
  • lines changed 1, context: html, text, full: html, text
    53dff34f95bdea27e7747c8bcecb03a7ae45bdfd Thu Aug 27 14:58:41 2026 -0700
    Whoops, ensuring the MethBase2 stuff is set to alpha, and doesn't escape before review. refs #36320
• src/hg/makeDb/trackDb/rabbit/oryCun2/dnaMethylation.html
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/rabbit/oryCun2/mb2_oryCun2_colors.json
  • lines changed 7, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/rabbit/oryCun2/mb2_oryCun2_metadata.tsv
  • lines changed 5, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/rabbit/oryCun2/methbase2.ra
  • lines changed 165, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/rabbit/oryCun2/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
  • lines changed 1, context: html, text, full: html, text
    53dff34f95bdea27e7747c8bcecb03a7ae45bdfd Thu Aug 27 14:58:41 2026 -0700
    Whoops, ensuring the MethBase2 stuff is set to alpha, and doesn't escape before review. refs #36320
• src/hg/makeDb/trackDb/rat/rn7/dnaMethylation.html
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/rat/rn7/mb2_rn7_colors.json
  • lines changed 24, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/rat/rn7/mb2_rn7_metadata.tsv
  • lines changed 202, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/rat/rn7/methbase2.ra
  • lines changed 7631, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/rat/rn7/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
  • lines changed 1, context: html, text, full: html, text
    53dff34f95bdea27e7747c8bcecb03a7ae45bdfd Thu Aug 27 14:58:41 2026 -0700
    Whoops, ensuring the MethBase2 stuff is set to alpha, and doesn't escape before review. refs #36320
• src/hg/makeDb/trackDb/rhesus/rheMac10/dnaMethylation.html
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/rhesus/rheMac10/mb2_rheMac10_colors.json
  • lines changed 24, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/rhesus/rheMac10/mb2_rheMac10_metadata.tsv
  • lines changed 271, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/rhesus/rheMac10/methbase2.ra
  • lines changed 10273, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/rhesus/rheMac10/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
  • lines changed 1, context: html, text, full: html, text
    53dff34f95bdea27e7747c8bcecb03a7ae45bdfd Thu Aug 27 14:58:41 2026 -0700
    Whoops, ensuring the MethBase2 stuff is set to alpha, and doesn't escape before review. refs #36320
• src/hg/makeDb/trackDb/sheep/oviAri4/dnaMethylation.html
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/sheep/oviAri4/mb2_oviAri4_colors.json
  • lines changed 24, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/sheep/oviAri4/mb2_oviAri4_metadata.tsv
  • lines changed 165, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/sheep/oviAri4/methbase2.ra
  • lines changed 6245, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/sheep/oviAri4/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
  • lines changed 1, context: html, text, full: html, text
    53dff34f95bdea27e7747c8bcecb03a7ae45bdfd Thu Aug 27 14:58:41 2026 -0700
    Whoops, ensuring the MethBase2 stuff is set to alpha, and doesn't escape before review. refs #36320
• src/hg/makeDb/trackDb/stickleback/gasAcu1/dnaMethylation.html
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/stickleback/gasAcu1/mb2_gasAcu1_colors.json
  • lines changed 6, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/stickleback/gasAcu1/mb2_gasAcu1_metadata.tsv
  • lines changed 61, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/stickleback/gasAcu1/methbase2.ra
  • lines changed 2293, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/stickleback/gasAcu1/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
  • lines changed 1, context: html, text, full: html, text
    53dff34f95bdea27e7747c8bcecb03a7ae45bdfd Thu Aug 27 14:58:41 2026 -0700
    Whoops, ensuring the MethBase2 stuff is set to alpha, and doesn't escape before review. refs #36320
• src/hg/makeDb/trackDb/tetraodon/tetNig2/dnaMethylation.html
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/tetraodon/tetNig2/mb2_tetNig2_colors.json
  • lines changed 5, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/tetraodon/tetNig2/mb2_tetNig2_metadata.tsv
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/tetraodon/tetNig2/methbase2.ra
  • lines changed 127, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/tetraodon/tetNig2/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
  • lines changed 1, context: html, text, full: html, text
    53dff34f95bdea27e7747c8bcecb03a7ae45bdfd Thu Aug 27 14:58:41 2026 -0700
    Whoops, ensuring the MethBase2 stuff is set to alpha, and doesn't escape before review. refs #36320
• src/hg/makeDb/trackDb/urchin/strPur2/dnaMethylation.html
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/urchin/strPur2/mb2_strPur2_colors.json
  • lines changed 8, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/urchin/strPur2/mb2_strPur2_metadata.tsv
  • lines changed 5, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/urchin/strPur2/methbase2.ra
  • lines changed 165, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/urchin/strPur2/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
  • lines changed 1, context: html, text, full: html, text
    53dff34f95bdea27e7747c8bcecb03a7ae45bdfd Thu Aug 27 14:58:41 2026 -0700
    Whoops, ensuring the MethBase2 stuff is set to alpha, and doesn't escape before review. refs #36320
• src/hg/makeDb/trackDb/xenTro/xenTro10/dnaMethylation.html
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/xenTro/xenTro10/mb2_xenTro10_colors.json
  • lines changed 7, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/xenTro/xenTro10/mb2_xenTro10_metadata.tsv
  • lines changed 16, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/xenTro/xenTro10/methbase2.ra
  • lines changed 583, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/xenTro/xenTro10/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
  • lines changed 1, context: html, text, full: html, text
    53dff34f95bdea27e7747c8bcecb03a7ae45bdfd Thu Aug 27 14:58:41 2026 -0700
    Whoops, ensuring the MethBase2 stuff is set to alpha, and doesn't escape before review. refs #36320
