Commits for angie
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v303_preview to v303_preview2 (2014-07-07 to 2014-07-14) v303
- I had assumed that each LRG would have a single source, but that wasincorrect; both names and urls were being concatenated. Since hgc
expects a single name and url, for now I'll just pick the first
non-empty name/url (there are sources with no names, just a contact
entry). After this LRG release, I can update hgc to handle comma-sep
names and urls. Then, next LRG release, this should be updated to
make comma-sep names and urls.
- src/hg/utils/automation/parseLrgXml.pl - lines changed 11, context: html, text, full: html, text
- Rebuilt LRG in hg19 and hg38 with corrected URLs for some sources whoseURLs have changed; eventually I expect these to be fixed in LRG xml.
- src/hg/makeDb/doc/hg19.txt - lines changed 15, context: html, text, full: html, text
- src/hg/makeDb/doc/hg38.txt - lines changed 14, context: html, text, full: html, text
- Added trackDb settings for initializing VCF track controls.This will be useful for CTs/hub tracks to turn off haplotype clustering
or apply minimum QUAL score / minimum minor allele frequency filters.
- src/hg/hgTracks/vcfTrack.c - lines changed 21, context: html, text, full: html, text
- src/hg/makeDb/trackDb/tagTypes.tab - lines changed 7, context: html, text, full: html, text
- Moved Regulatory annotations out of 'Select More Annotations' into theirown top-level section because they are not just another annotation source --
they cause us to assign a specific consequence type. Also, as Jonathan suggested,
I'm suppressing regulatory annotation info for gene-consequence lines of outputs.
That makes the output a lot less redundant while still providing details for
RegulatoryFeature lines of output.
- src/hg/lib/annoFormatVep.c - lines changed 4, context: html, text, full: html, text
- Added missing target=_blank to external link.
- src/hg/makeDb/trackDb/pubs.html - lines changed 1, context: html, text, full: html, text
- Added several missing target=_blank to external links.
- src/hg/makeDb/trackDb/pubs.html - lines changed 3, context: html, text, full: html, text
- hgConvert was missing a call to setUdcCacheDir, so it was using the default /tmp/udcCache/.
- src/hg/hgConvert/hgConvert.c - lines changed 1, context: html, text, full: html, text
- Added COSMIC as an optional annotation. refs #11228
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