All File Changes

v395_base to v396_preview (2020-03-09 to 2020-03-16) v396

• src/hg/cirm/gateway/htdocs/cirmIndex.html
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    281f91e4d0d2603d5cce2566f2b7483535365c62 Mon Mar 9 17:57:27 2020 -0700
    Add '<' to click able icon closed as addressed in code review
• src/hg/hgMirror/hgMirror
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    21d5d63590ae47d277ebe83a048f3ded1f446783 Mon Mar 16 01:06:03 2020 -0700
    fixing ncbiRefSeq in offline mode on gbib, email from user
• src/hg/hgTables/hic.c
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    60079bc1898e003d9f1397176baaee00e431b011 Tue Mar 10 14:36:41 2020 -0700
    Changes to support better chr mappings in .hic files depended on a non-NULL assembly name, which was not previously assumed. Fixing what I broke, refs #24988
• src/hg/hgTracks/hgTracks.c
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    cc7cbe4be1f3034c493d1a07549b6e4aadea0a5c Wed Mar 4 16:35:45 2020 -0800
    Fix problem with nonempty track names on hubs when using hideEmptySubtracks. refs #23665
• src/hg/htdocs/goldenPath/help/gbic.html
  • lines changed 14, context: html, text, full: html, text
    00ebc6c645c3a9d8e668d3670031b53d8180d235 Tue Mar 10 11:10:54 2020 -0700
    Adding a note about how to add other partitions for GBiC data, refs #25056
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    3ae0ec6ec7b6478bc8f1c9feab82fb9d8e0d9806 Tue Mar 10 11:19:11 2020 -0700
    Adding an HTML anchor to the partition section, refs #25056
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    36f54a92956a350a2e61453b47c52e4286a1f942 Thu Mar 12 07:10:13 2020 -0700
    adding more details to gbic.html refs #25123
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    654d0bd1cd798505efc917087541d450e5da9e66 Thu Mar 12 11:02:42 2020 -0700
    Replacing double quotes with the HTML entity and making each line less than 100 characters, refs #25123
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 13, context: html, text, full: html, text
    bc5169d72588f7a162dfde36bf10cb71f7a7c017 Wed Mar 11 13:21:33 2020 -0700
    Updated trackDb docs to v2 syntax of hideEmptySubtracks setting. refs #23365
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    cc31b8b1614ac2a3566171a3aca3d11d9295629b Thu Mar 12 10:08:42 2020 -0700
    Fix typo. refs #23365
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
  • lines changed 11, context: html, text, full: html, text
    bc5169d72588f7a162dfde36bf10cb71f7a7c017 Wed Mar 11 13:21:33 2020 -0700
    Updated trackDb docs to v2 syntax of hideEmptySubtracks setting. refs #23365
  • lines changed 1, context: html, text, full: html, text
    cc31b8b1614ac2a3566171a3aca3d11d9295629b Thu Mar 12 10:08:42 2020 -0700
    Fix typo. refs #23365
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 44, context: html, text, full: html, text
    bc5169d72588f7a162dfde36bf10cb71f7a7c017 Wed Mar 11 13:21:33 2020 -0700
    Updated trackDb docs to v2 syntax of hideEmptySubtracks setting. refs #23365
• src/hg/htdocs/images/phylo/wuhCor1_119way.png
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    f29e6e6fe0b3ff481c572970b0cb777822922d14 Fri Mar 13 11:19:59 2020 -0700
    phylo tree for wuhCor1 119 way refs #25090
• src/hg/htdocs/images/phylo/wuhCor1_44way.png
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    dfcf0922f105edcd7676f0e1cadf26ccdcb7c05c Sat Mar 14 14:07:38 2020 -0700
    image for 44-way alignment refs #25090
• src/hg/htdocs/training/index.html
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    74757c3e4a3e30a4e208d55d552b8e8815f78d58 Wed Mar 11 12:35:00 2020 -0700
