Commits for wong

v266_base to v267_preview (2012-04-24 to 2012-05-01) v267

• removed deprecated types from extended types list
  • src/hg/utils/automation/Encode.pm - lines changed 1, context: html, text, full: html, text
• shouldnt have removed gappedPeak
  
  • src/hg/utils/automation/Encode.pm - lines changed 1, context: html, text, full: html, text
• restructuring for the enw validateFiles
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 308, context: html, text, full: html, text
• restructiring for new validateFiles and .as and .sql locations
  • src/hg/encode/encodeLoad/doEncodeLoad.pl - lines changed 10, context: html, text, full: html, text
• Merge branch 'master' into newValidateFiles
  • src/hg/utils/automation/Encode.pm - lines changed 5, context: html, text, full: html, text
• filtering on bam only for validation settings
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 3, context: html, text, full: html, text
• reworked installSchemas to actually work and modified make to compensate
  • src/hg/encode/encodeLoad/installSqlSchemas.pl - lines changed 52, context: html, text, full: html, text
  • src/hg/encode/encodeLoad/makefile - lines changed 1, context: html, text, full: html, text
• restored the object type after some discoveries were made about how the files were uploaded
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 6, context: html, text, full: html, text
• removed some debugging prints
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 9, context: html, text, full: html, text
• forgot to pull variable out
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 1, context: html, text, full: html, text
• Merge branch 'newValidateFiles'
• revoking old TssHmm's
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 17, context: html, text, full: html, text
• added in seqPlayform where known
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 313, context: html, text, full: html, text
• resolving merge
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.ra - lines changed 7, context: html, text, full: html, text
• reverting an error made earlier
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.ra - lines changed 1, context: html, text, full: html, text
• missed this metaDAta somehow
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 45, context: html, text, full: html, text
• fixing metadata errors
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 13, context: html, text, full: html, text
• adding a reference
  • python/lib/ucscgenomics/qa/encode/tableCheck.py - lines changed 1, context: html, text, full: html, text
• trackDb fixes and promotes tier 2.5 cell lines
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.ra - lines changed 115, context: html, text, full: html, text
• adding treatment to expVars
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra - lines changed 2, context: html, text, full: html, text
• removing a bad search and replace change
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.ra - lines changed 1, context: html, text, full: html, text
• removing space that was causing default to not be checked
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.ra - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• removing another bad search and replace
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.ra - lines changed 1, context: html, text, full: html, text
• qa fixes
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.ra - lines changed 67, context: html, text, full: html, text
• more qa fixes
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.ra - lines changed 8, context: html, text, full: html, text
• qa fixes for html riken
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.html - lines changed 5, context: html, text, full: html, text
• more html fixes for riken, this time capitalization
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.html - lines changed 2, context: html, text, full: html, text
• changed alignments to off, and removed replicate from fileSortOrder
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.ra - lines changed 16, context: html, text, full: html, text
• changed max window on minus to be the same as plus
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.ra - lines changed 1, context: html, text, full: html, text