All File Changes

v398_preview to v398_preview2 (2020-04-27 to 2020-05-04) v398

• src/hg/hgBlat/hgBlat.c
  • lines changed 4, context: html, text, full: html, text
    c75304f57269fdf2dbe9029f6d051b88e6d0bd50 Thu Apr 23 23:59:49 2020 -0700
    fixing up some text for hgBlat, also, only print it for nucleotide search
• src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c
  • lines changed 9, context: html, text, full: html, text
    832926811b278d5c656957e1565acdde48522def Mon Apr 27 17:59:12 2020 -0700
    Update GTEx gene track click handler and track settings to handle V8 (add Kidney Medulla tissue, support TPM and RPKM). refs #25130
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 5, context: html, text, full: html, text
    ba6e961593b24def506fa73e55d31542fb780a88 Mon Apr 27 12:35:33 2020 -0700
    Revert "adding multipleListOnlyAnd and multipleListOnlyOr to bigBed handling code. refs #25136" This reverts commit 86b389767dc3185b8fd02cbe21276d65df7f1667.
  • lines changed 80, context: html, text, full: html, text
    fecc0bfffd30dccc9998aa0c2e5a6064d487bbb1 Fri Apr 10 15:39:54 2020 -0700
    Initial work on merging multiple bigBed items that span the window, refs #25133
  • lines changed 5, context: html, text, full: html, text
    e8969bff1017d3fc8ca3e45be2040d79d41bc2a0 Wed Apr 29 06:52:05 2020 -0700
    Revert "Revert "adding multipleListOnlyAnd and multipleListOnlyOr to bigBed handling code. refs #25136"" This reverts commit ba6e961593b24def506fa73e55d31542fb780a88.
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    577c7537344e58f1538843f38e084f6e175b5ca3 Wed Apr 29 11:34:27 2020 -0700
    fix warning: suggest parentheses around ‘&&’ within ‘||’ [-Werror=parentheses]
  • lines changed 8, context: html, text, full: html, text
    e99bf5acd96a085eb5581d147209c6f2d5e63556 Wed Apr 29 12:07:09 2020 -0700
    Fixing compile err/warn and simplifying. Not fixing functionality if this is wrong ;-)
• src/hg/hgTracks/gtexTracks.c
  • lines changed 9, context: html, text, full: html, text
    f0add51e132dbab425e76cabc6626a31a74f47e9 Tue Apr 28 12:29:40 2020 -0700
    Support TPM in GTEx V8 gene expression. refs #25130
  • lines changed 8, context: html, text, full: html, text
    9796c4d65f1f1fcd8eae91e158b68bbf8ee8698f Wed Apr 29 12:01:38 2020 -0700
    Add map box on entire gene graph for click to hgc. refs #25465
• src/hg/hgTracks/imageV2.c
  • lines changed 12, context: html, text, full: html, text
    fecc0bfffd30dccc9998aa0c2e5a6064d487bbb1 Fri Apr 10 15:39:54 2020 -0700
    Initial work on merging multiple bigBed items that span the window, refs #25133
• src/hg/hgTracks/simpleTracks.c
  • lines changed 2, context: html, text, full: html, text
    4fb6df366f380117bae142682857a813176bb204 Sat May 2 13:47:10 2020 -0700
    increase label width from 17 to 23 characters
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    7bc17a364b67139d78eed6ea6a589f6d7c9826cc Mon May 4 09:18:12 2020 -0700
    label width down to 20
• src/hg/hgTracks/vcfTrack.c
  • lines changed 2, context: html, text, full: html, text
    0de7cb7d6e9595fcb877544d666e099f7562314d Tue Apr 28 12:46:36 2020 -0700
    tg->visibility isn't always set for subtracks if they're parallel loading
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    8523f0b59275db50e5f84bceb61040431ea57155 Tue Apr 28 13:28:17 2020 -0700
    Applying Braney's fix for vcfTabixLoadItems in 0de7cb7d to vcfLoadItems for consistency. refs #25462
• src/hg/hgc/gtexClick.c
  • lines changed 4, context: html, text, full: html, text
    832926811b278d5c656957e1565acdde48522def Mon Apr 27 17:59:12 2020 -0700
    Update GTEx gene track click handler and track settings to handle V8 (add Kidney Medulla tissue, support TPM and RPKM). refs #25130
• src/hg/hgc/hgcData/gtexBoxplot.R
  • lines changed 17, context: html, text, full: html, text
    832926811b278d5c656957e1565acdde48522def Mon Apr 27 17:59:12 2020 -0700
    Update GTEx gene track click handler and track settings to handle V8 (add Kidney Medulla tissue, support TPM and RPKM). refs #25130
• src/hg/hgc/hgcData/gtexColorsV8.R
  • lines changed 119, context: html, text, full: html, text
    832926811b278d5c656957e1565acdde48522def Mon Apr 27 17:59:12 2020 -0700
    Update GTEx gene track click handler and track settings to handle V8 (add Kidney Medulla tissue, support TPM and RPKM). refs #25130
  • lines changed 6, context: html, text, full: html, text
    f0add51e132dbab425e76cabc6626a31a74f47e9 Tue Apr 28 12:29:40 2020 -0700
    Support TPM in GTEx V8 gene expression. refs #25130
• src/hg/htdocs/covid19.html
  • lines changed 16, context: html, text, full: html, text
    a94079e43a772ac582ae64c12c1c66c4897aed09 Thu Apr 30 10:56:36 2020 -0700
    Updated transmission graphic and added two links requested by DavidH. refs #25217
  • lines changed 26, context: html, text, full: html, text
    1a4a1243ebec2eeef6d3dd005c8f6ece5d4b584f Thu Apr 30 12:08:25 2020 -0700
    A few more links from DH. refs #25217
