All File Changes

v493_preview to v493_preview2 (2026-01-12 to 2026-01-19) v493

• confs/asia.hg.conf
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    619ca05f585205e93e72e2703685a5a9efad6c17 Sun Jan 18 01:11:19 2026 -0800
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 1, context: html, text, full: html, text
    619ca05f585205e93e72e2703685a5a9efad6c17 Sun Jan 18 01:11:19 2026 -0800
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
  • lines changed 1, context: html, text, full: html, text
    619ca05f585205e93e72e2703685a5a9efad6c17 Sun Jan 18 01:11:19 2026 -0800
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 1, context: html, text, full: html, text
    619ca05f585205e93e72e2703685a5a9efad6c17 Sun Jan 18 01:11:19 2026 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/hgGateway/hgGateway.html
  • lines changed 1, context: html, text, full: html, text
    60289f7d3a6cb349a7608d07dbcf2a092c3cd27f Wed Jan 14 11:35:54 2026 -0800
    Fix span to be a closing tag, pointed out by code review, refs #36813
• src/hg/hgTables/pal.c
  • lines changed 1, context: html, text, full: html, text
    ac25efe0149be547d5ed2ef57feeb584f04ab64e Tue Jan 13 12:54:56 2026 -0800
    Revert "Allows bigGenePred to used like genePred and provide CDS FASTA output from Table Browser. fixes #34712" This reverts commit 22d5ed169d378a1fbc1b5f76488771be106c9b1f. This was failing for genbank dog assembly GCF_014441545.1 and augustus track with bigGenePred type. Alas We do not have a quick fix available.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 72, context: html, text, full: html, text
    fcb6dc8dfa166136193177c895ca181200850e4d Mon Jan 19 06:02:31 2026 -0800
    changing superTrack TrackUi quite a bit. Removing dropdowns and replacing them with buttons. Also adding buttons for setting all tracks or all visible tracks to a visibility. While at it, making a change to the js-query-library function (inversed the order of arguments) which was requested months ago by Brian, but I forgot to make the change after code review. Also shortening the "source data version" label to just "version". refs #36917. I changed the library function hTvDropDownClassVisOnlyAndExtra() rather than copying the code. This was because I was hesitant to copy/paste all this code into a second function, which would have been the only alternative, as the function cannot be reused as-is. So I modified the function to return the list of visibilities. It's never clear whether it's better to modify functions or copy/paste code. here, not breaking the function into smaller parts, so copy/pasting it, would risk requiring more future copy/pasted code. But the risk is to break existing tracks.
• src/hg/hgTracks/bigBedTrack.c
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    adc2acdfe8380d7db963b023106b6b33afae77c7 Fri Jan 16 15:18:26 2026 -0800
    make bigBedOnePath be on by default
• src/hg/hgTracks/config.c
  • lines changed 1, context: html, text, full: html, text
    12947e6dc054b98b4bb372cf381b40169638aa65 Thu Jan 15 14:44:26 2026 -0800
    Make ability to do hgc in popups on by default, still need the cart variable doHgcInPopUp (which also defaults to true) to control whether the popup actually shows up, refs #36953
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    4f8248a37b7dafb77e84f0c40d7b0152d296269f Thu Jan 15 14:41:56 2026 -0800
    Make grey bar icons default to always on, refs #36956
  • lines changed 2, context: html, text, full: html, text
    12947e6dc054b98b4bb372cf381b40169638aa65 Thu Jan 15 14:44:26 2026 -0800
    Make ability to do hgc in popups on by default, still need the cart variable doHgcInPopUp (which also defaults to true) to control whether the popup actually shows up, refs #36953
  • lines changed 1, context: html, text, full: html, text
    fcb6dc8dfa166136193177c895ca181200850e4d Mon Jan 19 06:02:31 2026 -0800
    changing superTrack TrackUi quite a bit. Removing dropdowns and replacing them with buttons. Also adding buttons for setting all tracks or all visible tracks to a visibility. While at it, making a change to the js-query-library function (inversed the order of arguments) which was requested months ago by Brian, but I forgot to make the change after code review. Also shortening the "source data version" label to just "version". refs #36917. I changed the library function hTvDropDownClassVisOnlyAndExtra() rather than copying the code. This was because I was hesitant to copy/paste all this code into a second function, which would have been the only alternative, as the function cannot be reused as-is. So I modified the function to return the list of visibilities. It's never clear whether it's better to modify functions or copy/paste code. here, not breaking the function into smaller parts, so copy/pasting it, would risk requiring more future copy/pasted code. But the risk is to break existing tracks.
