source: trunk/yat/omic/BamFile.cc @ 2993

Last change on this file since 2993 was 2993, checked in by Peter, 9 years ago

conform GPL header to same style as in other yat files

  • Property svn:eol-style set to native
  • Property svn:keywords set to Id
File size: 3.0 KB
Line 
1
2// $Id: BamFile.cc 2993 2013-03-03 07:38:22Z peter $
3
4/*
5  Copyright (C) 2012, 2013 Peter Johansson
6
7  This file is part of the yat library, http://dev.thep.lu.se/yat
8
9  The yat library is free software; you can redistribute it and/or
10  modify it under the terms of the GNU General Public License as
11  published by the Free Software Foundation; either version 3 of the
12  License, or (at your option) any later version.
13
14  The yat library is distributed in the hope that it will be useful,
15  but WITHOUT ANY WARRANTY; without even the implied warranty of
16  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17  General Public License for more details.
18
19  You should have received a copy of the GNU General Public License
20  along with this program. If not, see <http://www.gnu.org/licenses/>.
21*/
22
23#include <config.h>
24
25#include "BamFile.h"
26#include "BamHeader.h"
27#include "config_bam.h"
28
29#include "yat/utility/Exception.h"
30
31#include YAT_BAM_HEADER
32
33#include <stdexcept>
34#include <string>
35#include <sstream>
36
37namespace theplu {
38namespace yat {
39namespace omic {
40
41  InBamFile::InBamFile(void)
42    : super_t(), index_(NULL)
43  {}
44
45
46  InBamFile::InBamFile(const std::string& fn)
47    : super_t(), index_(NULL)
48  {
49    open(fn);
50  }
51
52
53  InBamFile::~InBamFile(void)
54  {
55    bam_index_destroy(index_);
56  }
57
58
59  const BamHeader& InBamFile::header(void) const
60  {
61    return header_;
62  }
63
64
65  const bam_index_t* InBamFile::index(void) const
66  {
67    if (!index_) {
68      index_ = bam_index_load(filename().c_str());
69      if (!index_) {
70        std::ostringstream ss;
71        ss << "cannot load bam index '" << filename() << ".bai'";
72        throw utility::runtime_error(ss.str());
73      }
74    }
75    return index_;
76  }
77
78
79  void InBamFile::open(const std::string& fn)
80  {
81    open_base(fn, "rb", NULL);
82    header_.header_ = sf_->header;
83    assert(header_.header_);
84  }
85
86
87  bool InBamFile::read(BamRead& read)
88  {
89    int result_ = samread(sf_, read.bam_);
90    if (result_<-1) {
91      std::ostringstream ss;
92      ss << "read(1): invalid bam file '" << filename() << "'";
93      if (result_ == -2)
94        ss << " truncated file";
95      else
96        ss << " error: " << result_;
97      throw utility::runtime_error(ss.str());
98    }
99    return result_>=0;
100  }
101
102
103  bool InBamFile::read(BamRead& read, bam_iter_t iter)
104  {
105    assert(sf_->type & 1); // no random access from sam files
106    int result_ = bam_iter_read(sf_->x.bam, iter, read.bam_);
107    if (result_<-1) {
108      std::ostringstream ss;
109      ss << "read(2): invalid bam file '" << filename() << "'";
110      if (result_ == -2)
111        ss << " truncated file";
112      else
113        ss << " error: " << result_;
114      throw utility::runtime_error(ss.str());
115    }
116    return result_>=0;
117  }
118
119
120  OutBamFile::OutBamFile(void)
121    : super_t() {}
122
123
124  OutBamFile::OutBamFile(const std::string& fn, const BamHeader& header)
125  {
126    open(fn, header);
127  }
128
129
130  void OutBamFile::open(const std::string& fn, const BamHeader& h)
131  {
132    open_base(fn, "wb", h.header_);
133  }
134
135
136  void OutBamFile::write(const BamRead& read)
137  {
138    if (!samwrite(sf_, read.bam_)) {
139      // FIXME if wanted perhaps we should throw an OutBamFile::error
140      // instead that can hold \a read
141      throw utility::runtime_error("OutBamFile::write failed");
142    }
143  }
144
145}}}
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