All File Changes

v453_preview2 to v453_base (2023-08-21 to 2023-08-28) v453

• src/hg/cgilib/cartJson.c
  • lines changed 8, context: html, text, full: html, text
    f5bc6b413957f25f24799f15e836757e4f82a668 Tue Aug 22 13:27:51 2023 -0700
    Make warnings show up in search results, refs #31965
• src/hg/cgilib/pcrResult.c
  • lines changed 30, context: html, text, full: html, text
    4163e36238919a24e50cbd911aa52fa3a07a7796 Thu Aug 24 10:58:38 2023 -0700
    Fix backwards compatibility bug I introduced when adding multiple pcr results, refs #32022
  • lines changed 30, context: html, text, full: html, text
    6794e8c75739e1c58957f1a5b5ed1bc6fb444133 Thu Aug 24 15:38:26 2023 -0700
    Revert "Fix backwards compatibility bug I introduced when adding multiple pcr results, refs #32022" This reverts commit 4163e36238919a24e50cbd911aa52fa3a07a7796.
• src/hg/hgSearch/hgSearch.c
  • lines changed 2, context: html, text, full: html, text
    f5bc6b413957f25f24799f15e836757e4f82a668 Tue Aug 22 13:27:51 2023 -0700
    Make warnings show up in search results, refs #31965
• src/hg/hgTracks/cds.c
  • lines changed 8, context: html, text, full: html, text
    4163e36238919a24e50cbd911aa52fa3a07a7796 Thu Aug 24 10:58:38 2023 -0700
    Fix backwards compatibility bug I introduced when adding multiple pcr results, refs #32022
  • lines changed 8, context: html, text, full: html, text
    6794e8c75739e1c58957f1a5b5ed1bc6fb444133 Thu Aug 24 15:38:26 2023 -0700
    Revert "Fix backwards compatibility bug I introduced when adding multiple pcr results, refs #32022" This reverts commit 4163e36238919a24e50cbd911aa52fa3a07a7796.
  • lines changed 8, context: html, text, full: html, text
    72275dee5bee0933472aac4cbbf051f712d76f83 Thu Aug 24 15:48:47 2023 -0700
    Separate out hgTracks only fix for broken old style pcr result track, refs #32028
• src/hg/hgTracks/hgTracks.c
  • lines changed 9, context: html, text, full: html, text
    e46da004a1ed5fdf64eb24662bf94e0eee2f3bf3 Tue Aug 22 10:15:31 2023 -0700
    Make hgTracks tutorial start automatically with special url variable startTutorial=true, refs #32004
  • lines changed 1, context: html, text, full: html, text
    38713472b37d9c8ebf55826b3d6f52edc7fba8f1 Wed Aug 23 15:24:47 2023 -0700
    one more edit of squishyPack control label
• src/hg/hgTracks/simpleTracks.c
  • lines changed 5, context: html, text, full: html, text
    54be876b42771b1aea2839a533e46c073134caf1 Wed Aug 23 10:36:24 2023 -0700
    Fix pgSnp items not scaling correctly when item is off the left side of the window, refs #32006
• src/hg/hgc/hgc.c
  • lines changed 5, context: html, text, full: html, text
    4163e36238919a24e50cbd911aa52fa3a07a7796 Thu Aug 24 10:58:38 2023 -0700
    Fix backwards compatibility bug I introduced when adding multiple pcr results, refs #32022
  • lines changed 5, context: html, text, full: html, text
    6794e8c75739e1c58957f1a5b5ed1bc6fb444133 Thu Aug 24 15:38:26 2023 -0700
    Revert "Fix backwards compatibility bug I introduced when adding multiple pcr results, refs #32022" This reverts commit 4163e36238919a24e50cbd911aa52fa3a07a7796.
