All File Changes

v407_preview2 to v407_base (2020-11-09 to 2020-11-16) v407

• confs/asia.hg.conf
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    692b44c7d284208b990c232eccbcf2abb79d9b99 Sun Nov 15 01:12:03 2020 -0800
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 4, context: html, text, full: html, text
    692b44c7d284208b990c232eccbcf2abb79d9b99 Sun Nov 15 01:12:03 2020 -0800
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
  • lines changed 1, context: html, text, full: html, text
    692b44c7d284208b990c232eccbcf2abb79d9b99 Sun Nov 15 01:12:03 2020 -0800
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 4, context: html, text, full: html, text
    692b44c7d284208b990c232eccbcf2abb79d9b99 Sun Nov 15 01:12:03 2020 -0800
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 1, context: html, text, full: html, text
    692b44c7d284208b990c232eccbcf2abb79d9b99 Sun Nov 15 01:12:03 2020 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/hgPublicSessions/hgPublicSessions.c
  • lines changed 8, context: html, text, full: html, text
    326e2863f25a00c91baa95df5d7e31d7ece175db Tue Nov 10 13:44:13 2020 -0800
    Adding URL searchability to hgPublicSessions using parameter 'search=blah', refs #18470
  • lines changed 20, context: html, text, full: html, text
    302062e64efcf0d93b1955d4890e7456c5fdd524 Fri Nov 13 09:50:56 2020 -0800
    hgPublicSessions: Do not overwrite previous search if there is no 'search' variable on the URL, refs #18470
• src/hg/hgTracks/hgTracks.c
  • lines changed 5, context: html, text, full: html, text
    2e02e6d00e98c4b404bf4f0b4bfb164d9390f1f6 Tue Nov 10 09:14:09 2020 -0800
    now passing fontSize to js and sending number of data values for mouseOver mean detection refs #21980
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    a010673c4c37e6c0b6bca9b4d5e3dd1e4744321b Thu Nov 12 12:42:20 2020 -0800
    dealing with carts that have knownGene in them when a different default gene track is specified
• src/hg/hgTracks/hgTracks.h
  • lines changed 8, context: html, text, full: html, text
    d08fc8ebe4a3ce6b6ccf85d099c64cb8d6f6f157 Fri Nov 13 17:14:15 2020 -0800
    convert mouseOverData into a slList instead of a static array refs #26505
• src/hg/hgTracks/simpleTracks.c
  • lines changed 2, context: html, text, full: html, text
    2f18a71851ebd3dd7926c75e12f6a93f70551b55 Tue Nov 10 13:39:20 2020 -0800
    changes in response to code review
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    2b9d8d6fe4ad7a276ec8294c6f615a5c2ed2ca79 Thu Nov 12 02:07:14 2020 -0800
    adding accession and strand to exon mouseover, refs #24395
• src/hg/hgTracks/wigTrack.c
  • lines changed 8, context: html, text, full: html, text
    2e02e6d00e98c4b404bf4f0b4bfb164d9390f1f6 Tue Nov 10 09:14:09 2020 -0800
    now passing fontSize to js and sending number of data values for mouseOver mean detection refs #21980
  • lines changed 21, context: html, text, full: html, text
    61b8f9bb3cd7d2b67e8c698c9657efd6df58b309 Thu Nov 12 20:52:14 2020 -0800
    better isolation of the mouseOver calculations refs #21980
  • lines changed 76, context: html, text, full: html, text
    a13101d076e8cf07adf14c4196ecade8b076da30 Fri Nov 13 17:03:44 2020 -0800
    convert mouseOverData into a slList instead of a static array refs #26505
• src/hg/hgc/vcfClick.c
  • lines changed 21, context: html, text, full: html, text
    5cdeda3ceacbf093b325e8ebd48e17c4ac03e6c6 Thu Nov 12 16:29:01 2020 -0800
