Read.h

//	Metal - A fast methylation alignment and calling tool for WGBS data.
//	Copyright (C) 2017  Jonas Fischer
//
//	This program is free software: you can redistribute it and/or modify
//	it under the terms of the GNU General Public License as published by
//	the Free Software Foundation, either version 3 of the License, or
//	(at your option) any later version.
//
//	This program is distributed in the hope that it will be useful,
//	but WITHOUT ANY WARRANTY; without even the implied warranty of
//	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
//	GNU General Public License for more details.
//
//	You should have received a copy of the GNU General Public License
//	along with this program.  If not, see <http://www.gnu.org/licenses/>.
//
//	Jonas Fischer	jonaspost@web.de

#ifndef READ_H
#define READ_H

#include <string>
#include <fstream>
#include <vector>

#include "structs.h"

class Read
{

    public:

        // ---- Ctors ----
        //
        Read();
        Read(std::string& seq, std::string& id);

        // ---------------

        // print the matching info of this read to ofs
        // FORMAT:
        //      Chromosome\tPosition\tKmerOverlap\tReadSeq\n*
        //      , where
        //      Chromosome is the index of the chromosome
        //      Position is the 0 based offset in the chromosome
        //      KmerOverlap is the number of kmers that match the position
        //          (up to ReadSize - MyConst::KMERLEN + 1)
        //      ReadSeq is the sequence of the read
        //
        //      done for each match
        //
        void printMatch(std::ofstream& ofs);


        // print the matching info to ofs in SAM format
        void printMatchSam(std::ofstream& ofs);

        std::string id;

        // (DNA) sequence of the read
        std::string seq;

        // The matching positions of the read
        MATCH::match mat;

        // flag stating if read has an N in sequence or is too small (< Kmerlength)
        // OR maps to multiple locations in the genome
        // if this is the case, it won't be processed
        bool isInvalid;

};

#endif /* READ_H */