All File Changes

v397_preview to v397_preview2 (2020-04-06 to 2020-04-13) v397

• confs/hgwbeta.hg.conf
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    3f16d08f8e643af1ad6a16021eb337fe4d457768 Sun Apr 12 01:11:34 2020 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/gateway/htdocs/cirmIndex.html
  • lines changed 49, context: html, text, full: html, text
    f60e3c01c53288fdc54d9a4c696b4dddbed24748 Tue Apr 7 15:36:22 2020 -0700
    icon are now all one clickable link
• src/hg/hgTracks/barChartTrack.c
  • lines changed 16, context: html, text, full: html, text
    7d70cdf40567dbcfd3a190c844d99046aced5637 Thu Apr 9 13:58:39 2020 -0700
    Add settings to define window sizes for small/medium/large graphs. Useful for small (e.g. virus) genomes. Prompted by Max barCharts on wuhCor1. refs #25339
• src/hg/hgTracks/hgTracks.c
  • lines changed 6, context: html, text, full: html, text
    3035fe4b8c8e8ac74f12417dd350e25f11290dd4 Sun Apr 12 09:42:43 2020 -0700
    support RNA genomes by repurposing hgPbOk in dbDb to specify whether the database is an RNA genome #25350
• src/hg/hgTracks/hgTracks.h
  • lines changed 3, context: html, text, full: html, text
    3035fe4b8c8e8ac74f12417dd350e25f11290dd4 Sun Apr 12 09:42:43 2020 -0700
    support RNA genomes by repurposing hgPbOk in dbDb to specify whether the database is an RNA genome #25350
• src/hg/hgTracks/imageV2.c
  • lines changed 2, context: html, text, full: html, text
    9d1737001e59efe00fa76072027ea50aff9e3fd2 Tue Apr 7 08:30:25 2020 -0700
    product function from null input
• src/hg/hgTracks/searchTracks.c
  • lines changed 3, context: html, text, full: html, text
    7b847e0c7367b7ad20e602eba314125cef27fe89 Thu Apr 9 14:29:48 2020 -0700
    put out a more useful error message when a user tries to use track search on an assembly hub
• src/hg/hgTracks/wigMafTrack.c
  • lines changed 2, context: html, text, full: html, text
    3035fe4b8c8e8ac74f12417dd350e25f11290dd4 Sun Apr 12 09:42:43 2020 -0700
    support RNA genomes by repurposing hgPbOk in dbDb to specify whether the database is an RNA genome #25350
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 58, context: html, text, full: html, text
    ef6f0f9b64982b66ad965ecc0010f36b7dfc91d8 Thu Apr 9 09:39:13 2020 -0700
    Adding 2020 publications with grant reference 5U41-HG002371
  • lines changed 33, context: html, text, full: html, text
    517037d52c60d325c4e28a4b60e0f3a50327b033 Thu Apr 9 09:54:28 2020 -0700
    Moving the 2019 pubs into the right place
• src/hg/htdocs/images/new.jpg
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    e43a27f20360771debc033e0d4fe82027018fd88 Mon Apr 6 17:26:15 2020 -0700
    adding thanks to ucsc team in credits
• src/hg/htdocs/inc/gbsFooter.html
  • lines changed 1, context: html, text, full: html, text
    7943d92ab6110c0fd3b416b4f01c966f741412c1 Wed Apr 8 09:01:27 2020 -0700
    add google analytics to some of the static pages refs #23969
• src/hg/htdocs/index.html
  • lines changed 1, context: html, text, full: html, text
    5afb7c00df05d61e1cbe878788d695f105ac8fc4 Thu Apr 9 09:51:11 2020 -0700
    adding analytics to home page refs #23969
• src/hg/inc/barChartUi.h
  • lines changed 2, context: html, text, full: html, text
    7d70cdf40567dbcfd3a190c844d99046aced5637 Thu Apr 9 13:58:39 2020 -0700
    Add settings to define window sizes for small/medium/large graphs. Useful for small (e.g. virus) genomes. Prompted by Max barCharts on wuhCor1. refs #25339
• src/hg/inc/hdb.h
  • lines changed 4, context: html, text, full: html, text
