Question on counting overlapping peaks

[HenriettaHolze]

Hi, I'm looking at a transcript with a shorter an longer version of an exon.
I was wondering how you count reads for those peaks?
Like reads that map partially to the shorter exon but fully to the longer, or reads that map to the longer but the junction shows they belong to the shorter? I supply my own peak list using the UTR and CDS regions from my gtf file at the moment. Thanks!