source: trunk/yat/omic/algorithm.h @ 3173

Last change on this file since 3173 was 3173, checked in by Peter, 8 years ago

a first version of BamPairIterator?. refs #784

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File size: 2.0 KB
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1#ifndef theplu_yat_omic_algorithm
2#define theplu_yat_omic_algorithm
3
4// $Id: algorithm.h 3173 2014-03-08 13:48:13Z peter $
5
6/*
7  Copyright (C) 2012, 2013 Peter Johansson
8
9  This file is part of the yat library, http://dev.thep.lu.se/yat
10
11  The yat library is free software; you can redistribute it and/or
12  modify it under the terms of the GNU General Public License as
13  published by the Free Software Foundation; either version 3 of the
14  License, or (at your option) any later version.
15
16  The yat library is distributed in the hope that it will be useful,
17  but WITHOUT ANY WARRANTY; without even the implied warranty of
18  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19  General Public License for more details.
20
21  You should have received a copy of the GNU General Public License
22  along with this program. If not, see <http://www.gnu.org/licenses/>.
23*/
24
25#include "BamPairIterator.h"
26#include "BamRead.h"
27#include "GenomicPosition.h"
28
29#include <boost/concept/assert.hpp>
30
31#include <iterator>
32#include <map>
33#include <string>
34#include <utility>
35
36namespace theplu {
37namespace yat {
38namespace omic {
39
40  /**
41     \c bam_pair_analyse performs an operation on bam read pairs as
42     defined by \a visitor. The function iterates over sorted input
43     range of reads; if read is first read, it is cached for later
44     use; if read is second read and mate is present in cache, \a
45     visitor operates on pair, i.e., \c Visitor (\c mate, \c read) is
46     called.
47
48     Type Requirements:
49     - \c Iterator must be an \input_iterator
50     - \c Iterator 's \c reference type must be convertible to BamRead
51     - \c Visitor must have an \c operator()(BamRead, BamRead) (or any
52       \c const or reference combination)
53
54     \note Input range \c [\a first, \a last \c ) must be sorted or behaviour is
55     undefined.
56
57     \since New in yat 0.10
58   */
59  template<class Iterator, class Visitor>
60  void bam_pair_analyse(Iterator first, Iterator last, Visitor& visitor)
61  {
62    BamPairIterator<Iterator> iter(first, last);
63    BamPairIterator<Iterator> end(last, last);
64    for (; iter!=end; ++iter)
65      visitor(iter->first, iter->second);
66  }
67
68}}}
69#endif
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