All File Changes

v494_base to v495_preview (2026-02-16 to 2026-02-23) v495

• confs/hgwdev.hg.conf
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    a4a3fc06fc13c3e5577f66cca38d9cb43f3aa2de Sun Feb 22 01:11:15 2026 -0800
    Installing updated hg.conf files from UCSC servers
• docs/hubs/contributedTracks.md
  • lines changed 4, context: html, text, full: html, text
    6d5744572234650664785eab8d4a443bc0908506 Wed Feb 18 09:34:00 2026 -0800
    adding link to hubBasics and email address, refs #37043
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 14, context: html, text, full: html, text
    d0976c9d524ee428053266757aa17c7ef1b66a12 Wed Feb 18 12:20:45 2026 -0800
    Libify the api key set/revoke methods, refs #36517
• src/hg/hgHubConnect/hgHubConnect.h
  • lines changed 2, context: html, text, full: html, text
    d0976c9d524ee428053266757aa17c7ef1b66a12 Wed Feb 18 12:20:45 2026 -0800
    Libify the api key set/revoke methods, refs #36517
• src/hg/hgHubConnect/hooks/pre-create.c
  • lines changed 1, context: html, text, full: html, text
    d0976c9d524ee428053266757aa17c7ef1b66a12 Wed Feb 18 12:20:45 2026 -0800
    Libify the api key set/revoke methods, refs #36517
• src/hg/hgHubConnect/hooks/pre-finish.c
  • lines changed 1, context: html, text, full: html, text
    d0976c9d524ee428053266757aa17c7ef1b66a12 Wed Feb 18 12:20:45 2026 -0800
    Libify the api key set/revoke methods, refs #36517
• src/hg/hgHubConnect/trackHubWizard.c
  • lines changed 70, context: html, text, full: html, text
    d0976c9d524ee428053266757aa17c7ef1b66a12 Wed Feb 18 12:20:45 2026 -0800
    Libify the api key set/revoke methods, refs #36517
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    cb73c8cc35a7f7d20284102ab00d0b102c1a5f30 Tue Feb 17 14:33:42 2026 -0800
    Make cf keyboard shortcut on hgTracks work even if not tracklist is present below the image, refs #34456
  • lines changed 1, context: html, text, full: html, text
    e9c3757c29ec6d08b6232e0a671fe5970bb58e2e Wed Feb 18 19:21:54 2026 -0800
    Feedback from CR, refs #37124
  • lines changed 6, context: html, text, full: html, text
    d17212c4b414a78dc5e95554953f3aa9a977ae63 Thu Feb 19 14:52:00 2026 -0800
    ps/pdf output wasn't displaying some highlights if too many were present in the cart. The highlight array is now dynamically allocated instead of a static limit of 4096, refs #36895
• src/hg/htdocs/goldenPath/help/quickLiftChain.html
  • lines changed 70, context: html, text, full: html, text
    e1428851a49899cefeeb3ed621aa19ea93334cdd Wed Feb 18 22:09:18 2026 -0800
    Updating the Alignment Differences track description page, refs #36942
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 5, context: html, text, full: html, text
    c18dbbabd21dc4ffc907e4651618fed0e483705e Wed Feb 18 09:19:05 2026 -0800
    fixes based on CR, refs #37125
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 1, context: html, text, full: html, text
    97b949a89c0bb48eca9a858b2df60e9e967a9fc7 Tue Feb 17 10:35:01 2026 -0800
    Code review edit, refs #37088
  • lines changed 34, context: html, text, full: html, text
    83b0f7d4e2913e2f42f2f822c8e933872591f36d Wed Feb 18 15:27:21 2026 -0800
    Announcing the JASPAR 2026 tracks, refs #36264
  • lines changed 8, context: html, text, full: html, text
    e5d0dcc14f3656db7b358b239477a9c3e19d9e51 Wed Feb 18 16:10:47 2026 -0800
    Updating the jaspar URLs for the assemblies, refs #36264
• src/hg/htdocs/images/QuickLift/quickLiftTrianglesMouseOver.png
  • lines changed 0, context: html, text, full: html, text
    e1428851a49899cefeeb3ed621aa19ea93334cdd Wed Feb 18 22:09:18 2026 -0800
    Updating the Alignment Differences track description page, refs #36942
