Getting length of total region aligned to cluster of paired end reads

Question

[arsala521]

Hi,

I have two sam files for alignment of two sets of paired-end reads. I can do the pairwise alignment if required. I want to determine the genomic length that is mapped to the cluster of paired-end reads. I uploaded a figure to clarify what I want. I basically need these two lengths.

Is there a way to get this? I looked into samtools view options but I couldn’t figure out a way. Not very much good in coding to write a code to do this.

Thank you