[BioC] Reading paired-end data into GRangesList

[Hubert Rehrauer]

Hi

I want to load paired-end data from Bam-Files into R in order to do 
expression counting. The complicating thing is, that the first read was 
aligned using a gapped alignment (i.e. the cigar string contains Ns).

How can this be done? I thought this would be a quite common task but I 
did not find any function that would do this. Neither scanBam nor 
readBamGappedAlignments are directly helpful with this.

For me the most obvious thing would be to hold the alignment of such a 
read as a GRangesList. In order to get there I would use scanBam to load 
the first read. Parse the  cigar string to identify the gaps, build a 
GRangesList and then add the alignment of the second read to the List. 
Do you have any better ideas?


best regards,
hubert