Commits for wong

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

• removed extra includes for dead RRBS track
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
• fixed dataVersions in hg18 tracks
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeChromatinMap.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra - lines changed 22, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleChIPseq.ra - lines changed 32, context: html, text, full: html, text
• addin in patch files for matrix and other corrections in uw tracks
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.patch.ra - lines changed 1488, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.patch.ra - lines changed 1383, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.patch.ra - lines changed 3582, context: html, text, full: html, text
• removing k562/NaBut from defaults
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.ra - lines changed 3, context: html, text, full: html, text
• reformed refereces properly
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeTfBindingSuper.html - lines changed 16, context: html, text, full: html, text
• ported to python, needs a good reviewing before full blown tool usage
  • src/hg/encode/qaAddTrackReferences/qaAddTrackReferences - lines changed 373, context: html, text, full: html, text
• moved regex into conditional, to prevent uninitialized errors when oldSettings exists, but doesn't have a metaData line
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 2, 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
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 1, 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/encodeValidate/doEncodeValidate.pl - lines changed 11, context: html, text, full: html, text
• revokoing entire Duke Affy Exon track
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeDukeAffyExon.ra - lines changed 108, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.release3.ra - lines changed 869, context: html, text, full: html, text
• replaced old submissions with V2's
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeDukeAffyExon.ra - lines changed 1983, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.release3.ra - lines changed 830, context: html, text, full: html, text
• added in new submissions for duke affy exon
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeDukeAffyExon.ra - lines changed 1008, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.release3.ra - lines changed 441, context: html, text, full: html, text
• added md5sums
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeDukeAffyExon.ra - lines changed 153, context: html, text, full: html, text
• notes for duke affy exon
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeDukeAffyExon.release3.notes - lines changed 590, context: html, text, full: html, text
• fixing makefile for python version
  • src/hg/encode/qaAddTrackReferences/makefile - lines changed 1, context: html, text, full: html, text
• expIds and dccAccession for known ones
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeDukeAffyExon.ra - lines changed 215, context: html, text, full: html, text
• changed html tag
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.release3.ra - lines changed 1, context: html, text, full: html, text
• added md5sums and composite level metaData
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylWgbs.ra - lines changed 10, context: html, text, full: html, text
• added a fatal error message for a missing composite level stanza
  • src/hg/encode/encodeQaInit/encodeQaInit - lines changed 3, context: html, text, full: html, text
• trackDb fixes for track functionality
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylWgbs.ra - lines changed 38, context: html, text, full: html, text
• changed to ascii apostrophe
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylWgbs.html - lines changed 1, context: html, text, full: html, text
• changes tabs to 4 spaces
  • src/hg/encode/encodeQaInit/encodeQaInit - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)