Commits for cricket

v257_preview to v257_preview2 (2011-09-06 to 2011-09-13) v257

• Adding the 4 new cell lines that would be Release 3
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibMethylRrbs.release2.notes - lines changed 917, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra - lines changed 487, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.html - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.ra - lines changed 134, context: html, text, full: html, text
• Fixing merge conflict
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.ra - lines changed 81, context: html, text, full: html, text
• Trying to fix the Tier 1 and Tier 2 mistake that I put in the .ra instead of the .new.ra
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.new.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.ra - lines changed 9, context: html, text, full: html, text
• Typo in HELAS3
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.ra - lines changed 1, context: html, text, full: html, text
• Adding md5sums
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra - lines changed 21, context: html, text, full: html, text
• Removed the html that goes with the deprecated track
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeYaleRnaSeq.html - lines changed 147, context: html, text, full: html, text
• MUNUS should be MINUS
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1, context: html, text, full: html, text
• wgEncodeCshlShortRnaSeq.new.html
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.ra - lines changed 20, context: html, text, full: html, text
• Making changes for Jacob on ticket 1634
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.html - lines changed 22, context: html, text, full: html, text
• Change Peggy's link to USC
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhRnaSeq.html - lines changed 2, context: html, text, full: html, text
• Ticket 383, changing the html and the view limits per Katrina requests
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhRnaSeq.html - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhRnaSeq.ra - lines changed 1, context: html, text, full: html, text
• Resolving merge conflict
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhRnaSeq.html - lines changed 4, context: html, text, full: html, text
• Fixed a broken link and changed Seq to seq and dropped orig assembly
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhRnaSeq.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhRnaSeq.ra - lines changed 12, context: html, text, full: html, text
• Remove the Yale mdb, it is SYDH
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeYaleRnaSeq.ra - lines changed 258, context: html, text, full: html, text
• Fixing references
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.html - lines changed 12, context: html, text, full: html, text
• Changing long labels to have no Strand and to have lowercase polyA
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra - lines changed 296, context: html, text, full: html, text
• One short label
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra - lines changed 1, context: html, text, full: html, text
• Changing the invalids line to have the same behaviour as the other notices
  • src/hg/makeDb/mdbUpdate/mdbPrint.c - lines changed 1, context: html, text, full: html, text
• Replacing the 1x75-Directional-HepG2-rep2 and rep1
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeCaltechRnaSeq.release2.notes - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 58, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.ra - lines changed 2, context: html, text, full: html, text
• Adding the md5sums
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 61, context: html, text, full: html, text
• Removing the view, since it is a single view track
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.new.html - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.new.ra - lines changed 67, context: html, text, full: html, text
• So the long awaited merge of metaTest into metaCheck is here. This is an arguments face lift because the original metaCheck was meant to be used in code not as a command line, so now there are defaults for all of the locations of the trackDb, metaDb, downloads dir but you can specify a different location.
  • src/hg/encode/metaCheck/README.txt - lines changed 20, context: html, text, full: html, text
  • src/hg/encode/metaCheck/metaCheck.c - lines changed 95, context: html, text, full: html, text
• Removed the unloaded data for Chia Pet
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra - lines changed 1475, context: html, text, full: html, text
• Added table names for the Junctions
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 55, context: html, text, full: html, text