[BioC] countOverlaps() only count positive strand (from GenomicRanges example)

[Jason]

Song Li <songli116 at ...> writes:

> 
> Hi Martin and Vincent,
> 
> Thank you for your replies, here is my code:
> 
> > strand(exonRanges)<-"*"
> Error in `strand<-`(`*tmp*`, value = "*") :
>   replacement 'value' is not an AtomicList with the same elementLengths as 'x'
> 
> > levels(strand(aligns))<-c('*','*','*')
> Error in function (classes, fdef, mtable)  :
>   unable to find an inherited method for function "strand<-", for
> signature "GappedAlignments"
> 
> It does not seem to be that straightforward.
> 
> I have been searching for ways to make modification to the
> GappedAlignments and GRangesList  objects.
> 
> Song
> 



I just encountered the same problem. 
What I did is this
 
aln <- grg(readBamGappedAlignments(bam))
strand(aln) = "*"
countOverlaps(exonRanges, aln)


Jason