    Quality of life improvements on VCF details page, put the info tag annotations in a collapsible table, and add a border to said table so it's easier to distinguish between different tags. Also fix a bug in INFO tabular tables where the trailing separator was causing extra table cells to print, refs #26451
• src/hg/htdocs/covid19.html
  • lines changed 49, context: html, text, full: html, text
    f75874a85e09a19a652ca8c06cd72be5fba5482f Thu Nov 12 08:59:08 2020 -0800
    Added section about hgPhyloPlace/UShER to CoViD-19 landing page. refs #26516
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    7bceb48e55a1c1f686fcb379c808a8fb5a06728e Fri Nov 13 11:21:01 2020 -0800
    Changing the date to today's date for the 'last updated' section, refs #26516
• src/hg/htdocs/goldenPath/help/bigLolly.html
  • lines changed 12, context: html, text, full: html, text
    778a63012afa9e04bd7afb17fd291f569016b20e Wed Nov 4 17:12:01 2020 -0800
    tweaks to bigLolly documentation
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 76, context: html, text, full: html, text
    39e3bc63e290466ec4484ccc5fb36ab94a15b232 Mon Nov 9 11:35:58 2020 -0800
    Readability edits and removing redundancy #26462
  • lines changed 1, context: html, text, full: html, text
    971e4bd169dab5e88878f0b7921f598c67cf0fec Mon Nov 9 11:51:14 2020 -0800
    Typo fix refs #26462
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    04910adfb418b9ad6e9c27c13de57a4c01ee9211 Mon Nov 9 12:04:33 2020 -0800
    Typo fixes and clarity improve refs #26462
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 8, context: html, text, full: html, text
    2b9d8d6fe4ad7a276ec8294c6f615a5c2ed2ca79 Thu Nov 12 02:07:14 2020 -0800
    adding accession and strand to exon mouseover, refs #24395
• src/hg/htdocs/images/covid19/UShER_example.png
  • lines changed 0, context: html, text, full: html, text
    f75874a85e09a19a652ca8c06cd72be5fba5482f Thu Nov 12 08:59:08 2020 -0800
    Added section about hgPhyloPlace/UShER to CoViD-19 landing page. refs #26516
• src/hg/htdocs/images/covid19/usher_logo.png
  • lines changed 0, context: html, text, full: html, text
    f75874a85e09a19a652ca8c06cd72be5fba5482f Thu Nov 12 08:59:08 2020 -0800
    Added section about hgPhyloPlace/UShER to CoViD-19 landing page. refs #26516
• src/hg/htdocs/style/mouseOver.css
  • lines changed 1, context: html, text, full: html, text
    cf4e6ee0203b3d9f463b43562ca21a20937c115f Tue Nov 10 09:21:36 2020 -0800
    text align right to keep the window from bouncing around refs #21980
• src/hg/htdocs/training/index.html
  • lines changed 10, context: html, text, full: html, text
    f8640e562a336ecb2ac88f7b71a9714c66bb96f3 Mon Nov 9 10:48:39 2020 -0800
    dropping ashg virt meeting and adding OHSU virt meeting
  • lines changed 1, context: html, text, full: html, text
    ff8135f868a74ef85bbe245400adf774e3b57b5c Mon Nov 9 12:18:15 2020 -0800
    fixing ref to hsgc meeting. not in nashville
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    42c276ca22c56f4afc32294df7ef280ad4620f79 Mon Nov 16 10:04:39 2020 -0800
    New version number v407
• src/hg/js/hgTracks.js
  • lines changed 56, context: html, text, full: html, text
    7ee3f386e0a4d9489d284ded95d19ba951468e7d Tue Nov 10 09:18:15 2020 -0800
    now using fontSize from browser for message box and number of data values for mouseOver mean detection refs and working in reverse display mode #21980
  • lines changed 1, context: html, text, full: html, text
    a8729cf45b0f11e737f376c2c1baf61b9cb2cf50 Tue Nov 10 09:27:37 2020 -0800
    correct font size when computing maximumWidth refs #21980
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    5dc51439a861d1cf4e7f6946c7b6317be3ef03b5 Wed Nov 11 22:41:17 2020 -0800
