All File Changes

v487_base to v488_preview (2025-09-01 to 2025-09-08) v488

• confs/asia.hg.conf
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    3f4301af5d63a9eec8ae1f8dda9159756a7f954b Sun Sep 7 01:11:19 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 3, context: html, text, full: html, text
    3f4301af5d63a9eec8ae1f8dda9159756a7f954b Sun Sep 7 01:11:19 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
  • lines changed 1, context: html, text, full: html, text
    3f4301af5d63a9eec8ae1f8dda9159756a7f954b Sun Sep 7 01:11:19 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 3, context: html, text, full: html, text
    3f4301af5d63a9eec8ae1f8dda9159756a7f954b Sun Sep 7 01:11:19 2025 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html
  • lines changed 12, context: html, text, full: html, text
    96002a53528b7a6f42b53fa1379f76b6bfd12664 Thu Sep 4 12:35:04 2025 -0700
    Aligning Q3 end to 2025-09-30 vs 2025-10-01 (which is start Q4) for SSPsyGene milestones
  • lines changed 12, context: html, text, full: html, text
    ef86606fd2c0af01d5769827b5a8bf83d4e01d45 Fri Sep 5 10:00:56 2025 -0700
    Ammending Broad's submit data to red diamond icon (critical milestone) for end of 2026 Q1 items
• src/hg/hgConvert/hgConvert.c
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    e341c576504ab46af7ad7d7a28cd4f81369e0fea Mon Sep 1 11:18:57 2025 -0700
    working to get quickLifts from genark hubs to work
• src/hg/hgPhyloPlace/parsimonyProto.c
  • lines changed 10, context: html, text, full: html, text
    232916a177e494f8e1b3543c7ed71d37b2f96191 Fri Sep 5 17:21:37 2025 -0700
    Handle .gz protobuf file
• src/hg/hgTracks/bedTrack.c
  • lines changed 1, context: html, text, full: html, text
    e341c576504ab46af7ad7d7a28cd4f81369e0fea Mon Sep 1 11:18:57 2025 -0700
    working to get quickLifts from genark hubs to work
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 1, context: html, text, full: html, text
    e341c576504ab46af7ad7d7a28cd4f81369e0fea Mon Sep 1 11:18:57 2025 -0700
    working to get quickLifts from genark hubs to work
  • lines changed 78, context: html, text, full: html, text
    458eb071b9214f95170c0e7d597f79cdc9bd04db Wed Sep 3 15:21:09 2025 -0700
    Revert "Fixes #35580 and #36250" This reverts commit 6a731cde7f73dcf905192439bdf064a73abf11d2. I will have to revert this for now and continue debugging on my branch.
  • lines changed 94, context: html, text, full: html, text
    4833b6c8e4583d27b99b06a6bdf0357fe786215d Mon Sep 8 01:45:07 2025 -0700
    Deals with multi-region and bigBeds so limitWiggle optimization works properly with all windows or regions. Fixes error test cases in rm35580 as well as full chromosome and recount3 and lrg and unusual tracks etc. fixes 35580
• src/hg/hgTracks/hgTracks.c
  • lines changed 39, context: html, text, full: html, text
    458eb071b9214f95170c0e7d597f79cdc9bd04db Wed Sep 3 15:21:09 2025 -0700
    Revert "Fixes #35580 and #36250" This reverts commit 6a731cde7f73dcf905192439bdf064a73abf11d2. I will have to revert this for now and continue debugging on my branch.
  • lines changed 39, context: html, text, full: html, text
    4833b6c8e4583d27b99b06a6bdf0357fe786215d Mon Sep 8 01:45:07 2025 -0700
    Deals with multi-region and bigBeds so limitWiggle optimization works properly with all windows or regions. Fixes error test cases in rm35580 as well as full chromosome and recount3 and lrg and unusual tracks etc. fixes 35580
• src/hg/hgTracks/hgTracks.h
  • lines changed 1, context: html, text, full: html, text
    458eb071b9214f95170c0e7d597f79cdc9bd04db Wed Sep 3 15:21:09 2025 -0700
    Revert "Fixes #35580 and #36250" This reverts commit 6a731cde7f73dcf905192439bdf064a73abf11d2. I will have to revert this for now and continue debugging on my branch.
