File Changes for cline

v252_base to v253_preview (2011-06-07 to 2011-06-14) v253

• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
  • lines changed 14, context: html, text, full: html, text
    Fixing Redmine bug 411: the refseq column in the kgXref table (which was built from genomic evidence) didn't always match knownToRefseq (which was built post-hoc according to transcript similarity heuristics). After looking into this for a while, I decided that no transcript heuristic would ever be perfect, and it was best to just grab the assignment from design-time evidence. hgMapToGene had a hook for this that almost worked: the -lookup switch. It almost worked because at the crucial lookup step, there was a bug in the code in which there was a hash lookup, a key-value pair, and value was being used as the key in place of key (i.e. 'val=lookup(hash,val)'). Now that that's fixed, the UCSC Genes script uses this -lookup switch to specify expected ucscGenes-refseq mappings from kgXref, to populate knownGeneMrna
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 383, context: html, text, full: html, text
    Merging some changes, mostly relating to alphabetizing and spacing
  • lines changed 4, context: html, text, full: html, text
    Addressing the stanzas where the orderUrl is N/A, which is apparently something that breaks the CGI
  • lines changed 2, context: html, text, full: html, text
    Cleaning up some missing vendor information that came up during this week's code review
  • lines changed 8, context: html, text, full: html, text
    Addressing the last of the feedback from this week's code review
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 1917, context: html, text, full: html, text
    Copying changes from alpha to beta
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.new.ra
  • lines changed 1, context: html, text, full: html, text
    Updated the submission IDs for the subtracks recently revoked and replaced with newer subtracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.ra
  • lines changed 2, context: html, text, full: html, text
    Updated the submission IDs for the subtracks recently revoked and replaced with newer subtracks
• src/hg/near/hgMapToGene/hgMapToGene.c
  • lines changed 1, context: html, text, full: html, text
    Fixing Redmine bug 411: the refseq column in the kgXref table (which was built from genomic evidence) didn't always match knownToRefseq (which was built post-hoc according to transcript similarity heuristics). After looking into this for a while, I decided that no transcript heuristic would ever be perfect, and it was best to just grab the assignment from design-time evidence. hgMapToGene had a hook for this that almost worked: the -lookup switch. It almost worked because at the crucial lookup step, there was a bug in the code in which there was a hash lookup, a key-value pair, and value was being used as the key in place of key (i.e. 'val=lookup(hash,val)'). Now that that's fixed, the UCSC Genes script uses this -lookup switch to specify expected ucscGenes-refseq mappings from kgXref, to populate knownGeneMrna