Commits for cricket

v270_preview2 to v270_base (2012-07-10 to 2012-07-17) v270

• Adding new data in, changing the matrix around a little bit
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwAffyExonArray.ra - lines changed 321, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.release3.ra - lines changed 267, context: html, text, full: html, text
• Fixing the numeric tags and adding Tier 1 label
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGisDnaPet.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyTiling.ra - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyRipSeq.ra - lines changed 39, context: html, text, full: html, text
• Changing cell labels and view labels, should be no visible change
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.ra - lines changed 17, context: html, text, full: html, text
• Promoting Tier 2 and cell line tag changes
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.ra - lines changed 31, context: html, text, full: html, text
• Tag change, no visible change
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.ra - lines changed 25, context: html, text, full: html, text
• Tag changes only, no visible changes
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHmm.ra - lines changed 10, context: html, text, full: html, text
• Adding the hyphens for H1-hesc
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.ra - lines changed 3, context: html, text, full: html, text
• Adding release 2 of FSU RepliChip
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliChip.release2.html - lines changed 150, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliChip.release2.ra - lines changed 105, context: html, text, full: html, text
• Changing the cell tags to promot tiers and to fix numeric tags
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release3.ra - lines changed 473, context: html, text, full: html, text
• Removing patch file, not sure what the goal was with this pathch
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.patch.ra - lines changed 870, context: html, text, full: html, text
• Preparing for pushQ, adding expIds, notes file, fixing names in the downloads files
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwAffyExonArray.release3.notes - lines changed 429, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwAffyExonArray.ra - lines changed 53, context: html, text, full: html, text
• Adding a notes files for UChicago
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeUchicagoTfbs.release2.notes - lines changed 420, context: html, text, full: html, text
• Trying to work on the html changes for Brian in ticket #6777
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.release3.html - lines changed 98, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.release3.ra - lines changed 1, context: html, text, full: html, text
• Increaseing to 10 mismatches
  • src/hg/encode/DAFs/3.0/mm9/wgEncodeCshlLongRnaSeq.daf - lines changed 2, context: html, text, full: html, text
• removing from the super track
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release3.ra - lines changed 1, context: html, text, full: html, text
• Answering ticket #5697Specifially, the long and short labels and
  
  1. In the track controls, Peaks are set to dense, but they should be set to pack.
  
  2. There is a cell line listed as "NCOR1", but the Input for it lists "COR1" in the matrix and in the Factor column below the matrix.
  
  3. In hgTrackUi, when sorting by the Replicated column, "Pooled" shows up before 1 and 2. It seems like "Pooled" should show up after 1 and 2.
  
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.release2.ra - lines changed 141, context: html, text, full: html, text
• Added release notes
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.release2.html - lines changed 5, context: html, text, full: html, text
• Changing the long and short labels, the defaults and adding the release notes
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.release2.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.release2.ra - lines changed 147, context: html, text, full: html, text
• adding accessions
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUchicagoTfbs.ra - lines changed 221, context: html, text, full: html, text
• Changing defaut views
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.release2.ra - lines changed 1, context: html, text, full: html, text
• Fixing the expIds
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra - lines changed 6, context: html, text, full: html, text
• Changed the way Inputs appeared in the matrix
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.release2.ra - lines changed 13, context: html, text, full: html, text
• Changed the short labels to add Sg and Pk
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.release2.ra - lines changed 54, context: html, text, full: html, text