  • lines changed 18, context: html, text, full: html, text
    4da7f36cc07a5babf2a5dfb898f66f58199f1502 Mon May 4 09:12:51 2020 -0700
    Add two more links (NYT) by request of DH. refs #25217
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 3, context: html, text, full: html, text
    da81d18085a8f37b93769d2113f3016eb3acbd96 Mon Apr 27 16:24:08 2020 -0700
    Documenting mergeSpannedItems setting for bigBed tracks, refs #25133
  • lines changed 2, context: html, text, full: html, text
    e4c2fec30dc9d455d711e69eda81105a7c9fd7cc Wed Apr 29 07:28:44 2020 -0700
    fixing doc typo found by Kate, no redmine
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
  • lines changed 3, context: html, text, full: html, text
    da81d18085a8f37b93769d2113f3016eb3acbd96 Mon Apr 27 16:24:08 2020 -0700
    Documenting mergeSpannedItems setting for bigBed tracks, refs #25133
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 14, context: html, text, full: html, text
    da81d18085a8f37b93769d2113f3016eb3acbd96 Mon Apr 27 16:24:08 2020 -0700
    Documenting mergeSpannedItems setting for bigBed tracks, refs #25133
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 117, context: html, text, full: html, text
    d64007232b5b5191becd4d3affa51a8641f09966 Tue Apr 28 16:12:38 2020 -0700
    News announcement for refSeq update refs #24547
  • lines changed 2, context: html, text, full: html, text
    7aef71a104ec1c3bb84dcff245b03dfc58d53358 Wed Apr 29 15:10:14 2020 -0700
    Fixing some forgot db declarations, no RM
  • lines changed 109, context: html, text, full: html, text
    801f36c6c9fe7974ce8c89427dd7417697c28ef5 Fri May 1 16:11:51 2020 -0700
    News release for 2nd coronavirus data release refs #25343
  • lines changed 7, context: html, text, full: html, text
    7d43c2d37ecf3af7e749b575537717442135e2b3 Mon May 4 09:34:38 2020 -0700
    Adding CD8 RosettaMHC track refs #25482
• src/hg/htdocs/images/covid19-transmission.apr28_2020.nextstrain.png
  • lines changed 0, context: html, text, full: html, text
    242d0a9e631b36a90103652c2947df0666843dc5 Thu Apr 30 10:56:55 2020 -0700
    Updated transmission graphic and added two links requested by DavidH. refs #25217
• src/hg/htdocs/images/gtexBodyMap.svg
  • lines changed 1, context: html, text, full: html, text
    1106b4995dcd8f12c168f50f44c7f724d8c0e901 Tue Apr 28 10:41:25 2020 -0700
    Update fibroblasts label as per GTEx V8 correction. refs #25130
• src/hg/htdocs/images/gtexBodyMapPage.svg
  • lines changed 1, context: html, text, full: html, text
    1106b4995dcd8f12c168f50f44c7f724d8c0e901 Tue Apr 28 10:41:25 2020 -0700
    Update fibroblasts label as per GTEx V8 correction. refs #25130
• src/hg/htdocs/images/gtexBodyMapSmall.svg
  • lines changed 1901, context: html, text, full: html, text
    1106b4995dcd8f12c168f50f44c7f724d8c0e901 Tue Apr 28 10:41:25 2020 -0700
    Update fibroblasts label as per GTEx V8 correction. refs #25130
• src/hg/htdocs/inc/gbPageStartHardcoded.html
  • lines changed 1, context: html, text, full: html, text
    851dd42ab83984ac7900a7a97c40bcb64d35407b Wed Apr 29 15:19:03 2020 -0700
    Adding wuhCor1 to the other nav bar, no RM
• src/hg/htdocs/indexNews.html
  • lines changed 14, context: html, text, full: html, text
    d64007232b5b5191becd4d3affa51a8641f09966 Tue Apr 28 16:12:38 2020 -0700
    News announcement for refSeq update refs #24547
  • lines changed 12, context: html, text, full: html, text
    801f36c6c9fe7974ce8c89427dd7417697c28ef5 Fri May 1 16:11:51 2020 -0700
    News release for 2nd coronavirus data release refs #25343
• src/hg/htdocs/style/HGStyle.css
  • lines changed 55, context: html, text, full: html, text
    0811c1da172a367fe55928a4869f77978ff83fdb Wed Apr 29 06:53:36 2020 -0700
    making bigbed extra filters a bit easier to see, refs #24850
• src/hg/htdocs/training/index.html
  • lines changed 2, context: html, text, full: html, text
    7d93ed6029c0355a18c49f62090ae513083e0a11 Mon Apr 27 15:13:25 2020 -0700
    Adding a : as part of code review input refs #25443
  • lines changed 1, context: html, text, full: html, text
    8e78eb3d0ffce96474362f21f438a1d3406fd7b8 Mon Apr 27 16:35:12 2020 -0700
    Changing id=help to id=guides to work properly code review refs #25443
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    46a412f67df059f41016a58d55686697d18950fd Thu Apr 30 15:46:48 2020 -0700
    marking more workshops as cancelled or postponed. added comment about doing webinar if needed
• src/hg/inc/bigBedFilter.h
  • lines changed 2, context: html, text, full: html, text
    a9759376f1c3dee161fe74a7e4c35aba756a4f50 Wed Apr 29 06:52:47 2020 -0700
    adding multiple list only defines, refs #25136""
• src/hg/inc/blatServers.h
  • lines changed 18, context: html, text, full: html, text
    e3871e1871d6158d4712b3ae6c41b62eb77ffcd1 Fri May 1 12:29:24 2020 -0700
    for Galt
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    9f2f4869f302d6af567f108a3d6ff2ee3665489f Fri May 1 13:29:09 2020 -0700
    real thing.
