All File Changes

v439_base to v440_preview (2022-10-31 to 2022-11-07) v440

• src/hg/hgGene/hgGene.c
  • lines changed 2, context: html, text, full: html, text
    5c213974bb28e98d1b10ad9a86063101e684e5e3 Mon Oct 31 12:16:52 2022 -0700
    add Jim's track duplication code
• src/hg/hgGene/hgGeneData/C_elegans/links.ra
  • lines changed 4, context: html, text, full: html, text
    af1e1199581918bd3acdf390c4cc34a264b93dcf Fri Nov 4 13:45:26 2022 -0700
    Adding alphafold links to hgGene for model organisms, refs #29817
• src/hg/hgGene/hgGeneData/D_melanogaster/dm1/links.ra
  • lines changed 4, context: html, text, full: html, text
    af1e1199581918bd3acdf390c4cc34a264b93dcf Fri Nov 4 13:45:26 2022 -0700
    Adding alphafold links to hgGene for model organisms, refs #29817
• src/hg/hgGene/hgGeneData/D_melanogaster/dm2/links.ra
  • lines changed 4, context: html, text, full: html, text
    af1e1199581918bd3acdf390c4cc34a264b93dcf Fri Nov 4 13:45:26 2022 -0700
    Adding alphafold links to hgGene for model organisms, refs #29817
• src/hg/hgGene/hgGeneData/D_melanogaster/dm3/links.ra
  • lines changed 4, context: html, text, full: html, text
    af1e1199581918bd3acdf390c4cc34a264b93dcf Fri Nov 4 13:45:26 2022 -0700
    Adding alphafold links to hgGene for model organisms, refs #29817
• src/hg/hgGene/hgGeneData/Human/links.ra
  • lines changed 1, context: html, text, full: html, text
    e892c5f7ed4d38cdd906a2f188462dd318a19ae9 Fri Nov 4 13:22:20 2022 -0700
    Fixing OMIM linkouts on hgGene, refs #30230
• src/hg/hgGene/hgGeneData/Rat/rn4/links.ra
  • lines changed 4, context: html, text, full: html, text
    af1e1199581918bd3acdf390c4cc34a264b93dcf Fri Nov 4 13:45:26 2022 -0700
    Adding alphafold links to hgGene for model organisms, refs #29817
• src/hg/hgGene/hgGeneData/S_cerevisiae/links.ra
  • lines changed 4, context: html, text, full: html, text
    af1e1199581918bd3acdf390c4cc34a264b93dcf Fri Nov 4 13:45:26 2022 -0700
    Adding alphafold links to hgGene for model organisms, refs #29817
• src/hg/hgGene/hgGeneData/Zebrafish/links.ra
  • lines changed 4, context: html, text, full: html, text
    af1e1199581918bd3acdf390c4cc34a264b93dcf Fri Nov 4 13:45:26 2022 -0700
    Adding alphafold links to hgGene for model organisms, refs #29817
• src/hg/hgGene/hgGeneData/links.ra
  • lines changed 7, context: html, text, full: html, text
    af1e1199581918bd3acdf390c4cc34a264b93dcf Fri Nov 4 13:45:26 2022 -0700
    Adding alphafold links to hgGene for model organisms, refs #29817
• src/hg/hgGene/hgGeneData/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    6b29a9f398148d8623c624dd4906d8e3087905c1 Fri Nov 4 13:34:18 2022 -0700
    Should be checking human IDs against the human Xref table, refs #30231
• src/hg/hgSearch/hgSearch.c
  • lines changed 1, context: html, text, full: html, text
    9241b00bb206e322963c1af9d92138a836d909dd Mon Oct 31 13:49:01 2022 -0700
    Fix off by one on redirect searches, fix lack of cgi encoding of search terms, refs #29693
  • lines changed 7, context: html, text, full: html, text
    19caadce837026ea1e2a45844b34efc4928d3efb Mon Oct 31 20:29:27 2022 -0700
    Fixes for searches noted in #30201 note 2. The hgTracks search bar strips commas out of queries for some reason, and work around a swapped chromStart/chromEnd bug found in an hgvs search, refs #30201
• src/hg/hgTables/hgTables.c
  • lines changed 10, context: html, text, full: html, text
    5c213974bb28e98d1b10ad9a86063101e684e5e3 Mon Oct 31 12:16:52 2022 -0700
    add Jim's track duplication code
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 115, context: html, text, full: html, text
    5c213974bb28e98d1b10ad9a86063101e684e5e3 Mon Oct 31 12:16:52 2022 -0700
    add Jim's track duplication code
• src/hg/hgTracks/gencodeTracks.c
  • lines changed 35, context: html, text, full: html, text
    6175649026c35358cc0871c3f2cdf39328736885 Sun Oct 30 20:44:31 2022 -0700
