libStatGen Software  1
SamFlag.h
1 /*
2  * Copyright (C) 2010 Regents of the University of Michigan
3  *
4  * This program is free software: you can redistribute it and/or modify
5  * it under the terms of the GNU General Public License as published by
6  * the Free Software Foundation, either version 3 of the License, or
7  * (at your option) any later version.
8  *
9  * This program is distributed in the hope that it will be useful,
10  * but WITHOUT ANY WARRANTY; without even the implied warranty of
11  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
12  * GNU General Public License for more details.
13  *
14  * You should have received a copy of the GNU General Public License
15  * along with this program. If not, see <http://www.gnu.org/licenses/>.
16  */
17 
18 #ifndef __SAM_FLAG_H__
19 #define __SAM_FLAG_H__
20 
21 #include <stdint.h>
22 
23 #ifdef DUPLICATE
24 #undef DUPLICATE
25 #endif
26 
27 /// Class for extracting information from a SAM Flag.
28 class SamFlag
29 {
30 public:
31  ///////////////////////
32  /// @name Constants for parsing a flag.
33  //@{
34  static const int16_t PAIRED = 0x0001;
35  static const int16_t PROPER_PAIR = 0x0002;
36  static const int16_t UNMAPPED = 0x0004;
37  static const int16_t MATE_UNMAPPED = 0x0008;
38  static const int16_t REVERSE = 0x0010;
39  static const int16_t MATE_REVERSED = 0x0020;
40  static const int16_t FIRST_READ = 0x0040;
41  static const int16_t SECOND_READ = 0x0080;
42  static const int16_t SECONDARY_ALIGNMENT = 0x0100;
43  static const int16_t FAILED_QUALITY = 0x0200;
44  static const int16_t DUPLICATE = 0x0400;
45  static const int16_t SUPPLEMENTARY_ALIGNMENT = 0x0800;
46  static const int16_t FRAGMENT_INFO = 0x00C0;
47  static const int16_t FRAGMENT_SHIFT = 6;
48  //@}
49 
50  ///////////////////////
51  /// @name Static methods for determining the contents of a flag.
52  //@{
53  static inline bool isMapped(uint16_t flag) {return(!(flag & UNMAPPED));}
54  static inline bool isMateMapped(uint16_t flag) {return(!(flag & MATE_UNMAPPED));}
55 
56  static inline bool isPaired(uint16_t flag) {return(flag & PAIRED);}
57  static inline bool isReverse(uint16_t flag) {return(flag & REVERSE);}
58  static inline bool isMateReverse(uint16_t flag) {return(flag & MATE_REVERSED);}
59  static inline bool isProperPair(uint16_t flag)
60  {
61  // Proper pair is only applicable if also paired.
62  return(isPaired(flag) && (flag & PROPER_PAIR));
63  }
64  static inline bool isDuplicate(uint16_t flag) {return(flag & DUPLICATE);}
65  static inline bool isQCFailure(uint16_t flag) {return(flag & FAILED_QUALITY);}
66 
67  static inline bool isSecondary(uint16_t flag) {return(flag & SECONDARY_ALIGNMENT);}
68 
69  /// Return if it is the first fragment or not
70  /// (if FIRST_READ is set and SECOND_READ is not).
71  static inline bool isFirstFragment(uint16_t flag)
72  {
73  // first fragment if FIRST_READ is set and SECOND_READ is not.
74  return((flag & FIRST_READ) && !(flag & SECOND_READ));
75  }
76  /// Return if it is the last fragment or not
77  /// (if FIRST_READ is not set and SECOND_READ is).
78  static inline bool isLastFragment(uint16_t flag)
79  {
80  // last fragment if FIRST_READ is not set and SECOND_READ is set.
81  return(!(flag & FIRST_READ) && (flag & SECOND_READ));
82  }
83  /// Return if it is a middle fragment or not
84  /// (if FIRST_READ is set and SECOND_READ is also set).
85  static inline bool isMidFragment(uint16_t flag)
86  {
87  // mid fragment if both FIRST_READ and SECOND_READ are set.
88  return((flag & FIRST_READ) && (flag & SECOND_READ));
89  }
90  /// Return if it is an unknown fragment fragment or not
91  /// (if FIRST_READ is not set and SECOND_READ is also not set).
92  static inline bool isUnknownFragment(uint16_t flag)
93  {
94  // unknown fragment index if neither FIRST_READ nor SECOND_READ are not.
95  return(!(flag & FIRST_READ) && !(flag & SECOND_READ));
96  }
97 
98  static inline uint8_t getFragmentType(uint16_t flag)
99  {
100  return((flag & FRAGMENT_INFO) >> FRAGMENT_SHIFT);
101  }
102 
103  /// Mark the passed in flag as unmapped.
104  static inline void setUnmapped(uint16_t& flag) { flag |= UNMAPPED;}
105  /// Mark the passed in flag as not duplicate.
106  static inline void setNotDuplicate(uint16_t& flag) { flag ^= DUPLICATE;}
107  /// Mark the passed in flag as not duplicate.
108  static inline void setDuplicate(uint16_t& flag) { flag |= DUPLICATE;}
109  //@}
110 
111 private:
112  SamFlag();
113 };
114 
115 
116 #endif
SamFlag::setNotDuplicate
static void setNotDuplicate(uint16_t &flag)
Mark the passed in flag as not duplicate.
Definition: SamFlag.h:106
SamFlag::setDuplicate
static void setDuplicate(uint16_t &flag)
Mark the passed in flag as not duplicate.
Definition: SamFlag.h:108
SamFlag::setUnmapped
static void setUnmapped(uint16_t &flag)
Mark the passed in flag as unmapped.
Definition: SamFlag.h:104
SamFlag::isLastFragment
static bool isLastFragment(uint16_t flag)
Return if it is the last fragment or not (if FIRST_READ is not set and SECOND_READ is).
Definition: SamFlag.h:78
SamFlag::isUnknownFragment
static bool isUnknownFragment(uint16_t flag)
Return if it is an unknown fragment fragment or not (if FIRST_READ is not set and SECOND_READ is also...
Definition: SamFlag.h:92
SamFlag
Class for extracting information from a SAM Flag.
Definition: SamFlag.h:29
SamFlag::isFirstFragment
static bool isFirstFragment(uint16_t flag)
Return if it is the first fragment or not (if FIRST_READ is set and SECOND_READ is not).
Definition: SamFlag.h:71
SamFlag::isMidFragment
static bool isMidFragment(uint16_t flag)
Return if it is a middle fragment or not (if FIRST_READ is set and SECOND_READ is also set).
Definition: SamFlag.h:85