• src/hg/hgTracks/imageV2.c
  • lines changed 3, context: html, text, full: html, text
    4f8248a37b7dafb77e84f0c40d7b0152d296269f Thu Jan 15 14:41:56 2026 -0800
    Make grey bar icons default to always on, refs #36956
• src/hg/hgTracks/simpleTracks.c
  • lines changed 12, context: html, text, full: html, text
    a733eb4377d20aad86d9e1b3657b00da2f9028fe Sat Jan 17 10:42:42 2026 -0800
    when quicklifting a genePred we need to reverse the exon frames if the strand changed
• src/hg/hgc/bigBedClick.c
  • lines changed 1, context: html, text, full: html, text
    adc2acdfe8380d7db963b023106b6b33afae77c7 Fri Jan 16 15:18:26 2026 -0800
    make bigBedOnePath be on by default
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    adc2acdfe8380d7db963b023106b6b33afae77c7 Fri Jan 16 15:18:26 2026 -0800
    make bigBedOnePath be on by default
• src/hg/htdocs/FAQ/FAQgenes.html
  • lines changed 57, context: html, text, full: html, text
    b714e3aa69abe5d109c72ca504240dece8d42666 Wed Jan 14 14:00:02 2026 -0800
    adding faq about exonFrame info in bed output, refs #24545
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 2, context: html, text, full: html, text
    6652018d9b67df1a64de3b9c6652bea0a3577532 Sun Jan 18 16:24:11 2026 -0800
    adding link to hub basics to page; changing trackDb definition page to relative link, refs #28347
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.js
  • lines changed 1, context: html, text, full: html, text
    2d7947d2ce33c3bc8515d2cd5fda05785e3dab44 Tue Jan 13 12:55:01 2026 -0800
    Fix bug in trackDbDoc searching where processed searched elements does not reset in between searches, refs #36831
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 113, context: html, text, full: html, text
    f29825cc3b3ce2c55f8aeb5b4756aa960f9905b2 Wed Jan 14 14:00:36 2026 -0800
    Releasing and announcing the new ENCODE4 cCREs track, refs #34109
• src/hg/htdocs/images/encode4cCREsNews.png
  • lines changed 0, context: html, text, full: html, text
    f29825cc3b3ce2c55f8aeb5b4756aa960f9905b2 Wed Jan 14 14:00:36 2026 -0800
    Releasing and announcing the new ENCODE4 cCREs track, refs #34109
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    f29825cc3b3ce2c55f8aeb5b4756aa960f9905b2 Wed Jan 14 14:00:36 2026 -0800
    Releasing and announcing the new ENCODE4 cCREs track, refs #34109
• src/hg/htdocs/liftRequest.html
  • lines changed 91, context: html, text, full: html, text
    5b211c300c02e8db4a5b4daedb1711122d9321d3 Fri Jan 16 11:47:18 2026 -0800
    initial content for the liftRequest function refs #31811
  • lines changed 10, context: html, text, full: html, text
    55c5be8236794e23ce8b00162917b5d3dbe83b7e Fri Jan 16 16:37:31 2026 -0800
    now checking for lift over existing and providing a download link refs #31811
  • lines changed 5, context: html, text, full: html, text
    0fd7a3dbdc484ff5bb2dd54193b5320e32bb6515 Sat Jan 17 15:53:54 2026 -0800
    correctly validates and saves email address to localStorage and gets back to hgGateway properly refs #31811
  • lines changed 15, context: html, text, full: html, text
    679ee3ed1c4d6f8ff2e2d4fdd7d72b83117c7c49 Sun Jan 18 22:12:13 2026 -0800
    provide links to browsers as well as lift over chain.gz files refs #31811
• src/hg/htdocs/style/HGStyle.css
  • lines changed 58, context: html, text, full: html, text
    fcb6dc8dfa166136193177c895ca181200850e4d Mon Jan 19 06:02:31 2026 -0800
    changing superTrack TrackUi quite a bit. Removing dropdowns and replacing them with buttons. Also adding buttons for setting all tracks or all visible tracks to a visibility. While at it, making a change to the js-query-library function (inversed the order of arguments) which was requested months ago by Brian, but I forgot to make the change after code review. Also shortening the "source data version" label to just "version". refs #36917. I changed the library function hTvDropDownClassVisOnlyAndExtra() rather than copying the code. This was because I was hesitant to copy/paste all this code into a second function, which would have been the only alternative, as the function cannot be reused as-is. So I modified the function to return the list of visibilities. It's never clear whether it's better to modify functions or copy/paste code. here, not breaking the function into smaller parts, so copy/pasting it, would risk requiring more future copy/pasted code. But the risk is to break existing tracks.
