Commits for angie
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v314_base to v315_preview (2015-03-30 to 2015-04-08) v315
- Turning off exon numbers for DGV, as b0b requested.
refs #7474
- src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 2, context: html, text, full: html, text
- Updated ExAC to release 0.3 and added subtrack with calling regions.
refs #14379
- src/hg/makeDb/doc/hg19.txt - lines changed 45, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/exac.html - lines changed 41, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/exacVariants.html - lines changed 39, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 18, context: html, text, full: html, text
- src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text
- A couple tweaks to ExAC description/metadata.
refs #14379
- src/hg/makeDb/trackDb/human/hg19/exac.html - lines changed 11, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 1, context: html, text, full: html, text
- Updating usage message in utils that now accept a URL for chrom.sizes.
resolves #14857
- src/utils/bedClip/bedClip.c - lines changed 6, context: html, text, full: html, text
- src/utils/bedGraphToBigWig/bedGraphToBigWig.c - lines changed 6, context: html, text, full: html, text
- src/utils/bedToBigBed/bedToBigBed.c - lines changed 6, context: html, text, full: html, text
- src/utils/wigToBigWig/wigToBigWig.c - lines changed 6, 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/bigBed.c - lines changed 1, context: html, text, full: html, text
- src/hg/hgTables/filterFields.c - lines changed 10, context: html, text, full: html, text
- src/hg/hgTables/hgTables.c - lines changed 25, context: html, text, full: html, text
- src/hg/hgTables/hgTables.h - 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/htdocs/style/HGStyle.css - 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
- src/hg/hgc/vcfClick.c - lines changed 110, context: html, text, full: html, text
- src/hg/htdocs/style/HGStyle.css - lines changed 5, 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
- 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/js/model/hgIntegrator/hgIntegratorModel.js - 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/inc/annoStreamDbKnownGene.h - lines changed 21, context: html, text, full: html, text
- src/hg/lib/annoFormatVep.c - lines changed 4, context: html, text, full: html, text
- src/hg/lib/annoStreamDbKnownGene.c - lines changed 178, context: html, text, full: html, text
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