All File Changes

v469_preview2 to v469_base (2024-07-29 to 2024-08-05) v469

• confs/hgwdev.hg.conf
  • lines changed 3, context: html, text, full: html, text
    1e0a74321fb6c24621358f8695b371f64d7785df Sun Aug 4 01:11:17 2024 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgBlat/hgBlat.c
  • lines changed 8, context: html, text, full: html, text
    d34fa1661ec45179035b50dc6ed47d8ea04835ac Thu Aug 1 13:28:48 2024 -0700
    Tweaking the hgBlat warning message that was added recently to flow better, no RM.
• src/hg/hgSearch/hgSearch.c
  • lines changed 2, context: html, text, full: html, text
    ccfa1e241fa0901145350afe59049b26f345df14 Tue Jul 30 15:34:54 2024 -0700
    Some style changes to hgSearch requested by Mark and Lou. One is fix resizing of columns when the window has been made small. Two is make font size of track titles larger, refs Mark email and #33503
• src/hg/hgSession/hgSession.c
  • lines changed 8, context: html, text, full: html, text
    eca99d569898b0e1f599d9336563db410c096400 Sun Aug 4 18:20:13 2024 -0700
    hgSession can only load sessions from URLs that are actually URLs, and no longer reports the content of bad settings (it was a security flaw). refs #34223
• src/hg/hgTracks/config.c
  • lines changed 11, context: html, text, full: html, text
    c3a239aa11cde08e85f3235b3e47861a507215cc Thu Aug 1 13:34:53 2024 -0700
    Add a configure page option for controlling whether hgc clicks open in pop-ups, refs #33216
  • lines changed 1, context: html, text, full: html, text
    ed64f2117c237ec58194baea7438d500052cef36 Thu Aug 1 17:49:24 2024 -0700
    Updating the configure page option text for the item details pop-up feature, refs #33216
• src/hg/hgTracks/hgTracks.c
  • lines changed 3, context: html, text, full: html, text
    c3a239aa11cde08e85f3235b3e47861a507215cc Thu Aug 1 13:34:53 2024 -0700
    Add a configure page option for controlling whether hgc clicks open in pop-ups, refs #33216
  • lines changed 3, context: html, text, full: html, text
    5a451c3cc7cb9b76708daa089fc443ad19158887 Sun Aug 4 16:58:55 2024 -0700
    Adding an hg.conf option to control max image height, refs #34152
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 66, context: html, text, full: html, text
    396c69214aa8d8b2267caa178377f24c796f579d Tue Jul 30 14:15:14 2024 -0700
    Staging the knownGene announcement for hg19, refs #32302
  • lines changed 5, context: html, text, full: html, text
    a33a189301f539896d9df28df9008b50f65d757f Fri Aug 2 12:09:41 2024 -0700
    Fixing up grammar, feedback from CR refs #34174
• src/hg/htdocs/inc/hgSearch.html
  • lines changed 36, context: html, text, full: html, text
    ccfa1e241fa0901145350afe59049b26f345df14 Tue Jul 30 15:34:54 2024 -0700
    Some style changes to hgSearch requested by Mark and Lou. One is fix resizing of columns when the window has been made small. Two is make font size of track titles larger, refs Mark email and #33503
• src/hg/htdocs/indexNews.html
  • lines changed 6, context: html, text, full: html, text
    d18a30a9620089db13af0c109396fd505aca438a Wed Jul 31 17:06:37 2024 -0700
    Adding the knownGene announcement to the index page, refs #32302
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    034516d1afe0c545d6d9f80aa041fb7c21a716e3 Mon Aug 5 12:31:42 2024 -0700
    New version number v469
• src/hg/js/hgSearch.js
  • lines changed 1, context: html, text, full: html, text
    ccfa1e241fa0901145350afe59049b26f345df14 Tue Jul 30 15:34:54 2024 -0700
    Some style changes to hgSearch requested by Mark and Lou. One is fix resizing of columns when the window has been made small. Two is make font size of track titles larger, refs Mark email and #33503
• src/hg/lib/cart.c
  • lines changed 5, context: html, text, full: html, text
    eca99d569898b0e1f599d9336563db410c096400 Sun Aug 4 18:20:13 2024 -0700
    hgSession can only load sessions from URLs that are actually URLs, and no longer reports the content of bad settings (it was a security flaw). refs #34223
• src/hg/makeDb/doc/enigma.txt
  • lines changed 2, context: html, text, full: html, text
    81b85e4efadaf4a8f10e3f3f5bfcbea597ce6838 Thu Aug 1 16:53:13 2024 -0700
    Adding a link so github users following the track description page can quickly find where the build scripts live, no RM.