• src/hg/inc/gtexInfo.h
  • lines changed 3, context: html, text, full: html, text
    832926811b278d5c656957e1565acdde48522def Mon Apr 27 17:59:12 2020 -0700
    Update GTEx gene track click handler and track settings to handle V8 (add Kidney Medulla tissue, support TPM and RPKM). refs #25130
• src/hg/inc/hui.h
  • lines changed 9, context: html, text, full: html, text
    fecc0bfffd30dccc9998aa0c2e5a6064d487bbb1 Fri Apr 10 15:39:54 2020 -0700
    Initial work on merging multiple bigBed items that span the window, refs #25133
• src/hg/js/hgGtexTrackSettings.js
  • lines changed 3, context: html, text, full: html, text
    832926811b278d5c656957e1565acdde48522def Mon Apr 27 17:59:12 2020 -0700
    Update GTEx gene track click handler and track settings to handle V8 (add Kidney Medulla tissue, support TPM and RPKM). refs #25130
  • lines changed 2, context: html, text, full: html, text
    fa261bb6a4e20cb44972593d383589f1e5e4edce Tue Apr 28 12:34:02 2020 -0700
    Redo tissue table, bed file, and related code to slot new kidney medulla tissue in (assign id) in proper alphabetical order. refs #25130
• src/hg/js/hgTracks.js
  • lines changed 46, context: html, text, full: html, text
    fecc0bfffd30dccc9998aa0c2e5a6064d487bbb1 Fri Apr 10 15:39:54 2020 -0700
    Initial work on merging multiple bigBed items that span the window, refs #25133
• src/hg/lib/blatServers.as
  • lines changed 1, context: html, text, full: html, text
    4b1e60cc4e12743f5d5194decfb10bda2942dc0c Thu Apr 30 22:32:27 2020 -0700
    adding missing canPcr field. should have been done long ago.
• src/hg/lib/blatServers.c
  • lines changed 30, context: html, text, full: html, text
    4b1e60cc4e12743f5d5194decfb10bda2942dc0c Thu Apr 30 22:32:27 2020 -0700
    adding missing canPcr field. should have been done long ago.
• src/hg/lib/blatServers.sql
  • lines changed 4, context: html, text, full: html, text
    4b1e60cc4e12743f5d5194decfb10bda2942dc0c Thu Apr 30 22:32:27 2020 -0700
    adding missing canPcr field. should have been done long ago.
• src/hg/lib/blatServers.tab
  • lines changed 6, context: html, text, full: html, text
    4b1e60cc4e12743f5d5194decfb10bda2942dc0c Thu Apr 30 22:32:27 2020 -0700
    adding missing canPcr field. should have been done long ago.
• src/hg/lib/genbankBed12.as
  • lines changed 18, context: html, text, full: html, text
    808fa9a4c306d2d85df51d5c7c8ea9976a0fb0f1 Thu Apr 30 11:41:48 2020 -0700
    adding genbankToBigGenePred tool, right now only for wuhCor1 assembly, but possibly useful elsewhere, as per emails with Braney
• src/hg/lib/genbankBigGenePred.as
  • lines changed 31, context: html, text, full: html, text
    808fa9a4c306d2d85df51d5c7c8ea9976a0fb0f1 Thu Apr 30 11:41:48 2020 -0700
    adding genbankToBigGenePred tool, right now only for wuhCor1 assembly, but possibly useful elsewhere, as per emails with Braney
  • lines changed 2, context: html, text, full: html, text
    dbcc7835da6ae05a32f309ba3f9ec6c52b966e55 Sat May 2 08:27:10 2020 -0700
    fixing duplicate table name, nightly auto email.
• src/hg/lib/gtexInfo.c
  • lines changed 13, context: html, text, full: html, text
    96962227b59e566541cf63670087bbed487a4682 Mon Apr 27 15:37:26 2020 -0700
    Straighten out tables names wrt versioning and add track for GTEx Gene track update to V8 (final). refs #25130
  • lines changed 7, context: html, text, full: html, text
    832926811b278d5c656957e1565acdde48522def Mon Apr 27 17:59:12 2020 -0700
    Update GTEx gene track click handler and track settings to handle V8 (add Kidney Medulla tissue, support TPM and RPKM). refs #25130
• src/hg/lib/gtexUi.c
  • lines changed 2, context: html, text, full: html, text
    832926811b278d5c656957e1565acdde48522def Mon Apr 27 17:59:12 2020 -0700
    Update GTEx gene track click handler and track settings to handle V8 (add Kidney Medulla tissue, support TPM and RPKM). refs #25130
• src/hg/lib/hui.c
  • lines changed 21, context: html, text, full: html, text
    fecc0bfffd30dccc9998aa0c2e5a6064d487bbb1 Fri Apr 10 15:39:54 2020 -0700
    Initial work on merging multiple bigBed items that span the window, refs #25133
  • lines changed 29, context: html, text, full: html, text
    a57e43af4d3436c4017a4744b9595b0dcbcf3891 Tue Apr 28 14:06:58 2020 -0700
    Move hideEmptySubtracks control on UI, by request of Ana. refs #23365
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    bc2f747c9f09b2f50e0a3427e884ec34e936bf07 Wed Apr 29 16:44:24 2020 -0700
    Add question mark with mouseover explanation next to hide empty subtracks checkbox. refs #23365
• src/hg/makeDb/doc/asmHubs/asmHubs.mk
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    67d50873eca0ae6f595367077c9735b7d348e5c2 Fri May 1 12:31:59 2020 -0700
    adding functions to build VGP index pages refs #23734
• src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
  • lines changed 29, context: html, text, full: html, text
    67d50873eca0ae6f595367077c9735b7d348e5c2 Fri May 1 12:31:59 2020 -0700
    adding functions to build VGP index pages refs #23734
• src/hg/makeDb/doc/asmHubs/mkGenomes.pl
  • lines changed 20, context: html, text, full: html, text
    67d50873eca0ae6f595367077c9735b7d348e5c2 Fri May 1 12:31:59 2020 -0700
    adding functions to build VGP index pages refs #23734
• src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
  • lines changed 28, context: html, text, full: html, text
    67d50873eca0ae6f595367077c9735b7d348e5c2 Fri May 1 12:31:59 2020 -0700
    adding functions to build VGP index pages refs #23734
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    951ae58cfc4a8b6b7dec665cbabb524abb4fc67a Fri May 1 13:09:53 2020 -0700
    add class column in the table for VGP genomes refs #23734
• src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
  • lines changed 19, context: html, text, full: html, text
    67d50873eca0ae6f595367077c9735b7d348e5c2 Fri May 1 12:31:59 2020 -0700
    adding functions to build VGP index pages refs #23734
• src/hg/makeDb/doc/asmHubs/trackData.pl
  • lines changed 132, context: html, text, full: html, text
    67d50873eca0ae6f595367077c9735b7d348e5c2 Fri May 1 12:31:59 2020 -0700
    adding functions to build VGP index pages refs #23734
• src/hg/makeDb/doc/asmHubs/vgp.asmId.commonName.tsv
  • lines changed 157, context: html, text, full: html, text
