Commits for cline

v255_preview to v255_preview2 (2011-07-26 to 2011-08-02) v255

• Many small bug fixes...
  • src/hg/encode/cellTypeParser.py - lines changed 3, context: html, text, full: html, text
• Changed the include structure to be consistent with Morgan's new library structure
  • src/hg/encode/antibodyWikiParser.py - lines changed 1, context: html, text, full: html, text
• Added an order URL for the Wold lab for the C2C12 cell line
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1, context: html, text, full: html, text
• moved cellTypeParser and antibodyWikiParser into separate subdirs, with makefiles that copy them into the bin directory. For both files, added a -noDownload option
  • src/hg/encode/antibodyWikiParser.py - lines changed 295, context: html, text, full: html, text
  • src/hg/encode/antibodyWikiParser/antibodyWikiParser.py - lines changed 306, context: html, text, full: html, text
  • src/hg/encode/antibodyWikiParser/makefile - lines changed 18, context: html, text, full: html, text
  • src/hg/encode/cellTypeParser.py - lines changed 196, context: html, text, full: html, text
  • src/hg/encode/cellTypeParser/cellTypeParser.py - lines changed 201, context: html, text, full: html, text
  • src/hg/encode/cellTypeParser/makefile - lines changed 18, context: html, text, full: html, text
• Fixed the makefiles
  • src/hg/encode/antibodyWikiParser/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/cellTypeParser/makefile - lines changed 1, context: html, text, full: html, text
• On closer examination, I see that this 'bug fix' that I made a while ago actually introduced a bug. Consequently, I'm un-fixing the 'fix'
  • src/hg/near/hgMapToGene/hgMapToGene.c - lines changed 1, context: html, text, full: html, text
• Added a new switch to hgMapToGene to override any derived mapping with a known value, if that value is known in advance. Used that switch to make sure that the values in the knownToRefSeq table are consistent with the UCSC Genes - RefSeq assignments in the kgXref table. This means that if a UCSC Genes transcript is derived (in part) from a RefSeq transcript, that RefSeq transcript will be listed in the knownToRefSeq table. UCSC Genes transcripts that are NOT derived from RefSeq transcripts will have entries in the knownToRefSeq table that identify the most-overlapping RefSeq
  • src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh - lines changed 12, context: html, text, full: html, text
  • src/hg/near/hgMapToGene/hgMapToGene.c - lines changed 30, context: html, text, full: html, text