All File Changes

v462_preview2 to v462_base (2024-03-04 to 2024-03-11) v462

• src/hg/hgTracks/hgTracks.c
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    be09c9c576ac324b050baa0fca50afe05bc788d5 Wed Mar 6 10:19:19 2024 -0800
    getting CRAM custom tracks to work
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    0592e9dee1e20d7d5131219664674bacc92cd641 Wed Mar 6 15:05:30 2024 -0800
    don't put out null "More Info.." link on hubs
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    f23ef9aa1e46695a8e0ed3eaf7003158eab21e33 Mon Mar 11 07:53:23 2024 -0700
    up the maximum maxItems to 100,000
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    0a812f51e1c6478a53dee82bd97fd46e33399f36 Wed Mar 6 14:53:03 2024 -0800
    support CRAM in hgc
• src/hg/htdocs/goldenPath/help/docker.html
  • lines changed 193, context: html, text, full: html, text
    e895130c7a1cca12c145224a815443788ba6efee Thu Mar 7 00:05:04 2024 -0800
    Creating a new GB Docker help page, refs #27056
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 60, context: html, text, full: html, text
    28d217636eb69c134a1478eaef916ba3cbfdc7b9 Tue Mar 5 13:32:49 2024 -0800
    Announcing the release of the JASPAR 2024 track, refs #31973
  • lines changed 55, context: html, text, full: html, text
    8e82cf9587f424d103eb44b54c690c3c5e7ba1d5 Thu Mar 7 14:38:01 2024 -0800
    Announcing the release of the new Prediction Scores super track and BayesDel track. Removed the duplicate "AbSplice Scores" announcement which I added by accident, refs #27766
• src/hg/htdocs/images/container_logs.png
  • lines changed 0, context: html, text, full: html, text
    e895130c7a1cca12c145224a815443788ba6efee Thu Mar 7 00:05:04 2024 -0800
    Creating a new GB Docker help page, refs #27056
• src/hg/htdocs/images/container_settings.png
  • lines changed 0, context: html, text, full: html, text
    e895130c7a1cca12c145224a815443788ba6efee Thu Mar 7 00:05:04 2024 -0800
    Creating a new GB Docker help page, refs #27056
• src/hg/htdocs/images/docker_image.png
  • lines changed 0, context: html, text, full: html, text
    e895130c7a1cca12c145224a815443788ba6efee Thu Mar 7 00:05:04 2024 -0800
    Creating a new GB Docker help page, refs #27056
• src/hg/htdocs/images/docker_optional_settings.png
  • lines changed 0, context: html, text, full: html, text
    e895130c7a1cca12c145224a815443788ba6efee Thu Mar 7 00:05:04 2024 -0800
    Creating a new GB Docker help page, refs #27056
• src/hg/htdocs/indexMeetings.html
  • lines changed 8, context: html, text, full: html, text
    f565bff04336208124ab37f69d975ea20f7d7f74 Fri Mar 8 13:33:28 2024 -0800
    Updating meetings page.
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    28d217636eb69c134a1478eaef916ba3cbfdc7b9 Tue Mar 5 13:32:49 2024 -0800
    Announcing the release of the JASPAR 2024 track, refs #31973
  • lines changed 12, context: html, text, full: html, text
    8e82cf9587f424d103eb44b54c690c3c5e7ba1d5 Thu Mar 7 14:38:01 2024 -0800
    Announcing the release of the new Prediction Scores super track and BayesDel track. Removed the duplicate "AbSplice Scores" announcement which I added by accident, refs #27766
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    b3ccd2e0dda6280a2218d9702da4c1906a9a9387 Mon Mar 11 10:41:25 2024 -0700
    New version number v462
• src/hg/js/hgSearch.js
  • lines changed 2, context: html, text, full: html, text
    a2787ccef4b1249013fc762adc2575d80709b9f1 Thu Mar 7 10:38:09 2024 -0800
    Encode the highlight parameter in hgSearch links to hgTracks because the value contains a '#' character, refs #33199
• src/hg/lib/customFactory.c
  • lines changed 2, context: html, text, full: html, text
    a2967835db0f5a17f28486f11a48c1a7d317bfe7 Wed Mar 6 10:16:46 2024 -0800
    get CRAM custom tracks to work, especially on hs1
  • lines changed 1, context: html, text, full: html, text
    60714310f765f28c36e8e3b8c6c688bdf7937e78 Thu Mar 7 16:59:45 2024 -0800
    skip hubnames when checking db in custom track against current db
• src/hg/lib/gwasCatalog.as
  • lines changed 1, context: html, text, full: html, text
    ee413d5fbaa279f619706ccc75c0a82770a2be8d Fri Mar 8 10:32:18 2024 -0800
    fix the gwasCatalog otto build.
