Commits for markd

v253_base to v254_preview (2011-06-28 to 2011-07-05) v254

• added filter to drop non-uniquely mapped cDNAs
  • src/hg/pslCDnaFilter/cDnaStats.c - lines changed 2, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/cDnaStats.h - lines changed 1, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/pslCDnaFilter.c - lines changed 26, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/uniqueMappedTest/filt.out - lines changed 7, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/uniqueMappedTest/keep.psl - lines changed 15, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/makefile - lines changed 8, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/usage.txt - lines changed 3, context: html, text, full: html, text
• added doc on track filters
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.html - lines changed 41, context: html, text, full: html, text
• include transcript and sequence positions and browser links in details page
  • src/hg/hgc/gencodeClick.c - lines changed 41, context: html, text, full: html, text
• fixed bug with haplotype filtesrs were some global need best were not correctly dropped and where some local near best where incorrectly dropped. Make -uniqueMapped haplotype chroms
  • src/hg/pslCDnaFilter/cDnaAligns.c - lines changed 69, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/cDnaAligns.h - lines changed 76, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/cDnaReader.c - lines changed 26, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/cDnaReader.h - lines changed 6, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/cDnaStats.h - lines changed 6, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/globalNearBestFilter.c - lines changed 48, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/globalNearBestFilter.h - lines changed 7, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/hapRegions.c - lines changed 225, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/hapRegions.h - lines changed 13, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/localNearBestFilter.c - lines changed 100, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/localNearBestFilter.h - lines changed 9, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/makefile - lines changed 6, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/overlapFilter.c - lines changed 9, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/overlapFilter.h - lines changed 7, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/pslCDnaFilter.c - lines changed 264, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/hapGlobalTest/filt.out - lines changed 3, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/hapGlobalTest/keep.psl - lines changed 3, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/hapLocalTest/filt.out - lines changed 2, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/hapLocalTest/keep.psl - lines changed 7, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/uniqueMappedHapTest/filt.out - lines changed 6, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/uniqueMappedHapTest/keep.psl - lines changed 10, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/usage.txt - lines changed 21, context: html, text, full: html, text