All File Changes

v436_preview to v436_preview2 (2022-08-15 to 2022-08-22) v436

• src/hg/hgTracks/bigRmskTrack.c
  • lines changed 17, context: html, text, full: html, text
    59ac146389c04b9e91c3bd7f658a28cb0f5e04d4 Sun Aug 14 10:12:11 2022 -0700
    show full label in label region (from RMH)
• src/hg/hgTracks/gencodeTracks.c
  • lines changed 23, context: html, text, full: html, text
    a93daa92b77f5717f8ff247cb049a46cd0f66409 Sun Aug 21 17:37:28 2022 -0700
    add transcriptRank column to wgEncodeGencodeAttrs in preperation for getting transcript ranks in upcomming gencode distribution. Import GENCODE V42 prerelease to test out creating column
• src/hg/htdocs/bigRmskTrackDesc.html
  • lines changed 216, context: html, text, full: html, text
    e417eb7ff33edef9c0b33bb67360a9fc39fc9105 Sun Aug 21 08:49:17 2022 -0700
    update bigRmsk track build documentation and provide a standard track description page
• src/hg/htdocs/goldenPath/help/bigRmsk.html
  • lines changed 310, context: html, text, full: html, text
    e417eb7ff33edef9c0b33bb67360a9fc39fc9105 Sun Aug 21 08:49:17 2022 -0700
    update bigRmsk track build documentation and provide a standard track description page
• src/hg/inc/encode/wgEncodeGencodeAttrs.h
  • lines changed 8, context: html, text, full: html, text
    a93daa92b77f5717f8ff247cb049a46cd0f66409 Sun Aug 21 17:37:28 2022 -0700
    add transcriptRank column to wgEncodeGencodeAttrs in preperation for getting transcript ranks in upcomming gencode distribution. Import GENCODE V42 prerelease to test out creating column
• src/hg/lib/encode/wgEncodeGencodeAttrs.c
  • lines changed 38, context: html, text, full: html, text
    a93daa92b77f5717f8ff247cb049a46cd0f66409 Sun Aug 21 17:37:28 2022 -0700
    add transcriptRank column to wgEncodeGencodeAttrs in preperation for getting transcript ranks in upcomming gencode distribution. Import GENCODE V42 prerelease to test out creating column
• src/hg/lib/encode/wgEncodeGencodeAttrs.sql
  • lines changed 1, context: html, text, full: html, text
    a93daa92b77f5717f8ff247cb049a46cd0f66409 Sun Aug 21 17:37:28 2022 -0700
    add transcriptRank column to wgEncodeGencodeAttrs in preperation for getting transcript ranks in upcomming gencode distribution. Import GENCODE V42 prerelease to test out creating column
• src/hg/lib/hgncBig62.as
  • lines changed 67, context: html, text, full: html, text
    8d6f251e885f2a8a3c6f32b4a3c0a47c11b00206 Sat Aug 20 15:23:42 2022 -0700
    add prototype HGNC track to hg38
• src/hg/lib/hui.c
  • lines changed 3, context: html, text, full: html, text
    0e96ee09b21a249e40d9174682fb97c29bbe45df Mon Aug 15 19:44:59 2022 -0700
    fix bug in recognizing old style filter names
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    ec578c077c200e7fc279e3cd69cf29c026c43ebf Mon Aug 22 09:19:11 2022 -0700
    adding GCF_024166365.1_mEleMax1_primary_haplotype Asiatic elephant per user request refs #29905
• src/hg/makeDb/doc/hg19.txt
  • lines changed 58, context: html, text, full: html, text
    3f5cb0af99b631cfd22ff7b37edc281c521510e1 Sat Aug 20 15:56:38 2022 -0700
    oops.. didn't add the hg19 makeDoc for hgnc
• src/hg/makeDb/doc/hg38/gencode.txt
  • lines changed 31, context: html, text, full: html, text
    a93daa92b77f5717f8ff247cb049a46cd0f66409 Sun Aug 21 17:37:28 2022 -0700
    add transcriptRank column to wgEncodeGencodeAttrs in preperation for getting transcript ranks in upcomming gencode distribution. Import GENCODE V42 prerelease to test out creating column
