All File Changes

v403_preview2 to v403_base (2020-08-17 to 2020-08-24) v403

• confs/asia.hg.conf
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    b09f991ed45d9ce7f07594c81643e6ebad61380c Sun Aug 23 01:11:36 2020 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
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    b09f991ed45d9ce7f07594c81643e6ebad61380c Sun Aug 23 01:11:36 2020 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
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    b09f991ed45d9ce7f07594c81643e6ebad61380c Sun Aug 23 01:11:36 2020 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgGene/hgGene.c
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    0b81078213eff40174d357fbc8632ed7077baec4 Fri Aug 21 09:47:38 2020 -0700
    changes to support the lack of native knownGene tables in an assembly.
• src/hg/hgGene/hgGeneData/links.ra
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    0b81078213eff40174d357fbc8632ed7077baec4 Fri Aug 21 09:47:38 2020 -0700
    changes to support the lack of native knownGene tables in an assembly.
• src/hg/hgGene/hgGeneData/otherOrgs.ra
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    0b81078213eff40174d357fbc8632ed7077baec4 Fri Aug 21 09:47:38 2020 -0700
    changes to support the lack of native knownGene tables in an assembly.
• src/hg/hgGene/links.c
  • lines changed 1, context: html, text, full: html, text
    0b81078213eff40174d357fbc8632ed7077baec4 Fri Aug 21 09:47:38 2020 -0700
    changes to support the lack of native knownGene tables in an assembly.
• src/hg/hgGene/otherOrgs.c
  • lines changed 3, context: html, text, full: html, text
    0b81078213eff40174d357fbc8632ed7077baec4 Fri Aug 21 09:47:38 2020 -0700
    changes to support the lack of native knownGene tables in an assembly.
• src/hg/hgSession/hgSession.c
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    e6f37ac836c15aef886fd4d10af0ab23f17b4b86 Wed Aug 19 15:54:31 2020 -0700
    Add a note about NOT adding CGI variables to the end of the URL in addSessionLink as it breaks short links when they are available
• src/hg/hgTracks/vcfTrack.c
  • lines changed 74, context: html, text, full: html, text
    7d992e15b156dca5c6601a989dc33a4bf229ce45 Thu Aug 20 10:14:08 2020 -0700
    Added support for highlightIds setting in VCF+treeFile custom tracks. refs #25943
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    2ab977674ff8aa920d078fa3c8e263298de74529 Mon Aug 17 15:54:37 2020 -0700
    Prevent page from crashing just because the list of alts includes an IUPAC ambiguous character that vpGenomicToTranscript doesn't know how to deal with. Use alpha channel for the highlighted samples so they don't hide the vertical guidelines. refs #25943
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    34ae341f397c44bda8ce0e2d59dcc3d18b5e519e Thu Aug 20 10:38:14 2020 -0700
    Use the new vcfParseGenotypesGtOnly for speed in haplotype displays.
• src/hg/hgc/hgc.c
  • lines changed 74, context: html, text, full: html, text
    a520a3e8703485e62c9bbabb43443f02a08c45ad Wed Aug 19 07:29:21 2020 -0700
    committing code for the "related tracks" feature. This will have no effect on the RR, as the table does not exist there. The main point of the commit is to allow chris to start modifying the code without a manual copy. refs #25721
• src/hg/htdocs/goldenPath/help/barChart.html
  • lines changed 12, context: html, text, full: html, text
    8df94986f343f4570b29822003a445d0a2ef9197 Wed Aug 19 16:04:45 2020 -0700
    Adding images to barChart.html #23679
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    d6083d92c7b4ea02711d5db375169d23fcb9ce26 Wed Aug 19 16:09:13 2020 -0700
    Modifying image addition #23679
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 52, context: html, text, full: html, text
    8fa80406a18bd1a3a5c3331d84d33e03971271e7 Tue Aug 18 12:28:21 2020 -0700
