All File Changes

v399_base to v400_preview (2020-06-01 to 2020-06-08) v400

• src/hg/hgTracks/hgTracks.h
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    c9d5c3eeb09a866dbc81d9732431c6ff0c096666 Sun Jun 7 15:46:27 2020 -0700
    Add maxWindowToDraw trackDb support to vcfPhasedTrio and limit 1000G phased trio track to 5MB. Also change up some of the UI labels, refs #25582
• src/hg/hgTracks/vcfTrack.c
  • lines changed 3, context: html, text, full: html, text
    c9d5c3eeb09a866dbc81d9732431c6ff0c096666 Sun Jun 7 15:46:27 2020 -0700
    Add maxWindowToDraw trackDb support to vcfPhasedTrio and limit 1000G phased trio track to 5MB. Also change up some of the UI labels, refs #25582
• src/hg/htdocs/ENCODE/dataSummaryMouse.html
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    5f6b0298f9be1e53c1eff9b89f6eee21af8a9145 Thu Jun 4 09:16:12 2020 -0700
    Fixing broken spreadsheet links Max found refs #25647
• src/hg/htdocs/covid19.html
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    f60979fd1b38862306b6060da3a00b3db632c9f5 Wed Jun 3 11:59:58 2020 -0700
    Updating link to hub to be relative to machine on covid19.html page
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 9, context: html, text, full: html, text
    69d2a32c5a3d72b28818c7ef59affd601ce25522 Fri Jun 5 19:00:14 2020 -0700
    standardized nominclature to key=<value> in #SHARE section. removed some whitespace
• src/hg/htdocs/goldenPath/help/trackDbIndexBb.html
  • lines changed 235, context: html, text, full: html, text
    3efabcabf4453c2ab402bb20230693af0e2e3963 Wed Jun 3 16:18:27 2020 -0700
    Help page for trackDbIndexBb utility refs #25532
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 2, context: html, text, full: html, text
    3a60e6f0c5e24242ee0a14cafb11bb158b4a5f03 Mon Jun 1 13:44:23 2020 -0700
    Feedback from CR refs #25662
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 4, context: html, text, full: html, text
    bc4db4f8be97bfcae35ebdf9ee70a903673c5e23 Thu Jun 4 09:19:14 2020 -0700
    Staging some publications in comments
• src/hg/js/autocomplete.js
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    0181c924ddf9e4c601fdd0f0bd3180e265ee50c3 Mon Jun 8 07:36:42 2020 -0700
    small js fix to allow copy/paste from position box on hgTracks, refs #25678
• src/hg/lib/encodeCcreCombined.as
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    76e480f51fbf36171248a26c9f24c3bd0e95af7f Thu Jun 4 11:38:18 2020 -0700
    Save build script and schema for CCRE track. refs #24668
• src/hg/lib/mafGene.c
  • lines changed 3, context: html, text, full: html, text
    dc9cd71799d3ded4fec70c2156cebfcc7118cbc8 Mon Jun 1 13:29:10 2020 -0700
    fix bug where 1bp exons weren't being counted.
• src/hg/lib/vcfUi.c
  • lines changed 3, context: html, text, full: html, text
    c9d5c3eeb09a866dbc81d9732431c6ff0c096666 Sun Jun 7 15:46:27 2020 -0700
    Add maxWindowToDraw trackDb support to vcfPhasedTrio and limit 1000G phased trio track to 5MB. Also change up some of the UI labels, refs #25582
• src/hg/makeDb/doc/canFam3.txt
  • lines changed 70, context: html, text, full: html, text
    cdff74ba43136ebbc37d590fe95d2eaf43c8fcb6 Fri Jun 5 09:37:29 2020 -0700
    liftOver and chainNet to canFam4 refs #25279
• src/hg/makeDb/doc/dm6/multiz124way.txt
  • lines changed 2, context: html, text, full: html, text
    592233336c30a579125ef5a52bd60be145c12521 Mon Jun 1 14:29:48 2020 -0700
    re-do mafGene alignments after bug fix
• src/hg/makeDb/doc/hg38/mane.txt
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    f003e879f8bd1b25f89bb33bbdd1cc09618f970d Mon Jun 1 12:04:50 2020 -0700
    new MANE 0.9 track
• src/hg/makeDb/doc/hg38/reg.txt
  • lines changed 53, context: html, text, full: html, text
    9e87a928af4260e37c2054af239b6b411058fd7e Thu Jun 4 11:24:29 2020 -0700
    Adding make docs for ENCODE CCRE tracks. refs #24668
  • lines changed 4, context: html, text, full: html, text
    76e480f51fbf36171248a26c9f24c3bd0e95af7f Thu Jun 4 11:38:18 2020 -0700