• src/hg/htdocs/style/liftRequest.css
  • lines changed 153, context: html, text, full: html, text
    5b211c300c02e8db4a5b4daedb1711122d9321d3 Fri Jan 16 11:47:18 2026 -0800
    initial content for the liftRequest function refs #31811
  • lines changed 8, context: html, text, full: html, text
    55c5be8236794e23ce8b00162917b5d3dbe83b7e Fri Jan 16 16:37:31 2026 -0800
    now checking for lift over existing and providing a download link refs #31811
• src/hg/hubApi/assemblyList.py
  • lines changed 14, context: html, text, full: html, text
    e4de17f9d12ae21128dc2c366297eb004b85c124 Sat Jan 17 09:43:34 2026 -0800
    adding more database assemblies to the topPriorities list refs #31811
• src/hg/hubApi/dataApi.h
  • lines changed 10, context: html, text, full: html, text
    16a4a0cbcbf56172a2e2e35dfe20c541d9cc46d7 Wed Jan 14 16:49:35 2026 -0800
    starting a liftRequest endpoint refs #31811
• src/hg/hubApi/genomePriority.py
  • lines changed 14, context: html, text, full: html, text
    3c238d1c5a14d3cc542bca1b3f059601d5f446aa Sat Jan 17 09:41:35 2026 -0800
    adding more database assemblies to the topPriorities list refs #31811
• src/hg/hubApi/hubApi.c
  • lines changed 2, context: html, text, full: html, text
    16a4a0cbcbf56172a2e2e35dfe20c541d9cc46d7 Wed Jan 14 16:49:35 2026 -0800
    starting a liftRequest endpoint refs #31811
• src/hg/hubApi/liftOver.c
  • lines changed 48, context: html, text, full: html, text
    16a4a0cbcbf56172a2e2e35dfe20c541d9cc46d7 Wed Jan 14 16:49:35 2026 -0800
    starting a liftRequest endpoint refs #31811
  • lines changed 2, context: html, text, full: html, text
    980804e6eacb85cb2f60ac064468eb307fe448d0 Wed Jan 14 16:57:26 2026 -0800
    starting a liftRequest endpoint refs #31811
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    d8e2f99f9cb8144a0a1c22cfe006d90241ada655 Thu Jan 15 12:27:30 2026 -0800
    testing connection to the branch libifyGenomeSearchBar refs #31811
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    d77dd5f4290f80a6212625afb08378b6c9a60a59 Thu Jan 15 15:33:03 2026 -0800
    now sending email to the google group but so far do not see it received there refs #31811
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    440a9e30c2a40cb5eced221d6512dd94471151c5 Fri Jan 16 11:44:57 2026 -0800
    using configuration specifications from hg.conf for the email addresses to and from for the chain request refs #31811
• src/hg/hubApi/tests/expected/list23.gz
  • lines changed 0, context: html, text, full: html, text
    b8c48272f7658078ce2e082c53ccd85cf6bade50 Mon Jan 19 09:17:04 2026 -0800
    swapping human genark genome out for a random virus
• src/hg/hubApi/tests/makefile
  • lines changed 3, context: html, text, full: html, text
    b8c48272f7658078ce2e082c53ccd85cf6bade50 Mon Jan 19 09:17:04 2026 -0800
    swapping human genark genome out for a random virus
• src/hg/inc/genePred.h
  • lines changed 1, context: html, text, full: html, text
    a733eb4377d20aad86d9e1b3657b00da2f9028fe Sat Jan 17 10:42:42 2026 -0800
    when quicklifting a genePred we need to reverse the exon frames if the strand changed
• src/hg/inc/hicUi.h
  • lines changed 7, context: html, text, full: html, text
    aaf862066887971c08f4fb632fff365a2d453450 Tue Jan 13 23:09:13 2026 -0800
    Changing Hi-C arc limit default to 10000 and turning it on by default, also correcting a typo. refs #36774
• src/hg/inc/hui.h
  • lines changed 4, context: html, text, full: html, text
    fcb6dc8dfa166136193177c895ca181200850e4d Mon Jan 19 06:02:31 2026 -0800
    changing superTrack TrackUi quite a bit. Removing dropdowns and replacing them with buttons. Also adding buttons for setting all tracks or all visible tracks to a visibility. While at it, making a change to the js-query-library function (inversed the order of arguments) which was requested months ago by Brian, but I forgot to make the change after code review. Also shortening the "source data version" label to just "version". refs #36917. I changed the library function hTvDropDownClassVisOnlyAndExtra() rather than copying the code. This was because I was hesitant to copy/paste all this code into a second function, which would have been the only alternative, as the function cannot be reused as-is. So I modified the function to return the list of visibilities. It's never clear whether it's better to modify functions or copy/paste code. here, not breaking the function into smaller parts, so copy/pasting it, would risk requiring more future copy/pasted code. But the risk is to break existing tracks.
