All File Changes

v406_preview to v406_preview2 (2020-10-12 to 2020-10-19) v406

• confs/hgwbeta.hg.conf
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    3839eb0afeef13722db9d17cc90c4276f562d70e Sun Oct 18 01:11:40 2020 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
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    3839eb0afeef13722db9d17cc90c4276f562d70e Sun Oct 18 01:11:40 2020 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgTracks/barChartTrack.c
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    303e913af55f68e47416249fefc71a069776c982 Wed Oct 14 12:02:24 2020 -0700
    Increase maximum number of barChart bars from 100 to 1000 (needed by Max). refs #26354
• src/hg/hgTracks/bedTrack.c
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    31faf99a48eae623ca44df250f1808673ee8d536 Wed Oct 14 06:59:27 2020 -0700
    fix one place where the difference between a type bigBed # can break if the actual bigBed has fewer columns
• src/hg/hgTracks/wigTrack.c
  • lines changed 96, context: html, text, full: html, text
    b707eeb51bad2091d226fc58e025fde1c7646c94 Fri Oct 16 16:09:40 2020 -0700
    initial prototype of wiggle mouse over values, it is really slow refs #21980
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    211722d8a12ca7202c4401453a93d7d606aa7d4f Mon Oct 19 08:45:04 2020 -0700
    turn off the wiggle mouse overs until better solution found refs #21980
• src/hg/hgc/clinvarSubLolly.c
  • lines changed 76, context: html, text, full: html, text
    ca1497842a28959b779f82251283f5cb8954466c Wed Oct 14 07:03:07 2020 -0700
    finalizing hgc page for Clinvar Submissions Summary track
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    f8c74d56568a37f357df961ed46d9704a2557948 Wed Oct 14 13:20:02 2020 -0700
    some tweaks for Ana.
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    3f4772e689c620fa0db33a2522e362cdcc216047 Sat Oct 17 07:24:30 2020 -0700
    almost done with the clinvar submissions track!
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    03c6f92bbb5b7240805877bb3e7ca3dc43fdc3f9 Mon Oct 19 09:09:18 2020 -0700
    make sure clinvar submissions will work on GBiB.
• src/hg/hgc/hgc.c
  • lines changed 22, context: html, text, full: html, text
    3f4772e689c620fa0db33a2522e362cdcc216047 Sat Oct 17 07:24:30 2020 -0700
    almost done with the clinvar submissions track!
• src/hg/hgc/hgc.h
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    3f4772e689c620fa0db33a2522e362cdcc216047 Sat Oct 17 07:24:30 2020 -0700
    almost done with the clinvar submissions track!
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 24, context: html, text, full: html, text
    a0dfc3a56c887efe60287e2f9ff43c9132592c98 Tue Oct 13 11:56:59 2020 -0700
    Creating announcements for refs #26321 and refs #25841
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    051fd339b2b278737722f62cf65dee1517ce20d9 Tue Oct 13 14:27:00 2020 -0700
    typo fix and style matching refs #26321
  • lines changed 118, context: html, text, full: html, text
    54d691020387ee93fee9cfeede5637dc002dbe92 Thu Oct 15 16:50:46 2020 -0700
    Announcing ensembl v101 update refs #26145
• src/hg/htdocs/inc/recTrackSets.hg19.tab
  • lines changed 7, context: html, text, full: html, text
    63810552a60993fe8a6d62b39b41308e23202a7a Fri Oct 16 13:59:39 2020 -0700
    Adding final sessions for feature release, and a link to the wiki refs #25601
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    a0dfc3a56c887efe60287e2f9ff43c9132592c98 Tue Oct 13 11:56:59 2020 -0700
    Creating announcements for refs #26321 and refs #25841
  • lines changed 12, context: html, text, full: html, text
    54d691020387ee93fee9cfeede5637dc002dbe92 Thu Oct 15 16:50:46 2020 -0700
    Announcing ensembl v101 update refs #26145
• src/hg/inc/barChartUi.h
  • lines changed 1, context: html, text, full: html, text
    303e913af55f68e47416249fefc71a069776c982 Wed Oct 14 12:02:24 2020 -0700
    Increase maximum number of barChart bars from 100 to 1000 (needed by Max). refs #26354
• src/hg/makeDb/doc/asmHubs/mammals.asmId.commonName.tsv
  • lines changed 107, context: html, text, full: html, text
    2390b850402fec79626ff5958af79779352c9d84 Thu Oct 15 08:54:38 2020 -0700
    clean up obsolete files refs #24748
• src/hg/makeDb/doc/asmHubs/mammals.commonName.asmId.orderList.tsv
  • lines changed 107, context: html, text, full: html, text
    2390b850402fec79626ff5958af79779352c9d84 Thu Oct 15 08:54:38 2020 -0700
