All File Changes

v397_base to v398_preview (2020-04-20 to 2020-04-27) v398

• confs/asia.hg.conf
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    bcac084e30f9026836bd2be0f322f722955480eb Sun Apr 26 01:11:51 2020 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
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    bcac084e30f9026836bd2be0f322f722955480eb Sun Apr 26 01:11:51 2020 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
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    bcac084e30f9026836bd2be0f322f722955480eb Sun Apr 26 01:11:51 2020 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
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    fc3a8ce57297d0b2bbff8f7acbb3cc90dfe601eb Mon Apr 20 23:41:28 2020 -0700
    Changing udc.localDir from /gbdb/hubs (which doesn't exist) to just /gbdb so I can install some files in /gbdb but make them custom tracks for now. refs #25188
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    bcac084e30f9026836bd2be0f322f722955480eb Sun Apr 26 01:11:51 2020 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 1, context: html, text, full: html, text
    bcac084e30f9026836bd2be0f322f722955480eb Sun Apr 26 01:11:51 2020 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/gateway/htdocs/cirmIndex.html
  • lines changed 29, context: html, text, full: html, text
    3720518672bd99bfcde455653e479ff9d5016b18 Mon Apr 20 17:05:02 2020 -0700
    Code Review for icon changes
• src/hg/cirm/gateway/htdocs/tools.html
  • lines changed 4, context: html, text, full: html, text
    fcf6915a32e7ef9843f3435e69a62e4c3c5c5675 Tue Apr 21 13:36:07 2020 -0700
    Changing image links for those we serve from our images directory to be relative links, no redmine.
• src/hg/hgTracks/bedTrack.c
  • lines changed 1, context: html, text, full: html, text
    f7148e5113be698a6fe208b4b233540be2000636 Thu Apr 23 11:30:36 2020 -0700
    Change note on longlabel when hide empty is on. Also, limit to composite track label (don't display on subtracks). refs #23365
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 1, context: html, text, full: html, text
    f7148e5113be698a6fe208b4b233540be2000636 Thu Apr 23 11:30:36 2020 -0700
    Change note on longlabel when hide empty is on. Also, limit to composite track label (don't display on subtracks). refs #23365
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    86b389767dc3185b8fd02cbe21276d65df7f1667 Mon Apr 27 05:53:35 2020 -0700
    adding multipleListOnlyAnd and multipleListOnlyOr to bigBed handling code. refs #25136
• src/hg/hgTracks/cds.c
  • lines changed 32, context: html, text, full: html, text
    298302978224472f8e84720e6c11272684346e6b Wed Apr 22 12:24:25 2020 -0700
    add some code to recognize ribosomal slips in codon display mode. Only works on the + stand right now for wuhCor1
• src/hg/hgTracks/cds.h
  • lines changed 12, context: html, text, full: html, text
    298302978224472f8e84720e6c11272684346e6b Wed Apr 22 12:24:25 2020 -0700
    add some code to recognize ribosomal slips in codon display mode. Only works on the + stand right now for wuhCor1
• src/hg/hgTracks/hgTracks.c
  • lines changed 24, context: html, text, full: html, text
    f7148e5113be698a6fe208b4b233540be2000636 Thu Apr 23 11:30:36 2020 -0700
    Change note on longlabel when hide empty is on. Also, limit to composite track label (don't display on subtracks). refs #23365
• src/hg/hgTracks/hgTracks.h
  • lines changed 3, context: html, text, full: html, text
    f7148e5113be698a6fe208b4b233540be2000636 Thu Apr 23 11:30:36 2020 -0700
    Change note on longlabel when hide empty is on. Also, limit to composite track label (don't display on subtracks). refs #23365
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    3dcfa772d1883dd243f418e7808d82b8096cb335 Fri Apr 24 08:34:25 2020 -0700