    Documenting VCF phased trio track, refs #26076
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
  • lines changed 51, context: html, text, full: html, text
    8fa80406a18bd1a3a5c3331d84d33e03971271e7 Tue Aug 18 12:28:21 2020 -0700
    Documenting VCF phased trio track, refs #26076
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 65, context: html, text, full: html, text
    8fa80406a18bd1a3a5c3331d84d33e03971271e7 Tue Aug 18 12:28:21 2020 -0700
    Documenting VCF phased trio track, refs #26076
• src/hg/htdocs/goldenPath/help/vcf.html
  • lines changed 41, context: html, text, full: html, text
    8fa80406a18bd1a3a5c3331d84d33e03971271e7 Tue Aug 18 12:28:21 2020 -0700
    Documenting VCF phased trio track, refs #26076
• src/hg/htdocs/goldenPath/newsarch.html
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    fb3bc03821d7cbc722fabd56cb4b533614bbe654 Fri Aug 21 15:47:52 2020 -0700
    adding message about wildfires
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    ae6f95d9f6961206f5dd821048e9614d2da59212 Fri Aug 21 15:59:58 2020 -0700
    removing errant endParen
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    8857d84b41e2991a1a4e7ab157df71599b46aed9 Fri Aug 21 16:37:16 2020 -0700
    small tweak
• src/hg/htdocs/images/barChartFull.png
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    8df94986f343f4570b29822003a445d0a2ef9197 Wed Aug 19 16:04:45 2020 -0700
    Adding images to barChart.html #23679
• src/hg/htdocs/images/barChartSquish.png
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    8df94986f343f4570b29822003a445d0a2ef9197 Wed Aug 19 16:04:45 2020 -0700
    Adding images to barChart.html #23679
• src/hg/htdocs/images/trioExample.png
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    8fa80406a18bd1a3a5c3331d84d33e03971271e7 Tue Aug 18 12:28:21 2020 -0700
    Documenting VCF phased trio track, refs #26076
• src/hg/htdocs/training/index.html
  • lines changed 23, context: html, text, full: html, text
    7d5faf8f6683f2aeb2f1e1072c5c0bca89c6833d Thu Aug 20 13:59:05 2020 -0700
    removed on Bar Harbor workshop, moved Nashville up, dropped Perth
• src/hg/inc/genePred.h
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    838bd75e5d5b859f5b81102933273b7c7e7e2114 Sun Aug 16 10:29:38 2020 -0700
    removed redundent function
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    e6cd18ccbe6e255de8cb54bc70da0e42fe9a73b5 Mon Aug 17 19:17:10 2020 -0700
    add report of location of frameshifts for use by CAT
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    5f7f06147265d248e99118adb21d85b08a882b1a Mon Aug 24 10:06:48 2020 -0700
    New version number v403
• src/hg/lib/genePred.c
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    838bd75e5d5b859f5b81102933273b7c7e7e2114 Sun Aug 16 10:29:38 2020 -0700
    removed redundent function
• src/hg/lib/hdb.c
  • lines changed 5, context: html, text, full: html, text
    0a825d5861f162d34ceae24e8c5f09863c9aea16 Sat Aug 22 06:22:16 2020 -0700
    fix up hgNearTest to know about separate knownGene databases
• src/hg/lib/hui.c
  • lines changed 22, context: html, text, full: html, text
    768289e6cf447f433a89c75856d60a3b018b53aa Thu Aug 20 11:00:29 2020 -0700
    add trackDb variables to allow the composite parent to forego the settings of the first track, and to show the configuration of a subtrack by default
• src/hg/lib/liftOver.c
  • lines changed 21, context: html, text, full: html, text
    261c6956765a12f489c8f210e86d327f80173f5c Fri Aug 21 19:25:56 2020 -0700
    Fixes bug found by Jonathan during code review that can have infinite loop. Code is now a little simpler and more reliable. refs#26088
• src/hg/lib/suggest.c
  • lines changed 6, context: html, text, full: html, text
    8c5ceb895b3852e45c5396169285247b7d2792ac Tue Aug 18 15:38:36 2020 -0700
    open the correct gene track when using hgSuggest with assembliees without knownGene