    marking tomorrow's ohsu worhshop as cancelled
• src/hg/inc/hui.h
  • lines changed 3, context: html, text, full: html, text
    17848d410ab4196fed212aba4d8f036769501205 Mon Feb 24 17:54:33 2020 -0800
    Change syntax of hideEmptySubtracks: add settings for multiBed and sources URLs. refs #23365
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    2bef4507d310c57d5462683dec8ad46b11f2a7e7 Tue Mar 3 15:16:55 2020 -0800
    Minor tweaks to compositeHideEmptySubtracks (new syntax). refs #23365
• src/hg/lib/hic.c
  • lines changed 4, context: html, text, full: html, text
    60079bc1898e003d9f1397176baaee00e431b011 Tue Mar 10 14:36:41 2020 -0700
    Changes to support better chr mappings in .hic files depended on a non-NULL assembly name, which was not previously assumed. Fixing what I broke, refs #24988
• src/hg/lib/hui.c
  • lines changed 29, context: html, text, full: html, text
    17848d410ab4196fed212aba4d8f036769501205 Mon Feb 24 17:54:33 2020 -0800
    Change syntax of hideEmptySubtracks: add settings for multiBed and sources URLs. refs #23365
  • lines changed 7, context: html, text, full: html, text
    2bef4507d310c57d5462683dec8ad46b11f2a7e7 Tue Mar 3 15:16:55 2020 -0800
    Minor tweaks to compositeHideEmptySubtracks (new syntax). refs #23365
  • lines changed 3, context: html, text, full: html, text
    00da38628aeeaaa58d2fff4202f7fd9107243d00 Sat Mar 14 13:54:48 2020 -0700
    tweak shorterDouble() to always use %.15g and call it in a few more places to get around %g's irritating practice of going into scientific notation too early.
• src/hg/lib/trackHub.c
  • lines changed 3, context: html, text, full: html, text
    17848d410ab4196fed212aba4d8f036769501205 Mon Feb 24 17:54:33 2020 -0800
    Change syntax of hideEmptySubtracks: add settings for multiBed and sources URLs. refs #23365
  • lines changed 1, context: html, text, full: html, text
    60079bc1898e003d9f1397176baaee00e431b011 Tue Mar 10 14:36:41 2020 -0700
    Changes to support better chr mappings in .hic files depended on a non-NULL assembly name, which was not previously assumed. Fixing what I broke, refs #24988
• src/hg/makeDb/doc/hg19.analysisSet.txt
  • lines changed 41, context: html, text, full: html, text
    cbe7391bbaffe17d27056884a9c33d0489e57f90 Mon Mar 9 11:39:29 2020 -0700
    adding hg19 analysis set, refs #25100
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    2ec22bc5fa605aebe9576301f7f238566d61e9e8 Tue Mar 10 04:00:22 2020 -0700
    adding indexed files for aligners, refs #25100
• src/hg/makeDb/doc/wuhCor1/multiz.txt
  • lines changed 1493, context: html, text, full: html, text
    80b709bb9a2d2cb227dd406dd6dd7e047b410bdd Mon Mar 9 23:20:41 2020 -0700
    first pass at a multiple alignment kinda like eboVir3 needs gene frames refs #25090
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    ef8d60a72021393316160d80c459dbe606ff25f3 Tue Mar 10 09:27:34 2020 -0700
    delete all the extra garbage beyond the last step performed refs #25090
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    3bdd6d28b65cfae5e9dd42bc65b56fe85368229f Tue Mar 10 13:49:39 2020 -0700
    add mafSnp display, add better coverage mafFrames table, tweak a few names in trackDb that were dashes instead of underbars
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    f7dff86f8009c87639bdc23592d9eacb16a23adb Fri Mar 13 15:43:37 2020 -0700
    done with 119 way alignment refs #25090
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    b499bd792a1d81575a926a2b907fdb5f34301afd Fri Mar 13 21:11:53 2020 -0700
    slight corrections found while running up the 44 way refs #25090
• src/hg/makeDb/doc/wuhCor1/multiz44.txt
