All File Changes

v421_preview2 to v421_base (2021-09-20 to 2021-09-27) v421

• confs/asia.hg.conf
  • lines changed 2, context: html, text, full: html, text
    5ee234fd2e186bd069a5192118f73a1bc4e80dbd Sun Sep 26 01:11:54 2021 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 2, context: html, text, full: html, text
    5ee234fd2e186bd069a5192118f73a1bc4e80dbd Sun Sep 26 01:11:54 2021 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 2, context: html, text, full: html, text
    5ee234fd2e186bd069a5192118f73a1bc4e80dbd Sun Sep 26 01:11:54 2021 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 2, context: html, text, full: html, text
    5ee234fd2e186bd069a5192118f73a1bc4e80dbd Sun Sep 26 01:11:54 2021 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/gateway/htdocs/images/Assays-3.png
  • lines changed 0, context: html, text, full: html, text
    cc0c2a3660afaec752782b9068c1770bce7b8bdb Mon Sep 20 13:19:12 2021 -0700
    Committing images for bestPractices.html that I committed previously. Images need to be committed too so that they actually show up on public and private sites, not just test site, no redmine
• src/hg/cirm/gateway/htdocs/images/Experiments.png
  • lines changed 0, context: html, text, full: html, text
    cc0c2a3660afaec752782b9068c1770bce7b8bdb Mon Sep 20 13:19:12 2021 -0700
    Committing images for bestPractices.html that I committed previously. Images need to be committed too so that they actually show up on public and private sites, not just test site, no redmine
• src/hg/cirm/gateway/htdocs/images/SampleDiagram.png
  • lines changed 0, context: html, text, full: html, text
    cc0c2a3660afaec752782b9068c1770bce7b8bdb Mon Sep 20 13:19:12 2021 -0700
    Committing images for bestPractices.html that I committed previously. Images need to be committed too so that they actually show up on public and private sites, not just test site, no redmine
• src/hg/cirm/gateway/htdocs/images/SampleProcessing.png
  • lines changed 0, context: html, text, full: html, text
    cc0c2a3660afaec752782b9068c1770bce7b8bdb Mon Sep 20 13:19:12 2021 -0700
    Committing images for bestPractices.html that I committed previously. Images need to be committed too so that they actually show up on public and private sites, not just test site, no redmine
• src/hg/cirm/gateway/htdocs/projects.html
  • lines changed 81, context: html, text, full: html, text
    4f4060a905c620c1bb0623fb19e8465bcea75ae4 Fri Aug 27 15:05:20 2021 -0700
    adding covid-19 projects to page, no redmine
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 2, context: html, text, full: html, text
    b638c1d328d8febc1d4cd8597b7cc358bebc39f3 Wed Sep 22 16:55:52 2021 -0700
    take out special handling of lrgTranscriptAli track in favor of the standard bigPsl routines
• src/hg/hgTracks/config.c
  • lines changed 4, context: html, text, full: html, text
    6ce1087262245e3d2d46198ac237d0d04126e1a3 Tue Sep 21 04:50:49 2021 -0700
    removing duplicated font-awesome integration into hgTracks, adding folder icon as a tag without a font dependency, removing link from the icon, and adding the icon to the config page, refs #28108
  • lines changed 4, context: html, text, full: html, text
    cb9d5c7ec853681999acfa42ce503f1846d546ae Fri Sep 24 05:03:21 2021 -0700
    fixing track vis color on config page, refs #26257
• src/hg/hgTracks/hgTracks.c
  • lines changed 21, context: html, text, full: html, text
    6ce1087262245e3d2d46198ac237d0d04126e1a3 Tue Sep 21 04:50:49 2021 -0700
