Commits for cricket

v264_preview to v264_preview2 (2012-02-21 to 2012-02-28) v264

• Adding the TSSHMM as displayed view, and fixing the release3.html line
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 534, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.ra - lines changed 577, context: html, text, full: html, text
• Changing tier to be non-cv determined
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 23, context: html, text, full: html, text
• Release notes and a long label change for Steve ticket 1634
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.html - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.ra - lines changed 1, context: html, text, full: html, text
• Extra .new files
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeChromSuper.new.html - lines changed 77, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.new.html - lines changed 164, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.new.ra - lines changed 277, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.new.html - lines changed 87, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.new.ra - lines changed 1475, context: html, text, full: html, text
• Removing the term species from the CV as it is really assembly, removing the one reference to species in hg18
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 37, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeNhgriBip.ra - lines changed 2, context: html, text, full: html, text
• Removing species as a metaDb var, see ticket 5111
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra - lines changed 1, context: html, text, full: html, text
• Changing the defualts on this track
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 3520, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.ra - lines changed 644, context: html, text, full: html, text
• Adding a release 3 for CSHL Short with many new cell lines
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra - lines changed 5855, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release3.html - lines changed 145, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release3.ra - lines changed 3590, context: html, text, full: html, text
• Added 5 more experiments
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 919, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.ra - lines changed 433, context: html, text, full: html, text
• Cleaning out freeze date from GENCODE files, they do not want to have ENCODE Versions
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV7.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV9.ra - lines changed 16, context: html, text, full: html, text
• Getting rid of the post Freeze dates
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHmm.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV9.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra - lines changed 8, context: html, text, full: html, text
• Fixed the doc to document and removed rnaExtract as a variable for short
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeCshlLongRnaSeq.daf - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeCshlShortRnaSeq.daf - lines changed 1, context: html, text, full: html, text
• Removing Gene Type with comments, see ticket #5111
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 49, context: html, text, full: html, text