Commits for braney

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

• fix gff3ToPsl to work on the negative strand
  • src/hg/utils/gff3ToPsl/gff3ToPsl.c - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/gff3ToPsl/tests/README - lines changed 11, context: html, text, full: html, text
  • src/hg/utils/gff3ToPsl/tests/expected/patch1test.2.axt - lines changed 6470966, context: html, text, full: html, text
  • src/hg/utils/gff3ToPsl/tests/expected/patch1test.psl - lines changed 266, context: html, text, full: html, text
  • src/hg/utils/gff3ToPsl/tests/input/GL339449.2bit - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/utils/gff3ToPsl/tests/input/GL339450_CM000671.gff - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/gff3ToPsl/tests/input/chrom.sizes - lines changed 26, context: html, text, full: html, text
  • src/hg/utils/gff3ToPsl/tests/input/locusToChrom.sed - lines changed 24, context: html, text, full: html, text
  • src/hg/utils/gff3ToPsl/tests/makefile - lines changed 3, context: html, text, full: html, text
  • src/lib/psl.c - lines changed 45, context: html, text, full: html, text
• fix gff3ToPsl to work with NCBI's gff alignments of haplotype chroms toreference chroms.
  
  • src/hg/utils/gff3ToPsl/gff3ToPsl.c - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/gff3ToPsl/tests/expected/patch1test.2.axt - lines changed 21329, context: html, text, full: html, text
  • src/hg/utils/gff3ToPsl/tests/expected/patch1test.2.stats - lines changed 267, context: html, text, full: html, text
  • src/hg/utils/gff3ToPsl/tests/expected/patch1test.psl - lines changed 266, context: html, text, full: html, text
  • src/hg/utils/gff3ToPsl/tests/input/GL339449.2bit - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/utils/gff3ToPsl/tests/input/GL339450_CM000671.gff - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/gff3ToPsl/tests/input/chrom.sizes - lines changed 26, context: html, text, full: html, text
  • src/hg/utils/gff3ToPsl/tests/input/haploMaps.gff - lines changed 269, context: html, text, full: html, text
  • src/hg/utils/gff3ToPsl/tests/input/locusToChrom.sed - lines changed 24, context: html, text, full: html, text
  • src/hg/utils/gff3ToPsl/tests/makefile - lines changed 7, context: html, text, full: html, text
  • src/lib/psl.c - lines changed 45, context: html, text, full: html, text
• a little update to a new HAL api
  • src/hg/hgTracks/snakeTrack.c - lines changed 2, context: html, text, full: html, text
• start the UCSC genes build for mm10
  • src/hg/makeDb/doc/proteins/140122.txt - lines changed 206, context: html, text, full: html, text
  • src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes14.csh - lines changed 1561, context: html, text, full: html, text
  • src/hg/makeDb/doc/uniProt/sp140122.txt - lines changed 62, 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/bedItemOverlapCount/tests/RunTest.sh - lines changed 3, context: html, text, full: html, text