• src/hg/makeDb/doc/hg19.gencode.txt
  • lines changed 47, context: html, text, full: html, text
    0f6f8c5cdfc1c5385c814102a4fa59afb08d2849 Wed Jul 31 23:45:27 2024 -0700
    import of GENCODE v47, v47lift37, and vM36 pre-releases
• src/hg/makeDb/doc/hg38/470way/speciesTable.pl
  • lines changed 1, context: html, text, full: html, text
    632322baa15b770a16d918f5c5135634f744f2a4 Wed Jul 31 18:13:46 2024 -0700
    Code review edits, forgot to add -h genome-centdb, refs #34171
  • lines changed 8, context: html, text, full: html, text
    a2ebb1194b2298b7748c30b8ded86ad734eb66ae Thu Aug 1 16:13:07 2024 -0700
    This table was creating links to non-released genome browsers, I added a new condition that checks for active=1 on the RR and only makes links to those, refs #34163
• src/hg/makeDb/doc/hg38/gencode.txt
  • lines changed 47, context: html, text, full: html, text
    0f6f8c5cdfc1c5385c814102a4fa59afb08d2849 Wed Jul 31 23:45:27 2024 -0700
    import of GENCODE v47, v47lift37, and vM36 pre-releases
• src/hg/makeDb/doc/hs1/hs1.GCF_003121395.1.lastz.log
  • lines changed 85, context: html, text, full: html, text
    48a70e2b7630a92c14d5cd1f1a5c5721d93b097d Tue Jul 30 15:09:23 2024 -0700
    build logs for lastz alignments refs #34179
• src/hg/makeDb/doc/hs1/hs1.GCF_028858775.1.lastz.log
  • lines changed 97, context: html, text, full: html, text
    48a70e2b7630a92c14d5cd1f1a5c5721d93b097d Tue Jul 30 15:09:23 2024 -0700
    build logs for lastz alignments refs #34179
• src/hg/makeDb/doc/hs1/hs1.GCF_028878055.1.lastz.log
  • lines changed 97, context: html, text, full: html, text
    48a70e2b7630a92c14d5cd1f1a5c5721d93b097d Tue Jul 30 15:09:23 2024 -0700
    build logs for lastz alignments refs #34179
• src/hg/makeDb/doc/hs1/hs1.GCF_028885625.1.lastz.log
  • lines changed 97, context: html, text, full: html, text
    48a70e2b7630a92c14d5cd1f1a5c5721d93b097d Tue Jul 30 15:09:23 2024 -0700
    build logs for lastz alignments refs #34179
• src/hg/makeDb/doc/hs1/hs1.GCF_028885655.1.lastz.log
  • lines changed 97, context: html, text, full: html, text
    48a70e2b7630a92c14d5cd1f1a5c5721d93b097d Tue Jul 30 15:09:23 2024 -0700
    build logs for lastz alignments refs #34179
• src/hg/makeDb/doc/hs1/hs1.GCF_029281585.1.lastz.log
  • lines changed 97, context: html, text, full: html, text
    48a70e2b7630a92c14d5cd1f1a5c5721d93b097d Tue Jul 30 15:09:23 2024 -0700
    build logs for lastz alignments refs #34179
• src/hg/makeDb/doc/hs1/hs1.GCF_029289425.1.lastz.log
  • lines changed 97, context: html, text, full: html, text
    48a70e2b7630a92c14d5cd1f1a5c5721d93b097d Tue Jul 30 15:09:23 2024 -0700
    build logs for lastz alignments refs #34179
• src/hg/makeDb/doc/mm39/gencode.txt
  • lines changed 24, context: html, text, full: html, text
    0f6f8c5cdfc1c5385c814102a4fa59afb08d2849 Wed Jul 31 23:45:27 2024 -0700
    import of GENCODE v47, v47lift37, and vM36 pre-releases
• src/hg/makeDb/outside/gencode/bin/gencodeGenerateTrackDbs
  • lines changed 4, context: html, text, full: html, text
    0f6f8c5cdfc1c5385c814102a4fa59afb08d2849 Wed Jul 31 23:45:27 2024 -0700
    import of GENCODE v47, v47lift37, and vM36 pre-releases
• src/hg/makeDb/outside/gencode/bin/gencodeGxfToAttrs
  • lines changed 20, context: html, text, full: html, text
    86a413987f2d1db20eb3b5db57c45b8da38178fc Fri Aug 2 22:24:04 2024 -0700