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    83b0f7d4e2913e2f42f2f822c8e933872591f36d Wed Feb 18 15:27:21 2026 -0800
    Announcing the JASPAR 2026 tracks, refs #36264
• src/hg/hubApi/apiUtils.c
  • lines changed 1, context: html, text, full: html, text
    ef8a176b2edbaf0a5c8e0d74a56a3536a30ff98a Fri Feb 13 11:41:45 2026 -0800
    remove unused forward declaration refs #37085
• src/hg/inc/hubSpaceKeys.h
  • lines changed 13, context: html, text, full: html, text
    d0976c9d524ee428053266757aa17c7ef1b66a12 Wed Feb 18 12:20:45 2026 -0800
    Libify the api key set/revoke methods, refs #36517
• src/hg/js/hgTracks.js
  • lines changed 12, context: html, text, full: html, text
    cb73c8cc35a7f7d20284102ab00d0b102c1a5f30 Tue Feb 17 14:33:42 2026 -0800
    Make cf keyboard shortcut on hgTracks work even if not tracklist is present below the image, refs #34456
• src/hg/lib/botDelay.c
  • lines changed 1, context: html, text, full: html, text
    d0976c9d524ee428053266757aa17c7ef1b66a12 Wed Feb 18 12:20:45 2026 -0800
    Libify the api key set/revoke methods, refs #36517
• src/hg/lib/hubSpaceKeys.c
  • lines changed 45, context: html, text, full: html, text
    d0976c9d524ee428053266757aa17c7ef1b66a12 Wed Feb 18 12:20:45 2026 -0800
    Libify the api key set/revoke methods, refs #36517
• src/hg/lib/trackDbCache.c
  • lines changed 1, context: html, text, full: html, text
    68ddd76f1be38e94450e3d1a73e63621ef2945a8 Fri Feb 20 16:50:48 2026 -0800
    make /dev/shm/trackDbCache the default directory for the trackDb cache refs #35945
• src/hg/lib/trackHub.c
  • lines changed 3, context: html, text, full: html, text
    e9c3757c29ec6d08b6232e0a671fe5970bb58e2e Wed Feb 18 19:21:54 2026 -0800
    Feedback from CR, refs #37124
• src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh
  • lines changed 1, context: html, text, full: html, text
    f4f10fdd8250edfa1fdbe6052f6cb84536996c9d Wed Feb 18 18:34:14 2026 -0800
    still need the hubUrl argument on the track count refs #37109
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    a1ed75f55ff4ad135992dcef08abd93a7ac916d4 Fri Feb 20 13:18:49 2026 -0800
    BRC update refs #34337
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    a1ed75f55ff4ad135992dcef08abd93a7ac916d4 Fri Feb 20 13:18:49 2026 -0800
    BRC update refs #34337
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 122, context: html, text, full: html, text
    a1ed75f55ff4ad135992dcef08abd93a7ac916d4 Fri Feb 20 13:18:49 2026 -0800
    BRC update refs #34337
• src/hg/makeDb/doc/hg38/gnomad.txt
  • lines changed 18, context: html, text, full: html, text
    2a58182f173ac7c5b7f28e39835ae79e4fe78466 Mon Feb 23 04:12:52 2026 -0800
    making gnomad coverage on hg38 always start at 0, feedback from Alistair Pagnamenta, refs #37041
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 1663, context: html, text, full: html, text
    a1ed75f55ff4ad135992dcef08abd93a7ac916d4 Fri Feb 20 13:18:49 2026 -0800
    BRC update refs #34337
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 5, context: html, text, full: html, text
    a1ed75f55ff4ad135992dcef08abd93a7ac916d4 Fri Feb 20 13:18:49 2026 -0800
    BRC update refs #34337
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    a1ed75f55ff4ad135992dcef08abd93a7ac916d4 Fri Feb 20 13:18:49 2026 -0800
    BRC update refs #34337
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    a1ed75f55ff4ad135992dcef08abd93a7ac916d4 Fri Feb 20 13:18:49 2026 -0800
    BRC update refs #34337
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    a1ed75f55ff4ad135992dcef08abd93a7ac916d4 Fri Feb 20 13:18:49 2026 -0800
    BRC update refs #34337
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
  • lines changed 19, context: html, text, full: html, text
