File Changes for braney

v295_preview to v295_preview2 (2014-01-20 to 2014-01-27) v295

• src/hg/bedItemOverlapCount/tests/RunTest.sh
  • lines changed 3, context: html, text, full: html, text
    fix the bedItemOverlapCount test script to have the correct sums and toactually exit with bad status if the tests fail.
    
• src/hg/hgTracks/snakeTrack.c
  • lines changed 2, context: html, text, full: html, text
    a little update to a new HAL api
• src/hg/makeDb/doc/proteins/140122.txt
  • lines changed 206, context: html, text, full: html, text
    start the UCSC genes build for mm10
• src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes14.csh
  • lines changed 1561, context: html, text, full: html, text
    start the UCSC genes build for mm10
• src/hg/makeDb/doc/uniProt/sp140122.txt
  • lines changed 62, context: html, text, full: html, text
    start the UCSC genes build for mm10
• src/hg/utils/gff3ToPsl/gff3ToPsl.c
  • lines changed 4, context: html, text, full: html, text
    fix gff3ToPsl to work on the negative strand
  • lines changed 4, context: html, text, full: html, text
    fix gff3ToPsl to work with NCBI's gff alignments of haplotype chroms toreference chroms.
    
• src/hg/utils/gff3ToPsl/tests/README
  • lines changed 11, context: html, text, full: html, text
    fix gff3ToPsl to work on the negative strand
• src/hg/utils/gff3ToPsl/tests/expected/patch1test.2.axt
  • lines changed 6470966, context: html, text, full: html, text
    fix gff3ToPsl to work on the negative strand
  • lines changed 21329, context: html, text, full: html, text
    fix gff3ToPsl to work with NCBI's gff alignments of haplotype chroms toreference chroms.
    
• src/hg/utils/gff3ToPsl/tests/expected/patch1test.2.stats
  • lines changed 267, context: html, text, full: html, text
    fix gff3ToPsl to work with NCBI's gff alignments of haplotype chroms toreference chroms.
    
• src/hg/utils/gff3ToPsl/tests/expected/patch1test.psl
  • lines changed 266, context: html, text, full: html, text
    fix gff3ToPsl to work on the negative strand
  • lines changed 266, context: html, text, full: html, text
    fix gff3ToPsl to work with NCBI's gff alignments of haplotype chroms toreference chroms.
    
• src/hg/utils/gff3ToPsl/tests/input/GL339449.2bit
  • lines changed 0, context: html, text, full: html, text
    fix gff3ToPsl to work on the negative strand
  • lines changed 0, context: html, text, full: html, text
    fix gff3ToPsl to work with NCBI's gff alignments of haplotype chroms toreference chroms.
    
• src/hg/utils/gff3ToPsl/tests/input/GL339450_CM000671.gff
  • lines changed 7, context: html, text, full: html, text
    fix gff3ToPsl to work on the negative strand
  • lines changed 7, context: html, text, full: html, text
    fix gff3ToPsl to work with NCBI's gff alignments of haplotype chroms toreference chroms.
    
• src/hg/utils/gff3ToPsl/tests/input/chrom.sizes
  • lines changed 26, context: html, text, full: html, text
    fix gff3ToPsl to work on the negative strand
  • lines changed 26, context: html, text, full: html, text
    fix gff3ToPsl to work with NCBI's gff alignments of haplotype chroms toreference chroms.
    
• src/hg/utils/gff3ToPsl/tests/input/haploMaps.gff
  • lines changed 269, context: html, text, full: html, text
    fix gff3ToPsl to work with NCBI's gff alignments of haplotype chroms toreference chroms.
    
• src/hg/utils/gff3ToPsl/tests/input/locusToChrom.sed
  • lines changed 24, context: html, text, full: html, text
    fix gff3ToPsl to work on the negative strand
  • lines changed 24, context: html, text, full: html, text
    fix gff3ToPsl to work with NCBI's gff alignments of haplotype chroms toreference chroms.
    
• src/hg/utils/gff3ToPsl/tests/makefile
  • lines changed 3, context: html, text, full: html, text
    fix gff3ToPsl to work on the negative strand
  • lines changed 7, context: html, text, full: html, text
    fix gff3ToPsl to work with NCBI's gff alignments of haplotype chroms toreference chroms.
    
• src/lib/psl.c
  • lines changed 45, context: html, text, full: html, text
    fix gff3ToPsl to work on the negative strand
  • lines changed 45, context: html, text, full: html, text
    fix gff3ToPsl to work with NCBI's gff alignments of haplotype chroms toreference chroms.