• src/hg/makeDb/trackDb/zebraFinch/taeGut2/dnaMethylation.html
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/zebraFinch/taeGut2/mb2_taeGut2_colors.json
  • lines changed 5, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/zebraFinch/taeGut2/mb2_taeGut2_metadata.tsv
  • lines changed 21, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/zebraFinch/taeGut2/methbase2.ra
  • lines changed 773, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/zebraFinch/taeGut2/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
  • lines changed 1, context: html, text, full: html, text
    53dff34f95bdea27e7747c8bcecb03a7ae45bdfd Thu Aug 27 14:58:41 2026 -0700
    Whoops, ensuring the MethBase2 stuff is set to alpha, and doesn't escape before review. refs #36320
• src/hg/makeDb/trackDb/zebrafish/danRer11/dnaMethylation.html
  • lines changed 4, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/zebrafish/danRer11/mb2_danRer11_colors.json
  • lines changed 24, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/zebrafish/danRer11/mb2_danRer11_metadata.tsv
  • lines changed 340, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/zebrafish/danRer11/methbase2.ra
  • lines changed 12855, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
• src/hg/makeDb/trackDb/zebrafish/danRer11/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700
    TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
  • lines changed 1, context: html, text, full: html, text
    53dff34f95bdea27e7747c8bcecb03a7ae45bdfd Thu Aug 27 14:58:41 2026 -0700
    Whoops, ensuring the MethBase2 stuff is set to alpha, and doesn't escape before review. refs #36320
• src/hg/utils/automation/doAssemblyHub.pl
  • lines changed 11, context: html, text, full: html, text
    5776ff26d2da71f6cf65909b53a3e9238a522a7e Tue Aug 25 10:30:18 2026 -0700
    adding gcOnFly track development refs #35958
• src/hg/utils/automation/doTandemDup.pl
  • lines changed 3, context: html, text, full: html, text
    83b6d1578c7e378077c303080246ad9f34bb4f31 Wed Aug 26 16:54:05 2026 -0700
    can now use much less memory for kmerPairs.pl no redmine
• src/hg/utils/cartTrackVarCatalog/cartTrackVarCatalog.py
  • lines changed 10, context: html, text, full: html, text
    19be3fe94ad785b9bd787fa4e425e7e3c4f2a1d5 Fri Aug 28 14:02:40 2026 -0700
    cartTrackVarCatalog: add facetSortOrder, refs #37838 <track>.facetSortOrder, written only by facetedComposite.js and read back at hgTrackUi.c:3314 to override trackDb's defaultSortField. Same 'field=+ field2=-' syntax as the composite sortOrder it was copied from.
• src/hg/utils/docent/README.md
  • lines changed 6, context: html, text, full: html, text
    3d8157de7ba1d2e846856deda743e0aae39b0dda Tue Aug 25 16:31:36 2026 -0700
    docent: use the shared Playwright install instead of a private ~/pwrec tree, refs #38188 PW_ENV in docent.mk and in the tests makefile named $(HOME)/pwrec, a tree that only existed in one home directory, so nobody else could run docent or its tests without setting the variable by hand. Both now default to /hive/groups/browser/uiTest/pw, one pinned copy of playwright, chromium, ffmpeg and js-yaml shared by every browser-driving test in the tree. A new PW_DIR variable still points either makefile at a private install. Nothing in docent.js changes except two comment lines. All nine docent tests and all three derivation baselines pass against the shared pin.
  • lines changed 11, context: html, text, full: html, text
    074123ba2fb70164a7aa364f7c8baf21d70f55a5 Thu Aug 27 09:04:05 2026 -0700
    docent: let expect: check the order rows were drawn in, refs #37892 rows: has been a set test, and exact: true only added "and nothing else", so no assertion in the language could fail because the rows came back in the wrong order. ordered: true adds that check: the named rows have to appear top to bottom in the order given. A row that was not drawn at all is reported once, by rows:, and skipped here rather than failing twice. A failure names the first pair that is inverted. The case that prompted it is #38032, a quickLift target returning its tracks in the order they were lifted rather than the order they have on the source. A tour of that bug passed every check on the broken build. Two tests: ordered asserts the hg38 order, and ordered.xfail names the same two rows backwards and has to fail, since a flag that cannot fail is only a second copy of the set test beside it.
• src/hg/utils/docent/docent.js
  • lines changed 4, context: html, text, full: html, text
    3d8157de7ba1d2e846856deda743e0aae39b0dda Tue Aug 25 16:31:36 2026 -0700
    docent: use the shared Playwright install instead of a private ~/pwrec tree, refs #38188 PW_ENV in docent.mk and in the tests makefile named $(HOME)/pwrec, a tree that only existed in one home directory, so nobody else could run docent or its tests without setting the variable by hand. Both now default to /hive/groups/browser/uiTest/pw, one pinned copy of playwright, chromium, ffmpeg and js-yaml shared by every browser-driving test in the tree. A new PW_DIR variable still points either makefile at a private install. Nothing in docent.js changes except two comment lines. All nine docent tests and all three derivation baselines pass against the shared pin.
  • lines changed 17, context: html, text, full: html, text
    074123ba2fb70164a7aa364f7c8baf21d70f55a5 Thu Aug 27 09:04:05 2026 -0700
    docent: let expect: check the order rows were drawn in, refs #37892 rows: has been a set test, and exact: true only added "and nothing else", so no assertion in the language could fail because the rows came back in the wrong order. ordered: true adds that check: the named rows have to appear top to bottom in the order given. A row that was not drawn at all is reported once, by rows:, and skipped here rather than failing twice. A failure names the first pair that is inverted. The case that prompted it is #38032, a quickLift target returning its tracks in the order they were lifted rather than the order they have on the source. A tour of that bug passed every check on the broken build. Two tests: ordered asserts the hg38 order, and ordered.xfail names the same two rows backwards and has to fail, since a flag that cannot fail is only a second copy of the set test beside it.
