Commits for vsmalladi

v236_base to v237_preview (2010-07-20 to 2010-07-27) v237

• Updated compsites to be default dense while supertrack is hide
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra - lines changed 1, context: html, text, full: html, text
• Updated the defaults for the tracks to be default, as the composite is set to default hide.
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeSydhHistone.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.ra - lines changed 1, context: html, text, full: html, text
• Updated Validtor to check assembly and if hg19 and 3 composites require inputType
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 1, context: html, text, full: html, text
• Updated type of termP to term
  • src/hg/encode/encodeValidate/config/cv.ra - lines changed 1, context: html, text, full: html, text
• Added 22 cell lines from UW.
  • src/hg/encode/encodeValidate/config/cv.ra - lines changed 279, context: html, text, full: html, text
• Fixed description for TAM treamtent for quantity of 2uM to 1 uM.
  • src/hg/encode/encodeValidate/config/cv.ra - lines changed 1, context: html, text, full: html, text
• Added 1 new treatment tamoxifen for Myers lab
  • src/hg/encode/encodeValidate/config/cv.ra - lines changed 5, context: html, text, full: html, text
• Remvoed orderUrl for GM12878 registered cell lines, not applicable
  • src/hg/encode/encodeValidate/config/cv.ra - lines changed 8, context: html, text, full: html, text
• Added 4 new cell lines for X-inactivation in GM12878 cell lines registered by the Myers lab
  • src/hg/encode/encodeValidate/config/cv.ra - lines changed 69, context: html, text, full: html, text
• Updated all Histone tracks to be consistent within the given super track. Short Labels and matrix display( factor and cell type order)
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeSydhHistone.ra - lines changed 22, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.ra - lines changed 148, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.ra - lines changed 9, context: html, text, full: html, text
• Updated long label for track
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.ra - lines changed 1, context: html, text, full: html, text
• Updated the order of the cell types in the matrix display.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.ra - lines changed 2, context: html, text, full: html, text
• Updated Open Chrom FAIRE-seq track short labels to match DNase-Seq. Also standardized treatment display headers between the two tracks
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.ra - lines changed 67, context: html, text, full: html, text
• Updated the check for Mouse Tissue category to spell out Tissue to match cv.ra, previously T was used.
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 1, context: html, text, full: html, text
• Updated the short lables and consistency notes.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.ra - lines changed 111, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra - lines changed 219, context: html, text, full: html, text
• Updated the metaData to be compliant with Hudson Alpha Expectations
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 420, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeHaibTfbs.ra - lines changed 7, context: html, text, full: html, text
• Removed old track for HAIB Methyl RRBS labeled encHaibRrbs from trackDb.wgEncode.ra
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 156, context: html, text, full: html, text
• Commented out the Revision history line that was causing problems
  • src/hg/encode/DAFs/2.0/uwMm9DnaseSeq.daf - lines changed 1, context: html, text, full: html, text
• Updated the validateFiles for fastq to check 1 in 1000 rather than the first 1000 lines, which was breaking (refer to Bug:390)
  • src/hg/encode/DAFs/2.0/uwMm9DnaseSeq.daf - lines changed 3, context: html, text, full: html, text
• Updated the Mouse cell type controlled vocabulary to be consistent with what was registered as well as update the CGIs to display the correct headers for mouse Cell Type
  • src/hg/encode/encodeValidate/config/cv.ra - lines changed 18, context: html, text, full: html, text
  • src/hg/encode/hgEncodeVocab/hgEncodeVocab.c - lines changed 1, context: html, text, full: html, text
• Changed OpenChromFaire to OpenChromDnase and visversa to be consistent with the data that is within each ra file
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.ra - lines changed 647, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.ra - lines changed 649, context: html, text, full: html, text
• Updated short labels and display standards for the UW DNaseI track
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra - lines changed 234, context: html, text, full: html, text