File Changes for wong

v258_preview to v258_preview2 (2011-09-27 to 2011-10-04) v258

• src/hg/encode/encodeDownloadReadme/encodeDownloadReadme.pl
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    cleaned up some whitespace stuff
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhTfbs.release1.notes
  • lines changed 184, context: html, text, full: html, text
    updated notes file
  • lines changed 89, context: html, text, full: html, text
    updated notes
  • lines changed 7, context: html, text, full: html, text
    updated notes
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUncBsuProt.release1.notes
  • lines changed 13, context: html, text, full: html, text
    updated notes files for unc bsu prot
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 12, context: html, text, full: html, text
    added 2 new treatments
  • lines changed 8, context: html, text, full: html, text
    put back in lines whose deletion broke things, corrected searchable term in dccRep
  • lines changed 9, context: html, text, full: html, text
    corrected incorrect lab name for antibodies registered.
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    missed an antibody
  • lines changed 5, context: html, text, full: html, text
    added in goat control entry
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 1162, context: html, text, full: html, text
    added new tracks to broad histone metaDb
  • lines changed 259, context: html, text, full: html, text
    loaded 2 new borad tracks
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethyl450.ra
  • lines changed 859, context: html, text, full: html, text
    added new tracks to Haib methyl 450
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 920, context: html, text, full: html, text
    added in 4321 and 4320
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    added a lot of haib tfbs tracks
  • lines changed 1184, context: html, text, full: html, text
    added in new haib tracks
  • lines changed 671, context: html, text, full: html, text
    added in new controls
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 336, context: html, text, full: html, text
    added in new tracks for open chrom chip
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 451, context: html, text, full: html, text
    added in new entries for open chrom dnase
  • lines changed 118, context: html, text, full: html, text
    added one track to open chrom dnase
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 257, context: html, text, full: html, text
    loaded 2 new tracks for sydh Histone
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 3, context: html, text, full: html, text
    added md5sums
  • lines changed 1409, context: html, text, full: html, text
    loaded new tracks into release 2 sydh TFBS
  • lines changed 7, context: html, text, full: html, text
    last second revoke and replace of an experiment
  • lines changed 31, context: html, text, full: html, text
    corrected controls and long labels for replacement experiment
  • lines changed 23, context: html, text, full: html, text
    added bai's to fileName field.
  • lines changed 63, context: html, text, full: html, text
    updated md5sums
  • lines changed 27, context: html, text, full: html, text
    cleanup SydhTfbs track
  • lines changed 54, context: html, text, full: html, text
    renamed K562/SetDb1/UCD to be consistent with the other objects in the experiment
  • lines changed 65, context: html, text, full: html, text
    added new control to sydh tfbs
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra
  • lines changed 5, context: html, text, full: html, text
    removed erroneous origAsembly hg19 term
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 1277, context: html, text, full: html, text
    added a lot of uw tracks
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    added a lot of DGF tracks
  • lines changed 108, context: html, text, full: html, text
    removed random accession=hg19 fields
  • lines changed 108, context: html, text, full: html, text
    removed origAssembly from DGF
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 115, context: html, text, full: html, text
    restored lost metadata
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
  • lines changed 70, context: html, text, full: html, text
    restored missing metadata
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    changed alpha to .new.ra for sydh tfbs
  • lines changed 1, context: html, text, full: html, text
    put it back to the .ra for sydh tfbs
  • lines changed 2, context: html, text, full: html, text
    alpha, beta, public on sydh TFBS trackDb
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.new.ra
  • lines changed 1, context: html, text, full: html, text
    inserted new antibody terms
  • lines changed 180, context: html, text, full: html, text
    added new tracks
  • lines changed 41, context: html, text, full: html, text
    loaded 2 new borad tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.ra
  • lines changed 353, context: html, text, full: html, text
    added new tracks to Haib methyl 450
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.new.ra
  • lines changed 122, context: html, text, full: html, text
    added in 4321 and 4320
  • lines changed 381, context: html, text, full: html, text
    added a lot of haib tfbs tracks
  • lines changed 1, context: html, text, full: html, text
    changed alpha to html character code
  • lines changed 752, context: html, text, full: html, text
    revamped long labels
  • lines changed 231, context: html, text, full: html, text
    added in new haib tracks
  • lines changed 82, context: html, text, full: html, text
    added in new controls
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.new.ra
  • lines changed 57, context: html, text, full: html, text
    added in new tracks for open chrom chip
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.new.ra
  • lines changed 98, context: html, text, full: html, text
    added in new entries for open chrom dnase
  • lines changed 6, context: html, text, full: html, text
    added in missing no treatments
  • lines changed 25, context: html, text, full: html, text
    added one track to open chrom dnase
  • lines changed 3, context: html, text, full: html, text
    added in missing non treatment
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.new.ra
  • lines changed 44, context: html, text, full: html, text
    loaded 2 new tracks for sydh Histone
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.new.ra
  • lines changed 17, context: html, text, full: html, text
    long labels for sydh tfbs
  • lines changed 28, context: html, text, full: html, text
    short labels sydh tfbs
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    added time to EtOH 36Hr treatment. We should consider adding this to the cv, as that term is inconsistent with the others.
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    objects that needed to be pushed got pushed to release2, uncomment this later
  • lines changed 278, context: html, text, full: html, text
    loaded new tracks into release 2 sydh TFBS
  • lines changed 3, context: html, text, full: html, text
    updated the info on a replaced track
  • lines changed 11, context: html, text, full: html, text
    added new control to sydh tfbs
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
  • lines changed 184, context: html, text, full: html, text
    merged non-released release1 with the WIP release2 to be the new release 1
  • lines changed 56, context: html, text, full: html, text
    removed bad experiments after once-over
  • lines changed 34, context: html, text, full: html, text
    last second revoke and replace of an experiment
  • lines changed 2, context: html, text, full: html, text
    corrected controls and long labels for replacement experiment
  • lines changed 14, context: html, text, full: html, text
    cleanup SydhTfbs track
  • lines changed 1, context: html, text, full: html, text
    cleaned up more trackDb
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.new.ra
  • lines changed 441, context: html, text, full: html, text
    added a lot of uw tracks
  • lines changed 281, context: html, text, full: html, text
    added a lot of DGF tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.html
  • lines changed 14, context: html, text, full: html, text
    changed html for uw histone
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra
  • lines changed 263, context: html, text, full: html, text
    fixed long labels UwHistone
  • lines changed 503, context: html, text, full: html, text
    fixed short labels
  • lines changed 425, context: html, text, full: html, text
    fixed longlabels in uwtfbs, added in treatments in uw histone tfbs and cleanup
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.ra
  • lines changed 328, context: html, text, full: html, text
    fixed longlabels in uwtfbs, added in treatments in uw histone tfbs and cleanup
  • lines changed 236, context: html, text, full: html, text
    short labels for uw tfbs