    increase the number of bases that extended DNA color choices will allow from 1 million to 5 million
• src/hg/htdocs/covid19.html
  • lines changed 12, context: html, text, full: html, text
    ba2f9d48847977cc17a538c598defc9b4fa9b82a Mon Apr 20 17:53:23 2020 -0700
    Add some links to new resources. refs #25217
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    7c025cd96c940db044dceaf8382674a3ce7a6f78 Mon Apr 20 18:12:31 2020 -0700
    Update graphic of COVID-19 transmission from NextStrain. refs #25217
  • lines changed 1, context: html, text, full: html, text
    d1365e7600640595b54a5b6fbe06009cf847ae98 Fri Apr 24 09:33:24 2020 -0700
    Updating the date for the COVID landing page, refs #25217
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    13ca54c6d443acbd973a3939c7424c68ccf1292d Fri Apr 24 15:54:33 2020 -0700
    small change to funding statement
• src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html
  • lines changed 2, context: html, text, full: html, text
    0647795ae5666e8a871f3b2a52c68f3e3c23dd5d Thu Apr 23 13:25:00 2020 -0700
    Removing a name= tag that was adding a break at the top of the page of wiggle help docs
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 8, context: html, text, full: html, text
    cad46decc9ba52f8fc2ce850fa14ed850d9ff1a6 Tue Apr 21 15:15:31 2020 -0700
    Brief edits to barChartSizeWindow section #25339
  • lines changed 10, context: html, text, full: html, text
    afad668b2bd287b7f26baf6892396d8a14f0f313 Mon Apr 27 06:05:38 2020 -0700
    adding documentation for multipleListOnlyOr and multipleListOnlyAnd filter statements, refs #25136
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 1, context: html, text, full: html, text
    5bc04b1a96f4edfb5abec265b6dcae15475521aa Mon Apr 20 16:00:08 2020 -0700
    fixed typo found by anna. refs #25396
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    26770707b996407c7cd39bb0688dc1ab0fcbf31e Mon Apr 20 16:09:39 2020 -0700
    fixed second instance of typo found by anna. refs #25396
  • lines changed 3, context: html, text, full: html, text
    4386c679f8362d80f7240a51930b4cc82d0d628f Fri Apr 24 12:52:30 2020 -0700
    editing funding statement
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    982b5bcbc18ff3816dcc364f7800cca2a6d2056f Fri Apr 24 19:15:41 2020 -0700
    newsarch announcement pLI and SV tracks refs #20394
• src/hg/htdocs/images/GnomadConstraintStructruralVarRelease.PNG
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    c3f1829e560e224aa385488eb352f9d67a133ad8 Fri Apr 24 13:32:14 2020 -0700
    adding screenshot for release announcment refs #20394
• src/hg/htdocs/images/covid19-transmission.apr2020.nextstrain.png
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    c2a5745b91c8212ce8707d2b10ee1f92321aceca Tue Apr 21 08:56:40 2020 -0700
    Updated graphic for COVID page. refs 25217
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    720ef0526d7f1b1f65704db24bd0ee5a0cfcd711 Fri Apr 24 19:25:14 2020 -0700
    added pLI and SV tracks to index news Apr.28 refs #20394
• src/hg/htdocs/training/index.html
  • lines changed 81, context: html, text, full: html, text
    766b5baa0dc8dfb4d0930e6c36ca29035becf364 Thu Apr 23 12:40:18 2020 -0700
    Adding help pages section on training index and also putting user guides into columns
  • lines changed 2, context: html, text, full: html, text
    dd089331ef1dbc90c7dd637d7fcc10cc5678c0a0 Thu Apr 23 12:47:45 2020 -0700
    Rewording new mirror links in training page
  • lines changed 9, context: html, text, full: html, text
    5b34d60e26db619bd854dfb196fc251a09f973d7 Thu Apr 23 13:13:03 2020 -0700
    using id instead of name for html anchors
• src/hg/js/makefile
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    167727d44236afb4eb9fa052c23b29c8ab137510 Tue Apr 21 15:15:50 2020 -0700
    add analytics.js to STATIC list refs #25322
• src/hg/lib/trackDbCache.c
