All File Changes

v398_base to v399_preview (2020-05-11 to 2020-05-18) v399

• confs/hgwbeta.hg.conf
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    8ffbb5ebb25b58c159007c8dc08d49b94d666c63 Sun May 17 01:11:52 2020 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
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    8ffbb5ebb25b58c159007c8dc08d49b94d666c63 Sun May 17 01:11:52 2020 -0700
    Installing updated hg.conf files from UCSC servers
• src/blat/blat.c
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    155197c63e3259d0922c5c3a0e859f4812129db4 Sun May 17 17:52:03 2020 -0700
    gfServer and blat and isPcr extended with new commandline option -noSimpRepMask to help with small genomes. refs #25477
• src/blat/version.doc
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    155197c63e3259d0922c5c3a0e859f4812129db4 Sun May 17 17:52:03 2020 -0700
    gfServer and blat and isPcr extended with new commandline option -noSimpRepMask to help with small genomes. refs #25477
• src/gfServer/gfServer.c
  • lines changed 8, context: html, text, full: html, text
    155197c63e3259d0922c5c3a0e859f4812129db4 Sun May 17 17:52:03 2020 -0700
    gfServer and blat and isPcr extended with new commandline option -noSimpRepMask to help with small genomes. refs #25477
• src/hg/hgBlat/hgBlat.c
  • lines changed 225, context: html, text, full: html, text
    03ad0cc3681e3a08fa2988990bdea9262faddc24 Mon May 18 00:31:03 2020 -0700
    Added All Results checkbox to hgBlat. Changed it to read tileSize etc from gfserver status so it can use whatever it finds. Correctly shows lengths and required lengths. Instead of limit 20 for dna it now detects min psl->match from genome size. Error messages and warnings should now be complete and correct about suggested and required minimum query lengths. In particular this is motivated by allowing extremely sensitive and short protein and dna queries on Sars-Cov2 (wuhCor1) as well as other microorganisms. refs #25477.
• src/hg/hgGene/ctd.c
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    3589900a038034a6c2112c308946f67889c11170 Fri May 15 11:40:30 2020 -0700
    fix URL to Comparative Toxicogenomics Database
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 12, context: html, text, full: html, text
    48c5bcc0735d09367f9853ebbd053aea3f94b262 Fri May 15 10:37:48 2020 -0700
    Fix bug in hub searching where a hub being down at the time we are trying to display it's search results caused a segfault, also removing remnants of hgHubConnect needing a special udcCache, which the CGI has not been using for months now, refs #25574
• src/hg/hgTables/vcf.c
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    e46073f856770bdfef4f7637eea8f9f9297aa139 Tue Nov 19 15:57:08 2019 -0800
    Initial commit of new track type vcfPhased trio. A line with ticks, one per haplotype per sample in the VCF, as specified by trackDb variables.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 102, context: html, text, full: html, text
    9599e99e622644fc958a1a6481b82778cfd9a27f Thu Feb 13 14:12:01 2020 -0800
    Initial cut adding supertrack info to member track UI. refs #24948
  • lines changed 37, context: html, text, full: html, text
    8149e01f1abf2d532e4bc0cd516713a536640006 Wed Feb 19 12:08:24 2020 -0800
    Tweak to match Ana's mock-up. Still in progress. refs #24948
  • lines changed 36, context: html, text, full: html, text
    2ed451a171f3939be436ccc3bf6f0800f9df2a3a Fri Feb 21 17:41:17 2020 -0800
    Implement collapsible panel with supertrack description, to appear at top of supertrack component track config page. refs #24948
  • lines changed 4, context: html, text, full: html, text
    bb2ae39fd12b2df4ec06b435e63f69da6097e21e Tue May 5 14:38:24 2020 -0700
    Add link to super-track HTML from supertrack member description collapsible panel. By request of Lou. refs #24668
  • lines changed 17, context: html, text, full: html, text
    b9d7723866095088387017765ea962f83e87bbfd Wed May 6 16:23:13 2020 -0700
    Add supertrack to supertrack member title bar. Part of attempt to make supertrack member UI page easier to understand (show hierarchy but subtly). refs #24948
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    9a54ece0b8406d393f065c03a0531d711ad6e5f3 Wed May 6 16:33:52 2020 -0700
    Take 2 on removing 'super-track' from supertrack blue bar. Off-shoot of discussion on better supertrack member track UI pages. refs #24948
  • lines changed 59, context: html, text, full: html, text
    1e695a4eb7c3df8d90db67d0859efb86fde53201 Wed May 6 17:51:49 2020 -0700
    Add collapsed panel with other tracks in supertrackand remove intro verbiage. Overall slim down the top material indicating hierarchy. Based on UI input from Ana and MarkD. refs #24948
  • lines changed 4, context: html, text, full: html, text
    4ad18f5e3c3e5b960a138161d8048cd7d3a2f34d Wed May 6 18:01:29 2020 -0700
    Fix styling. refs #24948
  • lines changed 121, context: html, text, full: html, text
    7597f413c7812055e03a9dd5177432be2a827571 Thu May 7 08:59:01 2020 -0700
    Remove second section, moving supertrack info into main section to simplify page. Expecting this to be final design (has hadded extensive UI review). refs #24948
  • lines changed 6, context: html, text, full: html, text
    60fb3562b8ca97c4e215049c9092e01eb6ce70cc Mon May 11 16:19:31 2020 -0700
    Switch back to listing all tracks in super (not 'other'). Request of MarkD. refs #24948
  • lines changed 2, context: html, text, full: html, text
    363ca5c576b616861e58d410da17f24cc562db96 Mon May 11 16:56:59 2020 -0700
    Use existing backdoor to allow HTML tags for styling in trackUi title bar. Request of MarkD to include parent short label in supertrack member title (show hierarchy), prompted motivation to expand styling. refs #24948
  • lines changed 140, context: html, text, full: html, text
    db7c8abb6d7674bb26f579eabb58bc080ce76fdd Tue May 12 07:04:05 2020 -0700
    adding a protease track to uniprot, refs #25192
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    f225bd9ef750fb706f2f14bd87e3512b43e23dc1 Wed May 13 13:50:34 2020 -0700
    Revert "adding a protease track to uniprot, refs #25192". I have no idea what happened here, looks like I typed git commit -a instead of git commit -m This reverts commit db7c8abb6d7674bb26f579eabb58bc080ce76fdd.
