// -*- 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 __ALIGNMENT_UTIL_HH
#define __ALIGNMENT_UTIL_HH

#include "alignment.hh"

#include "blt_util/pos_range.hh"


// Provides the bounds of an alignment
//
// note that for normal indel intersection test leading/trailing
// indels will be missed if using this range
//
known_pos_range
get_strict_alignment_range(const alignment& al);

// Provides the bounds of an alignment when edge indels
// are converted to match.
//
known_pos_range
get_soft_clip_alignment_range(const alignment& al);

// Provides the bounds of an alignment when edge indels and soft clip
// are converted to match.
//
known_pos_range
get_alignment_range(const alignment& al);


// Provides the largest reasonable bounds of an alignment by
// including any leading and trailing edge sequence and requiring that
// the end of the alignment range is equal to at least the
// start+read_length:
//
known_pos_range
get_alignment_zone(const alignment& al,
                   const unsigned seq_length);

#if 0
// Shift all indels as far "to the left" as possible -- note that
// some indels may be lost. Returns true if the alignment was changed.
//
bool
normalize_alignment(alignment& al,
                    const std::string& read_seq,
                    const std::string& ref_seq);
#endif

#endif