// -*- 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_CALL_PPROB_DIGT_HH
#define __STARLING_INDEL_CALL_PPROB_DIGT_HH

#include "indel.hh"
#include "starling_diploid_indel.hh"
#include "starling_indel_report_info.hh"

#include "starling/starling_shared.hh"

#include <iosfwd>


// \brief call an indel @ pos by calculating the posterior probability
/// of all possible genotypes for a diploid individual.
///
void
starling_indel_call_pprob_digt(const starling_options& client_opt,
                               const starling_deriv_options& client_dopt,
                               const double indel_error_prob,
                               const double ref_error_prob,
                               const indel_key& ik,
                               const indel_data& id,
                               starling_diploid_indel& dindel);


// debuging output -- produces labels
//
void
write_starling_diploid_indel(const starling_diploid_indel& dgt,
                             const starling_indel_report_info& iri,
                             std::ostream& os);

// file output -- data only
//
void
write_starling_diploid_indel_file(const starling_diploid_indel& dgt,
                                  const starling_indel_report_info& iri,
                                  std::ostream& os);

#endif