• src/hg/makeDb/doc/ambMex2/initialBuild.txt
  • lines changed 198, context: html, text, full: html, text
    180fdd5b8ed0b1d93cde304e58816ee64eb9f7f0 Mon Aug 17 12:22:20 2020 -0700
    have 2bit masked with custom repeat library refs #23367
• src/hg/makeDb/doc/hg38/lastzRuns.txt
  • lines changed 76, context: html, text, full: html, text
    5dbad70c3a1445cc3a505b451c623f9aa7bcca3b Mon Aug 17 12:46:26 2020 -0700
    lastz chainNet hg38 to canFam5 in progress refs #25917
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    d083e4c81c2db4fcf9e2b250bdd779ef55a3a3ba Mon Aug 17 13:15:24 2020 -0700
    starting lastz chainNet for mm39 refs #22271
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    a8c34aed0a71d4674178d116c7a8ec99186377b2 Tue Aug 18 08:51:45 2020 -0700
    lastz chainNet to canFam5 complete refs #25917
• src/hg/makeDb/doc/mm10.txt
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    0fee4835763cc67799a462b1d0c90d66a40f2f02 Mon Aug 17 12:45:51 2020 -0700
    lastz chainNet mm10 to canFam5 in progress refs #25917
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    a8c34aed0a71d4674178d116c7a8ec99186377b2 Tue Aug 18 08:51:45 2020 -0700
    lastz chainNet to canFam5 complete refs #25917
• src/hg/makeDb/doc/mm39/lastzRuns.txt
  • lines changed 69, context: html, text, full: html, text
    5ea80cd83327f973e24ee93695b321a77fd8bbd9 Mon Aug 17 12:49:16 2020 -0700
    starting lastz chainNet to canFam5 refs #25917
• src/hg/makeDb/doc/ucscGenes/hg38.gencodeV35.sh
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    0b81078213eff40174d357fbc8632ed7077baec4 Fri Aug 21 09:47:38 2020 -0700
    changes to support the lack of native knownGene tables in an assembly.
• src/hg/makeDb/genbank/etc/align.dbs
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    f5e6b5d6bdf224b0dac7a6982e10e029215196b4 Mon Aug 17 12:21:08 2020 -0700
    Added ambMex2 refs #23367
• src/hg/makeDb/genbank/etc/genbank.conf
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    9d0b167a9ea9f20e7d06fb51e4688672eb583f9d Mon Aug 17 12:19:47 2020 -0700
    Added ambMex2; refs #23367
• src/hg/makeDb/genbank/etc/hgwdev.dbs
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    f5e6b5d6bdf224b0dac7a6982e10e029215196b4 Mon Aug 17 12:21:08 2020 -0700
    Added ambMex2 refs #23367
• src/hg/makeDb/trackDb/human/trackDb.clinvarTest.ra
  • lines changed 2, context: html, text, full: html, text
    768289e6cf447f433a89c75856d60a3b018b53aa Thu Aug 20 11:00:29 2020 -0700
    add trackDb variables to allow the composite parent to forego the settings of the first track, and to show the configuration of a subtrack by default
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    768289e6cf447f433a89c75856d60a3b018b53aa Thu Aug 20 11:00:29 2020 -0700
    add trackDb variables to allow the composite parent to forego the settings of the first track, and to show the configuration of a subtrack by default
• src/hg/makeDb/trackDb/trackDb.chainNet.euarchontoglires.ra
  • lines changed 54, context: html, text, full: html, text
    102ab1cb5a7f8f8b1ed1197e69b204f340252501 Tue Aug 18 08:58:37 2020 -0700
    adding mm39 chainNet definition refs #22271
• src/hg/makeDb/trackDb/trackDb.chainNet.mammal.ra
  • lines changed 55, context: html, text, full: html, text
    fbf1a3a1fac7fdd4ad7bd169e966fe28c9a01f7f Tue Aug 18 09:08:22 2020 -0700
    adding canFam5 definitions refs #25917
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra
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    7dfe7eaf228d1e26f812a9cfe811bd52cf60d9a9 Mon Aug 17 10:45:01 2020 -0700
    Add 'tableBrowser off' setting for Nextstrain Variants and SARS-CoV-2 Phylogeny at GISAID's request. refs #26072
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
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    7dfe7eaf228d1e26f812a9cfe811bd52cf60d9a9 Mon Aug 17 10:45:01 2020 -0700
