rhead: changes by commit

branch to review (2010-01-19 to 2010-01-26) v224

• Switched all chainFelCat3 and netFelCat3 tracks to be composite chainNetFelCat3 tracks.
  • src/hg/makeDb/trackDb/dog/canFam2/trackDb.ra 1.44 - lines changed: 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dog/trackDb.ra 1.33 - lines changed: 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra 1.84 - lines changed: 18, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra 1.38 - lines changed: 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.ra 1.583 - lines changed: 30, context: html, text, full: html, text
• Got a little overzealous on last commit. Changing this back so felCat3 stays in the placental group.
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra 1.85 - lines changed: 18, context: html, text, full: html, text
• Set all of the net tracks within composite chainNet tracks to full.
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra 1.40 - lines changed: 65, context: html, text, full: html, text
• Switching equCab1 and equCab2 chains and nets to composites. EquCab1 is currently on RR for hg18, mm8, panTro2 and rn4. EquCab1 is on RR for canFam2, galGal3, hg19, mm9, monDom5, ornaAna1.
  • src/hg/makeDb/trackDb/chicken/galGal3/trackDb.chainNet.ra 1.2 - lines changed: 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/trackDb.ra 1.18 - lines changed: 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dog/canFam2/trackDb.chainNet.ra 1.3 - lines changed: 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dog/trackDb.ra 1.35 - lines changed: 28, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra 1.499 - lines changed: 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.chainNet.ra 1.4 - lines changed: 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/trackDb.ra 1.185 - lines changed: 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/platypus/trackDb.ra 1.14 - lines changed: 27, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra 1.42 - lines changed: 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.ra 1.585 - lines changed: 28, context: html, text, full: html, text
• Removing blocks for monDom2 chains and nets. These do not exist anywhere.
  • src/hg/makeDb/trackDb/trackDb.ra 1.588 - lines changed: 22, context: html, text, full: html, text
• Removed blocks for chains and nets to monDom2.
  • src/hg/makeDb/trackDb/zebrafish/danRer3/trackDb.ra 1.57 - lines changed: 7, context: html, text, full: html, text
• Removing release alphas on chainNetMonDom tracks. Also changing color to black, to make the chain longLabels show up against white.
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra 1.48 - lines changed: 10, context: html, text, full: html, text
• Changing opossum net and chain tracks to composites. The following assemblies are currently live on the RR: calJac1 canFam2 cavPor3 danRer4 danRer5 galGal2 galGal3 hg17 hg18 hg19 mm8 mm9 ornAna1 panTro2 ponAbe2 rheMac2 rn4 xenTro2.
  • src/hg/makeDb/trackDb/chicken/galGal3/trackDb.ra 1.19 - lines changed: 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro2/trackDb.ra 1.50 - lines changed: 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dog/canFam2/trackDb.ra 1.47 - lines changed: 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg17/trackDb.chainNet.ra 1.12 - lines changed: 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg17/trackDb.ra 1.440 - lines changed: 50, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/trackDb.ra 1.457 - lines changed: 29, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra 1.500 - lines changed: 40, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra 1.76 - lines changed: 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/trackDb.ra 1.190 - lines changed: 28, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/orangutan/trackDb.ra 1.11 - lines changed: 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/platypus/ornAna1/trackDb.ra 1.20 - lines changed: 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.ra 1.593 - lines changed: 51, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/xenTro/xenTro2/trackDb.ra 1.22 - lines changed: 27, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/trackDb.ra 1.64 - lines changed: 41, context: html, text, full: html, text
• Changed all entries to have a color of black and an altColor of dark brown. The old altColor of tan was showing up on chains within composites and was nearly impossible to see.
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra 1.50 - lines changed: 96, context: html, text, full: html, text