File Changes for vsmalladi

v263_preview to v263_preview2 (2012-01-31 to 2011-02-07) v263

• src/hg/encode/DAFs/3.0/hg19/wgEncodeUmassDekker5C.daf
  • lines changed 24, context: html, text, full: html, text
    Updated DAF to have all views. Added new view PrimerPeaks for Peaks determined at primer level. Also added validte None for Primer. Redmine #225.
  • lines changed 6, context: html, text, full: html, text
    Removed required tags in the DAF, this allows for views such as Primers not being required for each Cell type. Also fixed spelling of bed 12. Redmine #225.
• src/hg/encode/DAFs/3.0/mm9/wgEncodeCaltechRnaSeq.daf
  • lines changed 2, context: html, text, full: html, text
    Fixed DAF to require replciates for Alignments. Redmine #4156.
• src/hg/encode/DAFs/3.0/mm9/wgEncodeCshlLongRnaSeq.daf
  • lines changed 14, context: html, text, full: html, text
    Added two new views Contigs and TranscriptDeNovo. Redmine #5986.
  • lines changed 8, context: html, text, full: html, text
    Removed required for views to allow partial submissions. Redmine #5986.
  • lines changed 2, context: html, text, full: html, text
    After tallking with the lab decided to changed type for contigs from bigBed to bedRnaElements. Redmine #5986.
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 1, context: html, text, full: html, text
    Added None as a valid term for region, as some files are not region specific. Redmine #225.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 7, context: html, text, full: html, text
    Updated DAF to have all views. Added new view PrimerPeaks for Peaks determined at primer level. Also added validte None for Primer. Redmine #225.
  • lines changed 18, context: html, text, full: html, text
    Added 3 new treatments for Snyder/Struhl lab
  • lines changed 6, context: html, text, full: html, text
    Removed the duplication of a 36hr 1 uM treatment registration.
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 6, context: html, text, full: html, text
    Removed extra stanza that should be commented out. Redmine #6798.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/makefile
  • lines changed 2, context: html, text, full: html, text
    Added first experiments to track. Redmine #4156.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechHist.ra
  • lines changed 64, context: html, text, full: html, text
    Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 210, context: html, text, full: html, text
    Added first experiments to track. Redmine #4156.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechTfbs.ra
  • lines changed 124, context: html, text, full: html, text
    Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 97, context: html, text, full: html, text
    Removed WC+ from labProtocolId string, based on lab information. Redmine #5986.
  • lines changed 97, context: html, text, full: html, text
    Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
  • lines changed 6, context: html, text, full: html, text
    Added back composite level meta-data was typed incorrectly in commit 66cb88518473df9e9dbc818fe28bd1eefed69a2e.
  • lines changed 6, context: html, text, full: html, text
    Removed errant stanza object wgEncodeCshlLongRnaSeqq.
  • lines changed 2989, context: html, text, full: html, text
    Added 18 experiments for track. Redmine #5986.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
  • lines changed 376, context: html, text, full: html, text
    Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrRnaSeq.ra
  • lines changed 115, context: html, text, full: html, text
    Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
  • lines changed 248, context: html, text, full: html, text
    Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuHistone.ra
  • lines changed 293, context: html, text, full: html, text
    Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
  • lines changed 239, context: html, text, full: html, text
    Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHist.ra
  • lines changed 28, context: html, text, full: html, text
    Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhRnaSeq.ra
  • lines changed 10, context: html, text, full: html, text
    Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 323, context: html, text, full: html, text
    Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 85, context: html, text, full: html, text
    Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 486, context: html, text, full: html, text
    Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwRnaSeq.ra
  • lines changed 206, context: html, text, full: html, text
    Update freeze date to be ENCODE Mar 2012 Freeze. Redmine #6581.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 3, context: html, text, full: html, text
    Added first experiments to track. Redmine #4156.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.ra
  • lines changed 91, context: html, text, full: html, text
    Added first experiments to track. Redmine #4156.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.ra
  • lines changed 487, context: html, text, full: html, text
    Added 18 experiments for track. Redmine #5986.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.html
  • lines changed 17, context: html, text, full: html, text
    Redmine #111 1. Reworded sentence "and interpret these as DNA sequences" -> "and interpreted as DNA sequences" 2. Added semicolon in second sentence of Peaks section in Display Conventions and Configuration 3. Made Credits section plural changed "was" -> "were" 4. Added period for Journal titles. Also italicized "et al." in Reference section
  • lines changed 2, context: html, text, full: html, text
    Redmine #111. 4. Fixed spacing between semicolons and italisize et al. and period after journal name.
  • lines changed 1, context: html, text, full: html, text
    Redmine #111. Forgot to close italics.
  • lines changed 4, context: html, text, full: html, text
    Redmine #111. 5. Updated 2 links that were being redirected.
  • lines changed 1, context: html, text, full: html, text
    Redmine #111. Moved period out of hyperlink for Weiss track.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.ra
  • lines changed 19, context: html, text, full: html, text
    1. Removed old RA stanzas that were resubmitted and object name was changed. Redmine #111.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.release2.ra
  • lines changed 19, context: html, text, full: html, text
    1. Removed old RA stanzas that were resubmitted and object name was changed. Redmine #111.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.html
  • lines changed 18, context: html, text, full: html, text
    Redmine #110 1. Reworded sentence "and interpret these as DNA sequences" -> "and interpreted as DNA sequences" 2. Added semicolon in second sentence of Peaks section in Display Conventions and Configuration 3. Made Credits section plural changed "was" -> "were" 4. Added period for Journal titles.
  • lines changed 5, context: html, text, full: html, text
    Redmine #110. 4. Fixed spacing between semicolons and italisize et al. and period after journal name.
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    Added first experiments to track. Redmine #4156.