Re: [Seqan-dev] adding contig to fragmentStore.contigStore

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

Hi Mat,

I do not think that this works right now.

What exactly are you trying to do? Do you want to load a file? Or is the file already in memory?

Maybe looking at the loadContigs function can help you to implement the required functionality?

http://trac.mi.fu-berlin.de/seqan/browser/trunk/seqan/core/include/seqan/store/store_io.h#L868

Bests,
Manuel

Am 06.05.2011 um 14:55 schrieb Mat:

> Hey guys!
> 
> Does anybody have an advice on how to add a single contig (from a CharString) to a contigStore? I only found "assingSeq()" which seems to work only on memory mapped files-?
> 
> I guess it should be something like:
> 
> ...
> CharString newContig;
> ..
> ..
> 
> unsigned seqOfs = length(TDataManager::getInstance()->fragStore.contigStore);
> resize(TDataManager::getInstance()->fragStore.contigStore, seqOfs + 1, Generous());
> resize(TDataManager::getInstance()->fragStore.contigNameStore, seqOfs + 1, Generous());
> 
> 
> assignSeq(TDataManager::getInstance()->fragStore.contigStore[seqOfs + i].seq, newContig, ?);
> 
> And how to add a name later on to the contigNameStore?
> 
> Thanks!
> <ATT00001..txt>