• src/hg/utils/docent/docent.mk
  • lines changed 5, context: html, text, full: html, text
    3d8157de7ba1d2e846856deda743e0aae39b0dda Tue Aug 25 16:31:36 2026 -0700
    docent: use the shared Playwright install instead of a private ~/pwrec tree, refs #38188 PW_ENV in docent.mk and in the tests makefile named $(HOME)/pwrec, a tree that only existed in one home directory, so nobody else could run docent or its tests without setting the variable by hand. Both now default to /hive/groups/browser/uiTest/pw, one pinned copy of playwright, chromium, ffmpeg and js-yaml shared by every browser-driving test in the tree. A new PW_DIR variable still points either makefile at a private install. Nothing in docent.js changes except two comment lines. All nine docent tests and all three derivation baselines pass against the shared pin.
• src/hg/utils/docent/tests/README.txt
  • lines changed 1, context: html, text, full: html, text
    3d8157de7ba1d2e846856deda743e0aae39b0dda Tue Aug 25 16:31:36 2026 -0700
    docent: use the shared Playwright install instead of a private ~/pwrec tree, refs #38188 PW_ENV in docent.mk and in the tests makefile named $(HOME)/pwrec, a tree that only existed in one home directory, so nobody else could run docent or its tests without setting the variable by hand. Both now default to /hive/groups/browser/uiTest/pw, one pinned copy of playwright, chromium, ffmpeg and js-yaml shared by every browser-driving test in the tree. A new PW_DIR variable still points either makefile at a private install. Nothing in docent.js changes except two comment lines. All nine docent tests and all three derivation baselines pass against the shared pin.
  • lines changed 4, context: html, text, full: html, text
    074123ba2fb70164a7aa364f7c8baf21d70f55a5 Thu Aug 27 09:04:05 2026 -0700
    docent: let expect: check the order rows were drawn in, refs #37892 rows: has been a set test, and exact: true only added "and nothing else", so no assertion in the language could fail because the rows came back in the wrong order. ordered: true adds that check: the named rows have to appear top to bottom in the order given. A row that was not drawn at all is reported once, by rows:, and skipped here rather than failing twice. A failure names the first pair that is inverted. The case that prompted it is #38032, a quickLift target returning its tracks in the order they were lifted rather than the order they have on the source. A tour of that bug passed every check on the broken build. Two tests: ordered asserts the hg38 order, and ordered.xfail names the same two rows backwards and has to fail, since a flag that cannot fail is only a second copy of the set test beside it.
• src/hg/utils/docent/tests/makefile
  • lines changed 2, context: html, text, full: html, text
    3d8157de7ba1d2e846856deda743e0aae39b0dda Tue Aug 25 16:31:36 2026 -0700
    docent: use the shared Playwright install instead of a private ~/pwrec tree, refs #38188 PW_ENV in docent.mk and in the tests makefile named $(HOME)/pwrec, a tree that only existed in one home directory, so nobody else could run docent or its tests without setting the variable by hand. Both now default to /hive/groups/browser/uiTest/pw, one pinned copy of playwright, chromium, ffmpeg and js-yaml shared by every browser-driving test in the tree. A new PW_DIR variable still points either makefile at a private install. Nothing in docent.js changes except two comment lines. All nine docent tests and all three derivation baselines pass against the shared pin.
• src/hg/utils/docent/tests/ordered.docent.yaml
  • lines changed 26, context: html, text, full: html, text
    074123ba2fb70164a7aa364f7c8baf21d70f55a5 Thu Aug 27 09:04:05 2026 -0700
    docent: let expect: check the order rows were drawn in, refs #37892 rows: has been a set test, and exact: true only added "and nothing else", so no assertion in the language could fail because the rows came back in the wrong order. ordered: true adds that check: the named rows have to appear top to bottom in the order given. A row that was not drawn at all is reported once, by rows:, and skipped here rather than failing twice. A failure names the first pair that is inverted. The case that prompted it is #38032, a quickLift target returning its tracks in the order they were lifted rather than the order they have on the source. A tour of that bug passed every check on the broken build. Two tests: ordered asserts the hg38 order, and ordered.xfail names the same two rows backwards and has to fail, since a flag that cannot fail is only a second copy of the set test beside it.
• src/hg/utils/docent/tests/ordered.xfail.docent.yaml
  • lines changed 19, context: html, text, full: html, text
    074123ba2fb70164a7aa364f7c8baf21d70f55a5 Thu Aug 27 09:04:05 2026 -0700
    docent: let expect: check the order rows were drawn in, refs #37892 rows: has been a set test, and exact: true only added "and nothing else", so no assertion in the language could fail because the rows came back in the wrong order. ordered: true adds that check: the named rows have to appear top to bottom in the order given. A row that was not drawn at all is reported once, by rows:, and skipped here rather than failing twice. A failure names the first pair that is inverted. The case that prompted it is #38032, a quickLift target returning its tracks in the order they were lifted rather than the order they have on the source. A tour of that bug passed every check on the broken build. Two tests: ordered asserts the hg38 order, and ordered.xfail names the same two rows backwards and has to fail, since a flag that cannot fail is only a second copy of the set test beside it.