• src/hg/lib/gwasCatalog.sql
  • lines changed 7, context: html, text, full: html, text
    ee413d5fbaa279f619706ccc75c0a82770a2be8d Fri Mar 8 10:32:18 2024 -0800
    fix the gwasCatalog otto build.
• src/hg/lib/hdb.c
  • lines changed 1, context: html, text, full: html, text
    a2967835db0f5a17f28486f11a48c1a7d317bfe7 Wed Mar 6 10:16:46 2024 -0800
    get CRAM custom tracks to work, especially on hs1
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    1926a54bc4e7c89416dc875a086f6d1952722474 Mon Mar 4 18:37:14 2024 -0800
    adding 1 to catch up VGP refs #29545
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    2515e30c3110a44bd96a953d76bacd27adff21bf Fri Mar 8 20:45:00 2024 -0800
    adding GCA_004302925.2_ASM430292v2 Cochliomyia_hominivorax primary screw-worm per user request refs #29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    1926a54bc4e7c89416dc875a086f6d1952722474 Mon Mar 4 18:37:14 2024 -0800
    adding 1 to catch up VGP refs #29545
• src/hg/makeDb/doc/hg38/gencode.txt
  • lines changed 39, context: html, text, full: html, text
    cf2ea277055c7881254552745ce3e38e0d23f9a5 Mon Mar 4 20:36:11 2024 -0800
    import of GENCODE V46 prerelease
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    2515e30c3110a44bd96a953d76bacd27adff21bf Fri Mar 8 20:45:00 2024 -0800
    adding GCA_004302925.2_ASM430292v2 Cochliomyia_hominivorax primary screw-worm per user request refs #29545
• src/hg/makeDb/doc/mm39/gencode.txt
  • lines changed 37, context: html, text, full: html, text
    ba39846fb30a64ba6df41c0aae781915ddf61c80 Mon Mar 4 22:15:06 2024 -0800
    import of GENCODE VM35
• src/hg/makeDb/doc/panTro2.txt
  • lines changed 26, context: html, text, full: html, text
    c72e86438227987b38863408b636fa101a4cea39 Mon Mar 4 16:48:30 2024 -0800
    liftOver to panTro5 per user request refs #33047
• src/hg/makeDb/doc/ucscGenes/hg38.gencodeV45.sh
  • lines changed 33, context: html, text, full: html, text
    4e0ed5b2547fe5c4305c6bd4d9336c4800ae0276 Wed Mar 6 10:41:33 2024 -0800
    Commit of files for knownGeneV45 build, refs #32414
• src/hg/makeDb/doc/ucscGenes/mm39.gencodeVM34.sh
  • lines changed 56, context: html, text, full: html, text
    e84397db43e064ebc8fb853773d1e48fbdc7aa46 Wed Mar 6 10:43:19 2024 -0800
    Makedoc for knownGeneVM34, refs #32415
• src/hg/makeDb/doc/uniProt/sp240202.txt
  • lines changed 111, context: html, text, full: html, text
    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/makeDb/doc/vgpAsmHub/vgp.alternate.orderList.tsv
  • lines changed 31, context: html, text, full: html, text
    9b8bb908c285ca4cd641ebcb9451ffda0b11ae2d Mon Mar 4 13:06:30 2024 -0800
    catching up 232 alternate assemblies refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt
  • lines changed 26, context: html, text, full: html, text
    9b8bb908c285ca4cd641ebcb9451ffda0b11ae2d Mon Mar 4 13:06:30 2024 -0800
    catching up 232 alternate assemblies refs #29545
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 9, context: html, text, full: html, text
    cf2ea277055c7881254552745ce3e38e0d23f9a5 Mon Mar 4 20:36:11 2024 -0800
    import of GENCODE V46 prerelease
  • lines changed 2, context: html, text, full: html, text
    ba39846fb30a64ba6df41c0aae781915ddf61c80 Mon Mar 4 22:15:06 2024 -0800
    import of GENCODE VM35
• src/hg/makeDb/outside/gencode/lib/gencode/gencodeTags.py
  • lines changed 7, context: html, text, full: html, text
    cf2ea277055c7881254552745ce3e38e0d23f9a5 Mon Mar 4 20:36:11 2024 -0800
    import of GENCODE V46 prerelease
• src/hg/makeDb/schema/all.joiner
  • lines changed 94, context: html, text, full: html, text
    cf2ea277055c7881254552745ce3e38e0d23f9a5 Mon Mar 4 20:36:11 2024 -0800
    import of GENCODE V46 prerelease
  • lines changed 94, context: html, text, full: html, text
    ba39846fb30a64ba6df41c0aae781915ddf61c80 Mon Mar 4 22:15:06 2024 -0800
    import of GENCODE VM35
• src/hg/makeDb/trackDb/human/enigma.html
  • lines changed 145, context: html, text, full: html, text
    3f6d3b9b6ecc50930f78bc9ce752b0b0950590d5 Mon Mar 11 09:58:47 2024 -0700
