From a bam file I have a set of reads. For each read I am only interested in a particular regions, baring there is a continuous sub-sequence (i.e no gaps) and that their are no inserts.
With pysam I have been able to check for overlap in the reads using:
.get_overlap(start_pos, end_pos) . Where I hit a road block is checking if an insert or deletion is within that region. Are there any built in pysam functions that would tell me this?