// -*- 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 __STARLING_INDEL_REPORT_INFO_HH
#define __STARLING_INDEL_REPORT_INFO_HH

#include "indel.hh"
#include "starling/starling_shared.hh"

#include <string>

extern const bool is_use_alt_indel;


struct starling_indel_report_info {

    starling_indel_report_info() :
        ref_repeat_count(0), indel_repeat_count(0),
        n_q30_ref_reads(0), n_q30_indel_reads(0), n_q30_alt_reads(0),
        n_other_reads(0), depth(0),
        it(INDEL::NONE) {}

    std::string desc;
    std::string ref_seq;
    std::string indel_seq;
    std::string ref_upstream;
    std::string ref_downstream;
    std::string repeat_unit;
    unsigned ref_repeat_count;
    unsigned indel_repeat_count;

    unsigned n_q30_ref_reads;
    unsigned n_q30_indel_reads;
    unsigned n_q30_alt_reads;
    unsigned n_other_reads;
    unsigned depth;

    // not directly reported, but handy to have pre-calculated:
    INDEL::index_t it;
};


// translate read path likelihoods to posterior probs
//
read_path_scores
indel_lnp_to_pprob(const starling_deriv_options& client_dopt,
                   const read_path_scores& read_path_lnp);


/// get strings for desc, indel and ref sequences that span only the
/// indel (or indel combination) and other information used to
/// summarize indel output
///
void
get_starling_indel_report_info(const starling_deriv_options& client_dopt,
                               const indel_key& ik,
                               const indel_data& id,
                               const std::string& ref_seq,
                               starling_indel_report_info& iri);

#endif