    3035fe4b8c8e8ac74f12417dd350e25f11290dd4 Sun Apr 12 09:42:43 2020 -0700
    support RNA genomes by repurposing hgPbOk in dbDb to specify whether the database is an RNA genome #25350
• src/hg/js/analytics.js
  • lines changed 45, context: html, text, full: html, text
    7943d92ab6110c0fd3b416b4f01c966f741412c1 Wed Apr 8 09:01:27 2020 -0700
    add google analytics to some of the static pages refs #23969
  • lines changed 1, context: html, text, full: html, text
    39944c1c9464a8116f26f301186218f516e80a23 Thu Apr 9 09:04:24 2020 -0700
    the default should be the gBiB i.e. anything but UCSC browsers refs #23969
• src/hg/lib/hdb.c
  • lines changed 9, context: html, text, full: html, text
    cc25d2f93765ed4a50551dda4e4db9bdff953df5 Mon Apr 6 15:46:45 2020 -0700
    simplification in response to code review #25308
  • lines changed 14, context: html, text, full: html, text
    3035fe4b8c8e8ac74f12417dd350e25f11290dd4 Sun Apr 12 09:42:43 2020 -0700
    support RNA genomes by repurposing hgPbOk in dbDb to specify whether the database is an RNA genome #25350
• src/hg/makeDb/doc/canFam3.txt
  • lines changed 18, context: html, text, full: html, text
    23ecb79c604a5e4981c3ff30bb26250104356b77 Thu Apr 9 15:24:20 2020 -0700
    liftOver to canFam4 refs #25279
• src/hg/makeDb/doc/wuhCor1/kim2020.txt
  • lines changed 9, context: html, text, full: html, text
    52ec50ee3467f26759aab70724d1e95b89150dc0 Thu Apr 9 06:54:22 2020 -0700
    adding Kim2020 tracks, refs #25332
• src/hg/makeDb/doc/wuhCor1/primers.txt
  • lines changed 9, context: html, text, full: html, text
    bc96e96e131b7402ca47636a4d558afe70f891b7 Thu Apr 9 07:54:36 2020 -0700
    adding makedoc for primers track, refs #25189
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    9409adc4fa106acfcbef704329fdf125897e576b Thu Apr 9 15:08:22 2020 -0700
    Added canFam4 - dog refs #25279
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 18, context: html, text, full: html, text
    1e338f677bcafb6379c56fcb592c8719102f83e5 Thu Apr 9 15:07:17 2020 -0700
    Added canFam4 dog; refs #25279
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 2, context: html, text, full: html, text
    9409adc4fa106acfcbef704329fdf125897e576b Thu Apr 9 15:08:22 2020 -0700
    Added canFam4 - dog refs #25279
• src/hg/makeDb/trackDb/human/chainNetPlacental.ra
  • lines changed 19, context: html, text, full: html, text
    744eb91b7ac3b786d58b9dad166ce47d6d12273a Fri Apr 10 11:30:52 2020 -0700
    adding canFam4 chainNet definitions refs #25279
• src/hg/makeDb/trackDb/human/hg19/defaultPriority.ra
  • lines changed 1, context: html, text, full: html, text
    75fa39c5c86c77560060f42f1b6a5ed5ec2964c5 Thu Apr 9 20:22:13 2020 -0700
    moved mRNAs track to first position in mRNAs bluegroup. It can go out next time QA has something on hg19 to go out
• src/hg/makeDb/trackDb/human/hg19/gnomadPLI.html
  • lines changed 2, context: html, text, full: html, text
    e43a27f20360771debc033e0d4fe82027018fd88 Mon Apr 6 17:26:15 2020 -0700
    adding thanks to ucsc team in credits
  • lines changed 1, context: html, text, full: html, text
    4278ce54b8270e020a3bd532efbe5523efee51c8 Mon Apr 6 17:27:50 2020 -0700
    ack. typo on lou's name
  • lines changed 1, context: html, text, full: html, text
    2cc52db58c00517321a0db164e472416e7715bcf Mon Apr 6 18:04:17 2020 -0700
    changed the accent on Anna'a name
  • lines changed 36, context: html, text, full: html, text
    cb2da027a20d47e21deb2a14398c776564e84680 Tue Apr 7 12:19:45 2020 -0700
