All File Changes

v483_preview to v483_preview2 (2025-05-26 to 2025-06-02) v483

• confs/asia.hg.conf
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    1968e23d706f2898d208524febbff064ee060ed0 Sun Jun 1 01:11:24 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 6, context: html, text, full: html, text
    1968e23d706f2898d208524febbff064ee060ed0 Sun Jun 1 01:11:24 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
  • lines changed 1, context: html, text, full: html, text
    1968e23d706f2898d208524febbff064ee060ed0 Sun Jun 1 01:11:24 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 7, context: html, text, full: html, text
    1968e23d706f2898d208524febbff064ee060ed0 Sun Jun 1 01:11:24 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 6, context: html, text, full: html, text
    1968e23d706f2898d208524febbff064ee060ed0 Sun Jun 1 01:11:24 2025 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgApi/hgApi.c
  • lines changed 17, context: html, text, full: html, text
    a7ad12187330204f9657482c84bebc349905bcc0 Tue May 27 16:22:26 2025 -0700
    Make hgApi use the cart. This makes db=hub_id work on requests to allow genark bigGenePred zoomToExon/Codon to work, refs #35799
• src/hg/hgConvert/hgConvert.c
  • lines changed 5, context: html, text, full: html, text
    0edefc9983679d6bbee96ccc100f7d41921def00 Wed May 28 12:25:49 2025 -0700
    working on track visibilities after quickLift
• src/hg/hgGateway/hgGateway.c
  • lines changed 2, context: html, text, full: html, text
    314f62455b39a4271649c732b6d55cd96f9bba82 Tue May 27 12:42:11 2025 -0700
    Remove CDN links to shepherd and replace with local copies, refs #35464
• src/hg/hgGene/hgGene.c
  • lines changed 45, context: html, text, full: html, text
    8165601dddc27978eb4a2fe2654ba81212e30473 Sat May 31 11:46:07 2025 -0700
    hgGene changes for quickLift
• src/hg/hgGene/hgGene.h
  • lines changed 1, context: html, text, full: html, text
    8165601dddc27978eb4a2fe2654ba81212e30473 Sat May 31 11:46:07 2025 -0700
    hgGene changes for quickLift
• src/hg/hgGene/links.c
  • lines changed 9, context: html, text, full: html, text
    8165601dddc27978eb4a2fe2654ba81212e30473 Sat May 31 11:46:07 2025 -0700
    hgGene changes for quickLift
• src/hg/hgGene/pathways.c
  • lines changed 1, context: html, text, full: html, text
    8165601dddc27978eb4a2fe2654ba81212e30473 Sat May 31 11:46:07 2025 -0700
    hgGene changes for quickLift
• src/hg/hgGene/sequence.c
  • lines changed 33, context: html, text, full: html, text
    8165601dddc27978eb4a2fe2654ba81212e30473 Sat May 31 11:46:07 2025 -0700
    hgGene changes for quickLift
• src/hg/hgTables/mainPage.c
  • lines changed 2, context: html, text, full: html, text
    314f62455b39a4271649c732b6d55cd96f9bba82 Tue May 27 12:42:11 2025 -0700
    Remove CDN links to shepherd and replace with local copies, refs #35464
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 3, context: html, text, full: html, text
    6ff14cbe503f6d3b20d61308887dc91a692ec507 Wed May 28 09:21:47 2025 -0700
    fix some problems with quickLift reported by QA refs #35609
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 8, context: html, text, full: html, text
    83ccf1c6b15c91b83723894b882f3af1e340882b Sun Jun 1 16:37:23 2025 -0700
    exon frames are in transcription strand order so if it's changed during quickLift we need to flip the order in the genePred
• src/hg/hgTracks/hgTracks.c
  • lines changed 2, context: html, text, full: html, text
    314f62455b39a4271649c732b6d55cd96f9bba82 Tue May 27 12:42:11 2025 -0700