  • lines changed 23, context: html, text, full: html, text
    877b1886b6e9ee73fa26477cbf83bbf16771bb3d Wed May 13 16:24:46 2020 -0700
    Restore ENCODE logo to track header (not supertrack). Remove uplink to all tracks in group from the supertrack link. Maybe we decided to remove this generally ?. refs #24948
• src/hg/hgTracks/hgTracks.c
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    e46073f856770bdfef4f7637eea8f9f9297aa139 Tue Nov 19 15:57:08 2019 -0800
    Initial commit of new track type vcfPhased trio. A line with ticks, one per haplotype per sample in the VCF, as specified by trackDb variables.
• src/hg/hgTracks/hgTracks.h
  • lines changed 3, context: html, text, full: html, text
    e46073f856770bdfef4f7637eea8f9f9297aa139 Tue Nov 19 15:57:08 2019 -0800
    Initial commit of new track type vcfPhased trio. A line with ticks, one per haplotype per sample in the VCF, as specified by trackDb variables.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 4, context: html, text, full: html, text
    e46073f856770bdfef4f7637eea8f9f9297aa139 Tue Nov 19 15:57:08 2019 -0800
    Initial commit of new track type vcfPhased trio. A line with ticks, one per haplotype per sample in the VCF, as specified by trackDb variables.
• src/hg/hgTracks/vcfTrack.c
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    39df62e630e31c0f8019bb350d64736ebe44220d Wed May 13 15:40:48 2020 -0700
    oops, forgot to call hReplaceGbdb on new tree file for VCF (and on .vcf.gz file for that matter). refs #25554
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    e46073f856770bdfef4f7637eea8f9f9297aa139 Tue Nov 19 15:57:08 2019 -0800
    Initial commit of new track type vcfPhased trio. A line with ticks, one per haplotype per sample in the VCF, as specified by trackDb variables.
• src/hg/hgc/hgc.c
  • lines changed 3, context: html, text, full: html, text
    e46073f856770bdfef4f7637eea8f9f9297aa139 Tue Nov 19 15:57:08 2019 -0800
    Initial commit of new track type vcfPhased trio. A line with ticks, one per haplotype per sample in the VCF, as specified by trackDb variables.
• src/hg/hgc/vcfClick.c
  • lines changed 5, context: html, text, full: html, text
    e8405a958dae40b261b2eadcd59a20edc64761f1 Wed May 13 15:25:04 2020 -0700
    VCF details and track controls: use "sample" instead of "haplotype" when displaying SARS-CoV-2 data because viruses are not diploid. refs #25409 Also don't display "leaf cluster" shape option, which applies only to the center-weighted haplotype clustering, unless that method is selected.
• src/hg/htdocs/FAQ/FAQlink.html
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    9ab80f9387e6e46cb1a19f85b3b696e915d8a62f Sun May 17 18:09:44 2020 -0700
    made zoomVariant link in index work by adding hashtag, fixed a typo, changed header of HGVS section to better match the index. adding new anchor tag, genes, for linking to gene names that is more descriptive, leaving the original link3 in place in case anyone outside links to it (we do not). weirdly, there is already an anchor in the doc called gene that is not used anywhere I can find
• src/hg/htdocs/covid19.html
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    1e4593e163722bd3878db5d83392b57525ec9ca2 Mon May 11 12:45:42 2020 -0700
    Update Nextstrain transmission graphic on COVID-19 page. refs #25217
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    85154a6ca6d1acae41c3dc7ac97d6f58d23496cb Mon May 11 12:58:36 2020 -0700
    Add info about our bioRxiv paper. refs #25217
  • lines changed 3, context: html, text, full: html, text
    e094a8fde03223a69c24d284e014a840212e28b8 Wed May 13 11:47:54 2020 -0700
    adding link to virus tutorial
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    a0c38076b917b3ac6fa6747c16088f4a17748435 Wed May 13 12:07:00 2020 -0700
    moved map link to separate line
• src/hg/htdocs/covid19/covid.css
  • lines changed 47, context: html, text, full: html, text
    909396cec2a8fcd0a220da40a82f29ecee4d5ec6 Tue May 12 03:38:49 2020 -0700
    removing old covid homepage, as per bob email
• src/hg/htdocs/covid19/index.html
  • lines changed 117, context: html, text, full: html, text
    909396cec2a8fcd0a220da40a82f29ecee4d5ec6 Tue May 12 03:38:49 2020 -0700
    removing old covid homepage, as per bob email
• src/hg/htdocs/goldenPath/help/hubQuickStartSearch.html
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    b438269cad04b002a7f51302ff76b12bcf76dfbc Wed May 13 14:39:45 2020 -0700
    Fixing incorrect assembly ref No RM
• src/hg/htdocs/goldenPath/help/mirror.html
  • lines changed 27, context: html, text, full: html, text
    db7c8abb6d7674bb26f579eabb58bc080ce76fdd Tue May 12 07:04:05 2020 -0700
    adding a protease track to uniprot, refs #25192
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    f225bd9ef750fb706f2f14bd87e3512b43e23dc1 Wed May 13 13:50:34 2020 -0700
    Revert "adding a protease track to uniprot, refs #25192". I have no idea what happened here, looks like I typed git commit -a instead of git commit -m This reverts commit db7c8abb6d7674bb26f579eabb58bc080ce76fdd.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
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    79142546956ba8b0d94175b6e0adcb0c5c01172d Wed May 13 16:56:19 2020 -0700
    Fixes to doc for hideEmptySubtracks settings, refs #23365
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 27, context: html, text, full: html, text
    315f8c88b06685bbacdf27400292e247ec027ea7 Mon May 11 17:42:16 2020 -0700
    releasing video about new coronavirus video
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    c11355d6a6a8fc022297b6db3dde96f902b98842 Mon May 11 19:04:26 2020 -0700
    fixed misspelling
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    bcd12add62adab155609ace31efc2ae413af62a6 Tue May 12 09:34:58 2020 -0700
    added a sentence about transcript
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    9429d8a90724a8ed4476c8757d5dd3399c360ba5 Wed May 13 11:46:56 2020 -0700
    adding some missing hyphens
• src/hg/htdocs/images/covid19-transmission.may8_2020.nextstrain.png
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    1e4593e163722bd3878db5d83392b57525ec9ca2 Mon May 11 12:45:42 2020 -0700
    Update Nextstrain transmission graphic on COVID-19 page. refs #25217
• src/hg/htdocs/images/phylo/wuhCor1_7way.png
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    8521ee7816a0dc0c5d862b76aba678948142127f Wed May 13 12:01:00 2020 -0700
    adding 7-way phylo tree image refs #25187
• src/hg/htdocs/images/titleVid20.jpg
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    315f8c88b06685bbacdf27400292e247ec027ea7 Mon May 11 17:42:16 2020 -0700
    releasing video about new coronavirus video
• src/hg/htdocs/indexNews.html
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    315f8c88b06685bbacdf27400292e247ec027ea7 Mon May 11 17:42:16 2020 -0700
    releasing video about new coronavirus video
• src/hg/htdocs/style/makefile
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    3e9c58fd7471ce612009bfd13c644d26923e1258 Mon May 11 11:43:06 2020 -0700
    add an rsync of htdocs/style/images
• src/hg/htdocs/training/index.html
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    315f8c88b06685bbacdf27400292e247ec027ea7 Mon May 11 17:42:16 2020 -0700
    releasing video about new coronavirus video
• src/hg/inc/vcfUi.h
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    e8405a958dae40b261b2eadcd59a20edc64761f1 Wed May 13 15:25:04 2020 -0700
    VCF details and track controls: use "sample" instead of "haplotype" when displaying SARS-CoV-2 data because viruses are not diploid. refs #25409 Also don't display "leaf cluster" shape option, which applies only to the center-weighted haplotype clustering, unless that method is selected.