  • lines changed 2, context: html, text, full: html, text
    a5378ba7d46c47d2c3d4b7dbdd0b7777ed7854ed Thu Apr 23 13:37:43 2020 -0700
    using mtime to keep track of access time was resulting in a race condition in recognizing new trackDb or hub contents. This change will require that trackDb cache be on a filesystem that updates atime (e.g. /dev/shm)
• src/hg/makeDb/avada/toBed.py
  • lines changed 18, context: html, text, full: html, text
    2adcc68f17866e32eab65cfd5c423583ddb50e3b Mon Apr 27 07:53:47 2020 -0700
    fixing duplicates in avada track, refs #25433
• src/hg/makeDb/doc/canFam4/initialBuild.txt
  • lines changed 263, context: html, text, full: html, text
    767c1233bac4f69e91864ca7100beee1f45e51d4 Mon Apr 20 14:32:43 2020 -0700
    lastz chainNet to mm10 and hg38 done refs #25279
• src/hg/makeDb/doc/gtex/V8.txt
  • lines changed 149, context: html, text, full: html, text
    a2ad2a8f3e71fe90a3c335f967ff3fcec9d37296 Thu Apr 23 10:38:28 2020 -0700
    Initial work for GTEx V8 gene expression track: parse files and load gene expression and metadata tables. refs #25130
• src/hg/makeDb/doc/hg19.txt
  • lines changed 46, context: html, text, full: html, text
    fffb37c69309b49959efe512c85b68424b27ffdf Thu Apr 23 06:12:23 2020 -0700
    adding makedoc, fixing field names, fixing track docs for problematic regions track, refs #24245
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    9a2b57b9b8f4d0db31b00a238a0047c6f25323bf Thu Apr 23 10:33:51 2020 -0700
    Fixing some typos
• src/hg/makeDb/doc/hg38/gtex.txt
  • lines changed 34, context: html, text, full: html, text
    a2ad2a8f3e71fe90a3c335f967ff3fcec9d37296 Thu Apr 23 10:38:28 2020 -0700
    Initial work for GTEx V8 gene expression track: parse files and load gene expression and metadata tables. refs #25130
• src/hg/makeDb/doc/hg38/lastzRuns.txt
  • lines changed 73, context: html, text, full: html, text
    bcd3e3119afb90a3c162b5ac668084c3f65c7fc1 Mon Apr 20 14:30:02 2020 -0700
    hg38 canFam4 chainNet refs #25279
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    52797440fc9be789b26f8f64fc70f9d40c9ca2c0 Fri Apr 24 15:41:54 2020 -0700
    Belated doc commit for hg38 lastz run against enhLutNer1, refs #21152
• src/hg/makeDb/doc/mm10.txt
  • lines changed 67, context: html, text, full: html, text
    ba48424667f579f95f96d49d1bc57467508d741f Mon Apr 20 14:28:42 2020 -0700
    mm10 canFam4 chainNet refs #25279
• src/hg/makeDb/doc/ncbiRefSeq/update.2020-04.txt
  • lines changed 63, context: html, text, full: html, text
    12a73dd0da50c7ff8569cd798d2a2b1266407bbf Mon Apr 20 15:34:52 2020 -0700
    build procedure for ncbiRefSeq genes refs #24547
• src/hg/makeDb/doc/ncbiRefSeq/updateOne
  • lines changed 117, context: html, text, full: html, text
    12a73dd0da50c7ff8569cd798d2a2b1266407bbf Mon Apr 20 15:34:52 2020 -0700
    build procedure for ncbiRefSeq genes refs #24547
• src/hg/makeDb/doc/wuhCor1/rnaStructRangan.txt
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    faeba1ede00712f52d33e8b1b5093df8723fce4d Fri Apr 24 17:47:02 2020 -0700
    new stuff from Manny
• src/hg/makeDb/outside/hgGtex/hgGtex.c
  • lines changed 5, context: html, text, full: html, text
    a2ad2a8f3e71fe90a3c335f967ff3fcec9d37296 Thu Apr 23 10:38:28 2020 -0700
    Initial work for GTEx V8 gene expression track: parse files and load gene expression and metadata tables. refs #25130
• src/hg/makeDb/schema/all.joiner
  • lines changed 8, context: html, text, full: html, text
    c9419666505c8bb67c8b514a082728dee8276df8 Mon Apr 20 14:24:53 2020 -0700
    adding rules for canFam4 refs #25279
• src/hg/makeDb/trackDb/ebola/gire2014.html
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    2a8638e662e67cd99d49f8bad466ef471696c109 Wed Apr 22 11:15:18 2020 -0700
    David H just noticed that the descriptions of white and black were swapped in VCF track descriptions! Oops.