• src/hg/utils/hgConfCatalog/hgConfAges.json
  • lines changed 125, context: html, text, full: html, text
    5dc55ce0216403150c4b82f912db3339202b300f Fri Aug 28 14:02:25 2026 -0700
    hgConfCatalog: cite the file, not the line, refs #37925 A stored line number is derived data. Thirteen of the last sixteen commits from nightlyRegister.sh changed nothing but line numbers, because one edit near the top of hgTracks.c moves fifteen at once. The line is now recomputed for display from the harvester, so that job commits only when a setting is genuinely new. Also repoints login.approvedReturn and sessionDataDir at the files that read them today, classifies cspResponseHeader as a release gate, and rebuilds the age cache at v502.
• src/hg/utils/hgConfCatalog/hgConfCatalog.py
  • lines changed 22, context: html, text, full: html, text
    7a03e53ac12bd080fee86c9e1184be4da154cabf Fri Aug 28 02:46:03 2026 -0700
    updating catalog
  • lines changed 488, context: html, text, full: html, text
    5dc55ce0216403150c4b82f912db3339202b300f Fri Aug 28 14:02:25 2026 -0700
    hgConfCatalog: cite the file, not the line, refs #37925 A stored line number is derived data. Thirteen of the last sixteen commits from nightlyRegister.sh changed nothing but line numbers, because one edit near the top of hgTracks.c moves fifteen at once. The line is now recomputed for display from the harvester, so that job commits only when a setting is genuinely new. Also repoints login.approvedReturn and sessionDataDir at the files that read them today, classifies cspResponseHeader as a release gate, and rebuilds the age cache at v502.
• src/hg/utils/hgConfCatalog/nightlyRegister.sh
  • lines changed 29, context: html, text, full: html, text
    5dc55ce0216403150c4b82f912db3339202b300f Fri Aug 28 14:02:25 2026 -0700
    hgConfCatalog: cite the file, not the line, refs #37925 A stored line number is derived data. Thirteen of the last sixteen commits from nightlyRegister.sh changed nothing but line numbers, because one edit near the top of hgTracks.c moves fifteen at once. The line is now recomputed for display from the harvester, so that job commits only when a setting is genuinely new. Also repoints login.approvedReturn and sessionDataDir at the files that read them today, classifies cspResponseHeader as a release gate, and rebuilds the age cache at v502.
• src/hg/utils/otto/dengue/buildTree.sh
  • lines changed 15, context: html, text, full: html, text
    de23dd389f8e8e35c41880a85d74e9838a4df8e4 Thu Jun 18 15:11:49 2026 -0700
    ssh to hgwdev for commands that need access to hgwdev-only directories, because these scripts run elsewhere now. Tweak shell variables usherDir and friends to make it easier to try out different build directories.
• src/hg/utils/otto/fluA/buildConcatTree.sh
  • lines changed 14, context: html, text, full: html, text
    8d5f0115cf9ab2b99f18a1467c0be02a6ae55de4 Thu Jun 18 15:18:03 2026 -0700
    Use taxonium overlay html to describe the trees. Adjust filters. ssh to hgwdev for commands that need access to hgwdev-only directories, because these scripts run elsewhere now. Tweak shell variables usherDir and friends to make it easier to try out different build directories.
• src/hg/utils/otto/fluA/buildConcatTreeD1.1.sh
  • lines changed 11, context: html, text, full: html, text
    8d5f0115cf9ab2b99f18a1467c0be02a6ae55de4 Thu Jun 18 15:18:03 2026 -0700
    Use taxonium overlay html to describe the trees. Adjust filters. ssh to hgwdev for commands that need access to hgwdev-only directories, because these scripts run elsewhere now. Tweak shell variables usherDir and friends to make it easier to try out different build directories.
• src/hg/utils/otto/fluA/buildTree.sh
  • lines changed 47, context: html, text, full: html, text
    8d5f0115cf9ab2b99f18a1467c0be02a6ae55de4 Thu Jun 18 15:18:03 2026 -0700
    Use taxonium overlay html to describe the trees. Adjust filters. ssh to hgwdev for commands that need access to hgwdev-only directories, because these scripts run elsewhere now. Tweak shell variables usherDir and friends to make it easier to try out different build directories.
• src/hg/utils/otto/fluA/taxonium_overlay.html
  • lines changed 52, context: html, text, full: html, text
    8d5f0115cf9ab2b99f18a1467c0be02a6ae55de4 Thu Jun 18 15:18:03 2026 -0700
    Use taxonium overlay html to describe the trees. Adjust filters. ssh to hgwdev for commands that need access to hgwdev-only directories, because these scripts run elsewhere now. Tweak shell variables usherDir and friends to make it easier to try out different build directories.
• src/hg/utils/otto/fluA/taxonium_overlay_b3_13.html
  • lines changed 89, context: html, text, full: html, text
    8d5f0115cf9ab2b99f18a1467c0be02a6ae55de4 Thu Jun 18 15:18:03 2026 -0700
    Use taxonium overlay html to describe the trees. Adjust filters. ssh to hgwdev for commands that need access to hgwdev-only directories, because these scripts run elsewhere now. Tweak shell variables usherDir and friends to make it easier to try out different build directories.
  • lines changed 1, context: html, text, full: html, text
    23d1d4ea2a7caf6ecc1c7f3c4e3b730e25456e63 Fri Aug 28 08:36:57 2026 -0700
    Fixing typo found by Claude.
• src/hg/utils/otto/fluA/taxonium_overlay_d1_1.html
  • lines changed 89, context: html, text, full: html, text
    8d5f0115cf9ab2b99f18a1467c0be02a6ae55de4 Thu Jun 18 15:18:03 2026 -0700
    Use taxonium overlay html to describe the trees. Adjust filters. ssh to hgwdev for commands that need access to hgwdev-only directories, because these scripts run elsewhere now. Tweak shell variables usherDir and friends to make it easier to try out different build directories.
