Re: [Seqan-dev] reading bam file problem

[Bernd Jagla <bernd.jagla@pasteur.fr>]

Thanks for making me dig a bit deeper...

I didn't know that I have to carry the context 
(BamIOContext<StringSet<CharString> > around when reading BAM files... 
For SAM files it apparently doesn't matter...

So, this problem is solved.

Sorry for any confusion that I might have caused...

Best,

Bernd

On 4/20/2012 11:04 AM, Holtgrewe, Manuel wrote:
> Bernd, without a minimal example and a small/minimal input file that present the problem we will not be able to help you.
> ________________________________________
> From: Bernd Jagla [bernd.jagla@pasteur.fr]
> Sent: Friday, April 20, 2012 11:01 AM
> To: seqan-dev@lists.fu-berlin.de
> Subject: [Seqan-dev] reading bam file problem
>
> Hi,
>
> I have another problem with reading bam files:
>
> I get the following error message when reading a bam record, after
> having read the bam header:
>
> Though I think that this problem might be related to the bgzip problem
> mentioned earlier, I don't understand why this causes a core-dump???
> Schouldn't the return value from readRecord be different than 0 if
> something goes wrong? Maybe it is just one record that is bad and we can
> still work on the others....
>
> Thanks for clarifying this,
>
> Best,
>
> Bernd
>
>
> /pasteur/solexa2/solexa_travail/PF2/programs/seqan/workspace/seqan/extras/include/seqan/bam_io/read_bam.h:208
> Assertion failed : static_cast<__uint64>(record.rId)<
> length(nameStore(context)) was: 0>= 0
>
> stack trace:
>     0          [0x452b9e]  seqan::ClassTest::fail() + 0xe
>     1          [0x44eeac]  int
> seqan::readRecord<seqan::Stream<seqan::Tag<seqan::Bgzf_>  >,
> seqan::StringSet<seqan::String<char, seqan::Alloc<void>  >,
> seqan::Owner<seqan::Tag<seqan::Default_>  >  >,
> seqan::NameStoreCache<seqan::StringSet<seqan::String<char,
> seqan::Alloc<void>  >, seqan::Owner<seqan::Tag<seqan::Default_>  >  >,
> seqan::String<char, seqan::Alloc<void>  >  >  >(seqan::BamAlignmentRecord&,
> seqan::BamIOContext<seqan::StringSet<seqan::String<char,
> seqan::Alloc<void>  >, seqan::Owner<seqan::Tag<seqan::Default_>  >  >,
> seqan::NameStoreCache<seqan::StringSet<seqan::String<char,
> seqan::Alloc<void>  >, seqan::Owner<seqan::Tag<seqan::Default_>  >  >,
> seqan::String<char, seqan::Alloc<void>  >  >  >&,
> seqan::Stream<seqan::Tag<seqan::Bgzf_>  >&, seqan::Tag<seqan::Bam_>
> const&) + 0x19c
>
>
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