  • lines changed 11, context: html, text, full: html, text
    e46073f856770bdfef4f7637eea8f9f9297aa139 Tue Nov 19 15:57:08 2019 -0800
    Initial commit of new track type vcfPhased trio. A line with ticks, one per haplotype per sample in the VCF, as specified by trackDb variables.
• src/hg/js/hui.js
  • lines changed 17, context: html, text, full: html, text
    db7c8abb6d7674bb26f579eabb58bc080ce76fdd Tue May 12 07:04:05 2020 -0700
    adding a protease track to uniprot, refs #25192
  • lines changed 17, context: html, text, full: html, text
    f225bd9ef750fb706f2f14bd87e3512b43e23dc1 Wed May 13 13:50:34 2020 -0700
    Revert "adding a protease track to uniprot, refs #25192". I have no idea what happened here, looks like I typed git commit -a instead of git commit -m This reverts commit db7c8abb6d7674bb26f579eabb58bc080ce76fdd.
• src/hg/js/subCfg.js
  • lines changed 39, context: html, text, full: html, text
    db7c8abb6d7674bb26f579eabb58bc080ce76fdd Tue May 12 07:04:05 2020 -0700
    adding a protease track to uniprot, refs #25192
  • lines changed 39, context: html, text, full: html, text
    f225bd9ef750fb706f2f14bd87e3512b43e23dc1 Wed May 13 13:50:34 2020 -0700
    Revert "adding a protease track to uniprot, refs #25192". I have no idea what happened here, looks like I typed git commit -a instead of git commit -m This reverts commit db7c8abb6d7674bb26f579eabb58bc080ce76fdd.
• src/hg/lib/customFactory.c
  • lines changed 18, context: html, text, full: html, text
    e46073f856770bdfef4f7637eea8f9f9297aa139 Tue Nov 19 15:57:08 2019 -0800
    Initial commit of new track type vcfPhased trio. A line with ticks, one per haplotype per sample in the VCF, as specified by trackDb variables.
• src/hg/lib/hui.c
  • lines changed 47, context: html, text, full: html, text
    db7c8abb6d7674bb26f579eabb58bc080ce76fdd Tue May 12 07:04:05 2020 -0700
    adding a protease track to uniprot, refs #25192
  • lines changed 47, context: html, text, full: html, text
    f225bd9ef750fb706f2f14bd87e3512b43e23dc1 Wed May 13 13:50:34 2020 -0700
    Revert "adding a protease track to uniprot, refs #25192". I have no idea what happened here, looks like I typed git commit -a instead of git commit -m This reverts commit db7c8abb6d7674bb26f579eabb58bc080ce76fdd.
• src/hg/lib/rnaSecStr.c
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    8c46bf4f26ab5833f1b9f23e4ec54f62ed60bf00 Thu May 14 15:48:28 2020 -0700
    changes in comment in response to code review
• src/hg/lib/trackDbCustom.c
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    e46073f856770bdfef4f7637eea8f9f9297aa139 Tue Nov 19 15:57:08 2019 -0800
    Initial commit of new track type vcfPhased trio. A line with ticks, one per haplotype per sample in the VCF, as specified by trackDb variables.
• src/hg/lib/vcfUi.c
  • lines changed 74, context: html, text, full: html, text
    e8405a958dae40b261b2eadcd59a20edc64761f1 Wed May 13 15:25:04 2020 -0700
    VCF details and track controls: use "sample" instead of "haplotype" when displaying SARS-CoV-2 data because viruses are not diploid. refs #25409 Also don't display "leaf cluster" shape option, which applies only to the center-weighted haplotype clustering, unless that method is selected.
  • lines changed 112, context: html, text, full: html, text
    e46073f856770bdfef4f7637eea8f9f9297aa139 Tue Nov 19 15:57:08 2019 -0800
    Initial commit of new track type vcfPhased trio. A line with ticks, one per haplotype per sample in the VCF, as specified by trackDb variables.
• src/hg/lib/web.c
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    b9d7723866095088387017765ea962f83e87bbfd Wed May 6 16:23:13 2020 -0700
    Add supertrack to supertrack member title bar. Part of attempt to make supertrack member UI page easier to understand (show hierarchy but subtly). refs #24948
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    306429a79f9eedb8614ad52c6f5e2ad60bc50449 Mon May 11 16:54:58 2020 -0700
    Reverting html and web lib changes for allowing tags in title bars. (For now, limiting to trackUi). refs #24948
• src/hg/makeDb/avada/avada.as
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    db7c8abb6d7674bb26f579eabb58bc080ce76fdd Tue May 12 07:04:05 2020 -0700
    adding a protease track to uniprot, refs #25192
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    f225bd9ef750fb706f2f14bd87e3512b43e23dc1 Wed May 13 13:50:34 2020 -0700
    Revert "adding a protease track to uniprot, refs #25192". I have no idea what happened here, looks like I typed git commit -a instead of git commit -m This reverts commit db7c8abb6d7674bb26f579eabb58bc080ce76fdd.