• src/hg/makeDb/trackDb/ebola/gire2014Missense.html
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    2a8638e662e67cd99d49f8bad466ef471696c109 Wed Apr 22 11:15:18 2020 -0700
    David H just noticed that the descriptions of white and black were swapped in VCF track descriptions! Oops.
• src/hg/makeDb/trackDb/ebola/gireIntraHost.html
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    2a8638e662e67cd99d49f8bad466ef471696c109 Wed Apr 22 11:15:18 2020 -0700
    David H just noticed that the descriptions of white and black were swapped in VCF track descriptions! Oops.
• src/hg/makeDb/trackDb/ebola/gireZebov.html
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    2a8638e662e67cd99d49f8bad466ef471696c109 Wed Apr 22 11:15:18 2020 -0700
    David H just noticed that the descriptions of white and black were swapped in VCF track descriptions! Oops.
• src/hg/makeDb/trackDb/ebola/gireZebovMissense.html
  • lines changed 2, context: html, text, full: html, text
    2a8638e662e67cd99d49f8bad466ef471696c109 Wed Apr 22 11:15:18 2020 -0700
    David H just noticed that the descriptions of white and black were swapped in VCF track descriptions! Oops.
• src/hg/makeDb/trackDb/human/clinvar.html
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    808cdc046593cff1a4b4d2db2762a4ef4b996dca Tue Apr 21 12:49:51 2020 -0700
    Changing track descriptions and labels of clinvar and lovd tracks to reflect changes to length cutoff for the cnv and short variants
• src/hg/makeDb/trackDb/human/hg19/gnomad.html
  • lines changed 49, context: html, text, full: html, text
    fe159028c8c7a0db9c5852b28d29645d4805c7d7 Tue Apr 21 09:04:59 2020 -0700
    changed description and display text no redmine
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    3276a53316fa86717bec2e25db74bbe77e066c1d Tue Apr 21 10:20:53 2020 -0700
    corrected typos SV size no redmine
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    1e7f8f09b0451038ce74d57dc33cdaa07442ca5f Wed Apr 22 14:33:35 2020 -0700
    Clearing up the main gnomAD page refs #20394
• src/hg/makeDb/trackDb/human/hg19/gnomadCoverage.html
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    a0586aa79488a2424009637d35bc32cf4b4b99bd Mon Apr 20 15:33:11 2020 -0700
    new description for gnomad Coverage subtrack and corrected typos refs #25395
• src/hg/makeDb/trackDb/human/hg19/gnomadPLI.html
  • lines changed 2, context: html, text, full: html, text
    6dfdb0f77aa475a782072bafaa8afd810f716b89 Mon Apr 20 15:18:34 2020 -0700
    corrected typos refs #25395
• src/hg/makeDb/trackDb/human/hg19/gnomadSv.html
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    6f36a1a58855fad1f7da807badd694a1ab77b55c Mon Apr 20 10:48:12 2020 -0700
    Adding a missing period found from my code review, refs #25397
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    c3f1ab644d13a971d33dc770e80e3680386167a8 Tue Apr 21 10:03:28 2020 -0700
    corrected typos, SV size, bold refs #24179
• src/hg/makeDb/trackDb/human/hg19/gnomadVariants.html
  • lines changed 128, context: html, text, full: html, text
    aab0c6bca1d8cc639ad41e8d20da2769d5f8fbe7 Tue Apr 21 14:58:08 2020 -0700
    changed description and variant filtes, replaced html link in ra no redmine
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    5ce1a195325878236bb06955896ffaf7947e6776 Tue Apr 21 15:39:53 2020 -0700
    changed description and variant filters no redmine
• src/hg/makeDb/trackDb/human/hg19/problematic.html
  • lines changed 30, context: html, text, full: html, text
    9ec7539041f81e363034a450d6db7ca3473726b5 Tue Apr 21 15:13:14 2020 -0700
    Updating labels, location, and text of the problematic regions track #24245
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    8ad5727d7e64fc0c94ee07cf4f4450dce8f1c511 Wed Apr 22 06:31:52 2020 -0700
    adding linnk to GET-RM browser to special regions track, refs #24245
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    fffb37c69309b49959efe512c85b68424b27ffdf Thu Apr 23 06:12:23 2020 -0700
    adding makedoc, fixing field names, fixing track docs for problematic regions track, refs #24245
• src/hg/makeDb/trackDb/human/hg19/tgpPhase1.html
  • lines changed 2, context: html, text, full: html, text
    2a8638e662e67cd99d49f8bad466ef471696c109 Wed Apr 22 11:15:18 2020 -0700
    David H just noticed that the descriptions of white and black were swapped in VCF track descriptions! Oops.