    a1ed75f55ff4ad135992dcef08abd93a7ac916d4 Fri Feb 20 13:18:49 2026 -0800
    BRC update refs #34337
• src/hg/makeDb/trackDb/drosophila/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    0db15879749b6753035c8f365e9d69b5987f4c79 Tue Feb 17 16:33:46 2026 -0800
    Adding assembly specific filters, and updating the track desc page based on author feedback, refs #36264
• src/hg/makeDb/trackDb/human/dnaMethylation.html
  • lines changed 1, context: html, text, full: html, text
    5f9d00bf2c7cc68a49c72aac71e91451680b6019 Tue Feb 17 08:00:59 2026 -0800
    Feedback from CR, refs #37093
• src/hg/makeDb/trackDb/human/genCC.ra
  • lines changed 2, context: html, text, full: html, text
    e124da635e46cce4ce2dc3eae2154339ee10d311 Fri Feb 20 17:13:37 2026 -0800
    Updating the type and urls linkout with the new GenCC file format, refs #37135
• src/hg/makeDb/trackDb/human/hg38/gnomadCoverage.ra
  • lines changed 4, context: html, text, full: html, text
    2a58182f173ac7c5b7f28e39835ae79e4fe78466 Mon Feb 23 04:12:52 2026 -0800
    making gnomad coverage on hg38 always start at 0, feedback from Alistair Pagnamenta, refs #37041
• src/hg/makeDb/trackDb/human/varFreqs.html
  • lines changed 8, context: html, text, full: html, text
    3f88af395a070d9e1db62a0e95b8c0650dc958dc Thu Feb 12 00:32:25 2026 -0800
    doc updates for mrgb varFreqs track
• src/hg/makeDb/trackDb/jaspar.html
  • lines changed 99, context: html, text, full: html, text
    0db15879749b6753035c8f365e9d69b5987f4c79 Tue Feb 17 16:33:46 2026 -0800
    Adding assembly specific filters, and updating the track desc page based on author feedback, refs #36264
  • lines changed 34, context: html, text, full: html, text
    f8fcc3e5fcb5fa70d28bf67d104519fc75f68b20 Wed Feb 18 09:03:02 2026 -0800
    Updating the emails and 2026 release description based on author feedback, refs #36261
  • lines changed 1, context: html, text, full: html, text
    f301ade11502e2fba8e5715b4d286c5007daca18 Fri Feb 20 13:58:47 2026 -0800
    Code review edits, refs ##37120
• src/hg/makeDb/trackDb/jaspar.ra
  • lines changed 1, context: html, text, full: html, text
    9fbca72bc539b50983cfec413d2fe3b6abdacc54 Tue Feb 17 19:49:04 2026 -0800
    Updating pennantIcon for the JASPAR 2026 TFBS track, refs #36264
• src/hg/makeDb/trackDb/mouse/mm10/cCREregistry.html
  • lines changed 121, context: html, text, full: html, text
    e309de9305cf4536b2813e100473272c7316fd82 Thu Feb 19 17:46:33 2026 -0800
    First draft of new encode cCREs track for mm10, refs #37131
• src/hg/makeDb/trackDb/mouse/mm10/cCREsSuper.html
  • lines changed 52, context: html, text, full: html, text
    e309de9305cf4536b2813e100473272c7316fd82 Thu Feb 19 17:46:33 2026 -0800
    First draft of new encode cCREs track for mm10, refs #37131
• src/hg/makeDb/trackDb/mouse/mm10/coreCollection.html
  • lines changed 143, context: html, text, full: html, text
    e309de9305cf4536b2813e100473272c7316fd82 Thu Feb 19 17:46:33 2026 -0800
    First draft of new encode cCREs track for mm10, refs #37131
• src/hg/makeDb/trackDb/mouse/mm10/encode.cCREs.override.ra
  • lines changed 34, context: html, text, full: html, text
    e309de9305cf4536b2813e100473272c7316fd82 Thu Feb 19 17:46:33 2026 -0800
    First draft of new encode cCREs track for mm10, refs #37131
• src/hg/makeDb/trackDb/mouse/mm10/encode4.ccres.ra
  • lines changed 1222, context: html, text, full: html, text
    e309de9305cf4536b2813e100473272c7316fd82 Thu Feb 19 17:46:33 2026 -0800
    First draft of new encode cCREs track for mm10, refs #37131
• src/hg/makeDb/trackDb/mouse/mm10/encodeCcreCombined.old.ra
  • lines changed 2, context: html, text, full: html, text
    e309de9305cf4536b2813e100473272c7316fd82 Thu Feb 19 17:46:33 2026 -0800
