// -*- 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_HH
#define __STARLING_READ_ALIGN_SCORE_HH

#include "indel_buffer.hh"
#include "starling_read.hh"
#include "starling_read_align_shared.hh"
#include "starling/starling_shared.hh"

#include <string>


double
score_candidate_alignment(const starling_options& client_opt,
                          const indel_buffer& ibuff,
                          const read_segment& rseg,
                          const candidate_alignment& cal,
                          const std::string& ref_seq);

#endif