  • lines changed 8, context: html, text, full: html, text
    c107da5a25ac3f3f58a747ff23d3533f0afedfa1 Wed May 13 15:31:25 2020 -0700
    adding back kim and ncbigene wuhCor1 changes after screwed up commit
• src/hg/makeDb/doc/wuhCor1/kim2020.txt
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    db7c8abb6d7674bb26f579eabb58bc080ce76fdd Tue May 12 07:04:05 2020 -0700
    adding a protease track to uniprot, refs #25192
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    f225bd9ef750fb706f2f14bd87e3512b43e23dc1 Wed May 13 13:50:34 2020 -0700
    Revert "adding a protease track to uniprot, refs #25192". I have no idea what happened here, looks like I typed git commit -a instead of git commit -m This reverts commit db7c8abb6d7674bb26f579eabb58bc080ce76fdd.
  • lines changed 18, context: html, text, full: html, text
    c107da5a25ac3f3f58a747ff23d3533f0afedfa1 Wed May 13 15:31:25 2020 -0700
    adding back kim and ncbigene wuhCor1 changes after screwed up commit
• src/hg/makeDb/doc/wuhCor1/multiz7way.txt
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    224c450fc89ff07b44d0405b92ce3320cfb92801 Wed May 13 12:01:34 2020 -0700
    adding 7-way display refs #25187
• src/hg/makeDb/doc/wuhCor1/ncbiGene.txt
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    db7c8abb6d7674bb26f579eabb58bc080ce76fdd Tue May 12 07:04:05 2020 -0700
    adding a protease track to uniprot, refs #25192
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    6f3fc4898bf6e398b31dcb0e1878f0f63a4eb28e Wed May 13 11:41:02 2020 -0700
    makeDoc for trix index for ncbiProteins
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    f225bd9ef750fb706f2f14bd87e3512b43e23dc1 Wed May 13 13:50:34 2020 -0700
    Revert "adding a protease track to uniprot, refs #25192". I have no idea what happened here, looks like I typed git commit -a instead of git commit -m This reverts commit db7c8abb6d7674bb26f579eabb58bc080ce76fdd.
  • lines changed 9, context: html, text, full: html, text
    c107da5a25ac3f3f58a747ff23d3533f0afedfa1 Wed May 13 15:31:25 2020 -0700
    adding back kim and ncbigene wuhCor1 changes after screwed up commit
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    bdc06272b74428b4b206745d07b0ac4c527444f8 Mon May 18 07:01:01 2020 -0700
    fixing the Orf1ab problem, refs #25114 as per email from Jason
• src/hg/makeDb/trackDb/encodeCcreCombined.html
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    2c78d69bf51c0282d97dd262b8f9005f1c5d3192 Tue May 12 16:32:36 2020 -0700
    Polish track config and draft track description. refs #24668
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    c1bf92e8d0500957bef941593240f66eabe8094d Wed May 13 10:30:24 2020 -0700
    Polish track description and generalize to include mouse. Add 4-char labels for classification and abbreviated accession label as per JK. Filter on the more user-friendly classification labels. refs #24668
• src/hg/makeDb/trackDb/human/dbVarCommon.html
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    3e1960b35a07377b46bd83b8fd04387f182c6bd6 Fri May 15 10:52:51 2020 -0700
    added three description pages for dbVar tracks refs #25424
• src/hg/makeDb/trackDb/human/dbVarConflict.html
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    3e1960b35a07377b46bd83b8fd04387f182c6bd6 Fri May 15 10:52:51 2020 -0700
    added three description pages for dbVar tracks refs #25424
• src/hg/makeDb/trackDb/human/dbVarCurated.html
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    3e1960b35a07377b46bd83b8fd04387f182c6bd6 Fri May 15 10:52:51 2020 -0700
    added three description pages for dbVar tracks refs #25424
• src/hg/makeDb/trackDb/human/hg19/problematic.html
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    8b9f5b03e7af5bfa300d3c3083f1c68becee73ba Mon May 11 13:41:33 2020 -0700
    Code review, adding dash #25545
• src/hg/makeDb/trackDb/human/hg38/hicAndMicroC.html
  • lines changed 5, context: html, text, full: html, text
    e08b667f9bc02586a366e39399886580b4c27c30 Fri May 15 13:29:43 2020 -0700
    Updating reference for Micro-C track on hg38, refs #25577
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 47, context: html, text, full: html, text
    e46073f856770bdfef4f7637eea8f9f9297aa139 Tue Nov 19 15:57:08 2019 -0800
    Initial commit of new track type vcfPhased trio. A line with ticks, one per haplotype per sample in the VCF, as specified by trackDb variables.
• src/hg/makeDb/trackDb/human/trackDb.dbVar.ra
  • lines changed 28, context: html, text, full: html, text
    d8291eebd92ce15d5ca00bdf8c7db1e36d7425b0 Wed May 13 18:27:08 2020 -0700
    change track names and add html pages refs #25424
• src/hg/makeDb/trackDb/makefile
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    888f7654e2cd538922ffea023abf83f9db522b88 Fri May 15 14:51:34 2020 -0700
    Added test target to trackDb/makefile that invokes tdbQuery -check -release={alpha,beta,public} -strict.
• src/hg/makeDb/trackDb/nscanGene.html
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    cdf97b3df98fc12b2b58df8c44a1b0e532fc27de Tue May 12 15:52:55 2020 -0700
    Updating http to https for panTro2, uiLinks cronjob.
• src/hg/makeDb/trackDb/tagTypes.tab
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    e46073f856770bdfef4f7637eea8f9f9297aa139 Tue Nov 19 15:57:08 2019 -0800
    Initial commit of new track type vcfPhased trio. A line with ticks, one per haplotype per sample in the VCF, as specified by trackDb variables.