    initial implementation of all gencode transcript rank filters, not GUI yet
  • lines changed 4, context: html, text, full: html, text
    6bd333f69401150f11cfa8d592165ad9b655f80f Wed Nov 2 23:01:02 2022 -0700
    added track hub control to set max transcripts
• src/hg/hgTracks/hgTracks.c
  • lines changed 76, context: html, text, full: html, text
    5c213974bb28e98d1b10ad9a86063101e684e5e3 Mon Oct 31 12:16:52 2022 -0700
    add Jim's track duplication code
• src/hg/hgc/gencodeClick.c
  • lines changed 17, context: html, text, full: html, text
    feeb6019339b80b90124476e6303e8dffb0f5f0b Sat Oct 29 14:59:04 2022 -0700
    Compute versione table names rather then get them from trackDb. I have no idea why I did it this way, but it causes problems because a table was missing
  • lines changed 121, context: html, text, full: html, text
    6175649026c35358cc0871c3f2cdf39328736885 Sun Oct 30 20:44:31 2022 -0700
    initial implementation of all gencode transcript rank filters, not GUI yet
• src/hg/hgc/hgc.c
  • lines changed 20, context: html, text, full: html, text
    5c213974bb28e98d1b10ad9a86063101e684e5e3 Mon Oct 31 12:16:52 2022 -0700
    add Jim's track duplication code
• src/hg/hgcentralTidy/hgcentralTidy.c
  • lines changed 1, context: html, text, full: html, text
    e17c7514a660c645f6387b17bc1128756d8a418a Wed Nov 2 22:58:15 2022 -0700
    bob has retired, so clay can get this email if there is an error. only happens very very rarely.
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 3, context: html, text, full: html, text
    c2e7dafc8f5c5d8a3500608a7c746e065813efc2 Tue Nov 1 18:10:17 2022 -0700
    Replacing the wiki page link with a UCSC page link, refs #28424
  • lines changed 9, context: html, text, full: html, text
    d901715bd990920719b5d2a89300de98fcd19f55 Thu Nov 3 10:19:58 2022 -0700
    Expanding a little on the figshare example of the docs, refs #30198
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 3, context: html, text, full: html, text
    ba9090c1767c6cab887fba49b2439f7cabc74e99 Tue Nov 1 17:50:58 2022 -0700
    Code review edits and updates for the public hub guidelines page, refs #28424
• src/hg/htdocs/goldenPath/help/hubQuickStart.html
  • lines changed 2, context: html, text, full: html, text
    c2e7dafc8f5c5d8a3500608a7c746e065813efc2 Tue Nov 1 18:10:17 2022 -0700
    Replacing the wiki page link with a UCSC page link, refs #28424
• src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
  • lines changed 2, context: html, text, full: html, text
    c2e7dafc8f5c5d8a3500608a7c746e065813efc2 Tue Nov 1 18:10:17 2022 -0700
    Replacing the wiki page link with a UCSC page link, refs #28424
• src/hg/htdocs/goldenPath/help/hubQuickStartGroups.html
  • lines changed 2, context: html, text, full: html, text
    c2e7dafc8f5c5d8a3500608a7c746e065813efc2 Tue Nov 1 18:10:17 2022 -0700
    Replacing the wiki page link with a UCSC page link, refs #28424
• src/hg/htdocs/goldenPath/help/publicHubGuidelines.html
  • lines changed 10, context: html, text, full: html, text
    ba9090c1767c6cab887fba49b2439f7cabc74e99 Tue Nov 1 17:50:58 2022 -0700
    Code review edits and updates for the public hub guidelines page, refs #28424
  • lines changed 4, context: html, text, full: html, text
    9ef756f18472a7b7f750f80bfa29836372aeaeb4 Tue Nov 1 18:07:03 2022 -0700
    Code review edits for the public hub guidelines page, refs #30206
• src/hg/htdocs/training/index.html
  • lines changed 1, context: html, text, full: html, text
    ba9090c1767c6cab887fba49b2439f7cabc74e99 Tue Nov 1 17:50:58 2022 -0700
    Code review edits and updates for the public hub guidelines page, refs #28424
  • lines changed 3, context: html, text, full: html, text
    d7524bde1ea485b2ca891c4329c6fa4ec9880f11 Thu Nov 3 10:22:03 2022 -0700
    Tweaking our new training constraints, no RM.
