Commits for cricket

v249_base to v250_preview (2011-03-29 to 2011-04-05) v250

• Removed errant Na in the file names of the fastqs
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 2575, context: html, text, full: html, text
• added mean+whiskers, fileSortOrder, changed release tags to new method, fixed subgroup labels, added missing information in the mdb
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra - lines changed 53, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra - lines changed 104, context: html, text, full: html, text
• Trying to commit again to deal with the fact that hgwdev hung on my previous git commit
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra - lines changed 45, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 5, context: html, text, full: html, text
• Making all versions of Minus and Plus Sig, Signal, Raw into MinusRawSignal
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 84, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 1003, context: html, text, full: html, text
• Making all versions of Minus and Plus Sig, Signal, Raw into MinusRawSignal, THIS TIME WITH MAGIC NUMBER
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 1, context: html, text, full: html, text
• Consolidate ExonsGene and ExonGen and remove Aligns as views
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 40, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 57, context: html, text, full: html, text
• continuing to consolidate views TranscriptGencV3 -> V3c, Fastq -> RawData
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibRnaSeq.ra - lines changed 31, context: html, text, full: html, text
• More re-shuffling of metadata terms and filetypes
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra - lines changed 405, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.ra - lines changed 52, context: html, text, full: html, text
• added fastq required, at suggestion of Brian
  • src/hg/encode/DAFs/2.0/gisChiaPet.daf - lines changed 2, context: html, text, full: html, text
• First draft at adding views to the CV
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 257, context: html, text, full: html, text
• Removed 4 experiments due to suspect files
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeGisRnaPet.release1.notes - lines changed 74, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra - lines changed 519, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra - lines changed 18, context: html, text, full: html, text
• Changed label for A549 to be correct from A459
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.ra - lines changed 1, context: html, text, full: html, text
• Standardized obtainedBy to lab names from PI names
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibGenotype.ra - lines changed 36, context: html, text, full: html, text
• changed long labels to have RIP-chip
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.ra - lines changed 26, context: html, text, full: html, text
• Changed the dataType to Genotype. This will make it consistent with other tracks that all data in the same composite has the same dataType
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibGenotype.ra - lines changed 91, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.ra - lines changed 2, context: html, text, full: html, text
• Added origAssembly for the lifted tracks
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.ra - lines changed 5, context: html, text, full: html, text
• Changed the colors in the tables, changed the table names to V2, changed the html to reflect the new colors of red, blue, orange
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaCnv.ra - lines changed 52, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaCnv.new.html - lines changed 95, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaCnv.new.ra - lines changed 4, context: html, text, full: html, text
• Release notes for Color Change for CNV
  • src/hg/makeDb/doc/encodeDccHg18/wgEncodeHudsonalphaCnv.release2.notes - lines changed 76, context: html, text, full: html, text
• Sort the Tier 1 to the top
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.ra - lines changed 12, context: html, text, full: html, text
• Changed the long labels for the Contigs, uncertain if we will display the Junctions
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra - lines changed 126, context: html, text, full: html, text
• Changed Tier 2 to sort to the top
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.ra - lines changed 13, context: html, text, full: html, text
• changed the target protien to be under antibody even though there is no antibody in this experiment so that the links would work
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunySwitchgear.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSunySwitchgear.ra - lines changed 3, context: html, text, full: html, text
• Recovered lost data
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBuOrchid.ra - lines changed 35, context: html, text, full: html, text