Re: [Seqan-dev] reading bam file problem

["Holtgrewe, Manuel" <manuel.holtgrewe@fu-berlin.de>]

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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