pchan: changes by file

review to branch (2009-07-27 to 2009-08-04) v212

• src/hg/archaeStuff/data/Genome-info-mods
  • 1.72 lines changed: 56, context: html, text, full: html, text
    add methVulc0, methInfe0, methFerv0
  • 1.71 lines changed: 13, context: html, text, full: html, text
    add natrMaga0 to multiz of all halophiles
• src/hg/archaeStuff/scripts/make-browser-2.0
  • 1.44 lines changed: 4, context: html, text, full: html, text
    add --cleanblast to delete private genomes from blastp and blastx hits
  • 1.43 lines changed: 10, context: html, text, full: html, text
    add igenics and blastx tracks
• src/hg/archaeStuff/scripts/archaeBrowser/Blast.pm
  • 1.20 lines changed: 3, context: html, text, full: html, text
    add index for target field in blast Hits table
  • 1.19 lines changed: 2, context: html, text, full: html, text
    replace die with PrintErrorAndExit
  • 1.18 lines changed: 356, context: html, text, full: html, text
    add igenics and blastx tracks
  • 1.17 lines changed: 1, context: html, text, full: html, text
    turn off spectum for self blastz by Todd
• src/hg/archaeStuff/scripts/archaeBrowser/CDS.pm
  • 1.17 lines changed: 6, context: html, text, full: html, text
    add support to old version of genePred
  • 1.16 lines changed: 1, context: html, text, full: html, text
    fix bug in parsing cds
  • 1.15 lines changed: 9, context: html, text, full: html, text
    replace die with PrintErrorAndExit
  • 1.14 lines changed: 135, context: html, text, full: html, text
    add igenics and blastx tracks
  • 1.13 lines changed: 15, context: html, text, full: html, text
    take precomputed .gp and .xra for TIGR genomes if files exist
• src/hg/archaeStuff/scripts/archaeBrowser/Organism.pm
  • 1.8 lines changed: 13, context: html, text, full: html, text
    add igenics and blastx tracks
• src/hg/archaeStuff/scripts/archaeBrowser/OrganismDb.pm
  • 1.38 lines changed: 93, context: html, text, full: html, text
    add --cleanblast to delete private genomes from blastp and blastx hits
• src/hg/archaeStuff/scripts/archaeBrowser/Track.pm
  • 1.13 lines changed: 4, context: html, text, full: html, text
    put N/A to description field of table html if value doesn't exist
• src/hg/makeDb/trackDb/lowelab/trackDb.ra
  • 1.80 lines changed: 12, context: html, text, full: html, text
    add igenics track; rename igenics microarray track to igenicsMicroarray
  • 1.79 lines changed: 12, context: html, text, full: html, text
    add BlastX_Related
• src/hg/makeDb/trackDb/lowelab/halMar1/trackDb.ra
  • 1.14 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/haloHalo1/trackDb.ra
  • 1.18 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/haloSali1/trackDb.ra
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/haloVolc1/trackDb.ra
  • 1.5 lines changed: 1, context: html, text, full: html, text
    add natrMaga0 to multiz
• src/hg/makeDb/trackDb/lowelab/haloWals1/trackDb.ra
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/methJann1/trackDb.ra
  • 1.13 lines changed: 1, context: html, text, full: html, text
    add methVulc0, methInfe0, methFerv0 to multiz
• src/hg/makeDb/trackDb/lowelab/natrPhar1/trackDb.ra
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Update multiz track