File Changes for angie

v291_base to v292_preview (2013-10-21 to 2013-10-28) v292

• src/hg/lib/annoGratorGpVar.c
  • lines changed 4, context: html, text, full: html, text
    If a genePred table includes the exonFrames column, beware... it maycontain transcripts with incomplete CDS that begin out-of-frame.
    So far we've been assuming that the CDS sequence begins in frame,
    which works fine for UCSC Genes and RefSeq. However, less tidy
    sets such as Ensembl and Gencode Comprehensive have lots of
    out-of-frame CDSs.
    In order to not have incorrect translation to peptide sequence,
    we need to use a padded CDS sequence. For example, if the
    first coding exon's frame is 1, we now add an 'N' at the beginning
    of the coding sequence to align it to the correct frame. We also
    look out for subsequent surprises in exonFrames, though I expect
    those to be rare. Of course, when the coding sequence is tweaked
    like that, care must be taken when modifying it with an alt allele.
    fixes #11990
    refs #11175
    
• src/hg/lib/annoStreamDb.c
  • lines changed 2, context: html, text, full: html, text
    When doing a single-region query, if we don't get any results fromthe query, set self->eof so there isn't infinite recursion in
    asdNextRow (thanks to nextRowFromBuffer setting self->needQuery
    because the buffer is empty).
    fixes #11988
    refs #11110
    
• src/hg/lib/gpFx.c
  • lines changed 119, context: html, text, full: html, text
    If a genePred table includes the exonFrames column, beware... it maycontain transcripts with incomplete CDS that begin out-of-frame.
    So far we've been assuming that the CDS sequence begins in frame,
    which works fine for UCSC Genes and RefSeq. However, less tidy
    sets such as Ensembl and Gencode Comprehensive have lots of
    out-of-frame CDSs.
    In order to not have incorrect translation to peptide sequence,
    we need to use a padded CDS sequence. For example, if the
    first coding exon's frame is 1, we now add an 'N' at the beginning
    of the coding sequence to align it to the correct frame. We also
    look out for subsequent surprises in exonFrames, though I expect
    those to be rare. Of course, when the coding sequence is tweaked
    like that, care must be taken when modifying it with an alt allele.
    fixes #11990
    refs #11175
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 13, context: html, text, full: html, text
    Regenerating snp138 tables with one last allele frequency fix.refs #11438, #11954