    Adding enigma tracks html page, refs #32914
• src/hg/makeDb/trackDb/human/hg19/bayesDel.ra
  • lines changed 8, context: html, text, full: html, text
    b5cb1b52fa5a14839fcb3ae669036ab1f2a79400 Tue Mar 5 17:19:04 2024 -0800
    Edits to the BayesDel track description page and adding the html page to the subtracks , refs #27766
  • lines changed 1, context: html, text, full: html, text
    8e82cf9587f424d103eb44b54c690c3c5e7ba1d5 Thu Mar 7 14:38:01 2024 -0800
    Announcing the release of the new Prediction Scores super track and BayesDel track. Removed the duplicate "AbSplice Scores" announcement which I added by accident, refs #27766
• src/hg/makeDb/trackDb/human/hg19/predictionScoresSuper.html
  • lines changed 89, context: html, text, full: html, text
    0c14f34f5bbc558a771d72960d9ea04a758e7ead Wed Mar 6 16:39:27 2024 -0800
    Moving predictionScoresSuper files for the BayesDel track from human to the hg19 directory due to data only being available for hg19, refs #27766
• src/hg/makeDb/trackDb/human/hg19/predictionScoresSuper.ra
  • lines changed 10, context: html, text, full: html, text
    0c14f34f5bbc558a771d72960d9ea04a758e7ead Wed Mar 6 16:39:27 2024 -0800
    Moving predictionScoresSuper files for the BayesDel track from human to the hg19 directory due to data only being available for hg19, refs #27766
  • lines changed 1, context: html, text, full: html, text
    8e82cf9587f424d103eb44b54c690c3c5e7ba1d5 Thu Mar 7 14:38:01 2024 -0800
    Announcing the release of the new Prediction Scores super track and BayesDel track. Removed the duplicate "AbSplice Scores" announcement which I added by accident, refs #27766
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    0c14f34f5bbc558a771d72960d9ea04a758e7ead Wed Mar 6 16:39:27 2024 -0800
    Moving predictionScoresSuper files for the BayesDel track from human to the hg19 directory due to data only being available for hg19, refs #27766
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra
  • lines changed 9, context: html, text, full: html, text
    4e0ed5b2547fe5c4305c6bd4d9336c4800ae0276 Wed Mar 6 10:41:33 2024 -0800
    Commit of files for knownGeneV45 build, refs #32414
• src/hg/makeDb/trackDb/human/hg38/knownGeneArchive.ra
  • lines changed 55, context: html, text, full: html, text
    4e0ed5b2547fe5c4305c6bd4d9336c4800ae0276 Wed Mar 6 10:41:33 2024 -0800
    Commit of files for knownGeneV45 build, refs #32414
• src/hg/makeDb/trackDb/human/hg38/knownGeneOldV44.html
  • lines changed 10, context: html, text, full: html, text
    4e0ed5b2547fe5c4305c6bd4d9336c4800ae0276 Wed Mar 6 10:41:33 2024 -0800
    Commit of files for knownGeneV45 build, refs #32414
• src/hg/makeDb/trackDb/human/hg38/knownGeneV45.html
  • lines changed 178, context: html, text, full: html, text
    4e0ed5b2547fe5c4305c6bd4d9336c4800ae0276 Wed Mar 6 10:41:33 2024 -0800
    Commit of files for knownGeneV45 build, refs #32414
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    cf2ea277055c7881254552745ce3e38e0d23f9a5 Mon Mar 4 20:36:11 2024 -0800
    import of GENCODE V46 prerelease
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    4e0ed5b2547fe5c4305c6bd4d9336c4800ae0276 Wed Mar 6 10:41:33 2024 -0800
    Commit of files for knownGeneV45 build, refs #32414
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV46.html
  • lines changed 47, context: html, text, full: html, text
    cf2ea277055c7881254552745ce3e38e0d23f9a5 Mon Mar 4 20:36:11 2024 -0800
    import of GENCODE V46 prerelease
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV46.ra
  • lines changed 247, context: html, text, full: html, text
    cf2ea277055c7881254552745ce3e38e0d23f9a5 Mon Mar 4 20:36:11 2024 -0800
    import of GENCODE V46 prerelease
• src/hg/makeDb/trackDb/human/jaspar.ra
  • lines changed 2, context: html, text, full: html, text
    28d217636eb69c134a1478eaef916ba3cbfdc7b9 Tue Mar 5 13:32:49 2024 -0800
    Announcing the release of the JASPAR 2024 track, refs #31973
• src/hg/makeDb/trackDb/human/predictionScoresSuper.html
