Commits for cricket

v271_preview to v271_preview2 (2012-07-24 to 2012-07-31) v271

• Tier 2 promotion
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.ra - lines changed 85, context: html, text, full: html, text
• Promoted tier 2.5 cell lines and collapsed the HCT116 line in the matrix to represnt both Stanford and Haib samples
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.ra - lines changed 64, context: html, text, full: html, text
• Promoting the tier 2.5 cell lines and fixing the tags for the phase and the views
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.ra - lines changed 191, context: html, text, full: html, text
• Updated tags for cell lines, should be no visible change
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.release1.ra - lines changed 11, context: html, text, full: html, text
• Adding 3 tables
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 88, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release4.ra - lines changed 27, context: html, text, full: html, text
• Changing the defintion of dccInternalNotes to specify a use for it. It looks like we may be reloading a lot of files
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1, context: html, text, full: html, text
• Adding the bedClusters fix for Gis Rna Pet
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeGisRnaPet.daf - lines changed 3, context: html, text, full: html, text
• Adding the EnsV65 views
  • src/hg/encode/DAFs/3.0/mm9/wgEncodeCshlLongRnaSeq.daf - lines changed 21, context: html, text, full: html, text
• Sorting out the V1, V3, V4 issue with NHEK, see ticket #7771
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 36, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release4.ra - lines changed 21, context: html, text, full: html, text
• Adding release notes, needed to use loose option because of Morgan changes for the rawdata see ticket #7771
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeRikenCage.release4.notes - lines changed 2170, context: html, text, full: html, text
• Adding release notes
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release4.html - lines changed 175, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release4.ra - lines changed 1, context: html, text, full: html, text
• Correcting alphabet
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.release1.ra - lines changed 11, context: html, text, full: html, text
• Merge branch 'CricketTier2'
• Correcting an error in expVars
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV4.ra - lines changed 3, context: html, text, full: html, text
• Removed the 4 from 4OHTAM according to ticket 8408
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release6.ra - lines changed 7, context: html, text, full: html, text
• Changed the rnaExtract to all, changed prostate to Prostate, changed two of the TssHmm files to be on by defualt
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release4.ra - lines changed 5, context: html, text, full: html, text
• Added some comments about the Cage label
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1, context: html, text, full: html, text
• Making Brians small edits
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release4.ra - lines changed 29, context: html, text, full: html, text
• Removing labProtocolId
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 497, context: html, text, full: html, text
• Adding new stanzas from submission 7727
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeFsuRepliChip.ra - lines changed 237, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliChip.release2.ra - lines changed 61, context: html, text, full: html, text
• Adding md5sums, expIds, accsssions, corrected H9ES
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeFsuRepliChip.ra - lines changed 39, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliChip.release2.ra - lines changed 2, context: html, text, full: html, text
• adding release notes
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeFsuRepliChip.release2.notes - lines changed 174, context: html, text, full: html, text
• Adding dataType
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV4.ra - lines changed 2, context: html, text, full: html, text
• Adding in dateUnrestricted
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeFsuRepliChip.ra - lines changed 11, context: html, text, full: html, text
• Changing some more white space after merging with previous commit
  • src/hg/makeDb/hgTrackDb/hgTrackDb.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/loadTracks - lines changed 2, context: html, text, full: html, text
• loadTracks did not belong in the previous commit, I am undoing it
  • src/hg/makeDb/trackDb/loadTracks - lines changed 2, context: html, text, full: html, text
• Changing this release 3 to release 4
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.release3.ra - lines changed 1531, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.release4.ra - lines changed 1531, context: html, text, full: html, text
• Starting to clean up long and short labels and adding the new html file
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.release4.html - lines changed 96, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.release4.ra - lines changed 33, context: html, text, full: html, text
• Updating more dateUnrestricted
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeFsuRepliChip.ra - lines changed 3, context: html, text, full: html, text
• Chainging more restriction dates
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeFsuRepliChip.ra - lines changed 19, context: html, text, full: html, text
• Preparing Uw Affy Exon Release 4, changing long labels, updating the origAssembly to only be there if needed, fixing differentiation.
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwAffyExonArray.release4.notes - lines changed 468, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwAffyExonArray.ra - lines changed 154, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.release4.ra - lines changed 10, context: html, text, full: html, text
• Adding release notes
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.release4.html - lines changed 2, context: html, text, full: html, text
• Adding in 4 replacement fastqs and dropping useless lines like treatment None
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 991, context: html, text, full: html, text