File Changes for wong

v271_preview to v271_preview2 (2012-07-24 to 2012-07-31) v271

• src/hg/encode/getTrackReferences/getTrackReferences
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    removed prog= so default behavior happens
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlLongRnaSeq.release2.notes
  • lines changed 6, context: html, text, full: html, text
    updating notes file
  • lines changed 6, context: html, text, full: html, text
    Revert "updating notes file"
    This reverts commit 2d35026eff77e39f04dc072b74cfce019585778d.
    
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 12, context: html, text, full: html, text
    restoring labProtocolId, as Cshl uses it for their submissions. This was causing mass failures.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    adding trackDb changes or affy rna chip
• src/hg/makeDb/trackDb/human/hg18/wgEncodeAffyRnaChip.patch.ra
  • lines changed 1000, context: html, text, full: html, text
    splitting affyrna into patch.ra and normal.ra
• src/hg/makeDb/trackDb/human/hg18/wgEncodeAffyRnaChip.ra
  • lines changed 105, context: html, text, full: html, text
    fixed the tags in affyRnaChip, comming in branch and testing hte shared branch thing
  • lines changed 108, context: html, text, full: html, text
    correcting cell tier tags
  • lines changed 108, context: html, text, full: html, text
    splitting affyrna into patch.ra and normal.ra
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadHmm.ra
  • lines changed 10, context: html, text, full: html, text
    fixed metadata and dates
  • lines changed 10, context: html, text, full: html, text
    Revert "fixed metadata and dates"
    This reverts commit fdd11ddb9f8b6e749175a07e86843ad18e0976fb.
    
  • lines changed 0, context: html, text, full: html, text
    correcting spacing and indentation
  • lines changed 10, context: html, text, full: html, text
    fixing cell tier tags
  • lines changed 0, context: html, text, full: html, text
    correcting cell tier tags
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.ra
  • lines changed 139, context: html, text, full: html, text
    fixed metadata and dates
  • lines changed 139, context: html, text, full: html, text
    Revert "fixed metadata and dates"
    This reverts commit fdd11ddb9f8b6e749175a07e86843ad18e0976fb.
    
  • lines changed 139, context: html, text, full: html, text
    fixing the rest of the tags
  • lines changed 141, context: html, text, full: html, text
    correcting cell tier tags
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlLongRnaSeq.ra
  • lines changed 49, context: html, text, full: html, text
    fixed metadata and dates
  • lines changed 49, context: html, text, full: html, text
    Revert "fixed metadata and dates"
    This reverts commit fdd11ddb9f8b6e749175a07e86843ad18e0976fb.
    
  • lines changed 21, context: html, text, full: html, text
    fixing the rest of the tags
  • lines changed 22, context: html, text, full: html, text
    correcting cell tier tags
  • lines changed 49, context: html, text, full: html, text
    more qa fixes for hg18 tag correction, this time correctin view tag errors
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlShortRnaSeq.ra
  • lines changed 98, context: html, text, full: html, text
    fixed metadata and dates
  • lines changed 98, context: html, text, full: html, text
    Revert "fixed metadata and dates"
    This reverts commit fdd11ddb9f8b6e749175a07e86843ad18e0976fb.
    
  • lines changed 48, context: html, text, full: html, text
    fizing tags for cshl short rna seq
  • lines changed 48, context: html, text, full: html, text
    Revert "fizing tags for cshl short rna seq"
    This reverts commit 3e65bac5c9b15997f7e1ab0a5649596de840d738.
    
  • lines changed 46, context: html, text, full: html, text
    fixing the rest of the tags
  • lines changed 46, context: html, text, full: html, text
    correcting cell tier tags
  • lines changed 5, context: html, text, full: html, text
    fixing things for QA
  • lines changed 98, context: html, text, full: html, text
    more qa fixes for hg18 tag correction, this time correctin view tag errors
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisDnaPet.ra
  • lines changed 7, context: html, text, full: html, text
    fixed metadata and dates
  • lines changed 7, context: html, text, full: html, text
    Revert "fixed metadata and dates"
    This reverts commit fdd11ddb9f8b6e749175a07e86843ad18e0976fb.
    
  • lines changed 8, context: html, text, full: html, text
    fixing the rest of the tags
  • lines changed 7, context: html, text, full: html, text
    correcting cell tier tags
  • lines changed 2, context: html, text, full: html, text
    fixing things for QA
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.ra
  • lines changed 170, context: html, text, full: html, text
    fixed metadata and dates
  • lines changed 170, context: html, text, full: html, text
    Revert "fixed metadata and dates"
    This reverts commit fdd11ddb9f8b6e749175a07e86843ad18e0976fb.
    
  • lines changed 87, context: html, text, full: html, text
    fixed tag errors for gis pet hg18
  • lines changed 87, context: html, text, full: html, text
    Revert "fixed tag errors for gis pet hg18"
    This reverts commit ad65cd56e8afaae71d73ed6deda9fdd6dee9857b.
    
