braney: changes by commit

review to branch (2009-11-17 to 2009-12-01) v220

• fix up some stuff with GisRnaSeq, fix clicking on control terms with CshlLongRna
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.661 - lines changed: 32, context: html, text, full: html, text
• add RNA to GIS RnaSeq
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.662 - lines changed: 18, context: html, text, full: html, text
• turn on some defaults for GIS DNA-pet
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.663 - lines changed: 10, context: html, text, full: html, text
• some defaults for Gis Rna Pet Loc
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.664 - lines changed: 25, context: html, text, full: html, text
• Uw Exon arrays
  • src/hg/encode/DAFs/UwExons.daf 1.1 - lines changed: 21, context: html, text, full: html, text
• duke affy exons
  • src/hg/encode/DAFs/DukeExons.daf 1.1 - lines changed: 21, context: html, text, full: html, text
• add settingsByView to CSHL long rna-seq
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.667 - lines changed: 1, context: html, text, full: html, text
• some long label changes, add settingsByView to GisPet
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.668 - lines changed: 81, context: html, text, full: html, text
• make GIS RNA-PET alignments bigBeds
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.675 - lines changed: 29, context: html, text, full: html, text
• make GisDnaPet use bigBeds
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.676 - lines changed: 5, context: html, text, full: html, text
• change CalTech RNA-seq track to color-by-strand
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.678 - lines changed: 48, context: html, text, full: html, text
• go back to color by cell type for Caltech RNA-seq track
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.679 - lines changed: 36, context: html, text, full: html, text
• change text describing colors to reflect colors by cell type (in Caltech RNA-seq track)
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.html 1.13 - lines changed: 14, context: html, text, full: html, text
• make viewLimits line into the right format
  • src/hg/makeDb/trackDb/human/trackDb.ra 1.472 - lines changed: 1, context: html, text, full: html, text
• take out pesky ancestors
  • src/hg/makeDb/trackDb/makefile 1.279 - lines changed: 3, context: html, text, full: html, text
• fix up little problem in multiz28way trackDb entry
  • src/hg/makeDb/trackDb/human/hg18/trackDb.ra 1.426 - lines changed: 1, context: html, text, full: html, text
• fix up tiny non-important error in multiz46way trackDb entry
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra 1.65 - lines changed: 1, context: html, text, full: html, text
• fix up some problems with some encode yale tracks
  • src/hg/makeDb/trackDb/human/hg16/trackDb.encode.ra 1.13 - lines changed: 8, context: html, text, full: html, text
• made subtrack processing check for more errors, fail on errors, and a lot easier to read without all the continues and huge functions. Confirmed that trackDb generated is the same as the old hgTrackDb (after fixing the 8 errors found in existing tracks). All of this is prep for automatically adding prefixes to subGroups for automatic sorting
  • src/hg/makeDb/hgTrackDb/hgTrackDb.c 1.55 - lines changed: 139, context: html, text, full: html, text
• add settingsByView to GisRnaSeq
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.682 - lines changed: 1, context: html, text, full: html, text
• a couple of new MethylSeq cell types
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.689 - lines changed: 39, context: html, text, full: html, text
• Riken CAGE viewlimits (why?)
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.690 - lines changed: 22, context: html, text, full: html, text