mary: changes by commit

branch to review (2010-05-04 to 2010-05-11) v231

• adding a .chainNet.ra file to override chainNets for panTro2
  • src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.chainNet.ra 1.1 - lines changed: 5, context: html, text, full: html, text
• removing unecessary lines from chainNetPanTro2 override
  • src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.chainNet.ra 1.2 - lines changed: 2, context: html, text, full: html, text
• adding include line to include new trackDb.chainNet.ra file
  • src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.ra 1.5 - lines changed: 2, context: html, text, full: html, text
• changing chainMinScore gap to 3000 for calJac3 as I was told to do by the script
  • src/hg/makeDb/trackDb/dog/trackDb.chainNet.ra 1.23 - lines changed: 1, context: html, text, full: html, text
• adding period
  • src/utils/qa/chain.csh 1.33 - lines changed: 1, context: html, text, full: html, text
• adding visibility overrides to make the default position for susScr2. Did affect susSCr1, but figured since it was only on dev this was ok
  • src/hg/makeDb/trackDb/pig/trackDb.chainNet.ra 1.3 - lines changed: 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/pig/trackDb.ra 1.3 - lines changed: 6, context: html, text, full: html, text
• adding matrix and chainMinScore overrides for ponAbe2 in calJac3
  • src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.chainNet.ra 1.3 - lines changed: 4, context: html, text, full: html, text
• moving chain/Net overrides for rheMac2 down one level for calJac3. interferring with calJac1 when on marmoset level
  • src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.chainNet.ra 1.4 - lines changed: 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/marmoset/trackDb.chainNet.ra 1.11 - lines changed: 2, context: html, text, full: html, text
• turning on genbank updates for susScr2
  • src/hg/makeDb/genbank/etc/rr.dbs 1.92 - lines changed: 1, context: html, text, full: html, text