  • lines changed 1, context: html, text, full: html, text
    23d1d4ea2a7caf6ecc1c7f3c4e3b730e25456e63 Fri Aug 28 08:36:57 2026 -0700
    Fixing typo found by Claude.
• src/hg/utils/otto/fluA/taxonium_overlay_h5n1_ha.html
  • lines changed 78, context: html, text, full: html, text
    8d5f0115cf9ab2b99f18a1467c0be02a6ae55de4 Thu Jun 18 15:18:03 2026 -0700
    Use taxonium overlay html to describe the trees. Adjust filters. ssh to hgwdev for commands that need access to hgwdev-only directories, because these scripts run elsewhere now. Tweak shell variables usherDir and friends to make it easier to try out different build directories.
• src/hg/utils/otto/fluA/taxonium_overlay_pb2.html
  • lines changed 74, context: html, text, full: html, text
    8d5f0115cf9ab2b99f18a1467c0be02a6ae55de4 Thu Jun 18 15:18:03 2026 -0700
    Use taxonium overlay html to describe the trees. Adjust filters. ssh to hgwdev for commands that need access to hgwdev-only directories, because these scripts run elsewhere now. Tweak shell variables usherDir and friends to make it easier to try out different build directories.
• src/hg/utils/otto/fluA/updateAndersenLab.sh
  • lines changed 7, context: html, text, full: html, text
    e22c5be5fb552757c886e7356db9d49eca8cdedb Thu Jun 18 15:13:24 2026 -0700
    Use TMPDIR -- this no longer runs on hgwdev.
• src/hg/utils/otto/measles/buildTree.sh
  • lines changed 9, context: html, text, full: html, text
    de23dd389f8e8e35c41880a85d74e9838a4df8e4 Thu Jun 18 15:11:49 2026 -0700
    ssh to hgwdev for commands that need access to hgwdev-only directories, because these scripts run elsewhere now. Tweak shell variables usherDir and friends to make it easier to try out different build directories.
• src/hg/utils/otto/mpxv/buildTree.sh
  • lines changed 15, context: html, text, full: html, text
    de23dd389f8e8e35c41880a85d74e9838a4df8e4 Thu Jun 18 15:11:49 2026 -0700
    ssh to hgwdev for commands that need access to hgwdev-only directories, because these scripts run elsewhere now. Tweak shell variables usherDir and friends to make it easier to try out different build directories.
• src/hg/utils/otto/mtb/taxonium.annotated.config.json
  • lines changed 2, context: html, text, full: html, text
    d356fdc7acdc6b715b559ad6cd8a72d651c282ee Fri Aug 28 08:31:06 2026 -0700
    Add genotype and None to colorByOptions -- they're not automatically included.
• src/hg/utils/otto/otto.crontab
  • lines changed 3, context: html, text, full: html, text
    085e756cd661df666ac2d9e1ff477363b709449a Fri Aug 28 15:43:25 2026 -0700
    Updating git to match the crontab running on /hive, no Redmine
• src/hg/utils/otto/ottoCompareGitVsHiveFiles.py
  • lines changed 27, context: html, text, full: html, text
    6886101fd2d0574daca5c9ce962a0de70ef61b19 Fri Aug 28 15:53:29 2026 -0700
    Implementing Lou's feedback from code review, refs #38177
• src/hg/utils/otto/refSeqHistorical/checkRefSeqHistoricalUpdate.sh
  • lines changed 2, context: html, text, full: html, text
    219f66fde04ded54d6992855d1fef738aa5b6a6f Thu Aug 27 17:12:34 2026 -0700
    Give the RefSeq Historical subtrack its own dataVersion, refs #35766 The Historical track inherited the composite's dataVersion file, which tracks the current RefSeq annotation release, so the track advertised RS_2025_08 while its data is RS_2024_08. This affected three places: the long label in the browser image (simpleTracks.c appends the version for any track whose name starts with ncbiRef), the track settings page, and the details pages. A subtrack may carry its own dataVersion; trackDbSetting reads the local value first and only climbs to the parent when there isn't one. Same pattern already used by clinGenHaplo and the nmdEsc* subtracks. Also adds the version file step to the makedoc, and a reminder to the weekly notifier mail so the next refresh doesn't leave it stale again. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/utils/otto/rsv/buildTree.sh
  • lines changed 13, context: html, text, full: html, text
    de23dd389f8e8e35c41880a85d74e9838a4df8e4 Thu Jun 18 15:11:49 2026 -0700
    ssh to hgwdev for commands that need access to hgwdev-only directories, because these scripts run elsewhere now. Tweak shell variables usherDir and friends to make it easier to try out different build directories.
• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.py
  • lines changed 8, context: html, text, full: html, text
    92ed679e589bc5f2f4bcc78dd89584e67e496cfc Fri Aug 28 08:20:24 2026 -0700
    Support representativeBacktrack for exclusions too. It occurs to me that if a representative is used in multiple places and has representativeBacktrack in any of them, the one that the script finds first will be applied to all. Pressed for time and not yet sure what to do about that. Probably should at least detect & warn.
• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
  • lines changed 8, context: html, text, full: html, text
    c210683fd63e352426e983f869c6c9aa389da3e1 Wed Aug 26 16:59:09 2026 -0700
    Add exceptions for some XFJ and XFG branches.
  • lines changed 1, context: html, text, full: html, text
    61e501ff1e558ceb89d89ce46acb8fae1cb46cfc Fri Aug 28 08:23:02 2026 -0700
    Add representativeBacktrack: 1 for exclusion of 23599 for XFJ.3.1 because representative was removed and added back with another masked mut putting it one node deeper in the pre-masking tree which caused the exclusion to be applied only to that little branch.
