hiram: changes by commit

review to branch (2010-02-10 to 2010-02-16) v225

• Adding calJac3 - Marmoset - Callithrix jacchus
  • src/hg/makeDb/genbank/etc/align.dbs 1.111 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwdev.dbs 1.115 - lines changed: 1, context: html, text, full: html, text
• add cpgIslandExt track
  • src/hg/makeDb/doc/tetNig2.txt 1.9 - lines changed: 8, context: html, text, full: html, text
• not loading split table is now the default
  • src/hg/utils/automation/doBlastzChainNet.pl 1.31 - lines changed: 9, context: html, text, full: html, text
• now adding dateReference to the trackVersion table entry
  • src/hg/utils/automation/doEnsGeneUpdate.pl 1.23 - lines changed: 9, context: html, text, full: html, text
• check source input for enough valid bases before running cpglh.exe
  • src/hg/utils/automation/doCpgIslands.pl 1.3 - lines changed: 7, context: html, text, full: html, text
• liftOver to calJac3 completed
  • src/hg/makeDb/doc/calJac1.txt 1.22 - lines changed: 12, context: html, text, full: html, text
• rerun the Panda lastz, and the calJac3
  • src/hg/makeDb/doc/hg19.txt 1.82 - lines changed: 68, context: html, text, full: html, text
• rerun the panda alignment, and starting the calJac3 marmoset
  • src/hg/makeDb/doc/canFam2.txt 1.27 - lines changed: 59, context: html, text, full: html, text
• last runs to Marmoset calJac3
  • src/hg/makeDb/doc/panTro2.txt 1.18 - lines changed: 63, context: html, text, full: html, text
  • src/hg/makeDb/doc/ponAbe2.txt 1.23 - lines changed: 61, context: html, text, full: html, text
  • src/hg/makeDb/doc/rheMac2.txt 1.20 - lines changed: 61, context: html, text, full: html, text
• rebuild Panda sequence with official genbank release
  • src/hg/makeDb/doc/ailMel1.txt 1.4 - lines changed: 81, context: html, text, full: html, text
• Add monDom5 for calJac3
  • src/hg/makeDb/trackDb/marmoset/trackDb.chainNet.ra 1.8 - lines changed: 5, context: html, text, full: html, text
• completed calJac3 lastz alignment
  • src/hg/makeDb/doc/canFam2.txt 1.28 - lines changed: 15, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm9.txt 1.125 - lines changed: 48, context: html, text, full: html, text
  • src/hg/makeDb/doc/monDom5.txt 1.19 - lines changed: 48, context: html, text, full: html, text
• done with a number of lastz runs
  • src/hg/makeDb/doc/calJac3.txt 1.3 - lines changed: 378, context: html, text, full: html, text
• all.joiner done and pushQ entries
  • src/hg/makeDb/doc/oryCun2.txt 1.6 - lines changed: 22, context: html, text, full: html, text