  • lines changed 3, context: html, text, full: html, text
    b5cb1b52fa5a14839fcb3ae669036ab1f2a79400 Tue Mar 5 17:19:04 2024 -0800
    Edits to the BayesDel track description page and adding the html page to the subtracks , refs #27766
  • lines changed 89, context: html, text, full: html, text
    0c14f34f5bbc558a771d72960d9ea04a758e7ead Wed Mar 6 16:39:27 2024 -0800
    Moving predictionScoresSuper files for the BayesDel track from human to the hg19 directory due to data only being available for hg19, refs #27766
• src/hg/makeDb/trackDb/human/predictionScoresSuper.ra
  • lines changed 10, context: html, text, full: html, text
    0c14f34f5bbc558a771d72960d9ea04a758e7ead Wed Mar 6 16:39:27 2024 -0800
    Moving predictionScoresSuper files for the BayesDel track from human to the hg19 directory due to data only being available for hg19, refs #27766
• src/hg/makeDb/trackDb/human/trackDb.enigmaTracks.ra
  • lines changed 5, context: html, text, full: html, text
    3f6d3b9b6ecc50930f78bc9ce752b0b0950590d5 Mon Mar 11 09:58:47 2024 -0700
    Adding enigma tracks html page, refs #32914
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    0c14f34f5bbc558a771d72960d9ea04a758e7ead Wed Mar 6 16:39:27 2024 -0800
    Moving predictionScoresSuper files for the BayesDel track from human to the hg19 directory due to data only being available for hg19, refs #27766
• src/hg/makeDb/trackDb/mouse/jaspar.ra
  • lines changed 2, context: html, text, full: html, text
    28d217636eb69c134a1478eaef916ba3cbfdc7b9 Tue Mar 5 13:32:49 2024 -0800
    Announcing the release of the JASPAR 2024 track, refs #31973
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    ba39846fb30a64ba6df41c0aae781915ddf61c80 Mon Mar 4 22:15:06 2024 -0800
    import of GENCODE VM35
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM35.html
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    ba39846fb30a64ba6df41c0aae781915ddf61c80 Mon Mar 4 22:15:06 2024 -0800
    import of GENCODE VM35
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM35.ra
  • lines changed 247, context: html, text, full: html, text
    ba39846fb30a64ba6df41c0aae781915ddf61c80 Mon Mar 4 22:15:06 2024 -0800
    import of GENCODE VM35
• src/hg/protein/spToDb/expected/test1/commentVal.txt
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/expected/test2/accToKeyword.txt
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/expected/test2/accToTaxon.txt
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/expected/test2/author.txt
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/expected/test2/citation.txt
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/expected/test2/citationRc.txt
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/expected/test2/citationRp.txt
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/expected/test2/comment.txt
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/expected/test2/commentType.txt
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/expected/test2/commentVal.txt
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/expected/test2/commonName.txt
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/expected/test2/description.txt
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/expected/test2/displayId.txt
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/expected/test2/extDb.txt
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/expected/test2/extDbRef.txt
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/expected/test2/feature.txt
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/expected/test2/featureClass.txt
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/expected/test2/featureId.txt
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/expected/test2/featureType.txt
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/expected/test2/gene.txt
  • lines changed 18, context: html, text, full: html, text
    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/expected/test2/geneLogic.txt
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/expected/test2/info.txt