    replace word mean with greek letter mu, much less space used refs #21980
  • lines changed 8, context: html, text, full: html, text
    49e91a5cadcd320b71d118e30ee2544f66da60d5 Fri Nov 13 10:59:27 2020 -0800
    trackDb does not seem to exist for every track name refs #21980
  • lines changed 18, context: html, text, full: html, text
    9b0b0bcba6332c559c8834d1b34c386b9692e485 Mon Nov 16 08:25:02 2020 -0800
    avoid wigMaf track types and composite tracks with children (overlayed wiggles) refs #21980
• src/hg/lib/gencodeBGP.as
  • lines changed 1, context: html, text, full: html, text
    bd5fe2550051753ba1945e13dd51854f2ae85144 Sat Nov 14 10:32:18 2020 -0800
    fix up some text for Mark
• src/hg/lib/hAnno.c
  • lines changed 1, context: html, text, full: html, text
    f40b6f8e5a763bffbf364d8e64bcf252f8aef27d Mon Nov 9 13:20:57 2020 -0800
    Add vcfPhasedTrio to supported hgIntegrator track types, refs #25873
• src/hg/lib/hdb.c
  • lines changed 3, context: html, text, full: html, text
    a010673c4c37e6c0b6bca9b4d5e3dd1e4744321b Thu Nov 12 12:42:20 2020 -0800
    dealing with carts that have knownGene in them when a different default gene track is specified
  • lines changed 3, context: html, text, full: html, text
    94d982ed8d81d8446b0497a6b38549398ffcfa47 Fri Nov 13 13:09:38 2020 -0800
    don't let default known gene searching break on track hubs
• src/hg/lib/hui.c
  • lines changed 3, context: html, text, full: html, text
    e355230ded4734b4640081ae2d0fd5247ceea25c Fri Nov 13 06:36:05 2020 -0800
    tiny change to data last updated text to make the difference between source database and UCSC data updates clearer, refs #23580
• src/hg/lib/tests/expected/hgvs/validTerms.txt
  • lines changed 2, context: html, text, full: html, text
    d6620ab7a89bf7c2779d5bebe836fe7850ca832a Wed Nov 11 14:43:06 2020 -0800
    Updating RefSeq accession version.
• src/hg/lib/tests/input/hgvs/validTerms.txt
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    d6620ab7a89bf7c2779d5bebe836fe7850ca832a Wed Nov 11 14:43:06 2020 -0800
    Updating RefSeq accession version.
• src/hg/makeDb/doc/hg19.gencode.txt
  • lines changed 31, context: html, text, full: html, text
    3421b6247b80f8884055fd32df67c09a6f4e9ac5 Thu Nov 12 17:11:19 2020 -0800
    import of gencode V35lift37
• src/hg/makeDb/doc/wuhCor1/pbm.txt
  • lines changed 8, context: html, text, full: html, text
    2b9d8d6fe4ad7a276ec8294c6f615a5c2ed2ca79 Thu Nov 12 02:07:14 2020 -0800
    adding accession and strand to exon mouseover, refs #24395
  • lines changed 1, context: html, text, full: html, text
    17d742023c599268d6b252879b3b939e163be539 Fri Nov 13 05:45:17 2020 -0800
    docs and makedoc page for the wuhCor1 pbm (beijing) track, refs #26518
• src/hg/makeDb/outside/gencode/bin/gencodeGenerateTrackDbsOldSchema
  • lines changed 703, context: html, text, full: html, text
    3421b6247b80f8884055fd32df67c09a6f4e9ac5 Thu Nov 12 17:11:19 2020 -0800
    import of gencode V35lift37
• src/hg/makeDb/outside/gencode/gencodeHgGene2Load.mk
  • lines changed 6, context: html, text, full: html, text
    c81057f76640a4fc61ed998801e1597421312205 Thu Nov 12 14:22:12 2020 -0800
    update for standard kent tree location and VM25 gencode
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 1, context: html, text, full: html, text
    3421b6247b80f8884055fd32df67c09a6f4e9ac5 Thu Nov 12 17:11:19 2020 -0800
    import of gencode V35lift37
• src/hg/makeDb/schema/all.joiner
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    3421b6247b80f8884055fd32df67c09a6f4e9ac5 Thu Nov 12 17:11:19 2020 -0800
