All File Changes

v416_base to v417_preview (2021-06-14 to 2021-06-21) v417

• confs/hgwbeta.hg.conf
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    fd96f546c3683a65174ef1ea403b42fc03178746 Sun Jun 20 01:11:46 2021 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 1, context: html, text, full: html, text
    0e3cd383acb8a9946add69acd91fbd7437c26a05 Mon Jun 14 10:56:44 2021 -0700
    fix bug in bigBed filtering #27713
• src/hg/hgTracks/recTrackSets.c
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    757272da1a6562f39ef8c5283aed15dbc3af7657 Tue Jun 15 09:53:12 2021 -0700
    Preserve left label region width. refs #27688
• src/hg/hgTracks/simpleTracks.c
  • lines changed 2, context: html, text, full: html, text
    185a4f642530a98b65189bf218d412f382462b8c Mon Jun 14 11:06:10 2021 -0700
    fix clicks on squished item tracks when in nextExon mode #27715
• src/hg/htdocs/covid19.html
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    5973558729768608f2b0fc68ee628f1c57c5e793 Tue Jun 15 13:18:39 2021 -0700
    Fixed static page cronjob 404 links, date 2021-06-15, no RM
• src/hg/inc/bigBedFilter.h
  • lines changed 1, context: html, text, full: html, text
    0e3cd383acb8a9946add69acd91fbd7437c26a05 Mon Jun 14 10:56:44 2021 -0700
    fix bug in bigBed filtering #27713
  • lines changed 1, context: html, text, full: html, text
    1334cc6d5faa01343d041c889c5e71dfd8a44757 Mon Jun 14 18:29:10 2021 -0700
    make the default filterType be multiple
• src/hg/lib/hdb.c
  • lines changed 2, context: html, text, full: html, text
    0194df3ad18b73a17bc652065e8ef9fcfaaa3188 Mon Jun 14 11:51:58 2021 -0700
    fix crash in hTrackDb() when database doesn't exist or has no trackDb
• src/hg/lib/hui.c
  • lines changed 17, context: html, text, full: html, text
    0e3cd383acb8a9946add69acd91fbd7437c26a05 Mon Jun 14 10:56:44 2021 -0700
    fix bug in bigBed filtering #27713
• src/hg/makeDb/trackDb/human/cadd.ra
  • lines changed 8, context: html, text, full: html, text
    b1ae66fdc9611229b379edc06fa5fb78cc03d45f Thu Jun 17 14:12:32 2021 -0700
    Renaming the caddAlpha.ra file, refs #27589
• src/hg/makeDb/trackDb/human/caddAlpha.ra
  • lines changed 94, context: html, text, full: html, text
    b1ae66fdc9611229b379edc06fa5fb78cc03d45f Thu Jun 17 14:12:32 2021 -0700
    Renaming the caddAlpha.ra file, refs #27589
• src/hg/makeDb/trackDb/human/hg19/dbSnpArchiveHg19.ra
  • lines changed 57, context: html, text, full: html, text
    ea7cde1457334fa71ce1a9fe7088eba1e9598845 Fri Jun 18 16:14:12 2021 -0700
    Reordering snp archive tracks, refs #26719
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.alpha.ra
  • lines changed 944, context: html, text, full: html, text
    0e3cd383acb8a9946add69acd91fbd7437c26a05 Mon Jun 14 10:56:44 2021 -0700
    fix bug in bigBed filtering #27713
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    0e3cd383acb8a9946add69acd91fbd7437c26a05 Mon Jun 14 10:56:44 2021 -0700
    fix bug in bigBed filtering #27713
• src/hg/makeDb/trackDb/human/hg38/dbSnpArchiveHg38.ra
  • lines changed 91, context: html, text, full: html, text
    ea7cde1457334fa71ce1a9fe7088eba1e9598845 Fri Jun 18 16:14:12 2021 -0700
    Reordering snp archive tracks, refs #26719
• src/hg/makeDb/trackDb/human/hg38/gnomad.alpha.ra
  • lines changed 116, context: html, text, full: html, text
    0e3cd383acb8a9946add69acd91fbd7437c26a05 Mon Jun 14 10:56:44 2021 -0700
    fix bug in bigBed filtering #27713
  • lines changed 1, context: html, text, full: html, text
    56b4dadf61ebe941a7b955d9999d75d3265809c8 Mon Jun 14 11:18:00 2021 -0700
    put gnomad 3_1_1 track in alpha trackDb
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 34, context: html, text, full: html, text
    56b4dadf61ebe941a7b955d9999d75d3265809c8 Mon Jun 14 11:18:00 2021 -0700
    put gnomad 3_1_1 track in alpha trackDb
• src/hg/makeDb/trackDb/human/hg38/trackDb.241wayBM.ra
  • lines changed 40, context: html, text, full: html, text
    76b6848019fb17a00bd1c3c7a4d87c71e3a3c099 Mon Jun 14 11:50:25 2021 -0700
    trying the bigMaf track refs #11636
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    0e3cd383acb8a9946add69acd91fbd7437c26a05 Mon Jun 14 10:56:44 2021 -0700
    fix bug in bigBed filtering #27713
