Getting End Location of Alignment from Bowtie 2

Question

[eholleman12]

I was wondering if anyone knows of a good way to figure out the end location of an alignment from a Bowtie search. I first attempted to use the CIGAR string but getting the length that corresponds to returns the length of the query sequence which is not what I'm looking for. Thanks!

[ATpoint]

but getting the length that corresponds to returns the length of the query sequence which is not what I'm looking for

What does that mean? Where is the problem?