    Save build script and schema for CCRE track. refs #24668
• src/hg/makeDb/doc/mm10.txt
  • lines changed 41, context: html, text, full: html, text
    9e87a928af4260e37c2054af239b6b411058fd7e Thu Jun 4 11:24:29 2020 -0700
    Adding make docs for ENCODE CCRE tracks. refs #24668
  • lines changed 4, context: html, text, full: html, text
    76e480f51fbf36171248a26c9f24c3bd0e95af7f Thu Jun 4 11:38:18 2020 -0700
    Save build script and schema for CCRE track. refs #24668
  • lines changed 58, context: html, text, full: html, text
    66a8e56296308c7ed601e188dd9374ebe4b3c5ec Fri Jun 5 09:42:01 2020 -0700
    finished lastz/chain/net to assembly hub sequence per user request refs #25625
• src/hg/makeDb/outside/encode3/ccre/README.txt
  • lines changed 3, context: html, text, full: html, text
    76e480f51fbf36171248a26c9f24c3bd0e95af7f Thu Jun 4 11:38:18 2020 -0700
    Save build script and schema for CCRE track. refs #24668
• src/hg/makeDb/outside/encode3/ccre/makeCcreCombined.pl
  • lines changed 45, context: html, text, full: html, text
    76e480f51fbf36171248a26c9f24c3bd0e95af7f Thu Jun 4 11:38:18 2020 -0700
    Save build script and schema for CCRE track. refs #24668
• src/hg/makeDb/trackDb/human/gtexGeneV8.html
  • lines changed 1, context: html, text, full: html, text
    7940db9b89ae1d8c004bad4259c42b4259ca89d4 Wed Jun 3 15:38:16 2020 -0700
    Fixing incomplete link for CR #25661
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
  • lines changed 4, context: html, text, full: html, text
    511c4c51f5c9746edf62b2db2b630a1d2567cd4c Wed Jun 3 16:40:13 2020 -0700
    Staging code changes allowing gnomAD linkouts on beta refs #25600
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    511c4c51f5c9746edf62b2db2b630a1d2567cd4c Wed Jun 3 16:40:13 2020 -0700
    Staging code changes allowing gnomAD linkouts on beta refs #25600
• src/hg/makeDb/trackDb/human/hg38/encodeCcreCombined.html
  • lines changed 24, context: html, text, full: html, text
    fc071e99eaa5a3e8bfd65374cfcf6b301a4ebb67 Fri Jun 5 16:09:39 2020 -0700
    Removing an extra space and parenthesis. Making the numbered list use the numbered list html tags, refs #24668
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 2, context: html, text, full: html, text
    511c4c51f5c9746edf62b2db2b630a1d2567cd4c Wed Jun 3 16:40:13 2020 -0700
    Staging code changes allowing gnomAD linkouts on beta refs #25600
• src/hg/makeDb/trackDb/human/hg38/mane.alpha.ra
  • lines changed 5, context: html, text, full: html, text
    c244b6a2dae416e4cd568ee616ef8c1155c148e8 Mon Jun 1 12:23:35 2020 -0700
    add MANE 0.9
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    c244b6a2dae416e4cd568ee616ef8c1155c148e8 Mon Jun 1 12:23:35 2020 -0700
    add MANE 0.9
  • lines changed 8, context: html, text, full: html, text
    c9d5c3eeb09a866dbc81d9732431c6ff0c096666 Sun Jun 7 15:46:27 2020 -0700
    Add maxWindowToDraw trackDb support to vcfPhasedTrio and limit 1000G phased trio track to 5MB. Also change up some of the UI labels, refs #25582
• src/hg/makeDb/trackDb/human/trackDb.clinGen.ra
  • lines changed 11, context: html, text, full: html, text
    a7cc65d78d137b46de65297827017cf637a80014 Fri Jun 5 13:41:27 2020 -0700
    changed tracks and filters names refs #25562
• src/hg/makeDb/trackDb/human/trackDb.clinvarTest.ra
  • lines changed 11, context: html, text, full: html, text
    741f6f744739c39f0165276bc8e08907d3cc6d7d Fri Jun 5 14:54:40 2020 -0700
    Making changes to clinVar track in response to Ana refs #24850
• src/hg/makeDb/trackDb/mouse/mm10/encodeCcreCombined.html
  • lines changed 33, context: html, text, full: html, text
    2b3f7407c9139c186222571ffe8f2e2d8c245c96 Fri Jun 5 16:01:50 2020 -0700
    Using numbered list tags for the classification of cCRE's and removing an extra space, refs #24668
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    c9d5c3eeb09a866dbc81d9732431c6ff0c096666 Sun Jun 7 15:46:27 2020 -0700
    Add maxWindowToDraw trackDb support to vcfPhasedTrio and limit 1000G phased trio track to 5MB. Also change up some of the UI labels, refs #25582