    First draft of new encode cCREs track for mm10, refs #37131
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.encode3.ra
  • lines changed 3, context: html, text, full: html, text
    e309de9305cf4536b2813e100473272c7316fd82 Thu Feb 19 17:46:33 2026 -0800
    First draft of new encode cCREs track for mm10, refs #37131
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    e309de9305cf4536b2813e100473272c7316fd82 Thu Feb 19 17:46:33 2026 -0800
    First draft of new encode cCREs track for mm10, refs #37131
• src/hg/makeDb/trackDb/sacCer/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    0db15879749b6753035c8f365e9d69b5987f4c79 Tue Feb 17 16:33:46 2026 -0800
    Adding assembly specific filters, and updating the track desc page based on author feedback, refs #36264
• src/hg/makeDb/trackDb/squirt/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    0db15879749b6753035c8f365e9d69b5987f4c79 Tue Feb 17 16:33:46 2026 -0800
    Adding assembly specific filters, and updating the track desc page based on author feedback, refs #36264
• src/hg/makeDb/trackDb/worm/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    0db15879749b6753035c8f365e9d69b5987f4c79 Tue Feb 17 16:33:46 2026 -0800
    Adding assembly specific filters, and updating the track desc page based on author feedback, refs #36264
• src/hg/utils/bigChainToChain/bigChainToChain.c
  • lines changed 40, context: html, text, full: html, text
    d9741ac7fe00ba4e2cc38bb8baab8c8b2ae6eec6 Fri Feb 13 18:23:42 2026 -0800
    Updated the following seven utilities bigBedToBed, bigMafToMafj, bigWigToWig, bigWigToBedGraph, bigGenePredToGenePred, bigPslToPsl, bigChainToChain, added support for multiple -range parameters that uses and validates Marks desired bed and position values, in a new callback function in the library bigBedCmdSupport.c. Also added the ability to quickly check allowed chromosomes so users see and error when specifying incorrect chromsome names, and it works with all the filter options. These utils also have a new -skipChromCheck option that users can use if the want to skip the check. These have no tests. I will make tests for these soon. refs #28109, #36925
  • lines changed 3, context: html, text, full: html, text
    c9b7830e130a43e817566cedfb1be819cc2164c5 Thu Feb 19 17:42:22 2026 -0800
    fix oops do not want duplicate usage line. refs #28109
• src/hg/utils/bigGenePredToGenePred/bigGenePredToGenePred.c
  • lines changed 41, context: html, text, full: html, text
    d9741ac7fe00ba4e2cc38bb8baab8c8b2ae6eec6 Fri Feb 13 18:23:42 2026 -0800
    Updated the following seven utilities bigBedToBed, bigMafToMafj, bigWigToWig, bigWigToBedGraph, bigGenePredToGenePred, bigPslToPsl, bigChainToChain, added support for multiple -range parameters that uses and validates Marks desired bed and position values, in a new callback function in the library bigBedCmdSupport.c. Also added the ability to quickly check allowed chromosomes so users see and error when specifying incorrect chromsome names, and it works with all the filter options. These utils also have a new -skipChromCheck option that users can use if the want to skip the check. These have no tests. I will make tests for these soon. refs #28109, #36925
  • lines changed 3, context: html, text, full: html, text
    c9b7830e130a43e817566cedfb1be819cc2164c5 Thu Feb 19 17:42:22 2026 -0800
    fix oops do not want duplicate usage line. refs #28109
• src/hg/utils/bigGenePredToGenePred/tests/input/basicTest.gp
  • lines changed 40, context: html, text, full: html, text
    b96a2a4fd4c75db180a03af13a1122db5ce6d512 Fri Feb 20 20:18:33 2026 -0800