• src/hg/htdocs/training/upcoming.html
  • lines changed 8, context: html, text, full: html, text
    33dd41a30fd101e1d1c92b0e9a7ee269d5aab59f Wed Nov 2 09:32:12 2022 -0700
    Updating trainings, no RM
• src/hg/inc/cart.h
  • lines changed 4, context: html, text, full: html, text
    5c213974bb28e98d1b10ad9a86063101e684e5e3 Mon Oct 31 12:16:52 2022 -0700
    add Jim's track duplication code
• src/hg/inc/dupTrack.h
  • lines changed 47, context: html, text, full: html, text
    5c213974bb28e98d1b10ad9a86063101e684e5e3 Mon Oct 31 12:16:52 2022 -0700
    add Jim's track duplication code
• src/hg/inc/gencodeTracksCommon.h
  • lines changed 20, context: html, text, full: html, text
    6175649026c35358cc0871c3f2cdf39328736885 Sun Oct 30 20:44:31 2022 -0700
    initial implementation of all gencode transcript rank filters, not GUI yet
• src/hg/js/hgGateway.js
  • lines changed 1, context: html, text, full: html, text
    9241b00bb206e322963c1af9d92138a836d909dd Mon Oct 31 13:49:01 2022 -0700
    Fix off by one on redirect searches, fix lack of cgi encoding of search terms, refs #29693
• src/hg/js/hgSearch.js
  • lines changed 11, context: html, text, full: html, text
    06600d01f3b25b00c9797d98c8a63a8bfafd4d07 Mon Oct 31 12:24:09 2022 -0700
    When doing a multi position search that redirects right to hgTracks, like 'NM_012090.5;NM_012421.4', when doing the redirect, turn the track on, refs #29693
  • lines changed 1, context: html, text, full: html, text
    9241b00bb206e322963c1af9d92138a836d909dd Mon Oct 31 13:49:01 2022 -0700
    Fix off by one on redirect searches, fix lack of cgi encoding of search terms, refs #29693
• src/hg/js/hgTracks.js
  • lines changed 1, context: html, text, full: html, text
    9241b00bb206e322963c1af9d92138a836d909dd Mon Oct 31 13:49:01 2022 -0700
    Fix off by one on redirect searches, fix lack of cgi encoding of search terms, refs #29693
  • lines changed 1, context: html, text, full: html, text
    19caadce837026ea1e2a45844b34efc4928d3efb Mon Oct 31 20:29:27 2022 -0700
    Fixes for searches noted in #30201 note 2. The hgTracks search bar strips commas out of queries for some reason, and work around a swapped chromStart/chromEnd bug found in an hgvs search, refs #30201
• src/hg/lib/cart.c
  • lines changed 19, context: html, text, full: html, text
    5c213974bb28e98d1b10ad9a86063101e684e5e3 Mon Oct 31 12:16:52 2022 -0700
    add Jim's track duplication code
• src/hg/lib/dupTrack.c
  • lines changed 251, context: html, text, full: html, text
    5c213974bb28e98d1b10ad9a86063101e684e5e3 Mon Oct 31 12:16:52 2022 -0700
    add Jim's track duplication code
• src/hg/lib/encode/wgEncodeGencodeAttrs.as
  • lines changed 1, context: html, text, full: html, text
    ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
    import of GENCODE V42 final release with addition of transcript rankings
• src/hg/lib/encode/wgEncodeGencodeAttrs.c
  • lines changed 2, context: html, text, full: html, text
    ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
    import of GENCODE V42 final release with addition of transcript rankings
• src/hg/lib/gencodeTracksCommon.c
  • lines changed 33, context: html, text, full: html, text
    6175649026c35358cc0871c3f2cdf39328736885 Sun Oct 30 20:44:31 2022 -0700
    initial implementation of all gencode transcript rank filters, not GUI yet
• src/hg/lib/hgFind.c
  • lines changed 8, context: html, text, full: html, text
    58025f52231b5081e9a8dee4372f36e85f25da90 Mon Oct 31 12:12:17 2022 -0700
    Allow knownGene snippet file to not exist and fall back to kgXref descriptions, refs #29693
• src/hg/lib/hui.c
  • lines changed 15, context: html, text, full: html, text
    6bd333f69401150f11cfa8d592165ad9b655f80f Wed Nov 2 23:01:02 2022 -0700
    added track hub control to set max transcripts
  • lines changed 9, context: html, text, full: html, text
    cbc16c6d771f324f8e752f41578648e4d11f9510 Fri Nov 4 10:39:34 2022 -0700
    enable All GENCODE maxTrans checking explictly in trackDb, so lift37 will not have it, since we don't have transcriptRanks for them, but want to keep the column in the attrs table'
• src/hg/lib/makefile
  • lines changed 2, context: html, text, full: html, text
    6175649026c35358cc0871c3f2cdf39328736885 Sun Oct 30 20:44:31 2022 -0700
    initial implementation of all gencode transcript rank filters, not GUI yet
  • lines changed 1, context: html, text, full: html, text
    5c213974bb28e98d1b10ad9a86063101e684e5e3 Mon Oct 31 12:16:52 2022 -0700
    add Jim's track duplication code
  • lines changed 3, context: html, text, full: html, text
    28a32014fae85f167f805fe51e3eee91df731732 Fri Nov 4 14:48:45 2022 -0700
