File Changes for cline

v261_preview2 to v261_base (2011-12-20 to 2012-01-03) v261

• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
  • lines changed 57, context: html, text, full: html, text
    To clean up numerous gene-misnaming bugs, refined the way the gene symbol and description are assigned. If a transcript overlaps a RefSeq (i.e. if it has an entry in the knownToRefSeq table), take the gene symbol and description from the RefSeq record. If there isn't an overlapping transcript, then do the other things: look at whatever protein was annotated for the CDS (with the caveat that this can go badly awry within families of paralogs), look at the evidence the transcript was based on, etc. For UCSC Genes, this makes things a bit more complicated because the knownToRefSeq table must be built before the kgXref table - but later the knownToRefSeq table must be updated to match the contents of the kgXref refseq column (which is set by a more sensitive process). So, I updated the UCSC Genes script to build a preliminary version of knownToRefSeq, built the kgXref table with that preliminary knownToRefSeq, and then updated knownToRefSeq from kgXref.
  • lines changed 73, context: html, text, full: html, text
    1. Switched the genome versions for certain related organisms after those versions turned out to have incomplete datasets. 2. As a stylistic thing, where the code references the root of the kent source tree as ~/kent, replaced that with the variable , to give developers greater ease in reorganizing their source trees. 3. Rearranged some of the steps for building the isPCR files to make more explicit what must be done by a superuser and what has to be done after the superuser commands are complete
  • lines changed 24, context: html, text, full: html, text
    Fixing Redmine Bug #5180, the gist of which is that the abParts should be excluded from the knownTo* tables. Added an exclude option to hgMapToGene, which contains a list of gene names to exclude from the table
• src/hg/near/hgMapToGene/hgMapToGene.c
  • lines changed 2, context: html, text, full: html, text
    In addition to requiring that a gene and a transcript either share a splice site or are both unspliced if they are going to be mapped together, require that they be on the same strand as well
  • lines changed 5, context: html, text, full: html, text
    Bug fix: I'd forgotten that strands are implemented as char[2], not just char. Now I'm comparing two strands properly
  • lines changed 29, context: html, text, full: html, text
    Fixing Redmine Bug #5180, the gist of which is that the abParts should be excluded from the knownTo* tables. Added an exclude option to hgMapToGene, which contains a list of gene names to exclude from the table
• src/hg/txGene/txGeneXref/txGeneXref.c
  • lines changed 60, context: html, text, full: html, text
    To clean up numerous gene-misnaming bugs, refined the way the gene symbol and description are assigned. If a transcript overlaps a RefSeq (i.e. if it has an entry in the knownToRefSeq table), take the gene symbol and description from the RefSeq record. If there isn't an overlapping transcript, then do the other things: look at whatever protein was annotated for the CDS (with the caveat that this can go badly awry within families of paralogs), look at the evidence the transcript was based on, etc. For UCSC Genes, this makes things a bit more complicated because the knownToRefSeq table must be built before the kgXref table - but later the knownToRefSeq table must be updated to match the contents of the kgXref refseq column (which is set by a more sensitive process). So, I updated the UCSC Genes script to build a preliminary version of knownToRefSeq, built the kgXref table with that preliminary knownToRefSeq, and then updated knownToRefSeq from kgXref.