// -*- 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_READ_ALIGN_SCORE_INDELS_HH
#define __STARLING_READ_ALIGN_SCORE_INDELS_HH


#include "depth_buffer.hh"
#include "indel_buffer.hh"
#include "starling_read_align_shared.hh"
#include "starling_read_segment.hh"
#include "starling/starling_shared.hh"

#include <set>
#include <vector>


typedef indel_buffer::iterator iiter;
typedef indel_buffer::const_iterator ciiter;

typedef std::map<indel_key,bool> indel_status_map_t;


// use the most likely alignment for each indel state for every indel
// in indel_status_map to generate data needed in indel calling:
//
void
score_indels(const starling_options& client_opt,
             const depth_buffer& db,
             const read_segment& rseg,
             indel_buffer& ibuff,
             const std::set<candidate_alignment>& cal_set,
             const bool is_incomplete_search,
             const std::vector<double>& cal_set_path_lnp,
             double max_path_lnp,
             const candidate_alignment* max_cal_ptr);

#endif