hiram: changes by file

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

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