kuhn: changes by commit

branch to review (2009-07-07 to 2009-07-15) v210

• added PapHam1 to chainlist and capitalized AplCal1
  • src/hg/makeDb/schema/all.joiner 1.722 - lines changed: 1, context: html, text, full: html, text
• dropped exit command that was in there for debugging
  • src/utils/qa/chain2.csh 1.12 - lines changed: 2, context: html, text, full: html, text
• added sort check for chain and net tables
  • src/utils/qa/chain2.csh 1.11 - lines changed: 15, context: html, text, full: html, text
  • src/utils/qa/net.csh 1.20 - lines changed: 28, context: html, text, full: html, text
• added TarSyr1 to list of chains
  • src/hg/makeDb/schema/all.joiner 1.723 - lines changed: 1, context: html, text, full: html, text
• added OtoGar1 to list of chains
  • src/hg/makeDb/schema/all.joiner 1.725 - lines changed: 1, context: html, text, full: html, text
• adjusted BLOCKQUOTE tag to put text over matrix tables
  • src/hg/makeDb/trackDb/human/hg19/hg19ChainNet.html 1.3 - lines changed: 4, context: html, text, full: html, text
• added MicMur1 to list of chains
  • src/hg/makeDb/schema/all.joiner 1.726 - lines changed: 1, context: html, text, full: html, text
• made separate files for the three chain/net tracks
  • src/hg/makeDb/trackDb/human/hg19/hg19mammalChainNet.html 1.1 - lines changed: 191, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/hg19primateChainNet.html 1.1 - lines changed: 191, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/hg19vertChainNet.html 1.1 - lines changed: 191, context: html, text, full: html, text
• added release alphas to control push to beta. made new html files for three chain/net sets. reversed order of three chain/net tracks to match order in Conservation track. adjusted order of views on details pages
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra 1.35 - lines changed: 24, context: html, text, full: html, text
• adjusted to only check one RR machine, as they all now share hgsqlrr
  • src/utils/qa/realTime.csh 1.12 - lines changed: 1, context: html, text, full: html, text
• changed to hgw8 for now, as hgw1 is out for upgrade
  • src/utils/qa/realTime.csh 1.13 - lines changed: 2, context: html, text, full: html, text
• dropped mantin of cgdToSgd
  • src/hg/makeDb/schema/all.joiner 1.727 - lines changed: 2, context: html, text, full: html, text