    67d50873eca0ae6f595367077c9735b7d348e5c2 Fri May 1 12:31:59 2020 -0700
    adding functions to build VGP index pages refs #23734
• src/hg/makeDb/doc/asmHubs/vgp.commonName.asmId.orderList.tsv
  • lines changed 157, context: html, text, full: html, text
    67d50873eca0ae6f595367077c9735b7d348e5c2 Fri May 1 12:31:59 2020 -0700
    adding functions to build VGP index pages refs #23734
• src/hg/makeDb/doc/gtex/V6.txt
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    d96751b9e97f16417a020a9f6356432e6d102bc1 Wed Apr 29 10:21:59 2020 -0700
    Correct tissue description, as per GTEx portal page for V8. refs #25130
• src/hg/makeDb/doc/gtex/V8.txt
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    96962227b59e566541cf63670087bbed487a4682 Mon Apr 27 15:37:26 2020 -0700
    Straighten out tables names wrt versioning and add track for GTEx Gene track update to V8 (final). refs #25130
  • lines changed 14, context: html, text, full: html, text
    fa261bb6a4e20cb44972593d383589f1e5e4edce Tue Apr 28 12:34:02 2020 -0700
    Redo tissue table, bed file, and related code to slot new kidney medulla tissue in (assign id) in proper alphabetical order. refs #25130
• src/hg/makeDb/doc/hg19.gencode.txt
  • lines changed 681, context: html, text, full: html, text
    f5183290e802b44254b3b4d381f369cee8390fca Wed Apr 29 11:09:57 2020 -0700
    moved gencode track doc to their own files for mm10 and hg19 as it is overwhelming the main file
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    8449958c66006a38a4515b46ad1e78d7f7f6ad81 Wed Apr 29 14:53:20 2020 -0700
    import of GENCODE 34lift37
• src/hg/makeDb/doc/hg19.txt
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    f5183290e802b44254b3b4d381f369cee8390fca Wed Apr 29 11:09:57 2020 -0700
    moved gencode track doc to their own files for mm10 and hg19 as it is overwhelming the main file
• src/hg/makeDb/doc/hg38/gencode.txt
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    b985a10e714b3fad02117a0eeba5a6b36bd0ca59 Wed Apr 29 12:53:43 2020 -0700
    loaded gencodeV34 final release
• src/hg/makeDb/doc/hg38/gtex.txt
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    55d5984bc5dd9e1d382c811ee9284771925a16b2 Tue Apr 28 12:37:30 2020 -0700
    Assign score field based on tissue medians. refs #25130
• src/hg/makeDb/doc/mm10.gencode.txt
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    f5183290e802b44254b3b4d381f369cee8390fca Wed Apr 29 11:09:57 2020 -0700
    moved gencode track doc to their own files for mm10 and hg19 as it is overwhelming the main file
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    7bd8c4f2fd1c56e7bb81ac0235944ab82cfabaea Wed Apr 29 13:46:43 2020 -0700
    import of GENCODE VM25
• src/hg/makeDb/doc/mm10.txt
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    f5183290e802b44254b3b4d381f369cee8390fca Wed Apr 29 11:09:57 2020 -0700
    moved gencode track doc to their own files for mm10 and hg19 as it is overwhelming the main file
• src/hg/makeDb/doc/vgpAsmHub/VGPlogo.png
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    67d50873eca0ae6f595367077c9735b7d348e5c2 Fri May 1 12:31:59 2020 -0700
    adding functions to build VGP index pages refs #23734
• src/hg/makeDb/doc/vgpAsmHub/hub.txt
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    67d50873eca0ae6f595367077c9735b7d348e5c2 Fri May 1 12:31:59 2020 -0700
    adding functions to build VGP index pages refs #23734
• src/hg/makeDb/doc/vgpAsmHub/makefile
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    67d50873eca0ae6f595367077c9735b7d348e5c2 Fri May 1 12:31:59 2020 -0700
    adding functions to build VGP index pages refs #23734
• src/hg/makeDb/doc/vgpAsmHub/vgp.taxId,asmId.class.txt
  • lines changed 157, context: html, text, full: html, text
    67d50873eca0ae6f595367077c9735b7d348e5c2 Fri May 1 12:31:59 2020 -0700
    adding functions to build VGP index pages refs #23734
• src/hg/makeDb/doc/wuhCor1/multiz.txt
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    48af17eb015e5c81e22f0cff23d181c50949aa5b Thu Apr 30 22:28:03 2020 -0700
    added 119-way strain name track refs #25090
• src/hg/makeDb/doc/wuhCor1/ncbiGene.txt
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    84b209a8c6517af21f733b68744e78897063fbf4 Thu Apr 30 16:10:51 2020 -0700
    some very basic makeDoc for NCBI Genes
• src/hg/makeDb/doc/wuhCor1/phastCons119way.txt
  • lines changed 3, context: html, text, full: html, text
    48af17eb015e5c81e22f0cff23d181c50949aa5b Thu Apr 30 22:28:03 2020 -0700
    added 119-way strain name track refs #25090
• src/hg/makeDb/doc/wuhCor1/snpView.44way.txt
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    d676882c7f64619f14d512a77fa9aed71890547e Sat May 2 10:39:17 2020 -0700
    tweak the mafSnp tables on wuhCor1 a bit to change codingVariants that aren't syn or nonsyn into missing data
• src/hg/makeDb/doc/wuhCor1/snpView.txt
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    48af17eb015e5c81e22f0cff23d181c50949aa5b Thu Apr 30 22:28:03 2020 -0700
    added 119-way strain name track refs #25090
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    d676882c7f64619f14d512a77fa9aed71890547e Sat May 2 10:39:17 2020 -0700
    tweak the mafSnp tables on wuhCor1 a bit to change codingVariants that aren't syn or nonsyn into missing data
• src/hg/makeDb/genbank/etc/genbank.conf
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    3b4ec517d97a4a4bd01864d969041635423e13e6 Fri May 1 15:53:55 2020 -0700
    Adding wuhCor1 to genbank build
• src/hg/makeDb/genbank/src/lib/gbGenome.c
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    3e639f123d181eccbafd9dd38eb448236f93c02d Mon May 4 09:06:48 2020 -0700
    Adding wuhCor1 definition to gbGenome genbank definition
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    d4e393a4c04fec20c85797eebea72a71921e843d Mon May 4 09:09:57 2020 -0700
    Forgot one line of wuhCor genbank definition
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    a4ef30418907a322b23993252a774143d92125d3 Mon May 4 09:53:26 2020 -0700
    Adding another name for Sars-Cov-2 to genbank pipeline
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
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    b985a10e714b3fad02117a0eeba5a6b36bd0ca59 Wed Apr 29 12:53:43 2020 -0700
    loaded gencodeV34 final release