• src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra
  • lines changed 55, context: html, text, full: html, text
    441bd60f9de5d7ab206028f5610788fb61e2d253 Mon Jun 1 14:22:41 2020 -0700
    trying out a chain net track on an assembly hub refs #25625
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    441bd60f9de5d7ab206028f5610788fb61e2d253 Mon Jun 1 14:22:41 2020 -0700
    trying out a chain net track on an assembly hub refs #25625
• src/hg/makeDb/trackDb/virus/wuhCor1/PhyloCSF_power.html
  • lines changed 31, context: html, text, full: html, text
    98826b7c647c43529bc0f08e34cb4eeb5f303d2f Fri Jun 5 06:04:58 2020 -0700
    tdb and doc updates for wuhCor1 phyloCSF track after feedback from authors, refs #25644
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    720b56ff2ab05dfb662737ea85cc1eedda2c2aea Fri Jun 5 14:00:02 2020 -0700
    changed from pull requests #35 and #36
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    5f189fc1f749283e467e30d4eeffdca15941e810 Fri Jun 5 14:01:58 2020 -0700
    rename HTML file to correspond to track name
• src/hg/makeDb/trackDb/virus/wuhCor1/PhyloCSF_smooth.html
  • lines changed 30, context: html, text, full: html, text
    98826b7c647c43529bc0f08e34cb4eeb5f303d2f Fri Jun 5 06:04:58 2020 -0700
    tdb and doc updates for wuhCor1 phyloCSF track after feedback from authors, refs #25644
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    720b56ff2ab05dfb662737ea85cc1eedda2c2aea Fri Jun 5 14:00:02 2020 -0700
    changed from pull requests #35 and #36
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    0007e1bce42c42e5ec0f8e5f53465bde012dcf8a Sat Jun 6 13:16:54 2020 -0700
    fixed typo
• src/hg/makeDb/trackDb/virus/wuhCor1/PhyloCSFpower.html
  • lines changed 61, context: html, text, full: html, text
    5f189fc1f749283e467e30d4eeffdca15941e810 Fri Jun 5 14:01:58 2020 -0700
    rename HTML file to correspond to track name
• src/hg/makeDb/trackDb/virus/wuhCor1/addgene.html
  • lines changed 34, context: html, text, full: html, text
    bbff98445c077f1eef4d988283f2ad5ce29a824f Mon Jun 8 05:10:48 2020 -0700
    adding addgene track for wuhCor1, refs #25683
• src/hg/makeDb/trackDb/virus/wuhCor1/addgene.ra
  • lines changed 11, context: html, text, full: html, text
    bbff98445c077f1eef4d988283f2ad5ce29a824f Mon Jun 8 05:10:48 2020 -0700
    adding addgene track for wuhCor1, refs #25683
  • lines changed 1, context: html, text, full: html, text
    d64f2b0000e1b02a8445827583dd9513a80e5493 Mon Jun 8 05:17:55 2020 -0700
    forgot outlink for addgene track, refs #25683
• src/hg/makeDb/trackDb/virus/wuhCor1/phylocsf.ra
  • lines changed 5, context: html, text, full: html, text
    98826b7c647c43529bc0f08e34cb4eeb5f303d2f Fri Jun 5 06:04:58 2020 -0700
    tdb and doc updates for wuhCor1 phyloCSF track after feedback from authors, refs #25644
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    bbff98445c077f1eef4d988283f2ad5ce29a824f Mon Jun 8 05:10:48 2020 -0700
    adding addgene track for wuhCor1, refs #25683
• src/hg/utils/hgvsToVcf/hgvsToVcf.c
  • lines changed 2, context: html, text, full: html, text
    bd2d35635bdfcfa6ddea367370bcab60b490291d Tue Jun 2 17:27:24 2020 -0700
    Make hgvsToVcf write error messages to stderr so comment lines don't mess up the VCF header
• src/hg/utils/hgvsToVcf/tests/expected/clinVarChanges.err
  • lines changed 14, context: html, text, full: html, text
    bd2d35635bdfcfa6ddea367370bcab60b490291d Tue Jun 2 17:27:24 2020 -0700
    Make hgvsToVcf write error messages to stderr so comment lines don't mess up the VCF header
• src/hg/utils/hgvsToVcf/tests/expected/clinVarChanges.vcf
  • lines changed 14, context: html, text, full: html, text
    bd2d35635bdfcfa6ddea367370bcab60b490291d Tue Jun 2 17:27:24 2020 -0700
    Make hgvsToVcf write error messages to stderr so comment lines don't mess up the VCF header
• src/hg/utils/hgvsToVcf/tests/expected/testShifting.err
  • lines changed 0, context: html, text, full: html, text