    Remove CDN links to shepherd and replace with local copies, refs #35464
  • lines changed 1, context: html, text, full: html, text
    bfe42ed2f82c1f6dec44ea6dec503284e7a68abd Wed May 28 15:54:21 2025 -0700
    Updating hgTracks to use the new popup menu for the javascript tutorials, refs #35716
  • lines changed 12, context: html, text, full: html, text
    b01267e746a100118ca7045113d78b5fa588e685 Fri May 30 17:10:30 2025 -0700
    when a composite has dense tracks the way we deal with center labels the draw routine leaves grek in the track when the decenders of the center label have been drawn even though the center label is not actually drawn, but hidden via CSS. Now in this condition we're drawing slightly smaller fonts for the center labels so they don't exceed the drawing box. refs #29500
• src/hg/hgTracks/hgTracks.h
  • lines changed 3, context: html, text, full: html, text
    b01267e746a100118ca7045113d78b5fa588e685 Fri May 30 17:10:30 2025 -0700
    when a composite has dense tracks the way we deal with center labels the draw routine leaves grek in the track when the decenders of the center label have been drawn even though the center label is not actually drawn, but hidden via CSS. Now in this condition we're drawing slightly smaller fonts for the center labels so they don't exceed the drawing box. refs #29500
• src/hg/hgTracks/searchTracks.c
  • lines changed 1, context: html, text, full: html, text
    bf1dc34e24d371fd8b9bbfacd94dca10b6c41bf7 Tue May 27 14:25:24 2025 -0700
    Make hgTracks trackSearch include hub results by default, refs #35807
• src/hg/hgTracks/simpleTracks.c
  • lines changed 4, context: html, text, full: html, text
    6ff14cbe503f6d3b20d61308887dc91a692ec507 Wed May 28 09:21:47 2025 -0700
    fix some problems with quickLift reported by QA refs #35609
  • lines changed 3, context: html, text, full: html, text
    5ef72df72099ffa752903955d8826bed3b81e4bb Thu May 29 18:21:53 2025 -0700
    Making the (?) a link instead of the entire 'codon phase', refs #33749
• src/hg/hgc/hgc.c
  • lines changed 24, context: html, text, full: html, text
    6ff14cbe503f6d3b20d61308887dc91a692ec507 Wed May 28 09:21:47 2025 -0700
    fix some problems with quickLift reported by QA refs #35609
  • lines changed 18, context: html, text, full: html, text
    36216d451fe6fc46f9c29af334ab73788b3024f6 Wed May 28 17:30:49 2025 -0700
    fixes error in hgc showAll for blat non-ct results and clicking on show full alignment. refs #32750
  • lines changed 10, context: html, text, full: html, text
    83ccf1c6b15c91b83723894b882f3af1e340882b Sun Jun 1 16:37:23 2025 -0700
    exon frames are in transcription strand order so if it's changed during quickLift we need to flip the order in the genePred
• src/hg/htdocs/goldenPath/help/bedMethyl.html
  • lines changed 92, context: html, text, full: html, text
    9cb1efe7ba7f45e80faf3c9a9c6af3833cbae850 Fri May 23 12:27:32 2025 -0700
    add bedMethyl.html skeleton so gitFiles will return it
• src/hg/htdocs/images/info-circle-svgrepo-com.svg
  • lines changed 7, context: html, text, full: html, text
    232168a2674f2b069da8d66e31d878f1f5a5aff7 Thu May 29 15:58:36 2025 -0700
    Adding an info icon, refs #31584
  • lines changed 7, context: html, text, full: html, text
    3f789d6ebcb62a51a5f8c31a61449120fc581249 Thu May 29 16:01:05 2025 -0700
    Accidentally pushed the image, refs #31584
• src/hg/htdocs/indexMeetings.html
  • lines changed 27, context: html, text, full: html, text
    cd51f3aac524834d5ce1047a460d4e11bea6e7be Thu May 29 11:22:44 2025 -0700
    Updating home page meetings based on b0b's upcoming workshops.