• src/hg/makeDb/trackDb/human/hg19/tgpPhase3.html
  • lines changed 2, context: html, text, full: html, text
    2a8638e662e67cd99d49f8bad466ef471696c109 Wed Apr 22 11:15:18 2020 -0700
    David H just noticed that the descriptions of white and black were swapped in VCF track descriptions! Oops.
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
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    a0586aa79488a2424009637d35bc32cf4b4b99bd Mon Apr 20 15:33:11 2020 -0700
    new description for gnomad Coverage subtrack and corrected typos refs #25395
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    456e183bd7af2579cb6a5ff127fac935fdc87257 Mon Apr 20 16:38:31 2020 -0700
    Adding the release tag for hgwbeta, refs #24179
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    aab0c6bca1d8cc639ad41e8d20da2769d5f8fbe7 Tue Apr 21 14:58:08 2020 -0700
    changed description and variant filtes, replaced html link in ra no redmine
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    99d28ff88b059d411bf2415c43f10c95e366f92f Fri Apr 24 14:24:55 2020 -0700
    Removing the release tags for the gnomAD-SV track for hg19 now that it is ready for the RR, refs #24179
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    9ec7539041f81e363034a450d6db7ca3473726b5 Tue Apr 21 15:13:14 2020 -0700
    Updating labels, location, and text of the problematic regions track #24245
  • lines changed 1, context: html, text, full: html, text
    77048d138349c38a700848e7196b7c799debc1cf Tue Apr 21 15:56:21 2020 -0700
    Fixing minor typo #24245
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    076363aac67ddedb99ff29f04b86b532d0fa3c0f Wed Apr 22 06:25:58 2020 -0700
    switching off score filter, refs #24245
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    9934dad94d6cdba294c865c1fc31197ec2ea9df5 Wed Apr 22 10:36:32 2020 -0700
    Fixing minor typo #25245
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    c91faca9a057cdc07728ee4fc655521bf21bace5 Fri Apr 24 14:52:28 2020 -0700
    Releasing problematic regions track #25245
• src/hg/makeDb/trackDb/human/hg38/tgpPhase3.html
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    2a8638e662e67cd99d49f8bad466ef471696c109 Wed Apr 22 11:15:18 2020 -0700
    David H just noticed that the descriptions of white and black were swapped in VCF track descriptions! Oops.
• src/hg/makeDb/trackDb/human/lovdComp.html
  • lines changed 2, context: html, text, full: html, text
    808cdc046593cff1a4b4d2db2762a4ef4b996dca Tue Apr 21 12:49:51 2020 -0700
    Changing track descriptions and labels of clinvar and lovd tracks to reflect changes to length cutoff for the cnv and short variants
• src/hg/makeDb/trackDb/human/trackDb.clinvar.ra
  • lines changed 2, context: html, text, full: html, text
    808cdc046593cff1a4b4d2db2762a4ef4b996dca Tue Apr 21 12:49:51 2020 -0700
    Changing track descriptions and labels of clinvar and lovd tracks to reflect changes to length cutoff for the cnv and short variants
• src/hg/makeDb/trackDb/human/trackDb.clinvarTest.ra
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    8fa777e7a626753ecf40a7471999dba3a984e272 Tue Apr 21 09:21:39 2020 -0700
    more clinvar improvements, refs #24850
  • lines changed 2, context: html, text, full: html, text
    808cdc046593cff1a4b4d2db2762a4ef4b996dca Tue Apr 21 12:49:51 2020 -0700
    Changing track descriptions and labels of clinvar and lovd tracks to reflect changes to length cutoff for the cnv and short variants
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    808cdc046593cff1a4b4d2db2762a4ef4b996dca Tue Apr 21 12:49:51 2020 -0700
    Changing track descriptions and labels of clinvar and lovd tracks to reflect changes to length cutoff for the cnv and short variants
• src/hg/makeDb/trackDb/mouse/mm10/strainSNPs.html
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    2a8638e662e67cd99d49f8bad466ef471696c109 Wed Apr 22 11:15:18 2020 -0700
    David H just noticed that the descriptions of white and black were swapped in VCF track descriptions! Oops.