    Merge branch 'master' into all-gencode-ranks
• src/hg/lib/web.c
  • lines changed 3, context: html, text, full: html, text
    5c213974bb28e98d1b10ad9a86063101e684e5e3 Mon Oct 31 12:16:52 2022 -0700
    add Jim's track duplication code
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 2, context: html, text, full: html, text
    6782b9af94bab6f4541b408d67178c9388b942c9 Thu Nov 3 14:36:00 2022 -0700
    adding two assemblies per user request refs #29545
  • lines changed 1, context: html, text, full: html, text
    3d50d0ade2f9c4d01c9995a9b048037b90db0af1 Fri Nov 4 10:06:44 2022 -0700
    adding Bovine herpesvirus per user request refs #29545
• src/hg/makeDb/doc/asmHubs/updateGenArkCentral.sh
  • lines changed 4, context: html, text, full: html, text
    40f099b5e7ab52c9c734f164bdbdbc6e8da39d69 Fri Nov 4 10:12:24 2022 -0700
    indicate row count before and after update refs #29545
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    3d50d0ade2f9c4d01c9995a9b048037b90db0af1 Fri Nov 4 10:06:44 2022 -0700
    adding Bovine herpesvirus per user request refs #29545
  • lines changed 1, context: html, text, full: html, text
    eb089b54da47529d7279e3e5658a450f89e626bd Fri Nov 4 10:35:43 2022 -0700
    correctly place herpesvirus in viral set not bacteria refs #29545
• src/hg/makeDb/doc/hg19.gencode.txt
  • lines changed 60, context: html, text, full: html, text
    1fe89284953dd069f7155892bdcb8306adea13ef Thu Nov 3 21:31:54 2022 -0700
    import of v42lift37
• src/hg/makeDb/doc/hg38/gencode.txt
  • lines changed 36, context: html, text, full: html, text
    ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
    import of GENCODE V42 final release with addition of transcript rankings
  • lines changed 2, context: html, text, full: html, text
    622669affcb25b3fe27c6f3ec188a01ec35b6f58 Thu Nov 3 11:07:28 2022 -0700
    got Ensembl version wrong
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    6782b9af94bab6f4541b408d67178c9388b942c9 Thu Nov 3 14:36:00 2022 -0700
    adding two assemblies per user request refs #29545
• src/hg/makeDb/doc/mm39/gencode.txt
  • lines changed 34, context: html, text, full: html, text
    f1a6509a2f33b00f4908de15d47f6625118b6a93 Thu Nov 3 12:46:19 2022 -0700
    import of All GENCODE VM31
• src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt
  • lines changed 1, context: html, text, full: html, text
    4c8867def29289f46a7afa4e2c1ccdbbf68c70c1 Thu Nov 3 10:27:13 2022 -0700
    adding definition for GCF_024166365.1_mEleMax1_primary_haplotype no redmine
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    eb089b54da47529d7279e3e5658a450f89e626bd Fri Nov 4 10:35:43 2022 -0700
    correctly place herpesvirus in viral set not bacteria refs #29545
• src/hg/makeDb/outside/gencode/bin/buildGencodeToUcscLift
  • lines changed 4, context: html, text, full: html, text
    ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
    import of GENCODE V42 final release with addition of transcript rankings
• src/hg/makeDb/outside/gencode/bin/gencodeGenerateTrackDbs
  • lines changed 17, context: html, text, full: html, text
    feeb6019339b80b90124476e6303e8dffb0f5f0b Sat Oct 29 14:59:04 2022 -0700
    Compute versione table names rather then get them from trackDb. I have no idea why I did it this way, but it causes problems because a table was missing
  • lines changed 4, context: html, text, full: html, text
    cbc16c6d771f324f8e752f41578648e4d11f9510 Fri Nov 4 10:39:34 2022 -0700
    enable All GENCODE maxTrans checking explictly in trackDb, so lift37 will not have it, since we don't have transcriptRanks for them, but want to keep the column in the attrs table'
  • lines changed 36, context: html, text, full: html, text
    e863249eae18325e041c2948722b98cb5a5643e4 Fri Nov 4 14:47:29 2022 -0700
    Dropped GENCODE 2-way pseudogenes from latest releases. These should have never been included
  • lines changed 1, context: html, text, full: html, text
    7e2ceb55c803eaeaf15b61d3b2d1b12792a0d127 Sat Nov 5 10:18:27 2022 -0700
    fixed GENCODE view reference
• src/hg/makeDb/outside/gencode/bin/gencodeGxfToAttrs
  • lines changed 36, context: html, text, full: html, text
    ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
    import of GENCODE V42 final release with addition of transcript rankings
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 5, context: html, text, full: html, text
    ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
    import of GENCODE V42 final release with addition of transcript rankings
  • lines changed 5, context: html, text, full: html, text
    f1a6509a2f33b00f4908de15d47f6625118b6a93 Thu Nov 3 12:46:19 2022 -0700
