File Changes for angie

v314_base to v315_preview (2015-03-30 to 2015-04-08) v315

• src/hg/hgTables/bigBed.c
  • lines changed 1, context: html, text, full: html, text
    hgTables fixes to support bigBed and VCF tracks that have no mysql table,
    only a bigDataUrl setting that may point to a local file.
    refs #15059
    
• src/hg/hgTables/filterFields.c
  • lines changed 10, context: html, text, full: html, text
    hgTables fixes to support bigBed and VCF tracks that have no mysql table,
    only a bigDataUrl setting that may point to a local file.
    refs #15059
    
• src/hg/hgTables/hgTables.c
  • lines changed 25, context: html, text, full: html, text
    hgTables fixes to support bigBed and VCF tracks that have no mysql table,
    only a bigDataUrl setting that may point to a local file.
    refs #15059
    
• src/hg/hgTables/hgTables.h
  • lines changed 4, context: html, text, full: html, text
    hgTables fixes to support bigBed and VCF tracks that have no mysql table,
    only a bigDataUrl setting that may point to a local file.
    refs #15059
    
• src/hg/hgTables/vcf.c
  • lines changed 20, context: html, text, full: html, text
    hgTables fixes to support bigBed and VCF tracks that have no mysql table,
    only a bigDataUrl setting that may point to a local file.
    refs #15059
    
• src/hg/hgc/hgc.c
  • lines changed 4, context: html, text, full: html, text
    Wrap hgc's track description html in a div with limited width, so if the
    page is extremely wide due to long details, the description text will
    wrap and you won't have to scroll back and forth to read it.
    
• src/hg/hgc/vcfClick.c
  • lines changed 110, context: html, text, full: html, text
    When VCF ##INFO description and data seem to have the same number of
    |-separated columns (and at least 3 apparent columns), display them
    as separate tables below the big table of INFO tags and settings
    because they can be quite large; for example, VEP annotations may
    have >40 |-separated columns for each alt allele & transcript.
    refs #14379
    
  • lines changed 1, context: html, text, full: html, text
    Use class stdTbl instead of making up new class.
    
• src/hg/htdocs/style/HGStyle.css
  • lines changed 5, context: html, text, full: html, text
    Wrap hgc's track description html in a div with limited width, so if the
    page is extremely wide due to long details, the description text will
    wrap and you won't have to scroll back and forth to read it.
    
  • lines changed 5, context: html, text, full: html, text
    When VCF ##INFO description and data seem to have the same number of
    |-separated columns (and at least 3 apparent columns), display them
    as separate tables below the big table of INFO tags and settings
    because they can be quite large; for example, VEP annotations may
    have >40 |-separated columns for each alt allele & transcript.
    refs #14379
    
  • lines changed 5, context: html, text, full: html, text
    Use class stdTbl instead of making up new class.
    
• src/hg/inc/annoStreamDbKnownGene.h
  • lines changed 21, context: html, text, full: html, text
    Added a special annoStreamer for knownGene, to tack on kgXref.geneSymbol
    at the end. Now in hgVai, the geneSymbol is shown instead of the protein ID.
    The new column is also available in hgIntegrator. Now users can get the
    gene symbol that goes with their items, without changing gene track.
    refs #11752 #14579
    
• src/hg/js/model/hgIntegrator/hgIntegratorModel.js
  • lines changed 4, context: html, text, full: html, text
    Remove track groups from incoming groupedTrackDb if they have no tracks.
    Currently this removes 'All Tracks' and 'All Tables'; if there is demand
    for those, they could be constructed at this stage.
    refs #14579
    
• src/hg/lib/annoFormatVep.c
  • lines changed 4, context: html, text, full: html, text
    Added a special annoStreamer for knownGene, to tack on kgXref.geneSymbol
    at the end. Now in hgVai, the geneSymbol is shown instead of the protein ID.
    The new column is also available in hgIntegrator. Now users can get the
    gene symbol that goes with their items, without changing gene track.
    refs #11752 #14579
    
• src/hg/lib/annoStreamDbKnownGene.c
  • lines changed 178, context: html, text, full: html, text
    Added a special annoStreamer for knownGene, to tack on kgXref.geneSymbol
    at the end. Now in hgVai, the geneSymbol is shown instead of the protein ID.
    The new column is also available in hgIntegrator. Now users can get the
    gene symbol that goes with their items, without changing gene track.
    refs #11752 #14579
    
• src/hg/lib/hAnno.c
  • lines changed 16, context: html, text, full: html, text
    Added a special annoStreamer for knownGene, to tack on kgXref.geneSymbol
    at the end. Now in hgVai, the geneSymbol is shown instead of the protein ID.
    The new column is also available in hgIntegrator. Now users can get the
    gene symbol that goes with their items, without changing gene track.
    refs #11752 #14579
    
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Added a special annoStreamer for knownGene, to tack on kgXref.geneSymbol
    at the end. Now in hgVai, the geneSymbol is shown instead of the protein ID.
    The new column is also available in hgIntegrator. Now users can get the
    gene symbol that goes with their items, without changing gene track.
    refs #11752 #14579
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 45, context: html, text, full: html, text
    Updated ExAC to release 0.3 and added subtrack with calling regions.
    refs #14379
    
• src/hg/makeDb/trackDb/human/hg19/exac.html
  • lines changed 41, context: html, text, full: html, text
    Updated ExAC to release 0.3 and added subtrack with calling regions.
    refs #14379
    
  • lines changed 11, context: html, text, full: html, text
    A couple tweaks to ExAC description/metadata.
    refs #14379
    
• src/hg/makeDb/trackDb/human/hg19/exacVariants.html
  • lines changed 39, context: html, text, full: html, text
    Updated ExAC to release 0.3 and added subtrack with calling regions.
    refs #14379
    
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 18, context: html, text, full: html, text
    Updated ExAC to release 0.3 and added subtrack with calling regions.
    refs #14379
    
  • lines changed 1, context: html, text, full: html, text
    A couple tweaks to ExAC description/metadata.
    refs #14379
    
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Turning off exon numbers for DGV, as b0b requested.
    refs #7474
    
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    Updated ExAC to release 0.3 and added subtrack with calling regions.
    refs #14379
    
• src/utils/bedClip/bedClip.c
  • lines changed 6, context: html, text, full: html, text
    Updating usage message in utils that now accept a URL for chrom.sizes.
    resolves #14857
    
• src/utils/bedGraphToBigWig/bedGraphToBigWig.c
  • lines changed 6, context: html, text, full: html, text
    Updating usage message in utils that now accept a URL for chrom.sizes.
    resolves #14857
    
• src/utils/bedToBigBed/bedToBigBed.c
  • lines changed 6, context: html, text, full: html, text
    Updating usage message in utils that now accept a URL for chrom.sizes.
    resolves #14857
    
• src/utils/wigToBigWig/wigToBigWig.c
  • lines changed 6, context: html, text, full: html, text
    Updating usage message in utils that now accept a URL for chrom.sizes.
    resolves #14857