Re: [Seqan-dev] match number of globalalignment

["Weese, David" <weese@campus.fu-berlin.de>]

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.
>