    import of All GENCODE VM31
  • lines changed 10, context: html, text, full: html, text
    1fe89284953dd069f7155892bdcb8306adea13ef Thu Nov 3 21:31:54 2022 -0700
    import of v42lift37
  • lines changed 13, context: html, text, full: html, text
    e863249eae18325e041c2948722b98cb5a5643e4 Fri Nov 4 14:47:29 2022 -0700
    Dropped GENCODE 2-way pseudogenes from latest releases. These should have never been included
• src/hg/makeDb/outside/gencode/lib/gencode/biotypes.py
  • lines changed 2, context: html, text, full: html, text
    ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
    import of GENCODE V42 final release with addition of transcript rankings
• src/hg/makeDb/outside/gencode/lib/gencode/gencodeGenes.py
  • lines changed 1, context: html, text, full: html, text
    ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
    import of GENCODE V42 final release with addition of transcript rankings
• src/hg/makeDb/outside/gencode/lib/gencode/gencodeTags.py
  • lines changed 1, context: html, text, full: html, text
    ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
    import of GENCODE V42 final release with addition of transcript rankings
• src/hg/makeDb/outside/gencode/makefile
  • lines changed 1, context: html, text, full: html, text
    ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
    import of GENCODE V42 final release with addition of transcript rankings
• src/hg/makeDb/outside/gencode/tests/expected/attrsPseudoGff3Tests.tsv
  • lines changed 2, context: html, text, full: html, text
    ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
    import of GENCODE V42 final release with addition of transcript rankings
• src/hg/makeDb/outside/gencode/tests/expected/attrsRankTest.tsv
  • lines changed 96, context: html, text, full: html, text
    ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
    import of GENCODE V42 final release with addition of transcript rankings
• src/hg/makeDb/outside/gencode/tests/expected/attrsSet1GtfTest.tsv
  • lines changed 82, context: html, text, full: html, text
    ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
    import of GENCODE V42 final release with addition of transcript rankings
• src/hg/makeDb/outside/gencode/tests/expected/attrsTagGff3Tests.tsv
  • lines changed 16, context: html, text, full: html, text
    ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
    import of GENCODE V42 final release with addition of transcript rankings
• src/hg/makeDb/outside/gencode/tests/expected/attrsTagGtfTests.tsv
  • lines changed 16, context: html, text, full: html, text
    ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
    import of GENCODE V42 final release with addition of transcript rankings
• src/hg/makeDb/outside/gencode/tests/expected/attrsV19GtfTest.tsv
  • lines changed 5, context: html, text, full: html, text
    ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
    import of GENCODE V42 final release with addition of transcript rankings
• src/hg/makeDb/outside/gencode/tests/expected/attrsV21Gff3Test.tsv
  • lines changed 117, context: html, text, full: html, text
    ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
    import of GENCODE V42 final release with addition of transcript rankings
• src/hg/makeDb/outside/gencode/tests/expected/attrsV21GtfTest.tsv
  • lines changed 117, context: html, text, full: html, text
    ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
    import of GENCODE V42 final release with addition of transcript rankings
• src/hg/makeDb/outside/gencode/tests/expected/attrsV27ParGff3Test.tsv
  • lines changed 15, context: html, text, full: html, text
    ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
    import of GENCODE V42 final release with addition of transcript rankings
• src/hg/makeDb/outside/gencode/tests/expected/attrsV27ParGtfTest.tsv
  • lines changed 15, context: html, text, full: html, text
    ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
    import of GENCODE V42 final release with addition of transcript rankings
• src/hg/makeDb/outside/gencode/tests/expected/buildGencodeToUcscLiftHs38Test.chain
  • lines changed 2277, context: html, text, full: html, text
    ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
    import of GENCODE V42 final release with addition of transcript rankings
• src/hg/makeDb/outside/gencode/tests/expected/makeAttrsTest.attrs.tab
  • lines changed 82, context: html, text, full: html, text
    ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
    import of GENCODE V42 final release with addition of transcript rankings
• src/hg/makeDb/outside/gencode/tests/expected/set1.attrs.tsv
