Hi Biostars,

I was wondering if someone has a convenient trick to calculate inner distance depth of PE reads?

For example, consider the below 2 PE reads;

PairedEnd1- R1 maps from chr1:100-125 & R2 maps from chr1:150-175
PairedEnd2- R1 maps from chr1:120-145 & R2 maps from chr1:170-195

Ultimately I'd like to have a table like;

pos, depth.mapped, depth.inner
chr1:122, 2, 0
chr1:130, 1, 1

TIA