File Changes for wong

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

• python/lib/ucscgenomics/ra.py
  • lines changed 5, context: html, text, full: html, text
    fixed a bug handling comments internal to stanzas
  • lines changed 4, context: html, text, full: html, text
    indent on wrong level, and added continue statements for some minor speed gains
  • lines changed 3, context: html, text, full: html, text
    wrong method used to add stanzas into raFile object
  • lines changed 25, context: html, text, full: html, text
    rewrote some of updatediff to take out the metaDb special case, it now does it ra-type agnostically
  • lines changed 7, context: html, text, full: html, text
    added comments and made variable names better
  • lines changed 47, context: html, text, full: html, text
    added in willy's ra->trackDb print option
  • lines changed 0, context: html, text, full: html, text
    removed extra space
• python/lib/ucscgenomics/ucscUtils.py
  • lines changed 2, context: html, text, full: html, text
    doesn't skip empty lines now
• src/hg/encode/encodeMkFilesList/encodeMkFilesList
  • lines changed 5, context: html, text, full: html, text
    widened the filemask and fixed a weird edge case bug
• src/hg/encode/encodeQaPrepareRelease/encodeQaPrepareRelease
  • lines changed 107, context: html, text, full: html, text
    refactored code to be more python like
  • lines changed 4, context: html, text, full: html, text
    missed an indent on refactor
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 4, 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/qaUpdateMetadata/qaUpdateMetadata
  • lines changed 1, context: html, text, full: html, text
    removed useless option
• src/hg/encode/raMerge/raMerge
  • lines changed 2, context: html, text, full: html, text
    structure of merged object changed, compensating
  • lines changed 4, context: html, text, full: html, text
    modifications for trackDb
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibGenotype.release2.notes
  • lines changed 359, context: html, text, full: html, text
    this is the real notes, last time I forgot the --loose option when saving
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 11, context: html, text, full: html, text
    added in some treatments for crawford
  • lines changed 4, context: html, text, full: html, text
    fixed tag and added labels to serum treatments from crawford lab
  • lines changed 6, context: html, text, full: html, text
    removing the datatype cnv entry, conflicts with CNV view
  • lines changed 666, context: html, text, full: html, text
    more pre-qa fixes
  • lines changed 1189, context: html, text, full: html, text
    resolving merge
  • lines changed 656, context: html, text, full: html, text
    my merge broke things, I'm reverting to 0bce6f57b2a869efad314fe3411f83984bae91fa
  • lines changed 7, context: html, text, full: html, text
    chiapet datatpye got merged wuth ruan lab entry
  • lines changed 6, context: html, text, full: html, text
    removing Cnv datatype again
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 7, context: html, text, full: html, text
    fixed chia-pet's entry in beta cv
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 19, context: html, text, full: html, text
    updated expIDs
  • lines changed 411, context: html, text, full: html, text
    added in new tracks to haib tfbs
  • lines changed 927, context: html, text, full: html, text
    changed dataVersion date
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeMapability.ra
  • lines changed 5, context: html, text, full: html, text
    changed dataVersion date
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 31, context: html, text, full: html, text
    changed dataVersion date
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 71, context: html, text, full: html, text
    updated md5sums
  • lines changed 91, context: html, text, full: html, text
    changed dataVersion date
  • lines changed 10, context: html, text, full: html, text
    added in bai's for open chrom dnase
  • lines changed 1, context: html, text, full: html, text
    forgot magic number
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
  • lines changed 15, context: html, text, full: html, text
    changed dataVersion date
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromSynth.ra
  • lines changed 11, context: html, text, full: html, text
    changed dataVersion date
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 121, context: html, text, full: html, text
    changed dataVersion date
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 151, context: html, text, full: html, text
    changed dataVersion date
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 384, context: html, text, full: html, text
    changed dataVersion date
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
  • lines changed 286, context: html, text, full: html, text
    changed dataVersion date
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeHaibTfbs.ra
  • lines changed 444, 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/wgEncodeMapability.ra
  • lines changed 5, 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/wgEncodeOpenChromDnase.ra
  • lines changed 3, 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/wgEncodeOpenChromFaire.ra
  • lines changed 6, 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/wgEncodeUwDnase.ra
  • lines changed 61, 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/wgEncodeUwHistone.ra
  • lines changed 247, 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/wgEncodeDukeAffyExon.new.ra
  • lines changed 2, context: html, text, full: html, text
    fixed a score filter thing, and changed type to broadpeak
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.release2.html
  • lines changed 7, context: html, text, full: html, text
    pre-qa fixes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.ra
  • lines changed 73, context: html, text, full: html, text
    added in new tracks to haib tfbs
  • lines changed 14, context: html, text, full: html, text
    removed metadata lines in trackDb
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.html
  • lines changed 6, context: html, text, full: html, text
    pre-QA fixed
  • lines changed 2, context: html, text, full: html, text
    more pre-qa fixes
  • lines changed 2, context: html, text, full: html, text
    my merge broke things, I'm reverting to 0bce6f57b2a869efad314fe3411f83984bae91fa
  • lines changed 2, context: html, text, full: html, text
    redoing a change i did, because of a revert
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.patch.ra
  • lines changed 559, context: html, text, full: html, text
    same dimension fix for patch now
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release2.ra
  • lines changed 559, context: html, text, full: html, text
    fixed numeral in dimentionNchecked bug in histone
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release3.ra
  • lines changed 638, context: html, text, full: html, text
    fixed dimensionNchecked bug in release 3 of histone
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release2.html
  • lines changed 3, context: html, text, full: html, text
    added in line about false discovery rates
  • lines changed 1, context: html, text, full: html, text
    spelling error
  • lines changed 1, context: html, text, full: html, text
    qa fixes for html
  • lines changed 2, context: html, text, full: html, text
    changed hypersensitivity to affinity
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release2.ra
  • lines changed 2, context: html, text, full: html, text
    fixed short labels, qa request
  • lines changed 69, context: html, text, full: html, text
    removed FDR from the labels
  • lines changed 14, context: html, text, full: html, text
    put in defaults
  • lines changed 400, context: html, text, full: html, text
    cleaned up trackDb stuff, and fixed the problem with the matrix
• src/hg/utils/automation/Encode.pm
  • lines changed 2, context: html, text, full: html, text
    updating dataVersion date