// -*- 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_UTIL_HH
#define __STARLING_READ_UTIL_HH

#include "alignment.hh"

#include "blt_common/blt_shared.hh"
#include "blt_util/bam_seq.hh"
#include "blt_util/blt_types.hh"
#include "blt_util/export_line_parser.hh"

#include <string>


// provide a key from the export line which follows the pattern used
// in export->SAM/BAM conversion
//
void
get_read_key_from_export_line(const export_line_parser& exl,
                              std::string& key);

// the position used to buffer alignments allows for the possibility that
// any leading soft-clip or insert sequence could really align to the reference:
//
pos_t
get_alignment_buffer_pos(const alignment& al);


#if 0
void
create_mismatch_filter_map(const blt_options& client_opt,
                           const alignment& al,
                           const std::string& ref_seq,
                           const std::string& read_seq,
                           const unsigned read_begin,
                           const unsigned read_end,
                           bool* mismatch_filter_map,
                           int* mismatch_count_ns);
#endif

void
create_mismatch_filter_map(const blt_options& client_opt,
                           const alignment& al,
                           const bam_seq_base& ref_seq,
                           const bam_seq_base& read_seq,
                           const unsigned read_begin,
                           const unsigned read_end,
                           bool* mismatch_filter_map,
                           int* mismatch_count_ns);
#endif