angie: changes by file

branch to review (2009-07-21 to 2009-07-27) v211

• src/hg/hgTracks/bamTrack.c
  • 1.4 lines changed: 27, context: html, text, full: html, text
    Libified the code that interfaces directly with libbam to open, fetch, close.
  • 1.3 lines changed: 177, context: html, text, full: html, text
    Added option (trackDb setting pairEndsByName) to join separate BAM records for paired ends into linkedFeaturesSeries paired-end items.
• src/hg/hgTracks/hgTracks.h
  • 1.186 lines changed: 5, context: html, text, full: html, text
    Added option (trackDb setting pairEndsByName) to join separate BAM records for paired ends into linkedFeaturesSeries paired-end items.
• src/hg/hgTracks/simpleTracks.c
  • 1.94 lines changed: 1, context: html, text, full: html, text
    Added option (trackDb setting pairEndsByName) to join separate BAM records for paired ends into linkedFeaturesSeries paired-end items.
• src/hg/hgc/hgc.c
  • 1.1561 lines changed: 6, context: html, text, full: html, text
    When htmStart'ing in a subdirectory of trash (showSomeAlignment), call htmStartDirDepth with depth=2 so that htmlWarnBox will generate a correct relative path to images.
• src/hg/inc/bamFile.h
  • 1.1 lines changed: 17, context: html, text, full: html, text
    Libified the code that interfaces directly with libbam to open, fetch, close.
• src/hg/lib/bamFile.c
  • 1.1 lines changed: 52, context: html, text, full: html, text
    Libified the code that interfaces directly with libbam to open, fetch, close.
• src/hg/lib/makefile
  • 1.392 lines changed: 4, context: html, text, full: html, text
    Libified the code that interfaces directly with libbam to open, fetch, close.
• src/hg/makeDb/trackDb/drosophila/bdtnpChipper.html
  • 1.4 lines changed: 7, context: html, text, full: html, text
    Added link to just-published article (not yet in pubmed, but it's open-access).
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.407 lines changed: 1, context: html, text, full: html, text
    bamNA12878: adding stripPrefix so we don't hardcode stripping of chr from chromName for bam tracks.
  • 1.406 lines changed: 1, context: html, text, full: html, text
    Added setting pairEndsByName.
  • 1.405 lines changed: 1, context: html, text, full: html, text
    Hide snp129 by default now that snp130 is released.
• src/inc/bbiFile.h
  • 1.11 lines changed: 2, context: html, text, full: html, text
    Added include needed by .c's that include this .h only, which should be OK.
• src/inc/htmshell.h
  • 1.21 lines changed: 7, context: html, text, full: html, text
    Added htmStartDirDepth, so htmlWarnBox can generate a relative path to images with the correct number of ../'s depending on where the HTML comes from (used only in hgc's alignment index/ and body/ files now). Cleaned up code a bit.
• src/lib/htmshell.c
  • 1.60 lines changed: 71, context: html, text, full: html, text
    Added htmStartDirDepth, so htmlWarnBox can generate a relative path to images with the correct number of ../'s depending on where the HTML comes from (used only in hgc's alignment index/ and body/ files now). Cleaned up code a bit.