Re: [Seqan-dev] sorting sam file by SortReadID()

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

With external do you mean something like samtools or sort, i.e. through the command line?

B
On Apr 10, 2012, at 4:40 PM, Holtgrewe, Manuel wrote:

> This is meant for sorting alignments in the FragmentStore.
> 
> You currently have to resort to an external tool for sorting SAM files without completely loading them into memory.
> 
> *m
> ________________________________________
> From: Bernd Jagla [bernd.jagla@pasteur.fr]
> Sent: Tuesday, April 10, 2012 3:01 PM
> To: seqan-dev@lists.fu-berlin.de
> Subject: [Seqan-dev] sorting sam file by SortReadID()
> 
> Hi,
> 
> I am trying to sort a sam/bam file by read-id and am using the following
> construct:
> 
>       sortAlignedReads(reader, SortReadId());
> 
> 
> 
> Unfortunately the compiler is complaining:
> 
> In file included from
> /pasteur/solexa2/solexa_travail/PF2/programs/seqan/workspace/seqan/core/include/seqan/store.h:63:
> /pasteur/solexa2/solexa_travail/PF2/programs/seqan/workspace/seqan/core/include/seqan/store/store_align.h:369:13:
> error: member reference base type 'const char' is not a
>       structure or union
>                 return a1.readId < a2.readId;
>                        ~~ ^
> /usr/lib/gcc/x86_64-redhat-linux6E/4.4.4/../../../../include/c++/4.4.4/bits/stl_algo.h:2128:8:
> note: in instantiation of member function 'seqan::_LessAlignedRead<char,
>       const seqan::Tag<seqan::SortReadId_> >::operator()' requested here
>           if (__comp(__val, *__first))
>               ^
> /usr/lib/gcc/x86_64-redhat-linux6E/4.4.4/../../../../include/c++/4.4.4/bits/stl_algo.h:3433:4:
> note: in instantiation of function template specialization
>       'std::__insertion_sort<char *, seqan::_LessAlignedRead<char,
> const seqan::Tag<seqan::SortReadId_> > >' requested here
>           std::__insertion_sort(__first, __last, __comp);
>           ^
> /usr/lib/gcc/x86_64-redhat-linux6E/4.4.4/../../../../include/c++/4.4.4/bits/stl_algo.h:5468:2:
> note: in instantiation of function template specialization
>       'std::__inplace_stable_sort<char *, seqan::_LessAlignedRead<char,
> const seqan::Tag<seqan::SortReadId_> > >' requested here
>         std::__inplace_stable_sort(__first, __last, __comp);
>         ^
> /pasteur/solexa2/solexa_travail/PF2/programs/seqan/workspace/seqan/core/include/seqan/store/store_align.h:433:2:
> note: in instantiation of function template
>       specialization 'std::stable_sort<char *,
> seqan::_LessAlignedRead<char, const seqan::Tag<seqan::SortReadId_> > >'
> requested here
>         std::stable_sort(
>         ^
> /pasteur/solexa2/solexa_travail/PF2/programs/seqan/workspace/seqan/sandbox/jagla/apps/sambamstat/sambamstat.h:286:5:
> note: in instantiation of function template
>       specialization 'seqan::sortAlignedReads<seqan::Stream<Bgzf>,
> seqan::SortReadId_>' requested here
>            sortAlignedReads(reader, SortReadId());
>            ^
> /pasteur/solexa2/solexa_travail/PF2/programs/seqan/workspace/seqan/sandbox/jagla/apps/sambamstat/sambamstat.h:340:16:
> note: in instantiation of function template
>       specialization 'doWork<seqan::Stream<Bgzf>,
> seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>,
> seqan::Alloc<void> >,
>       seqan::Owner<seqan::Tag<seqan::Default_> >,
> seqan::Tag<seqan::Bam_> >' requested here
>         return doWork(bamStream, seqs, options, Bam());
>                ^
> 4 warnings and 15 errors generated.
> make[2]: ***
> [sandbox/jagla/apps/sambamstat/CMakeFiles/sambamstat.dir/sambamstat.cpp.o]
> Error 1
> make[1]: ***
> [sandbox/jagla/apps/sambamstat/CMakeFiles/sambamstat.dir/all] Error 2
> make: *** [all] Error 2
> 
> I also attach the the cpp and .h files..
> 
> Thanks for having a look at this ...
> 
> Bernd
> 
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