All File Changes

v317_preview to v317_preview2 (2015-05-18 to 2015-05-25) v317

• cirmNotes.txt
  • lines changed 18, context: html, text, full: html, text
    Some basic notes about the assignment, I am piping stats directly into the file, and worry it will be overwritten. Hence, git
    
• confs/hgwdev.hg.conf
  • lines changed 12, context: html, text, full: html, text
    A few recent changes to dev's hg.conf
    
• src/hg/cirm/cdw/cirmTags/cirmTags.c
  • lines changed 79, context: html, text, full: html, text
    Working on some cirm tag verifcation for Jim
    
  • lines changed 14, context: html, text, full: html, text
    This code runs on a Excel file (.xlsx) t
    
• src/hg/cirm/cdw/cirmTags/makefile
  • lines changed 3, context: html, text, full: html, text
    Working on some cirm tag verifcation for Jim
    
• src/hg/expData/expData.c
  • lines changed 465, context: html, text, full: html, text
    Changed the graph generation a bit, now the nodes are weighted based on children
    
• src/hg/expData/forceLayout.json
  • lines changed 247, context: html, text, full: html, text
    Changed the graph generation a bit, now the nodes are weighted based on children
    
• src/hg/expData/makefile
  • lines changed 3, context: html, text, full: html, text
    Changed the graph generation a bit, now the nodes are weighted based on children
    
• src/hg/expData/radialDend.html
  • lines changed 109, context: html, text, full: html, text
    Changed the graph generation a bit, now the nodes are weighted based on children
    
• src/hg/expMatrixToJson/expData.c
  • lines changed 465, context: html, text, full: html, text
    Changed the graph generation a bit, now the nodes are weighted based on children
    
• src/hg/expMatrixToJson/expMatrixToJson.c
  • lines changed 499, context: html, text, full: html, text
    Changed the graph generation a bit, now the nodes are weighted based on children
    
  • lines changed 11, context: html, text, full: html, text
    The binary tree is now a weighted binary tree
    
• src/hg/expMatrixToJson/forceLayout.json
  • lines changed 247, context: html, text, full: html, text
    Changed the graph generation a bit, now the nodes are weighted based on children
    
• src/hg/expMatrixToJson/makefile
  • lines changed 3, context: html, text, full: html, text
    Changed the graph generation a bit, now the nodes are weighted based on children
    
• src/hg/expMatrixToJson/radialDend.html
  • lines changed 109, context: html, text, full: html, text
    Changed the graph generation a bit, now the nodes are weighted based on children
    
• src/hg/hgGene/hgGene.c
  • lines changed 5, context: html, text, full: html, text
    get GENCODE ID from knownGene table if Gencode models #14639
    
• src/hg/hgTracks/extTools.c
  • lines changed 192, context: html, text, full: html, text
    implementing the external tools "send to" menu, refs #15113
    
• src/hg/hgTracks/extTools.h
  • lines changed 27, context: html, text, full: html, text
    implementing the external tools "send to" menu, refs #15113
    
• src/hg/hgTracks/extTools.ra
  • lines changed 371, context: html, text, full: html, text
    implementing the external tools "send to" menu, refs #15113
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 4, context: html, text, full: html, text
    if hideTracks is on the command line, set the visibilities of the other
    tracks based on URL even if they are the default visibilities in
    trackDb refs #15299
    
  • lines changed 1, context: html, text, full: html, text
    changed a grammar nit in comment. nothing to see here, except b0b's preoccupation with distinction between its and it's
    
  • lines changed 76, context: html, text, full: html, text
    adding keyboard shortcuts, refs #15370
    
  • lines changed 38, context: html, text, full: html, text
    implementing the external tools "send to" menu, refs #15113
    
• src/hg/hgTracks/mainMain.c
  • lines changed 15, context: html, text, full: html, text
    implementing the external tools "send to" menu, refs #15113
    
• src/hg/hgTracks/makefile
  • lines changed 1, context: html, text, full: html, text
    implementing the external tools "send to" menu, refs #15113
    
• src/hg/hgTracks/menu.c
  • lines changed 109, context: html, text, full: html, text
    implementing the external tools "send to" menu, refs #15113
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    take out spurious printf #15399
    