    import of gencode V35lift37
• src/hg/makeDb/trackDb/human/covidHgiGwas.ra
  • lines changed 1, context: html, text, full: html, text
    1cc7074f2d1b95838058636db75560afad9abc02 Thu Nov 12 15:42:03 2020 -0800
    Making changes to release COVID Risk var track #26351
• src/hg/makeDb/trackDb/human/covidMuts.html
  • lines changed 18, context: html, text, full: html, text
    0c85ef2a7ae60b49c2ce4f3175a9f3a54cda412f Mon Nov 9 13:56:11 2020 -0800
    Restore lost Description section, and remove section about multi-region. refs #26351
  • lines changed 24, context: html, text, full: html, text
    622e9ba577122e4b2c61504ca2f92a2f75d93c8e Tue Nov 10 16:14:24 2020 -0800
    Polishing description and methods sections of track description, with Ana. refs 326351
  • lines changed 16, context: html, text, full: html, text
    1cc7074f2d1b95838058636db75560afad9abc02 Thu Nov 12 15:42:03 2020 -0800
    Making changes to release COVID Risk var track #26351
• src/hg/makeDb/trackDb/human/hg15/trackDb.ra
  • lines changed 14, context: html, text, full: html, text
    9d644b359a9a38b90ec8845bbabbe24171cea274 Fri Nov 13 13:30:27 2020 -0800
    move "track knownGene" down to lower levels so hg38 can get by without having one even though the table exists
• src/hg/makeDb/trackDb/human/hg16/trackDb.ra
  • lines changed 12, context: html, text, full: html, text
    9d644b359a9a38b90ec8845bbabbe24171cea274 Fri Nov 13 13:30:27 2020 -0800
    move "track knownGene" down to lower levels so hg38 can get by without having one even though the table exists
• src/hg/makeDb/trackDb/human/hg17/trackDb.ra
  • lines changed 13, context: html, text, full: html, text
    9d644b359a9a38b90ec8845bbabbe24171cea274 Fri Nov 13 13:30:27 2020 -0800
    move "track knownGene" down to lower levels so hg38 can get by without having one even though the table exists
• src/hg/makeDb/trackDb/human/hg18/defaultPriority.ra
  • lines changed 4, context: html, text, full: html, text
    9d644b359a9a38b90ec8845bbabbe24171cea274 Fri Nov 13 13:30:27 2020 -0800
    move "track knownGene" down to lower levels so hg38 can get by without having one even though the table exists
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 18, context: html, text, full: html, text
    9d644b359a9a38b90ec8845bbabbe24171cea274 Fri Nov 13 13:30:27 2020 -0800
    move "track knownGene" down to lower levels so hg38 can get by without having one even though the table exists
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
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    488f5657d433c5446eba5d2b54f2812fea64fb3d Mon Nov 9 12:59:48 2020 -0800
    Removing gene filter from gnomAD variants track, refs #25010
• src/hg/makeDb/trackDb/human/hg38/mane.alpha.ra
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    c43a457205b7a475c8fe94c05770459b43a5ba8d Fri Nov 13 16:49:52 2020 -0800
    Releasing MANE update v.92 refs #26431
• src/hg/makeDb/trackDb/human/hg38/mane.html
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    d49a342b60814e4477d190972bff2823babc08e4 Tue Nov 10 15:31:29 2020 -0800
    Staging new MANE update on beta, and updating desc page refs #26431
• src/hg/makeDb/trackDb/human/hg38/mane.ra
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    c43a457205b7a475c8fe94c05770459b43a5ba8d Fri Nov 13 16:49:52 2020 -0800
    Releasing MANE update v.92 refs #26431
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    d49a342b60814e4477d190972bff2823babc08e4 Tue Nov 10 15:31:29 2020 -0800
    Staging new MANE update on beta, and updating desc page refs #26431