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/expected/test2/keyword.txt
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/expected/test2/organelle.txt
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/expected/test2/otherAcc.txt
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/expected/test2/pathogenHost.txt
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/expected/test2/protein.txt
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/expected/test2/proteinEvidence.txt
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/expected/test2/proteinEvidenceType.txt
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/expected/test2/rcType.txt
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/expected/test2/rcVal.txt
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
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• src/hg/protein/spToDb/expected/test2/reference.txt
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
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• src/hg/protein/spToDb/expected/test2/referenceAuthors.txt
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/expected/test2/taxon.txt
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/input/test1
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/input/test2
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/makefile
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/spDb.sql
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/spDbTables.as
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/protein/spToDb/spToDb.c
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    f2cc86e3506c2d5fefe00dbe85e7f05f0f33f43f Wed Mar 6 11:33:33 2024 -0800
    Updates for new uniProt import, refs #30476
• src/hg/utils/automation/doNcbiRefSeq.pl
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    4c31f852319ea0972f600913d61fa0a480a366bf Mon Mar 4 16:33:21 2024 -0800
    update md5sum.txt file in bigZips/genes refs #33088
• src/hg/utils/automation/doRepeatModeler.pl
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    669727c799747d9b4f298497a8c110c295b77d9c Tue Mar 5 09:52:29 2024 -0800
    add a symlink to get the families.stk.gz file delivered no redmine
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    89613f6e172824ae07651362a788cfa5ce22e762 Tue Mar 5 10:05:56 2024 -0800
    add link for rmod.log file to get it delivered to hgdownload no redmine
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    b5ae994376f6ea39fdca045b159a3cb942a36c82 Wed Mar 6 21:40:27 2024 -0800
    correct reference target for symlink of repeat modeler files to top level build dir no redmine
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    0b4bbb965c6248e94e8b1d0d3d9bc4d2a7bf0763 Thu Mar 7 22:35:55 2024 -0800
    forgot the .gz on the families.stk symLink no redmine
• src/hg/utils/genePredToBigGenePred/genePredToBigGenePred.c
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    d060221305367f769d02aabc4a8e675b8cf03524 Tue Mar 5 23:29:13 2024 -0800
    Updating help message note about converting the bigGenePred to a bigBed, #15448
• src/hg/utils/otto/knownGene/buildTo.sh
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    904412b7994f145e262ec606b47a725750b7edce Wed Mar 6 10:58:24 2024 -0800
    Some updates for the knownGene pipeline, refs #32414
• src/hg/utils/otto/knownGene/genIspcrMail.sh
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    904412b7994f145e262ec606b47a725750b7edce Wed Mar 6 10:58:24 2024 -0800
    Some updates for the knownGene pipeline, refs #32414
• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
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    c1d527b5f7544b6a5a3fc0bf49938ae61955a1a8 Tue Mar 5 11:00:42 2024 -0800
    More masked sites in BA.2.86 from inspection of tree in taxonium, and JN.1 from github issue.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
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    d82c094239e4c63924fd100693f3bc79b0349441 Tue Mar 5 11:01:19 2024 -0800
    More new lineages and more Ns for newly branch-specific-masked sites.
