Commits for angie

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

• Regenerating snp138 tables with one last allele frequency fix.refs #11438, #11954
  
  • src/hg/makeDb/doc/hg19.txt - lines changed 13, 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/annoStreamDb.c - lines changed 2, 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/annoGratorGpVar.c - lines changed 4, context: html, text, full: html, text
  • src/hg/lib/gpFx.c - lines changed 119, context: html, text, full: html, text