    Add 'tableBrowser off' setting for Nextstrain Variants and SARS-CoV-2 Phylogeny at GISAID's request. refs #26072
• src/hg/near/hgNear/hgNear.c
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    fb00da5974d75ff6cb2ebbce5ad7f2a072a5ec8d Thu Aug 20 09:18:01 2020 -0700
    remove dependency on hgNearData, which is release controlled
• src/hg/near/hgNearTest/hgNearTest.c
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    0a825d5861f162d34ceae24e8c5f09863c9aea16 Sat Aug 22 06:22:16 2020 -0700
    fix up hgNearTest to know about separate knownGene databases
• src/hg/utils/otto/decipher/buildDecipher
  • lines changed 35, context: html, text, full: html, text
    942b9930eaefb78d4e542e4f27e956ceb7a3ee34 Mon Aug 17 15:54:38 2020 -0700
    Update decipher to bigBed, refs #25841
• src/hg/utils/otto/decipher/checkDecipher.sh
  • lines changed 17, context: html, text, full: html, text
    942b9930eaefb78d4e542e4f27e956ceb7a3ee34 Mon Aug 17 15:54:38 2020 -0700
    Update decipher to bigBed, refs #25841
• src/hg/utils/otto/decipher/decipher.tables
  • lines changed 4, context: html, text, full: html, text
    942b9930eaefb78d4e542e4f27e956ceb7a3ee34 Mon Aug 17 15:54:38 2020 -0700
    Update decipher to bigBed, refs #25841
• src/hg/utils/otto/decipher/makefile
  • lines changed 1, context: html, text, full: html, text
    942b9930eaefb78d4e542e4f27e956ceb7a3ee34 Mon Aug 17 15:54:38 2020 -0700
    Update decipher to bigBed, refs #25841
• src/hg/utils/otto/decipher/processDecipher.py
  • lines changed 153, context: html, text, full: html, text
    162bc86b24eb5186560aabb1c2eedf919602f89b Tue Aug 18 12:29:16 2020 -0700
    Forgot to commit helper script for turning decipher into bigBed, refs #25841
• src/hg/utils/transMapPslToGenePred/makefile
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    e6cd18ccbe6e255de8cb54bc70da0e42fe9a73b5 Mon Aug 17 19:17:10 2020 -0700
    add report of location of frameshifts for use by CAT
• src/hg/utils/transMapPslToGenePred/tests/README
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    e6cd18ccbe6e255de8cb54bc70da0e42fe9a73b5 Mon Aug 17 19:17:10 2020 -0700
    add report of location of frameshifts for use by CAT
• src/hg/utils/transMapPslToGenePred/tests/expected/cds2InsertTest.fs.tsv
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    e6cd18ccbe6e255de8cb54bc70da0e42fe9a73b5 Mon Aug 17 19:17:10 2020 -0700
    add report of location of frameshifts for use by CAT
• src/hg/utils/transMapPslToGenePred/tests/expected/codingFillTest.fs.tsv
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    e6cd18ccbe6e255de8cb54bc70da0e42fe9a73b5 Mon Aug 17 19:17:10 2020 -0700
    add report of location of frameshifts for use by CAT
• src/hg/utils/transMapPslToGenePred/tests/expected/fill30Test.fs.tsv
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    e6cd18ccbe6e255de8cb54bc70da0e42fe9a73b5 Mon Aug 17 19:17:10 2020 -0700
    add report of location of frameshifts for use by CAT
• src/hg/utils/transMapPslToGenePred/tests/expected/fillTest.fs.tsv
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    e6cd18ccbe6e255de8cb54bc70da0e42fe9a73b5 Mon Aug 17 19:17:10 2020 -0700
    add report of location of frameshifts for use by CAT
• src/hg/utils/transMapPslToGenePred/tests/expected/musTest.fs.tsv
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    e6cd18ccbe6e255de8cb54bc70da0e42fe9a73b5 Mon Aug 17 19:17:10 2020 -0700
    add report of location of frameshifts for use by CAT
• src/hg/utils/transMapPslToGenePred/tests/expected/nonCodingFillTest.fs.tsv
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    e6cd18ccbe6e255de8cb54bc70da0e42fe9a73b5 Mon Aug 17 19:17:10 2020 -0700
    add report of location of frameshifts for use by CAT
• src/hg/utils/transMapPslToGenePred/tests/expected/tmAstMex1NoMergeTests.fs.tsv
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    e6cd18ccbe6e255de8cb54bc70da0e42fe9a73b5 Mon Aug 17 19:17:10 2020 -0700