  • lines changed 83, context: html, text, full: html, text
    6175649026c35358cc0871c3f2cdf39328736885 Sun Oct 30 20:44:31 2022 -0700
    initial implementation of all gencode transcript rank filters, not GUI yet
• src/hg/makeDb/outside/gencode/tests/input/v42.gff3
  • lines changed 2334, context: html, text, full: html, text
    ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
    import of GENCODE V42 final release with addition of transcript rankings
• src/hg/makeDb/outside/gencode/tests/input/v42.transcript_rankings.txt
  • lines changed 95, context: html, text, full: html, text
    ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
    import of GENCODE V42 final release with addition of transcript rankings
• src/hg/makeDb/outside/gencode/tests/makefile
  • lines changed 7, context: html, text, full: html, text
    ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
    import of GENCODE V42 final release with addition of transcript rankings
• src/hg/makeDb/schema/all.joiner
  • lines changed 95, context: html, text, full: html, text
    f1a6509a2f33b00f4908de15d47f6625118b6a93 Thu Nov 3 12:46:19 2022 -0700
    import of All GENCODE VM31
  • lines changed 90, context: html, text, full: html, text
    1fe89284953dd069f7155892bdcb8306adea13ef Thu Nov 3 21:31:54 2022 -0700
    import of v42lift37
  • lines changed 3, context: html, text, full: html, text
    e863249eae18325e041c2948722b98cb5a5643e4 Fri Nov 4 14:47:29 2022 -0700
    Dropped GENCODE 2-way pseudogenes from latest releases. These should have never been included
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    1fe89284953dd069f7155892bdcb8306adea13ef Thu Nov 3 21:31:54 2022 -0700
    import of v42lift37
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
  • lines changed 4, context: html, text, full: html, text
    1fe89284953dd069f7155892bdcb8306adea13ef Thu Nov 3 21:31:54 2022 -0700
    import of v42lift37
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV42lift37.html
  • lines changed 32, context: html, text, full: html, text
    1fe89284953dd069f7155892bdcb8306adea13ef Thu Nov 3 21:31:54 2022 -0700
    import of v42lift37
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV42lift37.ra
  • lines changed 210, context: html, text, full: html, text
    1fe89284953dd069f7155892bdcb8306adea13ef Thu Nov 3 21:31:54 2022 -0700
    import of v42lift37
  • lines changed 2, context: html, text, full: html, text
    e863249eae18325e041c2948722b98cb5a5643e4 Fri Nov 4 14:47:29 2022 -0700
    Dropped GENCODE 2-way pseudogenes from latest releases. These should have never been included
• src/hg/makeDb/trackDb/human/hg38/topmed.ra
  • lines changed 6, context: html, text, full: html, text
    703c19fb9ef448e04fd95bc0e3817b0f8fc28777 Tue Nov 1 05:50:18 2022 -0700
    adding testing track for topmed
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    cba1de530393888e6afe3e9a3caffd27d985242e Tue Nov 1 05:52:52 2022 -0700
    adding testing track for topmed, 2
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeSuper.html
  • lines changed 4, context: html, text, full: html, text
    ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
    import of GENCODE V42 final release with addition of transcript rankings
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV42.html
  • lines changed 2, context: html, text, full: html, text
    ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
    import of GENCODE V42 final release with addition of transcript rankings
  • lines changed 1, context: html, text, full: html, text
    622669affcb25b3fe27c6f3ec188a01ec35b6f58 Thu Nov 3 11:07:28 2022 -0700
    got Ensembl version wrong
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV42.ra
  • lines changed 6, context: html, text, full: html, text
    ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
    import of GENCODE V42 final release with addition of transcript rankings
  • lines changed 15, context: html, text, full: html, text
    feeb6019339b80b90124476e6303e8dffb0f5f0b Sat Oct 29 14:59:04 2022 -0700
    Compute versione table names rather then get them from trackDb. I have no idea why I did it this way, but it causes problems because a table was missing
  • lines changed 6, context: html, text, full: html, text
    622669affcb25b3fe27c6f3ec188a01ec35b6f58 Thu Nov 3 11:07:28 2022 -0700
    got Ensembl version wrong
  • lines changed 1, context: html, text, full: html, text
    cbc16c6d771f324f8e752f41578648e4d11f9510 Fri Nov 4 10:39:34 2022 -0700
    enable All GENCODE maxTrans checking explictly in trackDb, so lift37 will not have it, since we don't have transcriptRanks for them, but want to keep the column in the attrs table'
