File Changes for wong

v268_base to v269_preview (2012-06-05 to 2012-06-12) v269

• python/lib/ucscGb/encode/mkChangeNotes.py
  • lines changed 5, context: html, text, full: html, text
    making output better to read
  • lines changed 4, context: html, text, full: html, text
    changed it so the top header will show all supplemental instead of just enw ones, same behavior as the rest of the categories
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 1, context: html, text, full: html, text
    missing a line to strip out whitespace from a command line argument. Dunno how I didn't catch this in testing.
  • lines changed 1, context: html, text, full: html, text
    this line should skip loop iteration, not break out of the subroutine.
• src/hg/encode/getTrackReferences/getTrackReferences
  • lines changed 175, context: html, text, full: html, text
    moving directory over to new name
  • lines changed 15, context: html, text, full: html, text
    adding a plain text mode
  • lines changed 5, context: html, text, full: html, text
    fixing some issues with plain text mode
  • lines changed 22, context: html, text, full: html, text
    found a python library that does what I did, so didn't need to reinvent this wheel
• src/hg/encode/getTrackReferences/makefile
  • lines changed 27, context: html, text, full: html, text
    moving directory over to new name
• src/hg/encode/qaAddTrackReferences/getTrackReferences
  • lines changed 175, context: html, text, full: html, text
    renaming to getTrackReferences
  • lines changed 175, context: html, text, full: html, text
    moving directory over to new name
• src/hg/encode/qaAddTrackReferences/makefile
  • lines changed 2, context: html, text, full: html, text
    correcting the makefile for name change
  • lines changed 27, context: html, text, full: html, text
    moving directory over to new name
• src/hg/encode/qaAddTrackReferences/qaAddTrackReferences
  • lines changed 1, context: html, text, full: html, text
    incorrect way of failover for the regex is corrected
  • lines changed 37, context: html, text, full: html, text
    reworked how the htmlStr is constructed according to Brooke's request redmine:7236
  • lines changed 175, context: html, text, full: html, text
    renaming to getTrackReferences
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlLongRnaSeq.release2.notes
  • lines changed 6, context: html, text, full: html, text
    updating notes files
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
  • lines changed 202, context: html, text, full: html, text
    md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 105, context: html, text, full: html, text
    adding in missing controls
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    starting release 3 for us affy exon redmine:6777
  • lines changed 1, context: html, text, full: html, text
    correcting spelling error
  • lines changed 1, context: html, text, full: html, text
    forgot to change this over to release 5
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAffyRnaChip.ra
  • lines changed 28, context: html, text, full: html, text
    accidently over wrote Katrina's version with a bad checkin, reverting.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.ra
  • lines changed 1, context: html, text, full: html, text
    lowered maxWindow to 100k bases, 1 million was getting memory errors
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl27.ra
  • lines changed 74, context: html, text, full: html, text
    fixing haib methyl array's tags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylSeq.ra
  • lines changed 30, context: html, text, full: html, text
    correcting my tracks on alpha tags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylWgbs.ra
  • lines changed 5, context: html, text, full: html, text
    correcting my tracks on alpha tags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release3.ra
  • lines changed 1048, context: html, text, full: html, text
    correcting my tracks on alpha tags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.release2.ra
  • lines changed 141, context: html, text, full: html, text
    correcting my tracks on alpha tags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release3.ra
  • lines changed 1847, context: html, text, full: html, text
    starting new release trackDbs for uw hsitone and open chrom dnase
  • lines changed 204, context: html, text, full: html, text
    correcting my tracks on alpha tags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.release2.ra
  • lines changed 76, context: html, text, full: html, text
    correcting my tracks on alpha tags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.ra
  • lines changed 17, context: html, text, full: html, text
    correcting the tags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release4.ra
  • lines changed 468, context: html, text, full: html, text
    correcting tags on riken cage for cricket
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.release3.ra
  • lines changed 1474, context: html, text, full: html, text
    starting release 3 for us affy exon redmine:6777
  • lines changed 159, context: html, text, full: html, text
    correcting tags for uwAffyEcon release 3
  • lines changed 164, context: html, text, full: html, text
    there was a tag error due to metadata in the cell subgroup, corrected now
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.release4.ra
  • lines changed 193, context: html, text, full: html, text
    correcting my tracks on alpha tags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release5.html
  • lines changed 14, context: html, text, full: html, text
    removed message that no longer applies
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release5.ra
  • lines changed 1, context: html, text, full: html, text
    changing viewlimits to 1:10 for Raw
  • lines changed 2, context: html, text, full: html, text
    changing the scorefilter to mathc the range of the data:
  • lines changed 625, context: html, text, full: html, text
    correcting the cell tier tags in UwDnase release 5
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.patch.ra
  • lines changed 6293, context: html, text, full: html, text
    removing patch, changes will go out in release5
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release5.ra
  • lines changed 6299, context: html, text, full: html, text
    starting new release trackDbs for uw hsitone and open chrom dnase
  • lines changed 724, context: html, text, full: html, text
    correcting my tracks on alpha tags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release4.ra
  • lines changed 373, context: html, text, full: html, text
    correcting my tracks on alpha tags
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • lines changed 50, context: html, text, full: html, text
    moving mapability over to it's own ra for moving to encode
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeMapability.ra
  • lines changed 50, context: html, text, full: html, text
    moving mapability over to it's own ra for moving to encode