markd: changes by file

branch to review (2010-02-16 to 2010-02-23) v226

• src/hg/hgc/hgc.c
  • 1.1597 lines changed: 5, context: html, text, full: html, text
    added details page for PAR tracks
• src/hg/hgc/makefile
  • 1.65 lines changed: 1, context: html, text, full: html, text
    added details page for PAR tracks
• src/hg/hgc/parClick.c
  • 1.2 lines changed: 6, context: html, text, full: html, text
    fixed bug when clicking on one par when both are displayed
  • 1.1 lines changed: 150, context: html, text, full: html, text
    added details page for PAR tracks
• src/hg/hgc/parClick.h
  • 1.1 lines changed: 8, context: html, text, full: html, text
    added details page for PAR tracks
• src/hg/inc/hgRelate.h
  • 1.17 lines changed: 10, context: html, text, full: html, text
    allow defaulting to TMPDIR directory
• src/hg/lib/hgConfig.c
  • 1.23 lines changed: 12, context: html, text, full: html, text
    check that all config files starting with dot are only readable by the owner
• src/hg/lib/hgRelate.c
  • 1.26 lines changed: 21, context: html, text, full: html, text
    allow defaulting to TMPDIR directory
• src/hg/makeDb/makefile
  • 1.43 lines changed: 2, context: html, text, full: html, text
    added hgPar to load PSL table describing PARs
• src/hg/makeDb/doc/hg18.txt
  • 1.398 lines changed: 6, context: html, text, full: html, text
    added PAR tracks
• src/hg/makeDb/doc/hg19.txt
  • 1.83 lines changed: 8, context: html, text, full: html, text
    added PAR tracks
• src/hg/makeDb/genbank/doc/to-do.txt
  • 1.121 lines changed: 2, context: html, text, full: html, text
    added some examples to look at
• src/hg/makeDb/hgPar/hgPar.c
  • 1.2 lines changed: 104, context: html, text, full: html, text
    used BED format for PAR
  • 1.1 lines changed: 105, context: html, text, full: html, text
    added hgPar to load PSL table describing PARs
• src/hg/makeDb/hgPar/makefile
  • 1.1 lines changed: 23, context: html, text, full: html, text
    added hgPar to load PSL table describing PARs
• src/hg/makeDb/hgPar/parSpec.as
  • 1.1 lines changed: 11, context: html, text, full: html, text
    added hgPar to load PSL table describing PARs
• src/hg/makeDb/hgPar/parSpec.c
  • 1.1 lines changed: 138, context: html, text, full: html, text
    added hgPar to load PSL table describing PARs
• src/hg/makeDb/hgPar/parSpec.h
  • 1.1 lines changed: 63, context: html, text, full: html, text
    added hgPar to load PSL table describing PARs
• src/hg/makeDb/hgPar/tests/makefile
  • 1.2 lines changed: 3, context: html, text, full: html, text
    used BED format for PAR
  • 1.1 lines changed: 13, context: html, text, full: html, text
    added hgPar to load PSL table describing PARs
• src/hg/makeDb/hgPar/tests/expected/par.bed
  • 1.1 lines changed: 4, context: html, text, full: html, text
    used BED format for PAR
• src/hg/makeDb/hgPar/tests/input/test.parspec
  • 1.3 lines changed: 0, context: html, text, full: html, text
    removed stray space
  • 1.2 lines changed: 2, context: html, text, full: html, text
    used BED format for PAR
  • 1.1 lines changed: 2, context: html, text, full: html, text
    added hgPar to load PSL table describing PARs
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.619 lines changed: 16, context: html, text, full: html, text
    added PAR tracks
• src/hg/makeDb/trackDb/human/par.html
  • 1.1 lines changed: 13, context: html, text, full: html, text
    added PAR tracks
• src/hg/pslCDnaFilter/cDnaAligns.c
  • 1.20 lines changed: 24, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/cDnaAligns.h
  • 1.14 lines changed: 5, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/pslCDnaFilter.c
  • 1.22 lines changed: 7, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/usage.txt
  • 1.12 lines changed: 4, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/tests/makefile
  • 1.14 lines changed: 11, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/tests/expected/ignoreIntronsTest/drop.psl
  • 1.1 lines changed: 1, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/tests/expected/ignoreIntronsTest/filt.out
  • 1.1 lines changed: 4, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/tests/expected/ignoreIntronsTest/keep.psl
  • 1.1 lines changed: 1, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/tests/expected/ignoreIntronsTest/weird.psl
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/tests/expected/noIgnoreIntronsTest/drop.psl
  • 1.1 lines changed: 1, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/tests/expected/noIgnoreIntronsTest/filt.out
  • 1.1 lines changed: 4, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/tests/expected/noIgnoreIntronsTest/keep.psl
  • 1.1 lines changed: 1, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/tests/expected/noIgnoreIntronsTest/weird.psl
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/tests/expected/weirdOverlappedFilterTest/drop.psl
  • 1.1 lines changed: 6, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/tests/expected/weirdOverlappedFilterTest/filt.out
  • 1.1 lines changed: 6, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/tests/expected/weirdOverlappedFilterTest/keep.psl
  • 1.1 lines changed: 11, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/tests/expected/weirdOverlappedFilterTest/weird.psl
  • 1.1 lines changed: 9, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency
• src/hg/pslCDnaFilter/tests/input/ignoreIntrons.psl
  • 1.1 lines changed: 3, context: html, text, full: html, text
    Added option to not give bonus score for apparent introns. Fix test naming inconsitency