File Changes for angie

v303_preview to v303_preview2 (2014-07-07 to 2014-07-14) v303

• src/hg/hgConvert/hgConvert.c
  • lines changed 1, context: html, text, full: html, text
    hgConvert was missing a call to setUdcCacheDir, so it was using the default /tmp/udcCache/.
• src/hg/hgTracks/vcfTrack.c
  • lines changed 21, 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/hgVai/hgVai.c
  • lines changed 22, 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.
    
  • lines changed 19, context: html, text, full: html, text
    Added COSMIC as an optional annotation. refs #11228
• src/hg/inc/cart.h
  • lines changed 3, 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/lib/annoFormatVep.c
  • lines changed 4, 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/cart.c
  • lines changed 10, 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/lib/vcfUi.c
  • 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/makeDb/doc/hg19.txt
  • lines changed 15, 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/hg38.txt
  • lines changed 14, 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/trackDb/pubs.html
  • lines changed 1, context: html, text, full: html, text
    Added missing target=_blank to external link.
  • lines changed 3, context: html, text, full: html, text
    Added several missing target=_blank to external links.
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 7, 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/utils/automation/parseLrgXml.pl
  • lines changed 11, context: html, text, full: html, text
    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.