Commits for vsmalladi

v254_base to v255_preview (2011-07-19 to 2011-07-26) v255

• Added replacment Peak files loaded from subId 4610. Updated notes files because 1 tag was changed in cv causing name of file and table to change.
  • src/hg/makeDb/doc/encodeDccMm9/wgEncodeSydhTfbs.release2.notes - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 67, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.newR2.ra - lines changed 13, context: html, text, full: html, text
• Loaded replacement peak file, but had to update name since tag changed in cv. Fixes Redmine #97, note 28.
  • src/hg/makeDb/doc/encodeDccMm9/wgEncodeSydhHistone.release1.notes - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHistone.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHistone.ra - lines changed 3, context: html, text, full: html, text
• Fixed parent/subTrack link from composite settings to view specific settings. Fixes: Redmine #4668 and #97, note 32.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHistone.ra - lines changed 1, context: html, text, full: html, text
• Fixed subTrack association to View configuration rather than composite configuration. Also fixed formatting into normal trackDb composite format.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.newR2.ra - lines changed 11, context: html, text, full: html, text
• Fixed rest of formatting and changed subTrack to parent to be consistent naming.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHistone.ra - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.newR2.ra - lines changed 31, context: html, text, full: html, text
• Fixed formating of trackDb to correct composite track format spacing. Changed naming of subTrack to parent so that track is consistent. Moved subIds that were listed above track as comment to match current formatting, these track came in over a year ago and had the old metadata formating line in the subTrack and that line was removed by Cricket. Fixes Redmine #97, note 34.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHistone.ra - lines changed 18, context: html, text, full: html, text
• Moved subIds that were listed above track as comment to match current formatting, these track came in over a year ago and had the old metadata formating line in the subTrack and that line was removed by Cricket.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.newR2.ra - lines changed 52, context: html, text, full: html, text
• Fixed working of descirption of Peaks and removed word usually to be correctly describing the Peaks for this composite track. Fixes Redmine #97, note 36.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHist.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.new.html - lines changed 1, context: html, text, full: html, text
• Updated ordering of references to be alphabetical. Also moved period out of hyperlink at the end of a title. Redmine #97, note 38. Updated the 'Contacts' link for Sherman Weisman to a new page. Redmine #97, note 39.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHist.html - lines changed 48, context: html, text, full: html, text
• Moved period out of hyperlink at the end of a title. Updated the 'Contacts' link for Sherman Weisman to a new page.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.new.html - lines changed 7, context: html, text, full: html, text
• Reworded first sentence of second paragraph of methods section, with recomendations from Katrina. Redmine #97, note 40.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHist.html - lines changed 2, context: html, text, full: html, text
• Reworded first sentence of second paragraph of methods section, with recomendations from QA.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.new.html - lines changed 2, context: html, text, full: html, text
• Updated line that states views present in track from 'ENCODE tracks typically contain one or more of the following views:' to 'This track contains the following views:'. Also standardized all Description about view's present paragraph to be the same in all tracks. Redmine #97, note 42.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHist.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhRnaSeq.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.new.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.html - lines changed 2, context: html, text, full: html, text
• First pass at the DAF for AWG uniform analysis track. Also added new view to cv to accomadate for data. Redmine #4522.
  • src/hg/encode/DAFs/2.0/awgUniform.daf - lines changed 54, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 30, context: html, text, full: html, text
• Removed reference to parentTable in metaDb for files. Term is not used in cv anymore.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra - lines changed 27, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 17, context: html, text, full: html, text