File Changes for wong

v264_preview to v264_preview2 (2012-02-21 to 2012-02-28) v264

• python/lib/ucscgenomics/mkChangeNotes.py
  • lines changed 2, context: html, text, full: html, text
    forgot parenthesis
  • lines changed 7, context: html, text, full: html, text
    changed some error handling stuff in mkChangeNotes, and made revoked gbdbs removed from the changed gbdbs list
• src/hg/encode/encodeMkFilesList/encodeMkFilesList
  • lines changed 3, context: html, text, full: html, text
    fixed usage
• src/hg/encode/encodeQaInit/encodeQaInit
  • lines changed 9, context: html, text, full: html, text
    corrections requested by others
  • lines changed 7, context: html, text, full: html, text
    fixed the enw fiels mail to also have file size
• src/hg/encode/qaAddTrackReferences/qaAddTrackReferences
  • lines changed 11, context: html, text, full: html, text
    made it so that suthor count can be defined on commant line
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeOpenChromDnase.release2.notes
  • lines changed 908, context: html, text, full: html, text
    regenerated notes
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwTfbs.release3.notes
  • lines changed 64, context: html, text, full: html, text
    regenerated notes
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethyl450.ra
  • lines changed 64, context: html, text, full: html, text
    changed post ENCDOE Jan 2011 Freeze to ENCODE Mar 2012 Freeze
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylArray.ra
  • lines changed 7, context: html, text, full: html, text
    changed post ENCDOE Jan 2011 Freeze to ENCODE Mar 2012 Freeze
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
  • lines changed 233, context: html, text, full: html, text
    changed post ENCDOE Jan 2011 Freeze to ENCODE Mar 2012 Freeze
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibRnaSeq.ra
  • lines changed 78, context: html, text, full: html, text
    short and long labels in trackDb, freeze date in etmaDb for haib rna seq fixes.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 309, context: html, text, full: html, text
    added in expIds and dccAcceession
  • lines changed 202, context: html, text, full: html, text
    fixed gzip md5sum bug
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
  • lines changed 81, context: html, text, full: html, text
    fixing md5sums for open Chrom Faire
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromSynth.ra
  • lines changed 18, context: html, text, full: html, text
    fixing md5sum gzip bug
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyGeneSt.ra
  • lines changed 121, context: html, text, full: html, text
    changed post ENCDOE Jan 2011 Freeze to ENCODE Mar 2012 Freeze
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhNsome.ra
  • lines changed 43, context: html, text, full: html, text
    changed post ENCDOE Jan 2011 Freeze to ENCODE Mar 2012 Freeze
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
  • lines changed 25, context: html, text, full: html, text
    expids for uw tfbs
  • lines changed 429, context: html, text, full: html, text
    added in expIds and dccAcceession
  • lines changed 409, context: html, text, full: html, text
    fixed gzip md5sum bug
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromSynth.ra
  • lines changed 18, context: html, text, full: html, text
    fixing md5sums for uw dgf and open chro synth, staging on beta
  • lines changed 18, context: html, text, full: html, text
    Revert "fixing md5sums for uw dgf and open chro synth, staging on beta" This reverts commit c1596ce2a293cd85862df52171dab56432a6ae5f.
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwDgf.ra
  • lines changed 98, context: html, text, full: html, text
    fixing md5sums for uw dgf and open chro synth, staging on beta
  • lines changed 98, context: html, text, full: html, text
    Revert "fixing md5sums for uw dgf and open chro synth, staging on beta" This reverts commit c1596ce2a293cd85862df52171dab56432a6ae5f.
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    changed incldue for WGBS
  • lines changed 2, context: html, text, full: html, text
    moving sydh histone to new release tag convention
  • lines changed 1, context: html, text, full: html, text
    trackDb.wgEncode.ra fix for duke affy exon
  • lines changed 3, context: html, text, full: html, text
    moved mapability to new release tags
  • lines changed 1, context: html, text, full: html, text
    trackDb fix for openchrom faire
  • lines changed 1, context: html, text, full: html, text
    include statement for 5c
  • lines changed 2, context: html, text, full: html, text
    setting up patch for mapability html change
  • lines changed 2, context: html, text, full: html, text
    Mapability track is done, no need for release 4
  • lines changed 2, context: html, text, full: html, text
    fixed some long labels that need to be patched in
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.new.html
  • lines changed 102, context: html, text, full: html, text
    moved duke affy exon to new convention for release tag
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.new.ra
  • lines changed 900, context: html, text, full: html, text
    moved duke affy exon to new convention for release tag
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.release3.html
  • lines changed 102, context: html, text, full: html, text
    moved duke affy exon to new convention for release tag
  • lines changed 3, context: html, text, full: html, text
    fixed temporary release notes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.release3.ra
  • lines changed 900, context: html, text, full: html, text
    moved duke affy exon to new convention for release tag
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibBisulfate.html
  • lines changed 61, context: html, text, full: html, text
    renaming the bisulfite track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibBisulfate.ra
  • lines changed 84, context: html, text, full: html, text
    renaming the bisulfite track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.html
  • lines changed 121, context: html, text, full: html, text
    moving haib mehtyl rrbs to rlease 3 tags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.ra
  • lines changed 1875, context: html, text, full: html, text
    moving haib mehtyl rrbs to rlease 3 tags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.release3.html
  • lines changed 121, context: html, text, full: html, text
    moving haib mehtyl rrbs to rlease 3 tags
  • lines changed 2, context: html, text, full: html, text
    fixed temporary release notes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.release3.ra
  • lines changed 1875, context: html, text, full: html, text
    moving haib mehtyl rrbs to rlease 3 tags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylWgbs.html
  • lines changed 61, context: html, text, full: html, text
    renaming the bisulfite track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylWgbs.ra
  • lines changed 84, context: html, text, full: html, text
    renaming the bisulfite track
  • lines changed 60, context: html, text, full: html, text
    cleaned up test WGBS track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.html
  • lines changed 16, context: html, text, full: html, text
    qa fixes to html
  • lines changed 1, context: html, text, full: html, text
    fixed genode misspelling
  • lines changed 1, context: html, text, full: html, text
    fixed misspelled gencode
  • lines changed 5, context: html, text, full: html, text
    added in naming convention for BAM reads
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.patch.ra
  • lines changed 870, context: html, text, full: html, text
    fixed some long labels that need to be patched in
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.ra
  • lines changed 4, context: html, text, full: html, text
    fixed some last second short labels
  • lines changed 40, context: html, text, full: html, text
    short and long labels in trackDb, freeze date in etmaDb for haib rna seq fixes.