• src/hg/makeDb/doc/hg38/hgnc.txt
  • lines changed 56, context: html, text, full: html, text
    8d6f251e885f2a8a3c6f32b4a3c0a47c11b00206 Sat Aug 20 15:23:42 2022 -0700
    add prototype HGNC track to hg38
• src/hg/makeDb/doc/hg38/multiz470way.txt
  • lines changed 2621, context: html, text, full: html, text
    55537db019790918919ae99fa0114582c4193fac Thu Aug 18 14:42:07 2022 -0700
    initial steps of this 470 way track refs #29898
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    ec578c077c200e7fc279e3cd69cf29c026c43ebf Mon Aug 22 09:19:11 2022 -0700
    adding GCF_024166365.1_mEleMax1_primary_haplotype Asiatic elephant per user request refs #29905
• src/hg/makeDb/outside/gencode/bin/gencodeGxfToAttrs
  • lines changed 6, context: html, text, full: html, text
    c64ea1371e5abf8908877f7c9e4164c2f7b54094 Sun Aug 21 19:37:48 2022 -0700
    include faked transcriptRank in initial TSV
• src/hg/makeDb/outside/gencode/bin/gencodeMakeAttrs
  • lines changed 2, context: html, text, full: html, text
    a93daa92b77f5717f8ff247cb049a46cd0f66409 Sun Aug 21 17:37:28 2022 -0700
    add transcriptRank column to wgEncodeGencodeAttrs in preperation for getting transcript ranks in upcomming gencode distribution. Import GENCODE V42 prerelease to test out creating column
  • lines changed 1, context: html, text, full: html, text
    c64ea1371e5abf8908877f7c9e4164c2f7b54094 Sun Aug 21 19:37:48 2022 -0700
    include faked transcriptRank in initial TSV
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 6, context: html, text, full: html, text
    a93daa92b77f5717f8ff247cb049a46cd0f66409 Sun Aug 21 17:37:28 2022 -0700
    add transcriptRank column to wgEncodeGencodeAttrs in preperation for getting transcript ranks in upcomming gencode distribution. Import GENCODE V42 prerelease to test out creating column
• src/hg/makeDb/outside/gencode/lib/gencode/biotypes.py
  • lines changed 3, context: html, text, full: html, text
    a93daa92b77f5717f8ff247cb049a46cd0f66409 Sun Aug 21 17:37:28 2022 -0700
    add transcriptRank column to wgEncodeGencodeAttrs in preperation for getting transcript ranks in upcomming gencode distribution. Import GENCODE V42 prerelease to test out creating column
• src/hg/makeDb/outside/gencode/lib/gencode/gencodeGenes.py
  • lines changed 5, context: html, text, full: html, text
    c64ea1371e5abf8908877f7c9e4164c2f7b54094 Sun Aug 21 19:37:48 2022 -0700
    include faked transcriptRank in initial TSV
• src/hg/makeDb/outside/gencode/lib/gencode/gencodeTags.py
  • lines changed 1, context: html, text, full: html, text
    a93daa92b77f5717f8ff247cb049a46cd0f66409 Sun Aug 21 17:37:28 2022 -0700
    add transcriptRank column to wgEncodeGencodeAttrs in preperation for getting transcript ranks in upcomming gencode distribution. Import GENCODE V42 prerelease to test out creating column
• src/hg/makeDb/outside/gencode/tests/expected/attrsPseudoGff3Tests.tsv
  • lines changed 3, context: html, text, full: html, text
    c64ea1371e5abf8908877f7c9e4164c2f7b54094 Sun Aug 21 19:37:48 2022 -0700
    include faked transcriptRank in initial TSV
• src/hg/makeDb/outside/gencode/tests/expected/attrsSet1GtfTest.tsv
  • lines changed 83, context: html, text, full: html, text
    c64ea1371e5abf8908877f7c9e4164c2f7b54094 Sun Aug 21 19:37:48 2022 -0700
    include faked transcriptRank in initial TSV
