Re: [Seqan-dev] Seed end offset

[Rahn, René <Rene.Rahn@fu-berlin.de>]

Hi Saliya,

On 21. Feb 2019, at 04:22, Saliya Ekanayake <esaliya@gmail.com> wrote:

Hi Devs,

Looking at the example on seeds at (https://seqan.readthedocs.io/en/seqan-v1.4.2/Tutorial/SeedAndExtend.html), I want to check if the seed end offset is exclusive or inclusive.

For example, in the string, 

"The quick BROWN fox jumped again!"

the seed ROW starts at 11 and ends at 13 (zero-based) indices. The example lists 14 as the end offset, so does that mean the last index should be exclusive?

Yes, the end of the seed is the position behind the last included element of the source, similar to the end iterator which points behind the last element of a range.

So in this example constructing the same seed with seed(11, 7, 3), where 3 is the size of the diagonal will give the same end positions 14 and 10.

I hope this helps,

best regards,

René

Thank you,
Saliya

--

Saliya Ekanayake, Ph.D

Postdoctoral Scholar

Performance and Algorithms Research (PAR) Group

Lawrence Berkeley National Laboratory

Phone: 510-486-5772

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René Rahn

Ph.D. Student (de.NBI - CIBI)

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Mail: rene.rahn@fu-berlin.de

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