• src/hg/makeDb/trackDb/trackDb.chainNet.laurasiatheria.ra
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    5c3ce92b86745b106cc7bec5c69b6f2d767aded6 Tue May 12 17:50:13 2020 -0700
    Removing the release tags for the Southern sea otter chain/nets for human and mouse, refs #21152
• src/hg/makeDb/trackDb/trackDb.encode3.ra
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    2c78d69bf51c0282d97dd262b8f9005f1c5d3192 Tue May 12 16:32:36 2020 -0700
    Polish track config and draft track description. refs #24668
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    c1bf92e8d0500957bef941593240f66eabe8094d Wed May 13 10:30:24 2020 -0700
    Polish track description and generalize to include mouse. Add 4-char labels for classification and abbreviated accession label as per JK. Filter on the more user-friendly classification labels. refs #24668
• src/hg/makeDb/trackDb/virus/wuhCor1/cons7way.html
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    917c57bb65f797b471d8b98bf415a1bd319d625e Wed May 13 12:43:08 2020 -0700
    documentation for 7-way refs #25090
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    9492fa97f1b5c87e59de34f9cdfd5954da86018c Wed May 13 12:48:20 2020 -0700
    fixup labels and table listing sequences correction refs #25090
• src/hg/makeDb/trackDb/virus/wuhCor1/ncbiGene.ra
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    e4491e9d8d52758491f8341d5bb5c00bfbfd8ea5 Wed May 13 11:32:57 2020 -0700
    some tweaks to labelFields and added a trix search to NCBI Proteins
• src/hg/makeDb/trackDb/virus/wuhCor1/ncbiProducts.html
  • lines changed 42, context: html, text, full: html, text
    3264a4b84faf347818be4940415a7cdbb8fa31ef Wed May 13 04:22:52 2020 -0700
    adding ncbi mature proteins desc page, refs #25114
• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainClade.html
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    7320e440fe5c1e94770d5fbc5ec30ea9242864c5 Tue May 12 10:18:52 2020 -0700
    Unfortunately GISAID has prevented Nextstrain from offering its latest ncov.json file for public download, so remove mentions of JSON from track descriptions. refs #25188, #25481
  • lines changed 1, context: html, text, full: html, text
    59749d287fb04a329cf873d4206d6657cb73fa76 Tue May 12 10:23:21 2020 -0700
    Update references to 'Nextstrain Vars' to 'Nextstrain Variants' now that 20-character shortLabels are in, yay. :) refs #25188
• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainFreq.html
  • lines changed 73, context: html, text, full: html, text
    54f7a5994a7093acf25a912e1348ca1ef181a08c Tue May 12 10:07:04 2020 -0700
    Changing Nextstrain Counts to Nextstrain Frequency and adding description. refs #25481
  • lines changed 11, context: html, text, full: html, text
    7320e440fe5c1e94770d5fbc5ec30ea9242864c5 Tue May 12 10:18:52 2020 -0700
    Unfortunately GISAID has prevented Nextstrain from offering its latest ncov.json file for public download, so remove mentions of JSON from track descriptions. refs #25188, #25481
  • lines changed 1, context: html, text, full: html, text
    59749d287fb04a329cf873d4206d6657cb73fa76 Tue May 12 10:23:21 2020 -0700
    Update references to 'Nextstrain Vars' to 'Nextstrain Variants' now that 20-character shortLabels are in, yay. :) refs #25188
• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainGene.html
  • lines changed 8, context: html, text, full: html, text
    7320e440fe5c1e94770d5fbc5ec30ea9242864c5 Tue May 12 10:18:52 2020 -0700
    Unfortunately GISAID has prevented Nextstrain from offering its latest ncov.json file for public download, so remove mentions of JSON from track descriptions. refs #25188, #25481
  • lines changed 1, context: html, text, full: html, text
    59749d287fb04a329cf873d4206d6657cb73fa76 Tue May 12 10:23:21 2020 -0700
    Update references to 'Nextstrain Vars' to 'Nextstrain Variants' now that 20-character shortLabels are in, yay. :) refs #25188
• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainSamples.html
  • lines changed 11, context: html, text, full: html, text
    7320e440fe5c1e94770d5fbc5ec30ea9242864c5 Tue May 12 10:18:52 2020 -0700
    Unfortunately GISAID has prevented Nextstrain from offering its latest ncov.json file for public download, so remove mentions of JSON from track descriptions. refs #25188, #25481
  • lines changed 68, context: html, text, full: html, text
    1f03198645ea9c851e031b83832e6412439c8130 Wed May 13 11:41:01 2020 -0700
    Nextstrain Variants description edits suggested by David with some clarifications/updates mixed in. refs #25409
  • lines changed 26, context: html, text, full: html, text
    5c4910deb5cbe427a10a75dd62f1912ae8a98a7b Thu May 14 10:19:02 2020 -0700
    Added Recurrent Bi-allelic subtrack and per-clade subtracks to Description section. refs #25409
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    f9d1e6b0d008cc1bb0265c59b2cdafd14dfed362 Thu May 14 10:50:44 2020 -0700
    Add a separate nextstrainSamplesDevOnly.html so that Recurrent Bi-allelic is described only on hgwdev. refs #25409
• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainSamplesDevOnly.html
  • lines changed 154, context: html, text, full: html, text
    f9d1e6b0d008cc1bb0265c59b2cdafd14dfed362 Thu May 14 10:50:44 2020 -0700
    Add a separate nextstrainSamplesDevOnly.html so that Recurrent Bi-allelic is described only on hgwdev. refs #25409
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.7way.ra
  • lines changed 5, context: html, text, full: html, text
    e78d5ab52e14ba5d2512b0fb4942f25105169eed Wed May 13 12:02:57 2020 -0700
    correcting names refs #25090
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    9492fa97f1b5c87e59de34f9cdfd5954da86018c Wed May 13 12:48:20 2020 -0700
    fixup labels and table listing sequences correction refs #25090
  • lines changed 1, context: html, text, full: html, text
    e8e6d8f264a736c1bf2edb59f78b326fd4ba92f0 Wed May 13 12:50:18 2020 -0700
    fixup labels refs #25090
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra
  • lines changed 70, context: html, text, full: html, text
    54f7a5994a7093acf25a912e1348ca1ef181a08c Tue May 12 10:07:04 2020 -0700
    Changing Nextstrain Counts to Nextstrain Frequency and adding description. refs #25481
  • lines changed 3, context: html, text, full: html, text
    1c4981bf11687b15ff48044ccf434f0157410a43 Tue May 12 10:45:56 2020 -0700
    Turning off autoScale for Nextstrain Frequency because it has a natural range of 0.0 to 1.0. refs #25481
  • lines changed 13, context: html, text, full: html, text
    f9d1e6b0d008cc1bb0265c59b2cdafd14dfed362 Thu May 14 10:50:44 2020 -0700
    Add a separate nextstrainSamplesDevOnly.html so that Recurrent Bi-allelic is described only on hgwdev. refs #25409
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    4fb9760710c1a7398a72b491975c862e4704f594 Fri May 15 11:34:36 2020 -0700
    Removing extra space between beta and public that caused tdbQuery cron check failure.
