ann: changes by commit

review to branch (2009-09-22 to 2009-09-29) v216

• this script gets the two variables needed for the chain description page ($chainMinScore and $chainLinearGap). similar to the getMatrixLines script which gets the $matrix variable
  • src/utils/qa/getChainLines.csh 1.1 - lines changed: 72, context: html, text, full: html, text
• new getChainLines script
  • src/utils/qa/makefile 1.114 - lines changed: 1, context: html, text, full: html, text
• we do not need the dollar-sign before the variable
  • src/utils/qa/getChainLines.csh 1.2 - lines changed: 2, context: html, text, full: html, text
• added call for new getChainLines script
  • src/utils/qa/chain.csh 1.25 - lines changed: 3, context: html, text, full: html, text
• ordered chain/net tracks wrt the opossum and each-other.
  • src/hg/makeDb/trackDb/opossum/monDom5/trackDb.ra 1.13 - lines changed: 71, context: html, text, full: html, text
• Brooke and Bob want it to be opposite of the Conservation line-up (which I think is incorrect:-)
  • src/hg/makeDb/trackDb/opossum/monDom5/trackDb.ra 1.14 - lines changed: 18, context: html, text, full: html, text
• added details about mm9 chain
  • src/hg/makeDb/trackDb/opossum/monDom5/trackDb.ra 1.15 - lines changed: 4, context: html, text, full: html, text
• added overrides for chain/net monDom4/5
  • src/hg/makeDb/trackDb/dog/canFam2/trackDb.ra 1.36 - lines changed: 12, context: html, text, full: html, text
• added chain vars for all orgs
  • src/hg/makeDb/trackDb/opossum/monDom5/trackDb.ra 1.19 - lines changed: 58, context: html, text, full: html, text