[Bioc-devel] strandless introns with VariantAnnotation::locateVariants()

[Robert Castelo]

hi,

currently, the annotation of variants in intronic regions by 
VariantAnnotation and the locateVariants() function does not assign 
strand to annotations in introns:

library(VariantAnnotation)
example(locateVariants)
loc_all[loc_all$LOCATION == "intron"]
GRanges object with 2 ranges and 9 metadata columns:
    seqnames         ranges strand | LOCATION  LOCSTART    LOCEND 
QUERYID        TXID         CDSID      GENEID
       <Rle>      <IRanges>  <Rle> | <factor> <integer> <integer> 
<integer> <character> <IntegerList> <character>
        chr1 [13302, 13302]      * |   intron       948       948 
   3           2                 100287102
        chr1 [13327, 13327]      * |   intron       973       973 
   4           2                 100287102
          PRECEDEID        FOLLOWID
    <CharacterList> <CharacterList>


   -------
   seqinfo: 1 sequence from hg19 genome; no seqlengths


however, introns are stranded, so I would suggest to include the strand 
information in variants annotated to intronic regions. After a quick 
look to the source code I believe the relevant line is within the 
private function .makeResult(), concretely at:

                 strand=strand(query)[xHits],

where is taking the strand of the query (the variant) while I guess it 
should be the subject (the annotation).


cheers,

robert.