  • lines changed 10, context: html, text, full: html, text
    add NCBI metadata to NCBI RefSeq track ( refs# 13673)
    
• src/hg/hgc/hgc.c
  • lines changed 90, context: html, text, full: html, text
    add NCBI metadata to NCBI RefSeq track ( refs# 13673)
    
  • lines changed 19, context: html, text, full: html, text
    hgc: tolerate the absence of two big Genbank tables in refseq, with a warning
    
  • lines changed 93, context: html, text, full: html, text
    implementing the external tools "send to" menu, refs #15113
    
• src/hg/hgc/hgc.h
  • lines changed 3, context: html, text, full: html, text
    implementing the external tools "send to" menu, refs #15113
    
• src/hg/hgc/lrgClick.c
  • lines changed 8, context: html, text, full: html, text
    implementing the external tools "send to" menu, refs #15113
    
• src/hg/htdocs/admin/403.html
  • lines changed 4, context: html, text, full: html, text
    Change some absolute links to relative in static docs
    
• src/hg/htdocs/admin/404.html
  • lines changed 4, context: html, text, full: html, text
    Change some absolute links to relative in static docs
    
• src/hg/htdocs/admin/500.html
  • lines changed 4, context: html, text, full: html, text
    Change some absolute links to relative in static docs
    
• src/hg/htdocs/goldenPath/help/query.html
  • lines changed 6, context: html, text, full: html, text
    Change some absolute links to relative in static docs
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.css
  • lines changed 2, context: html, text, full: html, text
    Add support for deprecated settings. And fix display of settings so those in groups show with proper level (instead of 'new'). refs #10015
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.js
  • lines changed 12, context: html, text, full: html, text
    Add support for deprecated settings. And fix display of settings so those in groups show with proper level (instead of 'new'). refs #10015
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html
  • lines changed 44, context: html, text, full: html, text
    Add support for deprecated settings. And fix display of settings so those in groups show with proper level (instead of 'new'). refs #10015
    
• src/hg/htdocs/images/shortcutHelp.png
  • lines changed 0, context: html, text, full: html, text
    adding keyboard shortcuts, refs #15370
    
• src/hg/htdocs/style/HGStyle.css
  • lines changed 1, context: html, text, full: html, text
    Removed the height constraint from absoluteModal so the modal wouldn't
    be taller than necessary (thus showing the section border bottom which
    looks clunky). This also simplifies the scrolling behavior -- no more
    scroll-within-scroll. However, it can leave the user looking at the
    bottom of the main page if they scroll down a large 'choose fields' list
    and click the Done button at the bottom of the tall modal.
    refs #14579
    
  • lines changed 4, context: html, text, full: html, text
    adding keyboard shortcuts, refs #15370
    
• src/hg/htdocs/style/nice_menu.css
  • lines changed 20, context: html, text, full: html, text
    implementing the external tools "send to" menu, refs #15113
    
• src/hg/inc/hui.h
  • lines changed 4, context: html, text, full: html, text
    implementing the external tools "send to" menu, refs #15113
    
• src/hg/inc/ncbiRefLink.h
  • lines changed 67, context: html, text, full: html, text
    add NCBI metadata to NCBI RefSeq track ( refs# 13673)
    
• src/hg/js/makefile
  • lines changed 1, context: html, text, full: html, text
    adding keyboard shortcuts, refs #15370
    
• src/hg/js/model/hgIntegrator/hgIntegratorModel.js
  • lines changed 3, context: html, text, full: html, text
    When the main model makes server requests after the CladeOrgDbMixin
    makes the server request to change the clade, org, db and position,
    the main model's server requests need to repeat the changing cgi vars.
    If they don't, then there's a race condition: if the main model's
    request(s) read the cart before CladeOrgDbMixin's changes have been
    written to the cart, but they take longer to complete, then they
    can write back old cart vars, squashing CladeOrgDbMixin's changes.
    So I added a function to get all of the cart variable changes that
    must be repeated by more-or-less simultaneous requests. Would be
    nice to have a more general way of handling this!
    refs #14579 note 52
    
  • lines changed 5, context: html, text, full: html, text
    hgIntegrator: omit bam and maf (wigMaf) tracks from the group/track/table menus
    because the underlying anno* libs don't support those types yet.
    refs #14579 note 52
    
