Commits for cricket

v256_base to v257_preview (2011-08-29 to 2011-09-06) v257

• Removing V2 that were not really V2, there never was a V1
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 9, context: html, text, full: html, text
• One more file that says V2 when there was never a V1
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 5, context: html, text, full: html, text
• dealt with fastqs and wrong error messages
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeCaltechRnaSeq.release2.notes - lines changed 424, context: html, text, full: html, text
• The view limits are set to 10
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhRnaSeq.ra - lines changed 2, context: html, text, full: html, text
• Reran the make change notes as there were so many difficulites
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhRnaSeq.release1.notes - lines changed 6, context: html, text, full: html, text
• Adding 13 new cell lines to this composite
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethyl450.ra - lines changed 287, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.ra - lines changed 123, context: html, text, full: html, text
• removing Astrocy
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl27.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.ra - lines changed 1, context: html, text, full: html, text
• Removing Astrocy
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.ra - lines changed 1, context: html, text, full: html, text
• Added back the 50 bigwigs that were replaced and are on the RR
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 1195, context: html, text, full: html, text
• adding new views
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.ra - lines changed 34, context: html, text, full: html, text
• Getting rid of Astrocy
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.ra - lines changed 14, context: html, text, full: html, text
• Adding new data and pulling old data
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra - lines changed 397, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.ra - lines changed 118, context: html, text, full: html, text
• Changing labels to have clone-fee clone-based
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra - lines changed 94, context: html, text, full: html, text
• Trying out the new labeling
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeYaleRnaSeq.ra - lines changed 9, context: html, text, full: html, text
• Added the SAM explaination and fixed Farhnam reference
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhRnaSeq.html - lines changed 6, context: html, text, full: html, text
• Fixing the snpDb error for Angie
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text
• Standardizing the cell line labels so that they play well with encodePatchTdb
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.new.ra - lines changed 60, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.new.ra - lines changed 22, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.new.ra - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.new.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.ra - lines changed 8, context: html, text, full: html, text
• Addressing Jacobs concerns #2020
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.html - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.ra - lines changed 2, context: html, text, full: html, text
• Standardizing labels for Tier1 and Tier2 so that encodePatchTDB works
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGisDnaPet.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.new.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.ra - lines changed 25, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyRipSeq.ra - lines changed 39, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhNsome.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhRnaSeq.ra - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeYaleRnaSeq.ra - lines changed 136, context: html, text, full: html, text
• Changing astrocy to NH-A
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra - lines changed 139, context: html, text, full: html, text
• Removing the UCSC accession column for an hg18 track
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMap.new.ra - lines changed 1, context: html, text, full: html, text
• Basic track description outline for new Single Cell RNA Seq track
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSc.html - lines changed 105, context: html, text, full: html, text
• removing the term run
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 11, context: html, text, full: html, text
• Changing the Tier 1 and Tier 2 cells to have 1 and 2 before the tag
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAffyRnaChip.ra - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.new.ra - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.new.ra - lines changed 19, context: html, text, full: html, text
• These were checked in prematurely before with the tags changed, they are fixed now.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.new.ra - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.ra - lines changed 5, context: html, text, full: html, text