• src/hg/utils/pslToBigPsl/pslToBigPsl.c
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    2322474c8ecc8f865350c14ea60a464248bd5c84 Fri Mar 8 00:02:10 2024 -0800
    make pslToBigPsl help slightly more helpful
• src/inc/bamFile.h
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    474b9ac55dcb8e3c4cc56b00d52bd210b7989038 Thu Mar 7 22:59:45 2024 -0800
    create PSLs for supplementary alignments that correct represent the query alignment. RM: 33209
• src/inc/srcVersion.h
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    b3ccd2e0dda6280a2218d9702da4c1906a9a9387 Mon Mar 11 10:41:25 2024 -0700
    New version number v462
• src/lib/bamFile.c
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    474b9ac55dcb8e3c4cc56b00d52bd210b7989038 Thu Mar 7 22:59:45 2024 -0800
    create PSLs for supplementary alignments that correct represent the query alignment. RM: 33209
• src/lib/hash.c
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    ecb1f5ac7ce97b744bd3c1b1f4f79652951fd20f Thu Mar 7 14:31:36 2024 -0800
    don't free mem in hash code that wasn't allocated from the heap in the first place
• src/utils/bamToPsl/bamToPsl.c
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    bd19d0f0854ea7e27017395d96715b61071b3391 Thu Mar 7 22:49:24 2024 -0800
    restructure code to make it easier to modify and then simplified by remove fasta checksum complexity checks that were added because of a missunderstanding about how supplemental alignments were represented
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    474b9ac55dcb8e3c4cc56b00d52bd210b7989038 Thu Mar 7 22:59:45 2024 -0800
    create PSLs for supplementary alignments that correct represent the query alignment. RM: 33209
• src/utils/bamToPsl/tests/chr9.NM_020469.2.blat.bam
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    2c3bfb6253d13a518eb2f3697d62224bdfa4aa54 Thu Mar 7 21:01:21 2024 -0800
    add new test cases that shows that bamToPsl is broken; restructure tests to match the rest
• src/utils/bamToPsl/tests/expected/test1.psl
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    2c3bfb6253d13a518eb2f3697d62224bdfa4aa54 Thu Mar 7 21:01:21 2024 -0800
    add new test cases that shows that bamToPsl is broken; restructure tests to match the rest
• src/utils/bamToPsl/tests/expected/test2.fa
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    49d67ce8f1bd5e1f0b5a5ae1133a8ffe507c50eb Thu Mar 7 22:52:20 2024 -0800
    added test case for fasta output
• src/utils/bamToPsl/tests/expected/test2.psl
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    2c3bfb6253d13a518eb2f3697d62224bdfa4aa54 Thu Mar 7 21:01:21 2024 -0800
    add new test cases that shows that bamToPsl is broken; restructure tests to match the rest
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    474b9ac55dcb8e3c4cc56b00d52bd210b7989038 Thu Mar 7 22:59:45 2024 -0800
    create PSLs for supplementary alignments that correct represent the query alignment. RM: 33209
• src/utils/bamToPsl/tests/expectedOut.psl
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    2c3bfb6253d13a518eb2f3697d62224bdfa4aa54 Thu Mar 7 21:01:21 2024 -0800
    add new test cases that shows that bamToPsl is broken; restructure tests to match the rest
• src/utils/bamToPsl/tests/input/chr9.NM_020469.2.blat.bam
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    2c3bfb6253d13a518eb2f3697d62224bdfa4aa54 Thu Mar 7 21:01:21 2024 -0800
    add new test cases that shows that bamToPsl is broken; restructure tests to match the rest
• src/utils/bamToPsl/tests/input/multimap.qsizes
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    2c3bfb6253d13a518eb2f3697d62224bdfa4aa54 Thu Mar 7 21:01:21 2024 -0800
    add new test cases that shows that bamToPsl is broken; restructure tests to match the rest
• src/utils/bamToPsl/tests/input/multimap.sam
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    2c3bfb6253d13a518eb2f3697d62224bdfa4aa54 Thu Mar 7 21:01:21 2024 -0800
    add new test cases that shows that bamToPsl is broken; restructure tests to match the rest
• src/utils/bamToPsl/tests/makefile
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    2c3bfb6253d13a518eb2f3697d62224bdfa4aa54 Thu Mar 7 21:01:21 2024 -0800
    add new test cases that shows that bamToPsl is broken; restructure tests to match the rest
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    4f600be98e2fe9e71637a704978a596029849ef4 Thu Mar 7 21:43:58 2024 -0800
    disable check of PSL, since bamToPsl is broken
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    49d67ce8f1bd5e1f0b5a5ae1133a8ffe507c50eb Thu Mar 7 22:52:20 2024 -0800
    added test case for fasta output
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    474b9ac55dcb8e3c4cc56b00d52bd210b7989038 Thu Mar 7 22:59:45 2024 -0800
    create PSLs for supplementary alignments that correct represent the query alignment. RM: 33209
• src/utils/qa/weeklybld/buildEnv.csh
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    3a40e7f28a18eaedf75388747f26e76e0611372a Mon Mar 11 10:40:46 2024 -0700
    v462 final build, refs #33051

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