File Changes for markd

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

• src/hg/hgc/gencodeClick.c
  • lines changed 41, context: html, text, full: html, text
    include transcript and sequence positions and browser links in details page
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.html
  • lines changed 41, context: html, text, full: html, text
    added doc on track filters
• src/hg/pslCDnaFilter/cDnaAligns.c
  • lines changed 69, 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.h
  • lines changed 76, 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/cDnaReader.c
  • lines changed 26, 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/cDnaReader.h
  • lines changed 6, 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/cDnaStats.c
  • lines changed 2, context: html, text, full: html, text
    added filter to drop non-uniquely mapped cDNAs
• src/hg/pslCDnaFilter/cDnaStats.h
  • lines changed 1, context: html, text, full: html, text
    added filter to drop non-uniquely mapped cDNAs
  • lines changed 6, 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/globalNearBestFilter.c
  • lines changed 48, 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/globalNearBestFilter.h
  • lines changed 7, 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/hapRegions.c
  • lines changed 225, 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/hapRegions.h
  • lines changed 13, 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/localNearBestFilter.c
  • lines changed 100, 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/localNearBestFilter.h
  • lines changed 9, 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/makefile
  • lines changed 6, 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/overlapFilter.c
  • lines changed 9, 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/overlapFilter.h
  • lines changed 7, 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/pslCDnaFilter.c
  • lines changed 26, context: html, text, full: html, text
    added filter to drop non-uniquely mapped cDNAs
  • lines changed 264, 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/tests/expected/hapGlobalTest/filt.out
  • lines changed 3, 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/tests/expected/hapGlobalTest/keep.psl
  • lines changed 3, 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/tests/expected/hapLocalTest/filt.out
  • lines changed 2, 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/tests/expected/hapLocalTest/keep.psl
  • lines changed 7, 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/tests/expected/uniqueMappedHapTest/filt.out
  • lines changed 6, 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/tests/expected/uniqueMappedHapTest/keep.psl
  • lines changed 10, 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/tests/expected/uniqueMappedTest/filt.out
  • lines changed 7, context: html, text, full: html, text
    added filter to drop non-uniquely mapped cDNAs
• src/hg/pslCDnaFilter/tests/expected/uniqueMappedTest/keep.psl
  • lines changed 15, context: html, text, full: html, text
    added filter to drop non-uniquely mapped cDNAs
• src/hg/pslCDnaFilter/tests/makefile
  • lines changed 8, context: html, text, full: html, text
    added filter to drop non-uniquely mapped cDNAs
  • lines changed 3, 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/usage.txt
  • lines changed 3, context: html, text, full: html, text
    added filter to drop non-uniquely mapped cDNAs
  • lines changed 21, 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