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

[Mat <matthias.dodt@mdc-berlin.de>]

Hi Manuel!

Yes, i already checked that. The new contig sequence get's created during runtime from several input sources (FASTA and SAM files).

cheers,

mat

Am 5/6/11 3:18 PM, schrieb Holtgrewe, Manuel:

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>

_______________________________________________
seqan-dev mailing list
seqan-dev@lists.fu-berlin.de
https://lists.fu-berlin.de/listinfo/seqan-dev