File Changes for wong

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

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