All File Changes

v493_preview2 to v493_base (2026-01-19 to 2026-01-26) v493

• confs/hgwbeta.hg.conf
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    0d2aae0eda9aad8255bced9aa142e457f1a25c5d Sun Jan 25 01:11:16 2026 -0800
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 7, context: html, text, full: html, text
    0d2aae0eda9aad8255bced9aa142e457f1a25c5d Sun Jan 25 01:11:16 2026 -0800
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 1, context: html, text, full: html, text
    0d2aae0eda9aad8255bced9aa142e457f1a25c5d Sun Jan 25 01:11:16 2026 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/cartDump/cartDump.c
  • lines changed 17, context: html, text, full: html, text
    b8b56383b460baeded0eb044c5c50998564f4b9d Sun Jan 25 22:35:48 2026 -0800
    Initial pass at making data types optional for the new faceted composite UI. refs #36320
• src/hg/cgilib/trackLayout.c
  • lines changed 8, context: html, text, full: html, text
    6e0d16475a09c3b72bd69f52f871671d8b1fee5d Thu Jan 22 16:41:30 2026 -0800
    allowing switching off the left side area, refs #36997
  • lines changed 8, context: html, text, full: html, text
    f60098c54a1a19f12520955d00ef774cae34d168 Mon Jan 26 05:51:47 2026 -0800
    Revert "allowing switching off the left side area, refs #36997" This reverts commit 6e0d16475a09c3b72bd69f52f871671d8b1fee5d because I found tracks that seem to hang the browser with label size set to 0 and I don't want to commit this now just before the build.
• src/hg/hgCustom/hgCustom.c
  • lines changed 1, context: html, text, full: html, text
    fdd22ab26c30d2cfbb0a2578e539b5b54b9f4c19 Thu Jan 22 17:30:46 2026 -0800
    Updating the custom track configuration text, refs #35492
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 1, context: html, text, full: html, text
    1f8adb2e2330efa72300e9e4b80095be31746168 Wed Jan 21 14:19:39 2026 -0800
    Encode the hubUrl on hgHubConnect retry hub button so if the url is bogus and has quotes it does not mess up the rest of the javascript, refs #36936
• src/hg/hgHubConnect/hooks/pre-create.c
  • lines changed 15, context: html, text, full: html, text
    c6d419ecfb6f122d7a0cb99c37f56c32c089bea3 Thu Jan 22 10:41:38 2026 -0800
    HubSpace changes: Allow users to overwrite already uploaded files, but warn them first. When a hub.txt file is being uploaded, don't auto-generate one. Check if the tracks being uploaded already exist in the hub.txt before adding a default stanza for it. Add some more checks in the hook files to prevent faulty uploads. Have the tus client clear localStorage on successful uploads so re-uploads of the same file don't cause confusing errors
• src/hg/hgHubConnect/hooks/pre-finish.c
  • lines changed 19, context: html, text, full: html, text
    c6d419ecfb6f122d7a0cb99c37f56c32c089bea3 Thu Jan 22 10:41:38 2026 -0800
    HubSpace changes: Allow users to overwrite already uploaded files, but warn them first. When a hub.txt file is being uploaded, don't auto-generate one. Check if the tracks being uploaded already exist in the hub.txt before adding a default stanza for it. Add some more checks in the hook files to prevent faulty uploads. Have the tus client clear localStorage on successful uploads so re-uploads of the same file don't cause confusing errors
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 1, context: html, text, full: html, text
    aab7ab11207b95e0edae3674a65144a159b2dbe3 Tue Jan 20 05:20:09 2026 -0800
    forgot semicolon in previous commit
  • lines changed 9, context: html, text, full: html, text
    478610d3be4abc22e330f4fbb154a2ac8ac4abfa Tue Jan 20 15:24:18 2026 -0800
    add strand filter option to oligoMatch track refs #36984 Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
  • lines changed 7, context: html, text, full: html, text
    5f99b76015eefbb14a2ac75ddcb56f8c1e17ca65 Wed Jan 21 00:01:19 2026 -0800
    Changes provided by Andrew Smith to tidy up the new composite UI, refs #36320
  • lines changed 13, context: html, text, full: html, text
    ad032e072d0427c066c425a88672288ed1b6c133 Wed Jan 21 08:13:31 2026 -0800
    fixes after code review and feedback from mark, refs #36978, and refs #36917
  • lines changed 72, context: html, text, full: html, text
    e6ee88658405177aee46ddb8902ae93aee5b1378 Thu Jan 22 16:36:14 2026 -0800
    Revert "changing superTrack TrackUi quite a bit. This reverts commit fcb6dc8dfa166136193177c895ca181200850e4d.