• src/hg/makeDb/outside/gencode/tests/expected/attrsTagGff3Tests.tsv
  • lines changed 17, context: html, text, full: html, text
    c64ea1371e5abf8908877f7c9e4164c2f7b54094 Sun Aug 21 19:37:48 2022 -0700
    include faked transcriptRank in initial TSV
• src/hg/makeDb/outside/gencode/tests/expected/attrsTagGtfTests.tsv
  • lines changed 17, context: html, text, full: html, text
    c64ea1371e5abf8908877f7c9e4164c2f7b54094 Sun Aug 21 19:37:48 2022 -0700
    include faked transcriptRank in initial TSV
• src/hg/makeDb/outside/gencode/tests/expected/attrsV19GtfTest.tsv
  • lines changed 6, context: html, text, full: html, text
    c64ea1371e5abf8908877f7c9e4164c2f7b54094 Sun Aug 21 19:37:48 2022 -0700
    include faked transcriptRank in initial TSV
• src/hg/makeDb/outside/gencode/tests/expected/attrsV21Gff3Test.tsv
  • lines changed 118, context: html, text, full: html, text
    c64ea1371e5abf8908877f7c9e4164c2f7b54094 Sun Aug 21 19:37:48 2022 -0700
    include faked transcriptRank in initial TSV
• src/hg/makeDb/outside/gencode/tests/expected/attrsV21GtfTest.tsv
  • lines changed 118, context: html, text, full: html, text
    c64ea1371e5abf8908877f7c9e4164c2f7b54094 Sun Aug 21 19:37:48 2022 -0700
    include faked transcriptRank in initial TSV
• src/hg/makeDb/outside/gencode/tests/expected/attrsV27ParGff3Test.tsv
  • lines changed 16, context: html, text, full: html, text
    c64ea1371e5abf8908877f7c9e4164c2f7b54094 Sun Aug 21 19:37:48 2022 -0700
    include faked transcriptRank in initial TSV
• src/hg/makeDb/outside/gencode/tests/expected/attrsV27ParGtfTest.tsv
  • lines changed 16, context: html, text, full: html, text
    c64ea1371e5abf8908877f7c9e4164c2f7b54094 Sun Aug 21 19:37:48 2022 -0700
    include faked transcriptRank in initial TSV
• src/hg/makeDb/outside/gencode/tests/expected/makeAttrsTest.attrs.tab
  • lines changed 82, context: html, text, full: html, text
    c64ea1371e5abf8908877f7c9e4164c2f7b54094 Sun Aug 21 19:37:48 2022 -0700
    include faked transcriptRank in initial TSV
• src/hg/makeDb/schema/all.joiner
  • lines changed 95, context: html, text, full: html, text
    a93daa92b77f5717f8ff247cb049a46cd0f66409 Sun Aug 21 17:37:28 2022 -0700
    add transcriptRank column to wgEncodeGencodeAttrs in preperation for getting transcript ranks in upcomming gencode distribution. Import GENCODE V42 prerelease to test out creating column
• src/hg/makeDb/trackDb/human/hg19/genotypeArrays.html
  • lines changed 4, context: html, text, full: html, text
    3a53fdf0f964d0c87e694202179c0b575835b38e Tue Aug 16 16:42:19 2022 -0700
    Adding what the colored annotations represent on the description page, refs #29309 #29492
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    0596c449025f12f6851d2b92e135e682aa3cf74d Wed Aug 17 11:17:36 2022 -0700
    Fixing the type for hg19 CytoSNP 850k track, refs #29492
• src/hg/makeDb/trackDb/human/hg38/genotypeArrays.html
  • lines changed 9, context: html, text, full: html, text
    3a53fdf0f964d0c87e694202179c0b575835b38e Tue Aug 16 16:42:19 2022 -0700
    Adding what the colored annotations represent on the description page, refs #29309 #29492
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    a93daa92b77f5717f8ff247cb049a46cd0f66409 Sun Aug 21 17:37:28 2022 -0700
    add transcriptRank column to wgEncodeGencodeAttrs in preperation for getting transcript ranks in upcomming gencode distribution. Import GENCODE V42 prerelease to test out creating column