  • lines changed 1, context: html, text, full: html, text
    4833b6c8e4583d27b99b06a6bdf0357fe786215d Mon Sep 8 01:45:07 2025 -0700
    Deals with multi-region and bigBeds so limitWiggle optimization works properly with all windows or regions. Fixes error test cases in rm35580 as well as full chromosome and recount3 and lrg and unusual tracks etc. fixes 35580
• src/hg/hgTracks/lrgTrack.c
  • lines changed 1, context: html, text, full: html, text
    f25f7ee54023f11c3dd7f6ed59c41defc9987520 Sun Sep 7 16:20:37 2025 -0700
    fix problem with lrg nextExon using wrong handler. fixes #36318
• src/hg/hgTracks/quickLift.c
  • lines changed 2, context: html, text, full: html, text
    365c52681ce18c77b192cb96bd5c62ba8c3dcfb1 Tue Sep 2 12:28:16 2025 -0700
    I'm changing the way that click-throughs on the Warning track work.
• src/hg/htdocs/goldenPath/help/assemblyHubHelp.html
  • lines changed 848, context: html, text, full: html, text
    5295d58d808a9ef30d0514558d943b7dbf4bd4f7 Tue Sep 2 16:03:33 2025 -0700
    Updating the GB page for the Assembly Hub Wiki, refs #34740
• src/hg/htdocs/goldenPath/help/posters.html
  • lines changed 504, context: html, text, full: html, text
    28aca3c30ac9ca206624654016671265c9be81f1 Mon Sep 1 11:44:23 2025 -0700
    Creating a gallery of posters page, refs #36182
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    b645de81448a7a6aff8500e3f23a035ff07c4a04 Mon Sep 1 12:07:35 2025 -0700
    Adding the correct UCSC_Proteomics_HUPO2015_Poster link to the gallery of posters page, refs #36182
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.css
  • lines changed 115, context: html, text, full: html, text
    39426d1f93ac5a32f9738821eba00c4905513c85 Thu Sep 4 16:03:23 2025 -0700
    Add a search bar to the trackDb settings document, that works just like regular ctrl+f/cmd+f but can find text that may be hidden on the page, refs #35618
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.js
  • lines changed 477, context: html, text, full: html, text
    39426d1f93ac5a32f9738821eba00c4905513c85 Thu Sep 4 16:03:23 2025 -0700
    Add a search bar to the trackDb settings document, that works just like regular ctrl+f/cmd+f but can find text that may be hidden on the page, refs #35618
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 12, context: html, text, full: html, text
    39426d1f93ac5a32f9738821eba00c4905513c85 Thu Sep 4 16:03:23 2025 -0700
    Add a search bar to the trackDb settings document, that works just like regular ctrl+f/cmd+f but can find text that may be hidden on the page, refs #35618
• src/hg/htdocs/indexMeetings.html
  • lines changed 16, context: html, text, full: html, text
    6505f25a3bb015b23f94bcf118887ab8a199daab Wed Sep 3 17:35:20 2025 -0700
    Removing old meeting from homepage, added a placeholder text so keep formatting changes to a min. No RM.
