angie: changes by commit

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

• Hide snp129 by default now that snp130 is released.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.ra 1.405 - lines changed: 1, 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/inc/htmshell.h 1.21 - lines changed: 7, context: html, text, full: html, text
  • src/lib/htmshell.c 1.60 - lines changed: 71, 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/hgc/hgc.c 1.1561 - lines changed: 6, 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/drosophila/bdtnpChipper.html 1.4 - lines changed: 7, 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/bamTrack.c 1.3 - lines changed: 177, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h 1.186 - lines changed: 5, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c 1.94 - lines changed: 1, context: html, text, full: html, text
• Added setting pairEndsByName.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.ra 1.406 - lines changed: 1, context: html, text, full: html, text
• Added include needed by .c's that include this .h only, which should be OK.
  • src/inc/bbiFile.h 1.11 - lines changed: 2, context: html, text, full: html, text
• bamNA12878: adding stripPrefix so we don't hardcode stripping of chr from chromName for bam tracks.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.ra 1.407 - lines changed: 1, context: html, text, full: html, text
• Libified the code that interfaces directly with libbam to open, fetch, close.
  • src/hg/hgTracks/bamTrack.c 1.4 - lines changed: 27, context: html, text, full: html, text
  • src/hg/inc/bamFile.h 1.1 - lines changed: 17, context: html, text, full: html, text
  • src/hg/lib/bamFile.c 1.1 - lines changed: 52, context: html, text, full: html, text
  • src/hg/lib/makefile 1.392 - lines changed: 4, context: html, text, full: html, text