Commits for cricket

v251_preview to v251_preview2 (2011-04-26 to 2011-05-03) v251

• Changing the expVars to not have localization
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 2, context: html, text, full: html, text
• Issue 2019, cleaning up the trackDb to incorporate changes from release 1 and removing all the V1 bigwigs from the metaDB
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 1216, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.ra - lines changed 19, context: html, text, full: html, text
• Renamed Paired to Aligns, renamed fastq V2 to fastq, dropped extra files
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 1487, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.ra - lines changed 64, context: html, text, full: html, text
• Removing Ilna from file names and metaData
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 248, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.ra - lines changed 104, context: html, text, full: html, text
• Added final fastq to the mdb
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra - lines changed 20, context: html, text, full: html, text
• Incorporating Julien's changes from the CRG regarding bioRep, labProtocolID, labExpId
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra - lines changed 217, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra - lines changed 306, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaSeq.ra - lines changed 55, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 424, context: html, text, full: html, text
• Changed Pooled when in fact, it was not pooled, only one rep was available
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 24, context: html, text, full: html, text
• Changed fileSortOrder to match in all files
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.ra - lines changed 1, context: html, text, full: html, text
• Putting items into the attic in both the trackDb and the meatDb
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra - lines changed 35, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.ra - lines changed 90, context: html, text, full: html, text
• Added a new fileSortOrder to be consistent with other transcriptome tracks
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra - lines changed 1, context: html, text, full: html, text
• Commented out the p-value after discussion with Katrina. Issue 37
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.ra - lines changed 2, context: html, text, full: html, text
• Added treatment and better validation settings
  • src/hg/encode/DAFs/2.0/caltechRnaSeq.daf - lines changed 3, context: html, text, full: html, text
• Removing the (Wold) and fixing the validation settings
  • src/hg/encode/DAFs/2.0/caltechElements.daf - lines changed 3, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/caltechRnaSeq.daf - lines changed 2, context: html, text, full: html, text
• Adding attic as a type of term and marking it as hidden
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 11, context: html, text, full: html, text
• Track 2254 notes 20 and 21, changed fileSortOrder, dropped bad GSMs, moved auxExp from htr8, fixed some long labels
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra - lines changed 85, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.ra - lines changed 53, context: html, text, full: html, text
• Changed the tags for several terms based on feedback from Tim from the code review. Also dropped a term that had been saying should be retired since 12-15-2010
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 12, context: html, text, full: html, text
• Resolving git merge conflict with cv.ra
• Added clusters and replacements Gm12878 data
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 1513, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.ra - lines changed 358, context: html, text, full: html, text
• Adding accession numbers
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAffyRnaChip.ra - lines changed 5122, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeDukeAffyExon.ra - lines changed 211, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaSeq.ra - lines changed 37, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeMapability.ra - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunySwitchgear.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwAffyExonArray.ra - lines changed 271, context: html, text, full: html, text
• Added replicated pooled so that make works, did not mean to check this in in the first place
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.ra - lines changed 3, context: html, text, full: html, text
• Added composite as an expVars as per Kate request
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromSynth.ra - lines changed 1, context: html, text, full: html, text