source: branches/0.10-stable/yat/omic/BamReadIterator.h @ 3014

Last change on this file since 3014 was 3014, checked in by Peter, 8 years ago

update copyright years

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1#ifndef theplu_yat_omic_bam_read_iterator
2#define theplu_yat_omic_bam_read_iterator
3
4// $Id: BamReadIterator.h 3014 2013-04-04 02:43:32Z peter $
5//
6// Copyright (C) 2012, 2013 Peter Johansson
7//
8// This program is free software; you can redistribute it and/or modify
9// it under the terms of the GNU General Public License as published by
10// the Free Software Foundation; either version 3 of the License, or
11// (at your option) any later version.
12//
13// This program is distributed in the hope that it will be useful, but
14// WITHOUT ANY WARRANTY; without even the implied warranty of
15// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
16// General Public License for more details.
17//
18// You should have received a copy of the GNU General Public License
19// along with this program. If not, see <http://www.gnu.org/licenses/>.
20
21#include "BamFile.h"
22#include "BamRead.h"
23#include "config_bam.h"
24
25#include YAT_SAM_HEADER
26
27#include <boost/iterator/iterator_facade.hpp>
28#include <boost/shared_ptr.hpp>
29
30#include <iterator>
31
32namespace theplu {
33namespace yat {
34namespace omic {
35
36  // forward declaration
37  class InBamFile;
38
39  /**
40     \brief class to iterate through a InBamFile
41
42     Iterator is a single pass \input_iterator which means iterator
43     can only be used read bam file. If creating two iterators working
44     on the same InBamFile, the iterators are not independent of each
45     other. Incrementing one, the behaviour of the other is undefined.
46
47     Iterator can either be constructed to iterate over entire bam
48     file or if a region is specified only over that region. When no
49     more elements are available, iterator turns into a end-of-file
50     iterator and is no longer dereferencable.
51
52     \see InBamFile
53
54     \since New in yat 0.10
55   */
56  class BamReadIterator
57    : public boost::iterator_facade<
58    BamReadIterator, const BamRead, std::input_iterator_tag
59    >
60  {
61  public:
62    /**
63       \brief Contructs end of file iterator.
64     */
65    BamReadIterator(void);
66
67    /**
68       Creates an iterator pointing to first BamRead in
69       InBamFile.
70
71       \param in file to iterate over
72     */
73    explicit BamReadIterator(InBamFile& in);
74
75    /**
76       Iterator that walks over specified region. Iterator iterates
77       over all BamReads in file \a in that overlap with specified
78       region and then it turns into an end-of-region iterator.
79
80       This function requires an index file is available, see
81       InBamFile::index().
82
83       All reads iterated over overlap with defined region, in other
84       words, iter->tid == \a tid; iter->pos() < \a end and iter->end()
85       > start
86
87       \param in file to iterate over
88       \param tid segment (chromosome) to iterate over
89       \param start left most position of specified region
90       \param end right most position of specified region
91     */
92    BamReadIterator(InBamFile& in, int32_t tid, int32_t start, int32_t end);
93  private:
94    friend class boost::iterator_core_access;
95    BamReadIterator::reference dereference(void) const;
96    bool equal(const BamReadIterator& other) const;
97    void increment(void);
98
99    /*
100       Interface class for the actor that handles difference between
101       an iterator that iterates the entire file and one that uses
102       index to iterate over a specific region.
103     */
104    class Actor
105    {
106    public:
107      explicit Actor(InBamFile*);
108      virtual ~Actor(void);
109      virtual void increment(void)=0;
110      InBamFile* in_;
111      BamRead read_;
112    };
113
114    // class used when region is entire file
115    class AllActor : public Actor
116    {
117    public:
118      AllActor(void);
119      explicit AllActor(InBamFile&);
120      void increment(void);
121    };
122
123    // class used when iterating over a sub-region of the bam file
124    class IndexActor : public Actor
125    {
126    public:
127      IndexActor(InBamFile& bf, int32_t tid, int32_t begin, int32_t end);
128      void increment(void);
129    private:
130      boost::shared_ptr<__bam_iter_t> iter_;
131    };
132
133    boost::shared_ptr<Actor> actor_;
134
135    struct IndexDestroyer
136    {
137      void operator()(bam_iter_t i) const
138      {
139        bam_iter_destroy(i);
140      }
141    };
142  };
143}}}
144#endif
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