  • lines changed 27, context: html, text, full: html, text
    e863249eae18325e041c2948722b98cb5a5643e4 Fri Nov 4 14:47:29 2022 -0700
    Dropped GENCODE 2-way pseudogenes from latest releases. These should have never been included
  • lines changed 1, context: html, text, full: html, text
    7e2ceb55c803eaeaf15b61d3b2d1b12792a0d127 Sat Nov 5 10:18:27 2022 -0700
    fixed GENCODE view reference
• src/hg/makeDb/trackDb/human/panelApp.html
  • lines changed 4, context: html, text, full: html, text
    ff4257af63b8ef729573df54c879eb05876b26ed Wed Nov 2 10:51:48 2022 -0700
    Adding note about the bug in refs# 30212
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    f1a6509a2f33b00f4908de15d47f6625118b6a93 Thu Nov 3 12:46:19 2022 -0700
    import of All GENCODE VM31
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeSuper.html
  • lines changed 4, context: html, text, full: html, text
    f1a6509a2f33b00f4908de15d47f6625118b6a93 Thu Nov 3 12:46:19 2022 -0700
    import of All GENCODE VM31
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM30.ra
  • lines changed 15, context: html, text, full: html, text
    feeb6019339b80b90124476e6303e8dffb0f5f0b Sat Oct 29 14:59:04 2022 -0700
    Compute versione table names rather then get them from trackDb. I have no idea why I did it this way, but it causes problems because a table was missing
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM31.html
  • lines changed 30, context: html, text, full: html, text
    f1a6509a2f33b00f4908de15d47f6625118b6a93 Thu Nov 3 12:46:19 2022 -0700
    import of All GENCODE VM31
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM31.ra
  • lines changed 271, context: html, text, full: html, text
    f1a6509a2f33b00f4908de15d47f6625118b6a93 Thu Nov 3 12:46:19 2022 -0700
    import of All GENCODE VM31
  • lines changed 1, context: html, text, full: html, text
    cbc16c6d771f324f8e752f41578648e4d11f9510 Fri Nov 4 10:39:34 2022 -0700
    enable All GENCODE maxTrans checking explictly in trackDb, so lift37 will not have it, since we don't have transcriptRanks for them, but want to keep the column in the attrs table'
  • lines changed 27, context: html, text, full: html, text
    e863249eae18325e041c2948722b98cb5a5643e4 Fri Nov 4 14:47:29 2022 -0700
    Dropped GENCODE 2-way pseudogenes from latest releases. These should have never been included
  • lines changed 1, context: html, text, full: html, text
    7e2ceb55c803eaeaf15b61d3b2d1b12792a0d127 Sat Nov 5 10:18:27 2022 -0700
    fixed GENCODE view reference
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    cbc16c6d771f324f8e752f41578648e4d11f9510 Fri Nov 4 10:39:34 2022 -0700
    enable All GENCODE maxTrans checking explictly in trackDb, so lift37 will not have it, since we don't have transcriptRanks for them, but want to keep the column in the attrs table'
• src/hg/makeDb/trackDb/wgEncodeGencodeCredits1.shared.html
  • lines changed 98, context: html, text, full: html, text
    5021f89a5ebb829503b4b900280862429c09bf92 Sat Nov 5 13:21:42 2022 -0700
    change GENCODE credits to link directly to GENCODE page
• src/hg/makeDb/trackDb/wgEncodeGencodeDisplay1.shared.html
  • lines changed 43, context: html, text, full: html, text
    cef070ed6c72e0247012855fa88e3e82144a7a9b Fri Nov 4 13:45:47 2022 -0700
    added all gencode transcript ranks to the track descriptions
  • lines changed 17, context: html, text, full: html, text
    e863249eae18325e041c2948722b98cb5a5643e4 Fri Nov 4 14:47:29 2022 -0700
    Dropped GENCODE 2-way pseudogenes from latest releases. These should have never been included
• src/hg/utils/automation/asmHubGatewayPage.pl
  • lines changed 1, context: html, text, full: html, text
    e22f7956c30a5490adb028364bbc2c1e45b2da8b Wed Nov 2 16:17:28 2022 -0700
    turn off mouse strain bigMaf tracks since they do not work and now with the new style copy link to paste buffer feature for gateway description pages refs #30199
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 9, context: html, text, full: html, text
    e22f7956c30a5490adb028364bbc2c1e45b2da8b Wed Nov 2 16:17:28 2022 -0700
    turn off mouse strain bigMaf tracks since they do not work and now with the new style copy link to paste buffer feature for gateway description pages refs #30199
• src/hg/utils/automation/doNcbiRefSeq.pl
  • lines changed 1, context: html, text, full: html, text
    cf6d10c6d02bad7a97ec933fff5acd453272ffe9 Wed Nov 2 22:59:55 2022 -0700
    fixed minor typo in this script where "z" was accidentally inserted in front of something that should just be cat since it is not a gzipped file.