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    5836c9c3fbf2aaa27fdc3e9f7fb65bcc7dc7c6d2 Fri Mar 13 21:10:47 2020 -0700
    adding 44-way alignment refs #25090
• src/hg/makeDb/doc/wuhCor1/nameList119.txt
  • lines changed 119, context: html, text, full: html, text
    fdd97f11b0aaa3ce471e18e2e996bfe096645183 Wed Mar 11 09:20:44 2020 -0700
    name correspondence list refs #25090
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    18c258cd4bfc1e391c89d8fa5e4e24d54fe83054 Thu Mar 12 14:24:21 2020 -0700
    fix the NMDC*-* names to be NMCD*_* refs #25090
• src/hg/makeDb/doc/wuhCor1/phastCons119way.txt
  • lines changed 358, context: html, text, full: html, text
    00e62e8a41d36887fdbbdb7519d54a3851fdaa57 Thu Mar 12 14:35:06 2020 -0700
    phastCons and phyloP track constructions refs #25090
• src/hg/makeDb/doc/wuhCor1/phastCons44way.txt
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    7366c05d85a7b46cb465a30b9eb60730e705a5e9 Fri Mar 13 21:35:17 2020 -0700
    phastCons and phyloP calculated for 44-way refs #25090
• src/hg/makeDb/doc/wuhCor1/snpView.44way.txt
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    5836c9c3fbf2aaa27fdc3e9f7fb65bcc7dc7c6d2 Fri Mar 13 21:10:47 2020 -0700
    adding 44-way alignment refs #25090
• src/hg/makeDb/doc/wuhCor1/snpView.txt
  • lines changed 48, context: html, text, full: html, text
    3bdd6d28b65cfae5e9dd42bc65b56fe85368229f Tue Mar 10 13:49:39 2020 -0700
    add mafSnp display, add better coverage mafFrames table, tweak a few names in trackDb that were dashes instead of underbars
• src/hg/makeDb/doc/wuhCor1/wuhCor1.119way.descriptiveName.nh
  • lines changed 119, context: html, text, full: html, text
    77bb82402f38ead533bd99c9848a9a911d302f4b Fri Mar 13 15:42:54 2020 -0700
    phylo trees used for downloads refs #25090
• src/hg/makeDb/doc/wuhCor1/wuhCor1.119way.nh
  • lines changed 119, context: html, text, full: html, text
    77bb82402f38ead533bd99c9848a9a911d302f4b Fri Mar 13 15:42:54 2020 -0700
    phylo trees used for downloads refs #25090
• src/hg/makeDb/trackDb/human/clinvar.html
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    f72322167bc143b5d6e9d6b81e6a0d0d0765b64c Wed Mar 11 01:56:00 2020 -0700
    adding note about mitochondrial genome on hg19, but commented out. QA should uncomment the note with the release of #24648. refs #24648
• src/hg/makeDb/trackDb/human/dbSnp153Composite.html
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    98f451794d0c9571ff8bd9433206041295ecfe2c Fri Mar 13 09:33:14 2020 -0700
    Expand the Data Access section to provide more details and examples for frequent MLQs. refs #25095
• src/hg/makeDb/trackDb/human/geneHancer.html
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    05466718bb09ec9ad8079aaf86a79dcfa81cf008 Fri Mar 13 11:35:47 2020 -0700
    clarified note about TB for geneHancer #25141
• src/hg/makeDb/trackDb/tagTypes.tab
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    17848d410ab4196fed212aba4d8f036769501205 Mon Feb 24 17:54:33 2020 -0800
    Change syntax of hideEmptySubtracks: add settings for multiBed and sources URLs. refs #23365
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    ad863edf952fc0609f53463a06e6a38d17c563b1 Mon Mar 9 23:21:53 2020 -0700
    initial view of 119-way alignment on wuhCor1 refs #25090
• src/hg/makeDb/trackDb/virus/wuhCor1/cons119way.html
  • lines changed 527, context: html, text, full: html, text
    b378ec33475f3fd10a4cc6667cf3cbf0989f04de Wed Mar 11 10:42:50 2020 -0700
    beginning description page refs #25090
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    f1a8ae4b8418c351bdc5d3ae8b8cae7dc2a90297 Wed Mar 11 15:12:58 2020 -0700