    removing duplicated font-awesome integration into hgTracks, adding folder icon as a tag without a font dependency, removing link from the icon, and adding the icon to the config page, refs #28108
• src/hg/hgc/bigBedClick.c
  • lines changed 1, context: html, text, full: html, text
    27b46974c742bba0d60bf92f74d4e17f8d16bb72 Fri Sep 24 13:01:43 2021 -0700
    remove supurious endSection()
• src/hg/hgc/hgc.c
  • lines changed 4, context: html, text, full: html, text
    b638c1d328d8febc1d4cd8597b7cc358bebc39f3 Wed Sep 22 16:55:52 2021 -0700
    take out special handling of lrgTranscriptAli track in favor of the standard bigPsl routines
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 1, context: html, text, full: html, text
    dd63f1db2fabe42eed12f9311b482f3c8fee4b94 Sun Sep 26 13:20:43 2021 -0700
    fixed single-char typo
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 27, context: html, text, full: html, text
    8ea0ade717747f936e7bda4f09bf848fe16a1c8f Fri Sep 24 17:18:41 2021 -0700
    Updating info and readability to let users know which assemblies we have and where refs #28205
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 1, context: html, text, full: html, text
    9291274db69ce9574770ca7908e63408de77358f Wed Sep 22 17:43:46 2021 -0700
    Adding colon from code review refs #28187
• src/hg/htdocs/inc/gbFooter.html
  • lines changed 2, context: html, text, full: html, text
    0f33cc4a0b242f6c3d2d266de14ab7de62431cd1 Fri Sep 24 13:19:36 2021 -0700
    Adding a link in the footer to FAQs & Search page, change approved by Lou, came up in CR where Lou enhanced the FAQ/index.hml refs #28192
• src/hg/htdocs/inc/gbFooterHardcoded.html
  • lines changed 1, context: html, text, full: html, text
    0f33cc4a0b242f6c3d2d266de14ab7de62431cd1 Fri Sep 24 13:19:36 2021 -0700
    Adding a link in the footer to FAQs & Search page, change approved by Lou, came up in CR where Lou enhanced the FAQ/index.hml refs #28192
• src/hg/htdocs/inc/gbsFooter.html
  • lines changed 2, context: html, text, full: html, text
    0f33cc4a0b242f6c3d2d266de14ab7de62431cd1 Fri Sep 24 13:19:36 2021 -0700
    Adding a link in the footer to FAQs & Search page, change approved by Lou, came up in CR where Lou enhanced the FAQ/index.hml refs #28192
• src/hg/htdocs/inc/jWestFooter.html
  • lines changed 2, context: html, text, full: html, text
    0f33cc4a0b242f6c3d2d266de14ab7de62431cd1 Fri Sep 24 13:19:36 2021 -0700
    Adding a link in the footer to FAQs & Search page, change approved by Lou, came up in CR where Lou enhanced the FAQ/index.hml refs #28192
• src/hg/htdocs/style/HGStyle.css
  • lines changed 2, context: html, text, full: html, text
    6ce1087262245e3d2d46198ac237d0d04126e1a3 Tue Sep 21 04:50:49 2021 -0700
    removing duplicated font-awesome integration into hgTracks, adding folder icon as a tag without a font dependency, removing link from the icon, and adding the icon to the config page, refs #28108
  • lines changed 4, context: html, text, full: html, text
    6792c1d5ca700a301d14fe7ea66e5e855598325a Thu Sep 23 05:28:32 2021 -0700
    aligning icons at the top, still looks somewhat strange, but better than before? refs #28108
• src/hg/inc/hui.h
  • lines changed 3, context: html, text, full: html, text
    8e2ec008050686045622d78cdb60a02b6da2b162 Tue Sep 21 10:50:14 2021 -0700
    adding missing file from previous commit
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    30eb18412a46f8376ba1b031d393159777a0590a Mon Sep 27 10:10:37 2021 -0700
    New version number v421
• src/hg/js/utils.js
  • lines changed 16, context: html, text, full: html, text
