nvbio::io::Alignment Struct Reference

Detailed description

A simple data-structure to represent an alignment

Definition at line 80 of file alignments.h.

#include <alignments.h>

Public Methods
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE	Alignment ()
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE	Alignment (const uint32 pos, const uint32 ed, const int32 score, const uint32 rc, const uint32 mate=0, const bool paired=false, const bool discordant=false)
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE int32	score () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE bool	is_aligned () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	alignment () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE bool	is_rc () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	ed () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	sink () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	mate () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE bool	is_paired () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE bool	is_unpaired () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE bool	is_concordant () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE bool	is_discordant () const

Static Public Methods
NVBIO_FORCEINLINE static NVBIO_HOST_DEVICE uint32	max_ed ()
NVBIO_FORCEINLINE static NVBIO_HOST_DEVICE int32	max_score ()
NVBIO_FORCEINLINE static NVBIO_HOST_DEVICE int32	min_score ()
NVBIO_HOST_DEVICE static NVBIO_FORCEINLINE Alignment	invalid ()

Public Members
uint32	m_score_sgn: 1
uint32	m_score:17
uint32	m_ed:10
uint32	m_rc:1
uint32	m_mate:1
uint32	m_paired:1
uint32	m_discordant:1
uint32	m_align

Constructor & Destructor Documentation

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE nvbio::io::Alignment::Alignment ( )

inline

Definition at line 91 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE nvbio::io::Alignment::Alignment ( const uint32  pos, const uint32  ed, const int32  score, const uint32  rc, const uint32  mate = 0, const bool  paired = false, const bool  discordant = false  )

inline

Definition at line 92 of file alignments.h.

Member Function Documentation

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::Alignment::alignment ( ) const

inline

Definition at line 115 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::Alignment::ed ( ) const

inline

Definition at line 117 of file alignments.h.

NVBIO_HOST_DEVICE static NVBIO_FORCEINLINE Alignment nvbio::io::Alignment::invalid ( )

inlinestatic

Definition at line 126 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE bool nvbio::io::Alignment::is_aligned ( ) const

inline

Definition at line 114 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE bool nvbio::io::Alignment::is_concordant ( ) const

inline

Definition at line 122 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE bool nvbio::io::Alignment::is_discordant ( ) const

inline

Definition at line 123 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE bool nvbio::io::Alignment::is_paired ( ) const

inline

Definition at line 120 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE bool nvbio::io::Alignment::is_rc ( ) const

inline

Definition at line 116 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE bool nvbio::io::Alignment::is_unpaired ( ) const

inline

Definition at line 121 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::Alignment::mate ( ) const

inline

Definition at line 119 of file alignments.h.

NVBIO_FORCEINLINE static NVBIO_HOST_DEVICE uint32 nvbio::io::Alignment::max_ed ( )

inlinestatic

Definition at line 83 of file alignments.h.

NVBIO_FORCEINLINE static NVBIO_HOST_DEVICE int32 nvbio::io::Alignment::max_score ( )

inlinestatic

Definition at line 86 of file alignments.h.

NVBIO_FORCEINLINE static NVBIO_HOST_DEVICE int32 nvbio::io::Alignment::min_score ( )

inlinestatic

Definition at line 89 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE int32 nvbio::io::Alignment::score ( ) const

inline

Definition at line 113 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::Alignment::sink ( ) const

inline

Definition at line 118 of file alignments.h.

Member Data Documentation

uint32 nvbio::io::Alignment::m_align

Definition at line 129 of file alignments.h.

uint32 nvbio::io::Alignment::m_discordant

Definition at line 128 of file alignments.h.

uint32 nvbio::io::Alignment::m_ed

Definition at line 128 of file alignments.h.

uint32 nvbio::io::Alignment::m_mate

Definition at line 128 of file alignments.h.

uint32 nvbio::io::Alignment::m_paired

Definition at line 128 of file alignments.h.

uint32 nvbio::io::Alignment::m_rc

Definition at line 128 of file alignments.h.

uint32 nvbio::io::Alignment::m_score

Definition at line 128 of file alignments.h.

uint32 nvbio::io::Alignment::m_score_sgn

Definition at line 128 of file alignments.h.

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

• E:/git/nvbio/nvbio/io/alignments.h