// -*- 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 __SNP_POS_INFO_HH
#define __SNP_POS_INFO_HH

#include "blt_util/qscore.hh"
#include "blt_util/seq_util.hh"

#include "stdint.h"

#include <iosfwd>
#include <vector>

//#define BC_DEBUG



struct base_call {
    base_call(const uint8_t init_base_id,
              const uint8_t init_qscore,
              const bool init_ifs,
#ifdef BC_DEBUG
              const unsigned init_read_pos,
              const unsigned init_read_pos,
#else
              const unsigned,
              const unsigned,
#endif
              const bool init_is_call_filter,
              const bool init_is_neighbor_mismatch)
        : qscore(init_qscore),
#ifdef BC_DEBUG
          read_pos(init_read_pos), read_size(init_read_size),
#endif
          base_id(init_base_id),
          is_fwd_strand(init_ifs),
          is_neighbor_mismatch(init_is_neighbor_mismatch),
          is_call_filter(init_is_call_filter) {}
    
    double
    error_prob() const {
        return qphred_to_error_prob(static_cast<int>(qscore));
    }

    uint16_t qscore:8;
    uint16_t base_id:4;
    uint16_t is_fwd_strand:1;
    uint16_t is_neighbor_mismatch:1;
    uint16_t is_call_filter:1; // filtered from snp-calling
#ifdef BC_DEBUG
    uint16_t read_pos; // zero-indexed cycle number
    uint16_t read_size;
#endif
};

std::ostream& operator<<(std::ostream& os,const base_call& bc);


struct snp_pos_info {

    snp_pos_info() { clear(); }

    void
    clear() {
        ref_base='N';
        calls.clear();
        is_n_ref_warn=false;
    }

    char ref_base; // always fwd-strand base
    bool is_n_ref_warn;
    std::vector<base_call> calls;
};

std::ostream& operator<<(std::ostream& os,const snp_pos_info& pci);


#endif