Hi Lemon,
On Tue, 13 Sep 2011 04:54:40 -0700 (PDT)
Lemon <lemon...@gmail.com> wrote:
> I have some segments start and end position on a reference sequence, I
> want to calculate the uncoverage region for the reference;
>
> for example: reference sequence length= 100,
>
> name [start,end]
> segment 1 [1,20]
> segment 2 [2,28]
> segment 3 [50,100]
> segment 4 [5,38]
>
> so uncover region = [38,49]
>
>
> now I already have %pos{start}=end structure for those segment
> position, could somebody give a good method?
>
I suggest you merge overlapping segments into big meta-segments using a sorted
array, one by one, and then see the uncovered regions between two adjacent
meta-segments.
Regards,
Shlomi Fish
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