    text changes description page refs #20394
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    bb3d7ddc40f4f319769a7567f4197b012564edf0 Tue Apr 7 13:56:01 2020 -0700
    fixing up pLI description page after feedback from Bob refs #20394
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
  • lines changed 2, context: html, text, full: html, text
    33eaea78314af55fc557ba515f61538e39ea24fb Mon Apr 6 10:52:52 2020 -0700
    Changing default labels to gene symbols refs #20394
  • lines changed 7, context: html, text, full: html, text
    cd34e8056e73728938124caffc346ac983ba6238 Mon Apr 6 13:59:56 2020 -0700
    gnomad structural variants track ready for QA, refs #24179
  • lines changed 3, context: html, text, full: html, text
    cb2da027a20d47e21deb2a14398c776564e84680 Tue Apr 7 12:19:45 2020 -0700
    text changes description page refs #20394
• src/hg/makeDb/trackDb/human/hg38/chainSelf.html
  • lines changed 1, context: html, text, full: html, text
    87ab356592ce2ba955978981c872bb178468b2f5 Mon Apr 6 15:40:22 2020 -0700
    Fixing in response to CR refs #25304
• src/hg/makeDb/trackDb/human/trackDb.clinvarTest.ra
  • lines changed 13, context: html, text, full: html, text
    9e041b5e2a4a27d79e1fa71c218952bf37c427b1 Fri Apr 10 04:22:18 2020 -0700
    fixing clinvar range filter, refs #24850
• src/hg/makeDb/trackDb/marmoset/calJac3/cons13way.html
  • lines changed 1, context: html, text, full: html, text
    3feee815404559366e8baf8bd6992acc1509dd21 Mon Apr 6 10:56:00 2020 -0700
    Updating redirected links found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.placentalsChainNet.ra
  • lines changed 19, context: html, text, full: html, text
    744eb91b7ac3b786d58b9dad166ce47d6d12273a Fri Apr 10 11:30:52 2020 -0700
    adding canFam4 chainNet definitions refs #25279
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 2, context: html, text, full: html, text
    7d70cdf40567dbcfd3a190c844d99046aced5637 Thu Apr 9 13:58:39 2020 -0700
    Add settings to define window sizes for small/medium/large graphs. Useful for small (e.g. virus) genomes. Prompted by Max barCharts on wuhCor1. refs #25339
• src/hg/makeDb/trackDb/trackDb.chainNet.mammal.ra
  • lines changed 216, context: html, text, full: html, text
    744eb91b7ac3b786d58b9dad166ce47d6d12273a Fri Apr 10 11:30:52 2020 -0700
    adding canFam4 chainNet definitions refs #25279
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 150, context: html, text, full: html, text
    744eb91b7ac3b786d58b9dad166ce47d6d12273a Fri Apr 10 11:30:52 2020 -0700
    adding canFam4 chainNet definitions refs #25279
• src/hg/makeDb/trackDb/virus/wuhCor1/cas13Crispr.html
  • lines changed 25, context: html, text, full: html, text
    4c36646e0554b3ab094bfa7d49c6f05f381a9ed1 Fri Apr 10 16:43:18 2020 -0700
    adding cas13 track to wuhCor1, no redmine yet.
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    f69c4aafb06ef1f4fa452a43bad6290be3b98c27 Sun Apr 12 07:25:57 2020 -0700
    fixing msdos linebreak discovered by nightly build error.
• src/hg/makeDb/trackDb/virus/wuhCor1/epitopes.html
  • lines changed 12, context: html, text, full: html, text
    87ab356592ce2ba955978981c872bb178468b2f5 Mon Apr 6 15:40:22 2020 -0700
    Fixing in response to CR refs #25304
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    8cd856f949ba05bffdbc6d249c0382adb342c0b5 Thu Apr 9 15:13:12 2020 -0700
    Update epitopes.html I changed the paper cited to be the paper that actually supplied the data shown in this track.
