pchan: changes by file

branch to review (2010-02-16 to 2010-02-23) v226

• src/hg/archaeStuff/data/Genome-info-meta
  • 1.14 lines changed: 12, context: html, text, full: html, text
    add multiz for IMG cistern spring, joseph coats, and monarch geyser
  • 1.13 lines changed: 11, context: html, text, full: html, text
    add Private in Tax_ID for all private metagenomes
• src/hg/archaeStuff/data/Genome-info-mods
  • 1.98 lines changed: 8, context: html, text, full: html, text
    add multiz for Synechococcus
• src/hg/archaeStuff/scripts/make-metagenome-info
  • 1.4 lines changed: 2, context: html, text, full: html, text
    fix locus tag for metagenomes when not exists in IMG
  • 1.3 lines changed: 1, context: html, text, full: html, text
    fix bug in formatting locus tag for IMG metagenome
  • 1.2 lines changed: 1, context: html, text, full: html, text
    fix problem when org name has slashes
  • 1.1 lines changed: 760, context: html, text, full: html, text
    create script to get metagenome info and sequences, initially from JGI IMG/M
• src/hg/archaeStuff/scripts/archaeBrowser/CDS.pm
  • 1.27 lines changed: 1, context: html, text, full: html, text
    fix locus tag for metagenomes when not exists in IMG
  • 1.26 lines changed: 1, context: html, text, full: html, text
    fix bug in formatting locus tag for IMG metagenome
  • 1.25 lines changed: 108, context: html, text, full: html, text
    add code to support IMG metagenome loading
• src/hg/archaeStuff/scripts/archaeBrowser/Constant.pm
  • 1.41 lines changed: 1, context: html, text, full: html, text
    add code to support IMG metagenome loading
• src/hg/archaeStuff/scripts/archaeBrowser/GenomeInfo.pm
  • 1.18 lines changed: 12, context: html, text, full: html, text
    add code to support IMG metagenome loading
• src/hg/archaeStuff/scripts/archaeBrowser/MultiAlignment.pm
  • 1.11 lines changed: 1, context: html, text, full: html, text
    fix tracksDb dir in multiz creation
• src/hg/archaeStuff/scripts/archaeBrowser/Organism.pm
  • 1.11 lines changed: 16, context: html, text, full: html, text
    add code to support IMG metagenome loading
• src/hg/archaeStuff/scripts/archaeBrowser/OrganismDb.pm
  • 1.53 lines changed: 4, context: html, text, full: html, text
    remove GOLD ID line if value does not exist
  • 1.52 lines changed: 9, context: html, text, full: html, text
    Use publication instead of isolation for metagenomes
  • 1.51 lines changed: 58, context: html, text, full: html, text
    add code to support IMG metagenome loading
• src/hg/archaeStuff/scripts/archaeBrowser/ncRNA.pm
  • 1.25 lines changed: 1, context: html, text, full: html, text
    fix locus tag for metagenomes when not exists in IMG
  • 1.24 lines changed: 1, context: html, text, full: html, text
    fix bug in formatting locus tag for IMG metagenome
  • 1.23 lines changed: 79, context: html, text, full: html, text
    add code to support IMG metagenome loading