All File Changes

v444_base to v445_preview (2023-02-20 to 2023-02-27) v445

• confs/hgwbeta.hg.conf
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    ca64aee85dbe16944eeba3cd4aee9b94ef9f712b Sun Feb 26 01:11:26 2023 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/hgGene/hgGeneData/Human/links.ra
  • lines changed 2, context: html, text, full: html, text
    726f0d82c65b613847011321bc7e9cd493311e92 Fri Feb 24 10:56:06 2023 -0800
    Update Stanford source links on hgGene to new princeton location, refs #30694
• src/hg/hgGene/hgGeneData/Mouse/links.ra
  • lines changed 2, context: html, text, full: html, text
    726f0d82c65b613847011321bc7e9cd493311e92 Fri Feb 24 10:56:06 2023 -0800
    Update Stanford source links on hgGene to new princeton location, refs #30694
• src/hg/hgGene/hgGeneData/Rat/links.ra
  • lines changed 2, context: html, text, full: html, text
    726f0d82c65b613847011321bc7e9cd493311e92 Fri Feb 24 10:56:06 2023 -0800
    Update Stanford source links on hgGene to new princeton location, refs #30694
• src/hg/hgGene/hgGeneData/Rat/rn4/links.ra
  • lines changed 2, context: html, text, full: html, text
    726f0d82c65b613847011321bc7e9cd493311e92 Fri Feb 24 10:56:06 2023 -0800
    Update Stanford source links on hgGene to new princeton location, refs #30694
• src/hg/hgTables/identifiers.c
  • lines changed 4, context: html, text, full: html, text
    81291d83afc22635047c8178c46d28aa7271d26b Thu Feb 23 14:47:50 2023 -0800
    Updating table schema references to the new data format description name, refs #30491
• src/hg/hgTables/mainPage.c
  • lines changed 3, context: html, text, full: html, text
    41e07184a720d35c7a981f2e019d961369bb637e Wed Feb 22 01:10:48 2023 -0800
    adding back BED output for wiggle data, as Hiram found that one can do peak calling on a wiggle file by using the filter option and minimum value, refs #30585
  • lines changed 6, context: html, text, full: html, text
    14292c6bc896a3768a781cf348b14208c5e172a9 Thu Feb 23 15:13:54 2023 -0800
    Tweaking the statement Max added after re-enabling BED output for signal tracks, refs #30585
  • lines changed 1, context: html, text, full: html, text
    849b83ab5df299bef66be9e3c545667e0cf49028 Fri Feb 24 17:17:09 2023 -0800
    Fixing wording of new wig box in hgTables, refs #30585
• src/hg/hgTables/usage.c
  • lines changed 2, context: html, text, full: html, text
    81291d83afc22635047c8178c46d28aa7271d26b Thu Feb 23 14:47:50 2023 -0800
    Updating table schema references to the new data format description name, refs #30491
• src/hg/hgTracks/bamTrack.c
  • lines changed 1, context: html, text, full: html, text
    cee60adf868375933ac0eb26e1b84048639e804f Fri Feb 24 11:07:54 2023 -0800
    ongoing work on snakes
• src/hg/hgTracks/halSnakeTrack.c
  • lines changed 2, context: html, text, full: html, text
    3757c263c0ab42b22d40abff7de40007fe70f76d Fri Feb 24 13:03:58 2023 -0800
    removed repeated function
• src/hg/hgTracks/hgTracks.h
  • lines changed 3, context: html, text, full: html, text
    cee60adf868375933ac0eb26e1b84048639e804f Fri Feb 24 11:07:54 2023 -0800
    ongoing work on snakes
• src/hg/hgTracks/recTrackSets.c
  • lines changed 7, context: html, text, full: html, text
    37e40ae31e02d615256bb9af43468ec2188afd24 Fri Feb 24 15:19:01 2023 -0800
    make recommended track sets merge with current cart instead of over-writing it. This is under hg.conf control (mergeRecommended=on)
• src/hg/hgTracks/simpleTracks.c
