File Changes for vsmalladi

origin/v233_branch to v234_preview (2010-06-07 to 2010-06-15) v234

• src/hg/encode/DAFs/2.0/dukeDnaseSeq.daf
  • lines changed 10, context: html, text, full: html, text
    Added fastq format as optional, specified bam files as downloadOnly and standardized compsite name
• src/hg/encode/DAFs/2.0/renMm9Tfbs.daf
  • lines changed 7, context: html, text, full: html, text
    Modifed Lab to LICR and grant to Ren, consistent with pi.ra. Changed compiste suffix to LicrChipSeq(not enought data to support just Tfbs) and changed long labels to Ren -> LICR
• src/hg/encode/DAFs/2.0/uncFaireSeq.daf
  • lines changed 3, context: html, text, full: html, text
    Changed fastq format as optional, specified bam files as downloadOnly and standardized compsite name
• src/hg/encode/DAFs/2.0/utAustinChipSeq.daf
  • lines changed 11, context: html, text, full: html, text
    Added fastq format as optional, specified bam files as downloadOnly and standardized compsite name
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 3, context: html, text, full: html, text
    Commented out the specific check for a lab inorder to write replicate to subgroups. The code has been checked in the unit test and will now write replicate as a subgroup regardless of lab. Have discussed with Brian about changes.
• src/hg/encode/encodeValidate/test/expected/chipseq/README.txt
  • lines changed 2, context: html, text, full: html, text
    Updated file names
• src/hg/encode/encodeValidate/test/expected/chipseq/fileDb.ra
  • lines changed 16, context: html, text, full: html, text
    Added fileDb.ra as this is generated by the pipeline at the moment
• src/hg/encode/encodeValidate/test/expected/chipseq/load.ra
  • lines changed 4, context: html, text, full: html, text
    Upated tablenames to include wgEncode
• src/hg/encode/encodeValidate/test/expected/chipseq/mdb.txt
  • lines changed 4, context: html, text, full: html, text
    Added mdb.txt to check the mdb.txt, might still need to update make file to verify everything in the file
• src/hg/encode/encodeValidate/test/expected/chipseq/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    Updated the metadata line to include only subId and dateSubmitted. updated track and subtrack names to include wgEncode and appropriate abreviations. Lastly updated type wig line to update to ENC-> WGENCODE
• src/hg/encode/encodeValidate/test/makefile
  • lines changed 2, context: html, text, full: html, text
    Added mdb.txt and fileDb.ra files to check between expected and actual. Uncommented line to print the file name
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 6250, context: html, text, full: html, text
    Updated metaDb to include new bam and broad peak files from June 7th freeze
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 7, context: html, text, full: html, text
    Updated the standardized lab UCD(Farnham) -> UCD
  • lines changed 599, context: html, text, full: html, text
    Checking in the file with the correct information. revision 1.4 was empty accidently. Updated Lab for submission 1122 and 1123 to UCD. Updated UCDavis -> UCD
  • lines changed 599, context: html, text, full: html, text
    Made Lab name consistent for all variants of UCD% -> UCD
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 12, context: html, text, full: html, text
    Removed ; (semicolns) accidently reintrodcued in labVersion
  • lines changed 81, context: html, text, full: html, text
    Made Lab name consistent for all variants of UCD% -> UCD and Harvard(Weissman) -> Harvard
  • lines changed 25, context: html, text, full: html, text
    Updated metaData with metaData for bam from sbumission 1246
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 1825, context: html, text, full: html, text
    Initial check in of Uw Histone( ChIP-seq) metadata file.