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    7bd8c4f2fd1c56e7bb81ac0235944ab82cfabaea Wed Apr 29 13:46:43 2020 -0700
    import of GENCODE VM25
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    8449958c66006a38a4515b46ad1e78d7f7f6ad81 Wed Apr 29 14:53:20 2020 -0700
    import of GENCODE 34lift37
• src/hg/makeDb/schema/all.joiner
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    8449958c66006a38a4515b46ad1e78d7f7f6ad81 Wed Apr 29 14:53:20 2020 -0700
    import of GENCODE 34lift37
• src/hg/makeDb/trackDb/armadillo/dasNov3/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
• src/hg/makeDb/trackDb/baboon/papAnu4/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
• src/hg/makeDb/trackDb/balAcu/balAcu1/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
• src/hg/makeDb/trackDb/birds/geoFor1/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
• src/hg/makeDb/trackDb/birds/melUnd1/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
• src/hg/makeDb/trackDb/bonobo/panPan2/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
• src/hg/makeDb/trackDb/bushbaby/otoGar3/trackDb.ra
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    a4004610e414e50484185ea4a0f291deba0e12ec Tue Apr 28 16:05:04 2020 -0700
    Adding last includes plus pennantIcon to last missing dbs for refseq updates refs #24547
• src/hg/makeDb/trackDb/calMil/calMil1/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
• src/hg/makeDb/trackDb/chicken/galGal6/refSeqComposite.ra
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    a4004610e414e50484185ea4a0f291deba0e12ec Tue Apr 28 16:05:04 2020 -0700
    Adding last includes plus pennantIcon to last missing dbs for refseq updates refs #24547
• src/hg/makeDb/trackDb/chlorocebus/chlSab2/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
• src/hg/makeDb/trackDb/criGri/criGriChoV1/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
• src/hg/makeDb/trackDb/dog/canFam3/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
• src/hg/makeDb/trackDb/elephant/loxAfr3/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
• src/hg/makeDb/trackDb/ferret/musFur1/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
• src/hg/makeDb/trackDb/frog/nanPar1/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
• src/hg/makeDb/trackDb/galVar/galVar1/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
• src/hg/makeDb/trackDb/guineaPig/cavPor3/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
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    e4a3deab7d351adfe571fd371171325dfa364639 Tue Apr 28 10:01:23 2020 -0700
    Adding pennantIcon and fixing some release tag issues refs #24547
• src/hg/makeDb/trackDb/guineaPig/cavPor3/trackDb.refGene.ra
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    e4a3deab7d351adfe571fd371171325dfa364639 Tue Apr 28 10:01:23 2020 -0700
    Adding pennantIcon and fixing some release tag issues refs #24547
• src/hg/makeDb/trackDb/hedgehog/eriEur2/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
• src/hg/makeDb/trackDb/horse/equCab2/nscanGene.html
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    fd972bf8dc704032335e18606e6e6ae33565b895 Thu Apr 30 10:07:20 2020 -0700
    Updating http to https for equCab2, uiLinks cronjob.
• src/hg/makeDb/trackDb/horse/equCab3/trackDb.ra
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    a4004610e414e50484185ea4a0f291deba0e12ec Tue Apr 28 16:05:04 2020 -0700
    Adding last includes plus pennantIcon to last missing dbs for refseq updates refs #24547
• src/hg/makeDb/trackDb/human/gtexGeneV8.html
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    5de72d67529fe096500e1009c53a83afaec25b96 Mon Apr 27 18:26:26 2020 -0700
    Update GTEx Gene track description for V8. refs #25130
• src/hg/makeDb/trackDb/human/hg19/gnomadVariants.html
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    088c5d1ae4044819d5f1a370b00c16cc7941d2a3 Wed Apr 29 15:07:46 2020 -0700
    textual corrections after CR refs #25449
• src/hg/makeDb/trackDb/human/hg19/problematic.html
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    57521b0e1fc1377cdf89dbda867f4d10e88838fe Tue Apr 28 17:55:50 2020 -0700
    Adding oxford comma for CR #25447
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    aacc8ecccb94495c77d09893ec4db897f57ec5b7 Fri May 1 12:18:36 2020 -0700
    add text to description page refs #24245
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
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    c5eb3af1ec48ee4d40c32d26c3486f1e60658b7b Wed Apr 29 15:45:09 2020 -0700
    forgot to include .ra file
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    80d0727da7c2b371c0f878d1fc2a8d10fd8fce10 Tue Apr 28 16:27:15 2020 -0700
    Fixing typos for #24245
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    679ac58542b7d783a88863aa779a630637b2aebf Thu Apr 30 11:18:36 2020 -0700
    take off trailing + on comments subtrack because we don't want score filters
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    d2066512153eb0c215c6102568f9790089611379 Fri May 1 12:17:47 2020 -0700
    change name UCSC unusual regions subtrack, correct typos refs #24245
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
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    8449958c66006a38a4515b46ad1e78d7f7f6ad81 Wed Apr 29 14:53:20 2020 -0700
    import of GENCODE 34lift37
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV34lift37.html
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    8449958c66006a38a4515b46ad1e78d7f7f6ad81 Wed Apr 29 14:53:20 2020 -0700
    import of GENCODE 34lift37
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV34lift37.ra
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    8449958c66006a38a4515b46ad1e78d7f7f6ad81 Wed Apr 29 14:53:20 2020 -0700
    import of GENCODE 34lift37
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeSuper.html
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    b985a10e714b3fad02117a0eeba5a6b36bd0ca59 Wed Apr 29 12:53:43 2020 -0700
    loaded gencodeV34 final release
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV30.html
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    f467fad2edc7840a410433f59651ff7422654d9e Mon Apr 27 11:12:09 2020 -0700
    Correcting link to Gencode v30 release, refs #25434
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV34.html
