errcorr.h

//
// Created by Vadim N. on 27/10/2015.
//

#ifndef YMIR_ERRCORR_H
#define YMIR_ERRCORR_H


#include "clonotype_builder.h"
#include "aligner.h"


namespace ymir {


    // class ErrorCorrector : public VDJAlignerBase {
    // public:


    //     ErrorCorrector(const VDJRecombinationGenes &genes, const SmithWatermanAligner &swa, const SmithWatermanNoGapAligner &swnga)
    //             : _genes(genes), _swa(swa), _swnga(swnga)
    //     {

    //     }


    //     Clonotype correctAndBuild(const std::string &sequence) const {
    //         // Smith-Waterman on all alleles of V and J
    //         SmithWatermanAligner swa();
    //         // Correct indel errors basing on the max alignment
    //         // Re-align with Smith-Waterman without indels
    //         SmithWatermanNoGapAligner swnga();

    //         // Remove alignments with less than threshold of the max alignment
    //         // Build clonotype
    //     }


    // protected:

    //     VDJRecombinationGenes _genes;
    //     float _threshold;
    //     AlignmentEventScore _v_score, _d_score, _j_score;
    //     SmithWatermanAligner _swa;
    //     SmithWatermanNoGapAligner _swnga;


    //     ErrorCorrector() {}


    //     void smith_waterman(const std::string &sequence) const {

    //     }

    // };
    
}

#endif //YMIR_ERRCORR_H