• src/hg/utils/otto/sarscov2phylo/combineMetadata.sh
  • lines changed 1, context: html, text, full: html, text
    b9f2ec794548c0db212574a8172c27d32ed47026 Fri Aug 28 08:24:26 2026 -0700
    Use csvtk grep because we hit a wall with grep -Fwf performance.
• src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
  • lines changed 6, context: html, text, full: html, text
    8e48fb87643184fc740bb980dbccd6309fee97c6 Thu Jun 18 15:22:24 2026 -0700
    Tweak shell variables usherDir and friends to make it easier to try out different build directories.
• src/hg/utils/otto/sarscov2phylo/find_recent_samples.py
  • lines changed 69, context: html, text, full: html, text
    6091af3e8fff91595ab6361974787afef032a342 Thu Jun 25 11:03:38 2026 -0700
    Fix second filtering to match first. Extract tree of sequences from the past year plus sequences within a radius of 5 edges of those.
• src/hg/utils/otto/sarscov2phylo/makeNewMaskedMaple.sh
  • lines changed 22, context: html, text, full: html, text
    637a3d134a395adf8eb77c177ff11aa6972146c0 Fri Aug 28 08:25:27 2026 -0700
    Use csvtk grep because we hit a wall with grep -Fwf performance.
• src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv
  • lines changed 6, context: html, text, full: html, text
    186567f2a1068c3f5d804de5f0907572e91ba914 Wed Jun 10 13:08:24 2026 -0700
    Added clades 25D - 25I.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
  • lines changed 34, context: html, text, full: html, text
    59c6cecaf508798f9e7c4f3cda836a6f0105ad9a Wed Jun 10 13:09:00 2026 -0700
    Added new lineages up through release 1.39.
  • lines changed 7, context: html, text, full: html, text
    f51e81544b68da673a608a8f8cb221c8f964af93 Thu Jun 18 15:20:35 2026 -0700
    Latest new lineages.
  • lines changed 96, context: html, text, full: html, text
    d433a2f3c25a7364956f5904c9e391d93eb3a3c8 Wed Aug 26 17:01:55 2026 -0700
    Many new lineages and a few tweaks.
  • lines changed 4, context: html, text, full: html, text
    d3954606ff07dd6169919e7059e53bc0d7e98b06 Fri Aug 28 08:27:34 2026 -0700
    Now that XFJ.3.1 is excluded from masking of 21617 (in JN.1), we can include A21617G in descendants of XFJ.3.1.
• src/hg/utils/otto/sarscov2phylo/prune_to_radius.py
  • lines changed 129, context: html, text, full: html, text
    6091af3e8fff91595ab6361974787afef032a342 Thu Jun 25 11:03:38 2026 -0700
    Fix second filtering to match first. Extract tree of sequences from the past year plus sequences within a radius of 5 edges of those.
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
  • lines changed 13, context: html, text, full: html, text
    014bee401f2fe14c79caf74d42b5f4f6cf797dd3 Thu Jun 18 15:23:11 2026 -0700
    Loosen filters to accommodate increasingly divergent sequences. Tweak shell variables usherDir and friends to make it easier to try out different build directories.
  • lines changed 24, context: html, text, full: html, text
    6091af3e8fff91595ab6361974787afef032a342 Thu Jun 25 11:03:38 2026 -0700
    Fix second filtering to match first. Extract tree of sequences from the past year plus sequences within a radius of 5 edges of those.
  • lines changed 12, context: html, text, full: html, text
    efdf71bc99d33cb9fc9327b8b8e05244dab81e08 Fri Aug 28 08:29:52 2026 -0700
    Scan the tree for split lineages, excluding some highly recurrent mutations.
• src/hg/utils/otto/sarscov2phylo/updateLineageTreePb.sh
  • lines changed 6, context: html, text, full: html, text
    0b095144508cbb36923bacffa0425003f8484042 Thu Jun 18 15:21:58 2026 -0700
    Simplify creation of pango.clade-mutations.reroot.tsv because matUtils annotate can handle multiple successive mutations at the same position now.
  • lines changed 29, context: html, text, full: html, text
    9949a453819bff3ae00234d5f65b73c903ea4b2f Fri Aug 28 08:13:40 2026 -0700
    Replace non-Pango extra labels with Pango labels before pangolin test runs because some new extra labels on older split lineages were causing regex failure in pangolin. Remove the BA.5.1_no29666 branch because it's always problematic.
  • lines changed 1, context: html, text, full: html, text
    ad81d8de49a9c061fb50958f72a017ae1436497d Fri Aug 28 08:17:19 2026 -0700
    Fix regex for rerooting pango.clade-mutations.tsv to also match B's empty mutation list. Bug caught by Claude automated review of 0b09514. Fortunately masked in latest pangolin-data release because the lineage B annotation was preserved when rerooting the tree and did not need re-annotating.
• src/hg/utils/otto/sarscov2phylo/updatePublic.sh
  • lines changed 3, context: html, text, full: html, text
    d0ed6814b11e78dfd69dbe071b296acf46b8e24a Fri Aug 28 08:28:16 2026 -0700
    If split lineages were found, report them.
• src/hg/utils/tdbQuery/tdbQuery.c
  • lines changed 157, context: html, text, full: html, text
    8d56c47e3c7d8cfedd92002ef9ce0ad3977e1f74 Tue Aug 25 12:08:01 2026 -0700
    tdbQuery: index record positions instead of rescanning the whole list, refs #35489 The parent/child position check called closestTdbAboveLevel once per child record, and that function walked the entire record list, called countAncestors on every candidate, and compared long file path names with strcmp. On the big assemblies this dominated the run. A profile of hg38 put 71.6% of samples on one line of that loop and another 16.6% in strcmp. Build the answer once instead. For each file, sort the record positions by line, then precompute for every position the closest record above it at or below each depth. A query is then a binary search plus one array lookup. The result is the same record the old scan returned. The test is still a strict "position before the child", and when two positions share a line the earliest in master list order still wins, which is what the backwards group walk in tdbFileIndexNew preserves. hg38 goes from 13.3 to 0.41 seconds with -release=beta, and from 49.1 to 0.64 seconds with no release. Summed over the 348 databases in the trackDb makefile, 45.7 to 14.0 seconds. The makefile test target, which queries all databases at once, goes from 84.7 to 10.5 seconds for alpha.
