Commits for wong

v265_preview2 to v265_base (2012-03-20 to 2012-03-27) v265

• added in new haib tracks
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 384, context: html, text, full: html, text
• replacing tracks with bigBed tracks
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeDukeAffyExon.ra - lines changed 510, context: html, text, full: html, text
• updated notes for duke affy exon
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeDukeAffyExon.release3.notes - lines changed 324, context: html, text, full: html, text
• updated md5sums
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeDukeAffyExon.ra - lines changed 153, context: html, text, full: html, text
• fixed some trackDb settings for duke affy exon
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.release3.ra - lines changed 262, context: html, text, full: html, text
• added in checks for bedRnaElement
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 12, context: html, text, full: html, text
• removed privacy from the cv, redmine #4143 comment 21
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra - lines changed 145, context: html, text, full: html, text
• adding in geo accession to hgfilui
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.ra - lines changed 1, context: html, text, full: html, text
• removed short labels from view parent stanzas
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.ra - lines changed 3, context: html, text, full: html, text
• Revert "added in checks for bedRnaElement" This reverts commit 50c00c11eca89cde855e23932882f8f8493c1ef8.
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 12, context: html, text, full: html, text
• removed privacy var form open chrom chip, missed last time
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra - lines changed 39, context: html, text, full: html, text
• qa fixes, viewlimits were off relative to the data, and set peaks to dense
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.ra - lines changed 5, context: html, text, full: html, text
• added md5sums, added in replacement bigWig v4, and revoked old one
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra - lines changed 52, context: html, text, full: html, text
• added in metaData from old submission
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra - lines changed 9, context: html, text, full: html, text
• reordered matrix, and other qa fixes
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.ra - lines changed 48, context: html, text, full: html, text
• updating notes file
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeOpenChromDnase.release2.notes - lines changed 128, context: html, text, full: html, text
• more alphabetization fixes
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.ra - lines changed 4, context: html, text, full: html, text
• updated submission id and date
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.ra - lines changed 1, context: html, text, full: html, text
• last second label changes for length purposes
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.ra - lines changed 2, context: html, text, full: html, text
• adding back in bedRnaElements checks for columns 7-9
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 12, context: html, text, full: html, text
• correcting html line
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.release3.ra - lines changed 1, context: html, text, full: html, text
• made a bypass for the pmc pathway, because ncbi changed how the xml is delivered in version 1.0 xml's. I need to rewrite the parsing mechanism to account for this, but this works for now.
  • src/hg/encode/qaAddTrackReferences/qaAddTrackReferences - lines changed 28, context: html, text, full: html, text
• fixed a lot of html errors in description page
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.html - lines changed 170, context: html, text, full: html, text
• staged new freeze dates to openChromChip
  • src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromChip.ra - lines changed 8, context: html, text, full: html, text
• qa fixes on .ra file
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.ra - lines changed 9, context: html, text, full: html, text
• html fixes for qa
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.html - lines changed 14, context: html, text, full: html, text
• put in parenthesis
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.html - lines changed 1, context: html, text, full: html, text
• Terry changed schools
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.html - lines changed 5, context: html, text, full: html, text
• splitting out the methyl27 track from the monolithic trackDb file
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra - lines changed 92, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethyl27.ra - lines changed 92, context: html, text, full: html, text
• removed unneeded colon
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.html - lines changed 1, context: html, text, full: html, text
• added treatment = None for all stanzas that didn't have it
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra - lines changed 291, context: html, text, full: html, text
• added in some expIds and dccAccessions
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra - lines changed 30, context: html, text, full: html, text
• removed all rep=1 and it's variants, replaced with .patch.ra's
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.patch.ra - lines changed 1257, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaSeq.patch.ra - lines changed 301, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethyl27.patch.ra - lines changed 92, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethylSeq.patch.ra - lines changed 324, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.patch.ra - lines changed 4562, context: html, text, full: html, text
• added in last expId
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra - lines changed 15, context: html, text, full: html, text
• adding in gencode v10 views
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 18, context: html, text, full: html, text