    add report of location of frameshifts for use by CAT
• src/hg/utils/transMapPslToGenePred/tests/expected/tmAstMex1NoMergeTests.mapped.gp
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    e6cd18ccbe6e255de8cb54bc70da0e42fe9a73b5 Mon Aug 17 19:17:10 2020 -0700
    add report of location of frameshifts for use by CAT
• src/hg/utils/transMapPslToGenePred/tests/input/tm-astMex1-hg38.ensembl.psl
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    e6cd18ccbe6e255de8cb54bc70da0e42fe9a73b5 Mon Aug 17 19:17:10 2020 -0700
    add report of location of frameshifts for use by CAT
• src/hg/utils/transMapPslToGenePred/tests/input/tm-astMex1.ensembl.gp
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    e6cd18ccbe6e255de8cb54bc70da0e42fe9a73b5 Mon Aug 17 19:17:10 2020 -0700
    add report of location of frameshifts for use by CAT
• src/hg/utils/transMapPslToGenePred/tests/makefile
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    e6cd18ccbe6e255de8cb54bc70da0e42fe9a73b5 Mon Aug 17 19:17:10 2020 -0700
    add report of location of frameshifts for use by CAT
• src/hg/utils/transMapPslToGenePred/transMapPslToGenePred.c
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    e6cd18ccbe6e255de8cb54bc70da0e42fe9a73b5 Mon Aug 17 19:17:10 2020 -0700
    add report of location of frameshifts for use by CAT
• src/inc/srcVersion.h
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    5f7f06147265d248e99118adb21d85b08a882b1a Mon Aug 24 10:06:48 2020 -0700
    New version number v403
• src/inc/vcf.h
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    39b3ad00ec43efa3dbd5a8b0836d7a6a00776528 Wed Jul 29 13:28:23 2020 -0700
    Added vcfParseGenotypesGtOnly to speed up parsing when we have tens of thousands of genotype columns and just want the genotypes not any associated details. refs #25943
• src/lib/linefile.c
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    9b043c5143cff7efe24ec0f9baf61c71104acc5a Thu Aug 20 10:06:41 2020 -0700
    Allow SARS-CoV-2 VCF to use GenBank or RefSeq ID instead of our chromified RefSeq ID. (Russ request, no RM)
• src/lib/vcf.c
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    9b043c5143cff7efe24ec0f9baf61c71104acc5a Thu Aug 20 10:06:41 2020 -0700
    Allow SARS-CoV-2 VCF to use GenBank or RefSeq ID instead of our chromified RefSeq ID. (Russ request, no RM)
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    39b3ad00ec43efa3dbd5a8b0836d7a6a00776528 Wed Jul 29 13:28:23 2020 -0700
    Added vcfParseGenotypesGtOnly to speed up parsing when we have tens of thousands of genotype columns and just want the genotypes not any associated details. refs #25943
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    fa61094c53e0c3bb6a6ef2b8235c0744aeb5f7c3 Wed Jul 29 18:22:22 2020 -0700
    Tolerate extra stuff (such as whitespace) after the VCF version number in ##fileformat line. (no RM, Russ ran into trouble with it)
• src/utils/chromToUcsc/chromToUcsc
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    56e876a710840529715cd8a5496f46e3e9d372cb Fri Aug 21 03:57:10 2020 -0700
    fixing general usage problems with chromToUcsc found by Matt, refs
• src/utils/chromToUcsc/tests/hg19.chromAlias.tsv
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    56e876a710840529715cd8a5496f46e3e9d372cb Fri Aug 21 03:57:10 2020 -0700
    fixing general usage problems with chromToUcsc found by Matt, refs
• src/utils/chromToUcsc/tests/makefile
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    56e876a710840529715cd8a5496f46e3e9d372cb Fri Aug 21 03:57:10 2020 -0700
    fixing general usage problems with chromToUcsc found by Matt, refs
• src/utils/qa/weeklybld/buildEnv.csh
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    3cbfdeebb6d99b98e910f31cda4ac0bd0e33c410 Mon Aug 24 10:05:44 2020 -0700
    v403 final build

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• files changed: 82