  • lines changed 30, context: html, text, full: html, text
    b8b56383b460baeded0eb044c5c50998564f4b9d Sun Jan 25 22:35:48 2026 -0800
    Initial pass at making data types optional for the new faceted composite UI. refs #36320
• src/hg/hgTracks/hgTracks.c
  • lines changed 2, context: html, text, full: html, text
    e7e155e57c9f0f1b456f614e254fe5e19d448d2b Tue Jan 20 01:43:10 2026 -0800
    changes after code review, refs #36932
  • lines changed 5, context: html, text, full: html, text
    478610d3be4abc22e330f4fbb154a2ac8ac4abfa Tue Jan 20 15:24:18 2026 -0800
    add strand filter option to oligoMatch track refs #36984 Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
  • lines changed 1, context: html, text, full: html, text
    f5623ef36caf6846ae476bdaba08e21d3ca450f3 Wed Jan 21 11:28:58 2026 -0800
    Small tweaks to the new hub error message, refs #36916
  • lines changed 1, context: html, text, full: html, text
    e6ee88658405177aee46ddb8902ae93aee5b1378 Thu Jan 22 16:36:14 2026 -0800
    Revert "changing superTrack TrackUi quite a bit. This reverts commit fcb6dc8dfa166136193177c895ca181200850e4d.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 3, context: html, text, full: html, text
    d972170022c5cbf6be7c1fdf31afba23d826608b Tue Jan 20 10:33:00 2026 -0800
    when quickLifting SQL genepreds be a little more forgiving of the alignment no RM
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    d972170022c5cbf6be7c1fdf31afba23d826608b Tue Jan 20 10:33:00 2026 -0800
    when quickLifting SQL genepreds be a little more forgiving of the alignment no RM
• src/hg/htdocs/FAQ/FAQgenes.html
  • lines changed 7, context: html, text, full: html, text
    dbed701b3a98a3c91c0e03766090dea21cc2ebb3 Wed Jan 21 10:35:18 2026 -0800
    making corrections based on CR feedback, refs #36979
  • lines changed 5, context: html, text, full: html, text
    0923e3a1c3c53c946f553f37351d262c1c6cff6f Sun Jan 25 10:20:04 2026 -0800
    minor changes from CR feedback, refs #36979
• src/hg/htdocs/goldenPath/help/assemblyHubHelp.html
  • lines changed 19, context: html, text, full: html, text
    ebe89ecc6be330409d78328e7197b4d1e956005b Sat Jan 24 17:16:39 2026 -0800
    Making some updates to the chromAuthority setting section, refs #33014
• src/hg/htdocs/goldenPath/help/decorator.html
  • lines changed 6, context: html, text, full: html, text
    b1cd59107c59752f09ae77652a11272763df1381 Mon Jan 26 06:22:15 2026 -0800
    adding feedback from Bob, no redmine ticket yet
  • lines changed 1, context: html, text, full: html, text
    9076f39d8a8cdedce400554dc22ef979d00d5a2e Mon Jan 26 06:24:28 2026 -0800
    small docs change
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 5, context: html, text, full: html, text
    50946adc9f3a5fc15fa4c3c1173eb75667ee5891 Wed Jan 21 10:36:21 2026 -0800
    adding some p tags based on CR, refs #36933
• src/hg/htdocs/goldenPath/help/mirrorManual.html
  • lines changed 26, context: html, text, full: html, text
    0f7434df22a1a4481eb046a635ae26bcee370c41 Wed Jan 21 01:40:23 2026 -0800
    small update to mirror docs page, no redmine
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 1, context: html, text, full: html, text
    e23c3cfcefbffc254b8a801b4438614c3b509cdb Wed Jan 21 11:06:45 2026 -0800
    Fixing typo in hicArcLimitEnabled explanation, refs #36774
  • lines changed 2, context: html, text, full: html, text
