pchan: changes by file

branch to review (2009-10-13 to 2009-10-20) v218

• src/hg/archaeStuff/data/Genome-info-mods
  • 1.91 lines changed: 16, context: html, text, full: html, text
    add Name_chg to haloSali1
  • 1.90 lines changed: 1, context: html, text, full: html, text
    change to use Hvo-genome.fa for haloVolc1_1
  • 1.89 lines changed: 1, context: html, text, full: html, text
    change blat port id again
  • 1.88 lines changed: 1, context: html, text, full: html, text
    fix blat port for haloVolc1_1
  • 1.87 lines changed: 21, context: html, text, full: html, text
    add Public_phylo for halophiles
• src/hg/archaeStuff/data/private-genomes.tab
  • 1.6 lines changed: 2, context: html, text, full: html, text
    replace spaces with tab
  • 1.5 lines changed: 5, context: html, text, full: html, text
    add schiPomb1 as private genome
  • 1.4 lines changed: 25, context: html, text, full: html, text
    add ynpyoung browser and nympLake_PGA2009 metagenome
• src/hg/archaeStuff/scripts/archaeBrowser/AlignmentCompare.pm
  • 1.5 lines changed: 65, context: html, text, full: html, text
    read annotRev cds.gp instead of genePred.tab if available for igenics and alignInfo
• src/hg/archaeStuff/scripts/archaeBrowser/CDS.pm
  • 1.21 lines changed: 4, context: html, text, full: html, text
    read annotRev cds.gp instead of genePred.tab if available for igenics and alignInfo
• src/hg/archaeStuff/scripts/archaeBrowser/GenomeInfo.pm
  • 1.16 lines changed: 7, context: html, text, full: html, text
    add public_phylo support to multiz
• src/hg/archaeStuff/scripts/archaeBrowser/MultiAlignment.pm
  • 1.10 lines changed: 4, context: html, text, full: html, text
    add public_phylo support to multiz
• src/hg/archaeStuff/scripts/archaeBrowser/Organism.pm
  • 1.10 lines changed: 8, context: html, text, full: html, text
    add public_phylo support to multiz
• src/hg/archaeStuff/scripts/archaeBrowser/RemovePriv.pm
  • 1.3 lines changed: 7, context: html, text, full: html, text
    remove snoRNA hits from alignInfo for public browser
• src/hg/hgc/lowelab.c
  • 1.38 lines changed: 101, context: html, text, full: html, text
    add support to annotRev tracks; use annotRev instead of genepred if available for blastp tracks detail page
• src/hg/makeDb/trackDb/lowelab/privateTracks.ra
  • 1.22 lines changed: 8, context: html, text, full: html, text
    add restricted tracks to ynpyoung browser
  • 1.21 lines changed: 12, context: html, text, full: html, text
    add haloferax private tracks
• src/hg/makeDb/trackDb/lowelab/halMar1/trackDb.ra
  • 1.19 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/haloHalo1/trackDb.ra
  • 1.23 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/haloSali1/trackDb.ra
  • 1.12 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/haloUtah1/trackDb.ra
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Update multiz track
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/haloVolc1_1/multizHalophiles.html
  • 1.1 lines changed: 161, context: html, text, full: html, text
    Details page for multiz track
• src/hg/makeDb/trackDb/lowelab/haloVolc1_1/trackDb.ra
  • 1.7 lines changed: 17, context: html, text, full: html, text
    Update multiz track
  • 1.6 lines changed: 10, context: html, text, full: html, text
    Update ultraConserved track
  • 1.5 lines changed: 14, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/haloVolc1_1/ultraConserved.html
  • 1.1 lines changed: 3, context: html, text, full: html, text
    New ultraConserved track
• src/hg/makeDb/trackDb/lowelab/haloWals1/trackDb.ra
  • 1.14 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/natrPhar1/trackDb.ra
  • 1.14 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/pyrAby1/trackDb.ra
  • 1.20 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/pyrFur2/trackDb.ra
  • 1.32 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/pyrHor1/trackDb.ra
  • 1.21 lines changed: 1, context: html, text, full: html, text
    Update multiz track