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

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

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