// -*- 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
///

#include "blt_common/blt_shared.hh"

#include "blt_util/log.hh"

#include <cstdlib>

#include <iomanip>
#include <iostream>


const char STDIN_FILENAME[] = "-";


const int DEFAULT_MIN_QSCORE(0);
const int DEFAULT_MIN_SINGLE_ALIGN_SCORE(10);
const int DEFAULT_MIN_PAIRED_ALIGN_SCORE(6);
const double DEFAULT_BACON_CALL_THRESH(10);
const double DEFAULT_BACON_HET_SNP_RATIO_THRESH(3);

// arbitrary... but things will be a total mess if not capped somewhere:
const unsigned MAX_FLANK_SIZE(50);



static
pos_range
get_report_range_limit(const pos_range& report_range,
                       const bool is_ref_set,
                       const pos_t ref_size){

    pos_range rrl;

    rrl.set_begin_pos((report_range.is_begin_pos ? report_range.begin_pos : 0));
    rrl.is_end_pos = (report_range.is_end_pos or is_ref_set);
    rrl.end_pos = (report_range.is_end_pos ? 
                   report_range.end_pos : 
                   (is_ref_set ? ref_size : 0));
    return rrl;
}



void
get_blt_deriv_options(const blt_options& client_opt,
                      const pos_t ref_size,
                      blt_deriv_options& client_dopt){

    client_dopt.report_range_limit=get_report_range_limit(client_opt.report_range,
                                                          client_opt.is_ref_set,
                                                          ref_size);
}



void
blt_read_counts::
report(std::ostream& os) const {
    os << "READ_COUNTS used: " << used
       << " align-score-filter: " << align_score_filter
       << " large-ref-deletion: " << large_ref_deletion
       << " unmapped: " << unmapped
       << " duplicate: " << duplicate
       << " primary-analysis-filter: " << primary_filter
       << " subsample-filter: " << subsample_filter << "\n";
}