// -*- mode: c++; indent-tabs-mode: nil; -*-
/** 
** Copyright (c) 2007-2010 Illumina, Inc. 
** 
** This software is covered by the "Illumina Genome Analyzer Software
** License Agreement" and the "Illumina Source Code License Agreement",
** and certain third party copyright/licenses, and any user of this
** source file is bound by the terms therein (see accompanying files
** Illumina_Genome_Analyzer_Software_License_Agreement.pdf and
** Illumina_Source_Code_License_Agreement.pdf and third party
** copyright/license notices).
** 
** This file is part of the Consensus Assessment of Sequence And VAriation 
** (CASAVA) software package. 
** 
** @file AssembledContig.hh
** 
** @brief An assembled contig.
** 
** @author Tony Cox, Ole Schulz-Trieglaff
**/

#ifndef ASSEMBLED_CONTIG_HH
#define ASSEMBLED_CONTIG_HH

#include<string>
#include<map>

struct AssembledContig {
    
    AssembledContig() : seedReadCount(0) {}

    // sequence
    std::string seq;
    // reads used for assembly of contig <read_no,mapping position to contig> 
    std::map<unsigned,int> contigReads;
    // no of reads containing the seeding kmer
    unsigned seedReadCount;
};

#endif