All File Changes

v494_preview2 to v494_base (2026-02-09 to 2026-02-16) v494

• docs/hubs/contributedTracks.md
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    de1c9682d7637f0e01724c3aa41401c1856fe882 Mon Feb 9 18:49:33 2026 -0800
    removing reference to UCSC database names, refs #37043
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    c4473ca7e4dd9383e7b03b8e306b1f57aa071ae3 Wed Feb 11 08:38:40 2026 -0800
    minor chnages to wording based on CR, refs #37095
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    f991be04e1a8010c3e6f63b620edf35ef45359f3 Wed Feb 11 08:44:09 2026 -0800
    Tweaks to requirements section, refs #37043
• src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html
  • lines changed 2, context: html, text, full: html, text
    fd45bd33807de0b6a9c4bce82db7a0413b32094c Tue Feb 10 10:26:18 2026 -0800
    Moving to active Zebrafish Beh. and LSFM mice after start of recent SFTP transfer from labs
• src/hg/hgGateway/hgGateway.html
  • lines changed 21, context: html, text, full: html, text
    ab5d95f27e2cfc363db9840c0514a7170b8547b1 Mon Feb 9 14:24:34 2026 -0800
    Add info icons to hgGateway, refs #34078
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 4, context: html, text, full: html, text
    8fcdc8d74c55bc1ea951d03cfe374491b87285b4 Fri Feb 13 16:40:26 2026 -0800
    When disconnecting an assembly hub on hgHubConnect, remove any of those assembly hub genomes from the recents list in localStorage. If the last connected db was one of those hubs, clear the db, org and genome cart variables and reset the db variable back to the default hg38, otherwise the first row of defaultDb is chosen as the current genome, refs #36535
• src/hg/hgSearch/hgSearch.c
  • lines changed 3, context: html, text, full: html, text
    ef13cc5d0f62179ede50ce59516f2c2b821cb7d7 Thu Feb 12 11:13:29 2026 -0800
    Oops forgot to update hgSearch when I cleaned up the species search bar changes and collated some functions together. Fix a separate bug where hgSearch was not properly setting the db= on the backend when a genark genome was selected from the auto-complete, refs #36232
• src/hg/hgTables/mainPage.c
  • lines changed 1, context: html, text, full: html, text
    0e46b7cc753347aa846d00af78f01390e80b3bcc Mon Feb 9 17:10:45 2026 -0800
    Adding an ID to the searchCell on hgTables. Updating the interactive tutorials since the new search feature breaks some of the tutorials. refs #37097
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 8, context: html, text, full: html, text
    1b4f89e8c61f36eb897687a47f8fa0971823e3d1 Thu Feb 12 13:12:17 2026 -0800
    create placeholder HTML for Alignment Differences track refs #36942
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    2fb7a9ce7a4d1d9b6c3c2a571643bfa09ec37a9c Thu Feb 12 14:48:24 2026 -0800
    support static HTML for quickLiftChain track
• src/hg/hgTracks/hgTracks.c
  • lines changed 2, context: html, text, full: html, text
    d77deb0a4cf433b8575e2068d8b099c473e6aab9 Tue Feb 10 12:52:08 2026 -0800
    Fixes from automated code review. refs #37087, #37060
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    79e20fc51607401bba064189e0ef5f44259cc969 Wed Feb 11 11:53:32 2026 -0800
    Shortening the confirmation message, as most users have small attention spans. Refs #36704
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    2fb7a9ce7a4d1d9b6c3c2a571643bfa09ec37a9c Thu Feb 12 14:48:24 2026 -0800
    support static HTML for quickLiftChain track
• src/hg/htdocs/goldenPath/help/quickLiftChain.html
  • lines changed 30, context: html, text, full: html, text
    a0014044bd80ea79079276eb762a96a3b9f89cba Thu Feb 12 12:56:40 2026 -0800
    add quickLiftChain placeholder
  • lines changed 28, context: html, text, full: html, text
    1b4f89e8c61f36eb897687a47f8fa0971823e3d1 Thu Feb 12 13:12:17 2026 -0800
