[Seqan-dev] Trouble Using Custom SeedSpec

[Brett Bowman <bnbowman@gmail.com>]

The algorithm I'm trying to implement with SeqAn (1.4.1) uses log-probabilities as scores, so I need to customize the Seed<> to change the default ScoreValue type:

(Following the docs here: http://docs.seqan.de/seqan/1.4.2-dox/?p=SimpleSeed)

"""

// Declare our Seed Config and associated Seed type

struct SeedConfig

{

    typedef size_t TPosition;

    typedef MakeSigned_<size_t>::Type TDiagonal;

    typedef size_t TSize;

    typedef float TScoreValue;   // Changed to Float to be compatible with existing scoring scheme

};

typedef Seed<Simple, SeedConfig> TSeed;

typedef SeedSet<SeedConfig> TSeedSet;

"""

But when I try to add seeds to my SeedSet, 

"""

TSeed seed = TSeed(queryPos, refPos, 12);

float score = 15.5;

setScore(seed, score);

std::cout << seed << " " << seqan::score(seed) << " " << score << std::endl;

 

if (!addSeed(seeds, seed, 0, Merge()))

{

     addSeed(seeds, seed, Single());

}

"""

I get the following error no matter what I try:

"""

/home/bbowman/git/SRSLI/src/C++/SparseAlignment.hpp:220:18: error: no matching function for call to 'addSeed'

            if (!addSeed(seeds, seed, 0, Merge()))

                 ^~~~~~~

/usr/include/seqan/seeds/seeds_seed_set_unordered.h:361:1: note: candidate function [with TSeedSpec = SeedConfig, TDistanceThreshold = int] not viable: no known conversion from

      'Seed<Simple, struct SeedConfig>' to 'const Seed<struct SeedConfig, (default) struct seqan::DefaultSeedConfig>' for 2nd argument

addSeed(SeedSet<TSeedSpec, Unordered> & seedSet,

"""

What am I missing?

Sincerely,

Brett