• src/hg/js/liftRequest.js
  • lines changed 93, context: html, text, full: html, text
    5b211c300c02e8db4a5b4daedb1711122d9321d3 Fri Jan 16 11:47:18 2026 -0800
    initial content for the liftRequest function refs #31811
  • lines changed 70, context: html, text, full: html, text
    55c5be8236794e23ce8b00162917b5d3dbe83b7e Fri Jan 16 16:37:31 2026 -0800
    now checking for lift over existing and providing a download link refs #31811
  • lines changed 48, context: html, text, full: html, text
    0fd7a3dbdc484ff5bb2dd54193b5320e32bb6515 Sat Jan 17 15:53:54 2026 -0800
    correctly validates and saves email address to localStorage and gets back to hgGateway properly refs #31811
  • lines changed 26, context: html, text, full: html, text
    679ee3ed1c4d6f8ff2e2d4fdd7d72b83117c7c49 Sun Jan 18 22:12:13 2026 -0800
    provide links to browsers as well as lift over chain.gz files refs #31811
• src/hg/js/utils.js
  • lines changed 4, context: html, text, full: html, text
    fcb6dc8dfa166136193177c895ca181200850e4d Mon Jan 19 06:02:31 2026 -0800
    changing superTrack TrackUi quite a bit. Removing dropdowns and replacing them with buttons. Also adding buttons for setting all tracks or all visible tracks to a visibility. While at it, making a change to the js-query-library function (inversed the order of arguments) which was requested months ago by Brian, but I forgot to make the change after code review. Also shortening the "source data version" label to just "version". refs #36917. I changed the library function hTvDropDownClassVisOnlyAndExtra() rather than copying the code. This was because I was hesitant to copy/paste all this code into a second function, which would have been the only alternative, as the function cannot be reused as-is. So I modified the function to return the list of visibilities. It's never clear whether it's better to modify functions or copy/paste code. here, not breaking the function into smaller parts, so copy/pasting it, would risk requiring more future copy/pasted code. But the risk is to break existing tracks.
• src/hg/lib/botDelay.c
  • lines changed 1, context: html, text, full: html, text
    8b35afcffcef1574bcf91ed352c660033929ee74 Thu Jan 15 12:21:33 2026 -0800
    Setting the new botdelay scheme (which we've been using for a while) to be the default, refs #36952
• src/hg/lib/hicUi.c
  • lines changed 5, context: html, text, full: html, text
    aaf862066887971c08f4fb632fff365a2d453450 Tue Jan 13 23:09:13 2026 -0800
    Changing Hi-C arc limit default to 10000 and turning it on by default, also correcting a typo. refs #36774
• src/hg/lib/hubConnect.c
  • lines changed 1, context: html, text, full: html, text
    3563a2ab31f9158639b47e035780088637ac0556 Sun Jan 18 16:56:09 2026 -0800
    make trackHubsCanAddGroups on by default refs #36955
• src/hg/lib/hui.c
  • lines changed 47, context: html, text, full: html, text
    fcb6dc8dfa166136193177c895ca181200850e4d Mon Jan 19 06:02:31 2026 -0800
    changing superTrack TrackUi quite a bit. Removing dropdowns and replacing them with buttons. Also adding buttons for setting all tracks or all visible tracks to a visibility. While at it, making a change to the js-query-library function (inversed the order of arguments) which was requested months ago by Brian, but I forgot to make the change after code review. Also shortening the "source data version" label to just "version". refs #36917. I changed the library function hTvDropDownClassVisOnlyAndExtra() rather than copying the code. This was because I was hesitant to copy/paste all this code into a second function, which would have been the only alternative, as the function cannot be reused as-is. So I modified the function to return the list of visibilities. It's never clear whether it's better to modify functions or copy/paste code. here, not breaking the function into smaller parts, so copy/pasting it, would risk requiring more future copy/pasted code. But the risk is to break existing tracks.