    Since it was present in 4 utils but missing and needed in 3 others, I have added bigWigToWig call in wigToBigWig test, and bigChainToChain to chainToBigChain test, and genePredToBigGenePred to bigGenePredToGenePred. Now all seven utilities properly run their inverse utilities so that they recreate the original input, verifying correctness. Requested in code-review by Mark. refs #28109, #36925
• src/hg/utils/bigGenePredToGenePred/tests/makefile
  • lines changed 3, context: html, text, full: html, text
    b96a2a4fd4c75db180a03af13a1122db5ce6d512 Fri Feb 20 20:18:33 2026 -0800
    Since it was present in 4 utils but missing and needed in 3 others, I have added bigWigToWig call in wigToBigWig test, and bigChainToChain to chainToBigChain test, and genePredToBigGenePred to bigGenePredToGenePred. Now all seven utilities properly run their inverse utilities so that they recreate the original input, verifying correctness. Requested in code-review by Mark. refs #28109, #36925
• src/hg/utils/bigMafToMaf/bigMafToMaf.c
  • lines changed 38, context: html, text, full: html, text
    d9741ac7fe00ba4e2cc38bb8baab8c8b2ae6eec6 Fri Feb 13 18:23:42 2026 -0800
    Updated the following seven utilities bigBedToBed, bigMafToMafj, bigWigToWig, bigWigToBedGraph, bigGenePredToGenePred, bigPslToPsl, bigChainToChain, added support for multiple -range parameters that uses and validates Marks desired bed and position values, in a new callback function in the library bigBedCmdSupport.c. Also added the ability to quickly check allowed chromosomes so users see and error when specifying incorrect chromsome names, and it works with all the filter options. These utils also have a new -skipChromCheck option that users can use if the want to skip the check. These have no tests. I will make tests for these soon. refs #28109, #36925
• src/hg/utils/bigPslToPsl/bigPslToPsl.c
  • lines changed 40, context: html, text, full: html, text
    d9741ac7fe00ba4e2cc38bb8baab8c8b2ae6eec6 Fri Feb 13 18:23:42 2026 -0800
    Updated the following seven utilities bigBedToBed, bigMafToMafj, bigWigToWig, bigWigToBedGraph, bigGenePredToGenePred, bigPslToPsl, bigChainToChain, added support for multiple -range parameters that uses and validates Marks desired bed and position values, in a new callback function in the library bigBedCmdSupport.c. Also added the ability to quickly check allowed chromosomes so users see and error when specifying incorrect chromsome names, and it works with all the filter options. These utils also have a new -skipChromCheck option that users can use if the want to skip the check. These have no tests. I will make tests for these soon. refs #28109, #36925
  • lines changed 3, context: html, text, full: html, text
    c9b7830e130a43e817566cedfb1be819cc2164c5 Thu Feb 19 17:42:22 2026 -0800
    fix oops do not want duplicate usage line. refs #28109
• src/hg/utils/chainToBigChain/tests/makefile
  • lines changed 3, context: html, text, full: html, text
    b96a2a4fd4c75db180a03af13a1122db5ce6d512 Fri Feb 20 20:18:33 2026 -0800
    Since it was present in 4 utils but missing and needed in 3 others, I have added bigWigToWig call in wigToBigWig test, and bigChainToChain to chainToBigChain test, and genePredToBigGenePred to bigGenePredToGenePred. Now all seven utilities properly run their inverse utilities so that they recreate the original input, verifying correctness. Requested in code-review by Mark. refs #28109, #36925
• src/hg/utils/chainToBigChain/tests/makefile.galt.save
  • lines changed 28, context: html, text, full: html, text
    b96a2a4fd4c75db180a03af13a1122db5ce6d512 Fri Feb 20 20:18:33 2026 -0800