• src/hg/makeDb/trackDb/virus/wuhCor1/artic.html
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    3bb8304651ce8d088aa7c294dbe0d3dace2f1e93 Wed Apr 22 07:32:17 2020 -0700
    adding artice network primers, refs #25416
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    3f201349ee7463196570c5b629f936d3c6410433 Fri Apr 24 11:23:28 2020 -0700
    removed funding statement in favor of a more comprehensive one on the gateway and portal
• src/hg/makeDb/trackDb/virus/wuhCor1/description.html
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    a304567c35fe557d6f89cf5a1e3cc11cd4e7c717 Fri Apr 24 13:01:46 2020 -0700
    corrected funding statement. refs #25436
• src/hg/makeDb/trackDb/virus/wuhCor1/epiValid.html
  • lines changed 5, context: html, text, full: html, text
    3f201349ee7463196570c5b629f936d3c6410433 Fri Apr 24 11:23:28 2020 -0700
    removed funding statement in favor of a more comprehensive one on the gateway and portal
• src/hg/makeDb/trackDb/virus/wuhCor1/epitopes.html
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    3f201349ee7463196570c5b629f936d3c6410433 Fri Apr 24 11:23:28 2020 -0700
    removed funding statement in favor of a more comprehensive one on the gateway and portal
• src/hg/makeDb/trackDb/virus/wuhCor1/kimNp.html
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    3f201349ee7463196570c5b629f936d3c6410433 Fri Apr 24 11:23:28 2020 -0700
    removed funding statement in favor of a more comprehensive one on the gateway and portal
• src/hg/makeDb/trackDb/virus/wuhCor1/kimRnaMod.html
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    ee6f4e7939c9b5f144c608ab97bdcc84a6dbdfd6 Wed Apr 22 11:00:44 2020 -0700
    Adding data access for refs #24245
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    3f201349ee7463196570c5b629f936d3c6410433 Fri Apr 24 11:23:28 2020 -0700
    removed funding statement in favor of a more comprehensive one on the gateway and portal
• src/hg/makeDb/trackDb/virus/wuhCor1/ncbiGeneBGP.html
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    3f201349ee7463196570c5b629f936d3c6410433 Fri Apr 24 11:23:28 2020 -0700
    removed funding statement in favor of a more comprehensive one on the gateway and portal
• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainClade.html
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    3f201349ee7463196570c5b629f936d3c6410433 Fri Apr 24 11:23:28 2020 -0700
    removed funding statement in favor of a more comprehensive one on the gateway and portal
• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainGene.html
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    3f201349ee7463196570c5b629f936d3c6410433 Fri Apr 24 11:23:28 2020 -0700
    removed funding statement in favor of a more comprehensive one on the gateway and portal
• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainSamples.html
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    2a8638e662e67cd99d49f8bad466ef471696c109 Wed Apr 22 11:15:18 2020 -0700
    David H just noticed that the descriptions of white and black were swapped in VCF track descriptions! Oops.
