On Wed, Mar 20, 2013 at 6:57 PM, Kasper Daniel Hansen <
kasperdanielhansen@gmail.com> wrote:

> Counting the space between the two reads is certainly used in some
> algorithms.
>
> But we should have the capability to not do so.
>
>
This is already supported to some extent. grglist() will exclude the space
and any N gaps, optionally D.


> Also, in both cases, we should be able to not double count if a base
> is covered by both reads, in case they overlap.
>
>
This comes about by calling reduce() on grglist().


> Kasper
>
> On Wed, Mar 20, 2013 at 7:00 PM, Dario Strbenac
> <d.strbenac@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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