angie: changes by commit

branch to review (2010-03-23 to 2010-03-30) v228

• Copying komp definitions to ikmc to support table rename requested by contributor (Carol Bult).
  • src/hg/makeDb/trackDb/mouse/ikmc.html 1.1 - lines changed: 117, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/trackDb.ra 1.211 - lines changed: 28, context: html, text, full: html, text
• Added an eCfgType for bam, to support bam in multi-view composites. (Should eCfgType be in hui instead of here?)
  • src/hg/inc/trackDb.h 1.54 - lines changed: 2, context: html, text, full: html, text
  • src/hg/lib/trackDbCustom.c 1.81 - lines changed: 2, context: html, text, full: html, text
• Moving bam configuration code from hgTrackUi to hui to support bam in multi-view composites.
  • src/hg/hgTrackUi/hgTrackUi.c 1.517 - lines changed: 101, context: html, text, full: html, text
  • src/hg/inc/hui.h 1.147 - lines changed: 3, context: html, text, full: html, text
  • src/hg/lib/hui.c 1.266 - lines changed: 99, context: html, text, full: html, text
• Use hAllocConnTrack instead of sqlConnect or hAllocConn to support profiles in hg.conf.
  • src/hg/hgGenome/bedList.c 1.6 - lines changed: 7, context: html, text, full: html, text
  • src/hg/hgGenome/hgGenome.c 1.66 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgGenome/hgGenome.h 1.39 - lines changed: 4, context: html, text, full: html, text
  • src/hg/hgGenome/import.c 1.17 - lines changed: 42, context: html, text, full: html, text
  • src/hg/hgTables/bedList.c 1.69 - lines changed: 3, context: html, text, full: html, text
  • src/hg/hgTables/custom.c 1.43 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.c 1.189 - lines changed: 14, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.h 1.139 - lines changed: 3, context: html, text, full: html, text
  • src/hg/hgTables/mainPage.c 1.147 - lines changed: 2, context: html, text, full: html, text
  • src/hg/hgTracks/bedGraph.c 1.21 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTracks/bedTrack.c 1.24 - lines changed: 8, context: html, text, full: html, text
  • src/hg/hgTracks/bigBedTrack.c 1.6 - lines changed: 6, context: html, text, full: html, text
  • src/hg/hgTracks/bigWigTrack.c 1.9 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h 1.203 - lines changed: 2, context: html, text, full: html, text
  • src/hg/hgc/hgc.c 1.1606 - lines changed: 1, context: html, text, full: html, text
• Hook ikmc into komp code, for table name change requested by contributor Carol Bult.
  • src/hg/hgc/hgc.c 1.1607 - lines changed: 4, context: html, text, full: html, text
• Renamed komp to ikmc as requested by contributor Carol Bult.
  • src/hg/makeDb/doc/mm9.txt 1.129 - lines changed: 3, context: html, text, full: html, text
• Added ikmc (new name of komp).
  • src/hg/makeDb/schema/all.joiner 1.775 - lines changed: 5, context: html, text, full: html, text
• Some really old changes: snp130 func annotation fixes, hapmap and 1000 genomes experimental work (some interrupted).
  • src/hg/makeDb/doc/hg18.txt 1.406 - lines changed: 400, context: html, text, full: html, text
• DGV: when both thickEnd and thickStart are set to chromStart, as they are since we stopped showing locus whiskers, don't print out separate positions for variant vs. locus because there's only the variant now.
  • src/hg/hgc/hgc.c 1.1608 - lines changed: 1, context: html, text, full: html, text
• When filling in searchDescription using tdb->longLabel, just omit the table name because it is often more confusing than informative.
  • src/hg/lib/hgFindSpecCustom.c 1.16 - lines changed: 1, context: html, text, full: html, text