    fa3c1fac7c358c843ad5eef08811b8ceedbb6037 Wed Jan 21 11:10:12 2026 -0800
    Updating the defaults in documentation for the hicArcLimit settings, refs #36774
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 1, context: html, text, full: html, text
    a132ee893c70eebe3fd5b41a0e41f5fa4c7d714c Tue Jan 20 17:19:47 2026 -0800
    Feedback from CR #36976
• src/hg/htdocs/liftRequest.html
  • lines changed 1, context: html, text, full: html, text
    a7702c08f9fc16dfb900a5efecb8b5f73a9acdd7 Mon Jan 19 13:29:37 2026 -0800
    restore the default hidden already exists window and eliminate the jQuery ajax calls with the standard jScript fetch() function refs #31811
  • lines changed 32, context: html, text, full: html, text
    df57ecff435188eeafe1d9505fb7a49c5941f764 Tue Jan 20 11:50:25 2026 -0800
    correctly appear and dismiss the liftExisting box and clean up the text documentation refs #31811
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    094c4d429df5c052a59dc6414e948f31e3f8d9ee Tue Jan 20 12:00:18 2026 -0800
    grammar correction from code review refs #36974
  • lines changed 4, context: html, text, full: html, text
    c25cbdabc6bf946780a6e3c8ab5efb4f8838232b Tue Jan 20 14:14:01 2026 -0800
    only needs jquery-ui does not need jquery or jquery.plugins refs #36974
• src/hg/htdocs/style/HGStyle.css
  • lines changed 58, context: html, text, full: html, text
    e6ee88658405177aee46ddb8902ae93aee5b1378 Thu Jan 22 16:36:14 2026 -0800
    Revert "changing superTrack TrackUi quite a bit. This reverts commit fcb6dc8dfa166136193177c895ca181200850e4d.
• src/hg/htdocs/style/liftRequest.css
  • lines changed 12, context: html, text, full: html, text
    df57ecff435188eeafe1d9505fb7a49c5941f764 Tue Jan 20 11:50:25 2026 -0800
    correctly appear and dismiss the liftExisting box and clean up the text documentation refs #31811
• src/hg/hubApi/liftOver.c
  • lines changed 16, context: html, text, full: html, text
    c9604780dd0b68875f447e935e4e89eac57f183d Mon Jan 19 13:30:56 2026 -0800
    write liftRequest entry into the hgcentral.ottoRequest table refs #31811
  • lines changed 1, context: html, text, full: html, text
    b6c8b1286c213a0dabca4a0728d647b8b505ee30 Mon Jan 19 14:03:54 2026 -0800
    improved ottoRequest table structure refs #31811
  • lines changed 6, context: html, text, full: html, text
    d397ac8c2ee2defbdcf2c148f0dd5d45a5a189ac Mon Jan 19 16:38:22 2026 -0800
    add a date stamp to the email refs #31811
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    01dcc7388be432075103008e61f99892db4230d0 Tue Jan 20 12:08:04 2026 -0800
    correction from code review refs #36974
  • lines changed 1, context: html, text, full: html, text
    9661cdfa5b5385b5e1e31b2ad691f54c7795e962 Wed Jan 21 21:55:51 2026 -0800
    adding the doneStatus to the row insert into the ottoTable refs #31811
• src/hg/inc/hui.h
  • lines changed 2, context: html, text, full: html, text
    478610d3be4abc22e330f4fbb154a2ac8ac4abfa Tue Jan 20 15:24:18 2026 -0800
    add strand filter option to oligoMatch track refs #36984 Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
  • lines changed 4, context: html, text, full: html, text
    e6ee88658405177aee46ddb8902ae93aee5b1378 Thu Jan 22 16:36:14 2026 -0800
    Revert "changing superTrack TrackUi quite a bit. This reverts commit fcb6dc8dfa166136193177c895ca181200850e4d.
