File Changes for wong

v270_base to v271_preview (2012-07-17 to 2012-07-24) v271

• src/hg/encode/encodeQaInit/encodeQaInit
  • lines changed 7, context: html, text, full: html, text
    added error message, and made autohelp off, also forgot to indent writeScriptOut last time
• src/hg/encode/encodeQaPrepareRelease/encodeQaPrepareRelease
  • lines changed 2, context: html, text, full: html, text
    make the selection more strict for detecting the composite name in a filename
• src/hg/encode/getTrackReferences/getTrackReferences
  • lines changed 2, context: html, text, full: html, text
    removing prog= so default behavior happens
• src/hg/encode/raDiff/raDiff
  • lines changed 5, context: html, text, full: html, text
    removed autohelp
  • lines changed 6, context: html, text, full: html, text
    added reverse mode
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwDnase.release6.notes
  • lines changed 2369, context: html, text, full: html, text
    adding in notes file for us dnase
  • lines changed 384, context: html, text, full: html, text
    updated notes
  • lines changed 5, context: html, text, full: html, text
    removed comma from file list
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwHistone.release5.notes
  • lines changed 2538, context: html, text, full: html, text
    added in first version of notes
  • lines changed 223, context: html, text, full: html, text
    updating notes to reflect K562/ZNF pull
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 12, context: html, text, full: html, text
    adding in saha treatments for open chrom
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 2731, context: html, text, full: html, text
    added in new haib tracks
  • lines changed 1093, context: html, text, full: html, text
    adding in new tracks for haib tfbs
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 937, context: html, text, full: html, text
    added in new open chrom dnase tracks
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwAffyExonArray.ra
  • lines changed 17, context: html, text, full: html, text
    removing K562/ZNF from dev as requested by richard
  • lines changed 17, context: html, text, full: html, text
    received an error reason
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 13, context: html, text, full: html, text
    removing K562/ZNF from dev as requested by richard
  • lines changed 13, context: html, text, full: html, text
    received an error reason
  • lines changed 983, context: html, text, full: html, text
    added in new uw dgf tracks
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 116, context: html, text, full: html, text
    cleaned up some metaData
  • lines changed 431, context: html, text, full: html, text
    adding expIds and accession
  • lines changed 91, context: html, text, full: html, text
    removing K562/ZNF from dev as requested by richard
  • lines changed 91, context: html, text, full: html, text
    received an error reason
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 489, context: html, text, full: html, text
    added in new histone tracks
  • lines changed 25, context: html, text, full: html, text
    added md5sums
  • lines changed 41, context: html, text, full: html, text
    added in expIds
  • lines changed 51, context: html, text, full: html, text
    removing K562/ZNF from dev as requested by richard
  • lines changed 51, context: html, text, full: html, text
    received an error reason
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    making initial patch for uw affy removal of k562 data
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release3.ra
  • lines changed 489, context: html, text, full: html, text
    added in new haib tracks
  • lines changed 193, context: html, text, full: html, text
    adding in new tracks for haib tfbs
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release3.ra
  • lines changed 193, context: html, text, full: html, text
    added in new open chrom dnase tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.patch.html
  • lines changed 96, context: html, text, full: html, text
    adding patch html
  • lines changed 4, context: html, text, full: html, text
    added patch notes
  • lines changed 2, context: html, text, full: html, text
    corrected revoke message for uw affy exon
  • lines changed 2, context: html, text, full: html, text
    more html corrections
  • lines changed 5, context: html, text, full: html, text
    removing more zinc finger related messages
  • lines changed 2, context: html, text, full: html, text
    clarifying revoke message
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.patch.ra
  • lines changed 1523, context: html, text, full: html, text
    making initial patch for uw affy removal of k562 data
  • lines changed 64, context: html, text, full: html, text
    removing the bad K562 Stanzas
  • lines changed 1, context: html, text, full: html, text
    adding patch html
  • lines changed 11, context: html, text, full: html, text
    added in some changed for the K562/ZNF revoke for uw affy exon
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.release4.ra
  • lines changed 80, context: html, text, full: html, text
    removing K562/ZNF stanzas from uw dnase
  • lines changed 518, context: html, text, full: html, text
    added in new uw dgf tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release6.html
  • lines changed 116, context: html, text, full: html, text
    added in new html
  • lines changed 8, context: html, text, full: html, text
    fixed uw dnase for qa
  • lines changed 2, context: html, text, full: html, text
    qa fixes for uw dnase mark 2
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release6.ra
  • lines changed 165, context: html, text, full: html, text
    fixed labels
  • lines changed 1, context: html, text, full: html, text
    added in new html
  • lines changed 488, context: html, text, full: html, text
    removing K562/ZNF data, adding replicate filterCompitste
  • lines changed 285, context: html, text, full: html, text
    fixed uw dnase for qa
  • lines changed 63, context: html, text, full: html, text
    qa fixes for uw dnase mark 2
  • lines changed 1, context: html, text, full: html, text
    added breaks for easier reading
  • lines changed 7, context: html, text, full: html, text
    changing control to Control
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release5.html
  • lines changed 94, context: html, text, full: html, text
    moving over to release 5 html
  • lines changed 2, context: html, text, full: html, text
    qa fixes for uw histone html file
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release5.ra
  • lines changed 109, context: html, text, full: html, text
    added in new histone tracks
  • lines changed 24, context: html, text, full: html, text
    fixed short and long labels
  • lines changed 1, context: html, text, full: html, text
    fixed too long label
  • lines changed 270, context: html, text, full: html, text
    removing bad K562 data
  • lines changed 1, context: html, text, full: html, text
    moving over to release 5 html
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 4291, context: html, text, full: html, text
    added in new cshl long mouse tracks
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    added in new cshl release 3 for mouse
  • lines changed 2, context: html, text, full: html, text
    forgot tags
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.release3.ra
  • lines changed 1325, context: html, text, full: html, text
    added in new cshl release 3 for mouse
  • lines changed 938, context: html, text, full: html, text
    added in new cshl long mouse tracks