[Seqan-dev] Trouble Hashing Kmers into Qgram Index

[Brett Bowman <bnbowman@gmail.com>]

Sorry to be a bother, but I decided to go back to the docs and start fresh and I'm still having issues.  

We're using Qgrams, so I trying to write a simple loop to search for all 12mers from a query sequence "seq" in the index formed from a StringSet of references "refSeq", building on the example code in the Q-Gram Index tutorial:

"""

  TFinder qgramFinder(index);

 for (size_t i = 0; i < length(seq)-12; i++)

 {

     TInfix::Type kmer = infix(seq, i, i+12);

     std::cout << kmer << std::endl;

     seqan::hash(indexShape(index), kmer);

     for (unsigned i = 0; i < length(getOccurrences(index, indexShape(index))); ++i)

     {

         std::cout << getOccurrences(index, indexShape(index))[i] << std::endl;

     }

     std::cout << std::endl;

 }

"""

but I'm getting a fairly obtuse error message I don't quite understand, and doesn't point me back to any specific lines in my code.

"""

/usr/include/seqan/index/shape_base.h:535:55: error: indirection requires pointer operand ('seqan::Segment<const seqan::String<seqan::SimpleType<unsigned

      char, seqan::Dna5_>, seqan::Alloc<void> >, seqan::InfixSegment>' invalid)

                        hash * ValueSize<TValue>::VALUE + ordValue((TValue)*it),

                                                                           ^~~

/usr/include/seqan/index/shape_base.h:548:22: note: in instantiation of function template specialization 'seqan::_hashFixedShape<unsigned long,

      seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Segment<const seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<void> >,

      seqan::InfixSegment>, 12>' requested here

                return me.hValue = _hashFixedShape(me.hValue, it, TValue(), UngappedShape<q>());

                                   ^

/home/bbowman/git/SRSLI/src/C++/SparseAlignment.hpp:102:16: note: in instantiation of function template specialization 'seqan::hash<seqan::SimpleType<unsigned

      char, seqan::Dna5_>, 12, seqan::Segment<const seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<void> >, seqan::InfixSegment>

      >' requested here

        seqan::hash(indexShape(index), kmer);

               ^

/home/bbowman/git/SRSLI/src/C++/main.cpp:86:9: note: in instantiation of function template specialization 'FindSeeds2<FindSeedsConfig<12,

      seqan::UngappedShape<12>, seqan::IndexQGram<seqan::UngappedShape<12>, seqan::Tag<seqan::Default_> > > >' requested here

        FindSeeds2(querySeedHits, refSetIndex, idxAndRecord.second.Seq);

"""

Suggestions?

Sincerely,

Brett