  • lines changed 4, context: html, text, full: html, text
    Trim some UI-only stuff from the querySpec sent when user clicks 'get output'.
    This should be refactored out with similar code in cartSendQuerySpec, but I'm
    not doing that just yet to avoid a merge conflict with a branch I'm working on.
    refs #14579
    
• src/hg/js/model/lib/CladeOrgDbMixin.js
  • lines changed 15, context: html, text, full: html, text
    When the main model makes server requests after the CladeOrgDbMixin
    makes the server request to change the clade, org, db and position,
    the main model's server requests need to repeat the changing cgi vars.
    If they don't, then there's a race condition: if the main model's
    request(s) read the cart before CladeOrgDbMixin's changes have been
    written to the cart, but they take longer to complete, then they
    can write back old cart vars, squashing CladeOrgDbMixin's changes.
    So I added a function to get all of the cart variable changes that
    must be repeated by more-or-less simultaneous requests. Would be
    nice to have a more general way of handling this!
    refs #14579 note 52
    
• src/hg/js/mousetrap.min.js
  • lines changed 11, context: html, text, full: html, text
    adding keyboard shortcuts, refs #15370
    
• src/hg/js/react/hgIntegrator/hgIntegrator.jsx
  • lines changed 3, context: html, text, full: html, text
    In the 'Choose Fields' dialog, put checkboxes and labels in separate columns so the label doesn't wrap around under the checkbox when squeezed.
    refs #14579
    
• src/hg/js/react/react.mk
  • lines changed 15, context: html, text, full: html, text
    common.mk: auto-detect hgwdev's installation of node.js tools.
    If jshint, jsxhint, jsx and/or uglifyjs are installed, set the corresponding
    JSHINT etc. variables; if not found, set variable to 'true' so makefile can
    invoke those steps without any effect (in which case the precompiled files
    in hg/js/react/bundle/ will not reflect any changes made to *.jsx).
    
• src/hg/lib/annoStreamWig.c
  • lines changed 3, context: html, text, full: html, text
    Add chrom, chromStart, chromEnd back into the autoSql for wig and bigWig annoStreamers.
    Now the columns can be selected/deselected the usual way instead of being fudged into
    the output with no choice.
    refs #14579
    
• src/hg/lib/cart.c
  • lines changed 3, context: html, text, full: html, text
    add a hg.conf option that makes sure that errAbort messages are always
    shown to the user, even when they are before a Content-type, refs #15332
    
• src/hg/lib/cartJson.c
  • lines changed 79, context: html, text, full: html, text
    hgIntegrator: omit bam and maf (wigMaf) tracks from the group/track/table menus
    because the underlying anno* libs don't support those types yet.
    refs #14579 note 52
    
• src/hg/lib/hAnno.c
  • lines changed 5, context: html, text, full: html, text
    Yikes, annoGrateBigWigNew was not properly hooked up before! So instead of getting
    wiggle values only for the primary item's position, each primary item got wiggle values
    for the whole position range, ick.
    refs #14579
    
• src/hg/lib/hui.c
  • lines changed 124, context: html, text, full: html, text
    implementing the external tools "send to" menu, refs #15113
    
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    add NCBI metadata to NCBI RefSeq track ( refs# 13673)
    
• src/hg/lib/ncbiRefLink.as
  • lines changed 9, context: html, text, full: html, text
    add NCBI metadata to NCBI RefSeq track ( refs# 13673)
    
• src/hg/lib/ncbiRefLink.c
  • lines changed 150, context: html, text, full: html, text
    add NCBI metadata to NCBI RefSeq track ( refs# 13673)
    
• src/hg/lib/ncbiRefLink.sql
  • lines changed 15, context: html, text, full: html, text
    add NCBI metadata to NCBI RefSeq track ( refs# 13673)
    
• src/hg/lib/sqlProg.c
  • lines changed 5, context: html, text, full: html, text
    fixed race condition on hgsql purging temporary files that caused errors when mulitple hgsql commands were run at the same thing. This is why /tmp was invented (no redmine)
    
• src/hg/lib/trackHubCheck.c
  • lines changed 11, context: html, text, full: html, text
    Change hard-coded paths and version to expected for production (v0, file on genome.ucsc.edu). refs #10015
    
  • lines changed 9, context: html, text, full: html, text
    Clean up error messages so count is correct. refs #10015
    