• src/hg/makeDb/trackDb/virus/wuhCor1/epitopes.ra
  • lines changed 2, context: html, text, full: html, text
    b32c24614a0f1a299474d6a47fbd13c2535c3c46 Fri Apr 10 06:16:27 2020 -0700
    making NCBI genes a default track again and hiding the UniProt full proteins track for now, refs #25332
• src/hg/makeDb/trackDb/virus/wuhCor1/kim2020.ra
  • lines changed 120, context: html, text, full: html, text
    ee4a1ee0daaee6d873ecffb909d1496a99512e15 Thu Apr 9 04:22:06 2020 -0700
    kim2020 track for wuhCor1, no redmine yet
  • lines changed 4, context: html, text, full: html, text
    52ec50ee3467f26759aab70724d1e95b89150dc0 Thu Apr 9 06:54:22 2020 -0700
    adding Kim2020 tracks, refs #25332
  • lines changed 6, context: html, text, full: html, text
    7d70cdf40567dbcfd3a190c844d99046aced5637 Thu Apr 9 13:58:39 2020 -0700
    Add settings to define window sizes for small/medium/large graphs. Useful for small (e.g. virus) genomes. Prompted by Max barCharts on wuhCor1. refs #25339
  • lines changed 1, context: html, text, full: html, text
    c69f0dd46608a5298ece019177f565eedbda7bb2 Fri Apr 10 07:17:18 2020 -0700
    accidentally showed the Kim 2020 track, hiding again now, refs #25332
• src/hg/makeDb/trackDb/virus/wuhCor1/kimNp.html
  • lines changed 33, context: html, text, full: html, text
    52ec50ee3467f26759aab70724d1e95b89150dc0 Thu Apr 9 06:54:22 2020 -0700
    adding Kim2020 tracks, refs #25332
• src/hg/makeDb/trackDb/virus/wuhCor1/kimRnaMod.html
  • lines changed 35, context: html, text, full: html, text
    52ec50ee3467f26759aab70724d1e95b89150dc0 Thu Apr 9 06:54:22 2020 -0700
    adding Kim2020 tracks, refs #25332
• src/hg/makeDb/trackDb/virus/wuhCor1/ncbiGeneBGP.html
  • lines changed 1, context: html, text, full: html, text
    e4ff3291cd6b32c9472e61aee808ff476bf9fc15 Fri Apr 10 15:02:07 2020 -0700
    renaming NCBI genes a little, preparing for full Genbank export coming next week, refs #25114
• src/hg/makeDb/trackDb/virus/wuhCor1/ncbiGeneBGP.ra
  • lines changed 1, context: html, text, full: html, text
    b32c24614a0f1a299474d6a47fbd13c2535c3c46 Fri Apr 10 06:16:27 2020 -0700
    making NCBI genes a default track again and hiding the UniProt full proteins track for now, refs #25332
  • lines changed 1, context: html, text, full: html, text
    e4ff3291cd6b32c9472e61aee808ff476bf9fc15 Fri Apr 10 15:02:07 2020 -0700
    renaming NCBI genes a little, preparing for full Genbank export coming next week, refs #25114
  • lines changed 1, context: html, text, full: html, text
    5b5a679382a739d2170c36ea9fe21135fd1194c8 Fri Apr 10 15:03:17 2020 -0700
    renaming NCBI genes again, refs #25114
• src/hg/makeDb/trackDb/virus/wuhCor1/pdb.html
  • lines changed 17, context: html, text, full: html, text
    69c3bae15bfd5d888ac4cd13bd3bf4f602c3f058 Tue Apr 7 13:38:17 2020 -0700
    Minor changes to display and description page of PDB track refs #25227
• src/hg/makeDb/trackDb/virus/wuhCor1/primers.html
  • lines changed 2, context: html, text, full: html, text
    52ec50ee3467f26759aab70724d1e95b89150dc0 Thu Apr 9 06:54:22 2020 -0700
    adding Kim2020 tracks, refs #25332
  • lines changed 19, context: html, text, full: html, text
    fe50c2671682b9dc63e3abff004cfe15c8de5d76 Thu Apr 9 07:47:05 2020 -0700
    update of primers docs page for wuhCor1, refs #25189
  • lines changed 2, context: html, text, full: html, text
    4c36646e0554b3ab094bfa7d49c6f05f381a9ed1 Fri Apr 10 16:43:18 2020 -0700
    adding cas13 track to wuhCor1, no redmine yet.