    clean up obsolete files refs #24748
• src/hg/makeDb/doc/asmHubs/primates.asmId.commonName.tsv
  • lines changed 23, context: html, text, full: html, text
    2390b850402fec79626ff5958af79779352c9d84 Thu Oct 15 08:54:38 2020 -0700
    clean up obsolete files refs #24748
• src/hg/makeDb/doc/asmHubs/primates.commonName.asmId.orderList.tsv
  • lines changed 23, context: html, text, full: html, text
    2390b850402fec79626ff5958af79779352c9d84 Thu Oct 15 08:54:38 2020 -0700
    clean up obsolete files refs #24748
• src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh
  • lines changed 1, context: html, text, full: html, text
    393d6e8e6a2d75158342a665d71093b3569ae0ee Thu Oct 15 08:57:51 2020 -0700
    rsync with delete is OK refs #23891
• src/hg/makeDb/doc/asmHubs/vertebrate.asmId.commonName.tsv
  • lines changed 25, context: html, text, full: html, text
    2390b850402fec79626ff5958af79779352c9d84 Thu Oct 15 08:54:38 2020 -0700
    clean up obsolete files refs #24748
• src/hg/makeDb/doc/asmHubs/vertebrate.commonName.asmId.orderList.tsv
  • lines changed 25, context: html, text, full: html, text
    2390b850402fec79626ff5958af79779352c9d84 Thu Oct 15 08:54:38 2020 -0700
    clean up obsolete files refs #24748
• src/hg/makeDb/doc/assemblyEquivalence/A.vs.B.sh
  • lines changed 1, context: html, text, full: html, text
    eb5f674d8ebadc542e4fbad84e465a629bdee6c7 Thu Oct 15 09:17:33 2020 -0700
    correctly create near mis list refs #24547
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    093ec075d6dd84496e38c5f5f110bf4b4c54298b Tue Oct 13 11:14:51 2020 -0700
    begin bacteria hub with an E. coli requested by user refs #26347
• src/hg/makeDb/doc/bacteriaAsmHub/hub.txt
  • lines changed 6, context: html, text, full: html, text
    093ec075d6dd84496e38c5f5f110bf4b4c54298b Tue Oct 13 11:14:51 2020 -0700
    begin bacteria hub with an E. coli requested by user refs #26347
• src/hg/makeDb/doc/bacteriaAsmHub/makefile
  • lines changed 26, context: html, text, full: html, text
    093ec075d6dd84496e38c5f5f110bf4b4c54298b Tue Oct 13 11:14:51 2020 -0700
    begin bacteria hub with an E. coli requested by user refs #26347
• src/hg/makeDb/doc/hg19.txt
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    3f4772e689c620fa0db33a2522e362cdcc216047 Sat Oct 17 07:24:30 2020 -0700
    almost done with the clinvar submissions track!
• src/hg/makeDb/doc/hg38/clinvarSubLolly.txt
  • lines changed 23, context: html, text, full: html, text
    3f4772e689c620fa0db33a2522e362cdcc216047 Sat Oct 17 07:24:30 2020 -0700
    almost done with the clinvar submissions track!
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 14, context: html, text, full: html, text
    272a25f286c4041d89fa5c159a1c2b59d6d78271 Thu Oct 15 09:19:39 2020 -0700
    add gene name to pop message for LRG track refs #24672
• src/hg/makeDb/doc/wuhCor1/phylogenetics.txt
  • lines changed 123, context: html, text, full: html, text
    0901c8be190c1112f7827fb2f00d2fe8d1dee84d Thu Oct 15 17:45:49 2020 -0700
    Added public-sequences-only version of SARS-CoV-2 Phylogeny track. refs #26364
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • lines changed 2, context: html, text, full: html, text
    14f3a39d26850ba87b223f259052b92dc9aff278 Sat Oct 17 06:32:47 2020 -0700
    add xrefBigDataUrl to trackDb variables that get parsed to replace $D in their urls.
• src/hg/makeDb/trackDb/human/clinvar.html
  • lines changed 42, context: html, text, full: html, text
    9a9506e810d1907bdf254c4ab01632be94bedfaf Mon Oct 19 07:22:13 2020 -0700
    added ClinVar Interpetations track description refs #26330
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    40afe6a0c034dd7d9d7c8c2f929c420f447067ee Mon Oct 19 07:38:36 2020 -0700
    corrected sentence dec page refs #26330
• src/hg/makeDb/trackDb/human/clinvarSubLolly.html
  • lines changed 1, context: html, text, full: html, text
    71b63c33bfccd2e143fff9a0759097bc83491614 Wed Oct 14 12:59:35 2020 -0700
    a placeholder for the Clinvar Submissions track
• src/hg/makeDb/trackDb/human/clinvarSubLolly.ra
  • lines changed 9, context: html, text, full: html, text
    ca1497842a28959b779f82251283f5cb8954466c Wed Oct 14 07:03:07 2020 -0700
    finalizing hgc page for Clinvar Submissions Summary track
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    3f4772e689c620fa0db33a2522e362cdcc216047 Sat Oct 17 07:24:30 2020 -0700
    almost done with the clinvar submissions track!