    create placeholder HTML for Alignment Differences track refs #36942
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 6, context: html, text, full: html, text
    13f35a13bfbf2b50c98220901dfbe836aee88213 Mon Feb 9 19:07:35 2026 -0800
    minor changes based on CR, refs #37095
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 7, context: html, text, full: html, text
    13f35a13bfbf2b50c98220901dfbe836aee88213 Mon Feb 9 19:07:35 2026 -0800
    minor changes based on CR, refs #37095
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 52, context: html, text, full: html, text
    a90c98b377900f57c19425f9396ee1d9df8d32c5 Mon Feb 9 15:46:05 2026 -0800
    Announcing the Mexico Biobank tracks and the Phased Variants container, refs #36259
• src/hg/htdocs/inc/gbPageStart.html
  • lines changed 1, context: html, text, full: html, text
    5c3b3ae39b7eb61b93be63c263a5f9a403b30f0d Fri Feb 13 14:21:18 2026 -0800
    Fixing edgecase in CDNs ticket, the JS was loading from the wrong location on that one page set to dynmatically load it (js/, not js/external/) and the local css we have doesn't have fontawesome arrows, so it was changed to use the ones we have. Refs #33998
• src/hg/htdocs/inc/gbPageStartHardcoded.html
  • lines changed 1, context: html, text, full: html, text
    5c3b3ae39b7eb61b93be63c263a5f9a403b30f0d Fri Feb 13 14:21:18 2026 -0800
    Fixing edgecase in CDNs ticket, the JS was loading from the wrong location on that one page set to dynmatically load it (js/, not js/external/) and the local css we have doesn't have fontawesome arrows, so it was changed to use the ones we have. Refs #33998
• src/hg/htdocs/inc/hgSearch.html
  • lines changed 2, context: html, text, full: html, text
    ef13cc5d0f62179ede50ce59516f2c2b821cb7d7 Thu Feb 12 11:13:29 2026 -0800
    Oops forgot to update hgSearch when I cleaned up the species search bar changes and collated some functions together. Fix a separate bug where hgSearch was not properly setting the db= on the backend when a genark genome was selected from the auto-complete, refs #36232
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    a90c98b377900f57c19425f9396ee1d9df8d32c5 Mon Feb 9 15:46:05 2026 -0800
    Announcing the Mexico Biobank tracks and the Phased Variants container, refs #36259
• src/hg/htdocs/staticStyle/gbStatic.css
  • lines changed 21, context: html, text, full: html, text
    5c3b3ae39b7eb61b93be63c263a5f9a403b30f0d Fri Feb 13 14:21:18 2026 -0800
    Fixing edgecase in CDNs ticket, the JS was loading from the wrong location on that one page set to dynmatically load it (js/, not js/external/) and the local css we have doesn't have fontawesome arrows, so it was changed to use the ones we have. Refs #33998
• src/hg/htdocs/style/gbStatic.css
  • lines changed 21, context: html, text, full: html, text
    5c3b3ae39b7eb61b93be63c263a5f9a403b30f0d Fri Feb 13 14:21:18 2026 -0800
    Fixing edgecase in CDNs ticket, the JS was loading from the wrong location on that one page set to dynmatically load it (js/, not js/external/) and the local css we have doesn't have fontawesome arrows, so it was changed to use the ones we have. Refs #33998
• src/hg/htdocs/style/jWest.css
  • lines changed 1, context: html, text, full: html, text
    b19189b90927a74b3a8c4de416d0e926e8430f02 Wed Feb 11 11:32:14 2026 -0800
    changing assembly name text in the recent genomes cards to be blue like the link text in the 'Genomes' dropdown, refs #34078
  • lines changed 1, context: html, text, full: html, text
    84a62d63711c77e5bacd96e8a3e6566dfe14e78a Wed Feb 11 15:20:44 2026 -0800
    Removing some of the white space padding around the new recent genomes menu, refs #36535
• src/hg/js/hgGateway.js
  • lines changed 28, context: html, text, full: html, text
    03d6935afd1f21e64a308f28fe738cd22c0c5b25 Mon Feb 9 14:05:16 2026 -0800