• src/hg/utils/urlCommandCatalog/urlCommandCatalog.py
  • lines changed 54, context: html, text, full: html, text
    ae642c6c0fb0fcc12c48e0e29168c08feedead8b Fri Aug 28 14:02:33 2026 -0700
    urlCommandCatalog: catalog hgSession's three save-form inputs, refs #37923 All three stay in the cart after the Save form: hgS_newSessionName is in 6400 of 6607 saved sessions, hgS_newSessionShare in 6398, hgS_newSessionDescription in 165. Each is removed in one of the JSON endpoints and none by the form path that posts them, so the first two were in the baseline on a reading the data does not support. New partialDrop= records which remove exists and which path it misses, since the persistence audit keys on the name alone and would otherwise call a real leak stale on every run.
• src/hg/utils/urlCommandCatalog/urlNamesNotCataloged.txt
  • lines changed 2, context: html, text, full: html, text
    ae642c6c0fb0fcc12c48e0e29168c08feedead8b Fri Aug 28 14:02:33 2026 -0700
    urlCommandCatalog: catalog hgSession's three save-form inputs, refs #37923 All three stay in the cart after the Save form: hgS_newSessionName is in 6400 of 6607 saved sessions, hgS_newSessionShare in 6398, hgS_newSessionDescription in 165. Each is removed in one of the JSON endpoints and none by the form path that posts them, so the first two were in the baseline on a reading the data does not support. New partialDrop= records which remove exists and which path it misses, since the persistence audit keys on the name alone and would otherwise call a real leak stale on every run.
• src/inc/perfTimer.h
  • lines changed 61, context: html, text, full: html, text
    5a3be3af33b76d69d1fc98ee76b9a37f96e96fc7 Wed Aug 26 00:36:52 2026 -0700
    Add opt-in per-phase request timing to the new hgBlat and hgSession pages, shown in a dialog with &measureTiming=1. refs #38157 New reusable perfTimer collector (lib/perfTimer.c) records labeled wall-clock intervals via clock1000() and emits them as JSON; hgBlat and hgSession attach a timing array to their payload when the existing measureTiming cart/CGI var is set. A shared gbShowTimingDialog helper in utils.js renders the server phases plus a client render-time row in a house-style modal, which opens automatically when measureTiming is on. Confirms the position band/locus annotation loop dominates hgSession, and run-BLAT plus locus lookups dominate hgBlat.
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    5a3be3af33b76d69d1fc98ee76b9a37f96e96fc7 Wed Aug 26 00:36:52 2026 -0700
    Add opt-in per-phase request timing to the new hgBlat and hgSession pages, shown in a dialog with &measureTiming=1. refs #38157 New reusable perfTimer collector (lib/perfTimer.c) records labeled wall-clock intervals via clock1000() and emits them as JSON; hgBlat and hgSession attach a timing array to their payload when the existing measureTiming cart/CGI var is set. A shared gbShowTimingDialog helper in utils.js renders the server phases plus a client render-time row in a house-style modal, which opens automatically when measureTiming is on. Confirms the position band/locus annotation loop dominates hgSession, and run-BLAT plus locus lookups dominate hgBlat.
• src/lib/memalloc.c
  • lines changed 11, context: html, text, full: html, text
    40288931d6f7e083f7b71fd97109c03d9916bc30 Thu Aug 27 09:30:25 2026 -0700
    When memalloc fails, it calls errAbort. But if the handler is a sophisticated one, it might try to call memalloc itself, resulting in an endless loop. Better to nip that in the bud. no ticket
• src/lib/perfTimer.c
  • lines changed 73, context: html, text, full: html, text
    5a3be3af33b76d69d1fc98ee76b9a37f96e96fc7 Wed Aug 26 00:36:52 2026 -0700
    Add opt-in per-phase request timing to the new hgBlat and hgSession pages, shown in a dialog with &measureTiming=1. refs #38157 New reusable perfTimer collector (lib/perfTimer.c) records labeled wall-clock intervals via clock1000() and emits them as JSON; hgBlat and hgSession attach a timing array to their payload when the existing measureTiming cart/CGI var is set. A shared gbShowTimingDialog helper in utils.js renders the server phases plus a client render-time row in a house-style modal, which opens automatically when measureTiming is on. Confirms the position band/locus annotation loop dominates hgSession, and run-BLAT plus locus lookups dominate hgBlat.
• src/product/scripts/trackDbCacheCleaner.sh
  • lines changed 184, context: html, text, full: html, text
    02f92c8818bdf0f54381cd1eb962f8f5c16dea7d Tue Aug 25 16:34:19 2026 -0700
    trackDbCacheCleaner: expire trackDb cache entries that nothing reads, refs #37551 The trackDb cache holds one directory per database or track hub. The browser expires a cache file only when a request visits its directory and finds the file older than the trackDb table or the hub, and nothing ever removes a directory. A hub URL that is requested once and never again keeps its cache files forever. A tmpfs cache directory hides this until the next reboot. A disk backed cache directory never hides it, and /data/trackDbCache on hgwdev had grown to 16G in 49,749 directories since it was created on May 13. trackDbCacheCleaner.sh removes a cache directory when nothing in it has been read for expireDays days, 30 by default. Last use is the newer of the access time and the modify time, so on a file system mounted noatime it falls back to the write time, which only ever keeps entries longer. A directory still in use is left alone, because the browser opens every file in a directory it visits and that keeps the access times current. The first run on hgwdev took 30 seconds and dropped /data/trackDbCache from 16G to 8.2G, removing 30,117 directories and 60,504 files. hg38, hg19 and mm39 were untouched, and an expired assembly rebuilt its entry on the next request.