• src/hg/htdocs/style/makefile
  • lines changed 1, context: html, text, full: html, text
    777c3f56fc294e6794a02af3ba1212bfe20e841f Tue May 27 12:35:41 2025 -0700
    Add shepherd CSS and JS lib to source tree, refs #35464
• src/hg/htdocs/style/shepherd.css
  • lines changed 9, context: html, text, full: html, text
    777c3f56fc294e6794a02af3ba1212bfe20e841f Tue May 27 12:35:41 2025 -0700
    Add shepherd CSS and JS lib to source tree, refs #35464
• src/hg/inc/genePred.h
  • lines changed 1, context: html, text, full: html, text
    83ccf1c6b15c91b83723894b882f3af1e340882b Sun Jun 1 16:37:23 2025 -0700
    exon frames are in transcription strand order so if it's changed during quickLift we need to flip the order in the genePred
• src/hg/inc/hui.h
  • lines changed 2, context: html, text, full: html, text
    6ff14cbe503f6d3b20d61308887dc91a692ec507 Wed May 28 09:21:47 2025 -0700
    fix some problems with quickLift reported by QA refs #35609
• src/hg/js/ajax.js
  • lines changed 1, context: html, text, full: html, text
    a7ad12187330204f9657482c84bebc349905bcc0 Tue May 27 16:22:26 2025 -0700
    Make hgApi use the cart. This makes db=hub_id work on requests to allow genark bigGenePred zoomToExon/Codon to work, refs #35799
• src/hg/js/external/makefile
  • lines changed 2, context: html, text, full: html, text
    777c3f56fc294e6794a02af3ba1212bfe20e841f Tue May 27 12:35:41 2025 -0700
    Add shepherd CSS and JS lib to source tree, refs #35464
• src/hg/js/external/shepherd.min.js
  • lines changed 0, context: html, text, full: html, text
    777c3f56fc294e6794a02af3ba1212bfe20e841f Tue May 27 12:35:41 2025 -0700
    Add shepherd CSS and JS lib to source tree, refs #35464
• src/hg/js/hgTracks.js
  • lines changed 3, context: html, text, full: html, text
    a7ad12187330204f9657482c84bebc349905bcc0 Tue May 27 16:22:26 2025 -0700
    Make hgApi use the cart. This makes db=hub_id work on requests to allow genark bigGenePred zoomToExon/Codon to work, refs #35799
• src/hg/js/utils.js
  • lines changed 1, context: html, text, full: html, text
    a7ad12187330204f9657482c84bebc349905bcc0 Tue May 27 16:22:26 2025 -0700
    Make hgApi use the cart. This makes db=hub_id work on requests to allow genark bigGenePred zoomToExon/Codon to work, refs #35799
• src/hg/lib/cart.c
  • lines changed 144, context: html, text, full: html, text
    27370697e01a3f1e80c90bb9a003560b959beed4 Tue May 27 14:51:05 2025 -0700
    adding cloudflare bot protection, refs #35790
  • lines changed 144, context: html, text, full: html, text
    3200d39bfd8e7c797f2d1d24e3c9567903da7f68 Tue May 27 16:51:10 2025 -0700
    Revert "adding cloudflare bot protection, refs #35790" This reverts commit 27370697e01a3f1e80c90bb9a003560b959beed4.
