tdreszer: changes by commit

branch to review (2009-09-29 to 2009-10-06) v217

• Initial version of UW Digital Genomic Footprinting DAF
  • src/hg/encode/DAFs/UwDgf.daf 1.1 - lines changed: 56, context: html, text, full: html, text
• Added antibody NFKB and treatment TNFa for Yale.
  • src/hg/encode/encodeValidate/config/cv.ra 1.131 - lines changed: 15, context: html, text, full: html, text
• Reverting Hiram's changes temporarily, since ENCODE pipeline is now failing validation left and right
  • src/hg/lib/wigAsciiToBinary.c 1.33 - lines changed: 19, context: html, text, full: html, text
• Added UW ChIPseq nad UW DNase. Reorganized a little
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.555 - lines changed: 1514, context: html, text, full: html, text
• Removed stray bad line. Changed UW DNase raw sig view range
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.556 - lines changed: 3, context: html, text, full: html, text
• Reorganized UW DNase
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.557 - lines changed: 1027, context: html, text, full: html, text
• Its ChIP-seq not ChIP-Seq
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.558 - lines changed: 146, context: html, text, full: html, text
• Left out UW ChIP HUVEC CTCF rep1 from last night's checkins
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.559 - lines changed: 31, context: html, text, full: html, text
• Did some Broad track reordering
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.560 - lines changed: 1179, context: html, text, full: html, text
• Finxed HeLa and HepG2 sort order in UW Dnase and ChIP
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.561 - lines changed: 35, context: html, text, full: html, text
• For Yale added NF-YA and NF-YB and renamed NFKB to NFkB
  • src/hg/encode/encodeValidate/config/cv.ra 1.132 - lines changed: 40, context: html, text, full: html, text
• Support bed3s
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.195 - lines changed: 4, context: html, text, full: html, text
• Sorry changing NFkB back to NFKB as this seems to be a valid term in the literature
  • src/hg/encode/encodeValidate/config/cv.ra 1.133 - lines changed: 1, context: html, text, full: html, text
• Finished up the Sep 2009 freeze submissions with Melissa's help
  • src/hg/makeDb/doc/encodeDccHg18/broadBernstein.txt 1.5 - lines changed: 121, context: html, text, full: html, text
• Added a lot of ChIPseq and DNase as part of the Sept 2009 freeze. Tracy Ballinger helped with trackDb, fileDb
  • src/hg/makeDb/doc/encodeDccHg18/uwStam.txt 1.1 - lines changed: 253, context: html, text, full: html, text
• Thought I should check in old stuff done for Gencode Release 3. Two issues still unresolved, though
  • src/hg/makeDb/doc/encodeDccHg18/gencode.txt 1.3 - lines changed: 336, context: html, text, full: html, text
• Tim adds some preliminary notes. No activity seen for Sept 2009 freeze
  • src/hg/makeDb/doc/encodeDccHg18/myers.txt 1.3 - lines changed: 46, context: html, text, full: html, text
• Finally checking in some antient notes
  • src/hg/makeDb/doc/encodeDccHg18/nhgriNreBipElnitski.txt 1.3 - lines changed: 17, context: html, text, full: html, text