• src/hg/inc/ottoRequest.h
  • lines changed 86, context: html, text, full: html, text
    73df4b22477525c05614cff79595806231dd64ed Mon Jan 19 14:03:15 2026 -0800
    starting the hgcentral table ottoRequest to record lift over request refs #31811
  • lines changed 3, context: html, text, full: html, text
    cf91694df806cf52913c294e6d2cf0452373f8fc Wed Jan 21 21:45:19 2026 -0800
    add a doneStatus and a completeTime elements to the table definition refs #31811
• src/hg/js/facetedComposite.js
  • lines changed 2, context: html, text, full: html, text
    5f99b76015eefbb14a2ac75ddcb56f8c1e17ca65 Wed Jan 21 00:01:19 2026 -0800
    Changes provided by Andrew Smith to tidy up the new composite UI, refs #36320
  • lines changed 25, context: html, text, full: html, text
    b8b56383b460baeded0eb044c5c50998564f4b9d Sun Jan 25 22:35:48 2026 -0800
    Initial pass at making data types optional for the new faceted composite UI. refs #36320
• src/hg/js/hgMyData.js
  • lines changed 6, context: html, text, full: html, text
    77351c0fa18c6b8da672a097790a1533c068b119 Tue Jan 20 15:20:10 2026 -0800
    cheapcgi.c:cgiEncode() encodes space to +, so we need to do the same in javascript, refs Max email
  • lines changed 4, context: html, text, full: html, text
    4f1f8506b8f8ad9e83f484032bab80866b9c6cd3 Tue Jan 20 15:58:57 2026 -0800
    Ensure hubUrl= links get encoded when the hubSpace UI generates them. userNames with spaces are encoded to '+' signs by cgiEncode, which need to be encoded to %2B so it will survive a cgiDecode by hgTracks later, so we not only encode space to '+' first, we then encode the '+' itself.
  • lines changed 87, context: html, text, full: html, text
    c6d419ecfb6f122d7a0cb99c37f56c32c089bea3 Thu Jan 22 10:41:38 2026 -0800
    HubSpace changes: Allow users to overwrite already uploaded files, but warn them first. When a hub.txt file is being uploaded, don't auto-generate one. Check if the tracks being uploaded already exist in the hub.txt before adding a default stanza for it. Add some more checks in the hook files to prevent faulty uploads. Have the tus client clear localStorage on successful uploads so re-uploads of the same file don't cause confusing errors
• src/hg/js/liftRequest.js
  • lines changed 63, context: html, text, full: html, text
    a7702c08f9fc16dfb900a5efecb8b5f73a9acdd7 Mon Jan 19 13:29:37 2026 -0800
    restore the default hidden already exists window and eliminate the jQuery ajax calls with the standard jScript fetch() function refs #31811
  • lines changed 21, context: html, text, full: html, text
    df57ecff435188eeafe1d9505fb7a49c5941f764 Tue Jan 20 11:50:25 2026 -0800
    correctly appear and dismiss the liftExisting box and clean up the text documentation refs #31811
• src/hg/js/tutorials/tutorialPopup.js
  • lines changed 1, context: html, text, full: html, text
    6e0f2a0aadf0ce61590fd13d801956fcc7c468b1 Wed Jan 21 16:36:31 2026 -0800
    Fixing a typo for the custom track tutorial text in the popup. The tutorial is only available for hg19, but the description says hg38, refs #34354
• src/hg/js/utils.js
  • lines changed 4, context: html, text, full: html, text
    e6ee88658405177aee46ddb8902ae93aee5b1378 Thu Jan 22 16:36:14 2026 -0800
    Revert "changing superTrack TrackUi quite a bit. This reverts commit fcb6dc8dfa166136193177c895ca181200850e4d.