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
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    5be8001bdbc86aedcbea1d8d03c09c423b7176c6 Tue May 12 09:04:57 2020 -0700
    adapting uniprot track labels
  • lines changed 8, context: html, text, full: html, text
    3fc38f5a8545b8bb11743b746c67856155682171 Fri May 15 14:47:24 2020 -0700
    add a lollipop track that captures the number of variants in the human sequences in the 119 way.
  • lines changed 10, context: html, text, full: html, text
    5bd8982a6e3337c383fce467b5fb6a5b9dfe5726 Mon May 18 06:33:39 2020 -0700
    adding conticelli et al rna editing track, no redmine yet
  • lines changed 7, context: html, text, full: html, text
    44c491fb0cbf2ea26b39a42458860dd76f18a8b5 Mon May 18 07:53:58 2020 -0700
    adding stringtie Kim track, mostly for Miten as an example
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.uniprot.ra
  • lines changed 11, context: html, text, full: html, text
    db7c8abb6d7674bb26f579eabb58bc080ce76fdd Tue May 12 07:04:05 2020 -0700
    adding a protease track to uniprot, refs #25192
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    69fdcef9274806b356b65ae8617fd04fc132e502 Wed May 13 13:50:26 2020 -0700
    renaming one uniprot track for wuhCor1
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    f225bd9ef750fb706f2f14bd87e3512b43e23dc1 Wed May 13 13:50:34 2020 -0700
    Revert "adding a protease track to uniprot, refs #25192". I have no idea what happened here, looks like I typed git commit -a instead of git commit -m This reverts commit db7c8abb6d7674bb26f579eabb58bc080ce76fdd.
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    cd89e9d0ffd48c6ec23b4c39f0065a3cdf6e3e74 Fri May 15 15:45:38 2020 -0700
    adding back uniprot protease trackDb stanzas, refs #25192
• src/hg/makeDb/trackDb/virus/wuhCor1/unipProtease.html
  • lines changed 31, context: html, text, full: html, text
    db7c8abb6d7674bb26f579eabb58bc080ce76fdd Tue May 12 07:04:05 2020 -0700
    adding a protease track to uniprot, refs #25192
  • lines changed 31, context: html, text, full: html, text
    f225bd9ef750fb706f2f14bd87e3512b43e23dc1 Wed May 13 13:50:34 2020 -0700
    Revert "adding a protease track to uniprot, refs #25192". I have no idea what happened here, looks like I typed git commit -a instead of git commit -m This reverts commit db7c8abb6d7674bb26f579eabb58bc080ce76fdd.
  • lines changed 31, context: html, text, full: html, text
    01c9e489a1e4a544d33cf3e5d21d2dd39d36e7df Wed May 13 13:54:38 2020 -0700
    adding uniprot protease track docs page, refs #25192
• src/hg/utils/automation/blastz-run-ucsc
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    3f7ec313053fa504911f69798236f571b8932e3f Sun May 17 13:55:40 2020 -0700
    fixup use of type command for debian dash shell refs #25528
• src/hg/utils/otto/nextstrainNcov/doUpdate.sh
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    a90606c0cc1d4650334172bdc0b193b2c19c1dbe Mon May 11 17:38:27 2020 -0700
    With Max's approval, convert the bedGraph Counts track to alt allele frequency (easier to explain, normalized to [0, 1]). Also, don't include ncov.json in the archive directories -- Trevor Bedford of Nextstrain said that GISAID doesn't want it available for public download. :( refs #25481, #25188
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    db96d28dd92f6ad538d7f07ef1ee600bbd599fa7 Tue May 12 09:47:32 2020 -0700
    Use more force when downloading latest ncov.json so the script doesn't die if there's a read-only ncov.json file in the way. refs #25188
• src/hg/utils/otto/nextstrainNcov/nextstrain.py
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    f6bebb8752bbd5f6f40713cc4ee93ed6c0804325 Mon May 11 16:06:38 2020 -0700
    Removed the warning about amino acid changes that don't match regex because they have added changes to '-' (as they did before for SNVs). refs #25188
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    0b18ad3971852efb98daabd60d55ec1cc1711612 Thu May 14 13:46:59 2020 -0700
    Python learning: the whole point of 'with open(...) as f' is that you don't have to remember to close f.
