Class for extracting information from a SAM Flag.
More...
#include <SamFlag.h>
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static bool | isMapped (uint16_t flag) |
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static bool | isMateMapped (uint16_t flag) |
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static bool | isPaired (uint16_t flag) |
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static bool | isReverse (uint16_t flag) |
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static bool | isMateReverse (uint16_t flag) |
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static bool | isProperPair (uint16_t flag) |
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static bool | isDuplicate (uint16_t flag) |
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static bool | isQCFailure (uint16_t flag) |
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static bool | isSecondary (uint16_t flag) |
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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). More...
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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). More...
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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). More...
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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 not set). More...
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static uint8_t | getFragmentType (uint16_t flag) |
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static void | setUnmapped (uint16_t &flag) |
| Mark the passed in flag as unmapped.
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static void | setNotDuplicate (uint16_t &flag) |
| Mark the passed in flag as not duplicate.
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static void | setDuplicate (uint16_t &flag) |
| Mark the passed in flag as not duplicate.
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static const int16_t | PAIRED = 0x0001 |
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static const int16_t | PROPER_PAIR = 0x0002 |
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static const int16_t | UNMAPPED = 0x0004 |
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static const int16_t | MATE_UNMAPPED = 0x0008 |
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static const int16_t | REVERSE = 0x0010 |
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static const int16_t | MATE_REVERSED = 0x0020 |
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static const int16_t | FIRST_READ = 0x0040 |
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static const int16_t | SECOND_READ = 0x0080 |
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static const int16_t | SECONDARY_ALIGNMENT = 0x0100 |
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static const int16_t | FAILED_QUALITY = 0x0200 |
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static const int16_t | DUPLICATE = 0x0400 |
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static const int16_t | SUPPLEMENTARY_ALIGNMENT = 0x0800 |
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static const int16_t | FRAGMENT_INFO = 0x00C0 |
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static const int16_t | FRAGMENT_SHIFT = 6 |
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Class for extracting information from a SAM Flag.
Definition at line 28 of file SamFlag.h.
◆ isFirstFragment()
static bool SamFlag::isFirstFragment |
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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.
74 return((flag & FIRST_READ) && !(flag & SECOND_READ));
◆ isLastFragment()
static bool SamFlag::isLastFragment |
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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.
81 return(!(flag & FIRST_READ) && (flag & SECOND_READ));
◆ isMidFragment()
static bool SamFlag::isMidFragment |
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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.
88 return((flag & FIRST_READ) && (flag & SECOND_READ));
◆ isUnknownFragment()
static bool SamFlag::isUnknownFragment |
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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.
95 return(!(flag & FIRST_READ) && !(flag & SECOND_READ));
The documentation for this class was generated from the following file: