[Seqan-dev] reading bam file problem

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

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