    Split tags into gene and transcript tags. This is only internal right now, not loaded in the database this way
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 28, context: html, text, full: html, text
    0f6f8c5cdfc1c5385c814102a4fa59afb08d2849 Wed Jul 31 23:45:27 2024 -0700
    import of GENCODE v47, v47lift37, and vM36 pre-releases
• src/hg/makeDb/outside/gencode/lib/gencode/gencodeGenes.py
  • lines changed 10, context: html, text, full: html, text
    86a413987f2d1db20eb3b5db57c45b8da38178fc Fri Aug 2 22:24:04 2024 -0700
    Split tags into gene and transcript tags. This is only internal right now, not loaded in the database this way
• src/hg/makeDb/outside/gencode/tests/expected/attrsPseudoGff3Tests.tsv
  • lines changed 3, context: html, text, full: html, text
    86a413987f2d1db20eb3b5db57c45b8da38178fc Fri Aug 2 22:24:04 2024 -0700
    Split tags into gene and transcript tags. This is only internal right now, not loaded in the database this way
• src/hg/makeDb/outside/gencode/tests/expected/attrsRankTest.tsv
  • lines changed 2, context: html, text, full: html, text
    86a413987f2d1db20eb3b5db57c45b8da38178fc Fri Aug 2 22:24:04 2024 -0700
    Split tags into gene and transcript tags. This is only internal right now, not loaded in the database this way
• src/hg/makeDb/outside/gencode/tests/expected/attrsSet1GtfTest.tsv
  • lines changed 34, context: html, text, full: html, text
    86a413987f2d1db20eb3b5db57c45b8da38178fc Fri Aug 2 22:24:04 2024 -0700
    Split tags into gene and transcript tags. This is only internal right now, not loaded in the database this way
• src/hg/makeDb/outside/gencode/tests/expected/attrsTagGff3Tests.tsv
  • lines changed 17, context: html, text, full: html, text
    86a413987f2d1db20eb3b5db57c45b8da38178fc Fri Aug 2 22:24:04 2024 -0700
    Split tags into gene and transcript tags. This is only internal right now, not loaded in the database this way
• src/hg/makeDb/outside/gencode/tests/expected/attrsTagGtfTests.tsv
  • lines changed 17, context: html, text, full: html, text
    86a413987f2d1db20eb3b5db57c45b8da38178fc Fri Aug 2 22:24:04 2024 -0700
    Split tags into gene and transcript tags. This is only internal right now, not loaded in the database this way
• src/hg/makeDb/outside/gencode/tests/expected/attrsV19GtfTest.tsv
  • lines changed 1, context: html, text, full: html, text
    86a413987f2d1db20eb3b5db57c45b8da38178fc Fri Aug 2 22:24:04 2024 -0700
    Split tags into gene and transcript tags. This is only internal right now, not loaded in the database this way
• src/hg/makeDb/outside/gencode/tests/expected/attrsV21Gff3Test.tsv
  • lines changed 26, context: html, text, full: html, text
    86a413987f2d1db20eb3b5db57c45b8da38178fc Fri Aug 2 22:24:04 2024 -0700
    Split tags into gene and transcript tags. This is only internal right now, not loaded in the database this way
• src/hg/makeDb/outside/gencode/tests/expected/attrsV21GtfTest.tsv
  • lines changed 26, context: html, text, full: html, text
    86a413987f2d1db20eb3b5db57c45b8da38178fc Fri Aug 2 22:24:04 2024 -0700
    Split tags into gene and transcript tags. This is only internal right now, not loaded in the database this way
• src/hg/makeDb/outside/gencode/tests/expected/attrsV27ParGff3Test.tsv
  • lines changed 16, context: html, text, full: html, text
