File Changes for wong

v264_base to v265_preview (2012-03-06 to 2012-03-13) v265

• src/hg/encode/encodeQaInit/encodeQaInit
  • lines changed 3, context: html, text, full: html, text
    added a fatal error message for a missing composite level stanza
  • lines changed 0, context: html, text, full: html, text
    changes tabs to 4 spaces
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 2, context: html, text, full: html, text
    moved regex into conditional, to prevent uninitialized errors when oldSettings exists, but doesn't have a metaData line
  • lines changed 1, context: html, text, full: html, text
    put check for defined sex variable in the conditional. It was causing errors when the cell was category = tissue and no sex defined in the DDF
  • lines changed 11, context: html, text, full: html, text
    made it so that if the cell is category=tissue, and sex is not defined in the ddf, the program gives an error. Also made it so that identical error lines are collapsed into one line, instead of flooding the screen.
• src/hg/encode/qaAddTrackReferences/makefile
  • lines changed 1, context: html, text, full: html, text
    fixing makefile for python version
• src/hg/encode/qaAddTrackReferences/qaAddTrackReferences
  • lines changed 373, context: html, text, full: html, text
    ported to python, needs a good reviewing before full blown tool usage
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeDukeAffyExon.release3.notes
  • lines changed 590, context: html, text, full: html, text
    notes for duke affy exon
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 8, context: html, text, full: html, text
    fixed dataVersions in hg18 tracks
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeChromatinMap.ra
  • lines changed 7, context: html, text, full: html, text
    fixed dataVersions in hg18 tracks
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra
  • lines changed 22, context: html, text, full: html, text
    fixed dataVersions in hg18 tracks
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleChIPseq.ra
  • lines changed 32, context: html, text, full: html, text
    fixed dataVersions in hg18 tracks
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeDukeAffyExon.ra
  • lines changed 108, context: html, text, full: html, text
    revokoing entire Duke Affy Exon track
  • lines changed 1983, context: html, text, full: html, text
    replaced old submissions with V2's
  • lines changed 1008, context: html, text, full: html, text
    added in new submissions for duke affy exon
  • lines changed 153, context: html, text, full: html, text
    added md5sums
  • lines changed 215, context: html, text, full: html, text
    expIds and dccAccession for known ones
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylWgbs.ra
  • lines changed 10, context: html, text, full: html, text
    added md5sums and composite level metaData
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    removed extra includes for dead RRBS track
  • lines changed 6, context: html, text, full: html, text
    addin in patch files for matrix and other corrections in uw tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.release3.ra
  • lines changed 869, context: html, text, full: html, text
    revokoing entire Duke Affy Exon track
  • lines changed 830, context: html, text, full: html, text
    replaced old submissions with V2's
  • lines changed 441, context: html, text, full: html, text
    added in new submissions for duke affy exon
  • lines changed 1, context: html, text, full: html, text
    changed html tag
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylWgbs.html
  • lines changed 1, context: html, text, full: html, text
    changed to ascii apostrophe
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylWgbs.ra
  • lines changed 38, context: html, text, full: html, text
    trackDb fixes for track functionality
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.ra
  • lines changed 3, context: html, text, full: html, text
    removing k562/NaBut from defaults
• src/hg/makeDb/trackDb/human/hg19/wgEncodeTfBindingSuper.html
  • lines changed 16, context: html, text, full: html, text
    reformed refereces properly
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.patch.ra
  • lines changed 1488, context: html, text, full: html, text
    addin in patch files for matrix and other corrections in uw tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.patch.ra
  • lines changed 1383, context: html, text, full: html, text
    addin in patch files for matrix and other corrections in uw tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.patch.ra
  • lines changed 3582, context: html, text, full: html, text
    addin in patch files for matrix and other corrections in uw tracks