[Seqan-dev] Two Alignment Questions

[Brett Bowman <bnbowman@gmail.com>]

1)  Is there an easy way to get the accuracy of an Alignment object, or is that something I need to calculate myself?

2)  bandedChainAlignment fails messily when given a Vector of Seeds instead of a String, where as other functions work fine (e.g. chainSeedsGlobally).  Why does it work for the one and not the other?  Excerpt from error message below.

"""

/usr/include/seqan/seeds/banded_chain_alignment_impl.h:1195:57: error: call to 'end' is ambiguous

    SEQAN_ASSERT(itEnd != static_cast<TSeedSetIterator>(end(seedSet)));

                                                        ^~~

/usr/include/seqan/basic/debug_test_system.h:2146:44: note: expanded from macro 'SEQAN_ASSERT'

                                          (_arg1), # _arg1)) {           \

                                           ^

/usr/include/seqan/seeds/banded_chain_alignment_profile.h:254:16: note: in instantiation of function template specialization

...

/usr/include/seqan/seeds/banded_chain_alignment.h:207:12: note: in instantiation of function template specialization

      'seqan::bandedChainAlignment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<void> >, seqan::Tag<seqan::ArrayGaps_>,

      std::vector<seqan::Seed<seqan::Tag<seqan::Simple_>, seqan::DefaultSeedConfig>, std::allocator<seqan::Seed<seqan::Tag<seqan::Simple_>, seqan::DefaultSeedConfig> > >, long,

      seqan::Tag<seqan::Simple_>, seqan::Tag<seqan::Simple_>, false, false, false, false, seqan::Tag<seqan::Default_> >' requested here

    return bandedChainAlignment(align, seedSet, scoreScheme, scoreScheme, alignConfig, bandExtension);

           ^

/home/bbowman/git/SRSLI/src/C++/SparseAlignment2.cpp:72:25: note: in instantiation of function template specialization

      'seqan::bandedChainAlignment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<void> >, seqan::Tag<seqan::ArrayGaps_>,

      std::vector<seqan::Seed<seqan::Tag<seqan::Simple_>, seqan::DefaultSeedConfig>, std::allocator<seqan::Seed<seqan::Tag<seqan::Simple_>, seqan::DefaultSeedConfig> > >, long,

      seqan::Tag<seqan::Simple_>, false, false, false, false, seqan::Tag<seqan::Default_> >' requested here

        long alnScore = bandedChainAlignment(alignment, *seedChain, scoring, globalConfig);

                        ^

/home/bbowman/git/SRSLI/src/C++/main.cpp:95:27: note: in instantiation of function template specialization 'RefChainsToAlignments<seqan::AlignConfig<false, true, true, false,

      seqan::Tag<seqan::Default_> > ()>' requested here

        auto alignments = RefChainsToAlignments(record->Seq,

                          ^

/usr/include/seqan/seeds/banded_chain_alignment_impl.h:583:1: note: candidate template ignored: substitution failure [with TSeedSet = std::vector<seqan::Seed<seqan::Tag<seqan::Simple_>,

      seqan::DefaultSeedConfig>, std::allocator<seqan::Seed<seqan::Tag<seqan::Simple_>, seqan::DefaultSeedConfig> > >]

_findFirstAnchor(TSeedSet const & seedSet, int bandExtension)

""" 

Sincerely,

-Brett