    86a413987f2d1db20eb3b5db57c45b8da38178fc Fri Aug 2 22:24:04 2024 -0700
    Split tags into gene and transcript tags. This is only internal right now, not loaded in the database this way
• src/hg/makeDb/outside/gencode/tests/expected/attrsV27ParGtfTest.tsv
  • lines changed 16, context: html, text, full: html, text
    86a413987f2d1db20eb3b5db57c45b8da38178fc Fri Aug 2 22:24:04 2024 -0700
    Split tags into gene and transcript tags. This is only internal right now, not loaded in the database this way
• src/hg/makeDb/schema/all.joiner
  • lines changed 278, context: html, text, full: html, text
    0f6f8c5cdfc1c5385c814102a4fa59afb08d2849 Wed Jul 31 23:45:27 2024 -0700
    import of GENCODE v47, v47lift37, and vM36 pre-releases
• src/hg/makeDb/scripts/enigma/BRCAmla.py
  • lines changed 343, context: html, text, full: html, text
    22355e64603a110b6da0bf1617509da9b0717c18 Thu Aug 1 16:45:52 2024 -0700
    Adding 3 more datasets to the ENIGMA MLA track. No RM.
• src/hg/makeDb/trackDb/chainNetGCF_003121395.ra
  • lines changed 96, context: html, text, full: html, text
    0ecf97803f8bb59bc58eac663040fb5351892899 Mon Aug 5 07:52:39 2024 -0700
    properly make chainNetGCF_003121395 and include alpha statement refs #34179
• src/hg/makeDb/trackDb/evaSnpContainer.html
  • lines changed 7, context: html, text, full: html, text
    a33a189301f539896d9df28df9008b50f65d757f Fri Aug 2 12:09:41 2024 -0700
    Fixing up grammar, feedback from CR refs #34174
• src/hg/makeDb/trackDb/human/hg19/knownGene.alpha.ra
  • lines changed 1, context: html, text, full: html, text
    837d957af47e54efac7d63cf3f71669f4d2ffcde Tue Jul 30 14:40:54 2024 -0700
    fix truncated squishyPackLabel
  • lines changed 42, context: html, text, full: html, text
    21367693c1d37c2abee28deebf657c0b6c096036 Wed Jul 31 15:47:45 2024 -0700
    Releasing the knownGene update for hg19, refs #32302
• src/hg/makeDb/trackDb/human/hg19/knownGene.ra
  • lines changed 42, context: html, text, full: html, text
    21367693c1d37c2abee28deebf657c0b6c096036 Wed Jul 31 15:47:45 2024 -0700
    Releasing the knownGene update for hg19, refs #32302
• src/hg/makeDb/trackDb/human/hg19/knownGeneArchive.ra
  • lines changed 3, context: html, text, full: html, text
    9fabdcc695925eda3dc1b87b23984333fd41cfa7 Tue Jul 30 15:16:03 2024 -0700
    Updating the long and short labels. Adding a priority value to make it appear third on hgTracks, refs #32302
  • lines changed 1, context: html, text, full: html, text
    49c7339031adbb5c34d98279faf98454edca2c31 Wed Jul 31 16:42:22 2024 -0700
    Updating the shortLabel for the knownGene archive, refs #34042
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    0f6f8c5cdfc1c5385c814102a4fa59afb08d2849 Wed Jul 31 23:45:27 2024 -0700
    import of GENCODE v47, v47lift37, and vM36 pre-releases
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 21, context: html, text, full: html, text
    21367693c1d37c2abee28deebf657c0b6c096036 Wed Jul 31 15:47:45 2024 -0700
    Releasing the knownGene update for hg19, refs #32302
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV47lift37.html
  • lines changed 32, context: html, text, full: html, text
    0f6f8c5cdfc1c5385c814102a4fa59afb08d2849 Wed Jul 31 23:45:27 2024 -0700
    import of GENCODE v47, v47lift37, and vM36 pre-releases
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV47lift37.ra
