All File Changes

v427_preview to v427_preview2 (2022-02-07 to 2022-02-14) v427

• src/hg/hgGene/domains.c
  • lines changed 15, context: html, text, full: html, text
    9575c7ded6204e195d050b3bc18b77e43359423c Mon Feb 7 14:37:55 2022 -0800
    remove links to PDB images which are no longer present. Change URL to structure to conform to current PDB site.
• src/hg/hgGene/hgGeneData/Human/hg38/links.ra
  • lines changed 2, context: html, text, full: html, text
    98f8d8fe3c4c43d4030a61ccec76e88c4719213a Thu Feb 10 11:51:25 2022 -0800
    upgrade to V39
• src/hg/hgTracks/barChartTrack.c
  • lines changed 3, context: html, text, full: html, text
    9ca1124c0c987a2669356f171ff681934cfebf16 Mon Feb 7 11:06:18 2022 -0800
    Fix disappearing barCharts when zooming in, refs #28876
• src/hg/hgTracks/wigTrack.c
  • lines changed 6, context: html, text, full: html, text
    d51631f0fa655b66dfd432cfb3ba95b3b058fa64 Thu Feb 10 12:00:02 2022 -0800
    change sequence logo view back to coming on at codon coloring level instead of base level since I cannot replicate the bug I was seeing.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 5, context: html, text, full: html, text
    13641ebfe529faefc2f6416ff56ec8593ac5d594 Tue Feb 8 16:27:07 2022 -0800
    Doc'ing new trackDb setting that stretches out barCharts to entire graph, refs #28804
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 5, context: html, text, full: html, text
    13641ebfe529faefc2f6416ff56ec8593ac5d594 Tue Feb 8 16:27:07 2022 -0800
    Doc'ing new trackDb setting that stretches out barCharts to entire graph, refs #28804
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 6, context: html, text, full: html, text
    13641ebfe529faefc2f6416ff56ec8593ac5d594 Tue Feb 8 16:27:07 2022 -0800
    Doc'ing new trackDb setting that stretches out barCharts to entire graph, refs #28804
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 35, context: html, text, full: html, text
    d98002da63a523f6de0e7c04936e458827a3b1ee Mon Feb 7 16:13:27 2022 -0800
    News release for 3 new GENCODE tracks, M28 and V39. Refs #28771 #28770 #28769
• src/hg/htdocs/indexNews.html
  • lines changed 6, context: html, text, full: html, text
    d98002da63a523f6de0e7c04936e458827a3b1ee Mon Feb 7 16:13:27 2022 -0800
    News release for 3 new GENCODE tracks, M28 and V39. Refs #28771 #28770 #28769
• src/hg/htdocs/mirror.html
  • lines changed 4, context: html, text, full: html, text
    87ee77e87dcff2ce2e3d1d5b04198446aa0f3be8 Tue Feb 8 15:29:58 2022 -0800
    Adding https links to mirror.html page. Refs #28892
• src/hg/makeDb/doc/asmHubs/lastzRuns.txt
  • lines changed 102, context: html, text, full: html, text
    658d2682457610e1373ee30ddc15ea47ef74ee04 Thu Feb 10 16:27:17 2022 -0800
    taeGut2 vs. geoFor1 lastz/chain/net run for user, refs #28840
  • lines changed 101, context: html, text, full: html, text
    77740770d513278f03c8cb1eac5f02c83c6c26c4 Thu Feb 10 16:40:31 2022 -0800
    Correcting makedoc location for taeGut2 vs. geoFor1 lastz/chain/net run for user, refs #28840
  • lines changed 107, context: html, text, full: html, text
    2ec8bd4117dbc3240979b3f03020452bb96461c4 Thu Feb 10 17:04:13 2022 -0800
    kinetoplastids GCA_000340355.2 vs. kinetoplastids GCF_000002845.2 lastz/chain/net run for user, refs #28824
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    1379a3b1ac6f01a2f16840ec51e17e2659b38ac2 Mon Feb 7 10:17:00 2022 -0800
    adding the chm13 T2T human assembly no redmine
  • lines changed 1, context: html, text, full: html, text
    8f14cbe0cb30b74ed5ee03c175f78c9203541d48 Tue Feb 8 16:11:47 2022 -0800
    adding invertebrate per user request, refs #28888
  • lines changed 1, context: html, text, full: html, text
    1a5e1d8d6237734a2c25600f06226e86ca486de3 Thu Feb 10 11:06:20 2022 -0800