• src/hg/hgc/vcfClick.c
  • lines changed 12, context: html, text, full: html, text
    1e6071743e73bccbc7d56a9e38e93cc1daabccfd Tue Aug 22 11:59:42 2023 -0700
    Make the INFO fields collapsible table have unique ids when there is more than one on an hgc page, refs #31987
• src/hg/htdocs/indexNews.html
  • lines changed 6, context: html, text, full: html, text
    45d64d64f40e2412d84eaf405a2c05b0e3ac5023 Fri Aug 25 13:37:24 2023 -0700
    I accidentally removed the javascript announcement, adding it back in, refs #32033
  • lines changed 1, context: html, text, full: html, text
    a1fb86d76a03fdc61aa2e90735e0b22ecc64c847 Fri Aug 25 13:45:27 2023 -0700
    Forgot to add a dash, refs #32033
• src/hg/inc/cartJson.h
  • lines changed 6, context: html, text, full: html, text
    f5bc6b413957f25f24799f15e836757e4f82a668 Tue Aug 22 13:27:51 2023 -0700
    Make warnings show up in search results, refs #31965
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    dd1b035041ad3777603524c4f8befdafc92074c0 Mon Aug 28 11:43:41 2023 -0700
    New version number v453
• src/hg/js/hgSearch.js
  • lines changed 6, context: html, text, full: html, text
    f5bc6b413957f25f24799f15e836757e4f82a668 Tue Aug 22 13:27:51 2023 -0700
    Make warnings show up in search results, refs #31965
  • lines changed 3, context: html, text, full: html, text
    0e7a265a6b8dab3ba98319422893f1121f72e729 Wed Aug 23 15:50:58 2023 -0700
    When there is a search warning but we still can get one result, keep the user on hgSearch instead of redirecting to hgTracks, refs #31965
  • lines changed 4, context: html, text, full: html, text
    b4d43329da1df630ed2a970921b5e135f3aa9771 Fri Aug 25 17:50:13 2023 -0700
    Fix typo in typeof check, caught by Lou no refs
• src/hg/js/hgTracks.js
  • lines changed 5, context: html, text, full: html, text
    e46da004a1ed5fdf64eb24662bf94e0eee2f3bf3 Tue Aug 22 10:15:31 2023 -0700
    Make hgTracks tutorial start automatically with special url variable startTutorial=true, refs #32004
• src/hg/js/tutorial.js
  • lines changed 8, context: html, text, full: html, text
    e46da004a1ed5fdf64eb24662bf94e0eee2f3bf3 Tue Aug 22 10:15:31 2023 -0700
    Make hgTracks tutorial start automatically with special url variable startTutorial=true, refs #32004
• src/hg/lib/hgFind.c
  • lines changed 4, context: html, text, full: html, text
    c57287f61a6f0e6233d6d01a572de8657028b998 Mon Aug 28 09:55:09 2023 -0700
    Fix bug in length spec search, if the user entered a length search, like chrA:X+Y, we first need to add Y to X before checking if the start and were a mistakenly swapped position, refs #32041,16721
• src/hg/lib/hui.c
  • lines changed 6, context: html, text, full: html, text
    38713472b37d9c8ebf55826b3d6f52edc7fba8f1 Wed Aug 23 15:24:47 2023 -0700
    one more edit of squishyPack control label
  • lines changed 1, context: html, text, full: html, text
    b56049171020ecac24906e2b2360fa89dacff72d Wed Aug 23 16:51:34 2023 -0700
    oops delete extra <B>
• src/hg/lib/jksql.c
  • lines changed 4, context: html, text, full: html, text
    bfc9e5fea7cdeda433effdeb36b2c43a64698006 Mon Aug 28 12:11:04 2023 +0200
    trying to work around mysql8/mariadb differences, email from Glenn Hickey and Mark
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    18802096ad7f602950846d47793b4880abb32dab Fri Aug 25 10:04:36 2023 -0700
    adding GCF_009828535.3_HMol_V3 silvery gibbon (v3 HMO894 2021 UC Santa Cruz) for an update refs #29545
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 172, context: html, text, full: html, text
    568883e90c09ae0acc3a53010b2fc2f098cffa68 Tue Aug 22 10:11:29 2023 -0700
    some experiments with same species liftover to HPRC assemblies does not work refs #31561
• src/hg/makeDb/doc/hg38/hprc90way.txt
  • lines changed 202, context: html, text, full: html, text
    80af0d3fbbffc1d7f1a42972fd4630812d4550ae Mon Aug 21 14:58:11 2023 -0700
    loading up a 90-way maf file refs #31561
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    18802096ad7f602950846d47793b4880abb32dab Fri Aug 25 10:04:36 2023 -0700
    adding GCF_009828535.3_HMol_V3 silvery gibbon (v3 HMO894 2021 UC Santa Cruz) for an update refs #29545