    hgGateway: rename category labels in the 'recents' section. external hub clicks on cards no longer remain selected after clicking. GenArk and native dbs are handled the same for UI purposes, refs #34078
  • lines changed 31, context: html, text, full: html, text
    ab5d95f27e2cfc363db9840c0514a7170b8547b1 Mon Feb 9 14:24:34 2026 -0800
    Add info icons to hgGateway, refs #34078
  • lines changed 82, context: html, text, full: html, text
    afcbfbdf1e2c8cb1a76a08ca90f1e16833296e28 Tue Feb 10 15:25:32 2026 -0800
    Fix hgGateway bugs found in #34078 note 39: fix show species tree link, when disconnecting a hub on hgHubConnect, remove the hub from localStorage, fix handling of native databases that don't follow canFam4, hg38, etc format (example GRCm38B), store public hub name in the item storage so we correctly detect clicks on public hubs in recents list, call draw species tree by default on page load even if it's hidden so we don't need to render it each time we call back to the server because connecting to hubs no longer go into the tree. refs #34078
  • lines changed 7, context: html, text, full: html, text
    4d4d5f3e0ce2470b5d033d21d0f489f2263dbeb0 Fri Feb 13 11:23:26 2026 -0800
    Making updates to the info icons for Recent Genomes and Connected Hub Assemblies on hgGateway, refs #34078
• src/hg/js/hgMyData.js
  • lines changed 23, context: html, text, full: html, text
    06a403144f20a2aa46ff4ee5f810f06e27869ef5 Tue Feb 10 16:05:26 2026 -0800
    Fix visual bug in hubSpaceUI, sometimes when adding new rows to the DataTable, we get confused and show the directory row and table headers twice, refs #36830
• src/hg/js/hgSearch.js
  • lines changed 40, context: html, text, full: html, text
    ef13cc5d0f62179ede50ce59516f2c2b821cb7d7 Thu Feb 12 11:13:29 2026 -0800
    Oops forgot to update hgSearch when I cleaned up the species search bar changes and collated some functions together. Fix a separate bug where hgSearch was not properly setting the db= on the backend when a genark genome was selected from the auto-complete, refs #36232
• src/hg/js/hgTracks.js
  • lines changed 3, context: html, text, full: html, text
    ada8fc4366a49a14ff6678bee0919b64a05e4f62 Fri Feb 13 13:20:51 2026 -0800
    Make right click titles correct, refs #37096
• src/hg/js/tutorials/customTrackTutorial.js
  • lines changed 2, context: html, text, full: html, text
    0e46b7cc753347aa846d00af78f01390e80b3bcc Mon Feb 9 17:10:45 2026 -0800
    Adding an ID to the searchCell on hgTables. Updating the interactive tutorials since the new search feature breaks some of the tutorials. refs #37097
• src/hg/js/tutorials/gatewayTutorial.js
  • lines changed 4, context: html, text, full: html, text
    0e46b7cc753347aa846d00af78f01390e80b3bcc Mon Feb 9 17:10:45 2026 -0800
    Adding an ID to the searchCell on hgTables. Updating the interactive tutorials since the new search feature breaks some of the tutorials. refs #37097
• src/hg/js/tutorials/tableBrowserTutorial.js
  • lines changed 6, context: html, text, full: html, text
    0e46b7cc753347aa846d00af78f01390e80b3bcc Mon Feb 9 17:10:45 2026 -0800
    Adding an ID to the searchCell on hgTables. Updating the interactive tutorials since the new search feature breaks some of the tutorials. refs #37097
• src/hg/js/utils.js
  • lines changed 4, context: html, text, full: html, text
    051f9d387aa2531eaae06445f1d4df13fed9f390 Mon Feb 9 15:43:06 2026 -0800
    Oops, when I switched most area elements created by hgTracks to stick the tooltips into the data-tooltip attribute, I forgot to update the javascript mapItem code to use that as the title instead of what I set as the default, refs #37081
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    8301c8be72b9ae478c27d1a8fb64ae6e762f4856 Tue Feb 10 12:36:49 2026 -0800
    remove debug console.log message code review refs #37089