• src/hg/lib/liftOver.c
  • lines changed 1, context: html, text, full: html, text
    a733eb4377d20aad86d9e1b3657b00da2f9028fe Sat Jan 17 10:42:42 2026 -0800
    when quicklifting a genePred we need to reverse the exon frames if the strand changed
• src/hg/makeDb/doc/hg19.txt
  • lines changed 39, context: html, text, full: html, text
    af06f485943b58470dccd7c832b97042f0c8ddb8 Sun Jan 18 21:44:31 2026 -0800
    Adding process_hgmd.py script, updating makedoc, and updating the hgmd track, refs #36779
• src/hg/makeDb/doc/hg38/hgmd.txt
  • lines changed 37, context: html, text, full: html, text
    af06f485943b58470dccd7c832b97042f0c8ddb8 Sun Jan 18 21:44:31 2026 -0800
    Adding process_hgmd.py script, updating makedoc, and updating the hgmd track, refs #36779
• src/hg/makeDb/doc/hg38/ncbiRefSeq.txt
  • lines changed 1, context: html, text, full: html, text
    af06f485943b58470dccd7c832b97042f0c8ddb8 Sun Jan 18 21:44:31 2026 -0800
    Adding process_hgmd.py script, updating makedoc, and updating the hgmd track, refs #36779
• src/hg/makeDb/doc/hg38/varFreqs.txt
  • lines changed 13, context: html, text, full: html, text
    c7b6da0a433f53fdf3c4137a67598d099d9ce1a5 Wed Jan 14 10:52:53 2026 -0800
    adding SFARI SPARK to varFreqs supertrack, refs #36642
• src/hg/makeDb/scripts/hgmd/process_hgmd.py
  • lines changed 423, context: html, text, full: html, text
    af06f485943b58470dccd7c832b97042f0c8ddb8 Sun Jan 18 21:44:31 2026 -0800
    Adding process_hgmd.py script, updating makedoc, and updating the hgmd track, refs #36779
• src/hg/makeDb/scripts/sparkMergeVcfAddCounts.sh
  • lines changed 74, context: html, text, full: html, text
    c7b6da0a433f53fdf3c4137a67598d099d9ce1a5 Wed Jan 14 10:52:53 2026 -0800
    adding SFARI SPARK to varFreqs supertrack, refs #36642
• src/hg/makeDb/trackDb/human/hg38/clsLongReadRna.html
  • lines changed 4, context: html, text, full: html, text
    c6b77b666eeacc402d28f9d9585458e7960d70a5 Wed Jan 14 17:32:42 2026 -0800
    Capitalizing and fixing the referenced gene models to reference the correct mouse release vs. the human GENCODE release on both. Refs #36908
• src/hg/makeDb/trackDb/human/hg38/coreCollection.html
  • lines changed 0, context: html, text, full: html, text
    be656b407a11f725049772fdd55761c3b20ce940 Wed Jan 14 13:57:40 2026 -0800
    Fixing small typo in track description page, refs #34109
• src/hg/makeDb/trackDb/human/hg38/encode.cCREs.override.ra
  • lines changed 2, context: html, text, full: html, text
    f29825cc3b3ce2c55f8aeb5b4756aa960f9905b2 Wed Jan 14 14:00:36 2026 -0800
    Releasing and announcing the new ENCODE4 cCREs track, refs #34109
• src/hg/makeDb/trackDb/human/hg38/encode3.ra
  • lines changed 4, context: html, text, full: html, text
    cc483764d1a461b7e918c18847e0d5a03eba537a Tue Jan 13 16:20:20 2026 -0800
    Releasing the cCREs track, refs #34109
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    cc483764d1a461b7e918c18847e0d5a03eba537a Tue Jan 13 16:20:20 2026 -0800
    Releasing the cCREs track, refs #34109
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    af06f485943b58470dccd7c832b97042f0c8ddb8 Sun Jan 18 21:44:31 2026 -0800
    Adding process_hgmd.py script, updating makedoc, and updating the hgmd track, refs #36779
• src/hg/makeDb/trackDb/human/varFreqs.html
  • lines changed 120, context: html, text, full: html, text
    c7b6da0a433f53fdf3c4137a67598d099d9ce1a5 Wed Jan 14 10:52:53 2026 -0800
    adding SFARI SPARK to varFreqs supertrack, refs #36642
• src/hg/makeDb/trackDb/human/varFreqs.ra
  • lines changed 11, context: html, text, full: html, text
    c7b6da0a433f53fdf3c4137a67598d099d9ce1a5 Wed Jan 14 10:52:53 2026 -0800
    adding SFARI SPARK to varFreqs supertrack, refs #36642
• src/hg/makeDb/trackDb/mouse/mm10/clsLongReadRna.html
