File Changes for wong

v261_preview to v261_preview2 (2011-12-13 to 2011-12-20) v261

• python/lib/ucscgenomics/mkChangeNotes.py
  • lines changed 1, context: html, text, full: html, text
    modifications for morgan's new ra.py changes
• python/lib/ucscgenomics/ra.py
  • lines changed 5, context: html, text, full: html, text
    corrected an error in morgan's modification
  • lines changed 1, context: html, text, full: html, text
    error in making the common set of stanzas, not intersection of self and self, that's just plain wrong
  • lines changed 1, context: html, text, full: html, text
    corrected backward changes
• src/hg/encode/qaUpdateMetadata/qaUpdateMetadata
  • lines changed 2, context: html, text, full: html, text
    changed comparison to public vs alpha instead of beta vs alpha
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeOpenChromSynth.release2.notes
  • lines changed 128, context: html, text, full: html, text
    notes for release2 open chrom synth
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeRikenCage.release2.notes
  • lines changed 418, context: html, text, full: html, text
    updated notes to reflect the restoring of revoked data
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 18, context: html, text, full: html, text
    moved comments out of lines with var val pairs
  • lines changed 1, context: html, text, full: html, text
    fixed regex to be more stringent
  • lines changed 5, context: html, text, full: html, text
    fixed some interferon descriptions, uncovered problems
  • lines changed 1, context: html, text, full: html, text
    forgot to escape the plus last time
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 21, context: html, text, full: html, text
    restored missing stanza from public
  • lines changed 4, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibGenotype.ra
  • lines changed 29, context: html, text, full: html, text
    fixed some metadata issues, added expIds and accessions
  • lines changed 2, context: html, text, full: html, text
    added md5sum
  • lines changed 5, context: html, text, full: html, text
    fixed some metadata issues caused by reloads
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromSynth.ra
  • lines changed 9, context: html, text, full: html, text
    added in treatment=None values
  • lines changed 17, context: html, text, full: html, text
    removed unnecessary origAessembly lines
  • lines changed 21, context: html, text, full: html, text
    added dcc accessions to synth
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 3586, context: html, text, full: html, text
    restored missing metaData form public
  • lines changed 152, context: html, text, full: html, text
    added revoke tags to all the restored metadata
  • lines changed 134, context: html, text, full: html, text
    added md5sums
  • lines changed 714, context: html, text, full: html, text
    removed stanzas from public that have no files left also added in dccaccessions and expids where possible
  • lines changed 13, context: html, text, full: html, text
    added bais
  • lines changed 6, context: html, text, full: html, text
    fleshed out replaced message
  • lines changed 74, context: html, text, full: html, text
    cleaned up the restored stanzas, there were many errors
  • lines changed 1340, context: html, text, full: html, text
    Revert "Removing the clusters again, we are getting new ones" This reverts commit 09d9948a9918c35ecb5ffe6ba9b2cdd4a12853e6.
  • lines changed 1267, context: html, text, full: html, text
    re-removed clusters from fresh file
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 1837, context: html, text, full: html, text
    metadata for batch job
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeBroadHistone.ra
  • lines changed 11, context: html, text, full: html, text
    filled in the rest of the dccAccessions
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeCshlShortRnaSeq.ra
  • lines changed 40, context: html, text, full: html, text
    rebuilt the beta.mdb.ra for cshl short's metaData update
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeRikenCage.ra
  • lines changed 5445, context: html, text, full: html, text
    remade the beta.mdb.ra for riken for dccaccession push
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    renamed openchromchip with release tag
  • lines changed 1, context: html, text, full: html, text
    changed over to release conventions for synth
  • lines changed 2, context: html, text, full: html, text
    fixed in trackDb
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.release2.html
  • lines changed 5, context: html, text, full: html, text
    added release 2 notes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.release2.ra
  • lines changed 112, context: html, text, full: html, text
    added obtained by to the subgroups becuase we have colliding objects without it
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.new.ra
  • lines changed 1112, context: html, text, full: html, text
    renamed openchromchip with release tag
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.release2.html
  • lines changed 315, context: html, text, full: html, text
    added in html for open chrom release 2
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.release2.ra
  • lines changed 1112, context: html, text, full: html, text
    renamed openchromchip with release tag
  • lines changed 10, context: html, text, full: html, text
    moved progfibro to be near the other fibroblasts
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.new.ra
  • lines changed 196, context: html, text, full: html, text
    changed over to release conventions for synth
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.html
  • lines changed 294, context: html, text, full: html, text
    added in html for synth release 2
  • lines changed 17, context: html, text, full: html, text
    open chrom synth release 2 fixes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.ra
  • lines changed 196, context: html, text, full: html, text
    changed over to release conventions for synth
  • lines changed 35, context: html, text, full: html, text
    pre-qa changes for synth
  • lines changed 11, context: html, text, full: html, text
    open chrom synth release 2 fixes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.html
  • lines changed 131, context: html, text, full: html, text
    moved html over
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.ra
  • lines changed 648, context: html, text, full: html, text
    batch loaded submissions
  • lines changed 4562, context: html, text, full: html, text
    rename to new convention
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release4.html
  • lines changed 131, context: html, text, full: html, text
    moved html over
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release4.ra
  • lines changed 4562, context: html, text, full: html, text
    rename to new convention
  • lines changed 4, context: html, text, full: html, text
    changed html tag, and collapsed cd20 cell lines into one
  • lines changed 54, context: html, text, full: html, text
    changed long labels