• src/hg/htdocs/style/HGStyle.css
  • lines changed 12, context: html, text, full: html, text
    06dd505658db9a9237b0eeba402b52aadfb25864 Wed Sep 3 15:46:36 2025 -0700
    Make active Table Browser buttons on Table Browser in color. Makes obvious to users that identifiers, filters, and intersections have been created and will affgect the table browser output. fixes #22159
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    c238a39a6b937ff44aa925539998029bc3429c62 Thu Sep 4 12:11:58 2025 -0700
    Adding red to the Clear buttons for Defined regions and Subtrack merge features, refs #22159
• src/hg/js/hgSearch.js
  • lines changed 1, context: html, text, full: html, text
    e8c18ea459195453190989275fa05f082ef84c6a Wed Sep 3 13:59:57 2025 -0700
    Add missing ampersand to redirect link when an hgSearch term resolves to a single position, refs #36068
• src/hg/lib/asmAlias.c
  • lines changed 3, context: html, text, full: html, text
    e341c576504ab46af7ad7d7a28cd4f81369e0fea Mon Sep 1 11:18:57 2025 -0700
    working to get quickLifts from genark hubs to work
• src/hg/lib/genomePriority.as
  • lines changed 5, context: html, text, full: html, text
    f6c778facb8d507287c93ae2c4027cd09e1e7b8b Mon Sep 1 23:31:40 2025 -0700
    improved priority business refs #32897
• src/hg/lib/genomePriority.c
  • lines changed 116, context: html, text, full: html, text
    f6c778facb8d507287c93ae2c4027cd09e1e7b8b Mon Sep 1 23:31:40 2025 -0700
    improved priority business refs #32897
• src/hg/lib/genomePriority.sql
  • lines changed 11, context: html, text, full: html, text
    f6c778facb8d507287c93ae2c4027cd09e1e7b8b Mon Sep 1 23:31:40 2025 -0700
    improved priority business refs #32897
• src/hg/lib/hdb.c
  • lines changed 7, context: html, text, full: html, text
    e341c576504ab46af7ad7d7a28cd4f81369e0fea Mon Sep 1 11:18:57 2025 -0700
    working to get quickLifts from genark hubs to work
• src/hg/lib/trackHub.c
  • lines changed 7, context: html, text, full: html, text
    e341c576504ab46af7ad7d7a28cd4f81369e0fea Mon Sep 1 11:18:57 2025 -0700
    working to get quickLifts from genark hubs to work
  • lines changed 3, context: html, text, full: html, text
    e5969c8ac3b73702710925bfc013c9fdbd8dbbdd Fri Sep 5 11:11:10 2025 -0700
    take out a fix that broke zooming out after an hgConvert
• src/hg/makeDb/doc/asmHubs/compareJsonLists.py
  • lines changed 47, context: html, text, full: html, text
    eaa0b77b060608e37c70bbc22f6aaa75aeb91c75 Mon Sep 1 22:54:28 2025 -0700
    helper script for minimalBuild.sh refs #29545
• src/hg/makeDb/doc/asmHubs/dynaBlatLinks.sh
  • lines changed 33, context: html, text, full: html, text
    911babaa75518844e606fa2e29ab92caaedaf377 Mon Sep 1 23:01:12 2025 -0700
    improved procedure
• src/hg/makeDb/doc/asmHubs/findEquiv.py
  • lines changed 14, context: html, text, full: html, text
    168c7a7081021c0656d309e61e00e070c66bfd2d Mon Sep 1 22:57:04 2025 -0700
    improved procedure refs #34917
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 28733, context: html, text, full: html, text
    6fa70b95c35a30c56deef04db5297b04740ff776 Mon Sep 1 22:11:56 2025 -0700
    move list out of source tree
• src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
  • lines changed 6, context: html, text, full: html, text
    d8388d5ea3fcd84481a3ac81633ef927dc40679c Mon Sep 1 22:55:17 2025 -0700
    adding the quickLift links refs #29545
• src/hg/makeDb/doc/asmHubs/updateLiftOverChain.pl
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    e1db15e52f8b00f85ecd45ea54f68f9a8949f8c2 Mon Sep 1 22:59:47 2025 -0700
    refine the check refs #35575
• src/hg/makeDb/doc/assemblyEquivalence/createNearMissRunList.pl
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    0a3f8c738cfc06e5f7154258dd8a19dbc471c8d7 Mon Sep 1 23:41:56 2025 -0700
    improvements
• src/hg/makeDb/doc/assemblyEquivalence/exact.sh