    adding mammal per user request, refs #28899
• src/hg/makeDb/doc/assemblyEquivalence/update.2022-01-18.txt
  • lines changed 50, context: html, text, full: html, text
    18bbec9e1a2ecbd3430515d8818ce2361f960535 Mon Feb 7 16:15:39 2022 -0800
    better matching to historical NCBI assemblies no redmine
• src/hg/makeDb/doc/hg38/mane.txt
  • lines changed 7, context: html, text, full: html, text
    bbad3a22ae7d64cb72f5af7e24963cf3c219fbe4 Sat Feb 12 10:03:39 2022 -0800
    import MANE v1.0
  • lines changed 4, context: html, text, full: html, text
    c924092bcdeb2b5e1b8e10f260854fa4ca9ac9c2 Sat Feb 12 13:14:03 2022 -0800
    a little clean-up of the doc
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    29ffb8065c750cbf6293cd240e3cb8c72a38233f Tue Feb 8 17:09:46 2022 -0800
    adding fly D.virilis 160 2020 per user request, refs #28888
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    75765ab110021bd43e6f6463e837fac4a2dacf94 Thu Feb 10 11:24:24 2022 -0800
    adding Saanen dairy goat per user request, refs #28899
  • lines changed 1, context: html, text, full: html, text
    d5e11c873647553ff6d8d9dbc9d2848d87f309fa Mon Feb 14 08:45:13 2022 -0800
    adding GCF_011100685.1_UU_Cfam_GSD_1.0 no redmine
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    1379a3b1ac6f01a2f16840ec51e17e2659b38ac2 Mon Feb 7 10:17:00 2022 -0800
    adding the chm13 T2T human assembly no redmine
• src/hg/makeDb/doc/taeGut2.txt
  • lines changed 101, context: html, text, full: html, text
    77740770d513278f03c8cb1eac5f02c83c6c26c4 Thu Feb 10 16:40:31 2022 -0800
    Correcting makedoc location for taeGut2 vs. geoFor1 lastz/chain/net run for user, refs #28840
• src/hg/makeDb/doc/ucscGenes/hg38.gencodeV39.log
  • lines changed 3674, context: html, text, full: html, text
    20473f03adfc10172e8cc39b23656e077aece62e Mon Feb 7 14:48:45 2022 -0800
    add GENCODE V39 log files to doc
• src/hg/makeDb/hgLoadWiggle/hgLoadWiggle.c
  • lines changed 1, context: html, text, full: html, text
    833cef3fe90d02e134871bb1a6763a5a8128c210 Tue Feb 8 17:28:24 2022 -0800
    Back-quoting new keyword `offset` in hgLoadWiggle. #refs #28799
• src/hg/makeDb/outside/gencode/bin/gencodeGenerateTrackDbs
  • lines changed 1, context: html, text, full: html, text
    98392a8bfe02501cabf97a1d1267bd97378a38e0 Wed Feb 9 20:06:41 2022 -0800
    simplify file location tracking
• src/hg/makeDb/outside/gencode/bin/gencodeGxfToAttrs
  • lines changed 35, context: html, text, full: html, text
    54691f7b728b08d1a095a5ccfd39e30e502d68cc Wed Feb 9 21:26:48 2022 -0800
    improve checking and reporting of GENCODE attribute errors
• src/hg/makeDb/outside/gencode/bin/gencodeGxfToGenePred
  • lines changed 4, context: html, text, full: html, text
    54691f7b728b08d1a095a5ccfd39e30e502d68cc Wed Feb 9 21:26:48 2022 -0800
    improve checking and reporting of GENCODE attribute errors
• src/hg/makeDb/outside/gencode/lib/gencode/gencodeGff3Parser.py
  • lines changed 1, context: html, text, full: html, text
    98392a8bfe02501cabf97a1d1267bd97378a38e0 Wed Feb 9 20:06:41 2022 -0800
    simplify file location tracking
• src/hg/makeDb/outside/gencode/lib/gencode/gencodeGtfParser.py
  • lines changed 1, context: html, text, full: html, text
    98392a8bfe02501cabf97a1d1267bd97378a38e0 Wed Feb 9 20:06:41 2022 -0800
    simplify file location tracking
• src/hg/makeDb/outside/gencode/lib/gencode/gencodeGxfParser.py
  • lines changed 10, context: html, text, full: html, text
    98392a8bfe02501cabf97a1d1267bd97378a38e0 Wed Feb 9 20:06:41 2022 -0800
    simplify file location tracking
  • lines changed 43, context: html, text, full: html, text
    54691f7b728b08d1a095a5ccfd39e30e502d68cc Wed Feb 9 21:26:48 2022 -0800
    improve checking and reporting of GENCODE attribute errors
• src/hg/makeDb/outside/gencode/lib/gencode/gencodeGxfRec.py