  • lines changed 2, context: html, text, full: html, text
    c43a457205b7a475c8fe94c05770459b43a5ba8d Fri Nov 13 16:49:52 2020 -0800
    Releasing MANE update v.92 refs #26431
• src/hg/makeDb/trackDb/human/trackDb.giab.ra
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    a92af473a83fd7ad2e01a581bfa859f1ded38462 Fri Nov 13 16:56:13 2020 -0800
    Adding visibility modes to the Genome in a Bottle views. Removing the 'visibility dense' lines since they are no longer needed in the children stanzas. refs #25873 and #24349
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    f3d4d8ef473ad5cb94357238a852b9ab99ebc189 Mon Nov 16 09:00:32 2020 -0800
    Changing the phased trio display for the Genome in a Bottle tracks to 'dense', refs #25873
• src/hg/makeDb/trackDb/human/trackDb.ra
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    cfe0eb35238d071ab6b9d32991b503a59c69c2d3 Tue Nov 10 16:14:50 2020 -0800
    Another take on track labels. refs #26351
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    1177b2afac8a65abd25600a8c4b060df888d73d2 Thu Nov 12 09:08:21 2020 -0800
    Another round on short label, input from Max and Ana. refs #26351
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    1cc7074f2d1b95838058636db75560afad9abc02 Thu Nov 12 15:42:03 2020 -0800
    Making changes to release COVID Risk var track #26351
  • lines changed 1, context: html, text, full: html, text
    6bea88e58628a47d2a2e059fd8afb1807e1f0355 Fri Nov 13 15:57:06 2020 -0800
    Staging the Genome in a Bottle tracks on hgwbeta for hg19 and hg38, refs #25873 and #24349
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    d6773312dae58699ac4712a47bb779269702b418 Mon Nov 16 07:05:06 2020 -0800
    fixing genomenom outlinks after email from their QA, refs #24157
• src/hg/makeDb/trackDb/mouse/trackDb.ra
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    9d644b359a9a38b90ec8845bbabbe24171cea274 Fri Nov 13 13:30:27 2020 -0800
    move "track knownGene" down to lower levels so hg38 can get by without having one even though the table exists
• src/hg/makeDb/trackDb/rat/trackDb.ra
  • lines changed 16, context: html, text, full: html, text
    9d644b359a9a38b90ec8845bbabbe24171cea274 Fri Nov 13 13:30:27 2020 -0800
    move "track knownGene" down to lower levels so hg38 can get by without having one even though the table exists
• src/hg/makeDb/trackDb/trackDb.ra
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    9d644b359a9a38b90ec8845bbabbe24171cea274 Fri Nov 13 13:30:27 2020 -0800
    move "track knownGene" down to lower levels so hg38 can get by without having one even though the table exists
• src/hg/makeDb/trackDb/virus/wuhCor1/iedb.html
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    a17e844df57237d5f44b8e758c6398ae1f7bf672 Fri Nov 13 07:02:19 2020 -0800
    updating iedb docs page a little after email from DavidH
• src/hg/makeDb/trackDb/virus/wuhCor1/pbm.html
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    17d742023c599268d6b252879b3b939e163be539 Fri Nov 13 05:45:17 2020 -0800
    docs and makedoc page for the wuhCor1 pbm (beijing) track, refs #26518
• src/hg/makeDb/trackDb/virus/wuhCor1/pbm.ra
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    bb65599525224d7282e55ab293d7ffa4db83fecb Mon Nov 9 11:02:28 2020 -0800
    adding protein antibody array for wuhCor1, no redmine yet but coming
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    80ecb6e9bc4a0b6248b2c2ddfa6fff38c0985e6a Thu Nov 12 08:52:11 2020 -0800
    adding protein microarray (beijing) track for wuhCor1, refs #26518
• src/hg/makeDb/trackDb/virus/wuhCor1/pbmIggCovid.ra
