File Changes for vsmalladi

v246_preview2 to v246_base (2011-01-18 to 2011-01-25) v246

• src/hg/encode/DAFs/2.0/stanfordNucleosome.daf
  • lines changed 2, context: html, text, full: html, text
    Updated BAM validation to look for 99.9% of file that agrese with 3 mismatches.
• src/hg/encode/DAFs/2.0/uChicagoTfbs.daf
  • lines changed 3, context: html, text, full: html, text
    Fixed DAF so that Peaks and Signal will not be required for all experiments. Inputs generate ALignments and Raw Data only and are subtracted from experiments with antibodies to generate Peaks and Signals.
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 2, context: html, text, full: html, text
    Fixed coding style to conform to camelCase of new subroutine. Also added whitespace after my decleration.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 2, context: html, text, full: html, text
    Fixed miss spelling of Provisional
  • lines changed 5, context: html, text, full: html, text
    Added new dataType Nucelosome.
  • lines changed 15, context: html, text, full: html, text
    Added new antibody for White lab: eGFP-NR4A1
  • lines changed 119, context: html, text, full: html, text
    Added 8 antibodies for Myers lab that did not have validation documents.
  • lines changed 6, context: html, text, full: html, text
    Added new Seq Platform AB SOLiD 3 Plus
  • lines changed 30, context: html, text, full: html, text
    Added new Control Terms for controls used when comparing for a specific antibody replicate. Lab doesn't use 1 run of a control to compare all results, but rather a control is run at the same time for each antibody specific experiment.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 1706, context: html, text, full: html, text
    Added 10 Chip-seq submissions for the Jan 2011 freeze.
  • lines changed 564, context: html, text, full: html, text
    Added 4 submissions for the Jan 2011 Freeze.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 3389, context: html, text, full: html, text
    Added 29 submissions for the Jan 2011 Freeze. Also, removed commented lines out of trackDb and reorder treatment and antibodies in alphabetical order.
  • lines changed 7, context: html, text, full: html, text
    Fixed controlId's for obj that had HeLaS3/None/Input/IgG-rab where cell line was miss spelled.
  • lines changed 641, context: html, text, full: html, text
    Added 5 submissions for the Jan 2011 Freeze.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
  • lines changed 367, context: html, text, full: html, text
    Added 10 Chip-seq submissions for the Jan 2011 freeze.
  • lines changed 73, context: html, text, full: html, text
    Added 4 submissions for the Jan 2011 Freeze.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
  • lines changed 521, context: html, text, full: html, text
    Added 29 submissions for the Jan 2011 Freeze. Also, removed commented lines out of trackDb and reorder treatment and antibodies in alphabetical order.
  • lines changed 1, context: html, text, full: html, text
    Reordered tratments alphabetically.Missed in last commit.
  • lines changed 101, context: html, text, full: html, text
    Added 5 submissions for the Jan 2011 Freeze.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.ra
  • lines changed 424, context: html, text, full: html, text
    Removed errant space in shortlabl for 1 subtrack. ast by ChIP-seq to subtrack long labels to following track settings style guide.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
  • lines changed 403, context: html, text, full: html, text
    Added 5 submissions with Peaks and Signals which previously only had raw data files.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
  • lines changed 537, context: html, text, full: html, text
    Added 7 submissions of Peaks and Signals which previously only had raw data files.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 3, context: html, text, full: html, text
    Added LICR Histone track.
  • lines changed 3, context: html, text, full: html, text
    Added 7 submissions of Peaks and Signals which previously only had raw data files.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.ra
  • lines changed 151, context: html, text, full: html, text
    Added 5 submissions with Peaks and Signals which previously only had raw data files.
  • lines changed 2, context: html, text, full: html, text
    Changed Long and Short labels to comply with track configuration standards.
  • lines changed 1, context: html, text, full: html, text
    Added noInherit on to both tracks.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.ra
  • lines changed 173, context: html, text, full: html, text
    Added 7 submissions of Peaks and Signals which previously only had raw data files.
  • lines changed 2, context: html, text, full: html, text
    Changed Long and Short labels to comply with track configuration standards.
  • lines changed 1, context: html, text, full: html, text
    Added noInherit on to both tracks.