• src/hg/makeDb/trackDb/human/covidHgeMuts.html
  • lines changed 67, context: html, text, full: html, text
    a2c387babdb3236fb6c4ccc4df89855c1cbe03db Wed Oct 14 04:59:50 2020 -0700
    new desc page refs #26351
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    01850216d9f1ce7c891126d4ec846d722d76d9a7 Wed Oct 14 11:52:04 2020 -0700
    added sentence to desc page refs #26351
• src/hg/makeDb/trackDb/human/covidHgiGwas.ra
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    5201447418f64f3adbca3999eed8373fce53e458 Wed Oct 14 06:22:27 2020 -0700
    added track to new covid-19 trackgroup
• src/hg/makeDb/trackDb/human/geneReviews.html
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    c52ecec1eb70d451431c061aa60a82b8dbc00863 Mon Oct 12 16:49:50 2020 -0700
    Adding Data Access and beta staging #25704
• src/hg/makeDb/trackDb/human/hg19/gnomadPext.html
  • lines changed 7, context: html, text, full: html, text
    f5cfb97be33ede9a901907f200b4d8edd4756c56 Mon Oct 12 10:29:36 2020 -0700
    Adding UCSC specific gnomAD pext methods and fixing shortLabels, refs #25869
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    bdb9debce951bd6e3a2fbee67d802a8559f0d298 Tue Oct 13 05:20:49 2020 -0700
    improved track description refs #25869
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    f11ce89586e7dca4c356b6bc7ed97b92c35ffef5 Tue Oct 13 05:33:48 2020 -0700
    improved track description refs #25869
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    8543135f3a146601d27d7b271128807c2e446351 Tue Oct 13 06:04:58 2020 -0700
    finished track desc page refs #25869
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
  • lines changed 54, context: html, text, full: html, text
    f5cfb97be33ede9a901907f200b4d8edd4756c56 Mon Oct 12 10:29:36 2020 -0700
    Adding UCSC specific gnomAD pext methods and fixing shortLabels, refs #25869
  • lines changed 82, context: html, text, full: html, text
    2bb705a0c628a9bfae92719fe7a4666dfb4684b4 Tue Oct 13 06:38:54 2020 -0700
    standarized tracks long and short labels refs #25869
• src/hg/makeDb/trackDb/human/trackDb.clinvar.ra
  • lines changed 23, context: html, text, full: html, text
    3f4772e689c620fa0db33a2522e362cdcc216047 Sat Oct 17 07:24:30 2020 -0700
    almost done with the clinvar submissions track!
• src/hg/makeDb/trackDb/human/trackDb.giab.ra
  • lines changed 2, context: html, text, full: html, text
    4431dfbe633f8baf571a0fd4b9e4482b59910c77 Fri Oct 16 14:10:51 2020 -0700
    Fixing weird zooming out and in bug on genome in a bottle trio tracks, refs #24349
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    c52ecec1eb70d451431c061aa60a82b8dbc00863 Mon Oct 12 16:49:50 2020 -0700
    Adding Data Access and beta staging #25704
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    f4b1331ddb92e4a13867471e8400df191c7570fc Tue Oct 13 14:54:00 2020 -0700
    Release tag removal post CGI release refs #26321
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    5d71702440f94762877c93a70c2bfdf85f602df6 Tue Oct 13 14:56:52 2020 -0700
    Adding pennantIcons refs #25841
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    921cc936d08da83f89b4060db00269de573f71a2 Tue Oct 13 15:07:50 2020 -0700
    Pennant icon adjust refs #25841
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    35ccc9ecce59749259cdf00b52fa3e5f30c6ae83 Wed Oct 14 06:14:13 2020 -0700
    new track done refs #26351
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    6412eff7c16dad1e752193baa53a7d0beba69c11 Wed Oct 14 11:15:56 2020 -0700
    improved track names refs #26351
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    b7cfcc88e5747f2a076da4668350bdef62cbd6cf Wed Oct 14 17:49:37 2020 -0700
    Polishing up track config. refs #26351
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    3f4772e689c620fa0db33a2522e362cdcc216047 Sat Oct 17 07:24:30 2020 -0700
    almost done with the clinvar submissions track!
• src/hg/makeDb/trackDb/tagTypes.tab
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    3f4772e689c620fa0db33a2522e362cdcc216047 Sat Oct 17 07:24:30 2020 -0700
    almost done with the clinvar submissions track!