  • lines changed 8, context: html, text, full: html, text
    cee60adf868375933ac0eb26e1b84048639e804f Fri Feb 24 11:07:54 2023 -0800
    ongoing work on snakes
• src/hg/hgTracks/snake.c
  • lines changed 71, context: html, text, full: html, text
    cee60adf868375933ac0eb26e1b84048639e804f Fri Feb 24 11:07:54 2023 -0800
    ongoing work on snakes
• src/hg/htdocs/ENCODE/FAQ/index.html
  • lines changed 2, context: html, text, full: html, text
    594e3295e115d96e05b3f5b67150704cc30ded0e Thu Feb 23 14:36:50 2023 -0800
    Updating docs since changing the table schema button to be more general data format description, refs #30491
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 1, context: html, text, full: html, text
    594e3295e115d96e05b3f5b67150704cc30ded0e Thu Feb 23 14:36:50 2023 -0800
    Updating docs since changing the table schema button to be more general data format description, refs #30491
• src/hg/htdocs/FAQ/FAQgenes.html
  • lines changed 2, context: html, text, full: html, text
    a5424bb96edb789bd8b46da2203069d9978dbc06 Wed Feb 22 11:50:24 2023 -0800
    Fixing 404 link for the Static Page Cronjob 2023-02-15, no RM
• src/hg/htdocs/goldenPath/gbdDescriptions.html
  • lines changed 2, context: html, text, full: html, text
    594e3295e115d96e05b3f5b67150704cc30ded0e Thu Feb 23 14:36:50 2023 -0800
    Updating docs since changing the table schema button to be more general data format description, refs #30491
• src/hg/htdocs/goldenPath/help/hgGeneGraph.html
  • lines changed 1, context: html, text, full: html, text
    594e3295e115d96e05b3f5b67150704cc30ded0e Thu Feb 23 14:36:50 2023 -0800
    Updating docs since changing the table schema button to be more general data format description, refs #30491
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 4, context: html, text, full: html, text
    594e3295e115d96e05b3f5b67150704cc30ded0e Thu Feb 23 14:36:50 2023 -0800
    Updating docs since changing the table schema button to be more general data format description, refs #30491
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 36, context: html, text, full: html, text
    8a904ce96a5b1e136073d1b569eba4274212dfdf Mon Feb 13 15:09:39 2023 -0800
    Announcing the release of the recombination rate track for hg38, refs #30044
  • lines changed 86, context: html, text, full: html, text
    f59f95929aa7cf2b8ec43fa12aa362aa2cc8142a Fri Feb 24 15:01:02 2023 -0800
    News release for new GENCODE tracks. Refs #30657
  • lines changed 1, context: html, text, full: html, text
    c988c01554db9f17455ca55e5bc42d3a94eeac9d Fri Feb 24 15:04:20 2023 -0800
    Fixing bonehead mistake of anchoring to next year.
• src/hg/htdocs/indexNews.html
  • lines changed 11, context: html, text, full: html, text
    8a904ce96a5b1e136073d1b569eba4274212dfdf Mon Feb 13 15:09:39 2023 -0800
    Announcing the release of the recombination rate track for hg38, refs #30044
  • lines changed 1, context: html, text, full: html, text
    4aa5c514326178f449f7e0b88cb34ee5df8ee396 Thu Feb 23 09:19:10 2023 -0800
    Fixing February typo, refs #30693
  • lines changed 12, context: html, text, full: html, text
    f59f95929aa7cf2b8ec43fa12aa362aa2cc8142a Fri Feb 24 15:01:02 2023 -0800
    News release for new GENCODE tracks. Refs #30657
  • lines changed 1, context: html, text, full: html, text
    c988c01554db9f17455ca55e5bc42d3a94eeac9d Fri Feb 24 15:04:20 2023 -0800
    Fixing bonehead mistake of anchoring to next year.