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    1395e00347b5e2aa8cdd2ad8039febd174fe951f Thu May 14 14:39:34 2020 -0700
    Fixing FORMAT column in per-clade and recurrent bi-allelic VCF output. (was causing about a million silent calls to vcfFileErr). refs #25188
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    5e880d2ed96fe5ad464fc9b98b07ea8dab70d7f6 Fri May 15 10:29:11 2020 -0700
    Back-mutations on the path to clade nodes cause duplicate blocks in the nextstrainClade bed, which causes sporadic bedToBigBed errors. Handle those by removing both the forward and back mutations because they cancel each other out in terms of the alleles at the clade node. Leave them in the variant string as a reminder that the tree has funky back-mutations. refs #25188
• src/hg/utils/refSeqGet/tests/expected/basicListTest.gp
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    259002a92c7e2b7f01f4bbbd079790eab6a6cec2 Wed May 13 10:01:45 2020 -0700
    Fixing refSeqGet tests
• src/hg/utils/refSeqGet/tests/expected/basicListTest.meta
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    259002a92c7e2b7f01f4bbbd079790eab6a6cec2 Wed May 13 10:01:45 2020 -0700
    Fixing refSeqGet tests
• src/hg/utils/refSeqGet/tests/expected/basicListTest.psl
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    259002a92c7e2b7f01f4bbbd079790eab6a6cec2 Wed May 13 10:01:45 2020 -0700
    Fixing refSeqGet tests
• src/hg/utils/refSeqGet/tests/expected/basicListTest.rna.fa
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    259002a92c7e2b7f01f4bbbd079790eab6a6cec2 Wed May 13 10:01:45 2020 -0700
    Fixing refSeqGet tests
• src/hg/utils/refSeqGet/tests/expected/versionedListTest.gp
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    259002a92c7e2b7f01f4bbbd079790eab6a6cec2 Wed May 13 10:01:45 2020 -0700
    Fixing refSeqGet tests
• src/hg/utils/refSeqGet/tests/expected/versionedListTest.meta
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    259002a92c7e2b7f01f4bbbd079790eab6a6cec2 Wed May 13 10:01:45 2020 -0700
    Fixing refSeqGet tests
• src/hg/utils/refSeqGet/tests/expected/versionedListTest.psl
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    259002a92c7e2b7f01f4bbbd079790eab6a6cec2 Wed May 13 10:01:45 2020 -0700
    Fixing refSeqGet tests
• src/hg/utils/refSeqGet/tests/expected/versionedListTest.rna.fa
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    259002a92c7e2b7f01f4bbbd079790eab6a6cec2 Wed May 13 10:01:45 2020 -0700
    Fixing refSeqGet tests
• src/hg/utils/refSeqGet/tests/input/versioned.acc
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    259002a92c7e2b7f01f4bbbd079790eab6a6cec2 Wed May 13 10:01:45 2020 -0700
    Fixing refSeqGet tests
• src/hg/utils/tdbQuery/tdbQuery.c
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    cf6c86d4ab35eecaebbaca76640393fd060af845 Fri May 15 14:35:22 2020 -0700
    Changed compatibleReleases to use recordMatchesRelease instead of sameString so that whitespace differences won't throw it off (and one record listing more releases than the other won't be a problem). Also changed buildReleaseBits to copy and clobber instead of clobbering and fixing (which could fail if there is a space before a comma). Also removed some logic for inheriting release from a parent because hgTrackDb doesn't do that.
• src/hg/utils/transMapPslToGenePred/transMapPslToGenePred.c
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    9543454d80c5c9ad8096398fba715c07ae8801b4 Mon May 11 12:23:22 2020 -0700
    fixed usage message
• src/inc/genoFind.h
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    155197c63e3259d0922c5c3a0e859f4812129db4 Sun May 17 17:52:03 2020 -0700
    gfServer and blat and isPcr extended with new commandline option -noSimpRepMask to help with small genomes. refs #25477
• src/inc/htmshell.h
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    b9d7723866095088387017765ea962f83e87bbfd Wed May 6 16:23:13 2020 -0700
    Add supertrack to supertrack member title bar. Part of attempt to make supertrack member UI page easier to understand (show hierarchy but subtly). refs #24948
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    306429a79f9eedb8614ad52c6f5e2ad60bc50449 Mon May 11 16:54:58 2020 -0700
    Reverting html and web lib changes for allowing tags in title bars. (For now, limiting to trackUi). refs #24948
• src/inc/memgfx.h
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    e46073f856770bdfef4f7637eea8f9f9297aa139 Tue Nov 19 15:57:08 2019 -0800
    Initial commit of new track type vcfPhased trio. A line with ticks, one per haplotype per sample in the VCF, as specified by trackDb variables.
• src/inc/vcf.h
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    e46073f856770bdfef4f7637eea8f9f9297aa139 Tue Nov 19 15:57:08 2019 -0800
    Initial commit of new track type vcfPhased trio. A line with ticks, one per haplotype per sample in the VCF, as specified by trackDb variables.
• src/isPcr/isPcr/isPcr.c
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    155197c63e3259d0922c5c3a0e859f4812129db4 Sun May 17 17:52:03 2020 -0700
    gfServer and blat and isPcr extended with new commandline option -noSimpRepMask to help with small genomes. refs #25477
• src/jkOwnLib/genoFind.c
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    155197c63e3259d0922c5c3a0e859f4812129db4 Sun May 17 17:52:03 2020 -0700
    gfServer and blat and isPcr extended with new commandline option -noSimpRepMask to help with small genomes. refs #25477
• src/lib/htmshell.c
  • lines changed 8, context: html, text, full: html, text
    b9d7723866095088387017765ea962f83e87bbfd Wed May 6 16:23:13 2020 -0700
    Add supertrack to supertrack member title bar. Part of attempt to make supertrack member UI page easier to understand (show hierarchy but subtly). refs #24948
  • lines changed 8, context: html, text, full: html, text
    306429a79f9eedb8614ad52c6f5e2ad60bc50449 Mon May 11 16:54:58 2020 -0700
    Reverting html and web lib changes for allowing tags in title bars. (For now, limiting to trackUi). refs #24948
• src/utils/apacheLogParse
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    db7c8abb6d7674bb26f579eabb58bc080ce76fdd Tue May 12 07:04:05 2020 -0700
    adding a protease track to uniprot, refs #25192
  • lines changed 40, context: html, text, full: html, text
    f225bd9ef750fb706f2f14bd87e3512b43e23dc1 Wed May 13 13:50:34 2020 -0700
    Revert "adding a protease track to uniprot, refs #25192". I have no idea what happened here, looks like I typed git commit -a instead of git commit -m This reverts commit db7c8abb6d7674bb26f579eabb58bc080ce76fdd.