    bd2d35635bdfcfa6ddea367370bcab60b490291d Tue Jun 2 17:27:24 2020 -0700
    Make hgvsToVcf write error messages to stderr so comment lines don't mess up the VCF header
• src/hg/utils/hgvsToVcf/tests/makefile
  • lines changed 4, context: html, text, full: html, text
    bd2d35635bdfcfa6ddea367370bcab60b490291d Tue Jun 2 17:27:24 2020 -0700
    Make hgvsToVcf write error messages to stderr so comment lines don't mess up the VCF header
• src/hg/utils/otto/nextstrainNcov/cladeColors.py
  • lines changed 31, context: html, text, full: html, text
    2e6ddaec223b5b760cbba134eee52d14a327fda3 Fri May 29 15:22:45 2020 -0700
    Adding tree manipulation python scripts and modules that I've been working on for David et al. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/lineageColors.py
  • lines changed 87, context: html, text, full: html, text
    2e6ddaec223b5b760cbba134eee52d14a327fda3 Fri May 29 15:22:45 2020 -0700
    Adding tree manipulation python scripts and modules that I've been working on for David et al. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/newick.py
  • lines changed 148, context: html, text, full: html, text
    2e6ddaec223b5b760cbba134eee52d14a327fda3 Fri May 29 15:22:45 2020 -0700
    Adding tree manipulation python scripts and modules that I've been working on for David et al. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/treeColorByLineage.py
  • lines changed 28, context: html, text, full: html, text
    2e6ddaec223b5b760cbba134eee52d14a327fda3 Fri May 29 15:22:45 2020 -0700
    Adding tree manipulation python scripts and modules that I've been working on for David et al. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/treeIntersectNextstrain.py
  • lines changed 128, context: html, text, full: html, text
    2e6ddaec223b5b760cbba134eee52d14a327fda3 Fri May 29 15:22:45 2020 -0700
    Adding tree manipulation python scripts and modules that I've been working on for David et al. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/utils.py
  • lines changed 25, context: html, text, full: html, text
    2e6ddaec223b5b760cbba134eee52d14a327fda3 Fri May 29 15:22:45 2020 -0700
    Adding tree manipulation python scripts and modules that I've been working on for David et al. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/virusNames.py
  • lines changed 132, context: html, text, full: html, text
    2e6ddaec223b5b760cbba134eee52d14a327fda3 Fri May 29 15:22:45 2020 -0700
    Adding tree manipulation python scripts and modules that I've been working on for David et al. sorta refs #25278, #25382
• src/utils/qa/weeklybld/buildEnv.csh
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    184c30f5c4805d2bf891aa75d9d2e073832788af Mon Jun 8 10:00:10 2020 -0700
    v400 preview1
• src/utils/trackDbIndexBb/tests/makefile
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    bb3d819885f31adab7cf3129f54962df1fd2e347 Wed Jun 3 16:27:41 2020 -0700
    Changing the three required arguments from keyword arguments to positional arguments refs #25532
• src/utils/trackDbIndexBb/tests/trackDbIndexBb
  • lines changed 3, context: html, text, full: html, text
    d660f59a95e2156f2d2deefd6658b6c54bab1b52 Tue Jun 2 14:35:45 2020 -0700
    Fixing the finish statement to reflect the new trackDb usage, no RM
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    bb3d819885f31adab7cf3129f54962df1fd2e347 Wed Jun 3 16:27:41 2020 -0700
    Changing the three required arguments from keyword arguments to positional arguments refs #25532
• src/utils/trackDbIndexBb/trackDbIndexBb
  • lines changed 3, context: html, text, full: html, text
    d660f59a95e2156f2d2deefd6658b6c54bab1b52 Tue Jun 2 14:35:45 2020 -0700
    Fixing the finish statement to reflect the new trackDb usage, no RM
  • lines changed 21, context: html, text, full: html, text
    bb3d819885f31adab7cf3129f54962df1fd2e347 Wed Jun 3 16:27:41 2020 -0700
    Changing the three required arguments from keyword arguments to positional arguments refs #25532

• lines changed: 1883
• files changed: 66