• src/hg/inc/cart.h
  • lines changed 1, context: html, text, full: html, text
    37e40ae31e02d615256bb9af43468ec2188afd24 Fri Feb 24 15:19:01 2023 -0800
    make recommended track sets merge with current cart instead of over-writing it. This is under hg.conf control (mergeRecommended=on)
• src/hg/js/hgTracks.js
  • lines changed 20, context: html, text, full: html, text
    71ba2b30f03c0fb2b80d766382c80c235d2b674c Thu Feb 23 09:04:00 2023 -0800
    Fix broken check all/clear all buttons on hgTracks download menu, refs #30024
  • lines changed 1, context: html, text, full: html, text
    bba1471486ee56648a0696fe248787a853634870 Thu Feb 23 11:16:34 2023 -0800
    Remove comment that is no longer relevant, refs #30672
• src/hg/lib/cart.c
  • lines changed 22, context: html, text, full: html, text
    37e40ae31e02d615256bb9af43468ec2188afd24 Fri Feb 24 15:19:01 2023 -0800
    make recommended track sets merge with current cart instead of over-writing it. This is under hg.conf control (mergeRecommended=on)
• src/hg/lib/chromAlias.c
  • lines changed 4, context: html, text, full: html, text
    f1b022e1885342482ef657f89b62caa1077e38b6 Thu Feb 23 01:29:59 2023 -0800
    adding a fix, possibly not an optimal one, to the chromAlias resolution, for cases where there is no alias yet for a sequence, this fix at least avoids a crash in hgTracks, refs #30578
• src/hg/lib/hgncBig62.as
  • lines changed 1, context: html, text, full: html, text
    7278b9e0a4d428d54eb563f25ccf65170aab9943 Mon Feb 20 17:09:26 2023 -0800
    Clarifying the bb as file, refs #30588
• src/hg/makeDb/doc/asmHubs/README.txt
  • lines changed 84, context: html, text, full: html, text
    edc007b0a1062502c0a898866561a6e9fd870b99 Wed Feb 22 11:25:12 2023 -0800
    updated instructions for a build procedure summary no redmine
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 2, context: html, text, full: html, text
    9ab271e61d082cb46af9d8355c3075d20bfcd115 Tue Feb 21 10:04:48 2023 -0800
    adding GCA_014183145.1_ASM1418314v1 fish Sciaenops_ocellatus per user request refs #29545
  • lines changed 187, context: html, text, full: html, text
    ab44d13777c71361b5466df580e12000e9398e3f Thu Feb 23 10:02:41 2023 -0800
    catching up 187 assemblies no redmine
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 23, context: html, text, full: html, text
    e69f0e510820b9a0d0c03e9dc28b39ae54dca247 Thu Feb 23 12:44:33 2023 -0800
    catching up 15 sequences no redmine
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 140, context: html, text, full: html, text
    0efe1dd3214edc702165e58835719d64fed38ad0 Thu Feb 23 14:46:51 2023 -0800
    adding 65 assemblies no redmine
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    ec3b834428f524f840766e982911999ecc7fb0d5 Tue Feb 21 10:14:18 2023 -0800
    adding GCA_014183145.1_ASM1418314v1 fish Sciaenops_ocellatus per user request refs #29545
  • lines changed 125, context: html, text, full: html, text
    ab43240882b3fde4cd5940004fc1b39261e7b401 Thu Feb 23 19:44:58 2023 -0800
    adding in 48 new assemblies no redmine
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    9e4a43d63c48374c421e91d2d004d212eb1179ca Fri Feb 24 08:50:55 2023 -0800
    correctly remove items that have moved to legacy no redmine
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 27, context: html, text, full: html, text
    8cd39951eaaf49dddecd4584b416e0c246b79768 Thu Feb 23 12:42:30 2023 -0800
    catching up with 10 additions no redmine
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 31, context: html, text, full: html, text
    e257810c69cfacfe1c507f809675e7f6ba081d30 Thu Feb 23 13:32:44 2023 -0800
    adding 26 assemblies no redmine
