Dear Experts, For some special application, I want to merge the read pairs of paired end reads from a BAM file, including the discordant reads, given that the genomic location is already known from the mapping to reference genome. I would mainly consider the following two conditions:

1- overlapping reads

1      7
=======>
    ||||
    <=========
     4      10

That would give me one read, like this.

1          10
============>

2- discordant reads.

Ref==============================================
         5          10^^^^^^^^^
         =====R1=====>|||||||||
                      |||||||||
                               <=====R2======
                               15          20

This one would result in:

        ================================>    
         5                             20

So, in other words, I want to reconstruct the missing fragment in the discordant pairs.

Are there any tools that can do that? Best wishes