All File Changes

v446_preview2 to v446_base (2023-03-27 to 2023-04-03) v446

• build/kent-core/makeKentCore
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    713ad294550b5a02a84247c1438e799cea0b911e Fri Mar 31 01:18:25 2023 -0700
    changes to kent-core, adding tags, see https://github.com/ucscGenomeBrowser/kent-core/issues/1
• src/hg/hgSearch/hgSearch.c
  • lines changed 10, context: html, text, full: html, text
    8fca283c4625a81c19eb71e87582e831771f03f6 Tue Mar 28 15:49:39 2023 -0700
    Make single position search coming from hgGateway go directly to hgTracks before drawing any html, refs Max email
• src/hg/hgTracks/imageV2.c
  • lines changed 4, context: html, text, full: html, text
    3a5d31716bb34526d02e20db823e8d5d0ae4a7d4 Mon Mar 27 14:36:58 2023 -0700
    some more error checking in the routine that collapses squishyPack tracks into a single imgTrack.
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 23, context: html, text, full: html, text
    72ed3a859583339f4178ff91515f758c59aaba2d Wed Mar 29 16:54:52 2023 -0700
    Announcing the release of the updated DGV tracks for hg19/hg38, refs #25566
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    72ed3a859583339f4178ff91515f758c59aaba2d Wed Mar 29 16:54:52 2023 -0700
    Announcing the release of the updated DGV tracks for hg19/hg38, refs #25566
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    07beac33fc2abb48bea11162ac9b833b7a0d383b Mon Apr 3 10:11:25 2023 -0700
    New version number v446
• src/hg/js/hgTracks.js
  • lines changed 4, context: html, text, full: html, text
    a2e927679baeff2c5cb03b265afa9fe96884c358 Tue Mar 28 14:16:39 2023 -0700
    Updating the new track speed message, refs #30591
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    4338ba13b766ee88e8b51ddd84dfc1363488e1bd Wed Mar 29 03:03:23 2023 -0700
    making performance warning box nicer based on feedback from Lou, refs #30591
  • lines changed 7, context: html, text, full: html, text
    80444b67d516cfc76198b8416b8f302aa7dabe25 Thu Mar 30 10:18:41 2023 -0700
    One more tweak to the speed message, refs #30591
• src/hg/lib/hgFind.c
  • lines changed 47, context: html, text, full: html, text
    67dcce67b7da61d4de46d360754b174294432a8c Wed Mar 29 16:22:39 2023 -0700
    Fix non-knownCanonical results not showing up in a knownGene search, refs #25078
• src/hg/lib/hui.c
  • lines changed 17, context: html, text, full: html, text
    f1d16c8dda5212308a33fa1642a07b7e8c28b047 Thu Mar 30 07:57:27 2023 -0700
    adding downloadUrl trackDb statement, no docs yet, refs #30904
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 5, context: html, text, full: html, text
    ada1ddb2e10cba1905097ec4b52496c4d6dc21b9 Mon Mar 27 12:42:46 2023 -0700
    HPRC almost done refs #30508
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    ae2dd63fb1a1921a7ad835eb5d5cf669ba900f5a Wed Mar 29 11:19:46 2023 -0700
    nearing end game for HPRC and a user request refs #30508
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    9aaf8df1f904ec62eceae14d5434f0d7b8ca4c2f Wed Mar 29 13:45:43 2023 -0700
    add 4 per user request refs #29545
• src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
  • lines changed 1, context: html, text, full: html, text
    eb19eff7d841ca40ae2f574641f8a61178fcfc5a Mon Mar 27 11:57:58 2023 -0700
    the thead elements can be sticky so they always are visible refs #30508
• src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
  • lines changed 1, context: html, text, full: html, text
    eb19eff7d841ca40ae2f574641f8a61178fcfc5a Mon Mar 27 11:57:58 2023 -0700
    the thead elements can be sticky so they always are visible refs #30508
  • lines changed 48, context: html, text, full: html, text
    47fa2308b393f3d1eea2310c58cdc46090356a62 Sun Apr 2 22:35:22 2023 -0700
    adding custom index page code for CCGP collection refs #30912
• src/hg/makeDb/doc/asmHubs/trackData.pl
  • lines changed 1, context: html, text, full: html, text
    eb19eff7d841ca40ae2f574641f8a61178fcfc5a Mon Mar 27 11:57:58 2023 -0700
    the thead elements can be sticky so they always are visible refs #30508
• src/hg/makeDb/doc/bigDbSnp.txt
  • lines changed 64, context: html, text, full: html, text
    61946925ad5049ff822bd5e4e76d00c3106797ee Tue Mar 28 16:45:14 2023 -0700
    re-ran dbsnp155 build after fixing bug rm30617. refs #30617.