  • lines changed 1, context: html, text, full: html, text
    fc0c8a5cec5b6ea9211d786ad765f343977dbda2 Fri Feb 24 08:51:09 2023 -0800
    correctly remove items that have moved to legacy no redmine
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 25, context: html, text, full: html, text
    a0c6d4fe11228219909f2167b018e8fb383899b3 Thu Feb 23 20:58:04 2023 -0800
    update has caused a number to move to legacy no redmine
  • lines changed 1, context: html, text, full: html, text
    e79092b1bcfc11fc1ff1e4a48e16e225f224d564 Thu Feb 23 21:55:03 2023 -0800
    need a definition for the single archaea which is on hgdownload no redmine
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 66, context: html, text, full: html, text
    a0c6d4fe11228219909f2167b018e8fb383899b3 Thu Feb 23 20:58:04 2023 -0800
    update has caused a number to move to legacy no redmine
  • lines changed 1, context: html, text, full: html, text
    2bb96d765745844678cce6bfb9bce559251c4702 Fri Feb 24 08:50:17 2023 -0800
    correct name for GCA_000845685.2_ViralProj14462 no redmine
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 39, context: html, text, full: html, text
    1c51cda29df19cd8a1d53fdaa2737458baaab21b Thu Feb 23 11:28:47 2023 -0800
    catching up 13 mammal assemblies no redmine
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 7, context: html, text, full: html, text
    a4bfa6f7e6523422644711be4c2c13333a8dc08c Thu Feb 23 12:59:48 2023 -0800
    catching up 5 sequences no redmine
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    b5c2003390bd6a3c4c7bc02d9c921e5b29a26f27 Thu Feb 23 10:29:51 2023 -0800
    update to slow loris assembly no redmine
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 6, context: html, text, full: html, text
    7cf46a28aa0dcdd04452cae7aa69c0bcfc1331dd Thu Feb 23 12:59:13 2023 -0800
    catching up 4 vertebrates no redmine
• src/hg/makeDb/doc/vgpAsmHub/vgp.alternate.orderList.tsv
  • lines changed 97, context: html, text, full: html, text
    83435b8a84bf60a2d2632a345e40fd61f670b9a5 Fri Feb 24 15:46:11 2023 -0800
    catching up the VGP alternate listing no redmine
• src/hg/makeDb/doc/vgpAsmHub/vgp.legacy.orderList.tsv
  • lines changed 14, context: html, text, full: html, text
    fe4e99030ede3daf6d7d368f60e1ebd6582ac7cf Fri Feb 24 14:45:11 2023 -0800
    catching up the VGP listings with current genomes no redmine
  • lines changed 14, context: html, text, full: html, text
    83435b8a84bf60a2d2632a345e40fd61f670b9a5 Fri Feb 24 15:46:11 2023 -0800
    catching up the VGP alternate listing no redmine
• src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv
  • lines changed 110, context: html, text, full: html, text
    fe4e99030ede3daf6d7d368f60e1ebd6582ac7cf Fri Feb 24 14:45:11 2023 -0800
    catching up the VGP listings with current genomes no redmine
• src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt
  • lines changed 55, context: html, text, full: html, text
    fe4e99030ede3daf6d7d368f60e1ebd6582ac7cf Fri Feb 24 14:45:11 2023 -0800
    catching up the VGP listings with current genomes no redmine
  • lines changed 85, context: html, text, full: html, text
    83435b8a84bf60a2d2632a345e40fd61f670b9a5 Fri Feb 24 15:46:11 2023 -0800
    catching up the VGP alternate listing no redmine
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    fd4633a9bab96bb77b10aa6ecf1667b6370d744d Fri Feb 24 08:51:34 2023 -0800
    correctly remove items that have moved to legacy no redmine
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    bc6d8c0971e27f2c535c7e9cb6c103d5ee9c15d0 Thu Feb 23 15:27:55 2023 -0800
    Squashing old pennantIcons and updating some GENCODE ones, refs #30657
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV42lift37.ra
  • lines changed 1, context: html, text, full: html, text
    bc6d8c0971e27f2c535c7e9cb6c103d5ee9c15d0 Thu Feb 23 15:27:55 2023 -0800
    Squashing old pennantIcons and updating some GENCODE ones, refs #30657
  • lines changed 1, context: html, text, full: html, text
    a4eee74618864ae995fb372bff6d5558351b9583 Thu Feb 23 16:45:55 2023 -0800
    Staging 5 new GENCODE tracks, refs #30657
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV43lift37.ra
  • lines changed 1, context: html, text, full: html, text
    a4eee74618864ae995fb372bff6d5558351b9583 Thu Feb 23 16:45:55 2023 -0800
    Staging 5 new GENCODE tracks, refs #30657
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 1, context: html, text, full: html, text
    bc6d8c0971e27f2c535c7e9cb6c103d5ee9c15d0 Thu Feb 23 15:27:55 2023 -0800
    Squashing old pennantIcons and updating some GENCODE ones, refs #30657
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra
  • lines changed 1, context: html, text, full: html, text
    a4eee74618864ae995fb372bff6d5558351b9583 Thu Feb 23 16:45:55 2023 -0800
    Staging 5 new GENCODE tracks, refs #30657
  • lines changed 54, context: html, text, full: html, text
    4b901eb0f53a8003cce7dcd598815f58066f73f2 Fri Feb 24 13:47:22 2023 -0800
    Staging and releasing the 5 new GENCODE tracks corresponding to V43 and VM32. Refs #30657
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra
  • lines changed 7, context: html, text, full: html, text
    4b901eb0f53a8003cce7dcd598815f58066f73f2 Fri Feb 24 13:47:22 2023 -0800
    Staging and releasing the 5 new GENCODE tracks corresponding to V43 and VM32. Refs #30657
• src/hg/makeDb/trackDb/human/hg38/knownGeneV43.html
  • lines changed 10, context: html, text, full: html, text
    a4eee74618864ae995fb372bff6d5558351b9583 Thu Feb 23 16:45:55 2023 -0800
    Staging 5 new GENCODE tracks, refs #30657
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    a7048503eb6fd7bf8c87ff628cd9ff10a1d88ffd Fri Feb 24 14:53:31 2023 -0800
    Fixing a small remaining old GENCODE number from the desc page.
• src/hg/makeDb/trackDb/human/hg38/recombRate.ra
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    8a904ce96a5b1e136073d1b569eba4274212dfdf Mon Feb 13 15:09:39 2023 -0800
    Announcing the release of the recombination rate track for hg38, refs #30044
  • lines changed 1, context: html, text, full: html, text
    91e37818e704b0bf01b3da3db49c07c4e60ab865 Fri Feb 24 17:30:57 2023 -0800
    Clarifying the track labels/desc based on user feedback, refs #30649
• src/hg/makeDb/trackDb/human/hg38/recombRate2.html
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    91e37818e704b0bf01b3da3db49c07c4e60ab865 Fri Feb 24 17:30:57 2023 -0800
    Clarifying the track labels/desc based on user feedback, refs #30649
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    bc6d8c0971e27f2c535c7e9cb6c103d5ee9c15d0 Thu Feb 23 15:27:55 2023 -0800
    Squashing old pennantIcons and updating some GENCODE ones, refs #30657
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    a4eee74618864ae995fb372bff6d5558351b9583 Thu Feb 23 16:45:55 2023 -0800
    Staging 5 new GENCODE tracks, refs #30657
  • lines changed 2, context: html, text, full: html, text
    4b901eb0f53a8003cce7dcd598815f58066f73f2 Fri Feb 24 13:47:22 2023 -0800
    Staging and releasing the 5 new GENCODE tracks corresponding to V43 and VM32. Refs #30657
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV42.ra
  • lines changed 1, context: html, text, full: html, text
    bc6d8c0971e27f2c535c7e9cb6c103d5ee9c15d0 Thu Feb 23 15:27:55 2023 -0800
    Squashing old pennantIcons and updating some GENCODE ones, refs #30657
  • lines changed 1, context: html, text, full: html, text
    a4eee74618864ae995fb372bff6d5558351b9583 Thu Feb 23 16:45:55 2023 -0800
    Staging 5 new GENCODE tracks, refs #30657
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV43.ra
  • lines changed 1, context: html, text, full: html, text
    a4eee74618864ae995fb372bff6d5558351b9583 Thu Feb 23 16:45:55 2023 -0800
    Staging 5 new GENCODE tracks, refs #30657
• src/hg/makeDb/trackDb/human/panelApp.ra
  • lines changed 1, context: html, text, full: html, text
    bc6d8c0971e27f2c535c7e9cb6c103d5ee9c15d0 Thu Feb 23 15:27:55 2023 -0800
    Squashing old pennantIcons and updating some GENCODE ones, refs #30657
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    bc6d8c0971e27f2c535c7e9cb6c103d5ee9c15d0 Thu Feb 23 15:27:55 2023 -0800
    Squashing old pennantIcons and updating some GENCODE ones, refs #30657
• src/hg/makeDb/trackDb/human/ukbDepletion.ra
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    bc6d8c0971e27f2c535c7e9cb6c103d5ee9c15d0 Thu Feb 23 15:27:55 2023 -0800
    Squashing old pennantIcons and updating some GENCODE ones, refs #30657
• src/hg/makeDb/trackDb/mouse/mm39/knownGene.alpha.ra
  • lines changed 1, context: html, text, full: html, text
    a4eee74618864ae995fb372bff6d5558351b9583 Thu Feb 23 16:45:55 2023 -0800
    Staging 5 new GENCODE tracks, refs #30657
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    4b901eb0f53a8003cce7dcd598815f58066f73f2 Fri Feb 24 13:47:22 2023 -0800
    Staging and releasing the 5 new GENCODE tracks corresponding to V43 and VM32. Refs #30657
• src/hg/makeDb/trackDb/mouse/mm39/knownGene.ra
  • lines changed 7, context: html, text, full: html, text
    4b901eb0f53a8003cce7dcd598815f58066f73f2 Fri Feb 24 13:47:22 2023 -0800
    Staging and releasing the 5 new GENCODE tracks corresponding to V43 and VM32. Refs #30657
• src/hg/makeDb/trackDb/mouse/mm39/knownGeneVM32.html
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    a4eee74618864ae995fb372bff6d5558351b9583 Thu Feb 23 16:45:55 2023 -0800
    Staging 5 new GENCODE tracks, refs #30657
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
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    bc6d8c0971e27f2c535c7e9cb6c103d5ee9c15d0 Thu Feb 23 15:27:55 2023 -0800
    Squashing old pennantIcons and updating some GENCODE ones, refs #30657
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
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    a4eee74618864ae995fb372bff6d5558351b9583 Thu Feb 23 16:45:55 2023 -0800
    Staging 5 new GENCODE tracks, refs #30657
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    4b901eb0f53a8003cce7dcd598815f58066f73f2 Fri Feb 24 13:47:22 2023 -0800
    Staging and releasing the 5 new GENCODE tracks corresponding to V43 and VM32. Refs #30657
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM31.ra
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    bc6d8c0971e27f2c535c7e9cb6c103d5ee9c15d0 Thu Feb 23 15:27:55 2023 -0800
    Squashing old pennantIcons and updating some GENCODE ones, refs #30657
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    a4eee74618864ae995fb372bff6d5558351b9583 Thu Feb 23 16:45:55 2023 -0800
    Staging 5 new GENCODE tracks, refs #30657
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM32.ra
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    a4eee74618864ae995fb372bff6d5558351b9583 Thu Feb 23 16:45:55 2023 -0800
    Staging 5 new GENCODE tracks, refs #30657
• src/hg/makefile
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    dede2d2b17c3c77141ba483d3c5491da7a9fc2be Wed Feb 22 13:32:21 2023 -0800
    adding pslSplitOnTarget to the userApps build refs #30675
• src/hg/utils/automation/makeDownloads.pl
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    81291d83afc22635047c8178c46d28aa7271d26b Thu Feb 23 14:47:50 2023 -0800
    Updating table schema references to the new data format description name, refs #30491
• src/hg/utils/otto/grcIncident/grcUpdate.sh
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    68c790ea17562c97c9c0d54346446196a11cbd6d Thu Feb 23 11:38:13 2023 -0800
    up to date with latest fixes no redmine
• src/hg/utils/otto/nextstrainNcov/nextstrain.py
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    6b76c158adf80081e080a8ebcb9157721663f1f5 Sun Feb 26 11:12:43 2023 -0800
    Updated nextstrain clades & coloring, got rid of extra files for ancient oldClades, fixed bug that caused errors for reverted deletions, got rid of unused and now incredibly verbose mutation-labels in newick.
• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.py
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    618f548682d24816a2898b4e29c5787ac591f67f Sun Feb 26 11:05:27 2023 -0800
    Adding comments after code review, thanks Jonathan.
• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
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    ac5d7c6726a1d4ccbea22592fa64de309869e9bf Sun Feb 26 11:03:27 2023 -0800
    Added many false reversions that were causing trouble in XBB, as well as a few for BQ.1, BQ.1.1, XBB.1(+27915) and XBB.1.5.
• src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv
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    01ea33002f66179857566a195021da375197557f Sun Feb 26 11:04:25 2023 -0800
    Added sequences for pango-designation#1637.
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
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    0b01886bcc0f6e4f6019edc35f03052b7aa49156 Sun Feb 26 11:06:33 2023 -0800
    Send verbose taxonium output to separate log file
• src/lib/udc.c
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    34269130c060acf47dd110def80020adf2c1c029 Thu Feb 23 20:20:26 2023 -0800
    removed WIFCONTINUED checks as that might not be available on some systems and is not needed
• src/product/installer/browserSetup.sh
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    88a60c7ebc4e3f7ddca6c0dcebd05db84f58fd19 Mon Feb 27 17:55:11 2023 +0100
    fixing py2 mysql build problem on fedora 37, refs #30684
• src/utils/chromToUcsc/chromToUcsc
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    2777956c1202283ecc5bf8b773b9ab82bab5d849 Thu Feb 23 12:01:05 2023 +0100
    adding genark support to chromToUcsc, refs #30454
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    29be125aaf00a06a7eb4a9e7c792119a41a6d622 Thu Feb 23 12:02:57 2023 +0100
    fixing typo in last commit, refs #30454
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    71fb2df68ba2d6c8164e8b5dcecd87a65934f0b5 Thu Feb 23 12:10:13 2023 +0100
    adding docs, refs #30454
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    28292a7173cf27b4da7f09b809a1d51aed180f15 Fri Feb 24 11:06:41 2023 +0100
    adding special case for hg38 to chromToUcsc, email from Hiram, no redmine
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    2567ad8ce3a3617f4d2ad81440d47d85246a0f0a Mon Feb 27 02:51:25 2023 -0800
    fixing chromToUcsc bug on py3 with uncompressed chromAlias files, no redmine, ran into this myself
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    22d92f453b687f1655db6a82b963d2df41632a4c Mon Feb 27 02:55:43 2023 -0800
    adding output directory option to chromToUcsc, no redmine
• src/utils/qa/weeklybld/buildEnv.csh
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    131d288c1e23674f35c1c1a051395683d51493b6 Mon Feb 27 10:01:17 2023 -0800
    v445 preview1

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