File Changes for vsmalladi

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v250_preview to v250_preview2 (2011-04-05 to 2011-04-12) v250

src/hg/encode/DAFs/2.0/broadChipSeq.daf
- lines changed 2, context: html, text, full: html, text
  Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
src/hg/encode/DAFs/2.0/haibChipSeq.daf
- lines changed 3, context: html, text, full: html, text
  Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
src/hg/encode/DAFs/2.0/licrMm9Histone.daf
- lines changed 2, context: html, text, full: html, text
  Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
src/hg/encode/DAFs/2.0/licrMm9Tfbs.daf
- lines changed 2, context: html, text, full: html, text
  Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
src/hg/encode/DAFs/2.0/psuMm9Histone.daf
- lines changed 2, context: html, text, full: html, text
  Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
src/hg/encode/DAFs/2.0/psuMm9Tfbs.daf
- lines changed 2, context: html, text, full: html, text
  Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
src/hg/encode/DAFs/2.0/stanfordChipSeq.daf
- lines changed 1, context: html, text, full: html, text
  Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
src/hg/encode/DAFs/2.0/stanfordHg19Hist.daf
- lines changed 2, context: html, text, full: html, text
  Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
src/hg/encode/DAFs/2.0/stanfordHg19HistInput.daf
- lines changed 2, context: html, text, full: html, text
  Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
src/hg/encode/DAFs/2.0/stanfordHg19Tfbs.daf
- lines changed 2, context: html, text, full: html, text
  Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
src/hg/encode/DAFs/2.0/stanfordHg19TfbsInput.daf
- lines changed 2, context: html, text, full: html, text
  Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
src/hg/encode/DAFs/2.0/stanfordMm9Hist.daf
- lines changed 2, context: html, text, full: html, text
  Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
src/hg/encode/DAFs/2.0/stanfordMm9Tfbs.daf
- lines changed 2, context: html, text, full: html, text
  Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
src/hg/encode/DAFs/2.0/stanfordMm9TfbsInput.daf
- lines changed 2, context: html, text, full: html, text
  Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
src/hg/encode/DAFs/2.0/stanfordNucleosome.daf
- lines changed 2, context: html, text, full: html, text
  Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
src/hg/encode/DAFs/2.0/uChicagoTfbs.daf
- lines changed 1, context: html, text, full: html, text
  Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
src/hg/encode/DAFs/2.0/uwChipSeq.daf
- lines changed 3, context: html, text, full: html, text
  Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
src/hg/encode/DAFs/2.0/uwTfbs.daf
- lines changed 3, context: html, text, full: html, text
  Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
src/hg/encode/DAFs/2.0/ydhrRnaSeq.daf
- lines changed 2, context: html, text, full: html, text
  Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
src/hg/encode/encodeValidate/config/fields.ra
- lines changed 15, context: html, text, full: html, text
  Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
- lines changed 5, context: html, text, full: html, text
  Sunsetted use of order from use in pipeline. Commented out initilization and use in Encode.pm and doEncodevalidate.pm. Commented out and retired term in fields.ra/ Redmine #1090.
src/hg/encode/encodeValidate/doEncodeValidate.pl
- lines changed 7, context: html, text, full: html, text
  Sunsetted use of order from use in pipeline. Commented out initilization and use in Encode.pm and doEncodevalidate.pm. Commented out and retired term in fields.ra/ Redmine #1090.
- lines changed 7, context: html, text, full: html, text
  Extended functionality to get sex,strain,age into meta-data from cv, for mouse ENCODE project if type=Cell Line and category not Tissue so that labs don't have to enter information every time and all mouse meta-data will be consistent against all tracks.
src/hg/makeDb/doc/encodeDccHg19/wgEncodeUchicagoTfbs.release1.notes
- lines changed 145, context: html, text, full: html, text
  Release 1 Notes for Uchicago track.
src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 1, context: html, text, full: html, text
  Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra
- lines changed 202, context: html, text, full: html, text
  Removed fileNames for RawSignal meta-data that were associated with tagAlign files as this was confusing to users. Redmine issue 792.
src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
- lines changed 3, context: html, text, full: html, text
  Forgot to add meta-data that fixed code review.
src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
- lines changed 19, context: html, text, full: html, text
  Replaced submission 3258 with 3875.
- lines changed 641, context: html, text, full: html, text
  Added 6 submission. One of them is a replacement submission 3875 for 3258.
src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
- lines changed 758, context: html, text, full: html, text
  Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
- lines changed 484, context: html, text, full: html, text
  Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 1, context: html, text, full: html, text
  Commented out 'include wgEncodeRegNorm.ra alpha' upon Jim's recommendation. The include prevents make of hg19, since file doesn't exist.