  • lines changed 1, context: html, text, full: html, text
    76b6848019fb17a00bd1c3c7a4d87c71e3a3c099 Mon Jun 14 11:50:25 2021 -0700
    trying the bigMaf track refs #11636
  • lines changed 2, context: html, text, full: html, text
    c0bf59436d960e9ad7ce1777febf6b81f8f49deb Tue Jun 15 16:16:35 2021 -0700
    Edited shortLabel and longLabel for ncbiRefSeqSelect, refs #27552
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    9cd8d110987899258391282618259b6706c58ae0 Tue Jun 15 16:55:48 2021 -0700
    Another edit to ncbiRefSeqSelect shortLabel and longLabel, refs #27552
• src/hg/makeDb/trackDb/human/revel.ra
  • lines changed 5, context: html, text, full: html, text
    ea7cde1457334fa71ce1a9fe7088eba1e9598845 Fri Jun 18 16:14:12 2021 -0700
    Reordering snp archive tracks, refs #26719
• src/hg/makeDb/trackDb/human/trackDb.clinvar.alpha.ra
  • lines changed 96, context: html, text, full: html, text
    0e3cd383acb8a9946add69acd91fbd7437c26a05 Mon Jun 14 10:56:44 2021 -0700
    fix bug in bigBed filtering #27713
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    0e3cd383acb8a9946add69acd91fbd7437c26a05 Mon Jun 14 10:56:44 2021 -0700
    fix bug in bigBed filtering #27713
  • lines changed 2, context: html, text, full: html, text
    c6f65dd5a4a2973e8dc285504541e19db8560014 Wed Jun 16 13:38:32 2021 -0700
    Updating release tags for cadd, refs #27589
  • lines changed 2, context: html, text, full: html, text
    af3d5a7fa71b7b548d6675d3eceb13d9dc6e3931 Thu Jun 17 14:17:42 2021 -0700
    Removing cadd release tags, refs #27589
• src/hg/makeDb/trackDb/makefile
  • lines changed 2, context: html, text, full: html, text
    10f674a1e8b0c153171383ed2e211c001fd36dec Mon Jun 14 20:19:23 2021 -0700
    add the creation of the cartVersion pseudo track to the beta trackDb build #27517
• src/hg/makeDb/trackDb/mouse/mm10/dbSnpArchiveMm10.ra
  • lines changed 8, context: html, text, full: html, text
    ea7cde1457334fa71ce1a9fe7088eba1e9598845 Fri Jun 18 16:14:12 2021 -0700
    Reordering snp archive tracks, refs #26719
• src/hg/utils/otto/sarscov2phylo/fixNcbiFastaNames.pl
  • lines changed 0, context: html, text, full: html, text
    b90cc537ccb7800ba8dc1caf25e54c835fd653a8 Wed Jun 16 17:50:21 2021 -0700
    Encountered new condition (missing metadata) and found that downstream scripts really expect a space before |.
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
  • lines changed 25, context: html, text, full: html, text
    cc57121245fc7a8dd659c359a2f8457a808335b8 Wed Jun 16 17:49:16 2021 -0700
    Use NCBI datasets tool instead of API, more robust and can exclude unwanted files. Handle the previous day's build failing by using ncbi.latest.
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
  • lines changed 353, context: html, text, full: html, text
    88c5c33485279c9687d7be15a85da2665c16e91d Wed Jun 16 17:52:44 2021 -0700
    Lots of work from the past month. De-dup COG-UK & GenBank; generate public tree from combined gisaidAndPublic tree.
• src/hg/utils/otto/sarscov2phylo/util.sh
  • lines changed 10, context: html, text, full: html, text
    e6e4ac7f750c6e2894752ef008325efee95ae6fc Wed Jun 16 17:47:08 2021 -0700
    Added vcfSamples function (grab VCF sample names from #CHROM header line, print one name per line)
• src/hg/utils/vcfRenameAndPrune/vcfRenameAndPrune.c
  • lines changed 2, context: html, text, full: html, text
    89e6b5b4e3b7cef642d825fbfca09c6111f3f4cd Wed Jun 16 17:34:53 2021 -0700
    Another case of too many VCF columns to keep an array of them on the stack.
• src/inc/memgfx.h
  • lines changed 25, context: html, text, full: html, text
    45f9f9211373510d8a65af4abb53555d44a6ac13 Fri Jun 18 14:50:34 2021 -0700
    fix alpha compositing so draw engine graphs can be composited on top of Javascript drawings (eg. highlights)
• src/utils/faFrag/faFrag.c
  • lines changed 27, context: html, text, full: html, text
    a31ae2470e4b225665e48c267e22bcca06bc6ddf Wed Jun 16 17:45:59 2021 -0700
    faFrag: support multi-sequence alignment fasta by fetching the same coords from each sequence in file.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    4921f655bc5bdc660b73b42b25a5bbbad530d25b Mon Jun 21 10:13:02 2021 -0700
    v417 preview1, refs #27655

• lines changed: 1986
• files changed: 38