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
|
/*
* Copyright (C) 2010 Regents of the University of Michigan
*
* This program 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.
*
* This program 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/>.
*/
#ifndef __SAM_FLAG_H__
#define __SAM_FLAG_H__
#include <stdint.h>
#ifdef DUPLICATE
#undef DUPLICATE
#endif
/// Class for extracting information from a SAM Flag.
class SamFlag
{
public:
///////////////////////
/// @name Constants for parsing a flag.
//@{
static const int16_t PAIRED = 0x0001;
static const int16_t PROPER_PAIR = 0x0002;
static const int16_t UNMAPPED = 0x0004;
static const int16_t MATE_UNMAPPED = 0x0008;
static const int16_t REVERSE = 0x0010;
static const int16_t MATE_REVERSED = 0x0020;
static const int16_t FIRST_READ = 0x0040;
static const int16_t SECOND_READ = 0x0080;
static const int16_t SECONDARY_ALIGNMENT = 0x0100;
static const int16_t FAILED_QUALITY = 0x0200;
static const int16_t DUPLICATE = 0x0400;
static const int16_t SUPPLEMENTARY_ALIGNMENT = 0x0800;
static const int16_t FRAGMENT_INFO = 0x00C0;
static const int16_t FRAGMENT_SHIFT = 6;
//@}
///////////////////////
/// @name Static methods for determining the contents of a flag.
//@{
static inline bool isMapped(uint16_t flag) {return(!(flag & UNMAPPED));}
static inline bool isMateMapped(uint16_t flag) {return(!(flag & MATE_UNMAPPED));}
static inline bool isPaired(uint16_t flag) {return(flag & PAIRED);}
static inline bool isReverse(uint16_t flag) {return(flag & REVERSE);}
static inline bool isMateReverse(uint16_t flag) {return(flag & MATE_REVERSED);}
static inline bool isProperPair(uint16_t flag)
{
// Proper pair is only applicable if also paired.
return(isPaired(flag) && (flag & PROPER_PAIR));
}
static inline bool isDuplicate(uint16_t flag) {return(flag & DUPLICATE);}
static inline bool isQCFailure(uint16_t flag) {return(flag & FAILED_QUALITY);}
static inline bool isSecondary(uint16_t flag) {return(flag & SECONDARY_ALIGNMENT);}
/// Return if it is the first fragment or not
/// (if FIRST_READ is set and SECOND_READ is not).
static inline bool isFirstFragment(uint16_t flag)
{
// first fragment if FIRST_READ is set and SECOND_READ is not.
return((flag & FIRST_READ) && !(flag & SECOND_READ));
}
/// Return if it is the last fragment or not
/// (if FIRST_READ is not set and SECOND_READ is).
static inline bool isLastFragment(uint16_t flag)
{
// last fragment if FIRST_READ is not set and SECOND_READ is set.
return(!(flag & FIRST_READ) && (flag & SECOND_READ));
}
/// Return if it is a middle fragment or not
/// (if FIRST_READ is set and SECOND_READ is also set).
static inline bool isMidFragment(uint16_t flag)
{
// mid fragment if both FIRST_READ and SECOND_READ are set.
return((flag & FIRST_READ) && (flag & SECOND_READ));
}
/// Return if it is an unknown fragment fragment or not
/// (if FIRST_READ is not set and SECOND_READ is also not set).
static inline bool isUnknownFragment(uint16_t flag)
{
// unknown fragment index if neither FIRST_READ nor SECOND_READ are not.
return(!(flag & FIRST_READ) && !(flag & SECOND_READ));
}
static inline uint8_t getFragmentType(uint16_t flag)
{
return((flag & FRAGMENT_INFO) >> FRAGMENT_SHIFT);
}
/// Mark the passed in flag as unmapped.
static inline void setUnmapped(uint16_t& flag) { flag |= UNMAPPED;}
/// Mark the passed in flag as not duplicate.
static inline void setNotDuplicate(uint16_t& flag) { flag ^= DUPLICATE;}
/// Mark the passed in flag as not duplicate.
static inline void setDuplicate(uint16_t& flag) { flag |= DUPLICATE;}
//@}
private:
SamFlag();
};
#endif
|