src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
- lines changed 50, context: html, text, full: html, text
  fixed some discrepencies in files missing raised on code review, redmine #3519.
src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
- lines changed 5, context: html, text, full: html, text
  Replaced submission 3258 with 3875.
- lines changed 2, context: html, text, full: html, text
  2 tracks were missing release alpha tags.
- lines changed 91, context: html, text, full: html, text
  Added 6 submission. One of them is a replacement submission 3875 for 3258.
src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.html
- lines changed 3, context: html, text, full: html, text
  Removed Data sets section as this doesn't match the Track Description Standards.
- lines changed 27, context: html, text, full: html, text
  Added track configuration section and added sentence about Peaks and Signals being from pooled data and replicate raw data is available for downlaod.
- lines changed 4, context: html, text, full: html, text
  Added two sentences describing use of IgG controls by lab.
src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.ra
- lines changed 9, context: html, text, full: html, text
  Updated settings for track view settings and controlled vocabullary links. Set minimal p value to be 5 -log(10^-5). Set signal range to be 0:50 and use vertical view range setting option. Updated windowing function to be mean=whiskers.
- lines changed 1, context: html, text, full: html, text
  Updated track with fileSortOrder option.
- lines changed 38, context: html, text, full: html, text
  Updated short and long lables in subtacks and Long label of track to follow standard. Will be checking with Kate before finallizing labels.
- lines changed 34, context: html, text, full: html, text
  Fixed long and short labels to match standards proposed by Kate. Also removed eGFP- that was infront of factor name and used pure factor target.
src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.new.html
- lines changed 1, context: html, text, full: html, text
  Fixed ftp link to link to Uw Dgf on hg19 and not hg18 YaleChipSeq.
src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.new.ra
- lines changed 1, context: html, text, full: html, text
  Removed <BR> lines for 'Assembly originally mapped to' and used shorter verbiage to 'Original Assembly'. Also removed one <BR> line for 'GEO Sample Assession' to put 'GEO Sample' on the same line.
src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.ra
- lines changed 1, context: html, text, full: html, text
  The following edit was done on .new.ra file but was failed to be copied over to this file, adding the change back :Removed <BR> lines for 'Assembly originally mapped to' and used shorter verbiage to 'Original Assembly'. Also removed one <BR> line for 'GEO Sample Assession' to put 'GEO Sample' on the same line.
src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
- lines changed 6, context: html, text, full: html, text
  Added experimental vars so that all mouse data can be given experiment Ids
- lines changed 7, context: html, text, full: html, text
  Fixed incorrect data-types in LICR tracks. Removed extra variable in expVars for UwDnase track.
src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
- lines changed 6, context: html, text, full: html, text
  Added experimental vars so that all mouse data can be given experiment Ids
- lines changed 5, context: html, text, full: html, text
  Fixed incorrect data-types in LICR tracks. Removed extra variable in expVars for UwDnase track.
src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuHistone.ra
- lines changed 6, context: html, text, full: html, text
  Added experimental vars so that all mouse data can be given experiment Ids
src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
- lines changed 6, context: html, text, full: html, text
  Added experimental vars so that all mouse data can be given experiment Ids
src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHistone.ra
- lines changed 6, context: html, text, full: html, text
  Added experimental vars so that all mouse data can be given experiment Ids
- lines changed 2, context: html, text, full: html, text
  Added treatment as expVar for two Sydh tracks. Also removed an extranous meta-data obj in wgEncodeSydhTfbs.ra
src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
- lines changed 6, context: html, text, full: html, text
  Added experimental vars so that all mouse data can be given experiment Ids
- lines changed 26, context: html, text, full: html, text
  Added treatment as expVar for two Sydh tracks. Also removed an extranous meta-data obj in wgEncodeSydhTfbs.ra
src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
- lines changed 6, context: html, text, full: html, text
  Added experimental vars so that all mouse data can be given experiment Ids
- lines changed 2, context: html, text, full: html, text
  Fixed incorrect data-types in LICR tracks. Removed extra variable in expVars for UwDnase track.
src/hg/utils/automation/Encode.pm
- lines changed 2, context: html, text, full: html, text
  Sunsetted use of order from use in pipeline. Commented out initilization and use in Encode.pm and doEncodevalidate.pm. Commented out and retired term in fields.ra/ Redmine #1090.

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