// -*- 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 __READ_UTIL_HH
#define __READ_UTIL_HH

#include "bam_seq.hh"


/// get the number of bases to skip off the end of the read given the
/// read on its alignment strand
///
void
get_read_align_strand_end_skip(const char* const read,
                               const unsigned read_size,
                               unsigned& end_skip);

void
get_read_fwd_strand_skip(const char* const read,
                         const unsigned read_size,
                         const bool is_fwd_strand,
                         unsigned& begin_skip,
                         unsigned& end_skip);

void
get_read_fwd_strand_skip(const bam_seq& bseq,
                         const bool is_fwd_strand,
                         unsigned& begin_skip,
                         unsigned& end_skip);

#endif