Commits for vsmalladi

v257_base to v258_preview (2011-09-19 to 2011-09-27) v258

• Added new terms to accomadate for Replication Timing data. Added the first draft of DAF for new composite.
  • src/hg/encode/DAFs/2.0/uwRepliSeq.daf - lines changed 72, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 62, context: html, text, full: html, text
• Forgot 3 views. Checked in an incomplete DAF last time.
  • src/hg/encode/DAFs/2.0/uwRepliSeq.daf - lines changed 10, context: html, text, full: html, text
• Merge branch 'master' into UwReliSeq
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 73, context: html, text, full: html, text
• Added no inherint on so that Signal tracks would show in browser.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechHist.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.ra - lines changed 1, context: html, text, full: html, text
• Removed duplicate DAF to wgEncodeCaltechHist.daf.
  • src/hg/encode/DAFs/3.0/mm9/wgEncodeCaltechHistone.daf - lines changed 62, context: html, text, full: html, text
• Updated the version number that doesn't include longLabelPrefix's, to send to lab.
  • src/hg/encode/DAFs/3.0/mm9/wgEncodePsuHistone.daf - lines changed 1, context: html, text, full: html, text
• Added RepliSeq DAF update.
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeUwRepliSeq.daf - lines changed 79, context: html, text, full: html, text
• Updated DAF view name from Valley -> Valleys and removed longLabels.
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeUwRepliSeq.daf - lines changed 8, context: html, text, full: html, text
• Added new release to fix Astrocy -> NH-A naming problem. Redmine #4995.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeDukeAffyExon.ra - lines changed 51, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.new.html - lines changed 100, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.new.ra - lines changed 905, context: html, text, full: html, text
• Updated track to be consitent and renamed Astrocy -> NH-A. Redmine #4495, Redmine #4142.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra - lines changed 160, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.new.ra - lines changed 13, context: html, text, full: html, text
• Deprecating use of Astrocy as this is duplicated by NH-A. Redmine #4495.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1, context: html, text, full: html, text
• Added Fixed release notes file. Fixes issue Redmine #4995.
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeDukeAffyExon.release2.notes - lines changed 272, context: html, text, full: html, text
• Resolved merge conflict in cv.ra for Astrocy cell line, deprecated value.
• Fixed spelling error of NH-A as NH-a.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra - lines changed 8, context: html, text, full: html, text
• Added 5 controls missing from Histone track.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechHist.ra - lines changed 426, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechHist.ra - lines changed 46, context: html, text, full: html, text