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    bb65599525224d7282e55ab293d7ffa4db83fecb Mon Nov 9 11:02:28 2020 -0800
    adding protein antibody array for wuhCor1, no redmine yet but coming
• src/hg/makeDb/trackDb/virus/wuhCor1/pbmIggHealthy.ra
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    bb65599525224d7282e55ab293d7ffa4db83fecb Mon Nov 9 11:02:28 2020 -0800
    adding protein antibody array for wuhCor1, no redmine yet but coming
• src/hg/makeDb/trackDb/virus/wuhCor1/pbmIgmCovid.ra
  • lines changed 79, context: html, text, full: html, text
    bb65599525224d7282e55ab293d7ffa4db83fecb Mon Nov 9 11:02:28 2020 -0800
    adding protein antibody array for wuhCor1, no redmine yet but coming
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    80ecb6e9bc4a0b6248b2c2ddfa6fff38c0985e6a Thu Nov 12 08:52:11 2020 -0800
    adding protein microarray (beijing) track for wuhCor1, refs #26518
• src/hg/makeDb/trackDb/virus/wuhCor1/pbmIgmHealthy.ra
  • lines changed 93, context: html, text, full: html, text
    bb65599525224d7282e55ab293d7ffa4db83fecb Mon Nov 9 11:02:28 2020 -0800
    adding protein antibody array for wuhCor1, no redmine yet but coming
  • lines changed 1, context: html, text, full: html, text
    80ecb6e9bc4a0b6248b2c2ddfa6fff38c0985e6a Thu Nov 12 08:52:11 2020 -0800
    adding protein microarray (beijing) track for wuhCor1, refs #26518
• src/hg/makeDb/trackDb/virus/wuhCor1/pyle.html
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    159c15c4786bf1550ee8249ba9984018fc767e45 Thu Nov 12 08:21:57 2020 -0800
    making change to pyle data, refs #26466
• src/hg/makeDb/trackDb/virus/wuhCor1/pyle.ra
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    159c15c4786bf1550ee8249ba9984018fc767e45 Thu Nov 12 08:21:57 2020 -0800
    making change to pyle data, refs #26466
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.uniprot.ra
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    aeca0c31ca5a7ab6f8cbdf6def6ca9092dc98f93 Fri Nov 13 06:44:14 2020 -0800
    forgot to remove the April 2020 comment in uniprot proteins. Also now showing by default, but only in dense, the UniProt full length proteins, after I forgot myself two times now to activate this track. The S protein start position is not the one shown on our chains track, because the active S protein has cleaved from the pre-protein, which is easy to forget on the genome browser, if the full proteins are not shown. No redmine, as this is a one-word change in trackDb.
• src/hg/makeDb/trackDb/virus/wuhCor1/unipCov2AliSwissprot.html
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    aeca0c31ca5a7ab6f8cbdf6def6ca9092dc98f93 Fri Nov 13 06:44:14 2020 -0800
    forgot to remove the April 2020 comment in uniprot proteins. Also now showing by default, but only in dense, the UniProt full length proteins, after I forgot myself two times now to activate this track. The S protein start position is not the one shown on our chains track, because the active S protein has cleaved from the pre-protein, which is easy to forget on the genome browser, if the full proteins are not shown. No redmine, as this is a one-word change in trackDb.
• src/hg/utils/hgvsToVcf/tests/expected/clinVarChanges.vcf
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    d6620ab7a89bf7c2779d5bebe836fe7850ca832a Wed Nov 11 14:43:06 2020 -0800
    Updating RefSeq accession version.
• src/hg/utils/hgvsToVcf/tests/input/clinVarChanges.txt
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    d6620ab7a89bf7c2779d5bebe836fe7850ca832a Wed Nov 11 14:43:06 2020 -0800
    Updating RefSeq accession version.