    table now has phylo distance and in that initial order refs #25090
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    f08f94b43b6fb0ba32688a4121476ee2fe0618b6 Wed Mar 11 16:14:56 2020 -0700
    correct outlinks for sequences not in genbank refs #25090
• src/hg/makeDb/trackDb/virus/wuhCor1/epitopes.html
  • lines changed 41, context: html, text, full: html, text
    62ff1f5ef09a7b6ed47597de0785df40bd2c699a Thu Mar 12 13:09:55 2020 -0700
    adding epitope date from Arkal Arjun Rao extracted from https://doi.org/10.1101/2020.02.12.946087 refs #25090
• src/hg/makeDb/trackDb/virus/wuhCor1/epitopes.ra
  • lines changed 38, context: html, text, full: html, text
    62ff1f5ef09a7b6ed47597de0785df40bd2c699a Thu Mar 12 13:09:55 2020 -0700
    adding epitope date from Arkal Arjun Rao extracted from https://doi.org/10.1101/2020.02.12.946087 refs #25090
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.119way.ra
  • lines changed 111, context: html, text, full: html, text
    ad863edf952fc0609f53463a06e6a38d17c563b1 Mon Mar 9 23:21:53 2020 -0700
    initial view of 119-way alignment on wuhCor1 refs #25090
  • lines changed 1, context: html, text, full: html, text
    3bdd6d28b65cfae5e9dd42bc65b56fe85368229f Tue Mar 10 13:49:39 2020 -0700
    add mafSnp display, add better coverage mafFrames table, tweak a few names in trackDb that were dashes instead of underbars
  • lines changed 4, context: html, text, full: html, text
    1451c6ef63b264a84ce40dc5085db67718d43a90 Tue Mar 10 14:59:55 2020 -0700
    correct species order and default off for all non SARS-CoV-2 refs #25090
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    b74f05e2e998de45ee84777a2661930b3c30a2e2 Wed Mar 11 16:16:14 2020 -0700
    order by calibrated phylo distance refs #25090
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    2981a383abe7b79b84d75f8a78ed7c83bb3938a4 Wed Mar 11 18:00:00 2020 -0700
    now with phastCons and phyloP refs #25090
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    8d510f50dd31bc24f96511c16fe75142eb8585c6 Sat Mar 14 09:05:46 2020 -0700
    now have a phylo image refs #25090
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    7c0e84c39639ef7cb9ae3d6b3e37a83735398032 Sat Mar 14 13:20:19 2020 -0700
    turn on 119-way by default. Change species order of outbreak strains to better reflect the SNPs
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.44way.ra
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    ff59ac0b712aadc6dc6d462cba18dbe628906cc7 Fri Mar 13 21:07:06 2020 -0700
    adding a 44-way conservation track refs #25090
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    9910dce6454426d225df14ccd99163c4061ab33a Sat Mar 14 14:17:56 2020 -0700
    correct viewLimits on phyloP track refs #25090
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
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    ad863edf952fc0609f53463a06e6a38d17c563b1 Mon Mar 9 23:21:53 2020 -0700
    initial view of 119-way alignment on wuhCor1 refs #25090
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    62ff1f5ef09a7b6ed47597de0785df40bd2c699a Thu Mar 12 13:09:55 2020 -0700
    adding epitope date from Arkal Arjun Rao extracted from https://doi.org/10.1101/2020.02.12.946087 refs #25090
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    37e77c100b8953e93eb776ebd69df2685fbfcadd Thu Mar 12 13:11:44 2020 -0700
    can not use labelFields on the ncbiGene genePred track refs #25090
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    ff59ac0b712aadc6dc6d462cba18dbe628906cc7 Fri Mar 13 21:07:06 2020 -0700
