Commits for wong

v262_preview to v262_preview2 (2012-01-10 to 2012-01-17) v262

• updated md5sums
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra - lines changed 71, context: html, text, full: html, text
• widened the filemask and fixed a weird edge case bug
  • src/hg/encode/encodeMkFilesList/encodeMkFilesList - lines changed 5, context: html, text, full: html, text
• added in some treatments for crawford
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 11, context: html, text, full: html, text
• this is the real notes, last time I forgot the --loose option when saving
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibGenotype.release2.notes - lines changed 359, context: html, text, full: html, text
• updated expIDs
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 19, context: html, text, full: html, text
• resolve merge
• fixed tag and added labels to serum treatments from crawford lab
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 4, context: html, text, full: html, text
• fixed a bug handling comments internal to stanzas
  • python/lib/ucscgenomics/ra.py - lines changed 5, context: html, text, full: html, text
• refactored code to be more python like
  • src/hg/encode/encodeQaPrepareRelease/encodeQaPrepareRelease - lines changed 107, context: html, text, full: html, text
• missed an indent on refactor
  • src/hg/encode/encodeQaPrepareRelease/encodeQaPrepareRelease - lines changed 4, context: html, text, full: html, text
• indent on wrong level, and added continue statements for some minor speed gains
  • python/lib/ucscgenomics/ra.py - lines changed 4, context: html, text, full: html, text
• wrong method used to add stanzas into raFile object
  • python/lib/ucscgenomics/ra.py - lines changed 3, context: html, text, full: html, text
• structure of merged object changed, compensating
  • src/hg/encode/raMerge/raMerge - lines changed 2, context: html, text, full: html, text
• fixed short labels, qa request
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release2.ra - lines changed 2, context: html, text, full: html, text
• pre-QA fixed
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.html - lines changed 6, context: html, text, full: html, text
• pre-qa fixes
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.release2.html - lines changed 7, context: html, text, full: html, text
• removed FDR from the labels
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release2.ra - lines changed 69, context: html, text, full: html, text
• added in line about false discovery rates
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release2.html - lines changed 3, context: html, text, full: html, text
• removing the datatype cnv entry, conflicts with CNV view
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 6, context: html, text, full: html, text
• more pre-qa fixes
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 666, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.html - lines changed 2, context: html, text, full: html, text
• resolving merge
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1189, context: html, text, full: html, text
• fixed a score filter thing, and changed type to broadpeak
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.new.ra - lines changed 2, context: html, text, full: html, text
• rewrote some of updatediff to take out the metaDb special case, it now does it ra-type agnostically
  • python/lib/ucscgenomics/ra.py - lines changed 25, context: html, text, full: html, text
• my merge broke things, I'm reverting to 0bce6f57b2a869efad314fe3411f83984bae91fa
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 656, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.html - lines changed 2, context: html, text, full: html, text
• redoing a change i did, because of a revert
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.html - lines changed 2, context: html, text, full: html, text
• chiapet datatpye got merged wuth ruan lab entry
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 7, context: html, text, full: html, text
• fixed chia-pet's entry in beta cv
  • src/hg/makeDb/trackDb/cv/beta/cv.ra - lines changed 7, context: html, text, full: html, text
• put in defaults
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release2.ra - lines changed 14, context: html, text, full: html, text
• spelling error
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release2.html - lines changed 1, context: html, text, full: html, text
• qa fixes for html
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release2.html - lines changed 1, context: html, text, full: html, text
• removing Cnv datatype again
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 6, context: html, text, full: html, text
• removed useless option
  • src/hg/encode/qaUpdateMetadata/qaUpdateMetadata - lines changed 1, context: html, text, full: html, text
• added comments and made variable names better
  • python/lib/ucscgenomics/ra.py - lines changed 7, context: html, text, full: html, text
• updating dataVersion date
  • src/hg/utils/automation/Encode.pm - lines changed 2, context: html, text, full: html, text
• added in new tracks to haib tfbs
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 411, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.ra - lines changed 73, context: html, text, full: html, text
• added in willy's ra->trackDb print option
  • python/lib/ucscgenomics/ra.py - lines changed 47, context: html, text, full: html, text
• removed metadata lines in trackDb
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.ra - lines changed 14, context: html, text, full: html, text
• changed dataVersion date
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 927, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeMapability.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra - lines changed 91, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromSynth.ra - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra - lines changed 121, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra - lines changed 151, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra - lines changed 384, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra - lines changed 286, context: html, text, full: html, text
• staging on beta for tracks that can go ahead and push the dataVersion change, my tracks only
  • src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeHaibTfbs.ra - lines changed 444, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeMapability.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromDnase.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromFaire.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwDnase.ra - lines changed 61, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwHistone.ra - lines changed 247, context: html, text, full: html, text
• added switch for mm9's different dataVersion, right now it's the same as hg19's though
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 4, context: html, text, full: html, text
• removed extra space
  • python/lib/ucscgenomics/ra.py - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• added in bai's for open chrom dnase
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra - lines changed 10, context: html, text, full: html, text
• forgot magic number
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra - lines changed 1, context: html, text, full: html, text
• changed hypersensitivity to affinity
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release2.html - lines changed 2, context: html, text, full: html, text
• cleaned up trackDb stuff, and fixed the problem with the matrix
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release2.ra - lines changed 400, context: html, text, full: html, text
• fixed numeral in dimentionNchecked bug in histone
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release2.ra - lines changed 559, context: html, text, full: html, text
• fixed dimensionNchecked bug in release 3 of histone
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release3.ra - lines changed 638, context: html, text, full: html, text
• same dimension fix for patch now
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.patch.ra - lines changed 559, context: html, text, full: html, text
• modifications for trackDb
  • src/hg/encode/raMerge/raMerge - lines changed 4, context: html, text, full: html, text
• doesn't skip empty lines now
  • python/lib/ucscgenomics/ucscUtils.py - lines changed 2, context: html, text, full: html, text