• src/inc/memgfx.h
  • lines changed 1, context: html, text, full: html, text
    0beae765b9e7f5bd4736c3afc8993b69b309f810 Fri Nov 4 14:40:53 2022 -0700
    Fix for overflowing color combinations when working with partial alpha values, refs #30227
• src/inc/portable.h
  • lines changed 3, context: html, text, full: html, text
    13531feb863db3591e2c7e61cf45289d3770bc7c Mon Oct 31 11:49:46 2022 -0700
    for bigWig and bigBed build utilities, check to make sure the file isn't a pipe
• src/lib/osunix.c
  • lines changed 14, context: html, text, full: html, text
    13531feb863db3591e2c7e61cf45289d3770bc7c Mon Oct 31 11:49:46 2022 -0700
    for bigWig and bigBed build utilities, check to make sure the file isn't a pipe
• src/lib/trix.c
  • lines changed 12, context: html, text, full: html, text
    8c2001c3a5c7f1b077d7379ec77dc9756b1fe100 Tue Nov 1 12:14:16 2022 -0700
    Wrap snippet code in an errCatch so we can still reset prefixSize when a supporting file is not found, refs #30200
• src/utils/bedGraphToBigWig/bedGraphToBigWig.c
  • lines changed 3, context: html, text, full: html, text
    13531feb863db3591e2c7e61cf45289d3770bc7c Mon Oct 31 11:49:46 2022 -0700
    for bigWig and bigBed build utilities, check to make sure the file isn't a pipe
• src/utils/bedToBigBed/bedToBigBed.c
  • lines changed 7, context: html, text, full: html, text
    13531feb863db3591e2c7e61cf45289d3770bc7c Mon Oct 31 11:49:46 2022 -0700
    for bigWig and bigBed build utilities, check to make sure the file isn't a pipe
• src/utils/qa/checkHubSearchTextUpdate
  • lines changed 4, context: html, text, full: html, text
    abf9d610fcc6e307ef233c2ae3ecbbaa541e5ba2 Fri Oct 28 17:09:34 2022 -0700
    Adding a few scripts
• src/utils/qa/previewUpdate
  • lines changed 32, context: html, text, full: html, text
    abf9d610fcc6e307ef233c2ae3ecbbaa541e5ba2 Fri Oct 28 17:09:34 2022 -0700
    Adding a few scripts
• src/utils/qa/removeHubPublic
  • lines changed 34, context: html, text, full: html, text
    abf9d610fcc6e307ef233c2ae3ecbbaa541e5ba2 Fri Oct 28 17:09:34 2022 -0700
    Adding a few scripts
• src/utils/qa/trackQaHelper
  • lines changed 241, context: html, text, full: html, text
    abf9d610fcc6e307ef233c2ae3ecbbaa541e5ba2 Fri Oct 28 17:09:34 2022 -0700
    Adding a few scripts
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    a38d971843e5cd742d6bcd7ba735e4d352565b4b Mon Nov 7 10:08:50 2022 -0800
    v440 preview1, refs #30233
• src/utils/wigToBigWig/wigToBigWig.c
  • lines changed 7, context: html, text, full: html, text
    13531feb863db3591e2c7e61cf45289d3770bc7c Mon Oct 31 11:49:46 2022 -0700
    for bigWig and bigBed build utilities, check to make sure the file isn't a pipe

• lines changed: 7958
• files changed: 142