  • lines changed 144, context: html, text, full: html, text
    43d1009151fe8dfff680d387ed6772491b17d51f Tue May 27 16:59:30 2025 -0700
    adding cloudflare bot protection, without extranous files, refs #35790
  • lines changed 1, context: html, text, full: html, text
    a885499d72f17dc8e16c629312a9b194aad7fc88 Fri May 30 12:05:41 2025 -0700
    let individual sandboxs opt out of captcha
• src/hg/lib/customFactory.c
  • lines changed 138, context: html, text, full: html, text
    99d93d87504dd96cb48f7730ca1162c2c94ffc82 Wed May 28 09:23:28 2025 -0700
    bedMethyl custom track factory
• src/hg/lib/genePred.c
  • lines changed 15, context: html, text, full: html, text
    83ccf1c6b15c91b83723894b882f3af1e340882b Sun Jun 1 16:37:23 2025 -0700
    exon frames are in transcription strand order so if it's changed during quickLift we need to flip the order in the genePred
• src/hg/lib/hui.c
  • lines changed 24, context: html, text, full: html, text
    6ff14cbe503f6d3b20d61308887dc91a692ec507 Wed May 28 09:21:47 2025 -0700
    fix some problems with quickLift reported by QA refs #35609
• src/hg/lib/trackHub.c
  • lines changed 77, context: html, text, full: html, text
    0edefc9983679d6bbee96ccc100f7d41921def00 Wed May 28 12:25:49 2025 -0700
    working on track visibilities after quickLift
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    0d7871621c30ea9a041d008cb65759ebc221dc43 Wed May 28 10:07:28 2025 -0700
    adding one per user request refs #29545
  • lines changed 2, context: html, text, full: html, text
    8ff33a8c8dfc26aa665aa38e011dda59e052cdd3 Wed May 28 14:03:10 2025 -0700
    adding a couple per user requests refs #29545
  • lines changed 312, context: html, text, full: html, text
    3da03b62ffcd33ec6eb723ab92f31498453ad8d6 Fri May 30 09:53:19 2025 -0700
    adding virus for BRC project and primates for HPRC refs #34337
  • lines changed 1, context: html, text, full: html, text
    48d4e3681256e047c5a7ecb7396a7f3309040898 Fri May 30 16:16:49 2025 -0700
    adding one per user request refs #29545
  • lines changed 51, context: html, text, full: html, text
    92634f0f5c8afcb109341543a5fc2fe978cba657 Sun Jun 1 13:25:03 2025 -0700
    adding updated HPRC assemblies refs #35415
• src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh
  • lines changed 7, context: html, text, full: html, text
    fb83822aeeef2f87fa0bf7d1daaea1f365e6d7b5 Mon Jun 2 08:57:54 2025 -0700
    hgdownload2 disk is full send no more data to hgdownload2 refs #35415
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    48d4e3681256e047c5a7ecb7396a7f3309040898 Fri May 30 16:16:49 2025 -0700
    adding one per user request refs #29545
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    8ff33a8c8dfc26aa665aa38e011dda59e052cdd3 Wed May 28 14:03:10 2025 -0700
    adding a couple per user requests refs #29545
• src/hg/makeDb/doc/hg19.gencode.txt
  • lines changed 3, context: html, text, full: html, text
    9b5f3d76a56c8f5e1957869c0faeea4be5182256 Sat May 31 12:56:22 2025 -0700
    GENCODE Versions V48lift38
• src/hg/makeDb/doc/hg38/gencode.txt
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    20a6e56606f88189952c7fac787e6c0b8275fbc8 Sat May 31 12:28:24 2025 -0700
    GENCODE Versions V48
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    0d7871621c30ea9a041d008cb65759ebc221dc43 Wed May 28 10:07:28 2025 -0700
    adding one per user request refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    dbb90af27dc59821641e5e6fd30edb9afe72e955 Tue May 27 08:53:59 2025 -0700
    eliminate the GRCh38 versions refs #29545
