File Changes for wong

v254_preview2 to v254_base (2011-07-12 to 2011-07-19) v254

• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 26, context: html, text, full: html, text
    marked up some more comments and removed deprecated lines from doEncodeValidate
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibTfbs.release1.notes
  • lines changed 6, context: html, text, full: html, text
    removbed files that I accidently restored through a git error from back in the day.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 7, context: html, text, full: html, text
    added provisional exonsgencv7 term
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 161, context: html, text, full: html, text
    changed dates for dateUnrestricted according to redmine 4331
  • lines changed 320, context: html, text, full: html, text
    removed fileIndex field
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 4201, context: html, text, full: html, text
    added a lot of cshl long tracks
  • lines changed 5, context: html, text, full: html, text
    removed fileIndex field
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 1199, context: html, text, full: html, text
    added a lot of subtracks to cshl short rna seq
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 166, context: html, text, full: html, text
    removed fileIndex field
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 79, context: html, text, full: html, text
    removed fileIndex field
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 110, context: html, text, full: html, text
    removed fileIndex field
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
  • lines changed 41, context: html, text, full: html, text
    removed fileIndex field
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 7, context: html, text, full: html, text
    commit hand made changes before i try out my script to mass change dates for a large paper
  • lines changed 28, context: html, text, full: html, text
    forgot to commit histone changes for K562b
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 173, context: html, text, full: html, text
    changed treatment to tnfa for experiment that were incorrect
  • lines changed 129, context: html, text, full: html, text
    loaded mdb for 4412, it was missing earlier
  • lines changed 385, context: html, text, full: html, text
    added in some missing meta data
  • lines changed 137, context: html, text, full: html, text
    removed K562b traces
  • lines changed 21, context: html, text, full: html, text
    changed control for gm12878 nfkb form std to iggrab
  • lines changed 78, context: html, text, full: html, text
    changed files names for adding iggrab to gm12878 nfkb
  • lines changed 489, context: html, text, full: html, text
    cleaned up a lot of stuff in sydh tfbs per redmine #69
  • lines changed 68, context: html, text, full: html, text
    commit hand made changes before i try out my script to mass change dates for a large paper
  • lines changed 8, context: html, text, full: html, text
    moved k562/mnased/setdb1 to release 2 also found one last k562b that i missed somehow
  • lines changed 86, context: html, text, full: html, text
    correct a typing error TFNa > TNFa
  • lines changed 42, context: html, text, full: html, text
    corrected some control errors, more to go
  • lines changed 8, context: html, text, full: html, text
    renamed mislabeled control
  • lines changed 127, context: html, text, full: html, text
    fixed metadata control issues
  • lines changed 100, context: html, text, full: html, text
    fixed even more metadata control issues, name changes in this one too
  • lines changed 158, context: html, text, full: html, text
    forgot to add tnfa to gm12878
  • lines changed 203, context: html, text, full: html, text
    reverted previous commit, it was done in error
  • lines changed 1977, context: html, text, full: html, text
    added dccaccesion expId's where missing and changed controlId over to dcc accession
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 98, context: html, text, full: html, text
    removed fileIndex field
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.html
  • lines changed 13, context: html, text, full: html, text
    added references to the pages according to redmine 4331
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra
  • lines changed 1014, context: html, text, full: html, text
    added a lot of cshl long tracks
  • lines changed 60, context: html, text, full: html, text
    subgroups didn't have pooled, but patchtdb didn't throw error
  • lines changed 8, context: html, text, full: html, text
    a previous search and replace error made chromatin > chromatim, corrected
  • lines changed 1, context: html, text, full: html, text
    mispelling in short label
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.ra
  • lines changed 437, context: html, text, full: html, text
    added a lot of subtracks to cshl short rna seq
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.html
  • lines changed 9, context: html, text, full: html, text
    corrected some errors in haib tfbs's html
  • lines changed 1, context: html, text, full: html, text
    fixed a word
  • lines changed 8, context: html, text, full: html, text
    correct some html errors
  • lines changed 1, context: html, text, full: html, text
    changed a word
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
  • lines changed 1, context: html, text, full: html, text
    changed supertrack view for haib to dense
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.html
  • lines changed 10, context: html, text, full: html, text
    added references to the pages according to redmine 4331
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.html
  • lines changed 21, context: html, text, full: html, text
    added references to the pages according to redmine 4331
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
  • lines changed 34, context: html, text, full: html, text
    changed files names for adding iggrab to gm12878 nfkb
  • lines changed 143, context: html, text, full: html, text
    cleaned up a lot of stuff in sydh tfbs per redmine #69
  • lines changed 16, context: html, text, full: html, text
    moved k562/mnased/setdb1 to release 2 also found one last k562b that i missed somehow
  • lines changed 5, context: html, text, full: html, text
    changed name for mislabeled control
  • lines changed 27, context: html, text, full: html, text
    added missing TNFa treatments to subgroups and labels
  • lines changed 18, context: html, text, full: html, text
    fixed even more metadata control issues, name changes in this one too
  • lines changed 5, context: html, text, full: html, text
    forgot to add tnfa to gm12878
  • lines changed 5, context: html, text, full: html, text
    reverted previous commit, it was done in error
  • lines changed 1, context: html, text, full: html, text
    put in filesort order for sydh tfbs, mainly a placeholder
  • lines changed 1, context: html, text, full: html, text
    corrected a typing error
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.ra
  • lines changed 1, context: html, text, full: html, text
    added geo accession sort field