Re: [Seqan-dev] usage of setStepSize

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

Hi Johannes,

the way you use setStepSize is absolutely right. It was a bug in the q-gram index construction, fixed in [10554].
http://trac.mi.fu-berlin.de/seqan/changeset/10554

Thanks for reporting,
David

Am 06.10.2011 um 14:42 schrieb Johannes Merkle:

> Hi,
> 
> I'm experiencing some odd behaviour when using the q-gram-index with a 
> different stepsize.
> The attached code (which is very similar to your tutorial, only with the 
> added setStepSize command and the OpenAddressing spec) returns wrong 
> results (0 and 7). Without the OpenAddressing spec it doesn't work at 
> all (see attached error message).
> 
> Am i using the setStepSize command incorrect or is this a bug?
> 
> Thanks,
> Johannes
> 
> 
> 
> Code:
> typedef Index<DnaString, IndexQGram< UngappedShape<3>, OpenAddressing > 
>> TIndex;
>     TIndex index("CATGATTACATA");
>     setStepSize(index,2);
>     hash(indexShape(index), "CAT");
>     for (unsigned i = 0; i < length(getOccurrences(index, 
> indexShape(index))); ++i)
>         std::cout << getOccurrences(index, indexShape(index))[i] << 
> std::endl;
> 
> Error Message:
> ...SeqAn\core\include\seqan/sequence/string_base.h:227 Assertion failed 
> : static_cast<TStringPos>(pos) < static_cast<TStringPos>(length(me)) 
> was: 254 >= 65 (Trying to access an element behind the last one!)
> 
> _______________________________________________
> seqan-dev mailing list
> seqan-dev@lists.fu-berlin.de
> https://lists.fu-berlin.de/listinfo/seqan-dev