• src/hg/makeDb/doc/ccgpAsmHub/CCGP_logo.png
  • lines changed 0, context: html, text, full: html, text
    0cdd9c7fee07aa3d5ef9f4a7dd9e3146f52421c3 Sun Apr 2 22:30:18 2023 -0700
    adding CCGP logo image refs #30912
• src/hg/makeDb/doc/ccgpAsmHub/ccgp.orderList.tsv
  • lines changed 24, context: html, text, full: html, text
    2cd36bf868d2c1dd42dd452f9b9724edd4ee67e9 Sun Apr 2 22:11:13 2023 -0700
    25 CCGP assemblies done refs #30912
• src/hg/makeDb/doc/ccgpAsmHub/ccgp.taxId.asmId.class.txt
  • lines changed 123, context: html, text, full: html, text
    54bfa01a40eae2477526f01136b15e3cc757126b Sun Apr 2 21:56:49 2023 -0700
    starting the taxId class list for CCGP assemblies refs #30912
• src/hg/makeDb/doc/hg38/hprcLastz.txt
  • lines changed 417, context: html, text, full: html, text
    50871bdc58d90912e30fdb66e2523de383ada100 Sat Apr 1 19:07:44 2023 -0700
    record of lastz runs HPRC genomes to hg38 refs #30508
  • lines changed 320, context: html, text, full: html, text
    166f7ceea61ae6355730d52f2ab9edf5b3542103 Sun Apr 2 14:50:37 2023 -0700
    record of lastz runs HPRC genomes to hg38 refs #30508
• src/hg/makeDb/doc/hprcAsmHub/hprc.orderList.tsv
  • lines changed 5, context: html, text, full: html, text
    07f3abdafbcc6ddc16923543827fe2cff304cb92 Mon Mar 27 13:01:43 2023 -0700
    HPRC almost done refs #30508
  • lines changed 11, context: html, text, full: html, text
    2be741b9b6d20b96b95fcf43a958f55c4dea7acc Wed Mar 29 11:29:28 2023 -0700
    nearing end game for HPRC refs #30508
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    d6c7fa4c35cbcbdaea914d8658b04d752348da80 Thu Mar 30 10:28:16 2023 -0700
    only one left to go refs #30508
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    c571219d92855a102ea156d7256a288750fcb147 Thu Mar 30 19:25:44 2023 -0700
    completed HPRC building refs #30508
• src/hg/makeDb/doc/hprcAsmHub/hub.txt
  • lines changed 3, context: html, text, full: html, text
    b20f086704c8878dddc4411af2b22ef21edf7c50 Thu Mar 30 19:36:44 2023 -0700
    correct title on the hub refs #30508
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 7, context: html, text, full: html, text
    c2613e3ae4bd2d87e4636f0f8f2fd7edade5f567 Wed Mar 29 15:45:48 2023 -0700
    adding assemblies requested by users refs #29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 31, context: html, text, full: html, text
    3ec2e23a21596e32f496a4725c2f62fcfa06c9c5 Mon Mar 27 12:59:52 2023 -0700
    HPRC almost done refs #30508
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    e2c655ad9c801455a788529461d13f8faea0a29d Wed Mar 29 11:26:20 2023 -0700
    nearing end game for HPRC refs #30508
  • lines changed 30, context: html, text, full: html, text
    469854e0db669fea70d5cea72340c4b5ef4c232e Sun Apr 2 21:08:37 2023 -0700
    up to date with all HPRC assemblies refs #30508
• src/hg/makeDb/trackDb/human/constraintSuper.ra
  • lines changed 1, context: html, text, full: html, text
    743cda1cb34617207849cba426c728be6bc73e90 Tue Mar 28 12:50:30 2023 -0700
    Squashing old pennantIcon
• src/hg/makeDb/trackDb/human/hg19/defaultPriority.ra
  • lines changed 3, context: html, text, full: html, text
    72ed3a859583339f4178ff91515f758c59aaba2d Wed Mar 29 16:54:52 2023 -0700
    Announcing the release of the updated DGV tracks for hg19/hg38, refs #25566
  • lines changed 1, context: html, text, full: html, text
    ed07e6b8d5f89a5720f55f5a306e6de6a79f64a3 Wed Mar 29 17:13:07 2023 -0700
    Updating pennantIcon dates for the updated DGV tracks for hg19/hg38, refs #25566
• src/hg/makeDb/trackDb/human/hg38/crossTissueMaps.html
  • lines changed 11, context: html, text, full: html, text
    4cdb607951bac8cd35b46f28b32c76599d925d9b Thu Mar 30 12:46:38 2023 -0700
    Updating the track description page and adding priority setting, refs #29954
• src/hg/makeDb/trackDb/human/hg38/crossTissueMaps.ra
  • lines changed 4, context: html, text, full: html, text
    4cdb607951bac8cd35b46f28b32c76599d925d9b Thu Mar 30 12:46:38 2023 -0700
    Updating the track description page and adding priority setting, refs #29954
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    72ed3a859583339f4178ff91515f758c59aaba2d Wed Mar 29 16:54:52 2023 -0700
    Announcing the release of the updated DGV tracks for hg19/hg38, refs #25566
  • lines changed 2, context: html, text, full: html, text