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    577c7537344e58f1538843f38e084f6e175b5ca3 Wed Apr 29 11:34:27 2020 -0700
    fix warning: suggest parentheses around ‘&&’ within ‘||’ [-Werror=parentheses]
• src/hg/makeDb/trackDb/human/trackDb.clinvarTest.ra
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    fecc0bfffd30dccc9998aa0c2e5a6064d487bbb1 Fri Apr 10 15:39:54 2020 -0700
    Initial work on merging multiple bigBed items that span the window, refs #25133
• src/hg/makeDb/trackDb/human/trackDb.gtex.ra
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    96962227b59e566541cf63670087bbed487a4682 Mon Apr 27 15:37:26 2020 -0700
    Straighten out tables names wrt versioning and add track for GTEx Gene track update to V8 (final). refs #25130
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    f83fd868fdf1863c36526277c3168b98934b88d2 Tue Apr 28 12:34:38 2020 -0700
    Update GTEx Gene track description for V8. refs #25130
• src/hg/makeDb/trackDb/latCha/latCha1/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
• src/hg/makeDb/trackDb/lizard/anoCar2/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
• src/hg/makeDb/trackDb/macaca/macFas5/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
• src/hg/makeDb/trackDb/manatee/triMan1/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
• src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
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    e4a3deab7d351adfe571fd371171325dfa364639 Tue Apr 28 10:01:23 2020 -0700
    Adding pennantIcon and fixing some release tag issues refs #24547
• src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.refGene.ra
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    e4a3deab7d351adfe571fd371171325dfa364639 Tue Apr 28 10:01:23 2020 -0700
    Adding pennantIcon and fixing some release tag issues refs #24547
• src/hg/makeDb/trackDb/microbat/myoLuc2/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
• src/hg/makeDb/trackDb/moleRat/hetGla2/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeSuper.html
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    7bd8c4f2fd1c56e7bb81ac0235944ab82cfabaea Wed Apr 29 13:46:43 2020 -0700
    import of GENCODE VM25
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM25.html
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    7bd8c4f2fd1c56e7bb81ac0235944ab82cfabaea Wed Apr 29 13:46:43 2020 -0700
    import of GENCODE VM25
• src/hg/makeDb/trackDb/orangutan/ponAbe3/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
• src/hg/makeDb/trackDb/panda/ailMel1/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
• src/hg/makeDb/trackDb/pika/ochPri3/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
• src/hg/makeDb/trackDb/rabbit/oryCun2/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
• src/hg/makeDb/trackDb/refSeqComposite.ra
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    e4a3deab7d351adfe571fd371171325dfa364639 Tue Apr 28 10:01:23 2020 -0700
    Adding pennantIcon and fixing some release tag issues refs #24547
• src/hg/makeDb/trackDb/rhino/cerSim1/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
• src/hg/makeDb/trackDb/saiBol/saiBol1/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
• src/hg/makeDb/trackDb/shrew/sorAra2/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
• src/hg/makeDb/trackDb/squirrel/speTri2/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
• src/hg/makeDb/trackDb/tagTypes.tab
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    fecc0bfffd30dccc9998aa0c2e5a6064d487bbb1 Fri Apr 10 15:39:54 2020 -0700
    Initial work on merging multiple bigBed items that span the window, refs #25133
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    432871a5ecd060804eccaed040a25f8d969981ef Thu Apr 30 16:01:34 2020 -0700
    Changing default selections to least-related sequences and making the labels more verbose refs #25090
• src/hg/makeDb/trackDb/targets.html
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    207229f284b91ec0bd2eaa856fe639d7786fe8e9 Mon Apr 27 12:26:51 2020 -0700
    adding T cell epitopes track, refs #25458
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    26ad7e5fe96a1b5070432af743fda80a385d52e8 Wed Apr 29 13:28:42 2020 -0700
    Moving the track desc page down to the wuhCor1 level refs #25458
• src/hg/makeDb/trackDb/tarsier/tarSyr2/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
• src/hg/makeDb/trackDb/tasmanianDevil/sarHar1/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
• src/hg/makeDb/trackDb/virus/wuhCor1/artic.html
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    1b57d6e546df31ddd01e6c521f52a0b4af8a4c53 Tue Apr 28 15:24:58 2020 -0700
    Adding data access section to ARTIC track refs #25416
• src/hg/makeDb/trackDb/virus/wuhCor1/cas13Crispr.html
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    fc64e514e36c00b4d457d3bf0747853895dcc651 Tue Apr 28 14:48:13 2020 -0700
    Fixing up the desc page for cas13 CRISPR track refs #25344
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    c1dd96464056bde5c4a743be533d27c05535a7cb Tue Apr 28 15:04:01 2020 -0700
    Adding data access section for cas13 CRISPR track refs #25344
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    716c4d1035a1ee92d7c578294960a992fe1ba650 Tue Apr 28 15:49:11 2020 -0700
    Making small html fix for readability no RM
• src/hg/makeDb/trackDb/virus/wuhCor1/crisprDet.html
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    8204f3686faa45ce0b031b2927f272fb1b11690e Tue Apr 28 14:30:03 2020 -0700
    Updating desc page for the crispr detection guides refs #25247
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    d4e4fb0192774a89920712be10bdb90b0e3c7352 Wed Apr 29 05:43:56 2020 -0700
    fixing crisprDet docs page, refs #25247
• src/hg/makeDb/trackDb/virus/wuhCor1/gordon.html
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    19ef0bf76151acd7bf6a2ef7cf30d683dbda30d1 Wed Apr 29 05:42:55 2020 -0700
    fixing gordon docs page, refs #25247
• src/hg/makeDb/trackDb/virus/wuhCor1/gordon2.html
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    19ef0bf76151acd7bf6a2ef7cf30d683dbda30d1 Wed Apr 29 05:42:55 2020 -0700
    fixing gordon docs page, refs #25247
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    3a0d7ebba74d84135ec239f3936da8bce479daa1 Wed Apr 29 08:17:01 2020 -0700
