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Re: [Seqan-dev] reading bam file problem

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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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