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    6b62d8bcb58c3d45932a777a98cbc63723aa7a71 Thu Oct 15 16:42:55 2020 -0700
    Adding pennantIcon to updated ensembl track refs #26145
• src/hg/makeDb/trackDb/virus/wuhCor1/epiValid.html
  • lines changed 8, context: html, text, full: html, text
    d7a8c3c2dcac96d1d0463f3bc9ab4ba802eb5551 Wed Oct 14 17:04:53 2020 -0700
    PennantIcon and minor desc changes to new track, refs #26305
• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainSamples.html
  • lines changed 36, context: html, text, full: html, text
    a8d3d26bf05988c409bc62277eb864a750f4a2d1 Mon Oct 12 16:58:13 2020 -0700
    Updating the Data Access section since GISAID can no longer be accessed from hgdownload. refs #26331
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    176038eaaa16835d634df82c94b93cfb316824ec Tue Oct 13 15:08:20 2020 -0700
    Some updates to links, methods, and data access section for Nextstrain Variants. refs #26331
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    68ee36685f97d8422e0a00937f62851e08fb9f61 Wed Oct 14 09:36:00 2020 -0700
    Adding a colon to match the other list elements, refs #26349
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    0b20304d7b3de6ad65caaf510e558376a4d5c2e1 Wed Oct 14 09:40:28 2020 -0700
    Adding double quotes around _blank and replacing double quotes with the HTML entity, refs #26349
• src/hg/makeDb/trackDb/virus/wuhCor1/sarsCov2PhyloPub.html
  • lines changed 297, context: html, text, full: html, text
    0901c8be190c1112f7827fb2f00d2fe8d1dee84d Thu Oct 15 17:45:49 2020 -0700
    Added public-sequences-only version of SARS-CoV-2 Phylogeny track. refs #26364
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
  • lines changed 53, context: html, text, full: html, text
    f4b1331ddb92e4a13867471e8400df191c7570fc Tue Oct 13 14:54:00 2020 -0700
    Release tag removal post CGI release refs #26321
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    d7a8c3c2dcac96d1d0463f3bc9ab4ba802eb5551 Wed Oct 14 17:04:53 2020 -0700
    PennantIcon and minor desc changes to new track, refs #26305
  • lines changed 44, context: html, text, full: html, text
    0901c8be190c1112f7827fb2f00d2fe8d1dee84d Thu Oct 15 17:45:49 2020 -0700
    Added public-sequences-only version of SARS-CoV-2 Phylogeny track. refs #26364
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 5, context: html, text, full: html, text
    1857a999455044505e7c0395b5b6b68b59c15906 Thu Oct 15 09:25:58 2020 -0700
    allow optional user data tracks in a trackDb (VGP work) refs #23891
• src/hg/utils/automation/doAssemblyHub.pl
  • lines changed 36, context: html, text, full: html, text
    4da1a14630708d887c3481e3b16df5044c86c59a Tue Oct 13 11:16:59 2020 -0700
    better batch size for xenoRefGene and fixup to handle assemblies without repeat masker and RM can not run on those species refs #26347
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    90b9985e1fc9106341b275badcd445531be9a48c Thu Oct 15 09:23:22 2020 -0700
    add noAugustus and noXenoRefSeq options for bacteria hub build refs #23891
• src/hg/utils/automation/doXenoRefGene.pl
  • lines changed 5, context: html, text, full: html, text
    4da1a14630708d887c3481e3b16df5044c86c59a Tue Oct 13 11:16:59 2020 -0700
    better batch size for xenoRefGene and fixup to handle assemblies without repeat masker and RM can not run on those species refs #26347
• src/hg/utils/automation/makePushQSql.pl
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    9767ea420ca35a45c6ed2c81f7bc7fde1ca30373 Thu Oct 15 09:22:16 2020 -0700
    adding more bigZips files for genes gtf files, and clarify wild card expansion ro redmine
• src/hg/utils/faToVcf/faToVcf.c
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    55093dc24432e86e100890a206c4bab473e74276 Fri Oct 16 15:59:25 2020 -0700
    faToVcf: add option -maskSites to remove variants at positions recommended for masking in in Problematic Sites VCF file.
• src/hg/utils/otto/omim/bigifyOmim.sh
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    3b0d251fc556419285eca98739c70f717a9ac9b7 Sat Oct 17 06:31:52 2020 -0700
    add Max's OMIM bigify scripts to tree
• src/hg/utils/otto/omim/omimGene2ToBigBed.py
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    3b0d251fc556419285eca98739c70f717a9ac9b7 Sat Oct 17 06:31:52 2020 -0700
    add Max's OMIM bigify scripts to tree
• src/utils/qa/weeklybld/buildEnv.csh
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    2fc69e65e0e67d7efd09c8cc30926ac71fa47ed6 Mon Oct 19 10:03:56 2020 -0700
    v406 preview2

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• files changed: 80