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    3f201349ee7463196570c5b629f936d3c6410433 Fri Apr 24 11:23:28 2020 -0700
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• src/hg/makeDb/trackDb/virus/wuhCor1/pdb.html
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    3f201349ee7463196570c5b629f936d3c6410433 Fri Apr 24 11:23:28 2020 -0700
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• src/hg/makeDb/trackDb/virus/wuhCor1/poranHla1.html
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    a565ce6c3b6db81fc738b0f19e318b82e1836d99 Thu Apr 23 06:57:37 2020 -0700
    Changesto new wuhCor1 epitopes track, cleaning up desc page refs #25384
• src/hg/makeDb/trackDb/virus/wuhCor1/poranHla2.html
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    a565ce6c3b6db81fc738b0f19e318b82e1836d99 Thu Apr 23 06:57:37 2020 -0700
    Changesto new wuhCor1 epitopes track, cleaning up desc page refs #25384
• src/hg/makeDb/trackDb/virus/wuhCor1/primers.html
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    3f201349ee7463196570c5b629f936d3c6410433 Fri Apr 24 11:23:28 2020 -0700
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• src/hg/makeDb/trackDb/virus/wuhCor1/publicAnnots.html
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    6e58d6a3c0f48add8588842ffa6acc78c3f0124a Thu Apr 23 15:13:36 2020 -0700
    Touching up the description page for user annotation track refs #25297
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    64ecd6f0867ad36b8d8b9ab90c87f2523fd26bc5 Thu Apr 23 15:39:20 2020 -0700
    Touching up the description page for user annotation track refs #25297
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    3f201349ee7463196570c5b629f936d3c6410433 Fri Apr 24 11:23:28 2020 -0700
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• src/hg/makeDb/trackDb/virus/wuhCor1/rnaStructRangan.html
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    faeba1ede00712f52d33e8b1b5093df8723fce4d Fri Apr 24 17:47:02 2020 -0700
    new stuff from Manny
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
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    9a20f2ebc987790ac14e33d5bc9b57c9899bd4c5 Mon Apr 20 10:44:13 2020 -0700
    move a release tag to be after the track definition
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    af33627e1fc86e7faa9c64f232a601957e0cbc2b Tue Apr 21 08:17:52 2020 -0700
    fixing up pdb wuhCor1 url, refs #25227
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    3bb8304651ce8d088aa7c294dbe0d3dace2f1e93 Wed Apr 22 07:32:17 2020 -0700
    adding artice network primers, refs #25416
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    a565ce6c3b6db81fc738b0f19e318b82e1836d99 Thu Apr 23 06:57:37 2020 -0700
    Changesto new wuhCor1 epitopes track, cleaning up desc page refs #25384
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    67c1fa374052371530df2c60202470d6aec356d8 Thu Apr 23 16:15:42 2020 -0700
    Adding filters to user annotation track refs #25365
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    faeba1ede00712f52d33e8b1b5093df8723fce4d Fri Apr 24 17:47:02 2020 -0700
    new stuff from Manny
• src/hg/makeDb/trackDb/virus/wuhCor1/unipCov2AliSwissprot.html
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    3f201349ee7463196570c5b629f936d3c6410433 Fri Apr 24 11:23:28 2020 -0700
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• src/hg/makeDb/trackDb/virus/wuhCor1/unipCov2Interest.html
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    3f201349ee7463196570c5b629f936d3c6410433 Fri Apr 24 11:23:28 2020 -0700
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• src/hg/makeDb/trackDb/virus/wuhCor1/uniprotCov2.html
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    3f201349ee7463196570c5b629f936d3c6410433 Fri Apr 24 11:23:28 2020 -0700
    removed funding statement in favor of a more comprehensive one on the gateway and portal
• src/hg/utils/automation/doBlastzChainNet.pl
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    3035b73d4fe070dbab1cc39491baa03e0e8c31a2 Sat Apr 25 16:22:20 2020 -0700
    use mkdir -p to fix some case where mkdir failed with -continue
• src/hg/utils/otto/clinvar/clinVarToBed
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    8fa777e7a626753ecf40a7471999dba3a984e272 Tue Apr 21 09:21:39 2020 -0700
