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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.


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