• src/utils/genbankToBigGenePred
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    e975034e529d38834c40b7c5b10519d2c06372f8 Wed May 13 08:11:17 2020 -0700
    making a few fixes to genbankToBigGenePred, refs #25114
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    bdc06272b74428b4b206745d07b0ac4c527444f8 Mon May 18 07:01:01 2020 -0700
    fixing the Orf1ab problem, refs #25114 as per email from Jason
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    a0ea77a19c81a4c1d0929d6f97994e1843309adb Mon May 18 08:06:53 2020 -0700
    fixing Orf1ab to ORF1ab, refs #25114
• src/utils/makefile
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    db7c8abb6d7674bb26f579eabb58bc080ce76fdd Tue May 12 07:04:05 2020 -0700
    adding a protease track to uniprot, refs #25192
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    9be83456f0cc46e79ebc460d75fe61ab9198c0c0 Tue May 12 11:00:18 2020 -0700
    Adding new util for indexing bigBeds, adding make tests and to list of user utilts refs #24479
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    f225bd9ef750fb706f2f14bd87e3512b43e23dc1 Wed May 13 13:50:34 2020 -0700
    Revert "adding a protease track to uniprot, refs #25192". I have no idea what happened here, looks like I typed git commit -a instead of git commit -m This reverts commit db7c8abb6d7674bb26f579eabb58bc080ce76fdd.
• src/utils/trackDbIndexBb/makefile
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    9be83456f0cc46e79ebc460d75fe61ab9198c0c0 Tue May 12 11:00:18 2020 -0700
    Adding new util for indexing bigBeds, adding make tests and to list of user utilts refs #24479
• src/utils/trackDbIndexBb/tests/expected/uniformDnase.multiBed.bb
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    9be83456f0cc46e79ebc460d75fe61ab9198c0c0 Tue May 12 11:00:18 2020 -0700
    Adding new util for indexing bigBeds, adding make tests and to list of user utilts refs #24479
• src/utils/trackDbIndexBb/tests/expected/uniformDnase.multiBedSources.tab
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    9be83456f0cc46e79ebc460d75fe61ab9198c0c0 Tue May 12 11:00:18 2020 -0700
    Adding new util for indexing bigBeds, adding make tests and to list of user utilts refs #24479
• src/utils/trackDbIndexBb/tests/in/hg19.chrom.sizes
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    9be83456f0cc46e79ebc460d75fe61ab9198c0c0 Tue May 12 11:00:18 2020 -0700
    Adding new util for indexing bigBeds, adding make tests and to list of user utilts refs #24479
• src/utils/trackDbIndexBb/tests/in/trackDb.smallExample.txt
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    9be83456f0cc46e79ebc460d75fe61ab9198c0c0 Tue May 12 11:00:18 2020 -0700
    Adding new util for indexing bigBeds, adding make tests and to list of user utilts refs #24479
• src/utils/trackDbIndexBb/tests/in/wgEncodeOpenChromDnaseGm12878Aln_5Reps.norm5.rawsignal.bw
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    9be83456f0cc46e79ebc460d75fe61ab9198c0c0 Tue May 12 11:00:18 2020 -0700
    Adding new util for indexing bigBeds, adding make tests and to list of user utilts refs #24479
• src/utils/trackDbIndexBb/tests/in/wgEncodeOpenChromDnaseH1hescAln_2Reps.norm5.rawsignal.bw
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    9be83456f0cc46e79ebc460d75fe61ab9198c0c0 Tue May 12 11:00:18 2020 -0700
    Adding new util for indexing bigBeds, adding make tests and to list of user utilts refs #24479
• src/utils/trackDbIndexBb/tests/in/wgEncodeOpenChromDnaseK562Aln_2Reps.norm5.rawsignal.bw
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    9be83456f0cc46e79ebc460d75fe61ab9198c0c0 Tue May 12 11:00:18 2020 -0700
    Adding new util for indexing bigBeds, adding make tests and to list of user utilts refs #24479
• src/utils/trackDbIndexBb/tests/in/wgEncodeUWDukeDnaseGM12878.fdr01peaks.hg19.bb
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    9be83456f0cc46e79ebc460d75fe61ab9198c0c0 Tue May 12 11:00:18 2020 -0700
    Adding new util for indexing bigBeds, adding make tests and to list of user utilts refs #24479
• src/utils/trackDbIndexBb/tests/in/wgEncodeUWDukeDnaseH1hESC.fdr01peaks.hg19.bb
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    9be83456f0cc46e79ebc460d75fe61ab9198c0c0 Tue May 12 11:00:18 2020 -0700
    Adding new util for indexing bigBeds, adding make tests and to list of user utilts refs #24479
• src/utils/trackDbIndexBb/tests/in/wgEncodeUWDukeDnaseK562.fdr01peaks.hg19.bb
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    9be83456f0cc46e79ebc460d75fe61ab9198c0c0 Tue May 12 11:00:18 2020 -0700
    Adding new util for indexing bigBeds, adding make tests and to list of user utilts refs #24479
• src/utils/trackDbIndexBb/tests/in/wgEncodeUwDnaseGm12878Aln_2Reps.norm5.rawsignal.bw
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    9be83456f0cc46e79ebc460d75fe61ab9198c0c0 Tue May 12 11:00:18 2020 -0700
    Adding new util for indexing bigBeds, adding make tests and to list of user utilts refs #24479
• src/utils/trackDbIndexBb/tests/in/wgEncodeUwDnaseH1hescAln_1Reps.norm5.rawsignal.bw
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    9be83456f0cc46e79ebc460d75fe61ab9198c0c0 Tue May 12 11:00:18 2020 -0700
    Adding new util for indexing bigBeds, adding make tests and to list of user utilts refs #24479
• src/utils/trackDbIndexBb/tests/in/wgEncodeUwDnaseK562Aln_2Reps.norm5.rawsignal.bw
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    9be83456f0cc46e79ebc460d75fe61ab9198c0c0 Tue May 12 11:00:18 2020 -0700
    Adding new util for indexing bigBeds, adding make tests and to list of user utilts refs #24479
• src/utils/trackDbIndexBb/tests/makefile
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    9be83456f0cc46e79ebc460d75fe61ab9198c0c0 Tue May 12 11:00:18 2020 -0700
    Adding new util for indexing bigBeds, adding make tests and to list of user utilts refs #24479
• src/utils/trackDbIndexBb/tests/trackDbIndexBb
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    9be83456f0cc46e79ebc460d75fe61ab9198c0c0 Tue May 12 11:00:18 2020 -0700
    Adding new util for indexing bigBeds, adding make tests and to list of user utilts refs #24479
• src/utils/trackDbIndexBb/trackDbIndexBb
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    9be83456f0cc46e79ebc460d75fe61ab9198c0c0 Tue May 12 11:00:18 2020 -0700
    Adding new util for indexing bigBeds, adding make tests and to list of user utilts refs #24479

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• files changed: 179