kent: changes by commit

branch to review (2010-02-02 to 2010-02-10) v225

• Making a single file rewriter for track in the middle.
  • src/hg/oneShot/tdbRewriteViewsToSubtracks1/makefile 1.1 - lines changed: 17, context: html, text, full: html, text
  • src/hg/oneShot/tdbRewriteViewsToSubtracks1/tdbRewriteViewsToSubtracks1.c 1.1 - lines changed: 696, context: html, text, full: html, text
• Clarifying some view info.
  • src/hg/makeDb/trackDb/README 1.99 - lines changed: 47, context: html, text, full: html, text
• Tweaking MATRIX section a bit as per Angie's suggestions.
  • src/hg/makeDb/trackDb/README 1.100 - lines changed: 6, context: html, text, full: html, text
• Adding trackDbUpdateOldTag function to convert older format trackDb tags to current format. Specifically converting superTrack, compositeTrack, and subTrack tags to use the new container and parent tags instead.
  • src/hg/inc/trackDb.h 1.53 - lines changed: 3, context: html, text, full: html, text
  • src/hg/lib/trackDbCustom.c 1.76 - lines changed: 40, context: html, text, full: html, text
• Getting rid of settingsByView stuff. Adding in converter to container/parent syntax. Fix to parent-not-found error message.
  • src/hg/utils/tdbQuery/tdbQuery.c 1.27 - lines changed: 63, context: html, text, full: html, text
  • src/hg/utils/tdbQuery/tdbRecord.c 1.6 - lines changed: 75, context: html, text, full: html, text
  • src/hg/utils/tdbQuery/tdbRecord.h 1.3 - lines changed: 4, context: html, text, full: html, text
• Getting to compile in Linux.
  • src/hg/utils/tdbQuery/tdbRecord.c 1.7 - lines changed: 5, context: html, text, full: html, text
• Ifdeffing out some of the new code until I finish baking it.
  • src/hg/lib/trackDbCustom.c 1.77 - lines changed: 12, context: html, text, full: html, text
• Taking out a half-baked change.
  • src/hg/utils/tdbQuery/tdbQuery.c 1.28 - lines changed: 3, context: html, text, full: html, text
• Fixed memory leaks.
  • src/lib/bigBed.c 1.26 - lines changed: 4, context: html, text, full: html, text
• Removing bigBedFileCreate which is no longer in library.
  • src/inc/bigBed.h 1.18 - lines changed: 30, context: html, text, full: html, text
• Making bigBedCoverageIntervals() static.
  • src/lib/bigBed.c 1.27 - lines changed: 1, context: html, text, full: html, text
• Moving bigBedFileOpen to a better place.
  • src/hg/hgTracks/bigBedTrack.c 1.4 - lines changed: 12, context: html, text, full: html, text
• Changing 'subTrack' to 'parent' internally. A backwards compatability routine will make it so either tag can be used in a trackDb file.
  • src/hg/hgTracks/simpleTracks.c 1.126 - lines changed: 1, context: html, text, full: html, text
  • src/hg/lib/hdb.c 1.418 - lines changed: 2, context: html, text, full: html, text
  • src/hg/lib/hui.c 1.258 - lines changed: 3, context: html, text, full: html, text
  • src/hg/lib/trackDbCustom.c 1.78 - lines changed: 8, context: html, text, full: html, text
  • src/hg/makeDb/hgTrackDb/hgTrackDb.c 1.61 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab 1.10 - lines changed: 1, context: html, text, full: html, text
  • src/hg/oneShot/freen/freen.c 1.97 - lines changed: 36, context: html, text, full: html, text
  • src/hg/utils/tdbQuery/tdbQuery.c 1.29 - lines changed: 3, context: html, text, full: html, text
• Hopefully fixing bigBed so that it works in dense mode on a clean cart _and_ it works with custom tracks. Have tested these two anyway.
  • src/hg/hgTracks/bigBedTrack.c 1.5 - lines changed: 33, context: html, text, full: html, text
• Making hgTracks be backwards compatible with older trackDb tables in case they didn't run hgTrackDb.
  • src/hg/lib/trackDbCustom.c 1.80 - lines changed: 30, context: html, text, full: html, text