Commits for cline

v248_preview to v248_preview2 (2011-02-22 to 2011-03-01) v248

• When recording a selenocysteine exception, save the specific information on the exception in the hash. This will be useful later in txCdsPick.c
  • src/hg/lib/genbank.c - lines changed 1, context: html, text, full: html, text
• When transferring information on a selenocysteine exception, grab the specific information on the exception now stored in the selenocysteine hash
  • src/hg/txCds/txCdsPick/txCdsPick.c - lines changed 3, context: html, text, full: html, text
• Minor HTML text editing, for clarity
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.html - lines changed 28, context: html, text, full: html, text
• Made a change in capitalization to make this data consistent with the files in the downloads directory
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra - lines changed 2, context: html, text, full: html, text
• Accepted a couple provisional stanzas. Drafted a validation regex for md5sums
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 5, context: html, text, full: html, text
• Copied a bunch of changes from alpha to beta
  • src/hg/makeDb/trackDb/cv/beta/cv.ra - lines changed 51, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRIPSuper.html - lines changed 88, context: html, text, full: html, text
• Set up the ENCODE RNA Binding Protein (RBP) supertrack page. Added the page to the set of ENCODE supertracks, and added the four SUNY RBP tracks to the supertrack
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRbpSuper.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyTiling.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSunySwitchgear.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSuper.ra - lines changed 7, context: html, text, full: html, text
• Incorporated some feedback from the Giddings lab
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.html - lines changed 59, context: html, text, full: html, text
• Added the localization to the long labels
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.ra - lines changed 2, context: html, text, full: html, text
• Simplified the argument list. Now this script takes only three arguments: the old directory (required), the new directory (required), and an optional argument for ctime
  • src/hg/txGene/txGeneValidation/compareModifiedFileSizes.csh - lines changed 16, context: html, text, full: html, text
• Added this track into the ENCODE RBP supertrack
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyRipSeq.ra - lines changed 1, context: html, text, full: html, text
• Added one more critical step: removing the temporary directory just created
  • src/hg/txGene/txGeneValidation/compareModifiedFileSizes.csh - lines changed 1, context: html, text, full: html, text
• Reversed the order of the first two arguments to make them consistent with the documentation
  • src/hg/txGene/txGeneValidation/compareModifiedFileSizes.csh - lines changed 3, context: html, text, full: html, text
• Accepted provisional changes, cleaned up one comment
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 2, context: html, text, full: html, text
• Copying a bunch of changes from alpha to beta
  • src/hg/makeDb/trackDb/cv/beta/cv.ra - lines changed 29, context: html, text, full: html, text
• Renamed several antibodies, in response to Redmine Bug # 2965
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 58, context: html, text, full: html, text
• Fixed a broken link introduced wen addressing Redmine bug 2965
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 3, context: html, text, full: html, text
• (1) Clarified the comments on expected values, especially concerning the interrelations between stanzas. (2) Added a couple stanzas to document expected values for familiar types (e.g. organism, tier). (3) Added data for one Farnham lab cell type that had been registered provisionally. (4) Fixed the antibody validation line convention of <antibody>_(<validationType>):<filename> as opposed to <antibody>_(<validationType>)_<PI>:<filename>. The reason: adding the name of the lab that validated the antibody adds no information, since it's the same as the lab that first entered the antibody. Having the name displayed in the validation column just adds clutter to the column
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 56, context: html, text, full: html, text