  • lines changed 5, context: html, text, full: html, text
    c6b77b666eeacc402d28f9d9585458e7960d70a5 Wed Jan 14 17:32:42 2026 -0800
    Capitalizing and fixing the referenced gene models to reference the correct mouse release vs. the human GENCODE release on both. Refs #36908
• src/hg/makeDb/trackDb/trackDb.cCREs.alpha.ra
  • lines changed 20, context: html, text, full: html, text
    cc483764d1a461b7e918c18847e0d5a03eba537a Tue Jan 13 16:20:20 2026 -0800
    Releasing the cCREs track, refs #34109
• src/hg/makeDb/trackDb/trackDb.encode3.ra
  • lines changed 2, context: html, text, full: html, text
    cc483764d1a461b7e918c18847e0d5a03eba537a Tue Jan 13 16:20:20 2026 -0800
    Releasing the cCREs track, refs #34109
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    cc483764d1a461b7e918c18847e0d5a03eba537a Tue Jan 13 16:20:20 2026 -0800
    Releasing the cCREs track, refs #34109
• src/hg/pslStats/pslStats.c
  • lines changed 5, context: html, text, full: html, text
    e86128cfb99722359894e3997b13b58783ca68ae Sat Jan 17 14:31:01 2026 -0800
    add number of aligned bases and alignment span
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    12fba0b2e8b85a7f3351a05dc0257211bcbb990d Sat Jan 17 23:00:43 2026 -0800
    add strand to pslStats output
• src/hg/pslStats/tests/expected/cdna2cdnaAlignTest.stats
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    e86128cfb99722359894e3997b13b58783ca68ae Sat Jan 17 14:31:01 2026 -0800
    add number of aligned bases and alignment span
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    12fba0b2e8b85a7f3351a05dc0257211bcbb990d Sat Jan 17 23:00:43 2026 -0800
    add strand to pslStats output
• src/hg/pslStats/tests/expected/tsvHeaderTest.stats
  • lines changed 32, context: html, text, full: html, text
    e86128cfb99722359894e3997b13b58783ca68ae Sat Jan 17 14:31:01 2026 -0800
    add number of aligned bases and alignment span
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    12fba0b2e8b85a7f3351a05dc0257211bcbb990d Sat Jan 17 23:00:43 2026 -0800
    add strand to pslStats output
• src/hg/pslStats/tests/expected/untransAlignTest.stats
  • lines changed 32, context: html, text, full: html, text
    e86128cfb99722359894e3997b13b58783ca68ae Sat Jan 17 14:31:01 2026 -0800
    add number of aligned bases and alignment span
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    12fba0b2e8b85a7f3351a05dc0257211bcbb990d Sat Jan 17 23:00:43 2026 -0800
    add strand to pslStats output
• src/hg/pslStats/tests/expected/untransAlignUnalnTest.stats
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    e86128cfb99722359894e3997b13b58783ca68ae Sat Jan 17 14:31:01 2026 -0800
    add number of aligned bases and alignment span
  • lines changed 32, context: html, text, full: html, text
    12fba0b2e8b85a7f3351a05dc0257211bcbb990d Sat Jan 17 23:00:43 2026 -0800
    add strand to pslStats output
• src/inc/cheapcgi.h
  • lines changed 1, context: html, text, full: html, text
    fcb6dc8dfa166136193177c895ca181200850e4d Mon Jan 19 06:02:31 2026 -0800
    changing superTrack TrackUi quite a bit. Removing dropdowns and replacing them with buttons. Also adding buttons for setting all tracks or all visible tracks to a visibility. While at it, making a change to the js-query-library function (inversed the order of arguments) which was requested months ago by Brian, but I forgot to make the change after code review. Also shortening the "source data version" label to just "version". refs #36917. I changed the library function hTvDropDownClassVisOnlyAndExtra() rather than copying the code. This was because I was hesitant to copy/paste all this code into a second function, which would have been the only alternative, as the function cannot be reused as-is. So I modified the function to return the list of visibilities. It's never clear whether it's better to modify functions or copy/paste code. here, not breaking the function into smaller parts, so copy/pasting it, would risk requiring more future copy/pasted code. But the risk is to break existing tracks.