  • lines changed 5, context: html, text, full: html, text
    98392a8bfe02501cabf97a1d1267bd97378a38e0 Wed Feb 9 20:06:41 2022 -0800
    simplify file location tracking
• src/hg/makeDb/outside/gencode/tests/expected/attrsErrorGff3Test.err
  • lines changed 9, context: html, text, full: html, text
    54691f7b728b08d1a095a5ccfd39e30e502d68cc Wed Feb 9 21:26:48 2022 -0800
    improve checking and reporting of GENCODE attribute errors
• src/hg/makeDb/outside/gencode/tests/expected/attrsErrorGtfTest.err
  • lines changed 9, context: html, text, full: html, text
    54691f7b728b08d1a095a5ccfd39e30e502d68cc Wed Feb 9 21:26:48 2022 -0800
    improve checking and reporting of GENCODE attribute errors
• src/hg/makeDb/outside/gencode/tests/input/attrErrors.gff3
  • lines changed 931, context: html, text, full: html, text
    54691f7b728b08d1a095a5ccfd39e30e502d68cc Wed Feb 9 21:26:48 2022 -0800
    improve checking and reporting of GENCODE attribute errors
• src/hg/makeDb/outside/gencode/tests/input/attrErrors.gtf
  • lines changed 940, context: html, text, full: html, text
    54691f7b728b08d1a095a5ccfd39e30e502d68cc Wed Feb 9 21:26:48 2022 -0800
    improve checking and reporting of GENCODE attribute errors
• src/hg/makeDb/outside/gencode/tests/makefile
  • lines changed 12, context: html, text, full: html, text
    54691f7b728b08d1a095a5ccfd39e30e502d68cc Wed Feb 9 21:26:48 2022 -0800
    improve checking and reporting of GENCODE attribute errors
• src/hg/makeDb/trackDb/human/hg19/genePredArchive.ra
  • lines changed 1, context: html, text, full: html, text
    742a27931ba252748a366e219db551b206b7e1df Thu Feb 10 09:05:41 2022 -0800
    Sqashing old pennantIcons, no RM
• src/hg/makeDb/trackDb/human/hg19/tgpArchive.ra
  • lines changed 1, context: html, text, full: html, text
    742a27931ba252748a366e219db551b206b7e1df Thu Feb 10 09:05:41 2022 -0800
    Sqashing old pennantIcons, no RM
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    54b3a479bfd89169a5a3c18693fd034dfb01810d Mon Feb 7 16:16:34 2022 -0800
    Adding pennantIcon and tweaking new visibilities for the 3 new GENCODE tracks, M28 and V39. Refs #28771 #28770 #28769
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV38lift37.ra
  • lines changed 1, context: html, text, full: html, text
    54b3a479bfd89169a5a3c18693fd034dfb01810d Mon Feb 7 16:16:34 2022 -0800
    Adding pennantIcon and tweaking new visibilities for the 3 new GENCODE tracks, M28 and V39. Refs #28771 #28770 #28769
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV39lift37.ra
  • lines changed 1, context: html, text, full: html, text
    54b3a479bfd89169a5a3c18693fd034dfb01810d Mon Feb 7 16:16:34 2022 -0800
    Adding pennantIcon and tweaking new visibilities for the 3 new GENCODE tracks, M28 and V39. Refs #28771 #28770 #28769
• src/hg/makeDb/trackDb/human/hg38/affyArchive.ra
  • lines changed 1, context: html, text, full: html, text
    742a27931ba252748a366e219db551b206b7e1df Thu Feb 10 09:05:41 2022 -0800
    Sqashing old pennantIcons, no RM
• src/hg/makeDb/trackDb/human/hg38/genePredArchive.ra
  • lines changed 1, context: html, text, full: html, text
    742a27931ba252748a366e219db551b206b7e1df Thu Feb 10 09:05:41 2022 -0800
    Sqashing old pennantIcons, no RM
• src/hg/makeDb/trackDb/human/hg38/mane.alpha.html
  • lines changed 3, context: html, text, full: html, text
    bbad3a22ae7d64cb72f5af7e24963cf3c219fbe4 Sat Feb 12 10:03:39 2022 -0800
    import MANE v1.0
• src/hg/makeDb/trackDb/human/hg38/mane.alpha.ra
  • lines changed 21, context: html, text, full: html, text
    bbad3a22ae7d64cb72f5af7e24963cf3c219fbe4 Sat Feb 12 10:03:39 2022 -0800
    import MANE v1.0
• src/hg/makeDb/trackDb/human/hg38/mane.ra
  • lines changed 1, context: html, text, full: html, text
    742a27931ba252748a366e219db551b206b7e1df Thu Feb 10 09:05:41 2022 -0800
    Sqashing old pennantIcons, no RM
• src/hg/makeDb/trackDb/human/hg38/omimGene2.html
  • lines changed 1, context: html, text, full: html, text
    ed45c0f09ccc43f2505d050349e02d4252928e3f Thu Feb 3 16:30:54 2022 -0800
    Tweaking wording for OMIM disclaimer based on CR feedback, refs #28856
• src/hg/makeDb/trackDb/human/hg38/omimLocation.html
  • lines changed 1, context: html, text, full: html, text
    ed45c0f09ccc43f2505d050349e02d4252928e3f Thu Feb 3 16:30:54 2022 -0800
    Tweaking wording for OMIM disclaimer based on CR feedback, refs #28856
• src/hg/makeDb/trackDb/human/hg38/tgpArchive.ra
  • lines changed 1, context: html, text, full: html, text
    742a27931ba252748a366e219db551b206b7e1df Thu Feb 10 09:05:41 2022 -0800
    Sqashing old pennantIcons, no RM
• src/hg/makeDb/trackDb/human/hg38/trackDb.241way.ra
  • lines changed 1, context: html, text, full: html, text
    742a27931ba252748a366e219db551b206b7e1df Thu Feb 10 09:05:41 2022 -0800
    Sqashing old pennantIcons, no RM
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    54b3a479bfd89169a5a3c18693fd034dfb01810d Mon Feb 7 16:16:34 2022 -0800
    Adding pennantIcon and tweaking new visibilities for the 3 new GENCODE tracks, M28 and V39. Refs #28771 #28770 #28769
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    742a27931ba252748a366e219db551b206b7e1df Thu Feb 10 09:05:41 2022 -0800
    Sqashing old pennantIcons, no RM
  • lines changed 2, context: html, text, full: html, text
    bbad3a22ae7d64cb72f5af7e24963cf3c219fbe4 Sat Feb 12 10:03:39 2022 -0800
    import MANE v1.0
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV38.ra
  • lines changed 1, context: html, text, full: html, text
    54b3a479bfd89169a5a3c18693fd034dfb01810d Mon Feb 7 16:16:34 2022 -0800
    Adding pennantIcon and tweaking new visibilities for the 3 new GENCODE tracks, M28 and V39. Refs #28771 #28770 #28769
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV39.ra
  • lines changed 1, context: html, text, full: html, text
    54b3a479bfd89169a5a3c18693fd034dfb01810d Mon Feb 7 16:16:34 2022 -0800
    Adding pennantIcon and tweaking new visibilities for the 3 new GENCODE tracks, M28 and V39. Refs #28771 #28770 #28769
• src/hg/makeDb/trackDb/human/jaspar.ra
  • lines changed 2, context: html, text, full: html, text
    160a2cdef67e1ef72132a99d1d66ea156970c662 Mon Feb 7 14:35:31 2022 -0800
    Adding filter trackDb vars to prevent composite track confusion, refs #28870
• src/hg/makeDb/trackDb/human/omimAvSnp.html
  • lines changed 1, context: html, text, full: html, text
    ed45c0f09ccc43f2505d050349e02d4252928e3f Thu Feb 3 16:30:54 2022 -0800
    Tweaking wording for OMIM disclaimer based on CR feedback, refs #28856
• src/hg/makeDb/trackDb/human/omimGene2.html
  • lines changed 1, context: html, text, full: html, text
    ed45c0f09ccc43f2505d050349e02d4252928e3f Thu Feb 3 16:30:54 2022 -0800
    Tweaking wording for OMIM disclaimer based on CR feedback, refs #28856
• src/hg/makeDb/trackDb/human/omimLocation.html
  • lines changed 1, context: html, text, full: html, text
    ed45c0f09ccc43f2505d050349e02d4252928e3f Thu Feb 3 16:30:54 2022 -0800
    Tweaking wording for OMIM disclaimer based on CR feedback, refs #28856
• src/hg/makeDb/trackDb/mouse/jaspar.ra
  • lines changed 1, context: html, text, full: html, text
    160a2cdef67e1ef72132a99d1d66ea156970c662 Mon Feb 7 14:35:31 2022 -0800
    Adding filter trackDb vars to prevent composite track confusion, refs #28870
• src/hg/makeDb/trackDb/mouse/mm39/knownGene.alpha.ra
  • lines changed 1, context: html, text, full: html, text
    742a27931ba252748a366e219db551b206b7e1df Thu Feb 10 09:05:41 2022 -0800
    Sqashing old pennantIcons, no RM
• src/hg/makeDb/trackDb/mouse/mm39/knownGene.ra
  • lines changed 1, context: html, text, full: html, text