    Fixing up the protein interaction desc page refs #25247
• src/hg/makeDb/trackDb/virus/wuhCor1/kim2020.ra
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    b37b09c21ea36d8e14179f0619ba4306e518f4e0 Tue Apr 28 07:55:21 2020 -0700
    adding wuhCor1 transcriptome track, refs #25468
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    c2232f0fb90e36e169de6f6acddbf6404bf2e1b0 Tue Apr 28 09:15:33 2020 -0700
    renaming transcript subtracks so the long label makes more sense, refs #25468
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    5db92eefaeb955d7a2a5b152b0ee9bfa9a979c69 Tue Apr 28 11:25:17 2020 -0700
    add . after type bigBed
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    cf7597bcca30b45f90c5ff4cd7a8f2227bf123d7 Wed Apr 29 05:45:26 2020 -0700
    hiding the kim 2020 transcriptome track', refs #25468
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    a67a875d9b30d3a5815f530c4685a03c3ea0e87f Wed Apr 29 14:42:36 2020 -0700
    Splitting transcriptome track to kim transcripts and transcriptomes refs #25468
• src/hg/makeDb/trackDb/virus/wuhCor1/kimTranscripts.html
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    a67a875d9b30d3a5815f530c4685a03c3ea0e87f Wed Apr 29 14:42:36 2020 -0700
    Splitting transcriptome track to kim transcripts and transcriptomes refs #25468
• src/hg/makeDb/trackDb/virus/wuhCor1/ncbiGene.ra
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    037036926221d64f84d7594254a78f008e10b777 Thu Apr 30 15:55:02 2020 -0700
    A version of NCBI genes generated from the genbank record instead of the GFF, changed the name of the shorter orf1ab to orf1a
• src/hg/makeDb/trackDb/virus/wuhCor1/ncbiGeneBGP.html
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    037036926221d64f84d7594254a78f008e10b777 Thu Apr 30 15:55:02 2020 -0700
    A version of NCBI genes generated from the genbank record instead of the GFF, changed the name of the shorter orf1ab to orf1a
• src/hg/makeDb/trackDb/virus/wuhCor1/poranHla1.html
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    edfe2154917b93dbca09f74b043c8d1d5dee2c34 Tue Apr 28 17:15:16 2020 -0700
    Making changes in response to CR refs #25448
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    601daea1de754b9eaaf2b710a9e23e8e4d9c321d Wed Apr 29 12:39:14 2020 -0700
    Fixing up the kim transcriptome desc page refs #25468
• src/hg/makeDb/trackDb/virus/wuhCor1/publicAnnots.html
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    f687ccdef74c5ad851a7e2e7ffe76b74dbbfbec4 Thu Apr 30 03:30:32 2020 -0700
    remove typo
• src/hg/makeDb/trackDb/virus/wuhCor1/rfam.html
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    be446d716d5a6e9026b13d9302ca63d662a50af2 Mon Apr 27 15:09:58 2020 -0700
    adding rfam track, ref #25463
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    13f5190912cd31652cb88eba31f365ee1d13304b Mon Apr 27 15:11:39 2020 -0700
    fixing unicode problem on rfam docs page, refs #25463
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    a9c2124ec25e136c5395478728731a8432cfb78d Wed Apr 29 13:09:26 2020 -0700
    Fixing up desc page for rFAM refs #25464
• src/hg/makeDb/trackDb/virus/wuhCor1/rnaStructRangan.html
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    b64309c98f9f63c226fb0e72af7a6ececa5bca00 Tue Apr 28 15:48:25 2020 -0700
    Touching up description page for Rangan RNA, adding references refs #25228
• src/hg/makeDb/trackDb/virus/wuhCor1/targets.html
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    26ad7e5fe96a1b5070432af743fda80a385d52e8 Wed Apr 29 13:28:42 2020 -0700
    Moving the track desc page down to the wuhCor1 level refs #25458
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    80e84c909e7d3b1c2487911fdb44818b9eaf0305 Wed Apr 29 14:01:00 2020 -0700
    Fixing up desc page for T cell epitopes track refs #25458
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.119way.ra
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    432871a5ecd060804eccaed040a25f8d969981ef Thu Apr 30 16:01:34 2020 -0700
    Changing default selections to least-related sequences and making the labels more verbose refs #25090
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra
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    7ae5638cd51f8a67da9dbfa08781d3a1baa4e614 Fri Apr 24 15:20:39 2020 -0700
    Adding nextstrainSamplesRb (recurrent bi-allelic) subtrack to trackDb. refs #25188
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    c2cadc008dd509ae89b4883203b173a8508e2aca Wed Apr 29 11:56:30 2020 -0700
    Setting a nextstrainSamples subtrack on by default so you see data when you switch from hide to pack on hgTracks NoRM
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    c35d862713639e092261001c5a1d6e74d725a1e1 Wed Apr 29 17:18:24 2020 -0700
    Oops, since nextstrainSamplesRb is not yet on beta/RR, use release tags so nextstrainSamplesAll is off by default on dev but on by default on beta/RR. refs #25475
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    ec2b3412815fe8a90c4f4fc2a20ceb38f407c22a Fri May 1 16:59:57 2020 -0700
    adding nextstrain counts, refs #25481
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
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    c1d89458d6796c16766ec77a62e96c38784f871f Mon Apr 27 10:18:26 2020 -0700
    Changing short and longLabel due to feedback refs #25297
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    cac2a1c8f8b04d51a51c4f561c82fbb6c0cd5725 Mon Apr 27 12:04:27 2020 -0700
    changing user annots label, refs #25297
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    7570f83b5d7ca8ca334df52f84bbd64300237317 Mon Apr 27 12:07:52 2020 -0700
    fixing merge conflict
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    207229f284b91ec0bd2eaa856fe639d7786fe8e9 Mon Apr 27 12:26:51 2020 -0700
    adding T cell epitopes track, refs #25458
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    be446d716d5a6e9026b13d9302ca63d662a50af2 Mon Apr 27 15:09:58 2020 -0700
    adding rfam track, ref #25463
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    c2232f0fb90e36e169de6f6acddbf6404bf2e1b0 Tue Apr 28 09:15:33 2020 -0700
    renaming transcript subtracks so the long label makes more sense, refs #25468
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    da125c7b2682fd607264cf3da6dc8e31ca19a36a Tue Apr 28 15:13:22 2020 -0700
