tdreszer: changes by commit

branch to review (2009-10-27 to 2009-11-03) v219

• A lot of work on HudsonAlpha TFSB
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.621 - lines changed: 651, context: html, text, full: html, text
• More cleanup of HAIB TFBS
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.622 - lines changed: 2065, context: html, text, full: html, text
• Straightened out GM12878 Taf1 and K562 Taf1 as per Flo's wishes
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.623 - lines changed: 70, context: html, text, full: html, text
• Limited the number of tracks shown by detault for Broad
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.624 - lines changed: 19, context: html, text, full: html, text
• Renamed some HudsonAlpha tables and cleaned up some metadata
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.625 - lines changed: 132, context: html, text, full: html, text
• Initial checking of my clean up of varias issues
  • src/hg/makeDb/doc/encodeDccHg18/haibChipSeq.txt 1.1 - lines changed: 376, context: html, text, full: html, text
• New DAF for Rami
  • src/hg/encode/DAFs/HAIBChIPseq.daf 1.1 - lines changed: 38, context: html, text, full: html, text
• Fixed bug that left matCB indeterminate though no subtracks match state.
  • src/hg/js/hui.js 1.42 - lines changed: 4, context: html, text, full: html, text
• Added labVersion=PCR2x to older GM12989 and K562 experiments for haibChip
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.627 - lines changed: 128, context: html, text, full: html, text
• Changed GM12878Taf1 to V2 and made Input(PCR2x) visible for haibChip
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.628 - lines changed: 74, context: html, text, full: html, text
• More attempts to straighten out 2 controls fro Gm12878 and K562 on haibChip
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.630 - lines changed: 66, context: html, text, full: html, text
• 4 more tracks to haibChip and more work to distinguish PCR2x input
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.631 - lines changed: 48, context: html, text, full: html, text
• Added explanitory note for PCR2x control
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.html 1.19 - lines changed: 8, context: html, text, full: html, text
• Removed wgEncodeHudsonalphaChipSeqProv provisional composite as its entire contents have been superseded by wgEncodeHudsonalphaChipSeq
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.634 - lines changed: 48, context: html, text, full: html, text
• New coloring scheme and V3c release
  • src/hg/makeDb/trackDb/human/wgEncodeGencode.html 1.4 - lines changed: 31, context: html, text, full: html, text
• Gencode v3c with new subtrack 2way consensus psuedogenes
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.635 - lines changed: 32, context: html, text, full: html, text
• Kayla noticed too many tables being eliminated and too few files being added.
  • src/hg/makeDb/doc/encodeDccHg18/broadChipSeq.notes.txt 1.6 - lines changed: 176, context: html, text, full: html, text
• Keeping up with the flood
  • src/hg/makeDb/doc/encodeDccHg18/haibChipSeq.txt 1.2 - lines changed: 177, context: html, text, full: html, text
  • src/hg/makeDb/doc/encodeDccHg18/uwStam.txt 1.3 - lines changed: 267, context: html, text, full: html, text
• Getting the url to use the OTT id which is now in the classes table turns out to be easy
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.636 - lines changed: 4, context: html, text, full: html, text
• This is Gencode's October 2009 freeze
  • src/hg/makeDb/trackDb/human/wgEncodeGencode.html 1.5 - lines changed: 1, context: html, text, full: html, text
• Added OTTER id search spec for gencode v3c and set gencode freeze to Oct 2009
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.638 - lines changed: 31, context: html, text, full: html, text