File Changes for braney

v328_preview2 to v328_base (2016-01-25 to 2016-02-08) v328

• src/hg/hgTracks/vcfTrack.c
  • lines changed 2, context: html, text, full: html, text
    close all the files that vcfTabix support opens
    
  • lines changed 2, context: html, text, full: html, text
    oops... VCF files were being closed twice sometimes
    
• src/hg/makeDb/trackDb/snail/bioGla0/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    added some frames to snail browser maf.
    
• src/hg/mouseStuff/simpleChain/simpleChain.c
  • lines changed 1, context: html, text, full: html, text
    fix simpleChain to output the correct values for the psl insert columns
    
• src/hg/utils/gff3ToPsl/gff3ToPsl.c
  • lines changed 1, context: html, text, full: html, text
    use strand, rather than targetStrand, in gff3ToPsl
    
  • lines changed 13, context: html, text, full: html, text
    make gff3ToPsl be a little more strand savvy
    
• src/hg/utils/gff3ToPsl/tests/expected/grch38ToGrch37Test.psl
  • lines changed 20, context: html, text, full: html, text
    make gff3ToPsl be a little more strand savvy
    
• src/hg/utils/gff3ToPsl/tests/expected/patch1test.psl
  • lines changed 266, context: html, text, full: html, text
    make gff3ToPsl be a little more strand savvy
    
• src/hg/utils/otto/gwas/perlParser.pl
  • lines changed 1, context: html, text, full: html, text
    get otto GWAS to understand cedilla
    
• src/lib/linefile.c
  • lines changed 5, context: html, text, full: html, text
    close all the files that vcfTabix support opens
    
  • lines changed 2, context: html, text, full: html, text
    oops... VCF files were being closed twice sometimes
    
  • lines changed 1, context: html, text, full: html, text
    tweak the linefile tabix code to assume .tbi indices.
    
• src/lib/vcf.c
  • lines changed 7, context: html, text, full: html, text
    oops... VCF files were being closed twice sometimes
    
  • lines changed 2, context: html, text, full: html, text
    one more time! Close vcf file if read in at open time