pchan: changes by commit

review to branch (2009-10-06 to 2009-10-13) v217

• created by Andrew Holmes for lowelab alignment feature track
  • src/hg/lib/alignInfo.sql 1.1 - lines changed: 21, context: html, text, full: html, text
• read private-genomes.tab to skip sync'ing and initdb; add --removepriv to clean up hits to private genomes in blastp, blastx, and alignFeatures tracks
  • src/hg/archaeStuff/scripts/archaeBrowser/Blast.pm 1.24 - lines changed: 158, context: html, text, full: html, text
  • src/hg/archaeStuff/scripts/archaeBrowser/Constant.pm 1.36 - lines changed: 72, context: html, text, full: html, text
  • src/hg/archaeStuff/scripts/archaeBrowser/OrganismDb.pm 1.44 - lines changed: 102, context: html, text, full: html, text
  • src/hg/archaeStuff/scripts/make-browser-2.0 1.49 - lines changed: 11, context: html, text, full: html, text
• add -removepriv to clean up private genome hits
  • src/hg/archaeStuff/scripts/archaeBrowser/RemovePriv.pm 1.1 - lines changed: 196, context: html, text, full: html, text
• comment out chainHalMar1 and blastzHalMar1
  • src/hg/makeDb/trackDb/lowelab/halMar1/trackDb.ra 1.18 - lines changed: 22, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lowelab/haloHalo1/trackDb.ra 1.22 - lines changed: 23, context: html, text, full: html, text
• delete old multiz track
  • src/hg/makeDb/trackDb/lowelab/peloCarb/trackDb.ra 1.4 - lines changed: 17, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lowelab/peloProp_DSM2379/trackDb.ra 1.4 - lines changed: 17, context: html, text, full: html, text
• mark all private genomes as private to haloferax collab browser
  • src/hg/archaeStuff/data/private-genomes.tab 1.2 - lines changed: 14, context: html, text, full: html, text
• add annotRev list to description page
  • src/hg/makeDb/trackDb/lowelab/description-template.html 1.14 - lines changed: 2, context: html, text, full: html, text
• add haloVolc1_1 from Halolex
  • src/hg/archaeStuff/data/Genome-info-mods 1.86 - lines changed: 33, context: html, text, full: html, text
• fix bug when cleaning up data in collab server; add --annotrev for revised annotation track; add annotRev list to description page
  • src/hg/archaeStuff/scripts/archaeBrowser/Blast.pm 1.25 - lines changed: 36, context: html, text, full: html, text
  • src/hg/archaeStuff/scripts/archaeBrowser/CDS.pm 1.19 - lines changed: 325, context: html, text, full: html, text
  • src/hg/archaeStuff/scripts/archaeBrowser/Constant.pm 1.37 - lines changed: 4, context: html, text, full: html, text
  • src/hg/archaeStuff/scripts/archaeBrowser/OrganismDb.pm 1.45 - lines changed: 3, context: html, text, full: html, text
  • src/hg/archaeStuff/scripts/archaeBrowser/RemovePriv.pm 1.2 - lines changed: 2, context: html, text, full: html, text
  • src/hg/archaeStuff/scripts/make-browser-2.0 1.50 - lines changed: 5, context: html, text, full: html, text
• Update annotRev track
  • src/hg/makeDb/trackDb/lowelab/haloVolc1_1/trackDb.ra 1.4 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lowelab/haloVolc1_1/trackDb.ra 1.3 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lowelab/haloVolc1_1/trackDb.ra 1.2 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lowelab/haloVolc1_1/trackDb.ra 1.1 - lines changed: 27, context: html, text, full: html, text
• add haloferax private browser and haloVolc1_1 as private genome
  • src/hg/archaeStuff/data/private-genomes.tab 1.3 - lines changed: 16, context: html, text, full: html, text
• make more coding changes to support annotRev in Blastp
  • src/hg/archaeStuff/scripts/archaeBrowser/Blast.pm 1.26 - lines changed: 21, context: html, text, full: html, text
  • src/hg/archaeStuff/scripts/archaeBrowser/CDS.pm 1.20 - lines changed: 35, context: html, text, full: html, text