    742a27931ba252748a366e219db551b206b7e1df Thu Feb 10 09:05:41 2022 -0800
    Sqashing old pennantIcons, no RM
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    54b3a479bfd89169a5a3c18693fd034dfb01810d Mon Feb 7 16:16:34 2022 -0800
    Adding pennantIcon and tweaking new visibilities for the 3 new GENCODE tracks, M28 and V39. Refs #28771 #28770 #28769
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM27.ra
  • lines changed 1, context: html, text, full: html, text
    54b3a479bfd89169a5a3c18693fd034dfb01810d Mon Feb 7 16:16:34 2022 -0800
    Adding pennantIcon and tweaking new visibilities for the 3 new GENCODE tracks, M28 and V39. Refs #28771 #28770 #28769
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM28.ra
  • lines changed 1, context: html, text, full: html, text
    54b3a479bfd89169a5a3c18693fd034dfb01810d Mon Feb 7 16:16:34 2022 -0800
    Adding pennantIcon and tweaking new visibilities for the 3 new GENCODE tracks, M28 and V39. Refs #28771 #28770 #28769
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    742a27931ba252748a366e219db551b206b7e1df Thu Feb 10 09:05:41 2022 -0800
    Sqashing old pennantIcons, no RM
• src/hg/makeDb/trackDb/virus/wuhCor1/resist.html
  • lines changed 13, context: html, text, full: html, text
    c5287575e5d368f49d7cebbd4ee461bc17f98262 Tue Feb 8 06:39:42 2022 -0800
    adding drug resistance track to wuhCor1, refs #28889
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
  • lines changed 12, context: html, text, full: html, text
    c5287575e5d368f49d7cebbd4ee461bc17f98262 Tue Feb 8 06:39:42 2022 -0800
    adding drug resistance track to wuhCor1, refs #28889
• src/hg/utils/otto/knownGene/buildTo.sh
  • lines changed 6, context: html, text, full: html, text
    339f301a906608e65e98d494054ef975a5b68f44 Thu Feb 10 12:43:04 2022 -0800
    take Lynx out of knownGene build
• src/hg/utils/otto/knownGene/copyFilesToAssembly.sh
  • lines changed 2, context: html, text, full: html, text
    bb0ba2f4936af96f32f4cbc01dfab0a8b0b957ea Thu Feb 10 12:41:32 2022 -0800
    more parameterization of knownGene build
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    9ac2372e602df87120cb3e778bf7b236e6ac6361 Mon Feb 14 10:14:25 2022 -0800
    v427 preview2, refs #28882
• src/utils/subColumn/subColumn.c
  • lines changed 16, context: html, text, full: html, text
    fe2dff20936a2f7d3cd570360b1d6fe0e1b65cc1 Thu Feb 10 14:15:36 2022 -0800
    add an option to subColumn to skip lines that don't match
• src/utils/subColumn/tests/expected/outputMiss.bed
  • lines changed 209, context: html, text, full: html, text
    c014326efaedb835a44760dbe4e2ed4c8e992412 Thu Feb 10 14:13:21 2022 -0800
    add some tests to subColumn
• src/utils/subColumn/tests/expected/passMissing.tab
  • lines changed 268, context: html, text, full: html, text
    c014326efaedb835a44760dbe4e2ed4c8e992412 Thu Feb 10 14:13:21 2022 -0800
    add some tests to subColumn
• src/utils/subColumn/tests/expected/skipMissing.tab
  • lines changed 59, context: html, text, full: html, text
    c014326efaedb835a44760dbe4e2ed4c8e992412 Thu Feb 10 14:13:21 2022 -0800
    add some tests to subColumn
• src/utils/subColumn/tests/input/colored.bed
  • lines changed 268, context: html, text, full: html, text
    c014326efaedb835a44760dbe4e2ed4c8e992412 Thu Feb 10 14:13:21 2022 -0800
    add some tests to subColumn
• src/utils/subColumn/tests/input/ensembl.tab
  • lines changed 194, context: html, text, full: html, text
    c014326efaedb835a44760dbe4e2ed4c8e992412 Thu Feb 10 14:13:21 2022 -0800
    add some tests to subColumn
• src/utils/subColumn/tests/makefile
  • lines changed 24, context: html, text, full: html, text
    c014326efaedb835a44760dbe4e2ed4c8e992412 Thu Feb 10 14:13:21 2022 -0800
    add some tests to subColumn

• lines changed: 7371
• files changed: 81