    Since it was present in 4 utils but missing and needed in 3 others, I have added bigWigToWig call in wigToBigWig test, and bigChainToChain to chainToBigChain test, and genePredToBigGenePred to bigGenePredToGenePred. Now all seven utilities properly run their inverse utilities so that they recreate the original input, verifying correctness. Requested in code-review by Mark. refs #28109, #36925
• src/hg/utils/hubCheck/hubCheck.c
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    e9c3757c29ec6d08b6232e0a671fe5970bb58e2e Wed Feb 18 19:21:54 2026 -0800
    Feedback from CR, refs #37124
• src/hg/utils/hubCheck/tests/expected/autoScaleHub.txt
  • lines changed 2, context: html, text, full: html, text
    e9c3757c29ec6d08b6232e0a671fe5970bb58e2e Wed Feb 18 19:21:54 2026 -0800
    Feedback from CR, refs #37124
• src/hg/utils/hubCheck/tests/expected/manyErrors.output.txt
  • lines changed 1, context: html, text, full: html, text
    e9c3757c29ec6d08b6232e0a671fe5970bb58e2e Wed Feb 18 19:21:54 2026 -0800
    Feedback from CR, refs #37124
• src/hg/utils/otto/genCC/doGenCC.py
  • lines changed 235, context: html, text, full: html, text
    1331fff6434827b6c138f9e18f3b5491917c63b0 Fri Feb 20 17:31:34 2026 -0800
    Many updates to the GenCC pipeline. 1 It was using GencodeV40 hardcoded; now it uses the latest GENCODE table. 2. Better handling of the comment field of the tsv, which used to include even HTML, so I wasn't parsing it correctly, leading to some items being excluded from the track. 3. Fixed a bug where I was treating numbers as strings, leading to a few corner cases (only came up in this latest GenCC update) where the coordinates were wrong. 4. GenCC emailed us that they are updating their format, much to our chagrin, since we usually just extend fields at the end to not break pipelines. I just adopted their new format, which changed the UUID to a versioned ID and added a version number field. So, overall, the field count went up by 1. 5. Handle multi-chrom genes (only a few) by picking the chrom with the most transcripts. 6. Add a fallback to look up genes missing from GENCODE by checking kgXref. Refs #37135
• src/inc/bigBedCmdSupport.h
  • lines changed 13, context: html, text, full: html, text
    d9741ac7fe00ba4e2cc38bb8baab8c8b2ae6eec6 Fri Feb 13 18:23:42 2026 -0800
    Updated the following seven utilities bigBedToBed, bigMafToMafj, bigWigToWig, bigWigToBedGraph, bigGenePredToGenePred, bigPslToPsl, bigChainToChain, added support for multiple -range parameters that uses and validates Marks desired bed and position values, in a new callback function in the library bigBedCmdSupport.c. Also added the ability to quickly check allowed chromosomes so users see and error when specifying incorrect chromsome names, and it works with all the filter options. These utils also have a new -skipChromCheck option that users can use if the want to skip the check. These have no tests. I will make tests for these soon. refs #28109, #36925
• src/lib/bigBedCmdSupport.c
  • lines changed 110, context: html, text, full: html, text
    d9741ac7fe00ba4e2cc38bb8baab8c8b2ae6eec6 Fri Feb 13 18:23:42 2026 -0800
    Updated the following seven utilities bigBedToBed, bigMafToMafj, bigWigToWig, bigWigToBedGraph, bigGenePredToGenePred, bigPslToPsl, bigChainToChain, added support for multiple -range parameters that uses and validates Marks desired bed and position values, in a new callback function in the library bigBedCmdSupport.c. Also added the ability to quickly check allowed chromosomes so users see and error when specifying incorrect chromsome names, and it works with all the filter options. These utils also have a new -skipChromCheck option that users can use if the want to skip the check. These have no tests. I will make tests for these soon. refs #28109, #36925
• src/utils/bigBedToBed/bigBedToBed.c
  • lines changed 38, context: html, text, full: html, text
