Commits for angie

v301_preview to v301_preview2 (2014-05-26 to 2014-06-02) v301

• Accidentally removed pgSnp tracks' dense mode left labels in a430d3db1;adding them back now.
  refs #13220, fixes #13344
  
  • src/hg/hgTracks/simpleTracks.c - lines changed 10, context: html, text, full: html, text
• When position was set to a chrom not present in a VCF+tabix file,annoStreamVcf just kept reading rows out of the file instead of
  paying attention to the return value of lineFileSetTabixRegion.
  This inefficiency led to carefulMem running into its 6G limit.
  Fix: if lineFileSetTabixRegion fails in asvSetRegion, set self->eof
  to prevent reading out rows from the wrong position. If we're trying
  to skip ahead to minChrom using lineFileSetTabixRegion in
  nextRowUnfiltered, and it fails, just keep current position in case
  the file has more chroms after minChrom.
  fixes #13343
  
  • src/lib/annoStreamVcf.c - lines changed 12, context: html, text, full: html, text
• Updated LRG tracks on hg19 and added to hg38. Also updated reference to NAR paper.refs #13359
  
  • src/hg/makeDb/doc/hg19.txt - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38.txt - lines changed 48, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/lrg.html - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/lrgTranscriptAli.html - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/automation/parseLrgXml.pl - lines changed 31, context: html, text, full: html, text