    Fixing trackDb stanza for cas13 CRISPR to enable a score filter and shading by score refs #25344
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    a21934e112439626fa6dd349ec8ec40b04738565 Wed Apr 29 06:49:38 2020 -0700
    moving crisprDet to map and seq group, refs #25247
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    f21ea0504b247456a891e08e58877d644c2f483c Thu Apr 30 08:49:17 2020 -0700
    Capitalizing some shortLabels, no RM
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    893fb2be6044ef6697d9f199af3179d88a5a8616 Thu Apr 30 14:50:17 2020 -0700
    Fixing the name of the track, the name should not be all caps. No RM
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    037036926221d64f84d7594254a78f008e10b777 Thu Apr 30 15:55:02 2020 -0700
    A version of NCBI genes generated from the genbank record instead of the GFF, changed the name of the shorter orf1ab to orf1a
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    94f0ea957bc608c6a17998aeca1a3c2776955bc0 Thu Apr 30 22:15:03 2020 -0700
    adding 119-way track with strain names refs #25090
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    e4f538f000e1714c36734071826625fd3750cb4a Fri May 1 14:57:10 2020 -0700
    updating ncbiGenes track #25114
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    c436774102f2cbc6e313ce1a36c885d433dd1d57 Sat May 2 11:43:22 2020 -0700
    Removing exon numbers and arrows from track refs #25482
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.strainName119way.ra
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    2478e0f72dfcd5d1c86b0a7a2107a9274e1f719b Thu Apr 30 22:17:32 2020 -0700
    adding 119-way track with strain names refs #25090
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    757f6bb40349e3d5075dd90a34f91c069a9493b2 Thu Apr 30 22:24:47 2020 -0700
    using cons119way.html for description refs #25090
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    de0ea7557618ed71c31f0866eb351fb7a92c5e34 Fri May 1 10:24:22 2020 -0700
    Fixing labels, defaults, and shortLabel names for multiple alignment tracks refs #25090
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.strainName44way.ra
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    de0ea7557618ed71c31f0866eb351fb7a92c5e34 Fri May 1 10:24:22 2020 -0700
    Fixing labels, defaults, and shortLabel names for multiple alignment tracks refs #25090
• src/hg/makeDb/trackDb/virus/wuhCor1/transcriptome.html
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    b37b09c21ea36d8e14179f0619ba4306e518f4e0 Tue Apr 28 07:55:21 2020 -0700
    adding wuhCor1 transcriptome track, refs #25468
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    601daea1de754b9eaaf2b710a9e23e8e4d9c321d Wed Apr 29 12:39:14 2020 -0700
    Fixing up the kim transcriptome desc page refs #25468
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    a67a875d9b30d3a5815f530c4685a03c3ea0e87f Wed Apr 29 14:42:36 2020 -0700
    Splitting transcriptome track to kim transcripts and transcriptomes refs #25468
• src/hg/makeDb/trackDb/xenTro/xenLae2/trackDb.ra
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    aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700
    Removing release tags for refseq genes update refs #24547
• src/hg/utils/automation/doAssemblyHub.pl
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    6a48e07c2fbefbf0a0e5e74662dd768ef93fca88 Wed Apr 29 11:27:30 2020 -0700
    adding ncbiRmsk option to use NCBI rm.out.gz file instead of cluster run and record versionInfo.txt of RepeatMasker operation refs #23734
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    db6d277aafb53f3f3d5bad08d3821ae98a29a045 Wed Apr 29 14:29:34 2020 -0700
    fix use of verbose() in ncbiGene refs #23734
• src/hg/utils/automation/doRepeatMasker.pl
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    6a48e07c2fbefbf0a0e5e74662dd768ef93fca88 Wed Apr 29 11:27:30 2020 -0700
    adding ncbiRmsk option to use NCBI rm.out.gz file instead of cluster run and record versionInfo.txt of RepeatMasker operation refs #23734
• src/hg/utils/otto/nextstrainNcov/doUpdate.sh
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    b98e1d0ccffb3a4c1d69f6c69ab98a842840aa57 Fri Apr 24 13:58:33 2020 -0700
    Adding VCF subtrack for David: filter to recurrent bi-allelic variants only. refs #25188
• src/hg/utils/otto/nextstrainNcov/nextstrain.py
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    b98e1d0ccffb3a4c1d69f6c69ab98a842840aa57 Fri Apr 24 13:58:33 2020 -0700
    Adding VCF subtrack for David: filter to recurrent bi-allelic variants only. refs #25188
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    769a92cab2445edae6ab5209e93162c1e7036dee Thu Apr 30 11:59:54 2020 -0700
    Make sure python doesn't gak if no submitting_lab is provided for some sample. refs #25188
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    72730b6971500837e39e21461e8fce00eebfc008 Fri May 1 10:21:30 2020 -0700
    Add internal node labels to the newick tree files that encode clade and the sequence of mutations leading to the node. This actually does not affect the track at this point, but helps in comparing the trees from different releases. refs #25188
• src/lib/linefile.c
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    1ad98d1567578b8ceb7db30bf0be128b225edd1d Mon Apr 27 14:59:36 2020 -0700
    lineFileNext for udc file didn't bother to set retSize and apparently it didn't matter until I wanted to use lineFile with udc in phyloOpenTree.
• src/lib/phyloTree.c
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    cdb062c333ee1200f4a744fd0736d9a27933629c Mon Apr 27 15:01:01 2020 -0700
    Use lineFileUdc instead of just lineFile, so URLs work. Now I can make a custom track with hapClusterMethod treeFile <url>.
• src/utils/genbankToBigGenePred
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    808fa9a4c306d2d85df51d5c7c8ea9976a0fb0f1 Thu Apr 30 11:41:48 2020 -0700
    adding genbankToBigGenePred tool, right now only for wuhCor1 assembly, but possibly useful elsewhere, as per emails with Braney
• src/utils/qa/weeklybld/buildEnv.csh
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    1542a6da7c8cb7c15f92df47a06c9ddaa6167797 Mon May 4 09:54:02 2020 -0700
    v398 preview2, refs #25471

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