I am filtering out reads in a BAM that do not overlap a set of regions by iterating over a list of SAMRecords and comparing their alignment starts and ends to the regions.
There's a queryOverlapping in the SAMFileReader Class that seems to be doing what i want. It queries record overlapping a range by passing in a range and a sequence. I don't understand why the sequence is necessary for such operation.
Any explanation?
Thanks.
There's a queryOverlapping in the SAMFileReader Class that seems to be doing what i want. It queries record overlapping a range by passing in a range and a sequence. I don't understand why the sequence is necessary for such operation.
Any explanation?
Thanks.