Re: [Seqan-dev] bug report readSequence()

["Siragusa, Enrico" <Enrico.Siragusa@fu-berlin.de>]

Hello,

Could you please create a GitHub issue (https://github.com/seqan/seqan/issues/new) including a small example to reproduce your problem?

Thanks,
Enrico

On 05 Nov 2015, at 13:17, Eik Dahms <eik.dahms@gmail.com> wrote:

> Hello,
> my sequence alphabet uses strictly "ACTG". This seems not to be causing this allocation error. Also it shouldn't work on any system then.
> 
> Cordially
> Eik Dahms
> 
> Christophe VROLAND <christophe.vroland@ed.univ-lille1.fr> schrieb am Fr., 30. Okt. 2015 um 13:49 Uhr:
> On 30/10/2015 13:21, Eik Dahms wrote:
>> Dear all,
>> 
>> i recently upgraded sequan from 1.4.0 to 2.0.0. I did not change my code. 
>> 
>> When i now try to run the program  i get the following allocation error when i try to read a sequence via readSequence() from a FaiIndex:
>> 
>> /seqan/basic/basic_exception.h:368 FAILED!  (Uncaught exception of type std::bad_alloc: std::bad_alloc)
>> 
>> This error occurs only on my laptop with 4GB RAM. When i run the program on a Server with 500GB RAM - it works.
>> 
>> It seems that the memory that is allocated, for the string that the sequence is read in, is to high.
>> 
>> I appended the stacktrace from gnu debugger.  
>> 
>> Thanks in advance !
>> Eik
>> 
>> 
>> 
>> 
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>> 
>> seqan-dev@lists.fu-berlin.de
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> Hello,
> I have ever got this problem when my sequence alphabet used in the code doesn't include all the alphabet of the sequence I try to read.
> You use a Dna5 alphabet, maybe, there's an other letter than "ACGTN" in your sequence (a "X" ?).
> 
> Cordially
> 
> 
> -- 
> Christophe VROLAND
> 
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