Class for extracting information from a SAM Flag.
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#include <SamFlag.h>
Class for extracting information from a SAM Flag.
Definition at line 28 of file SamFlag.h.
◆ getFragmentType()
static uint8_t SamFlag::getFragmentType |
( |
uint16_t |
flag | ) |
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inlinestatic |
Definition at line 98 of file SamFlag.h.
99 {
100 return((flag & FRAGMENT_INFO) >> FRAGMENT_SHIFT);
101 }
◆ isDuplicate()
static bool SamFlag::isDuplicate |
( |
uint16_t |
flag | ) |
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inlinestatic |
Definition at line 64 of file SamFlag.h.
64{return(flag & DUPLICATE);}
◆ isFirstFragment()
static bool SamFlag::isFirstFragment |
( |
uint16_t |
flag | ) |
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inlinestatic |
Return if it is the first fragment or not (if FIRST_READ is set and SECOND_READ is not).
Definition at line 71 of file SamFlag.h.
72 {
73
74 return((flag & FIRST_READ) && !(flag & SECOND_READ));
75 }
◆ isLastFragment()
static bool SamFlag::isLastFragment |
( |
uint16_t |
flag | ) |
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inlinestatic |
Return if it is the last fragment or not (if FIRST_READ is not set and SECOND_READ is).
Definition at line 78 of file SamFlag.h.
79 {
80
81 return(!(flag & FIRST_READ) && (flag & SECOND_READ));
82 }
◆ isMapped()
static bool SamFlag::isMapped |
( |
uint16_t |
flag | ) |
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inlinestatic |
Definition at line 53 of file SamFlag.h.
53{return(!(flag & UNMAPPED));}
◆ isMateMapped()
static bool SamFlag::isMateMapped |
( |
uint16_t |
flag | ) |
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inlinestatic |
Definition at line 54 of file SamFlag.h.
54{return(!(flag & MATE_UNMAPPED));}
◆ isMateReverse()
static bool SamFlag::isMateReverse |
( |
uint16_t |
flag | ) |
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inlinestatic |
Definition at line 58 of file SamFlag.h.
58{return(flag & MATE_REVERSED);}
◆ isMidFragment()
static bool SamFlag::isMidFragment |
( |
uint16_t |
flag | ) |
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inlinestatic |
Return if it is a middle fragment or not (if FIRST_READ is set and SECOND_READ is also set).
Definition at line 85 of file SamFlag.h.
86 {
87
88 return((flag & FIRST_READ) && (flag & SECOND_READ));
89 }
◆ isPaired()
static bool SamFlag::isPaired |
( |
uint16_t |
flag | ) |
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inlinestatic |
Definition at line 56 of file SamFlag.h.
56{return(flag & PAIRED);}
◆ isProperPair()
static bool SamFlag::isProperPair |
( |
uint16_t |
flag | ) |
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inlinestatic |
Definition at line 59 of file SamFlag.h.
60 {
61
62 return(isPaired(flag) && (flag & PROPER_PAIR));
63 }
◆ isQCFailure()
static bool SamFlag::isQCFailure |
( |
uint16_t |
flag | ) |
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inlinestatic |
Definition at line 65 of file SamFlag.h.
65{return(flag & FAILED_QUALITY);}
◆ isReverse()
static bool SamFlag::isReverse |
( |
uint16_t |
flag | ) |
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inlinestatic |
Definition at line 57 of file SamFlag.h.
57{return(flag & REVERSE);}
◆ isSecondary()
static bool SamFlag::isSecondary |
( |
uint16_t |
flag | ) |
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inlinestatic |
Definition at line 67 of file SamFlag.h.
67{return(flag & SECONDARY_ALIGNMENT);}
◆ isUnknownFragment()
static bool SamFlag::isUnknownFragment |
( |
uint16_t |
flag | ) |
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inlinestatic |
Return if it is an unknown fragment fragment or not (if FIRST_READ is not set and SECOND_READ is also not set).
Definition at line 92 of file SamFlag.h.
93 {
94
95 return(!(flag & FIRST_READ) && !(flag & SECOND_READ));
96 }
◆ setDuplicate()
static void SamFlag::setDuplicate |
( |
uint16_t & |
flag | ) |
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inlinestatic |
Mark the passed in flag as not duplicate.
Definition at line 108 of file SamFlag.h.
◆ setNotDuplicate()
static void SamFlag::setNotDuplicate |
( |
uint16_t & |
flag | ) |
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inlinestatic |
Mark the passed in flag as not duplicate.
Definition at line 106 of file SamFlag.h.
◆ setUnmapped()
static void SamFlag::setUnmapped |
( |
uint16_t & |
flag | ) |
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inlinestatic |
◆ DUPLICATE
const int16_t SamFlag::DUPLICATE = 0x0400 |
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static |
◆ FAILED_QUALITY
const int16_t SamFlag::FAILED_QUALITY = 0x0200 |
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static |
◆ FIRST_READ
const int16_t SamFlag::FIRST_READ = 0x0040 |
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static |
◆ FRAGMENT_INFO
const int16_t SamFlag::FRAGMENT_INFO = 0x00C0 |
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static |
◆ FRAGMENT_SHIFT
const int16_t SamFlag::FRAGMENT_SHIFT = 6 |
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static |
◆ MATE_REVERSED
const int16_t SamFlag::MATE_REVERSED = 0x0020 |
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static |
◆ MATE_UNMAPPED
const int16_t SamFlag::MATE_UNMAPPED = 0x0008 |
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static |
◆ PAIRED
const int16_t SamFlag::PAIRED = 0x0001 |
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static |
◆ PROPER_PAIR
const int16_t SamFlag::PROPER_PAIR = 0x0002 |
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static |
◆ REVERSE
const int16_t SamFlag::REVERSE = 0x0010 |
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static |
◆ SECOND_READ
const int16_t SamFlag::SECOND_READ = 0x0080 |
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static |
◆ SECONDARY_ALIGNMENT
const int16_t SamFlag::SECONDARY_ALIGNMENT = 0x0100 |
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static |
◆ SUPPLEMENTARY_ALIGNMENT
const int16_t SamFlag::SUPPLEMENTARY_ALIGNMENT = 0x0800 |
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static |
◆ UNMAPPED
const int16_t SamFlag::UNMAPPED = 0x0004 |
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static |
The documentation for this class was generated from the following file: