All File Changes

v442_preview to v442_preview2 (2022-12-19 to 2023-01-03) v442

• src/hg/hgCustom/hgCustom.c
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    f832c0f046e1a08ebf9fc1070c0cc11cd1192462 Wed Dec 21 14:41:59 2022 -0800
    Fix database check in hgCustom custom track update procedure by stripping quotes from the new config db setting, refs #3201
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 6, context: html, text, full: html, text
    17743793f41d56eb703ba368534cbdad0c1b735e Sat Dec 31 13:09:33 2022 -0800
    When parsing GB accession out of full name, look for | so we skip over embedded reference accession in isolate name. Reported in https://github.com/cov-lineages/pango-designation/issues/1494
• src/hg/htdocs/goldenPath/help/blatSpec.html
  • lines changed 1, context: html, text, full: html, text
    deea5ecd50c17260a1d3e43ed7c36af0401241d7 Sat Dec 31 14:58:42 2022 -0800
    Fixing 404 link for the Static Page Cronjob 2022-12-15, no RM
• src/hg/js/hgGateway.js
  • lines changed 1, context: html, text, full: html, text
    ee93b178ce4495b2d0d27d79e6831620a4e7370a Thu Dec 22 10:08:15 2022 -0800
    Remove leading and trailing whitespace before checking for standard range specifiers or before a chromosome name lookup, refs #30415
• src/hg/js/hgTracks.js
  • lines changed 1, context: html, text, full: html, text
    ee93b178ce4495b2d0d27d79e6831620a4e7370a Thu Dec 22 10:08:15 2022 -0800
    Remove leading and trailing whitespace before checking for standard range specifiers or before a chromosome name lookup, refs #30415
• src/hg/js/utils.js
  • lines changed 6, context: html, text, full: html, text
    ee93b178ce4495b2d0d27d79e6831620a4e7370a Thu Dec 22 10:08:15 2022 -0800
    Remove leading and trailing whitespace before checking for standard range specifiers or before a chromosome name lookup, refs #30415
• src/hg/makeDb/doc/assemblyEquivalence/update.2022-11-14.txt
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    c0934691ab46714dedde3271b09d15f55d4a4471 Thu Dec 22 22:43:59 2022 -0800
    this is progress with an important note about cleaning up left over garbage
• src/hg/makeDb/doc/hg38/gencode.txt
  • lines changed 29, context: html, text, full: html, text
    fa5d9035c64f21008b496bc74780a9d0fcc3f2c3 Thu Dec 29 15:26:11 2022 -0800
    import of GENCODE V43 pre-release
• src/hg/makeDb/doc/mm39/gencode.txt
  • lines changed 31, context: html, text, full: html, text
    c9e0b8fd8911a369f435237837516a6f378297e8 Thu Dec 29 16:15:37 2022 -0800
    import of GENCODE VM32 pre-release
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 4, context: html, text, full: html, text
    fa5d9035c64f21008b496bc74780a9d0fcc3f2c3 Thu Dec 29 15:26:11 2022 -0800
    import of GENCODE V43 pre-release
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    c9e0b8fd8911a369f435237837516a6f378297e8 Thu Dec 29 16:15:37 2022 -0800
    import of GENCODE VM32 pre-release
• src/hg/makeDb/schema/all.joiner
  • lines changed 94, context: html, text, full: html, text
    fa5d9035c64f21008b496bc74780a9d0fcc3f2c3 Thu Dec 29 15:26:11 2022 -0800
    import of GENCODE V43 pre-release
  • lines changed 94, context: html, text, full: html, text
    c9e0b8fd8911a369f435237837516a6f378297e8 Thu Dec 29 16:15:37 2022 -0800
    import of GENCODE VM32 pre-release
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    20e4aa9f3d5e0ffe045017a0be5308767bf84640 Mon Dec 19 12:27:17 2022 -0800
    Turning off default track that users constatnly turn off themselves, refs #30373
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    bebd4961b4d82e7da9a553cfc7950871f39bea7b Tue Dec 20 14:11:00 2022 -0800
    Fixing a bone headed move (setting alpha instead of fixing visibilities), refs #30373
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 1, context: html, text, full: html, text
    bebd4961b4d82e7da9a553cfc7950871f39bea7b Tue Dec 20 14:11:00 2022 -0800
    Fixing a bone headed move (setting alpha instead of fixing visibilities), refs #30373
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra
  • lines changed 21, context: html, text, full: html, text
    9ccb1b32f902ada14438df38d9cf8a1fd40ad6f8 Fri Dec 30 08:48:46 2022 -0800
    switch to knownGene V43
• src/hg/makeDb/trackDb/human/hg38/knownGeneV43.html
  • lines changed 140, context: html, text, full: html, text
    9ccb1b32f902ada14438df38d9cf8a1fd40ad6f8 Fri Dec 30 08:48:46 2022 -0800
    switch to knownGene V43
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    fa5d9035c64f21008b496bc74780a9d0fcc3f2c3 Thu Dec 29 15:26:11 2022 -0800
    import of GENCODE V43 pre-release
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    20e4aa9f3d5e0ffe045017a0be5308767bf84640 Mon Dec 19 12:27:17 2022 -0800
    Turning off default track that users constatnly turn off themselves, refs #30373
  • lines changed 1, context: html, text, full: html, text
    bebd4961b4d82e7da9a553cfc7950871f39bea7b Tue Dec 20 14:11:00 2022 -0800
    Fixing a bone headed move (setting alpha instead of fixing visibilities), refs #30373
  • lines changed 2, context: html, text, full: html, text
    9ccb1b32f902ada14438df38d9cf8a1fd40ad6f8 Fri Dec 30 08:48:46 2022 -0800
    switch to knownGene V43
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV43.html
  • lines changed 47, context: html, text, full: html, text
    fa5d9035c64f21008b496bc74780a9d0fcc3f2c3 Thu Dec 29 15:26:11 2022 -0800
    import of GENCODE V43 pre-release
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV43.ra
  • lines changed 247, context: html, text, full: html, text
    fa5d9035c64f21008b496bc74780a9d0fcc3f2c3 Thu Dec 29 15:26:11 2022 -0800
    import of GENCODE V43 pre-release
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.ra
  • lines changed 1, context: html, text, full: html, text
    bebd4961b4d82e7da9a553cfc7950871f39bea7b Tue Dec 20 14:11:00 2022 -0800
    Fixing a bone headed move (setting alpha instead of fixing visibilities), refs #30373
• src/hg/makeDb/trackDb/mouse/mm39/knownGene.alpha.ra
  • lines changed 6, context: html, text, full: html, text
    af9a22e5fe719fb867173cdaa084b62a1ed31192 Sat Dec 31 09:20:03 2022 -0800
    VM32 knownGene trackDb
• src/hg/makeDb/trackDb/mouse/mm39/knownGeneVM32.html
  • lines changed 142, context: html, text, full: html, text
    af9a22e5fe719fb867173cdaa084b62a1ed31192 Sat Dec 31 09:20:03 2022 -0800
    VM32 knownGene trackDb
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.chainNet.ra
  • lines changed 4, context: html, text, full: html, text
    d08be258b2272b1ca51a89759cb88027fd6df84d Tue Dec 20 10:57:03 2022 -0800
    fixup gbdb locations for chain nets to GCF_009829145.1 no redmine
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    c9e0b8fd8911a369f435237837516a6f378297e8 Thu Dec 29 16:15:37 2022 -0800
    import of GENCODE VM32 pre-release
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    af9a22e5fe719fb867173cdaa084b62a1ed31192 Sat Dec 31 09:20:03 2022 -0800
    VM32 knownGene trackDb
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.rbestNet.ra
  • lines changed 4, context: html, text, full: html, text
    d08be258b2272b1ca51a89759cb88027fd6df84d Tue Dec 20 10:57:03 2022 -0800
    fixup gbdb locations for chain nets to GCF_009829145.1 no redmine
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.syntenicNet.ra
  • lines changed 4, context: html, text, full: html, text
    d08be258b2272b1ca51a89759cb88027fd6df84d Tue Dec 20 10:57:03 2022 -0800
    fixup gbdb locations for chain nets to GCF_009829145.1 no redmine
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM32.html
  • lines changed 30, context: html, text, full: html, text
    c9e0b8fd8911a369f435237837516a6f378297e8 Thu Dec 29 16:15:37 2022 -0800
    import of GENCODE VM32 pre-release
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM32.ra
  • lines changed 247, context: html, text, full: html, text
    c9e0b8fd8911a369f435237837516a6f378297e8 Thu Dec 29 16:15:37 2022 -0800
    import of GENCODE VM32 pre-release
• src/hg/utils/automation/asmHubRepeatMasker.sh
  • lines changed 12, context: html, text, full: html, text
    4dc9aaa85b70bdd4fd58d77b323147e28dbe16e6 Sat Dec 24 13:01:30 2022 -0800
