Re: [Seqan-dev] Is it thread safe to use Seqan for sequence alignment?

[Tianyang Li 李天阳 Tommy Li <tmy1018@gmail.com>]

Hi Rene,

Thank you very much!

Best,
Tianyang

On Mon, Jul 30, 2012 at 4:37 PM, Rahn, René <rene.maerker@fu-berlin.de> wrote:
> Dear Tianyang,
>
> if I get you right, then you want to compute all alignments within a set of
> sequences in multiple threads. In this case you should be fine with our
> alignment algorithms as there are no manipulations of shared data structures
> involved. The only issue that has to be addressed by your program is the
> management of the alignment data structures in which you can store the
> alignment. Each thread would require its own alignment data structure to
> write the alignment, otherwise multiple threads would manipulate the same
> data structure, which is not handled by our alignment algorithms or data
> structures.
>
> Kind regards,
>
> René
>
> On Jul 30, 2012, at 5:09 AM, Tianyang Li 李天阳 Tommy Li wrote:
>
> Hi,
>
> Sorry for sending this email directly to all of you, but I was
> wondering if I can use Seqan's alignment functions in a multithreading
> setting?
>
> If not, are there other C/C++ libraries that you would recommend?
>
> Thanks!
>
> Best,
> Tianyang
>
> On Sun, Jul 29, 2012 at 10:21 PM, Tianyang Li 李天阳 Tommy Li
> <tmy1018@gmail.com> wrote:
>
> Hi,
>
>
> I have a question about Seqan's thread safety.
>
>
> Currently I'd like to use Seqan to do Smith-Waterman alignment of
>
> nucleotide  sequences, and I'd like to speed it up by multi-threading.
>
>
> But I'm not sure about whether it'll be thread safe to do so.
>
>
> Thanks!
>
>
> Best,
>
> Tianyang
>
>
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>
> ---
>
> René Rahn
> Ph.D. Student
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