• src/hg/makeDb/doc/mm39/gencode.txt
  • lines changed 6, context: html, text, full: html, text
    d0507a008bc27f625eaf356b3fb967abb070f697 Sat May 31 12:44:55 2025 -0700
    GENCODE Version VM37
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    8ff33a8c8dfc26aa665aa38e011dda59e052cdd3 Wed May 28 14:03:10 2025 -0700
    adding a couple per user requests refs #29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 40, context: html, text, full: html, text
    3da03b62ffcd33ec6eb723ab92f31498453ad8d6 Fri May 30 09:53:19 2025 -0700
    adding virus for BRC project and primates for HPRC refs #34337
  • lines changed 51, context: html, text, full: html, text
    92634f0f5c8afcb109341543a5fc2fe978cba657 Sun Jun 1 13:25:03 2025 -0700
    adding updated HPRC assemblies refs #35415
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
  • lines changed 282, context: html, text, full: html, text
    3da03b62ffcd33ec6eb723ab92f31498453ad8d6 Fri May 30 09:53:19 2025 -0700
    adding virus for BRC project and primates for HPRC refs #34337
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 4, context: html, text, full: html, text
    20a6e56606f88189952c7fac787e6c0b8275fbc8 Sat May 31 12:28:24 2025 -0700
    GENCODE Versions V48
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    d0507a008bc27f625eaf356b3fb967abb070f697 Sat May 31 12:44:55 2025 -0700
    GENCODE Version VM37
• src/hg/makeDb/trackDb/human/bayesDel.ra
  • lines changed 8, context: html, text, full: html, text
    27370697e01a3f1e80c90bb9a003560b959beed4 Tue May 27 14:51:05 2025 -0700
    adding cloudflare bot protection, refs #35790
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    c71040cb944749df70f7e5817d94705d58bb354b Tue May 27 14:51:05 2025 -0700
    adding mutscore to pathogenicity scores, refs #35806
• src/hg/makeDb/trackDb/human/constraintSuper.html
  • lines changed 4, context: html, text, full: html, text
    680c0cb830ff738f2e9e8fe559a0b2cb894945a6 Fri May 30 15:42:30 2025 -0700
    Adding a hypen for 'non-coding', and add a link to the references section on the track description page for the linsight track, refs #35730
• src/hg/makeDb/trackDb/human/constraintSuper.ra
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    f8b7b2114ddbfd0d6a482f8bb9bde1de53bd79a4 Fri May 30 16:25:51 2025 -0700
    Staging the linsight track on hgwbeta, refs #35730
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    a33c70ec65ab927c51c1e244f81b2134342eaa2f Fri May 30 17:11:17 2025 -0700
    Releasing the linsight track for hg19, refs 335730
• src/hg/makeDb/trackDb/human/hg19/bayesDel.ra
  • lines changed 8, context: html, text, full: html, text
    3200d39bfd8e7c797f2d1d24e3c9567903da7f68 Tue May 27 16:51:10 2025 -0700
    Revert "adding cloudflare bot protection, refs #35790" This reverts commit 27370697e01a3f1e80c90bb9a003560b959beed4.
• src/hg/makeDb/trackDb/human/hg19/predictionScoresSuper.ra
  • lines changed 1, context: html, text, full: html, text
    3200d39bfd8e7c797f2d1d24e3c9567903da7f68 Tue May 27 16:51:10 2025 -0700
    Revert "adding cloudflare bot protection, refs #35790" This reverts commit 27370697e01a3f1e80c90bb9a003560b959beed4.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    27370697e01a3f1e80c90bb9a003560b959beed4 Tue May 27 14:51:05 2025 -0700
    adding cloudflare bot protection, refs #35790
  • lines changed 1, context: html, text, full: html, text
    3200d39bfd8e7c797f2d1d24e3c9567903da7f68 Tue May 27 16:51:10 2025 -0700
    Revert "adding cloudflare bot protection, refs #35790" This reverts commit 27370697e01a3f1e80c90bb9a003560b959beed4.