    fixup new rmToTrackHub.pl usage no redmine
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 5, context: html, text, full: html, text
    9df5ecf8842547ecb2a7c6fd2338a3f3a6fb5e26 Tue Dec 20 10:39:21 2022 -0800
    setup the custom RepeatModeler lib for download reference no redmine
• src/hg/utils/automation/doAssemblyHub.pl
  • lines changed 1, context: html, text, full: html, text
    5c6eeb845281a9cf407dcadd3480b1c65bfb48c7 Wed Dec 21 11:00:05 2022 -0800
    mistaken left on forced UCSC names for alt sequences no redmine
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    249f1c6c7231ede3da49dd949eaffb491e5d48cf Fri Dec 23 08:39:41 2022 -0800
    correct processing of alternatie and patch sequences no redmine
• src/hg/utils/automation/doBlastzChainNet.pl
  • lines changed 25, context: html, text, full: html, text
    24d667a6353af7e3d009ff35beb21f85dc40984d Tue Dec 20 10:40:08 2022 -0800
    correctly make symLinks for chainNet files at the time they actually exist no redmine
• src/hg/utils/automation/doRecipBest.pl
  • lines changed 12, context: html, text, full: html, text
    24d667a6353af7e3d009ff35beb21f85dc40984d Tue Dec 20 10:40:08 2022 -0800
    correctly make symLinks for chainNet files at the time they actually exist no redmine
• src/hg/utils/automation/doRepeatModeler.pl
  • lines changed 1, context: html, text, full: html, text
    d7d65ade9824fda1d981e1f9692860e243dd76a1 Mon Dec 26 21:01:46 2022 -0800
    "do not have the same name bash script as doRepeatMasker.pl no redmine
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    b032eee9e1cec0a1cb46ccff207a7a99b0a94e00 Wed Dec 28 22:17:38 2022 -0800
    run repeatModeler in /dev/shm for better performance no redmine
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    4f202ee8fcfdcec142628ab0da1ba73fe81b72fb Sat Dec 31 10:52:42 2022 -0800
    correctly use the tmpDir for parasol no redmine
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    f0f02218613a6cce438e7ce73694f7539587118d Mon Jan 2 09:33:12 2023 -0800
    preserve the do.log during the rsync no redmine
• src/hg/utils/hubCheck/tests/expected/autoScaleHub.txt
  • lines changed 2, context: html, text, full: html, text
    6314cc588f1f1c45248ecf085bc8bda5cf7f2f2a Tue Dec 20 11:10:30 2022 -0800
    Fix hubCheck tests after error message change, refs #13428
• src/hg/utils/otto/knownGene/addIspcrToCentral.sh
  • lines changed 9, context: html, text, full: html, text
    ef38617cd32fd57c007e05a6ed1d1311dd87599c Sat Dec 31 13:53:21 2022 -0800
    add a couple of tiny utilities used in the knownGene build
• src/hg/utils/otto/knownGene/genIspcrMail.sh
  • lines changed 8, context: html, text, full: html, text
    ef38617cd32fd57c007e05a6ed1d1311dd87599c Sat Dec 31 13:53:21 2022 -0800
    add a couple of tiny utilities used in the knownGene build
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
  • lines changed 16, context: html, text, full: html, text
    da0e133025899dc28777e841a961f45fc4591297 Sat Dec 10 18:27:16 2022 -0800
    A few new lineages, path tweaks and pango masks for pango-designation release v1.17
  • lines changed 5, context: html, text, full: html, text
    1c1a233dd8be4d16c15abdffdb8da88ee9b5a34b Wed Dec 14 19:46:30 2022 -0800
    Make it clear that C15240T is not a part of BQ.1.1 -- that was a tree-building/sequence problem.
• src/utils/qa/makefile
  • lines changed 1, context: html, text, full: html, text
    ae81cb8abefcb52cf51929ca0f2435727ec31a6b Fri Dec 30 20:45:37 2022 -0800
    Updating makedoc for python script to get monthly top hgSearch result terms, refs #30372
• src/utils/qa/searchedTermsCron.py
  • lines changed 130, context: html, text, full: html, text
    ec4ebc312a17073e6052de6da0368acd21104806 Fri Dec 30 19:54:21 2022 -0800
    Adding a python script to get monthly top hgSearch result terms, refs #30372
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    23b50ba3c34381d85d4bb7d5bd77aaa21b8ebcbb Tue Jan 3 10:09:19 2023 -0800
    v442 preview2, refs #30409

• lines changed: 1933
• files changed: 52