    ed07e6b8d5f89a5720f55f5a306e6de6a79f64a3 Wed Mar 29 17:13:07 2023 -0700
    Updating pennantIcon dates for the updated DGV tracks for hg19/hg38, refs #25566
  • lines changed 1, context: html, text, full: html, text
    d622a5637f75013962bc590aa56266cd763d3240 Thu Mar 30 17:31:54 2023 -0700
    Updating source data version for the DGV track, refs #25566
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    54c56698083e7bd2697e4b261ec232d1642a3157 Fri Mar 31 02:47:37 2023 -0700
    forgot to commit tagTypes change with last commit, refs #30904
• src/hg/snp/dbSnpJsonToTab/dbSnpJsonToTab.c
  • lines changed 71, context: html, text, full: html, text
    e9401d3358499d9ffa04eb076dfe18a12769d959 Tue Mar 28 16:43:15 2023 -0700
    fixing dbSnpJsonToTab part of the dbSnp pipeline, our code was not handling clinvar records that had multiple significances, even though the json clearly shows it can be a list. Also the jsonQuery code is great at fetching a list of elements that match your query, but it just sticks them all together, and has no idea which came from which so maintaining the grouping and order was tricky. Used Angies suggestion to html-encode the commas so the rest of the code just things it is a single string without any commas in it so it can work properly inside the comma-separated list. It also reports in Warnings.tab the comma-separated ones re-encoded so you can double check those RS ids worked correctly in the browser, it also lists the multiple-sigs list for easy viewing for the pipeline-runner. fixes #30617
• src/hg/utils/automation/AsmHub.pm
  • lines changed 12, context: html, text, full: html, text
    595d44078d99eb1f717f097e2e4c886c450b2fe1 Tue Mar 28 12:19:29 2023 -0700
    adding download links on the gene track description pages for the GTF file no redmine
• src/hg/utils/automation/asmHubAugustusGene.pl
  • lines changed 9, context: html, text, full: html, text
    595d44078d99eb1f717f097e2e4c886c450b2fe1 Tue Mar 28 12:19:29 2023 -0700
    adding download links on the gene track description pages for the GTF file no redmine
• src/hg/utils/automation/asmHubNcbiRefSeq.pl
  • lines changed 26, context: html, text, full: html, text
    595d44078d99eb1f717f097e2e4c886c450b2fe1 Tue Mar 28 12:19:29 2023 -0700
    adding download links on the gene track description pages for the GTF file no redmine
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 1, context: html, text, full: html, text
    7c0c6f08b3e53af0c02ec2f198ef1592584dccd9 Sat Apr 1 19:18:30 2023 -0700
    correctly remove rmsk.customLib.fa.gz link refs #30508
• src/hg/utils/automation/asmHubXenoRefGene.pl
  • lines changed 20, context: html, text, full: html, text
    595d44078d99eb1f717f097e2e4c886c450b2fe1 Tue Mar 28 12:19:29 2023 -0700
    adding download links on the gene track description pages for the GTF file no redmine
• src/hg/utils/bigMafToMaf/bigMafToMaf.c
  • lines changed 65, context: html, text, full: html, text
    0077bc3d653ba288e13b6ad75857ed5d6c4b51cd Sun Apr 2 10:45:31 2023 -0700
    decode bigMaf in chunks so as not to use absurd about of memory
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
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    421c01571a0e23866205154958ad31e1fdc91ff2 Thu Mar 30 12:02:57 2023 -0700
    More new lineages. Now up to pango-designation release v1.19.
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    5529da7ba80ea1c30db7bce1ae40a9729ce2c73d Thu Mar 30 18:00:35 2023 -0700
    Oops, forgot to mask UTR sites 261 and 29742 for pangolin.
• src/hg/utils/vcfToHgvs/tests/expected/stopLoss.tab
  • lines changed 21, context: html, text, full: html, text
    eeda64a71cfc7fe13b91130dcf6e6cdc22767059 Thu Mar 30 17:19:13 2023 -0700
    Make test was failing for utility vcfToHgvs. The stopLoss for the test NM_005572.3 just picked up more alignments from hg38. Added these to the expected list.
• src/inc/srcVersion.h
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    07beac33fc2abb48bea11162ac9b833b7a0d383b Mon Apr 3 10:11:25 2023 -0700
    New version number v446
• src/utils/qa/weeklybld/buildEnv.csh
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    1adbad53f9eb4018d231a73c7b9d073d58ed99da Mon Apr 3 10:09:10 2023 -0700
    v446 final build, refs #30851

• lines changed: 1600
• files changed: 54