Commits for wong

v265_preview to v265_preview2 (2012-03-13 to 2012-03-20) v265

• fixed a bug where a cvDefined=no term was still trying to be validated against the cv
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 11, context: html, text, full: html, text
• added files as a cv typeOfTerm
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 10, context: html, text, full: html, text
• added in a new subroutine to validate the ddf header against the cv instead of fields.ra
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 31, context: html, text, full: html, text
• i forgot about the perl hash bug where you need to confirm values in an intermediate nested hash, becuase if you don't, it get automatically created, and that creates phantom entries in the cv term hash
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 4, context: html, text, full: html, text
• chnged it so that validateFieldList dones't allow ddf's to be processed with fields.ra
  • src/hg/utils/automation/Encode.pm - lines changed 6, context: html, text, full: html, text
• removed unecessary comment
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 1, context: html, text, full: html, text
• fixing the cell lines names caused by the perl hash bug.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 42, context: html, text, full: html, text
• pushQDescription is no longer used, however a blank value isn't allowed in load.ra, so i put a fake '1' in place of it
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 1, context: html, text, full: html, text
• fixed daf version to allow 2.0 and 3.0 for now, will need to remove once all labs are up to date
  • src/hg/utils/automation/Encode.pm - lines changed 3, context: html, text, full: html, text
• added in parent hpc-l cell line (WIlly)
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 18, context: html, text, full: html, text
• willy's chia pet fixes
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeGisChiaPet.release1.notes - lines changed 232, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.html - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.ra - lines changed 1, context: html, text, full: html, text
• added in new track (Willy)
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.ra - lines changed 258, context: html, text, full: html, text
• added in defaults
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.ra - lines changed 4, context: html, text, full: html, text
• added in replacement tracks and new tracks for open chrom dnase
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra - lines changed 387, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.ra - lines changed 109, context: html, text, full: html, text
• changed Encode.pm to allow two daf versions, 2.0 and 3.0, correctly this time, unless is the right conditional
  • src/hg/utils/automation/Encode.pm - lines changed 3, context: html, text, full: html, text
• added in Terry's release notes for open chrom DNAse
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.html - lines changed 11, context: html, text, full: html, text