  • lines changed 82, context: html, text, full: html, text
    fixing the rest of the tags
  • lines changed 85, context: html, text, full: html, text
    correcting cell tier tags
  • lines changed 5, context: html, text, full: html, text
    fixing things for QA
  • lines changed 170, context: html, text, full: html, text
    more qa fixes for hg18 tag correction, this time correctin view tag errors
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaSeq.ra
  • lines changed 47, context: html, text, full: html, text
    fixed metadata and dates
  • lines changed 47, context: html, text, full: html, text
    Revert "fixed metadata and dates"
    This reverts commit fdd11ddb9f8b6e749175a07e86843ad18e0976fb.
    
  • lines changed 20, context: html, text, full: html, text
    fixed gisrna seq tags
  • lines changed 20, context: html, text, full: html, text
    Revert "fixed gisrna seq tags"
    This reverts commit 4066509926bc9530018d96135126dc8c7a214554.
    
  • lines changed 19, context: html, text, full: html, text
    fixing the rest of the tags
  • lines changed 20, context: html, text, full: html, text
    correcting cell tier tags
  • lines changed 48, context: html, text, full: html, text
    more qa fixes for hg18 tag correction, this time correctin view tag errors
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.ra
  • lines changed 122, context: html, text, full: html, text
    fixed metadata and dates
  • lines changed 122, context: html, text, full: html, text
    Revert "fixed metadata and dates"
    This reverts commit fdd11ddb9f8b6e749175a07e86843ad18e0976fb.
    
  • lines changed 62, context: html, text, full: html, text
    fixing tags for riken cage
  • lines changed 62, context: html, text, full: html, text
    Revert "fixing tags for riken cage"
    This reverts commit 2a44d0254c171c351833b144781630eea5dda7b5.
    
  • lines changed 59, context: html, text, full: html, text
    fixing the rest of the tags
  • lines changed 60, context: html, text, full: html, text
    correcting cell tier tags
  • lines changed 4, context: html, text, full: html, text
    fixing things for QA
  • lines changed 122, context: html, text, full: html, text
    more qa fixes for hg18 tag correction, this time correctin view tag errors
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwChIPSeq.ra
  • lines changed 300, context: html, text, full: html, text
    fixed metadata and dates
  • lines changed 300, context: html, text, full: html, text
    Revert "fixed metadata and dates"
    This reverts commit fdd11ddb9f8b6e749175a07e86843ad18e0976fb.
    
  • lines changed 300, context: html, text, full: html, text
    fixing the rest of the tags
  • lines changed 294, context: html, text, full: html, text
    correcting cell tier tags
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.ra
  • lines changed 230, context: html, text, full: html, text
    fixed metadata and dates
  • lines changed 230, context: html, text, full: html, text
    Revert "fixed metadata and dates"
    This reverts commit fdd11ddb9f8b6e749175a07e86843ad18e0976fb.
    
  • lines changed 230, context: html, text, full: html, text
    fixed tags in uw dnase seq
  • lines changed 230, context: html, text, full: html, text
    Revert "fixed tags in uw dnase seq"
    This reverts commit 2154fc5e2abf17b785892cc4c2b7bb599efc1abf.
    
  • lines changed 230, context: html, text, full: html, text
    fixing the rest of the tags
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 2045, context: html, text, full: html, text
    loaded a lot of broad histone tracks
  • lines changed 3338, context: html, text, full: html, text
    added in new broad tracks
  • lines changed 696, context: html, text, full: html, text
    addedi in lat of Broad histone tracks
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 928, context: html, text, full: html, text
    loaded protocols and transcipt denovos for cshl long
  • lines changed 97, context: html, text, full: html, text
    removed tableNames from transcipt denovos cshl long
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
  • lines changed 69, context: html, text, full: html, text
    adding in replacement clusters for gisRnaPet
  • lines changed 13, context: html, text, full: html, text
    aded md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 2185, context: html, text, full: html, text
    added new haib tracks
  • lines changed 6007, context: html, text, full: html, text
    adding in more haib tfbs tracks
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 881, context: html, text, full: html, text
    added in new tracks for open chrom chip
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwAffyExonArray.ra
  • lines changed 321, context: html, text, full: html, text
    added in last uw affy exon tracks
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 145, context: html, text, full: html, text
    corrected some metaDb errors
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    added in last uw affy exon tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release3.ra
  • lines changed 393, context: html, text, full: html, text
    loaded a lot of broad histone tracks
  • lines changed 487, context: html, text, full: html, text
    added in new broad tracks
  • lines changed 90, context: html, text, full: html, text
    addedi in lat of Broad histone tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release3.ra
  • lines changed 388, context: html, text, full: html, text
    added new haib tracks
  • lines changed 1061, context: html, text, full: html, text
    adding in more haib tfbs tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.release2.ra
  • lines changed 130, context: html, text, full: html, text
    added in new tracks for open chrom chip
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.release3.ra
  • lines changed 72, context: html, text, full: html, text
    added in last uw affy exon tracks
  • lines changed 73, context: html, text, full: html, text
    moving patch changes in and correcting tags
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 3894, context: html, text, full: html, text
    added in enw cshl mouse long tracks
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeMapability.ra
  • lines changed 16, context: html, text, full: html, text
    fixed metadata and dates
  • lines changed 16, context: html, text, full: html, text
    Revert "fixed metadata and dates"
    This reverts commit fdd11ddb9f8b6e749175a07e86843ad18e0976fb.
    
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.release3.ra
  • lines changed 304, context: html, text, full: html, text
    added in enw cshl mouse long tracks