[BioC] Calculate Outer Positions of GappedAlignmentPairs

[Kasper Daniel Hansen]

Counting the space between the two reads is certainly used in some algorithms.

But we should have the capability to not do so.

Also, in both cases, we should be able to not double count if a base
is covered by both reads, in case they overlap.

Kasper

On Wed, Mar 20, 2013 at 7:00 PM, Dario Strbenac
<d.strbenac at garvan.org.au> wrote:
> Thanks for the addition ! I was about to take up the challenge to create and submit an implementation.
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