    cb9d5c7ec853681999acfa42ce503f1846d546ae Fri Sep 24 05:03:21 2021 -0700
    fixing track vis color on config page, refs #26257
• src/hg/lib/hui.c
  • lines changed 21, context: html, text, full: html, text
    6ce1087262245e3d2d46198ac237d0d04126e1a3 Tue Sep 21 04:50:49 2021 -0700
    removing duplicated font-awesome integration into hgTracks, adding folder icon as a tag without a font dependency, removing link from the icon, and adding the icon to the config page, refs #28108
• src/hg/makeDb/doc/hg19.txt
  • lines changed 41, context: html, text, full: html, text
    15e40046b987f458aa1d8413fe95a2e3d6a3ca60 Thu Sep 23 09:06:34 2021 -0700
    Fixing double append bug when creating gnomAD pli and missense constraint tracks, found by Jonathan in Bob email
• src/hg/makeDb/doc/hg38/gencode.txt
  • lines changed 8, context: html, text, full: html, text
    bd0945ac583598387ea83c8b3c20593bd934b06a Sat Sep 25 16:29:23 2021 -0700
    reload V38 with new changes
• src/hg/makeDb/doc/hg38/gtex.txt
  • lines changed 196, context: html, text, full: html, text
    5e75c13af084da1dbfdfc81a248eaa00903819ed Fri Sep 24 14:27:57 2021 -0700
    Changes to makedoc for gtex based on CR. Added two scripts and as file contents to makrdoc. refs #27947 #28163
• src/hg/makeDb/doc/hg38/patchUpdate.13.txt
  • lines changed 168, context: html, text, full: html, text
    c737428fa84b744e8d13bb5f8a7d83282729f084 Wed Sep 15 21:32:05 2021 -0700
    make doc for hg38 patch13. refs #25091
• src/hg/makeDb/gnomad/combine.awk
  • lines changed 42, context: html, text, full: html, text
    15e40046b987f458aa1d8413fe95a2e3d6a3ca60 Thu Sep 23 09:06:34 2021 -0700
    Fixing double append bug when creating gnomAD pli and missense constraint tracks, found by Jonathan in Bob email
• src/hg/makeDb/outside/gencode/bin/buildGencodeToUcscLift
  • lines changed 153, context: html, text, full: html, text
    f8e605d52fb7a05d5c5b19d3d6a14e7e554c0a0a Sat Sep 25 13:59:34 2021 -0700
    change ensembl to ucsc names (programs, files, variables) to be gencode to ucsc, as gencode does not actually use ensembl names, it use ENCODE, which uses UCSC for primary assembly and GenBank access or other sequences
• src/hg/makeDb/outside/gencode/bin/ensToUcscMkLift
  • lines changed 99, context: html, text, full: html, text
    5601f85204f7a4d863c54dd0217c3e7704c4ef73 Sat Sep 25 13:42:42 2021 -0700
    up gencode mapping to use assembly reports rather than ensemblToUcsc, due to problems with the ensemblToUcsc process and weird ensembl reverse-complemented sequences
  • lines changed 153, context: html, text, full: html, text
    f8e605d52fb7a05d5c5b19d3d6a14e7e554c0a0a Sat Sep 25 13:59:34 2021 -0700
    change ensembl to ucsc names (programs, files, variables) to be gencode to ucsc, as gencode does not actually use ensembl names, it use ENCODE, which uses UCSC for primary assembly and GenBank access or other sequences
• src/hg/makeDb/outside/gencode/bin/gencodeExonSupportToTable
  • lines changed 4, context: html, text, full: html, text
    f8e605d52fb7a05d5c5b19d3d6a14e7e554c0a0a Sat Sep 25 13:59:34 2021 -0700
    change ensembl to ucsc names (programs, files, variables) to be gencode to ucsc, as gencode does not actually use ensembl names, it use ENCODE, which uses UCSC for primary assembly and GenBank access or other sequences
• src/hg/makeDb/outside/gencode/bin/gencodeGenerateTrackDbs
  • lines changed 178, context: html, text, full: html, text
    352d3ef1b538bbebc21acf30fad247d49af09c02 Sat Sep 25 16:29:13 2021 -0700