  • lines changed 1, context: html, text, full: html, text
    c71040cb944749df70f7e5817d94705d58bb354b Tue May 27 14:51:05 2025 -0700
    adding mutscore to pathogenicity scores, refs #35806
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
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    9b5f3d76a56c8f5e1957869c0faeea4be5182256 Sat May 31 12:56:22 2025 -0700
    GENCODE Versions V48lift38
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV48lift37.html
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    9b5f3d76a56c8f5e1957869c0faeea4be5182256 Sat May 31 12:56:22 2025 -0700
    GENCODE Versions V48lift38
• src/hg/makeDb/trackDb/human/hg38/encode4.html
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    17710ebe183000560daf8e3cfb56a86eaa382f58 Mon May 19 09:48:53 2025 -0700
    making tweaks to ENCODE long read transcripts track desc + config, refs #31368
• src/hg/makeDb/trackDb/human/hg38/encode4.ra
  • lines changed 6, context: html, text, full: html, text
    17710ebe183000560daf8e3cfb56a86eaa382f58 Mon May 19 09:48:53 2025 -0700
    making tweaks to ENCODE long read transcripts track desc + config, refs #31368
• src/hg/makeDb/trackDb/human/hg38/encode4LongRnaTranscripts.html
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    dff11e35ecb7bf69a571c414f5659c0aafccd555 Fri May 30 14:40:20 2025 -0700
    renaming encode4 ra+html -> encode4LongRnaTranscripts ra+html, refs #31368
• src/hg/makeDb/trackDb/human/hg38/encode4LongRnaTranscripts.ra
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    dff11e35ecb7bf69a571c414f5659c0aafccd555 Fri May 30 14:40:20 2025 -0700
    renaming encode4 ra+html -> encode4LongRnaTranscripts ra+html, refs #31368
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    56a768368a17f700743be90f02caa9843d5eeaf2 Fri May 30 15:10:51 2025 -0700
    changing html parameter, refs #31368
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    2961060a5326cd722ad604e48a1df6b386eb35a0 Fri May 30 16:04:44 2025 -0700
    various changes for encode4LongRnaTranscripts tracks on mm10 + hg38, refs #31368
• src/hg/makeDb/trackDb/human/hg38/knownGeneArchive.ra
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    a6cc2c4bb7c8794478931fcb160d67b55e539408 Fri May 30 16:46:34 2025 -0700
    Removing the knownGeneV47 alpha release tag in the knownGeneArchive track, refs #35186
• src/hg/makeDb/trackDb/human/hg38/long_read_transcripts.html
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    2961060a5326cd722ad604e48a1df6b386eb35a0 Fri May 30 16:04:44 2025 -0700
    various changes for encode4LongRnaTranscripts tracks on mm10 + hg38, refs #31368
• src/hg/makeDb/trackDb/human/hg38/long_read_transcripts.ra
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    d1d6367f12d687564a36f426171e376f811ca28c Fri May 30 14:55:05 2025 -0700
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    2961060a5326cd722ad604e48a1df6b386eb35a0 Fri May 30 16:04:44 2025 -0700
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    20a6e56606f88189952c7fac787e6c0b8275fbc8 Sat May 31 12:28:24 2025 -0700
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• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV48.html
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    20a6e56606f88189952c7fac787e6c0b8275fbc8 Sat May 31 12:28:24 2025 -0700
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    2961060a5326cd722ad604e48a1df6b386eb35a0 Fri May 30 16:04:44 2025 -0700
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    2961060a5326cd722ad604e48a1df6b386eb35a0 Fri May 30 16:04:44 2025 -0700
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    d1d6367f12d687564a36f426171e376f811ca28c Fri May 30 14:55:05 2025 -0700
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    2961060a5326cd722ad604e48a1df6b386eb35a0 Fri May 30 16:04:44 2025 -0700
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    d0507a008bc27f625eaf356b3fb967abb070f697 Sat May 31 12:44:55 2025 -0700
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    d0507a008bc27f625eaf356b3fb967abb070f697 Sat May 31 12:44:55 2025 -0700
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• src/inc/common.mk
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