  • lines changed 22, context: html, text, full: html, text
    4088b6e57be69de4f37e00beefb13969a34eb09e Tue Aug 25 16:40:27 2026 -0700
    trackDbCacheCleaner: do not abandon the run when one removal fails, refs #37551 A cache directory can be owned by any user who ran a command line utility, not just by apache, so a removal can fail on permissions. With set -beEu that aborted the whole run part way through, leaving a half cleaned cache and printing no summary at all. Count the failures instead, warn about the first ten, and finish the rest of the cleaning. A run with any failure reports FAILED and exits 1, so a cron notices, and the next run retries what was left behind.
• src/utils/genark/genark
  • lines changed 340, context: html, text, full: html, text
    024157529eaaa41e89d10d7db2750e6d13a00a62 Wed Aug 26 03:01:39 2026 -0700
    genark: add syncFtp to update the local NCBI genomes mirror New subcommand that brings /hive/data/outside/ncbi/genomes/{GCA,GCF} up to date with NCBI. It fetches the current assembly_summary files for GenBank and RefSeq, diffs them against the last synced copy to find assemblies that are new or have changed, mirrors those with lftp using the exclude list from fetchLftp.sh, and appends one row per affected assembly to changes.tsv so later steps know what moved. With -n it works out the whole change set and writes changes.tsv without downloading any assembly data.
• src/utils/qa/checkHTTPS
  • lines changed 1, context: html, text, full: html, text
    79ef45749671d72edb96b09fc6a56d8af0837e5a Tue Aug 25 16:10:48 2026 -0700
    Remove cirmdcm.soe.ucsc.edu from the checkHTTPS site certificate expiration check. No RM. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/utils/qa/weeklybld/makeStrictBeta.csh
  • lines changed 8, context: html, text, full: html, text
    0b36c1276f7fd41e8ba9ad53bbdb20c1d438913d Tue Aug 25 12:08:14 2026 -0700
    trackDb: build the trix once per database, and run the beta make in parallel, refs #35489 The trackDb make for a final build takes about 18 minutes. It is not one slow step. It is 348 per-database chains of short processes and network round trips, run strictly one after another. Two changes. First, stop building the same trix twice. The beta recipe called buildTrix once for hgwbeta and again for hgwdev, with identical inputs and only the destination differing. buildTrix now takes -alsoTo=machine:path, so the index is built once and sent to both places. It also assembles the files in a temporary directory under their final names, so each destination takes one rsync instead of one per file. That takes the trix step from ten ssh connections per database down to two, and it no longer leaves .offsets files behind in the trackDb directory. Second, run the make in parallel. The header comment warning against this was out of date. hgTrackDb and hgFindSpec put their temporary files in TMPDIR under process-unique names, and every other file and table a recipe writes is already named after its database, so the per-database chains do not collide. Two makes at once are still unsafe, because they share table names, and the comment now says that instead. makeStrictBeta.csh passes -O -j 8. Set TRACKDB_MAKE_JOBS to change the job count. Going much above 8 wants ssh connection sharing first, or hgwbeta's sshd starts refusing connections. Measured over all 348 databases, with the output compared line by line against a serial run each time: 321 seconds today, 194 with the tdbQuery fix alone, 81 with -j 8 alone, and 39 with both. The -j 8 figure lands on the hg38 chain, which is why the tdbQuery fix matters more than its share of the total suggests.
• src/utils/redmineCli
  • lines changed 6, context: html, text, full: html, text
    f4996889d4fcf17c5290b81d1863c06fa3738e40 Tue Aug 25 12:09:32 2026 -0700
    redmineCli: add --target-version filter to the list subcommand. No RM.
• src/utils/ts/README
  • lines changed 15, context: html, text, full: html, text
    4f9164cb6142e7468325253a67c6ac8a6a3d1f91 Tue Aug 25 09:54:31 2026 -0700
    ts: give each ticket sandbox its own udc cache, refs #37867 Every parked instance and the live sandbox shared trash/udcCache, so a cache entry written by one instance was read by all of them. A sparse or bad entry from one build reappeared under another, which breaks the freeze. Each ticket now gets trash/udcCache/ts/NNNNN. It stays in the shared trash, so the trash cleaner ages it out like any other udc cache, and it stays data, so sync does not clear it. remove deletes it, since it sits inside the shared trash and not in the sandbox directory. conf now sets it too, so an instance frozen before this existed does not need a re-freeze.
• src/utils/ts/ts
  • lines changed 28, context: html, text, full: html, text
    4f9164cb6142e7468325253a67c6ac8a6a3d1f91 Tue Aug 25 09:54:31 2026 -0700
    ts: give each ticket sandbox its own udc cache, refs #37867 Every parked instance and the live sandbox shared trash/udcCache, so a cache entry written by one instance was read by all of them. A sparse or bad entry from one build reappeared under another, which breaks the freeze. Each ticket now gets trash/udcCache/ts/NNNNN. It stays in the shared trash, so the trash cleaner ages it out like any other udc cache, and it stays data, so sync does not clear it. remove deletes it, since it sits inside the shared trash and not in the sandbox directory. conf now sets it too, so an instance frozen before this existed does not need a re-freeze.

• lines changed: 720944
• files changed: 428