File Changes for angie

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

• src/hg/hgTracks/simpleTracks.c
  • lines changed 10, context: html, text, full: html, text
    Accidentally removed pgSnp tracks' dense mode left labels in a430d3db1;adding them back now.
    refs #13220, fixes #13344
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 6, 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/hg38.txt
  • lines changed 48, 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/trackDb/human/lrg.html
  • lines changed 8, 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/trackDb/human/lrgTranscriptAli.html
  • lines changed 8, 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/trackDb/human/trackDb.ra
  • lines changed 2, 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/utils/automation/parseLrgXml.pl
  • lines changed 31, context: html, text, full: html, text
    Updated LRG tracks on hg19 and added to hg38. Also updated reference to NAR paper.refs #13359
    
• src/lib/annoStreamVcf.c
  • lines changed 12, 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