braney: changes by file

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

• src/hg/encode/DAFs/DukeExons.daf
  • 1.1 lines changed: 21, context: html, text, full: html, text
    duke affy exons
• src/hg/encode/DAFs/UwExons.daf
  • 1.1 lines changed: 21, context: html, text, full: html, text
    Uw Exon arrays
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • 1.55 lines changed: 139, 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/trackDb/makefile
  • 1.279 lines changed: 3, context: html, text, full: html, text
    take out pesky ancestors
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.472 lines changed: 1, context: html, text, full: html, text
    make viewLimits line into the right format
• src/hg/makeDb/trackDb/human/hg16/trackDb.encode.ra
  • 1.13 lines changed: 8, context: html, text, full: html, text
    fix up some problems with some encode yale tracks
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.426 lines changed: 1, context: html, text, full: html, text
    fix up little problem in multiz28way trackDb entry
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.690 lines changed: 22, context: html, text, full: html, text
    Riken CAGE viewlimits (why?)
  • 1.689 lines changed: 39, context: html, text, full: html, text
    a couple of new MethylSeq cell types
  • 1.682 lines changed: 1, context: html, text, full: html, text
    add settingsByView to GisRnaSeq
  • 1.679 lines changed: 36, context: html, text, full: html, text
    go back to color by cell type for Caltech RNA-seq track
  • 1.678 lines changed: 48, context: html, text, full: html, text
    change CalTech RNA-seq track to color-by-strand
  • 1.676 lines changed: 5, context: html, text, full: html, text
    make GisDnaPet use bigBeds
  • 1.675 lines changed: 29, context: html, text, full: html, text
    make GIS RNA-PET alignments bigBeds
  • 1.668 lines changed: 81, context: html, text, full: html, text
    some long label changes, add settingsByView to GisPet
  • 1.667 lines changed: 1, context: html, text, full: html, text
    add settingsByView to CSHL long rna-seq
  • 1.664 lines changed: 25, context: html, text, full: html, text
    some defaults for Gis Rna Pet Loc
  • 1.663 lines changed: 10, context: html, text, full: html, text
    turn on some defaults for GIS DNA-pet
  • 1.662 lines changed: 18, context: html, text, full: html, text
    add RNA to GIS RnaSeq
  • 1.661 lines changed: 32, context: html, text, full: html, text
    fix up some stuff with GisRnaSeq, fix clicking on control terms with CshlLongRna
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.html
  • 1.13 lines changed: 14, 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/hg19/trackDb.ra
  • 1.65 lines changed: 1, context: html, text, full: html, text
    fix up tiny non-important error in multiz46way trackDb entry