• src/hg/utils/hubCheck/hubCheck.c
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    702afb4c46543f3a415c0e31e3671f85b78e22ba Mon Nov 9 12:37:34 2020 -0800
    hubCheck for assembly hubs now warns when twoBitPath, htmlPath and descriptionUrl are missing or are malformed, refs #26459
• src/hg/utils/hubCheck/tests/expected/genomesConfigErrors.output.txt
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    702afb4c46543f3a415c0e31e3671f85b78e22ba Mon Nov 9 12:37:34 2020 -0800
    hubCheck for assembly hubs now warns when twoBitPath, htmlPath and descriptionUrl are missing or are malformed, refs #26459
• src/hg/utils/hubCheck/tests/expected/supertrackChild.txt
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    702afb4c46543f3a415c0e31e3671f85b78e22ba Mon Nov 9 12:37:34 2020 -0800
    hubCheck for assembly hubs now warns when twoBitPath, htmlPath and descriptionUrl are missing or are malformed, refs #26459
• src/hg/utils/hubCheck/tests/input/genomesConfigErrorsHub.txt
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    702afb4c46543f3a415c0e31e3671f85b78e22ba Mon Nov 9 12:37:34 2020 -0800
    hubCheck for assembly hubs now warns when twoBitPath, htmlPath and descriptionUrl are missing or are malformed, refs #26459
• src/hg/utils/hubCheck/tests/input/misconfigGenomes.txt
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    702afb4c46543f3a415c0e31e3671f85b78e22ba Mon Nov 9 12:37:34 2020 -0800
    hubCheck for assembly hubs now warns when twoBitPath, htmlPath and descriptionUrl are missing or are malformed, refs #26459
• src/hg/utils/hubCheck/tests/input/noErrors.araTha1.trackDb.txt
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    702afb4c46543f3a415c0e31e3671f85b78e22ba Mon Nov 9 12:37:34 2020 -0800
    hubCheck for assembly hubs now warns when twoBitPath, htmlPath and descriptionUrl are missing or are malformed, refs #26459
• src/hg/utils/hubCheck/tests/makefile
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    702afb4c46543f3a415c0e31e3671f85b78e22ba Mon Nov 9 12:37:34 2020 -0800
    hubCheck for assembly hubs now warns when twoBitPath, htmlPath and descriptionUrl are missing or are malformed, refs #26459
• src/hg/utils/otto/dbVar/giabSv.as
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    4543dba7eee24c7463b60ae9fb5e5f6ac78a95ad Fri Nov 13 10:23:19 2020 -0800
    Forgot to commit updated autoSql for genome in a bottle sv track, refs #24349
• src/hg/utils/otto/dbVar/processNstd175.py
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    5afa332cc12c75f441ffaf7fa2d9a219ec1f219b Fri Nov 13 10:22:20 2020 -0800
    Remove the superfluous fields 'Reference Seq' and 'Variant Seq' from the genome in a bottle sv track, refs #24349
• src/hg/utils/vcfToBed/vcfToBed.c
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    e2863d01dfb07e37992f4130c8cccb699370a398 Thu Nov 12 09:46:29 2020 -0800
    Fix boneheaded startsWith() mistake in vcfToBed
• src/hg/utils/vcfToHgvs/tests/expected/stopLoss.tab
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    d6620ab7a89bf7c2779d5bebe836fe7850ca832a Wed Nov 11 14:43:06 2020 -0800
    Updating RefSeq accession version.
• src/inc/srcVersion.h
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    42c276ca22c56f4afc32294df7ef280ad4620f79 Mon Nov 16 10:04:39 2020 -0800
    New version number v407
• src/utils/chromToUcsc/chromToUcsc
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    a5b8dc9064dc31482e96b5a1f4e4ce6a2cd8523a Mon Nov 16 05:08:43 2020 -0800
    allowing wiggle files in chromToUcsc, no redmine, came up when trying to process a lemur single cell dataset
• src/utils/chromToUcsc/makefile
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    43dd678817261131b81c42a160112c05cdc49032 Mon Nov 16 05:17:42 2020 -0800
    tiny fix to chromToUcsc makefile: changing times is not permitted in /cluster/bin/x86_64/chromToUcsc, no redmine
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    4650a06fc393355729d0f8c5ed74d4b81dd814f9 Mon Nov 16 07:53:20 2020 -0800
    adding back the -p to makefile, after feedback from Braney, no redmine
• src/utils/chromToUcsc/tests/expected/hg19.bed
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    a5b8dc9064dc31482e96b5a1f4e4ce6a2cd8523a Mon Nov 16 05:08:43 2020 -0800
    allowing wiggle files in chromToUcsc, no redmine, came up when trying to process a lemur single cell dataset
• src/utils/chromToUcsc/tests/in/hg19.bed
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    a5b8dc9064dc31482e96b5a1f4e4ce6a2cd8523a Mon Nov 16 05:08:43 2020 -0800
    allowing wiggle files in chromToUcsc, no redmine, came up when trying to process a lemur single cell dataset
• src/utils/makefile
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    8423ff7c26baa30c51e490ded78c8d97a197076a Wed Nov 11 10:16:01 2020 -0800
    Adding vcfFilter to top-level build, but not as a public util at this time because it assumes monoploid genotypes.
