clipOverlap in outward facing pairs

[statgen]

clipOverlap in outward facing pairs

[mktrost]

Here is the reasoning behind the extra clips you see:
Paired-end sequences from each end of a DNA fragment. Based on that, the start position of the forward strand corresponds with one end of the DNA fragment. If the reverse strand extends beyond the forward strand's start position, it is actually going past the end of the DNA fragment being sequenced, so ClipOverlap clips that extra sequence. Similar logic applies to clipping the part of a forward strand that goes past the end of the reverse strand.
Reading past the end of the fragment results in adaptors being read, which you don't want in your SAM/BAM file, since they are not part of the DNA sequence, so we clip anything that goes beyond the "length" of the fragment as indicated by the start of the forward & reverse reads.

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