tdreszer: changes by commit

review to branch (2009-06-30 to 2009-07-07) v210

• Inital check-in of Encode Gencode Classes table
  • src/hg/lib/encode/wgEncodeGencodeClasses.as 1.1 - lines changed: 14, context: html, text, full: html, text
  • src/hg/lib/encode/wgEncodeGencodeClasses.sql 1.1 - lines changed: 23, context: html, text, full: html, text
• Resubmitted Yale/K562 peaks, input. Fixed some metadata, standardized ChIP-seq
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.387 - lines changed: 299, context: html, text, full: html, text
• Collapsed K562 and K562b into a single column. Not the best solution, but neither was 2 columns quite right.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.388 - lines changed: 28, context: html, text, full: html, text
• Also collapsed HepG2 and HepG2b into a single column.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.389 - lines changed: 6, context: html, text, full: html, text
• submittedDataVersion=Vn needed to be added to metadata
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.186 - lines changed: 1, context: html, text, full: html, text
• Moving Rosetta uniqueness track into Mapability
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.390 - lines changed: 25, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeMapability.html 1.11 - lines changed: 29, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra 1.465 - lines changed: 18, context: html, text, full: html, text
• Rosetta uniqueness should be consistent
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.391 - lines changed: 1, context: html, text, full: html, text
• Snyder wanted some cell line order changes
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.398 - lines changed: 270, context: html, text, full: html, text
• Laura Elnotski wishes BiP to be Bi-Pro
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.402 - lines changed: 1, context: html, text, full: html, text
• ENCODE NHGRI Bidirectional promoters has no '-'.
  • src/hg/makeDb/trackDb/chimp/panTro2/trackDb.ra 1.36 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau4/trackDb.ra 1.11 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dog/canFam2/trackDb.ra 1.30 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.403 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra 1.53 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn4/trackDb.ra 1.36 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra 1.41 - lines changed: 2, context: html, text, full: html, text
• Added vaule|label to 'filterBy' and allowed filterBy to work with score for ENCODE NHGRI Bips
  • src/hg/inc/hui.h 1.133 - lines changed: 11, context: html, text, full: html, text
• Added value|label to 'filterBy' and allowed filterBy to work with score for ENCODE NHGRI Bips
  • src/hg/lib/hui.c 1.219 - lines changed: 68, context: html, text, full: html, text
• Added filterBy using 'score' so that ENCODE NHGRI BiPs can filter on annotations
  • src/hg/hgTracks/simpleTracks.c 1.89 - lines changed: 3, context: html, text, full: html, text
• Removed an extra .. from a help link
  • src/hg/lib/hui.c 1.220 - lines changed: 2, context: html, text, full: html, text
• Very minor work towards making the imgBox portal. Mostly just want to check in some format changes before too much dust gathers
  • src/hg/hgTracks/hgTracks.c 1.1580 - lines changed: 6, context: html, text, full: html, text
  • src/hg/hgTracks/imageV2.c 1.4 - lines changed: 194, context: html, text, full: html, text
  • src/hg/hgTracks/imageV2.h 1.3 - lines changed: 99, context: html, text, full: html, text
• Cleaned up.
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeMapability.html 1.12 - lines changed: 10, context: html, text, full: html, text
• Last minute addition of another reference.
  • src/hg/makeDb/trackDb/wgEncodeNhgriBip.html 1.3 - lines changed: 55, context: html, text, full: html, text
• Cleanup for Mapability. BiPs now use new 'filterBy score'.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.405 - lines changed: 10, context: html, text, full: html, text
• Elnitski BiPs have no score filter at all since all scores are 800 for this species
  • src/hg/makeDb/trackDb/chimp/panTro2/trackDb.ra 1.37 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau4/trackDb.ra 1.12 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dog/canFam2/trackDb.ra 1.31 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra 1.54 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn4/trackDb.ra 1.37 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra 1.42 - lines changed: 2, context: html, text, full: html, text