SamFlag Class Reference

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

#include <SamFlag.h>

List of all members.

Static Public Member Functions
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	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.
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	FRAGMENT_INFO = 0x00C0
static const int16_t	FRAGMENT_SHIFT = 6

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Detailed Description

Class for extracting information from a SAM Flag.

Definition at line 28 of file SamFlag.h.

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Member Function Documentation

static bool SamFlag::isFirstFragment

(

uint16_t

flag

)

[inline, static]

Return if it is the first fragment or not (if FIRST_READ is set and SECOND_READ is not).

Definition at line 68 of file SamFlag.h.

    {
        // first fragment if FIRST_READ is set and SECOND_READ is not.
        return((flag & FIRST_READ) && !(flag & SECOND_READ));
    }

static bool SamFlag::isLastFragment

(

uint16_t

flag

)

[inline, static]

Return if it is the last fragment or not (if FIRST_READ is not set and SECOND_READ is).

Definition at line 75 of file SamFlag.h.

    {
        // last fragment if FIRST_READ is not set and SECOND_READ is set.
        return(!(flag & FIRST_READ) && (flag & SECOND_READ));
    }

static bool SamFlag::isMidFragment

(

uint16_t

flag

)

[inline, static]

Return if it is a middle fragment or not (if FIRST_READ is set and SECOND_READ is also set).

Definition at line 82 of file SamFlag.h.

    {
        // mid fragment if both FIRST_READ and SECOND_READ are set.
        return((flag & FIRST_READ) && (flag & SECOND_READ));
    }

static bool SamFlag::isUnknownFragment

(

uint16_t

flag

)

[inline, static]

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 89 of file SamFlag.h.

    {
        // unknown fragment index if neither FIRST_READ nor SECOND_READ are not.
        return(!(flag & FIRST_READ) && !(flag & SECOND_READ));
    }

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

• bam/SamFlag.h