• src/utils/qa/weeklybld/buildEnv.csh
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    76403c1cb07f197f9dbd5d8948cead8d7c1911a7 Mon Nov 16 10:01:41 2020 -0800
    v407 final build
• src/utils/vcfFilter/makefile
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    f501def66bb2db196a4ada2a7eff65d03af33171 Wed Nov 11 10:12:45 2020 -0800
    New util vcfFilter for SARS-CoV-2 work; expects monoploid genotypes, would need extension for diploid.
• src/utils/vcfFilter/tests/expected/testMinAc1Gt.vcf
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    f501def66bb2db196a4ada2a7eff65d03af33171 Wed Nov 11 10:12:45 2020 -0800
    New util vcfFilter for SARS-CoV-2 work; expects monoploid genotypes, would need extension for diploid.
• src/utils/vcfFilter/tests/expected/testMinAc1GtExclude.vcf
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    f501def66bb2db196a4ada2a7eff65d03af33171 Wed Nov 11 10:12:45 2020 -0800
    New util vcfFilter for SARS-CoV-2 work; expects monoploid genotypes, would need extension for diploid.
• src/utils/vcfFilter/tests/expected/testMinAc1NoGt.vcf
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    f501def66bb2db196a4ada2a7eff65d03af33171 Wed Nov 11 10:12:45 2020 -0800
    New util vcfFilter for SARS-CoV-2 work; expects monoploid genotypes, would need extension for diploid.
• src/utils/vcfFilter/tests/expected/testMinAc2RenameGt.vcf
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    f501def66bb2db196a4ada2a7eff65d03af33171 Wed Nov 11 10:12:45 2020 -0800
    New util vcfFilter for SARS-CoV-2 work; expects monoploid genotypes, would need extension for diploid.
• src/utils/vcfFilter/tests/expected/testRenameGt.vcf
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    f501def66bb2db196a4ada2a7eff65d03af33171 Wed Nov 11 10:12:45 2020 -0800
    New util vcfFilter for SARS-CoV-2 work; expects monoploid genotypes, would need extension for diploid.
• src/utils/vcfFilter/tests/expected/testRenameNoGt.vcf
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    f501def66bb2db196a4ada2a7eff65d03af33171 Wed Nov 11 10:12:45 2020 -0800
    New util vcfFilter for SARS-CoV-2 work; expects monoploid genotypes, would need extension for diploid.
• src/utils/vcfFilter/tests/input/exclude.vcf
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    f501def66bb2db196a4ada2a7eff65d03af33171 Wed Nov 11 10:12:45 2020 -0800
    New util vcfFilter for SARS-CoV-2 work; expects monoploid genotypes, would need extension for diploid.
• src/utils/vcfFilter/tests/input/subset.vcf
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    f501def66bb2db196a4ada2a7eff65d03af33171 Wed Nov 11 10:12:45 2020 -0800
    New util vcfFilter for SARS-CoV-2 work; expects monoploid genotypes, would need extension for diploid.
• src/utils/vcfFilter/tests/makefile
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    f501def66bb2db196a4ada2a7eff65d03af33171 Wed Nov 11 10:12:45 2020 -0800
    New util vcfFilter for SARS-CoV-2 work; expects monoploid genotypes, would need extension for diploid.
• src/utils/vcfFilter/vcfFilter.c
  • lines changed 376, context: html, text, full: html, text
    f501def66bb2db196a4ada2a7eff65d03af33171 Wed Nov 11 10:12:45 2020 -0800
    New util vcfFilter for SARS-CoV-2 work; expects monoploid genotypes, would need extension for diploid.

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• files changed: 119