source: trunk/yat/omic/algorithm.h @ 3175

#ifndef theplu_yat_omic_algorithm
#define theplu_yat_omic_algorithm

// $Id: algorithm.h 3175 2014-03-15 08:15:51Z peter $

/*
  Copyright (C) 2012, 2013 Peter Johansson

  This file is part of the yat library, http://dev.thep.lu.se/yat

  The yat library is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License as
  published by the Free Software Foundation; either version 3 of the
  License, or (at your option) any later version.

  The yat library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  General Public License for more details.

  You should have received a copy of the GNU General Public License
  along with this program. If not, see <http://www.gnu.org/licenses/>.
*/

#include "BamPairIterator.h"
#include "BamRead.h"
#include "GenomicPosition.h"

#include <boost/concept/assert.hpp>

#include <iterator>
#include <map>
#include <string>
#include <utility>

namespace theplu {
namespace yat {
namespace omic {

  /**
     \c bam_pair_analyse performs an operation on bam read pairs as
     defined by \a visitor. The function iterates over sorted input
     range of reads; if read is first read, it is cached for later
     use; if read is second read and mate is present in cache, \a
     visitor operates on pair, i.e., \c Visitor (\c mate, \c read) is
     called.

     Type Requirements:
     - \c Iterator must be an \input_iterator
     - \c Iterator 's \c reference type must be convertible to BamRead
     - \c Visitor must have an \c operator()(BamRead, BamRead) (or any
       \c const or reference combination)

     \note Input range \c [\a first, \a last \c ) must be sorted or behaviour is
     undefined.

     \since New in yat 0.10
   */
  template<class Iterator, class Visitor>
  void bam_pair_analyse(Iterator first, Iterator last, Visitor& visitor)
  {
    BamPairIterator<Iterator> iter(first, last);
    BamPairIterator<Iterator> end(last, last);
    for (; iter!=end; ++iter)
      visitor(iter->first(), iter->second());
  }

}}}
#endif