• src/hg/makeDb/doc/ucscGenes/mm39.gencodeVM33.sh
  • lines changed 47, context: html, text, full: html, text
    6eed61012da9293c065a6b0f901a4f7c70ddb215 Tue Aug 22 13:30:08 2023 -0700
    makedoc for GENCODE VM33 knownGene build, refs #30841
• src/hg/makeDb/trackDb/crisprAll.ra
  • lines changed 1, context: html, text, full: html, text
    b02172165258117e726f871325d249202b193e2b Tue Aug 22 17:10:48 2023 -0700
    Clarifying the crispr message that regional queries can also fail, refs #18515
• src/hg/makeDb/trackDb/human/chainNetPrimate.ra
  • lines changed 10, context: html, text, full: html, text
    25a09db69fab1cdea5d0e52746627048d23d2aa7 Thu Aug 24 20:21:57 2023 -0700
    add chain definition for GCA_018873775.2_hg01243.v3.0 to the primate composite refs #31844
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra
  • lines changed 2, context: html, text, full: html, text
    38713472b37d9c8ebf55826b3d6f52edc7fba8f1 Wed Aug 23 15:24:47 2023 -0700
    one more edit of squishyPack control label
• src/hg/makeDb/trackDb/human/hg38/trackDb.hprc90way.ra
  • lines changed 72, context: html, text, full: html, text
    165cf7071f83306d069fc2ae5ab48ccd13ffe9ef Mon Aug 21 13:49:26 2023 -0700
    adding a maf file alignment for the HPRC 90-way refs #31561
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    4cc2e8711aebda1711e13524c18fdce488898570 Mon Aug 21 13:52:49 2023 -0700
    adding a maf file alignment for the HPRC 90-way refs #31561
• src/hg/makeDb/trackDb/mouse/mm39/knownGeneArchive.ra
  • lines changed 24, context: html, text, full: html, text
    e497be05a9447aa0a374e80ae95450718a5b99a4 Tue Aug 22 22:59:09 2023 -0700
    Adding VM32 knownGene to the knownGeneArchive supertrack on mm39, refs #30841
• src/hg/makeDb/trackDb/mouse/mm39/knownGeneVM33.html
  • lines changed 32, context: html, text, full: html, text
    0b397c55c159a8a218af56f9f00ab8341c0892e2 Fri Aug 18 15:23:24 2023 -0700
    Updating html for VM33 knownGene, refs #30841
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 5, context: html, text, full: html, text
    dd7396650c2b83b7e8536eb63a076e46e350aba7 Mon Aug 21 13:50:41 2023 -0700
    tagTypes for HPRC 90-way groups refs #31561
• src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra
  • lines changed 98, context: html, text, full: html, text
    478769000cef7d4756c3cdc13c0d61d698f08a2b Thu Aug 24 19:39:05 2023 -0700
    adding chainNet definitions for GCA_018873775.2_hg01243.v3.0 refs #31844
• src/hg/utils/automation/doXenoRefGene.pl
  • lines changed 5, context: html, text, full: html, text
    5f33fc0ebd5b0d47a27fb88cb78eff9aa0278e25 Thu Aug 24 13:52:09 2023 -0700
    add -ram argument to allow smaller ram size on the paraRun, this should be an argument to the paraRun setup no redmine
• src/hg/utils/gff3ToGenePred/tests/expected/errDupIdDiffParentsTest.out
  • lines changed 3, context: html, text, full: html, text
    43bc39cf7ce2525cc9b11251ec10272b9f889910 Thu Aug 24 08:57:53 2023 -0700
    fixed incoorect check for discontinue features with multiple parents
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    dd1b035041ad3777603524c4f8befdafc92074c0 Mon Aug 28 11:43:41 2023 -0700
    New version number v453
• src/lib/gff3.c
  • lines changed 24, context: html, text, full: html, text
    43bc39cf7ce2525cc9b11251ec10272b9f889910 Thu Aug 24 08:57:53 2023 -0700
    fixed incoorect check for discontinue features with multiple parents
• src/lib/tests/expected/gff3ErrorCasesTest.err
  • lines changed 3, context: html, text, full: html, text
    43bc39cf7ce2525cc9b11251ec10272b9f889910 Thu Aug 24 08:57:53 2023 -0700
    fixed incoorect check for discontinue features with multiple parents
• src/utils/qa/qaTestScript.py
  • lines changed 5, context: html, text, full: html, text
    2a4d1aa7d6d2ce32e3eb17b099ac4a23dc0fcfcc Sat Aug 26 14:36:35 2023 -0700
    Updating hgPcr target Genes track test case and other updates for the selenium qa testing script, refs #30817
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    59f74a36a565af499bf1bd4b8d2e6b43cc3a0797 Mon Aug 28 11:42:07 2023 -0700
    v453 final build, refs #31976

• lines changed: 898
• files changed: 47