• src/inc/common.h
  • lines changed 3, context: html, text, full: html, text
    fcb6dc8dfa166136193177c895ca181200850e4d Mon Jan 19 06:02:31 2026 -0800
    changing superTrack TrackUi quite a bit. Removing dropdowns and replacing them with buttons. Also adding buttons for setting all tracks or all visible tracks to a visibility. While at it, making a change to the js-query-library function (inversed the order of arguments) which was requested months ago by Brian, but I forgot to make the change after code review. Also shortening the "source data version" label to just "version". refs #36917. I changed the library function hTvDropDownClassVisOnlyAndExtra() rather than copying the code. This was because I was hesitant to copy/paste all this code into a second function, which would have been the only alternative, as the function cannot be reused as-is. So I modified the function to return the list of visibilities. It's never clear whether it's better to modify functions or copy/paste code. here, not breaking the function into smaller parts, so copy/pasting it, would risk requiring more future copy/pasted code. But the risk is to break existing tracks.
• src/lib/cheapcgi.c
  • lines changed 4, context: html, text, full: html, text
    fcb6dc8dfa166136193177c895ca181200850e4d Mon Jan 19 06:02:31 2026 -0800
    changing superTrack TrackUi quite a bit. Removing dropdowns and replacing them with buttons. Also adding buttons for setting all tracks or all visible tracks to a visibility. While at it, making a change to the js-query-library function (inversed the order of arguments) which was requested months ago by Brian, but I forgot to make the change after code review. Also shortening the "source data version" label to just "version". refs #36917. I changed the library function hTvDropDownClassVisOnlyAndExtra() rather than copying the code. This was because I was hesitant to copy/paste all this code into a second function, which would have been the only alternative, as the function cannot be reused as-is. So I modified the function to return the list of visibilities. It's never clear whether it's better to modify functions or copy/paste code. here, not breaking the function into smaller parts, so copy/pasting it, would risk requiring more future copy/pasted code. But the risk is to break existing tracks.
• src/lib/common.c
  • lines changed 8, context: html, text, full: html, text
    fcb6dc8dfa166136193177c895ca181200850e4d Mon Jan 19 06:02:31 2026 -0800
    changing superTrack TrackUi quite a bit. Removing dropdowns and replacing them with buttons. Also adding buttons for setting all tracks or all visible tracks to a visibility. While at it, making a change to the js-query-library function (inversed the order of arguments) which was requested months ago by Brian, but I forgot to make the change after code review. Also shortening the "source data version" label to just "version". refs #36917. I changed the library function hTvDropDownClassVisOnlyAndExtra() rather than copying the code. This was because I was hesitant to copy/paste all this code into a second function, which would have been the only alternative, as the function cannot be reused as-is. So I modified the function to return the list of visibilities. It's never clear whether it's better to modify functions or copy/paste code. here, not breaking the function into smaller parts, so copy/pasting it, would risk requiring more future copy/pasted code. But the risk is to break existing tracks.

• lines changed: 2345
• files changed: 85