Commits for cricket

v250_base to v251_preview (2011-04-19 to 2011-04-26) v251

• Hand changed the attic files that the renamer could not do so that growprot was not in the object name and that Yale became Stanford
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra - lines changed 107, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.ra - lines changed 5, context: html, text, full: html, text
• 2 more files renamed to add Duke, using renamer
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra - lines changed 27, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.ra - lines changed 4, context: html, text, full: html, text
• Revoking labExpID SL941 as it should have been SL1914. Waiting for replacement data.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra - lines changed 20, context: html, text, full: html, text
• This was a test of the renamer. There was a list of files to rename in issue 3011. Venkat should be asked to double check this check in.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 577, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 267, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra - lines changed 116, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra - lines changed 76, context: html, text, full: html, text
• More renamer work. The list is in Bug3011 in the MM9 file. Venkat should check off on this change
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 293, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.newR2.ra - lines changed 20, context: html, text, full: html, text
• Added the ver first accession number and exp ID
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeBuOrchid.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBuOrchid.ra - lines changed 5, context: html, text, full: html, text
• Removed fileIndex from composites where it was only in some of the stanzas
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisDnaPet.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaSeq.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylSeq.ra - lines changed 45, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 630, context: html, text, full: html, text
• Removed fileIndex and changed the Denovo and Exon to files not tables
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 229, context: html, text, full: html, text
• Changed the TranscriptGencV3c from tables into files
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 113, context: html, text, full: html, text
• Changed the BTO numbers for Cell lines as specified by the NHGRI. Melissa should review this
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 16, context: html, text, full: html, text
• added the url for Jennifer Condon
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1, context: html, text, full: html, text
• Issue 1440 Note 15. I am changing to add fileSortOrder to display the new accession numbers for both hg18 and hg19.
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeBuOrchid.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeBuOrchid.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBuOrchid.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeBuOrchid.ra - lines changed 2, context: html, text, full: html, text
• fixed a weird error of expVars showing up in a table object
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBuOrchid.ra - lines changed 2, context: html, text, full: html, text
• Adding GeneSt and Tiling as dataTypes
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 28, context: html, text, full: html, text
• Starting a Release 2 for Tiling
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyTiling.new.ra - lines changed 3, context: html, text, full: html, text
• Issue 37, Note 48, Items: 8,9,10 and 17, as well as the addition of md5sums and the changing of dataType to GeneST, these changes are all being reviewed by Katrina
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyGeneSt.ra - lines changed 97, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.ra - lines changed 6, context: html, text, full: html, text
• To be reviewed by Katrina. This is a major rewrite of the track description. It is in process
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.html - lines changed 57, context: html, text, full: html, text
• Issue 37, removing dccaccession and expId from mdb, adding clarifications in .html about the signal value and score, fixing ripInput to RIP-Input
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyGeneSt.ra - lines changed 49, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.html - lines changed 39, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.ra - lines changed 1, context: html, text, full: html, text
• Remove restrictionEnzyme from expVars
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaMethylSeq.ra - lines changed 2, context: html, text, full: html, text
• Changed dataType GeneSt to RipGeneSt at request of CV maven
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyGeneSt.ra - lines changed 48, context: html, text, full: html, text
• Issue 37 note 58 and 59, changed the dataType, updated the md5sums, fixed the greyValue by adding a min
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyGeneSt.ra - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.ra - lines changed 3, context: html, text, full: html, text
• The magic number is uptodate now
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyGeneSt.ra - lines changed 49, context: html, text, full: html, text
• Changed datatype from RipChip to RipTiling
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyTiling.ra - lines changed 9, context: html, text, full: html, text
• added attic=auxExp for attic files
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 12, context: html, text, full: html, text
• Changing Cnv to Genotype for dataType
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaCnv.ra - lines changed 7, context: html, text, full: html, text
• Added attic=auxExp for auxillary experiments
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra - lines changed 44, context: html, text, full: html, text
• Changed the dataType to be MethylArray instead of Methyl27 and added labVersion to indicate that Methyl27 was used
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaMethyl27.ra - lines changed 13, context: html, text, full: html, text
• Changed the dataType to be MethylArray instead of Methyl27 and added labVersion to indicate that Methyl27 was used
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylArray.ra - lines changed 147, context: html, text, full: html, text
• Changed the lab name to comply with the cv.ra
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeNhgriBip.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeNhgriNRE.ra - lines changed 5, context: html, text, full: html, text
• Added rnaExtract=polyA for all tracks not certain if it is right
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleRNAseq.ra - lines changed 20, context: html, text, full: html, text
• Labeled with the attic=auxExp for auxiallary experminets
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra - lines changed 15, context: html, text, full: html, text
• Started reviewing the karyotype information compared to vendor, Jeff is taking over
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 20, context: html, text, full: html, text
• Changing the Methyl27 to MethylArray for dataType. This should be reviewed by Melissa. The reasoning is that we also will have some data from Methyl450 and these data are to be considered together.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 4, context: html, text, full: html, text
• Changed rnaExtract at request of the lab. Will need to run renamer
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibRnaSeq.ra - lines changed 168, context: html, text, full: html, text