  • lines changed 28, context: html, text, full: html, text
    0a3f8c738cfc06e5f7154258dd8a19dbc471c8d7 Mon Sep 1 23:41:56 2025 -0700
    improvements
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    99ec03901d84f8b2af5c0ca1e9956f6110291ab9 Mon Sep 1 22:03:31 2025 -0700
    adding a couple per user request refs #29545
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
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    99ec03901d84f8b2af5c0ca1e9956f6110291ab9 Mon Sep 1 22:03:31 2025 -0700
    adding a couple per user request refs #29545
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
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    99ec03901d84f8b2af5c0ca1e9956f6110291ab9 Mon Sep 1 22:03:31 2025 -0700
    adding a couple per user request refs #29545
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    99ec03901d84f8b2af5c0ca1e9956f6110291ab9 Mon Sep 1 22:03:31 2025 -0700
    adding a couple per user request refs #29545
• src/hg/makeDb/trackDb/evaSnp.ra
  • lines changed 5, context: html, text, full: html, text
    23695c919a70e8c75ec5c8c32eefefe2cf80875e Fri Sep 5 14:24:42 2025 -0700
    Second round of mouseOver display updates for popular tracks, refs #36020
• src/hg/makeDb/trackDb/human/dosageSensitivityCollins2022.ra
  • lines changed 2, context: html, text, full: html, text
    23695c919a70e8c75ec5c8c32eefefe2cf80875e Fri Sep 5 14:24:42 2025 -0700
    Second round of mouseOver display updates for popular tracks, refs #36020
• src/hg/makeDb/trackDb/human/hg38/gnomad.constraint.public.ra
  • lines changed 16, context: html, text, full: html, text
    527576d959bdfbaa9a62c21ad3cc196f2deabe44 Mon Sep 1 10:16:37 2025 -0700
    More mouseOver display updates for popular tracks, refs #36020
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 2, context: html, text, full: html, text
    527576d959bdfbaa9a62c21ad3cc196f2deabe44 Mon Sep 1 10:16:37 2025 -0700
    More mouseOver display updates for popular tracks, refs #36020
• src/hg/makeDb/trackDb/human/hg38/problematic.ra
  • lines changed 9, context: html, text, full: html, text
    6dd96d3eddd8ec78bd0f0a1b100a9618c852bdaa Mon Sep 1 15:34:46 2025 -0700
    Making problematic track a default for hg38 with show empty subtracks on, refs #31062
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    23695c919a70e8c75ec5c8c32eefefe2cf80875e Fri Sep 5 14:24:42 2025 -0700
    Second round of mouseOver display updates for popular tracks, refs #36020
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    527576d959bdfbaa9a62c21ad3cc196f2deabe44 Mon Sep 1 10:16:37 2025 -0700
    More mouseOver display updates for popular tracks, refs #36020
• src/hg/makeDb/trackDb/uniprot.ra
  • lines changed 17, context: html, text, full: html, text
    23695c919a70e8c75ec5c8c32eefefe2cf80875e Fri Sep 5 14:24:42 2025 -0700
    Second round of mouseOver display updates for popular tracks, refs #36020
• src/hg/phyloPng/makefile
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    455a0b2500ffc2c3b4c2c11733d3103c3d3fb53e Mon Sep 1 23:34:56 2025 -0700
    do not need the -lm specification on the library link
• src/hg/utils/automation/asmHubChainNetTrackDb.pl
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    87f551dfb14925f9e7e1d6f23d798fef313fd73c Mon Sep 1 23:25:33 2025 -0700
    new chain net construction and update genePred names
• src/hg/utils/automation/asmHubChainNetTrackDb.sh
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    87f551dfb14925f9e7e1d6f23d798fef313fd73c Mon Sep 1 23:25:33 2025 -0700
    new chain net construction and update genePred names
• src/hg/utils/automation/asmHubChromAlias.pl
  • lines changed 37, context: html, text, full: html, text
    87f551dfb14925f9e7e1d6f23d798fef313fd73c Mon Sep 1 23:25:33 2025 -0700
    new chain net construction and update genePred names
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 18, context: html, text, full: html, text