    d9741ac7fe00ba4e2cc38bb8baab8c8b2ae6eec6 Fri Feb 13 18:23:42 2026 -0800
    Updated the following seven utilities bigBedToBed, bigMafToMafj, bigWigToWig, bigWigToBedGraph, bigGenePredToGenePred, bigPslToPsl, bigChainToChain, added support for multiple -range parameters that uses and validates Marks desired bed and position values, in a new callback function in the library bigBedCmdSupport.c. Also added the ability to quickly check allowed chromosomes so users see and error when specifying incorrect chromsome names, and it works with all the filter options. These utils also have a new -skipChromCheck option that users can use if the want to skip the check. These have no tests. I will make tests for these soon. refs #28109, #36925
• src/utils/bigWigToBedGraph/bigWigToBedGraph.c
  • lines changed 38, context: html, text, full: html, text
    d9741ac7fe00ba4e2cc38bb8baab8c8b2ae6eec6 Fri Feb 13 18:23:42 2026 -0800
    Updated the following seven utilities bigBedToBed, bigMafToMafj, bigWigToWig, bigWigToBedGraph, bigGenePredToGenePred, bigPslToPsl, bigChainToChain, added support for multiple -range parameters that uses and validates Marks desired bed and position values, in a new callback function in the library bigBedCmdSupport.c. Also added the ability to quickly check allowed chromosomes so users see and error when specifying incorrect chromsome names, and it works with all the filter options. These utils also have a new -skipChromCheck option that users can use if the want to skip the check. These have no tests. I will make tests for these soon. refs #28109, #36925
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    c9b7830e130a43e817566cedfb1be819cc2164c5 Thu Feb 19 17:42:22 2026 -0800
    fix oops do not want duplicate usage line. refs #28109
• src/utils/bigWigToWig/bigWigToWig.c
  • lines changed 37, context: html, text, full: html, text
    d9741ac7fe00ba4e2cc38bb8baab8c8b2ae6eec6 Fri Feb 13 18:23:42 2026 -0800
    Updated the following seven utilities bigBedToBed, bigMafToMafj, bigWigToWig, bigWigToBedGraph, bigGenePredToGenePred, bigPslToPsl, bigChainToChain, added support for multiple -range parameters that uses and validates Marks desired bed and position values, in a new callback function in the library bigBedCmdSupport.c. Also added the ability to quickly check allowed chromosomes so users see and error when specifying incorrect chromsome names, and it works with all the filter options. These utils also have a new -skipChromCheck option that users can use if the want to skip the check. These have no tests. I will make tests for these soon. refs #28109, #36925
• src/utils/genePredCompare
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    15286a4682e55985f6da7de23e7c700eef4bb436 Fri Feb 6 04:01:09 2026 -0800
    adding genePredCompare tool to kent repo, see https://github.com/galaxyproject/brc-analytics/issues/1131
• src/utils/makefile
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    15286a4682e55985f6da7de23e7c700eef4bb436 Fri Feb 6 04:01:09 2026 -0800
    adding genePredCompare tool to kent repo, see https://github.com/galaxyproject/brc-analytics/issues/1131
• src/utils/wigToBigWig/tests/makefile
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    b96a2a4fd4c75db180a03af13a1122db5ce6d512 Fri Feb 20 20:18:33 2026 -0800
    Since it was present in 4 utils but missing and needed in 3 others, I have added bigWigToWig call in wigToBigWig test, and bigChainToChain to chainToBigChain test, and genePredToBigGenePred to bigGenePredToGenePred. Now all seven utilities properly run their inverse utilities so that they recreate the original input, verifying correctness. Requested in code-review by Mark. refs #28109, #36925

• lines changed: 4831
• files changed: 79