  • lines changed 210, context: html, text, full: html, text
    0f6f8c5cdfc1c5385c814102a4fa59afb08d2849 Wed Jul 31 23:45:27 2024 -0700
    import of GENCODE v47, v47lift37, and vM36 pre-releases
• src/hg/makeDb/trackDb/human/hg38/cons470way.html
  • lines changed 54, context: html, text, full: html, text
    a2ebb1194b2298b7748c30b8ded86ad734eb66ae Thu Aug 1 16:13:07 2024 -0700
    This table was creating links to non-released genome browsers, I added a new condition that checks for active=1 on the RR and only makes links to those, refs #34163
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    0f6f8c5cdfc1c5385c814102a4fa59afb08d2849 Wed Jul 31 23:45:27 2024 -0700
    import of GENCODE v47, v47lift37, and vM36 pre-releases
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV47.html
  • lines changed 47, context: html, text, full: html, text
    0f6f8c5cdfc1c5385c814102a4fa59afb08d2849 Wed Jul 31 23:45:27 2024 -0700
    import of GENCODE v47, v47lift37, and vM36 pre-releases
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV47.ra
  • lines changed 247, context: html, text, full: html, text
    0f6f8c5cdfc1c5385c814102a4fa59afb08d2849 Wed Jul 31 23:45:27 2024 -0700
    import of GENCODE v47, v47lift37, and vM36 pre-releases
• src/hg/makeDb/trackDb/human/hs1/hs1PrimateChainNet.html
  • lines changed 196, context: html, text, full: html, text
    f97df06161eb19e3014503551f0c97bc83d5b33f Tue Jul 30 13:26:36 2024 -0700
    description page for primate alignments to hs1 refs #34149
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    0f6f8c5cdfc1c5385c814102a4fa59afb08d2849 Wed Jul 31 23:45:27 2024 -0700
    import of GENCODE v47, v47lift37, and vM36 pre-releases
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM36.html
  • lines changed 30, context: html, text, full: html, text
    0f6f8c5cdfc1c5385c814102a4fa59afb08d2849 Wed Jul 31 23:45:27 2024 -0700
    import of GENCODE v47, v47lift37, and vM36 pre-releases
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM36.ra
  • lines changed 247, context: html, text, full: html, text
    0f6f8c5cdfc1c5385c814102a4fa59afb08d2849 Wed Jul 31 23:45:27 2024 -0700
    import of GENCODE v47, v47lift37, and vM36 pre-releases
• src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra
  • lines changed 1, context: html, text, full: html, text
    ff4ca2ad8f8510a8cfa661148a68c25c464df177 Fri Aug 2 16:44:59 2024 -0700
    making track chainNetGCF_003121395.1 release alpha so it will not leak out on hs1 refs #34179
  • lines changed 97, context: html, text, full: html, text
    0ecf97803f8bb59bc58eac663040fb5351892899 Mon Aug 5 07:52:39 2024 -0700
    properly make chainNetGCF_003121395 and include alpha statement refs #34179
• src/hg/utils/automation/asmHubChainNetComposite.pl
  • lines changed 11, context: html, text, full: html, text
    febcba57979e8638ada173f0d26eba18cd51b3a8 Tue Jul 30 13:29:27 2024 -0700
    can be used for a UCSC database assembly with special arguments refs #34149
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    034516d1afe0c545d6d9f80aa041fb7c21a716e3 Mon Aug 5 12:31:42 2024 -0700
    New version number v469
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    2d31076b5f15aa61bf43fd05f2213562a66c46fb Mon Aug 5 12:30:48 2024 -0700
    v469 final build, refs #34168

• lines changed: 3188
• files changed: 68