Clipping bases from non-overlapping regions of mate reads in BAM file

Question

[lechu]

I'm looking for a tool that, given a paired-end BAM file, would (soft or hard) clip all the bases from non-overlapping part of read mates, leaving only the overlapping region. Ideas for ugly hacks of existing tool are welcome as well.

[Pierre Lindenbaum]

see paired-end bam clip bases outside insert range