    more clinvar improvements, refs #24850
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    a85f07414441c0ad4d8310620fe5c40a33f2f5fd Tue Apr 21 11:12:07 2020 -0700
    Changing lovd and clinvar otto scripts, structural variant cutoff is now >= 50bp, which brings gnomad, dbVar, clinvar, and lovd into harmony
• src/hg/utils/otto/clinvar/clinvar.as
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    8fa777e7a626753ecf40a7471999dba3a984e272 Tue Apr 21 09:21:39 2020 -0700
    more clinvar improvements, refs #24850
• src/hg/utils/otto/lovd/checkAndLoad.sh
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    a85f07414441c0ad4d8310620fe5c40a33f2f5fd Tue Apr 21 11:12:07 2020 -0700
    Changing lovd and clinvar otto scripts, structural variant cutoff is now >= 50bp, which brings gnomad, dbVar, clinvar, and lovd into harmony
• src/hg/utils/otto/nextstrainNcov/doUpdate.sh
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    8548ce2dc690933cbc0ba86b02260401fdc1682e Sun Apr 19 12:00:01 2020 -0700
    Add timestamp to ncov.json filename since there can be interesting changes within a single day and we need to have reproducible analyses. refs #25188
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    03c00c97bfb4666cbc74b63bf06a62948ff643ee Sun Apr 19 14:36:54 2020 -0700
    Add -f now that I'm write-protecting the timestamped ncov.json copies. refs #25188
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    17ef8d906cb3af6d9426b80b1962e1948f5e9ade Mon Apr 20 23:51:42 2020 -0700
    Automatically update the experimental custom tracks for David so that they stay in sync with the updated VCF. refs #25188
• src/hg/utils/otto/nextstrainNcov/makefile
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    17ef8d906cb3af6d9426b80b1962e1948f5e9ade Mon Apr 20 23:51:42 2020 -0700
    Automatically update the experimental custom tracks for David so that they stay in sync with the updated VCF. refs #25188
• src/hg/utils/otto/nextstrainNcov/nextstrain.py
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    4baf9e8d58909435aeff4102172d4b6c76e9ed0c Sun Apr 19 11:43:07 2020 -0700
    Better Nextstrain VCF (merge SNVs at same pos, add BACKMUTS); new output file .varPaths. refs #25188 VCF improvements: * Merge SNVs at the same position (multiple alt alleles like C>A and C>T, serial mutations like T>G and G>A, and back-mutations like G>T and T>G) into a single VCF record with accurate allele counts. * Add BACKMUTS to INFO to highlight samples with back-mutations. The new output file nextstrainSamples.varPaths shows the sequence of variants that occur at nodes in the path from the root of the tree to the sample's leaf, for each sample. This gives some insight into the strucure of the tree and how many mutations the various samples have; by comparing .varPaths files from different NextStrain releases, we can also see that the order of ancestors and descendants is sometimes shuffled from one release to the next.
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    b22c1c39b539a7e6167cf41983d09ce6cbf243e8 Mon Apr 20 21:16:43 2020 -0700
    Add submitting_lab to .varPaths file. Compute tree parsimony score for each recurrent biallelic variant for David. refs #25188
• src/inc/basicBed.h
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    433ed3d13a7fd8e09901031c223c54d5abc77178 Fri Apr 24 13:11:54 2020 -0700
    add a flag to bedToBigBed to allow exons to have 1bp overlapping
• src/lib/basicBed.c
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    433ed3d13a7fd8e09901031c223c54d5abc77178 Fri Apr 24 13:11:54 2020 -0700
    add a flag to bedToBigBed to allow exons to have 1bp overlapping
• src/lib/net.c
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    08b1be37724c83f2dab17f71b5494963f34180b7 Fri Apr 24 08:16:21 2020 -0700
    expand the size of a buffer in net.c to 8k instead of 2000
• src/utils/bedToBigBed/bedToBigBed.c
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    433ed3d13a7fd8e09901031c223c54d5abc77178 Fri Apr 24 13:11:54 2020 -0700
    add a flag to bedToBigBed to allow exons to have 1bp overlapping
• src/utils/qa/weeklybld/buildEnv.csh
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    2e5f6cee6de726f2def8e0f95d4873ac168a0faa Mon Apr 27 10:02:43 2020 -0700
    v398 preview1

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