arq5x/bedtools — pull request #72 by dawe (2013-05-28 08:26:20+00:00)
Title: Intersect library fragments and not alignment in multibamcov

I've added an option to multiBamCov which extends one read (R1, right now) for properly paired alignments to the size of ISIZE before the intersection with the bed file. This should, in principle, count intersection of library fragments in place of alignments. I thought this can be useful to have a proper count when dealing with ChIP/MeDIP experiments.
A similar option may be considered for genomecov when -bg option is enabled