// -*- mode: c++; indent-tabs-mode: nil; -*-
//
// Copyright 2009 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).
//
//

/// \file
///
/// \author Chris Saunders
///

#ifndef __POS_BASECALL_BUFFER_HH
#define __POS_BASECALL_BUFFER_HH

#include "blt_common/snp_pos_info.hh"
#include "blt_util/blt_types.hh"

#include <iosfwd>
#include <map>
#include <string>


struct pos_basecall_buffer {

    pos_basecall_buffer(const std::string& ref_seq) : _ref_seq(ref_seq) {}

    void
    insert_pos_basecall(const pos_t pos,
                        const base_call& bc){
        _pdata[pos].calls.push_back(bc);
    }

    // returns NULL for empty pos
    //
    snp_pos_info*
    get_pos(const pos_t pos) {
        const piter i(_pdata.find(pos));
        if(i==_pdata.end()) return NULL;
        return &(i->second);
    }

    void
    clear_pos(const pos_t pos) {
        const piter i(_pdata.find(pos));
        if(i!=_pdata.end()) _pdata.erase(i);
    }

#if 0
    iterator pos_iter(const pos_t pos) {
        return _pdata.lower_bound(pos);
    }
    const_iterator pos_iter(const pos_t pos) const {
        return _pdata.lower_bound(pos);
    }

    // debug dumpers:
    void
    dump_pos(const pos_t pos, std::ostream& os) const;

    void
    dump(std::ostream& os) const;
#endif

private:
    typedef std::map<pos_t,snp_pos_info> pdata_t;
    typedef pdata_t::iterator piter;
    typedef pdata_t::const_iterator pciter;

    const std::string& _ref_seq;
    pdata_t _pdata;
};


#endif