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    afcbfbdf1e2c8cb1a76a08ca90f1e16833296e28 Tue Feb 10 15:25:32 2026 -0800
    Fix hgGateway bugs found in #34078 note 39: fix show species tree link, when disconnecting a hub on hgHubConnect, remove the hub from localStorage, fix handling of native databases that don't follow canFam4, hg38, etc format (example GRCm38B), store public hub name in the item storage so we correctly detect clicks on public hubs in recents list, call draw species tree by default on page load even if it's hidden so we don't need to render it each time we call back to the server because connecting to hubs no longer go into the tree. refs #34078
  • lines changed 4, context: html, text, full: html, text
    3fb0b5d2a3d9d8b4429ab8ce25cdb8e00ddccf4a Fri Feb 13 13:56:04 2026 -0800
    Fix links to genark or public hubs to attach hub id onto links in the menu bar. The problem arises because when using hgGateway to connect to an assembly hub, it returns the 'genome' as the organism name which is not a valid value for the 'genome' field when used by hgTracks, refs #36535
• src/hg/lib/bigBedFind.c
  • lines changed 51, context: html, text, full: html, text
    ab2163a1bcc671f938eee484695ad77df98b4d79 Fri Feb 13 11:15:47 2026 -0800
    Add special item search descriptions to MANE and HGNC tracks, refs #34483
  • lines changed 1, context: html, text, full: html, text
    98f3f818e3a65d19b24f701aba31b425783b0034 Fri Feb 13 16:31:44 2026 -0800
    Oops hfs can be null for assembly hub searches, refs #37114
• src/hg/lib/cart.c
  • lines changed 10, context: html, text, full: html, text
    8fcdc8d74c55bc1ea951d03cfe374491b87285b4 Fri Feb 13 16:40:26 2026 -0800
    When disconnecting an assembly hub on hgHubConnect, remove any of those assembly hub genomes from the recents list in localStorage. If the last connected db was one of those hubs, clear the db, org and genome cart variables and reset the db variable back to the default hg38, otherwise the first row of defaultDb is chosen as the current genome, refs #36535
• src/hg/lib/hubConnect.c
  • lines changed 1, context: html, text, full: html, text
    1b4f89e8c61f36eb897687a47f8fa0971823e3d1 Thu Feb 12 13:12:17 2026 -0800
    create placeholder HTML for Alignment Differences track refs #36942
  • lines changed 1, context: html, text, full: html, text
    2fb7a9ce7a4d1d9b6c3c2a571643bfa09ec37a9c Thu Feb 12 14:48:24 2026 -0800
    support static HTML for quickLiftChain track
• src/hg/lib/trackHub.c
  • lines changed 10, context: html, text, full: html, text
    64675c24b3136d06f2123a1039a034114bd597b6 Thu Feb 12 13:35:41 2026 -0800
    Improving error messages mostly on hubCheck, with a few trackHub.c cases. Overall making the messages more informative to tell users what went wrong and what they can do to fix it, refs #35718
• src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh
  • lines changed 4, context: html, text, full: html, text
    78a47c721e9903c1f1f879ebbcf7bef4a8038ee7 Fri Feb 13 15:48:51 2026 -0800
    properly test tracks on hgwdev from their /gbdb/genark hubs location refs #37109
• src/hg/makeDb/doc/hg38/jaspar.txt
  • lines changed 3, context: html, text, full: html, text
    566f26928ab033f905f3fd87493ec5d94db4c59d Mon Feb 9 17:11:08 2026 -0800
    Adding the hgFixed table for the PFMs show up on the TFs hgc pages, refs #36264
• src/hg/makeDb/doc/hgFixed.txt
  • lines changed 12, context: html, text, full: html, text
    566f26928ab033f905f3fd87493ec5d94db4c59d Mon Feb 9 17:11:08 2026 -0800
    Adding the hgFixed table for the PFMs show up on the TFs hgc pages, refs #36264
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    7bb8ecf3a5d724c453e36901b74e027333843a30 Mon Feb 9 15:57:54 2026 -0800