  • lines changed 2, context: html, text, full: html, text
    turned show names for alignments to off
  • lines changed 41, context: html, text, full: html, text
    fixed label in matrix and log and short
  • lines changed 1, context: html, text, full: html, text
    entity in label, ebcause underscores get translated into spaces by cgi
  • lines changed 1, context: html, text, full: html, text
    reordered treatments
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.ra
  • lines changed 3, context: html, text, full: html, text
    fixed some qa stuff, removed replicate link for cv, and makde rep multi select
• src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.html
  • lines changed 1, context: html, text, full: html, text
    fixed link at terry's request
  • lines changed 1, context: html, text, full: html, text
    Revert "fixed link at terry's request" This reverts commit b4e1b70c8476a11f71d048e6221a26fe4a2135a2.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.new.html
  • lines changed 146, context: html, text, full: html, text
    properly moving mapability name to release tag convention
• src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.new.ra
  • lines changed 137, context: html, text, full: html, text
    moved mapability to new release tags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.patch.html
  • lines changed 146, context: html, text, full: html, text
    setting up patch for mapability html change
• src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.patch.ra
  • lines changed 137, context: html, text, full: html, text
    setting up patch for mapability html change
• src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.release4.html
  • lines changed 137, context: html, text, full: html, text
    moved mapability to new release tags
  • lines changed 177, context: html, text, full: html, text
    properly moving mapability name to release tag convention
  • lines changed 1, context: html, text, full: html, text
    setting up patch for mapability html change
  • lines changed 146, context: html, text, full: html, text
    Mapability track is done, no need for release 4
• src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.release4.ra
  • lines changed 137, context: html, text, full: html, text
    properly moving mapability name to release tag convention
  • lines changed 1, context: html, text, full: html, text
    setting up patch for mapability html change
  • lines changed 137, context: html, text, full: html, text
    Mapability track is done, no need for release 4
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.html
  • lines changed 10, context: html, text, full: html, text
    release notes 2 first draft
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.ra
  • lines changed 277, context: html, text, full: html, text
    fixed short and long labels
  • lines changed 7, context: html, text, full: html, text
    removed bad track in trackDb
  • lines changed 36, context: html, text, full: html, text
    removed the parental cell lines for ones with donors
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.new.ra
  • lines changed 694, context: html, text, full: html, text
    moving open Chrom faire to release tags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.release2.html
  • lines changed 307, context: html, text, full: html, text
    moving open Chrom faire to release tags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.release2.ra
  • lines changed 694, context: html, text, full: html, text
    moving open Chrom faire to release tags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.new.html
  • lines changed 174, context: html, text, full: html, text
    moving sydh histone to new release tag convention
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.new.ra
  • lines changed 516, context: html, text, full: html, text
    moving sydh histone to new release tag convention
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.release3.html
  • lines changed 174, context: html, text, full: html, text
    moving sydh histone to new release tag convention
  • lines changed 3, context: html, text, full: html, text
    temporary release notes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.release3.ra
  • lines changed 516, context: html, text, full: html, text
    moving sydh histone to new release tag convention
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.new.ra
  • lines changed 12, context: html, text, full: html, text
    moved uw5c to release tag conventions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.release2.html
  • lines changed 131, context: html, text, full: html, text
    moved uw5c to release tag conventions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.release2.ra
  • lines changed 12, context: html, text, full: html, text
    moved uw5c to release tag conventions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release3.html
  • lines changed 11, context: html, text, full: html, text
    fixes to uw tfbs html for QA
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release3.ra
  • lines changed 8, context: html, text, full: html, text
    fixed determined by qA