Commits for wong

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

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