    Fixing JASPAR visibilities on mm10 and hg19, I created the 2026 update, but those two assemblies don't have the 2026 track and need the 2024 on by default instead. Refs #37082
• src/hg/makeDb/trackDb/human/phasedVars.ra
  • lines changed 1, context: html, text, full: html, text
    f09641f323f37ad2148098cfd4c2148e961be05b Mon Feb 9 17:15:18 2026 -0800
    Adding the penantIcon for the Phased Variants track, refs #36259
• src/hg/makeDb/trackDb/jaspar.html
  • lines changed 1, context: html, text, full: html, text
    ff44390948a53ad9147abac1c39752932b81502c Tue Feb 10 13:31:32 2026 -0800
    Typo feedback from CR. Refs #37093
  • lines changed 37, context: html, text, full: html, text
    29756f1e91ffb40869bee417c95f233c3ceadbff Tue Feb 10 16:14:41 2026 -0800
    Updating the jaspar track description page, refs #36264
• src/hg/makeDb/trackDb/jaspar.ra
  • lines changed 1, context: html, text, full: html, text
    566f26928ab033f905f3fd87493ec5d94db4c59d Mon Feb 9 17:11:08 2026 -0800
    Adding the hgFixed table for the PFMs show up on the TFs hgc pages, refs #36264
  • lines changed 2, context: html, text, full: html, text
    75c863a2ea9c43bfa455f69fd444eba3f0b63305 Tue Feb 10 17:25:33 2026 -0800
    Removing 'showCfg on' because that needs a composite with multiple children, and for some assemblies this is the first JASPAR release. Refs #36264
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    7bb8ecf3a5d724c453e36901b74e027333843a30 Mon Feb 9 15:57:54 2026 -0800
    Fixing JASPAR visibilities on mm10 and hg19, I created the 2026 update, but those two assemblies don't have the 2026 track and need the 2024 on by default instead. Refs #37082
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 2, context: html, text, full: html, text
    5e8e9e71229d664fe260e7d6943357586a47dbe2 Fri Feb 13 08:58:36 2026 -0800
    fix bug in ix links for ncbiGene tracks refs #37109
  • lines changed 1, context: html, text, full: html, text
    9029dffcc033ff1b3b403f78af0faf37a055044f Fri Feb 13 09:03:44 2026 -0800
    fix bug in ix links for ncbiGene tracks refs #37109
• src/hg/utils/hubCheck/hubCheck.c
  • lines changed 18, context: html, text, full: html, text
    64675c24b3136d06f2123a1039a034114bd597b6 Thu Feb 12 13:35:41 2026 -0800
    Improving error messages mostly on hubCheck, with a few trackHub.c cases. Overall making the messages more informative to tell users what went wrong and what they can do to fix it, refs #35718
  • lines changed 23, context: html, text, full: html, text
    2cb1f903afe83b27c2561fb2cff129d27878a46a Thu Feb 12 15:23:10 2026 -0800
    Adding a new flag, -allowWarnings, to hubCheck so that it doesn't exit out when it raises warnings. This way it doesn't break pipelines on common warning complaints like track desc pages, refs #30723
• src/hg/utils/hubCheck/tests/expected/allowWarnings.output.txt
  • lines changed 10, context: html, text, full: html, text
    99c8b296447db2356a7669bcf6ee2c7ea89d138f Fri Feb 13 14:23:09 2026 -0800
    Forgot to commit the make tests for the new allowWarnings flag, refs #30723
• src/hg/utils/hubCheck/tests/expected/autoScaleHub.txt
  • lines changed 9, context: html, text, full: html, text
    64675c24b3136d06f2123a1039a034114bd597b6 Thu Feb 12 13:35:41 2026 -0800
    Improving error messages mostly on hubCheck, with a few trackHub.c cases. Overall making the messages more informative to tell users what went wrong and what they can do to fix it, refs #35718
• src/hg/utils/hubCheck/tests/expected/badGroups.output.txt
  • lines changed 2, context: html, text, full: html, text
    64675c24b3136d06f2123a1039a034114bd597b6 Thu Feb 12 13:35:41 2026 -0800
    Improving error messages mostly on hubCheck, with a few trackHub.c cases. Overall making the messages more informative to tell users what went wrong and what they can do to fix it, refs #35718
• src/hg/utils/hubCheck/tests/expected/badSubGroups.output.txt