    87f551dfb14925f9e7e1d6f23d798fef313fd73c Mon Sep 1 23:25:33 2025 -0700
    new chain net construction and update genePred names
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    5acd42ee6f0f2031ce020ff60a2fd1ffa9d7940a Tue Sep 2 13:49:47 2025 -0700
    reset default gene name display on RefSeq gene tracks refs #36206
• src/hg/utils/automation/doIdKeys.pl
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    87f551dfb14925f9e7e1d6f23d798fef313fd73c Mon Sep 1 23:25:33 2025 -0700
    new chain net construction and update genePred names
• src/hg/utils/automation/doRepeatMasker.pl
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    07239334f514fc80e68aba6968335e56853e3177 Tue Sep 2 11:23:25 2025 -0700
    upgrade to version 4.2.1
• src/hg/utils/automation/doRepeatModeler.pl
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    a7d8fc835322d9017fdd5d932c22aaf2b3f5c56e Tue Sep 2 11:12:17 2025 -0700
    updated to version 2.0.7
• src/hg/utils/automation/doXenoRefGene.pl
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    87f551dfb14925f9e7e1d6f23d798fef313fd73c Mon Sep 1 23:25:33 2025 -0700
    new chain net construction and update genePred names
• src/hg/utils/automation/gpToIx.pl
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    87f551dfb14925f9e7e1d6f23d798fef313fd73c Mon Sep 1 23:25:33 2025 -0700
    new chain net construction and update genePred names
• src/hg/utils/automation/makeGenomeDb.pl
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    87f551dfb14925f9e7e1d6f23d798fef313fd73c Mon Sep 1 23:25:33 2025 -0700
    new chain net construction and update genePred names
• src/hg/utils/gff3ToGenePred/tests/expected/bogusQuotesTest.out
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    53404d29a092a6b47f0583377e3d7c336c54ff2d Fri Sep 5 12:09:42 2025 -0700
    indicate which GFF3 errors can be treated as a warning
• src/hg/utils/gff3ToGenePred/tests/expected/errCases1Test.out
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    53404d29a092a6b47f0583377e3d7c336c54ff2d Fri Sep 5 12:09:42 2025 -0700
    indicate which GFF3 errors can be treated as a warning
• src/hg/utils/otto/fluA/updateAndersenLab.sh
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    0e7d82dd8faf78dd7e8a0a4ed8f29c9215382c37 Fri Sep 5 17:24:40 2025 -0700
    Strip comma from host component of name, so it doesn't mess up newick parsing in usher.
• src/hg/utils/otto/genArk/README
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    a20c0e1ae1ef0957b267321b78e43e1dbd91092c Mon Sep 1 23:43:36 2025 -0700
    mention the alphaBetaPush.pl procedure
• src/hg/utils/phyloTrees/asciiTree.pl
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    56aff44eacee07bc3679dd18fe70ad621f6142d5 Mon Sep 1 23:45:50 2025 -0700
    allow stdin as argument to asciiTree and updated perl issues for binaryTree
• src/hg/utils/phyloTrees/binaryTree.pl
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    56aff44eacee07bc3679dd18fe70ad621f6142d5 Mon Sep 1 23:45:50 2025 -0700
    allow stdin as argument to asciiTree and updated perl issues for binaryTree
• src/lib/gff3.c
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    53404d29a092a6b47f0583377e3d7c336c54ff2d Fri Sep 5 12:09:42 2025 -0700
    indicate which GFF3 errors can be treated as a warning
• src/lib/tests/expected/gff3ErrorCasesTest.err
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    bbe59bb755808b616717f3094bc573b644820fca Sat Sep 6 05:07:27 2025 -0700
    fixed expected test result
• src/product/ex.hg.conf
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    1b59701306d7524a51b12706290361a36a1b280d Fri Sep 5 19:35:39 2025 -0700
    Improving the wording of this hg.conf to better describe how it is set, and to be more descriptive to mirror operators who look at the file.

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• files changed: 76