1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
|
// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
//
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted (subject to the limitations in the
// disclaimer below) provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
//
// * Neither the name of Pacific Biosciences nor the names of its
// contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
// SUCH DAMAGE.
// Author: Derek Barnett
#ifndef MEMORYUTILS_H
#define MEMORYUTILS_H
#include "pbbam/Config.h"
#include "pbbam/BamHeader.h"
#include "pbbam/BamRecord.h"
#include "pbbam/BamRecordImpl.h"
#include <htslib/bgzf.h>
#include <htslib/sam.h>
#include <memory>
namespace PacBio {
namespace BAM {
class BamHeader;
namespace internal {
// intended for use with PBBAM_SHARED_PTR<T>, std::unique_ptr<T>, etc
struct HtslibBgzfDeleter
{
void operator()(BGZF* bgzf)
{
if (bgzf)
bgzf_close(bgzf);
bgzf = nullptr;
}
};
struct HtslibFileDeleter
{
void operator()(samFile* file)
{
if (file)
sam_close(file);
file = nullptr;
}
};
struct HtslibHeaderDeleter
{
void operator()(bam_hdr_t* hdr)
{
if (hdr)
bam_hdr_destroy(hdr);
hdr = nullptr;
}
};
struct HtslibIndexDeleter
{
void operator()(hts_idx_t* index)
{
if (index)
hts_idx_destroy(index);
index = nullptr;
}
};
struct HtslibIteratorDeleter
{
void operator()(hts_itr_t* iter)
{
if (iter)
hts_itr_destroy(iter);
iter = nullptr;
}
};
struct HtslibRecordDeleter
{
void operator()(bam1_t* b)
{
if (b)
bam_destroy1(b);
b = nullptr;
}
};
class BamHeaderMemory
{
public:
static BamHeader FromRawData(bam_hdr_t* header);
static PBBAM_SHARED_PTR<bam_hdr_t> MakeRawHeader(const BamHeader& header);
// static PBBAM_SHARED_PTR<bam_hdr_t> MakeRawHeader(const BamHeader& header);
};
class BamRecordMemory
{
public:
static const BamRecordImpl& GetImpl(const BamRecord& r);
static const BamRecordImpl& GetImpl(const BamRecord* r);
static PBBAM_SHARED_PTR<bam1_t> GetRawData(const BamRecord& r);
static PBBAM_SHARED_PTR<bam1_t> GetRawData(const BamRecord* r);
static PBBAM_SHARED_PTR<bam1_t> GetRawData(const BamRecordImpl& impl);
static PBBAM_SHARED_PTR<bam1_t> GetRawData(const BamRecordImpl* impl);
static void UpdateRecordTags(const BamRecord& r);
static void UpdateRecordTags(const BamRecordImpl& r);
};
inline const BamRecordImpl& BamRecordMemory::GetImpl(const BamRecord& r)
{ return r.impl_; }
inline const BamRecordImpl& BamRecordMemory::GetImpl(const BamRecord* r)
{ return r->impl_; }
inline PBBAM_SHARED_PTR<bam1_t> BamRecordMemory::GetRawData(const BamRecord& r)
{ return GetRawData(r.impl_); }
inline PBBAM_SHARED_PTR<bam1_t> BamRecordMemory::GetRawData(const BamRecord* r)
{ return GetRawData(r->impl_); }
inline PBBAM_SHARED_PTR<bam1_t> BamRecordMemory::GetRawData(const BamRecordImpl& impl)
{ return impl.d_; }
inline PBBAM_SHARED_PTR<bam1_t> BamRecordMemory::GetRawData(const BamRecordImpl* impl)
{ return impl->d_; }
inline void BamRecordMemory::UpdateRecordTags(const BamRecord& r)
{ UpdateRecordTags(r.impl_); }
inline void BamRecordMemory::UpdateRecordTags(const BamRecordImpl& r)
{ r.UpdateTagMap(); }
} // namespace internal
} // namespace BAM
} // namespace PacBio
#endif // MEMORYUTILS_H
|