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    64675c24b3136d06f2123a1039a034114bd597b6 Thu Feb 12 13:35:41 2026 -0800
    Improving error messages mostly on hubCheck, with a few trackHub.c cases. Overall making the messages more informative to tell users what went wrong and what they can do to fix it, refs #35718
• src/hg/utils/hubCheck/tests/expected/badType.output.txt
  • lines changed 10, context: html, text, full: html, text
    64675c24b3136d06f2123a1039a034114bd597b6 Thu Feb 12 13:35:41 2026 -0800
    Improving error messages mostly on hubCheck, with a few trackHub.c cases. Overall making the messages more informative to tell users what went wrong and what they can do to fix it, refs #35718
• src/hg/utils/hubCheck/tests/expected/goodGroups.output.txt
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    64675c24b3136d06f2123a1039a034114bd597b6 Thu Feb 12 13:35:41 2026 -0800
    Improving error messages mostly on hubCheck, with a few trackHub.c cases. Overall making the messages more informative to tell users what went wrong and what they can do to fix it, refs #35718
• src/hg/utils/hubCheck/tests/expected/manyErrors.output.txt
  • lines changed 39, context: html, text, full: html, text
    64675c24b3136d06f2123a1039a034114bd597b6 Thu Feb 12 13:35:41 2026 -0800
    Improving error messages mostly on hubCheck, with a few trackHub.c cases. Overall making the messages more informative to tell users what went wrong and what they can do to fix it, refs #35718
• src/hg/utils/hubCheck/tests/expected/noCompositeGroup.output.txt
  • lines changed 1, context: html, text, full: html, text
    64675c24b3136d06f2123a1039a034114bd597b6 Thu Feb 12 13:35:41 2026 -0800
    Improving error messages mostly on hubCheck, with a few trackHub.c cases. Overall making the messages more informative to tell users what went wrong and what they can do to fix it, refs #35718
• src/hg/utils/hubCheck/tests/expected/noLongLabel.txt
  • lines changed 3, context: html, text, full: html, text
    64675c24b3136d06f2123a1039a034114bd597b6 Thu Feb 12 13:35:41 2026 -0800
    Improving error messages mostly on hubCheck, with a few trackHub.c cases. Overall making the messages more informative to tell users what went wrong and what they can do to fix it, refs #35718
• src/hg/utils/hubCheck/tests/expected/output1.txt
  • lines changed 1, context: html, text, full: html, text
    64675c24b3136d06f2123a1039a034114bd597b6 Thu Feb 12 13:35:41 2026 -0800
    Improving error messages mostly on hubCheck, with a few trackHub.c cases. Overall making the messages more informative to tell users what went wrong and what they can do to fix it, refs #35718
• src/hg/utils/hubCheck/tests/expected/supertrackChild.txt
  • lines changed 9, context: html, text, full: html, text
    64675c24b3136d06f2123a1039a034114bd597b6 Thu Feb 12 13:35:41 2026 -0800
    Improving error messages mostly on hubCheck, with a few trackHub.c cases. Overall making the messages more informative to tell users what went wrong and what they can do to fix it, refs #35718
• src/hg/utils/hubCheck/tests/makefile
  • lines changed 2, context: html, text, full: html, text
    64675c24b3136d06f2123a1039a034114bd597b6 Thu Feb 12 13:35:41 2026 -0800
    Improving error messages mostly on hubCheck, with a few trackHub.c cases. Overall making the messages more informative to tell users what went wrong and what they can do to fix it, refs #35718
  • lines changed 5, context: html, text, full: html, text
    2cb1f903afe83b27c2561fb2cff129d27878a46a Thu Feb 12 15:23:10 2026 -0800
    Adding a new flag, -allowWarnings, to hubCheck so that it doesn't exit out when it raises warnings. This way it doesn't break pipelines on common warning complaints like track desc pages, refs #30723

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• files changed: 73