Gaps within reads causing variation in data

Question

[Ron]

Hi,

I am using pysam to calculate the read counts per allele.Large gaps within reads (mostly due to introns in RNA-seq data) are for some reason sometimes read as either ref or alt allele.This is resulting in variation in number of counts(reads)for reference allele and alternate alleles.

These are coded as < or > in pileup files.

The gaps shouldn't be read as anything. They should be skipped completely.Is there any way this can be taken care of in pysam? Or any suggestions on how to deal with this?

This question is related to my earlier post.

Cheers,
Ron