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV42.html
  • lines changed 47, context: html, text, full: html, text
    a93daa92b77f5717f8ff247cb049a46cd0f66409 Sun Aug 21 17:37:28 2022 -0700
    add transcriptRank column to wgEncodeGencodeAttrs in preperation for getting transcript ranks in upcomming gencode distribution. Import GENCODE V42 prerelease to test out creating column
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV42.ra
  • lines changed 286, context: html, text, full: html, text
    a93daa92b77f5717f8ff247cb049a46cd0f66409 Sun Aug 21 17:37:28 2022 -0700
    add transcriptRank column to wgEncodeGencodeAttrs in preperation for getting transcript ranks in upcomming gencode distribution. Import GENCODE V42 prerelease to test out creating column
• src/hg/makeDb/trackDb/human/lrg.html
  • lines changed 8, context: html, text, full: html, text
    bb81d6d10b9c22486ee6745375383d9a8d136230 Fri Aug 19 03:10:28 2022 -0700
    documenting refseqgene alias for lrg, very confusing, refs #29891
• src/hg/makeDb/trackDb/human/lrgTranscriptAli.html
  • lines changed 7, context: html, text, full: html, text
    bb81d6d10b9c22486ee6745375383d9a8d136230 Fri Aug 19 03:10:28 2022 -0700
    documenting refseqgene alias for lrg, very confusing, refs #29891
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    8ce2ae468ca2cb4e668c5c9b9630878480ce3b44 Tue Aug 16 16:48:34 2022 -0700
    Adding a green "Note" pennantIcon about dbSNP 153 getting nested soon into dbSNP archive, refs #27751
  • lines changed 2, context: html, text, full: html, text
    bb81d6d10b9c22486ee6745375383d9a8d136230 Fri Aug 19 03:10:28 2022 -0700
    documenting refseqgene alias for lrg, very confusing, refs #29891
  • lines changed 16, context: html, text, full: html, text
    8d6f251e885f2a8a3c6f32b4a3c0a47c11b00206 Sat Aug 20 15:23:42 2022 -0700
    add prototype HGNC track to hg38
  • lines changed 1, context: html, text, full: html, text
    757be1c964abd03dd10608f1db98ef850716da55 Sun Aug 21 17:17:56 2022 -0700
    Adding a pennantIcon for the dbSNP build 155 release, refs #27751
• src/hg/makeDb/trackDb/uniprotAlpha.html
  • lines changed 2, context: html, text, full: html, text
    48323273924a067a8a30a31fecf2265ccfa59905 Fri Aug 19 08:28:07 2022 -0700
    tiny change to uniprot docs page, #28560
• src/hg/utils/otto/ncbiRefSeq/runHg38.sh
  • lines changed 3, context: html, text, full: html, text
    1ed40bfa70579f764d1110fa4aa5467e6e5b78d9 Fri Aug 19 11:09:34 2022 -0700
    update the file to watch for the next versions of this track refs #29891
• src/utils/apacheLogParse
  • lines changed 19, context: html, text, full: html, text
    8796e12036760665e5e7ae83ad30cbbb48d302c9 Thu Aug 18 11:16:56 2022 -0700
    updating apacheLogParse, no redmine
  • lines changed 8, context: html, text, full: html, text
    a700c66c67b692c50b3d1e69eadc593c14b5fe1e Fri Aug 19 02:53:47 2022 -0700
    updating apache log parse, no redmine
• src/utils/mafSort.pl
  • lines changed 106, context: html, text, full: html, text
    c937ed5d9ffb20f8cfcbe18152a3f65929a3853c Thu Aug 18 12:11:37 2022 -0700
    maf sort command used to clean up maf files refs #29898
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    0c8747e94cde369b76c68fc3c1e8dbe2b80345ec Mon Aug 22 10:40:37 2022 -0700
    v436 preview2, refs #29878

• lines changed: 4569
• files changed: 51