• src/hg/lib/botDelay.c
  • lines changed 22, context: html, text, full: html, text
    51d5e2f822a1f5333d2b4c91a0eff20980900768 Thu Jan 22 17:13:45 2026 -0800
    botDelay needs to explain that it failed to connect to the bottleneck server so that we know what to fix when it happens, refs #36992
• src/hg/lib/hubSpace.c
  • lines changed 6, context: html, text, full: html, text
    c6d419ecfb6f122d7a0cb99c37f56c32c089bea3 Thu Jan 22 10:41:38 2026 -0800
    HubSpace changes: Allow users to overwrite already uploaded files, but warn them first. When a hub.txt file is being uploaded, don't auto-generate one. Check if the tracks being uploaded already exist in the hub.txt before adding a default stanza for it. Add some more checks in the hook files to prevent faulty uploads. Have the tus client clear localStorage on successful uploads so re-uploads of the same file don't cause confusing errors
• src/hg/lib/hui.c
  • lines changed 47, context: html, text, full: html, text
    e6ee88658405177aee46ddb8902ae93aee5b1378 Thu Jan 22 16:36:14 2026 -0800
    Revert "changing superTrack TrackUi quite a bit. This reverts commit fcb6dc8dfa166136193177c895ca181200850e4d.
• src/hg/lib/ottoRequest.as
  • lines changed 11, context: html, text, full: html, text
    73df4b22477525c05614cff79595806231dd64ed Mon Jan 19 14:03:15 2026 -0800
    starting the hgcentral table ottoRequest to record lift over request refs #31811
  • lines changed 2, context: html, text, full: html, text
    cf91694df806cf52913c294e6d2cf0452373f8fc Wed Jan 21 21:45:19 2026 -0800
    add a doneStatus and a completeTime elements to the table definition refs #31811
• src/hg/lib/ottoRequest.c
  • lines changed 243, context: html, text, full: html, text
    73df4b22477525c05614cff79595806231dd64ed Mon Jan 19 14:03:15 2026 -0800
    starting the hgcentral table ottoRequest to record lift over request refs #31811
  • lines changed 32, context: html, text, full: html, text
    cf91694df806cf52913c294e6d2cf0452373f8fc Wed Jan 21 21:45:19 2026 -0800
    add a doneStatus and a completeTime elements to the table definition refs #31811
• src/hg/lib/ottoRequest.sql
  • lines changed 16, context: html, text, full: html, text
    73df4b22477525c05614cff79595806231dd64ed Mon Jan 19 14:03:15 2026 -0800
    starting the hgcentral table ottoRequest to record lift over request refs #31811
  • lines changed 2, context: html, text, full: html, text
    cf91694df806cf52913c294e6d2cf0452373f8fc Wed Jan 21 21:45:19 2026 -0800
    add a doneStatus and a completeTime elements to the table definition refs #31811
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    390353c4fea824e8431fd1e6b4a5fa660ed9e14f Wed Jan 21 21:53:13 2026 -0800
    completeTime should be default null and add indexes on doneStatus and requestTime change comment to longtext from longblob refs #31811
• src/hg/lib/trackDbCustom.c
  • lines changed 7, context: html, text, full: html, text
    b62b7ebcba1539338903f821930af33f823a1513 Wed Jan 21 13:18:29 2026 -0800
    enable bigBeds with 3 or 4 fields to still use bigBed filters refs #28501
• src/hg/lib/userdata.c
  • lines changed 43, context: html, text, full: html, text
    c6d419ecfb6f122d7a0cb99c37f56c32c089bea3 Thu Jan 22 10:41:38 2026 -0800
    HubSpace changes: Allow users to overwrite already uploaded files, but warn them first. When a hub.txt file is being uploaded, don't auto-generate one. Check if the tracks being uploaded already exist in the hub.txt before adding a default stanza for it. Add some more checks in the hook files to prevent faulty uploads. Have the tus client clear localStorage on successful uploads so re-uploads of the same file don't cause confusing errors
• src/hg/makeDb/doc/asmHubs/quickLiftCatchUp.sh
  • lines changed 14, context: html, text, full: html, text
    a4984ed4a91768bac66cecaf7593bc0b7fca453f Mon Jan 19 14:12:05 2026 -0800
    correctly recognize files in a blat directory refs #35575
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    c40b817e7eb787c9242a7d0ecacc99663ee8ee31 Thu Jan 22 18:18:10 2026 -0800