• src/hg/makeDb/trackDb/virus/wuhCor1/publicAnnots.html
  • lines changed 7, context: html, text, full: html, text
    913e198cc062676337bef2e795fabcb896272d40 Fri Apr 10 15:25:03 2020 -0700
    adding hub link to user annotation track docs, refs #25297
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    69c3bae15bfd5d888ac4cd13bd3bf4f602c3f058 Tue Apr 7 13:38:17 2020 -0700
    Minor changes to display and description page of PDB track refs #25227
  • lines changed 1, context: html, text, full: html, text
    9e2b142138375378c3d62889c6e1f613f5e1c052 Thu Apr 9 04:22:42 2020 -0700
    kim2020 track for wuhCor1 include, no redmine yet
  • lines changed 12, context: html, text, full: html, text
    1d2b7601cae229ed13d4b644905892ccb356de19 Fri Apr 10 16:11:57 2020 -0700
    making url clickable in user annotations track, refs #25297
  • lines changed 1, context: html, text, full: html, text
    4c36646e0554b3ab094bfa7d49c6f05f381a9ed1 Fri Apr 10 16:43:18 2020 -0700
    adding cas13 track to wuhCor1, no redmine yet.
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.uniprot.ra
  • lines changed 19, context: html, text, full: html, text
    b32c24614a0f1a299474d6a47fbd13c2535c3c46 Fri Apr 10 06:16:27 2020 -0700
    making NCBI genes a default track again and hiding the UniProt full proteins track for now, refs #25332
• src/hg/makeDb/trackDb/virus/wuhCor1/unipCov2AliSwissprot.html
  • lines changed 10, context: html, text, full: html, text
    87ab356592ce2ba955978981c872bb178468b2f5 Mon Apr 6 15:40:22 2020 -0700
    Fixing in response to CR refs #25304
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    6f2549c5937cfec3bb7a661f582efd5a500e46a3 Mon Apr 6 16:29:31 2020 -0700
    Commenting out archive comment since it's current empty, and the uniprot is pre-release so we do not want to archive it refs #25192
• src/hg/makeDb/trackDb/virus/wuhCor1/unipCov2Interest.html
  • lines changed 10, context: html, text, full: html, text
    87ab356592ce2ba955978981c872bb178468b2f5 Mon Apr 6 15:40:22 2020 -0700
    Fixing in response to CR refs #25304
• src/hg/makeDb/trackDb/virus/wuhCor1/uniprotCov2.html
  • lines changed 16, context: html, text, full: html, text
    87ab356592ce2ba955978981c872bb178468b2f5 Mon Apr 6 15:40:22 2020 -0700
    Fixing in response to CR refs #25304
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    6f2549c5937cfec3bb7a661f582efd5a500e46a3 Mon Apr 6 16:29:31 2020 -0700
    Commenting out archive comment since it's current empty, and the uniprot is pre-release so we do not want to archive it refs #25192
• src/hg/utils/automation/doNcbiRefSeq.pl
  • lines changed 16, context: html, text, full: html, text
    be2fb5e3a2af8d3e1f73c1cc5c6bd5ff05bad8a5 Wed Apr 8 07:52:51 2020 -0700
    handle the problem of duplicate contigs and make all download files including archive refs #24547
• src/hg/utils/automation/makeDownloads.pl
  • lines changed 9, context: html, text, full: html, text
    6a2fbc6a437200b34de1956a93231d481ddb41b3 Wed Apr 8 07:53:45 2020 -0700
    correct READE for bigZips/genes/ refs #24547
• src/hg/utils/otto/mastermind/mastermindToBed.py
  • lines changed 5, context: html, text, full: html, text
    fcdf15b53464989f3345eaaab1f7c07e270934cf Wed Apr 8 09:02:04 2020 -0700
    Fixing weird chars in mastermind otto script, no refs
• src/product/installer/browserSetup.sh
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    5946bbc1e1251090797941c70ca147915ce495d5 Wed Apr 8 11:32:57 2020 -0700
    This should be executable
• src/utils/qa/weeklybld/buildEnv.csh
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    4c91377c0db174dc514a1755c7fae9bad6202222 Mon Apr 13 10:00:13 2020 -0700
    v397 preview2

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• files changed: 77