    adding a 44-way conservation track refs #25090
• src/hg/makeDb/trackDb/zebrafish/danRer10/trackDb.12way.ra
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    8c8cfb9ac4462733d42554c68b5338ea959569d5 Mon Mar 9 14:39:13 2020 -0700
    adding 12-way multiz no redmine
• src/hg/makeDb/trackDb/zebrafish/danRer10/trackDb.ra
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    8c8cfb9ac4462733d42554c68b5338ea959569d5 Mon Mar 9 14:39:13 2020 -0700
    adding 12-way multiz no redmine
• src/hg/utils/otto/clinvar/clinVarToBed
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    6149c6794aa3b64b8d2cecd3f3a948bfa7d0a5d8 Wed Mar 11 03:42:42 2020 -0700
    adapting clinvar colors for refs #25118, and tiny mouseover fix
• src/hg/utils/phyloTrees/binaryTree.pl
  • lines changed 12, context: html, text, full: html, text
    49eae9eda65782332874d75f644479b1a5b0b51b Fri Mar 13 09:45:24 2020 -0700
    add name quoting option refs #25090
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    e00236df7c5e59c822460caa58e662972af379cf Fri Mar 13 10:02:00 2020 -0700
    the quotes should be 'single' quotes refs #25090
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    2c221611ba1fe1da89314c8b9aad0bc9f5998e5c Fri Mar 13 11:28:26 2020 -0700
    add bothNames option to allow both names in output when translateName refs #25090
• src/lib/common.c
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    00da38628aeeaaa58d2fff4202f7fd9107243d00 Sat Mar 14 13:54:48 2020 -0700
    tweak shorterDouble() to always use %.15g and call it in a few more places to get around %g's irritating practice of going into scientific notation too early.
• src/product/installer/browserSetup.sh
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    499be1e252e75390ae5e00d39dff4829a35a294f Mon Mar 9 17:03:26 2020 -0700
    fix browserSetup.sh update to match the documentation. Allows user to specify a list of assemblies to update, or leave blank to update all assemblies. refs #rm25111.
• src/utils/bedFixBlockOverlaps
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    12b98c83c904de4e3e9d1d2f140781678936b90f Mon Mar 16 04:49:27 2020 -0700
    py3 changes for bedFixBlockOverlaps, no redmine
• src/utils/bedGraphToBigWig/bedGraphToBigWig.c
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    cf848a6f3c75bdb85e7030779e193fe837020566 Mon Mar 16 08:47:34 2020 -0700
    Add version numbers to wigToBig and bedGraphToBigWig, and increment the version number for bedToBigBed since we've made some changes without incrementing it. refs #25163
• src/utils/bedToBigBed/bedToBigBed.c
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    cf848a6f3c75bdb85e7030779e193fe837020566 Mon Mar 16 08:47:34 2020 -0700
    Add version numbers to wigToBig and bedGraphToBigWig, and increment the version number for bedToBigBed since we've made some changes without incrementing it. refs #25163
• src/utils/doClinvarLift
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    76607ba1c1c488b88d7121ce6e78c2cb5d0c59ca Tue Mar 10 02:51:37 2020 -0700
    changes after code review, refs #25105
• src/utils/qa/weeklybld/buildEnv.csh
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    43abd69ff8426442f018c1672dbe4999a1220fa4 Mon Mar 16 10:12:31 2020 -0700
    v396 preview1
• src/utils/wigToBigWig/wigToBigWig.c
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    cf848a6f3c75bdb85e7030779e193fe837020566 Mon Mar 16 08:47:34 2020 -0700
    Add version numbers to wigToBig and bedGraphToBigWig, and increment the version number for bedToBigBed since we've made some changes without incrementing it. refs #25163

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