    removed code for failed gencode/hgGene redo
• src/hg/makeDb/outside/gencode/bin/gencodeGenerateTrackDbsOldSchema
  • lines changed 2, context: html, text, full: html, text
    5601f85204f7a4d863c54dd0217c3e7704c4ef73 Sat Sep 25 13:42:42 2021 -0700
    up gencode mapping to use assembly reports rather than ensemblToUcsc, due to problems with the ensemblToUcsc process and weird ensembl reverse-complemented sequences
  • lines changed 707, context: html, text, full: html, text
    352d3ef1b538bbebc21acf30fad247d49af09c02 Sat Sep 25 16:29:13 2021 -0700
    removed code for failed gencode/hgGene redo
• src/hg/makeDb/outside/gencode/bin/gencodeGxfToAttrs
  • lines changed 1, context: html, text, full: html, text
    5601f85204f7a4d863c54dd0217c3e7704c4ef73 Sat Sep 25 13:42:42 2021 -0700
    up gencode mapping to use assembly reports rather than ensemblToUcsc, due to problems with the ensemblToUcsc process and weird ensembl reverse-complemented sequences
• src/hg/makeDb/outside/gencode/bin/gencodeGxfToGenePred
  • lines changed 4, context: html, text, full: html, text
    f8e605d52fb7a05d5c5b19d3d6a14e7e554c0a0a Sat Sep 25 13:59:34 2021 -0700
    change ensembl to ucsc names (programs, files, variables) to be gencode to ucsc, as gencode does not actually use ensembl names, it use ENCODE, which uses UCSC for primary assembly and GenBank access or other sequences
• src/hg/makeDb/outside/gencode/gencodeHgGeneLoad.mk
  • lines changed 8, context: html, text, full: html, text
    f8e605d52fb7a05d5c5b19d3d6a14e7e554c0a0a Sat Sep 25 13:59:34 2021 -0700
    change ensembl to ucsc names (programs, files, variables) to be gencode to ucsc, as gencode does not actually use ensembl names, it use ENCODE, which uses UCSC for primary assembly and GenBank access or other sequences
  • lines changed 421, context: html, text, full: html, text
    352d3ef1b538bbebc21acf30fad247d49af09c02 Sat Sep 25 16:29:13 2021 -0700
    removed code for failed gencode/hgGene redo
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 2, context: html, text, full: html, text
    5601f85204f7a4d863c54dd0217c3e7704c4ef73 Sat Sep 25 13:42:42 2021 -0700
    up gencode mapping to use assembly reports rather than ensemblToUcsc, due to problems with the ensemblToUcsc process and weird ensembl reverse-complemented sequences
  • lines changed 10, context: html, text, full: html, text
    f8e605d52fb7a05d5c5b19d3d6a14e7e554c0a0a Sat Sep 25 13:59:34 2021 -0700
    change ensembl to ucsc names (programs, files, variables) to be gencode to ucsc, as gencode does not actually use ensembl names, it use ENCODE, which uses UCSC for primary assembly and GenBank access or other sequences
  • lines changed 12, context: html, text, full: html, text
    bd0945ac583598387ea83c8b3c20593bd934b06a Sat Sep 25 16:29:23 2021 -0700
    reload V38 with new changes
• src/hg/makeDb/outside/gencode/tests/expected/buildGencodeToUcscLiftHs37Test.chain
  • lines changed 612, context: html, text, full: html, text
    f8e605d52fb7a05d5c5b19d3d6a14e7e554c0a0a Sat Sep 25 13:59:34 2021 -0700
    change ensembl to ucsc names (programs, files, variables) to be gencode to ucsc, as gencode does not actually use ensembl names, it use ENCODE, which uses UCSC for primary assembly and GenBank access or other sequences
• src/hg/makeDb/outside/gencode/tests/expected/buildGencodeToUcscLiftHs38Test.chain
  • lines changed 1280, context: html, text, full: html, text
    f8e605d52fb7a05d5c5b19d3d6a14e7e554c0a0a Sat Sep 25 13:59:34 2021 -0700
    change ensembl to ucsc names (programs, files, variables) to be gencode to ucsc, as gencode does not actually use ensembl names, it use ENCODE, which uses UCSC for primary assembly and GenBank access or other sequences
• src/hg/makeDb/outside/gencode/tests/expected/buildGencodeToUcscLiftMm38Test.chain
  • lines changed 478, context: html, text, full: html, text
    f8e605d52fb7a05d5c5b19d3d6a14e7e554c0a0a Sat Sep 25 13:59:34 2021 -0700
    change ensembl to ucsc names (programs, files, variables) to be gencode to ucsc, as gencode does not actually use ensembl names, it use ENCODE, which uses UCSC for primary assembly and GenBank access or other sequences
• src/hg/makeDb/outside/gencode/tests/expected/ensToUcscMkLiftHs37Test.chain
  • lines changed 742, context: html, text, full: html, text
    5601f85204f7a4d863c54dd0217c3e7704c4ef73 Sat Sep 25 13:42:42 2021 -0700
    up gencode mapping to use assembly reports rather than ensemblToUcsc, due to problems with the ensemblToUcsc process and weird ensembl reverse-complemented sequences
  • lines changed 612, context: html, text, full: html, text
    f8e605d52fb7a05d5c5b19d3d6a14e7e554c0a0a Sat Sep 25 13:59:34 2021 -0700
    change ensembl to ucsc names (programs, files, variables) to be gencode to ucsc, as gencode does not actually use ensembl names, it use ENCODE, which uses UCSC for primary assembly and GenBank access or other sequences
• src/hg/makeDb/outside/gencode/tests/expected/ensToUcscMkLiftHs38Test.chain
  • lines changed 1976, context: html, text, full: html, text
    5601f85204f7a4d863c54dd0217c3e7704c4ef73 Sat Sep 25 13:42:42 2021 -0700
    up gencode mapping to use assembly reports rather than ensemblToUcsc, due to problems with the ensemblToUcsc process and weird ensembl reverse-complemented sequences
  • lines changed 1280, context: html, text, full: html, text
    f8e605d52fb7a05d5c5b19d3d6a14e7e554c0a0a Sat Sep 25 13:59:34 2021 -0700
    change ensembl to ucsc names (programs, files, variables) to be gencode to ucsc, as gencode does not actually use ensembl names, it use ENCODE, which uses UCSC for primary assembly and GenBank access or other sequences
• src/hg/makeDb/outside/gencode/tests/expected/ensToUcscMkLiftMm38Test.chain
  • lines changed 471, context: html, text, full: html, text
    5601f85204f7a4d863c54dd0217c3e7704c4ef73 Sat Sep 25 13:42:42 2021 -0700
    up gencode mapping to use assembly reports rather than ensemblToUcsc, due to problems with the ensemblToUcsc process and weird ensembl reverse-complemented sequences
  • lines changed 478, context: html, text, full: html, text
    f8e605d52fb7a05d5c5b19d3d6a14e7e554c0a0a Sat Sep 25 13:59:34 2021 -0700
    change ensembl to ucsc names (programs, files, variables) to be gencode to ucsc, as gencode does not actually use ensembl names, it use ENCODE, which uses UCSC for primary assembly and GenBank access or other sequences
• src/hg/makeDb/outside/gencode/tests/expected/exonSupport1Test.exons
  • lines changed 10, context: html, text, full: html, text
    5601f85204f7a4d863c54dd0217c3e7704c4ef73 Sat Sep 25 13:42:42 2021 -0700
    up gencode mapping to use assembly reports rather than ensemblToUcsc, due to problems with the ensemblToUcsc process and weird ensembl reverse-complemented sequences
• src/hg/makeDb/outside/gencode/tests/expected/specialCases1Test.gp
  • lines changed 5, context: html, text, full: html, text
    5601f85204f7a4d863c54dd0217c3e7704c4ef73 Sat Sep 25 13:42:42 2021 -0700
    up gencode mapping to use assembly reports rather than ensemblToUcsc, due to problems with the ensemblToUcsc process and weird ensembl reverse-complemented sequences
• src/hg/makeDb/outside/gencode/tests/expected/specialCases1Test.unmapped.gp
  • lines changed 10, context: html, text, full: html, text
    5601f85204f7a4d863c54dd0217c3e7704c4ef73 Sat Sep 25 13:42:42 2021 -0700
    up gencode mapping to use assembly reports rather than ensemblToUcsc, due to problems with the ensemblToUcsc process and weird ensembl reverse-complemented sequences
• src/hg/makeDb/outside/gencode/tests/input/GCF_000001405.25_GRCh37.p13_assembly_report.txt
  • lines changed 333, context: html, text, full: html, text
    5601f85204f7a4d863c54dd0217c3e7704c4ef73 Sat Sep 25 13:42:42 2021 -0700
    up gencode mapping to use assembly reports rather than ensemblToUcsc, due to problems with the ensemblToUcsc process and weird ensembl reverse-complemented sequences
• src/hg/makeDb/outside/gencode/tests/input/GCF_000001405.39_GRCh38.p13_assembly_report.txt
  • lines changed 703, context: html, text, full: html, text
    5601f85204f7a4d863c54dd0217c3e7704c4ef73 Sat Sep 25 13:42:42 2021 -0700
    up gencode mapping to use assembly reports rather than ensemblToUcsc, due to problems with the ensemblToUcsc process and weird ensembl reverse-complemented sequences
• src/hg/makeDb/outside/gencode/tests/input/GCF_000001635.26_GRCm38.p6_assembly_report.txt
  • lines changed 282, context: html, text, full: html, text
    5601f85204f7a4d863c54dd0217c3e7704c4ef73 Sat Sep 25 13:42:42 2021 -0700
    up gencode mapping to use assembly reports rather than ensemblToUcsc, due to problems with the ensemblToUcsc process and weird ensembl reverse-complemented sequences
• src/hg/makeDb/outside/gencode/tests/makefile
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    5601f85204f7a4d863c54dd0217c3e7704c4ef73 Sat Sep 25 13:42:42 2021 -0700
    up gencode mapping to use assembly reports rather than ensemblToUcsc, due to problems with the ensemblToUcsc process and weird ensembl reverse-complemented sequences
  • lines changed 28, context: html, text, full: html, text
    f8e605d52fb7a05d5c5b19d3d6a14e7e554c0a0a Sat Sep 25 13:59:34 2021 -0700
    change ensembl to ucsc names (programs, files, variables) to be gencode to ucsc, as gencode does not actually use ensembl names, it use ENCODE, which uses UCSC for primary assembly and GenBank access or other sequences
• src/hg/makeDb/trackDb/human/geneHancer.html
  • lines changed 1, context: html, text, full: html, text
    60e2f1cf879afe3838a24e9bc0448b8c6ebf842e Fri Sep 24 14:30:08 2021 -0700
    Fixing formatting for quote char encoding, no redmine
• src/hg/makeDb/trackDb/human/hg19/gnomadPLI.html
  • lines changed 1, context: html, text, full: html, text
    53e2c936687f25ddc57775b80b912a1eb01ec641 Wed Sep 22 15:02:09 2021 -0700
    added a hyphen
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    f64d899aca1924ee0340f50145e70fd715ad3d0e Wed Sep 22 15:04:01 2021 -0700
    dropped a comma
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    5eead6e61c87f9d5fbe37ac42dc2254485716b4b Wed Sep 22 15:54:35 2021 -0700
    tweaks to wording
• src/hg/makeDb/trackDb/human/hg19/gnomadPext.html
  • lines changed 1, context: html, text, full: html, text
    5eead6e61c87f9d5fbe37ac42dc2254485716b4b Wed Sep 22 15:54:35 2021 -0700
    tweaks to wording
• src/hg/makeDb/trackDb/human/hg19/knownGene.alpha.ra
  • lines changed 39, context: html, text, full: html, text
    c9f4f4f59fa2576f5ec3bbd2b2886d3dc270f04e Wed Sep 22 19:02:17 2021 -0700
    switch the primary gene set on hg19 to V38lift37
  • lines changed 1, context: html, text, full: html, text
    60f24be747f18c670816b2e660dc1bb0ea8d3e6d Fri Sep 24 12:24:24 2021 -0700
    start using gencodeV38lift37 has primary gene set
• src/hg/makeDb/trackDb/human/hg19/knownGeneArchive.ra
  • lines changed 42, context: html, text, full: html, text
    76d463f1dcd4e0f752497032b2790100684df4dd Wed Sep 22 19:04:47 2021 -0700
    add hg19 knownGene archive
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
  • lines changed 1, context: html, text, full: html, text
    606dcebbac71bf95a60991cff9a77f91d824ecd0 Wed Sep 22 15:37:06 2021 -0700
    Fixing outlinks for gnomAD, no RM
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    c9f4f4f59fa2576f5ec3bbd2b2886d3dc270f04e Wed Sep 22 19:02:17 2021 -0700
    switch the primary gene set on hg19 to V38lift37
• src/hg/makeDb/trackDb/human/hg38/description.html
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    dfb97de7386e6b19a2eba8767a1d72b0232d5fb2 Tue Sep 21 12:32:50 2021 -0700
    Since web browsers are de-emphasizing FTP, we want to put HTTP first and FTP second.
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    daa672e431d5851ec7ff6ff92787b51a5665878c Thu Sep 23 19:23:54 2021 -0700
    fixed total chrom number to 640. refs #25091
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    953d44e2eda13dde89e684c2a53c2d779d02b18d Thu Sep 23 19:33:49 2021 -0700
    fixed url link. refs #25091
• src/hg/makeDb/trackDb/human/hg38/fetalGeneAtlas.html
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    f040d9bbdbef39d57e33fcd8f8eaa5c89ec2e6fa Tue Sep 21 10:43:35 2021 -0700
    Corrected the type of RNA-seq being used. refs #28059
• src/hg/makeDb/trackDb/human/hg38/gtexEqtl.ra
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    f5a8ec22fccfa23e5e1c51e0522b1aba4043bc22 Fri Sep 24 13:20:55 2021 -0700
    Some parts of the as file changed, so needed to change some of the trackDb settings, refs #27947
• src/hg/makeDb/trackDb/human/hg38/heartCellAtlas.html
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    8444df82d18ebc5163fd6ebc813ccabec745e16b Tue Sep 21 10:39:29 2021 -0700
    Added a note in the description based on my correspondence with Sarah Teichmann. refs #27727
• src/hg/makeDb/trackDb/human/hg38/placentaVentoTormo.ra
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    ce0e013f4d9fa9b68d4820c422b647e963584551 Tue Sep 21 10:45:36 2021 -0700
    Expanded the last two cell types based on my correspondence with Roser Vento. refs #26967
• src/hg/makeDb/trackDb/human/jaspar.ra
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    b1d94bf0fff50fe7d59af3c857b4e588a0d9ed44 Mon Sep 20 15:44:33 2021 -0700
    Accepting suggestions to minimize redundancy and add urls to JASPAR track refs #27061
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    fb664a2b84ad7f691d9ebb5aa3a85a1c1f42f024 Fri Sep 24 12:11:01 2021 -0700
    Releasing JASPAR tracks refs #27061
• src/hg/makeDb/trackDb/human/mastermind.html
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    55f08b2574488233f39f51a18362f1be97598b86 Wed Sep 22 14:54:51 2021 -0700
    pluralized paper to papers
• src/hg/makeDb/trackDb/human/trackDb.ra
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    63bfb6e037471cc05850d31f55c5d2afade219e1 Mon Sep 20 16:12:30 2021 -0700
    Releasing the LRG update refs #24672
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    2e704546ad7c7fe8f624328e3abb21b8048eeded Wed Sep 22 15:41:23 2021 -0700
    Revert "Releasing the LRG update refs #24672" This reverts commit 63bfb6e037471cc05850d31f55c5d2afade219e1.
