Commits for braney

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

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