  • lines changed 31, context: html, text, full: html, text
    Add support for deprecated settings. And fix display of settings so those in groups show with proper level (instead of 'new'). refs #10015
    
• src/hg/lib/web.c
  • lines changed 1, context: html, text, full: html, text
    add a hg.conf option that makes sure that errAbort messages are always
    shown to the user, even when they are before a Content-type, refs #15332
    
• src/hg/makeDb/doc/bisBis1/initialBuild.txt
  • lines changed 495, context: html, text, full: html, text
    running up genbank refs #15388
    
• src/hg/makeDb/doc/danRer10/ncbiGene.txt
  • lines changed 14, context: html, text, full: html, text
    add NCBI metadata to NCBI RefSeq track ( refs# 13673)
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 6, context: html, text, full: html, text
    adding microsat track to hg38 correcting instructions for hg19 refs #15398
    
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 21, context: html, text, full: html, text
    adding microsat track to hg38 correcting instructions for hg19 refs #15398
    
• src/hg/makeDb/doc/hg38/hg38Patch3.txt
  • lines changed 3, context: html, text, full: html, text
    load up the net track refs #15413
    
  • lines changed 9, context: html, text, full: html, text
    correctly indicate the loading of the chain/net tables on the hg38Patch3 db refs #15143
    
• src/hg/makeDb/doc/hg38/ncbiGene.txt
  • lines changed 16, context: html, text, full: html, text
    add NCBI metadata to NCBI RefSeq track ( refs# 13673)
    
• src/hg/makeDb/doc/mm10.txt
  • lines changed 15, context: html, text, full: html, text
    add NCBI metadata to NCBI RefSeq track ( refs# 13673)
    
• src/hg/makeDb/doc/ornAna2/initialBuild.txt
  • lines changed 479, context: html, text, full: html, text
    loading genbank and running augustus refs #15098
    
• src/hg/makeDb/doc/ornAna2/ucscCompositeAgp.pl
  • lines changed 62, context: html, text, full: html, text
    loading genbank and running augustus refs #15098
    
• src/hg/makeDb/doc/ornAna2/unlocalized.pl
  • lines changed 79, context: html, text, full: html, text
    loading genbank and running augustus refs #15098
    
• src/hg/makeDb/doc/ornAna2/unplaced.pl
  • lines changed 48, context: html, text, full: html, text
    loading genbank and running augustus refs #15098
    
• src/hg/makeDb/doc/panPan1.txt
  • lines changed 7, context: html, text, full: html, text
    rerun genbank to get mrna.native.load on yes refs #8231
    
• src/hg/makeDb/doc/rn6.txt
  • lines changed 15, context: html, text, full: html, text
    add NCBI metadata to NCBI RefSeq track ( refs# 13673)
    
• src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes15.csh
  • lines changed 16, context: html, text, full: html, text
    loaded the blastTabs on the other species for mm10 ucsc genes refs
    
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 6, context: html, text, full: html, text
    turning on refseq.mrna.native for panPan1 refs #8231
    
  • lines changed 3, context: html, text, full: html, text
    correct entries for bisBis1 refs 15388
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 9, context: html, text, full: html, text
    adding hg38Patch3 rules refs #15413
    
  • lines changed 1, context: html, text, full: html, text
    Added altSeqLiftOverPslP3 to hg38 tablesIgnored; refs #15143
    
• src/hg/makeDb/trackDb/augustusGene.html
  • lines changed 52, context: html, text, full: html, text
    adding description page for augustusGene refs #13088
    
• src/hg/makeDb/trackDb/gorilla/gorGor3/trackDb.chainNet.ra
  • lines changed 1, context: html, text, full: html, text
    Chain/net trackDb shuffling for the release of new tarSyr2 chain/net tracks, refs #15112
    
• src/hg/makeDb/trackDb/human/chainNetLegacy.ra
  • lines changed 16, context: html, text, full: html, text
    Chain/net trackDb shuffling for the release of new tarSyr2 chain/net tracks, refs #15112
    
• src/hg/makeDb/trackDb/human/chainNetPrimate.ra
  • lines changed 16, context: html, text, full: html, text
    Chain/net trackDb shuffling for the release of new tarSyr2 chain/net tracks, refs #15112
    