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    09a878c5030e368099828acb25bdc4ab8d2d46e8 Wed Sep 22 17:05:00 2021 -0700
    rename lrgBigPsl to lrgTranscriptAli as it once was
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    fb664a2b84ad7f691d9ebb5aa3a85a1c1f42f024 Fri Sep 24 12:11:01 2021 -0700
    Releasing JASPAR tracks refs #27061
• src/hg/utils/otto/lrg/buildLrg.sh
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    5740a341fc29a4d30268ad488d19a88d6e5401e7 Thu Sep 23 11:15:20 2021 -0700
    Prepare LRG otto job for switchover to ottomeister, only update when data has changed, refs #24672
• src/hg/utils/otto/otto.crontab
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    f78e3d4a78d011b07f57c8fe0a8dd7cdbddd9d26 Thu Sep 23 15:19:21 2021 -0700
    Updating otto crontab, no RM
• src/hg/utils/otto/sarscov2phylo/combineMetadata.sh
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    6068fc9cbd3f8aa5f70f0535a5086423cf0c8d4c Wed Sep 22 20:42:55 2021 -0700
    Move the construction of new.masked.vcf.gz out of updateCombinedTree.sh into makeNewMaskedVcf.sh and move out the metadata stuff into combineMetadata.sh.
• src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
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    724c2bc191aa30074eb93775ede264f38058d6bc Wed Sep 22 17:53:14 2021 -0700
    Always use -f (so reruns don't fail).
• src/hg/utils/otto/sarscov2phylo/gbMetadataAddBioSample.pl
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    4bfc83ad307e5017054b4852d17dc0b82f1997c5 Wed Sep 22 17:53:41 2021 -0700
    Better formatting of date mismatches for reporting to labs.
• src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh
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    6068fc9cbd3f8aa5f70f0535a5086423cf0c8d4c Wed Sep 22 20:42:55 2021 -0700
    Move the construction of new.masked.vcf.gz out of updateCombinedTree.sh into makeNewMaskedVcf.sh and move out the metadata stuff into combineMetadata.sh.
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
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    724c2bc191aa30074eb93775ede264f38058d6bc Wed Sep 22 17:53:14 2021 -0700
    Always use -f (so reruns don't fail).
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    6068fc9cbd3f8aa5f70f0535a5086423cf0c8d4c Wed Sep 22 20:42:55 2021 -0700
    Move the construction of new.masked.vcf.gz out of updateCombinedTree.sh into makeNewMaskedVcf.sh and move out the metadata stuff into combineMetadata.sh.
• src/inc/common.mk
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    8b3a01986b2cf3fc0bd975fe0f3bf06abb37123d Mon Sep 20 14:46:31 2021 -0700
    fix build on Mac OSX with freetype and mariadbclient libraries no redmine
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    da47fe7e559f64f870af274fe6ae2b0ff89354ba Fri Sep 24 14:17:21 2021 -0700
    restore previous behavior for freetype libs on hgwdev no redmine
• src/inc/srcVersion.h
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    30eb18412a46f8376ba1b031d393159777a0590a Mon Sep 27 10:10:37 2021 -0700
    New version number v421
• src/utils/makefile
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    dc98c2a3d02cea597839f3be202b7262e62d54ed Tue Sep 21 08:47:36 2021 -0700
    disable compiling findMotif on Apple M1 CPUs (arm64) due to using SSE instructions
• src/utils/qa/weeklybld/buildEnv.csh
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    bf1165178d46473f8ed0531ad3a3e88e43e649b5 Mon Sep 27 10:09:26 2021 -0700
    v421 final build, refs #28170

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