    adding some per user requests refs #29545
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    c40b817e7eb787c9242a7d0ecacc99663ee8ee31 Thu Jan 22 18:18:10 2026 -0800
    adding some per user requests refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 1, context: html, text, full: html, text
    033456bc068a20c98d73f74ec366dbdf8a01000e Mon Jan 19 14:13:07 2026 -0800
    NCBI name change for GCA_018852605.2 refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 6, context: html, text, full: html, text
    c40b817e7eb787c9242a7d0ecacc99663ee8ee31 Thu Jan 22 18:18:10 2026 -0800
    adding some per user requests refs #29545
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    c40b817e7eb787c9242a7d0ecacc99663ee8ee31 Thu Jan 22 18:18:10 2026 -0800
    adding some per user requests refs #29545
• src/hg/makeDb/scripts/hgmd/process_hgmd.py
  • lines changed 57, context: html, text, full: html, text
    aea35b33f28e89b22c07ba448a5659b9ca6c5fb8 Sat Jan 24 16:44:26 2026 -0800
    Updating script so it now automatically detects and uses the most recent ncbiRefSeq patch version available (p15, p14, p13, etc.), refs #36779
• src/hg/makeDb/trackDb/human/varFreqs.html
  • lines changed 4, context: html, text, full: html, text
    ad032e072d0427c066c425a88672288ed1b6c133 Wed Jan 21 08:13:31 2026 -0800
    fixes after code review and feedback from mark, refs #36978, and refs #36917
• src/hg/utils/automation/HgAutomate.pm
  • lines changed 8, context: html, text, full: html, text
    984d172a4eb5f434baa386930496e6af3289c4c8 Sat Jan 24 08:17:32 2026 -0800
    better detection of busy/idle nodes
• src/hg/utils/bigChainToChain/bigChainToChain.c
  • lines changed 89, context: html, text, full: html, text
    c17649d6f7028b83bad1bca0f64ac9d7ba834691 Tue Jan 20 16:40:40 2026 -0800
    Fixes from code review for utils bigMafToMaf bigBedToBed. Added routines to shared library bigBedCmdSupport. Added code to the other utilities bigChainToChain bigGenePredToGenePred bigPslToPsl bigWigToBedGraph bigWigToWig. refs #28109, 36925
• src/hg/utils/bigGenePredToGenePred/bigGenePredToGenePred.c
  • lines changed 86, context: html, text, full: html, text
    c17649d6f7028b83bad1bca0f64ac9d7ba834691 Tue Jan 20 16:40:40 2026 -0800
    Fixes from code review for utils bigMafToMaf bigBedToBed. Added routines to shared library bigBedCmdSupport. Added code to the other utilities bigChainToChain bigGenePredToGenePred bigPslToPsl bigWigToBedGraph bigWigToWig. refs #28109, 36925
• src/hg/utils/bigMafToMaf/bigMafToMaf.c
  • lines changed 71, context: html, text, full: html, text
    c17649d6f7028b83bad1bca0f64ac9d7ba834691 Tue Jan 20 16:40:40 2026 -0800
    Fixes from code review for utils bigMafToMaf bigBedToBed. Added routines to shared library bigBedCmdSupport. Added code to the other utilities bigChainToChain bigGenePredToGenePred bigPslToPsl bigWigToBedGraph bigWigToWig. refs #28109, 36925
• src/hg/utils/bigPslToPsl/bigPslToPsl.c
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    c17649d6f7028b83bad1bca0f64ac9d7ba834691 Tue Jan 20 16:40:40 2026 -0800
    Fixes from code review for utils bigMafToMaf bigBedToBed. Added routines to shared library bigBedCmdSupport. Added code to the other utilities bigChainToChain bigGenePredToGenePred bigPslToPsl bigWigToBedGraph bigWigToWig. refs #28109, 36925
• src/inc/bigBedCmdSupport.h
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    c17649d6f7028b83bad1bca0f64ac9d7ba834691 Tue Jan 20 16:40:40 2026 -0800
    Fixes from code review for utils bigMafToMaf bigBedToBed. Added routines to shared library bigBedCmdSupport. Added code to the other utilities bigChainToChain bigGenePredToGenePred bigPslToPsl bigWigToBedGraph bigWigToWig. refs #28109, 36925
• src/inc/cheapcgi.h
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    e6ee88658405177aee46ddb8902ae93aee5b1378 Thu Jan 22 16:36:14 2026 -0800
    Revert "changing superTrack TrackUi quite a bit. This reverts commit fcb6dc8dfa166136193177c895ca181200850e4d.