• src/hg/makeDb/trackDb/human/hg38/alpha.7way.ra
  • lines changed 1, context: html, text, full: html, text
    Added note to 7-way description page about problems with rhesus, mouse and dog; changes 7-way visibility setting to hide with release of 20-way; refs #15144
    
• src/hg/makeDb/trackDb/human/hg38/betaPublic.7way.ra
  • lines changed 1, context: html, text, full: html, text
    Added note to 7-way description page about problems with rhesus, mouse and dog; changes 7-way visibility setting to hide with release of 20-way; refs #15144
    
• src/hg/makeDb/trackDb/human/hg38/cons7way.html
  • lines changed 8, context: html, text, full: html, text
    Added note to 7-way description page about problems with rhesus, mouse and dog; changes 7-way visibility setting to hide with release of 20-way; refs #15144
    
• src/hg/makeDb/trackDb/human/hg38/hg38Patch3.ra
  • lines changed 2, context: html, text, full: html, text
    fixup search rule for hg38Patch3 tables refs #15143
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding microsat track to hg38 correcting instructions for hg19 refs #15398
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeSuper.html
  • lines changed 174, context: html, text, full: html, text
    Added missing description for gencode supertrack (#15374)
    
  • lines changed 50, context: html, text, full: html, text
    Made corrections to update page from GRCh37 to GRCh38; fixed references; refs #15115
    
• src/hg/makeDb/trackDb/human/newChainNet.ra
  • lines changed 14, context: html, text, full: html, text
    Commenting out extra tarSyr1 chain/net entries. May remove completely later. (no redmine)
    
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.euarchontoglireChainNet.ra
  • lines changed 20, context: html, text, full: html, text
    Chain/net trackDb shuffling for the release of new tarSyr2 chain/net tracks, refs #15112
    
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.previousVersionsChainNet.ra
  • lines changed 16, context: html, text, full: html, text
    Chain/net trackDb shuffling for the release of new tarSyr2 chain/net tracks, refs #15112
    
• src/hg/makeDb/trackDb/tarsier/tarSyr2/cons20way.html
  • lines changed 1, context: html, text, full: html, text
    Removing erroneous asterisk on 20way desc page, changing default vis. for NCBI RefGene track, refs #15112 #13673
    
• src/hg/makeDb/trackDb/tarsier/tarSyr2/trackDb.20way.ra
  • lines changed 1, context: html, text, full: html, text
    making check boxes appear in phylo order, refs #15112
    
  • lines changed 1, context: html, text, full: html, text
    Turning off SNP mode for now, refs #15112
    
• src/hg/makeDb/trackDb/tarsier/tarSyr2/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    Removing erroneous asterisk on 20way desc page, changing default vis. for NCBI RefGene track, refs #15112 #13673
    
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    adding description page for augustusGene refs #13088
    
• src/hg/utils/gff3ToGenePred/gff3ToGenePred.c
  • lines changed 19, context: html, text, full: html, text
    add NCBI metadata to NCBI RefSeq track ( refs# 13673)
    
• src/hg/utils/hubCheck/hubCheck.c
  • lines changed 3, context: html, text, full: html, text
    Clean up error messages so count is correct. refs #10015
    
• src/inc/common.mk
  • lines changed 30, context: html, text, full: html, text
    common.mk: auto-detect hgwdev's installation of node.js tools.
    If jshint, jsxhint, jsx and/or uglifyjs are installed, set the corresponding
    JSHINT etc. variables; if not found, set variable to 'true' so makefile can
    invoke those steps without any effect (in which case the precompiled files
    in hg/js/react/bundle/ will not reflect any changes made to *.jsx).
    
