Re: [Seqan-dev] match number of globalalignment

[Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>]

This gives an example

http://trac.seqan.de/browser/trunk/seqan/extras/demos/bam_stats.cpp#L196

On 01/13/2012 08:24 PM, Weese, David wrote:
> Hi,
>
> You can iterate with two iterators it1, it2 simultaneously over the two rows of the align object, see Task 1 of http://trac.seqan.de/wiki/Tutorial/Alignments.
> A match occurs whenever both isGap(it1) and isGap(it2) are false. Simply count them.
>
> Regards,
> David
>
> --
> David Weese				weese@inf.fu-berlin.de
> Freie Universität Berlin		http://www.inf.fu-berlin.de/
> Institut für Informatik			Phone: +49 30 838 75246
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>
> Am 13.01.2012 um 20:11 schrieb Beifang Niu:
>
> > Hi David,
> >
> > One example for  match number is the following:
> >
> > If I got the alignment using global alignment, the match number is 5.
> >
> > AACCGT
> >   | |    | | |
> > AATCGT
> >
> > I just can get the alignment using globalalignment but how can I get the match number of base pairs ?
> >
> > thanks,
> > Beifang.
>
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