• src/inc/common.h
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    e6ee88658405177aee46ddb8902ae93aee5b1378 Thu Jan 22 16:36:14 2026 -0800
    Revert "changing superTrack TrackUi quite a bit. This reverts commit fcb6dc8dfa166136193177c895ca181200850e4d.
• src/lib/bigBedCmdSupport.c
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    c17649d6f7028b83bad1bca0f64ac9d7ba834691 Tue Jan 20 16:40:40 2026 -0800
    Fixes from code review for utils bigMafToMaf bigBedToBed. Added routines to shared library bigBedCmdSupport. Added code to the other utilities bigChainToChain bigGenePredToGenePred bigPslToPsl bigWigToBedGraph bigWigToWig. refs #28109, 36925
• src/lib/cheapcgi.c
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    e6ee88658405177aee46ddb8902ae93aee5b1378 Thu Jan 22 16:36:14 2026 -0800
    Revert "changing superTrack TrackUi quite a bit. This reverts commit fcb6dc8dfa166136193177c895ca181200850e4d.
• src/lib/common.c
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    e6ee88658405177aee46ddb8902ae93aee5b1378 Thu Jan 22 16:36:14 2026 -0800
    Revert "changing superTrack TrackUi quite a bit. This reverts commit fcb6dc8dfa166136193177c895ca181200850e4d.
• src/product/mirrorManual.txt
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    0f7434df22a1a4481eb046a635ae26bcee370c41 Wed Jan 21 01:40:23 2026 -0800
    small update to mirror docs page, no redmine
• src/userApps/fetchKentSource.sh
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    dbfd9531e33085b16b29ad64e16b6fe0becb6c8b Mon Jan 19 14:09:18 2026 -0800
    show the du -hsc measurement of the kent source code checked out
• src/utils/bigBedToBed/bigBedToBed.c
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    c17649d6f7028b83bad1bca0f64ac9d7ba834691 Tue Jan 20 16:40:40 2026 -0800
    Fixes from code review for utils bigMafToMaf bigBedToBed. Added routines to shared library bigBedCmdSupport. Added code to the other utilities bigChainToChain bigGenePredToGenePred bigPslToPsl bigWigToBedGraph bigWigToWig. refs #28109, 36925
• src/utils/bigWigToBedGraph/bigWigToBedGraph.c
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    c17649d6f7028b83bad1bca0f64ac9d7ba834691 Tue Jan 20 16:40:40 2026 -0800
    Fixes from code review for utils bigMafToMaf bigBedToBed. Added routines to shared library bigBedCmdSupport. Added code to the other utilities bigChainToChain bigGenePredToGenePred bigPslToPsl bigWigToBedGraph bigWigToWig. refs #28109, 36925
• src/utils/bigWigToWig/bigWigToWig.c
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    c17649d6f7028b83bad1bca0f64ac9d7ba834691 Tue Jan 20 16:40:40 2026 -0800
    Fixes from code review for utils bigMafToMaf bigBedToBed. Added routines to shared library bigBedCmdSupport. Added code to the other utilities bigChainToChain bigGenePredToGenePred bigPslToPsl bigWigToBedGraph bigWigToWig. refs #28109, 36925
• src/utils/qa/qaTestScript.py
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    d0087461767a481a8eac755b42126bf3b796d3b9 Sun Jan 25 13:48:32 2026 -0800
    Adding GenArk (GCF_014441545.1) Table Browser test case that came up in a build patch, refs #36937

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• files changed: 93