• src/inc/errAbort.h
  • lines changed 4, context: html, text, full: html, text
    add a hg.conf option that makes sure that errAbort messages are always
    shown to the user, even when they are before a Content-type, refs #15332
    
• src/inc/jsonWrite.h
  • lines changed 5, context: html, text, full: html, text
    hgIntegrator: omit bam and maf (wigMaf) tracks from the group/track/table menus
    because the underlying anno* libs don't support those types yet.
    refs #14579 note 52
    
• src/inc/sqlNum.h
  • lines changed 3, context: html, text, full: html, text
    implementing the external tools "send to" menu, refs #15113
    
• src/lib/annoFormatTab.c
  • lines changed 1, context: html, text, full: html, text
    hgIntegrator: instead of comma-separated lists of wiggle values that get
    quite long for large regions, output the average of values in a region.
    I got a couple requests for this at the Biology of Genomes poster session.
    refs #14579
    
  • lines changed 57, context: html, text, full: html, text
    Add chrom, chromStart, chromEnd back into the autoSql for wig and bigWig annoStreamers.
    Now the columns can be selected/deselected the usual way instead of being fudged into
    the output with no choice.
    refs #14579
    
• src/lib/annoStreamBigWig.c
  • lines changed 3, context: html, text, full: html, text
    Add chrom, chromStart, chromEnd back into the autoSql for wig and bigWig annoStreamers.
    Now the columns can be selected/deselected the usual way instead of being fudged into
    the output with no choice.
    refs #14579
    
• src/lib/bbiWrite.c
  • lines changed 6, context: html, text, full: html, text
    make sure that chroms are sorted in a case-sensitive manner in
    bedToBigBed because otherwise the indexes don't work #15400
    
• src/lib/errAbort.c
  • lines changed 20, context: html, text, full: html, text
    add a hg.conf option that makes sure that errAbort messages are always
    shown to the user, even when they are before a Content-type, refs #15332
    
• src/lib/jsonWrite.c
  • lines changed 18, context: html, text, full: html, text
    hgIntegrator: omit bam and maf (wigMaf) tracks from the group/track/table menus
    because the underlying anno* libs don't support those types yet.
    refs #14579 note 52
    
• src/lib/osunix.c
  • lines changed 1, context: html, text, full: html, text
    fixed race condition on hgsql purging temporary files that caused errors when mulitple hgsql commands were run at the same thing. This is why /tmp was invented (no redmine)
    
• src/lib/sqlNum.c
  • lines changed 24, context: html, text, full: html, text
    implementing the external tools "send to" menu, refs #15113
    
• src/product/ex.hg.conf
  • lines changed 6, context: html, text, full: html, text
    documenting showEarlyErrors hg.conf option, refs #15332
    
• src/tagStorm/jsonToTagStorm/errCheck.sh
  • lines changed 41, context: html, text, full: html, text
    A shell script that Hiram gave me, runs a program and compares the error to a text file. Good for testing.
    
• src/tagStorm/jsonToTagStorm/jsonToTagStorm.c
  • lines changed 10, context: html, text, full: html, text
    Added warning and error messages for bad inputs
    
• src/tagStorm/tagStormToJson/tagStormToJson.c
  • lines changed 12, context: html, text, full: html, text
    Some minor refactoring to make the .json files smaller
    
• src/utils/bedToBigBed/bedToBigBed.c
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    make sure that chroms are sorted in a case-sensitive manner in
    bedToBigBed because otherwise the indexes don't work #15400
    
• src/utils/bedToBigBed/tests/expected/notSorted.err
  • lines changed 1, context: html, text, full: html, text
    make sure that chroms are sorted in a case-sensitive manner in
    bedToBigBed because otherwise the indexes don't work #15400
    
• src/utils/bedToBigBed/tests/input/notSorted.bed
  • lines changed 3, context: html, text, full: html, text
    make sure that chroms are sorted in a case-sensitive manner in
    bedToBigBed because otherwise the indexes don't work #15400
    
• src/utils/bedToBigBed/tests/input/notSorted.chrom.sizes
  • lines changed 3, context: html, text, full: html, text
    make sure that chroms are sorted in a case-sensitive manner in
    bedToBigBed because otherwise the indexes don't work #15400
    
• src/utils/bedToBigBed/tests/makefile
  • lines changed 7, context: html, text, full: html, text
    make sure that chroms are sorted in a case-sensitive manner in
    bedToBigBed because otherwise the indexes don't work #15400
    
  • lines changed 2, context: html, text, full: html, text
    make sure tests are run out of ${BINDIR} in bedToBigBed #15400
    
• src/utils/bigWigCluster/bigWigCluster.c
  • lines changed 2, context: html, text, full: html, text
    REFS #15377 fixing an issue with the usage statement
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 8, context: html, text, full: html, text
    v317 preview2 refs #15355
    

• lines changed: 6008
• files changed: 132