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SamFlag Class Reference

Class for extracting information from a SAM Flag. More...

#include <SamFlag.h>

Static Public Attributes

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
 

Static methods for determining the contents of a flag.

static bool isMapped (uint16_t flag)
 
static bool isMateMapped (uint16_t flag)
 
static bool isPaired (uint16_t flag)
 
static bool isReverse (uint16_t flag)
 
static bool isMateReverse (uint16_t flag)
 
static bool isProperPair (uint16_t flag)
 
static bool isDuplicate (uint16_t flag)
 
static bool isQCFailure (uint16_t flag)
 
static bool isSecondary (uint16_t flag)
 
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).
 
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).
 
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).
 
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).
 
static uint8_t getFragmentType (uint16_t flag)
 
static void setUnmapped (uint16_t &flag)
 Mark the passed in flag as unmapped.
 
static void setNotDuplicate (uint16_t &flag)
 Mark the passed in flag as not duplicate.
 
static void setDuplicate (uint16_t &flag)
 Mark the passed in flag as not duplicate.
 

Detailed Description

Class for extracting information from a SAM Flag.

Definition at line 28 of file SamFlag.h.

The documentation for this class was generated from the following file: