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nvbio::io::BestPairedAlignments Struct Reference
IO

Detailed description

A simple data-structure to hold the best 2 paired alignments

Definition at line 227 of file alignments.h.

#include <alignments.h>

Public Methods

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE BestPairedAlignments ()
 
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE BestPairedAlignments (const BestAlignments &a, const BestAlignments &o)
 
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE BestPairedAlignments (const BestAlignments &a)
 
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE bool 		is_paired () const
 
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE bool 		is_aligned () const
 
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE bool 		has_second_paired () const
 
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE bool 		has_second_unpaired () const
 
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE bool 		has_second () const
 
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE int32 		best_score () const
 
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE uint32 		best_ed () const
 
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE uint32 		best_alignment_pos () const
 
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE int32 		second_score () const
 
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE uint32 		second_ed () const
 
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE uint32 		second_alignment_pos () const
 
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE
BestAlignments 		best_anchor () const
 
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE
BestAlignments 		best_opposite () const
 
template<uint32 I>
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE
PairedAlignments 		pair () const
 
template<uint32 I>
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE const
Alignment & 		alignment () const
 
template<uint32 I>
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE Alignment & 		alignment ()
 
template<uint32 I>
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE const
Alignment & 		opposite_alignment () const
 
template<uint32 I>
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE Alignment & 		opposite_alignment ()
 
template<uint32 I>
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE uint32 		alignment_pos () const
 
template<uint32 I>
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE uint32 		opposite_alignment_pos () const
 
template<uint32 I>
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE int32 		score () const
 
template<uint32 I>
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE uint32 		ed () const
 
template<uint32 I>
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE bool 		is_aligned () const
 
template<uint32 I>
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE bool 		is_rc () const
 
template<uint32 I>
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE bool 		is_opposite_rc () const
 
template<uint32 I>
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE uint32 		anchor_mate () const
 
template<uint32 I>
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE uint32 		opposite_mate () const
 
template<uint32 I>
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE int32 		anchor_score () const
 
template<uint32 I>
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE uint32 		anchor_ed () const
 
template<uint32 I>
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE int32 		opposite_score () const
 
template<uint32 I>
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE uint32 		opposite_ed () const
 
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE
BestAlignments 		anchor () const
 
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE
BestAlignments 		opposite () const
 
NVBIO_HOST_DEVICE
NVBIO_FORCEINLINE
BestAlignments 		mate (const uint32 m) const
 

Public Members

Alignment m_a1
 
Alignment m_a2
 
Alignment m_o1
 
Alignment m_o2
 

Constructor & Destructor Documentation

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE nvbio::io::BestPairedAlignments::BestPairedAlignments ( )
inline

Definition at line 230 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE nvbio::io::BestPairedAlignments::BestPairedAlignments ( const BestAlignments &  a,
const BestAlignments &  o 
)
inline

Definition at line 233 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE nvbio::io::BestPairedAlignments::BestPairedAlignments ( const BestAlignments &  a)
inline

Definition at line 236 of file alignments.h.

Member Function Documentation

template<uint32 I>
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const Alignment& nvbio::io::BestPairedAlignments::alignment ( ) const
inline

Definition at line 259 of file alignments.h.

template<uint32 I>
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE Alignment& nvbio::io::BestPairedAlignments::alignment ( )
inline

Definition at line 263 of file alignments.h.

template<uint32 I>
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::BestPairedAlignments::alignment_pos ( ) const
inline

Definition at line 275 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE BestAlignments nvbio::io::BestPairedAlignments::anchor ( ) const
inline

Definition at line 326 of file alignments.h.

template<uint32 I>
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::BestPairedAlignments::anchor_ed ( ) const
inline

Definition at line 315 of file alignments.h.

template<uint32 I>
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::BestPairedAlignments::anchor_mate ( ) const
inline

Definition at line 303 of file alignments.h.

template<uint32 I>
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE int32 nvbio::io::BestPairedAlignments::anchor_score ( ) const
inline

Definition at line 311 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::BestPairedAlignments::best_alignment_pos ( ) const
inline

Definition at line 245 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE BestAlignments nvbio::io::BestPairedAlignments::best_anchor ( ) const
inline

Definition at line 250 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::BestPairedAlignments::best_ed ( ) const
inline

Definition at line 244 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE BestAlignments nvbio::io::BestPairedAlignments::best_opposite ( ) const
inline

Definition at line 251 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE int32 nvbio::io::BestPairedAlignments::best_score ( ) const
inline

Definition at line 243 of file alignments.h.

template<uint32 I>
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::BestPairedAlignments::ed ( ) const
inline

Definition at line 287 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE bool nvbio::io::BestPairedAlignments::has_second ( ) const
inline

Definition at line 242 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE bool nvbio::io::BestPairedAlignments::has_second_paired ( ) const
inline

Definition at line 240 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE bool nvbio::io::BestPairedAlignments::has_second_unpaired ( ) const
inline

Definition at line 241 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE bool nvbio::io::BestPairedAlignments::is_aligned ( ) const
inline

Definition at line 239 of file alignments.h.

template<uint32 I>
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE bool nvbio::io::BestPairedAlignments::is_aligned ( ) const
inline

Definition at line 291 of file alignments.h.

template<uint32 I>
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE bool nvbio::io::BestPairedAlignments::is_opposite_rc ( ) const
inline

Definition at line 299 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE bool nvbio::io::BestPairedAlignments::is_paired ( ) const
inline

Definition at line 238 of file alignments.h.

template<uint32 I>
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE bool nvbio::io::BestPairedAlignments::is_rc ( ) const
inline

Definition at line 295 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE BestAlignments nvbio::io::BestPairedAlignments::mate ( const uint32  m) const
inline

Definition at line 332 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE BestAlignments nvbio::io::BestPairedAlignments::opposite ( ) const
inline

Definition at line 329 of file alignments.h.

template<uint32 I>
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const Alignment& nvbio::io::BestPairedAlignments::opposite_alignment ( ) const
inline

Definition at line 267 of file alignments.h.

template<uint32 I>
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE Alignment& nvbio::io::BestPairedAlignments::opposite_alignment ( )
inline

Definition at line 271 of file alignments.h.

template<uint32 I>
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::BestPairedAlignments::opposite_alignment_pos ( ) const
inline

Definition at line 279 of file alignments.h.

template<uint32 I>
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::BestPairedAlignments::opposite_ed ( ) const
inline

Definition at line 323 of file alignments.h.

template<uint32 I>
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::BestPairedAlignments::opposite_mate ( ) const
inline

Definition at line 307 of file alignments.h.

template<uint32 I>
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE int32 nvbio::io::BestPairedAlignments::opposite_score ( ) const
inline

Definition at line 319 of file alignments.h.

template<uint32 I>
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE PairedAlignments nvbio::io::BestPairedAlignments::pair ( ) const
inline

Definition at line 255 of file alignments.h.

template<uint32 I>
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE int32 nvbio::io::BestPairedAlignments::score ( ) const
inline

Definition at line 283 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::BestPairedAlignments::second_alignment_pos ( ) const
inline

Definition at line 248 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::BestPairedAlignments::second_ed ( ) const
inline

Definition at line 247 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE int32 nvbio::io::BestPairedAlignments::second_score ( ) const
inline

Definition at line 246 of file alignments.h.

Member Data Documentation

Alignment nvbio::io::BestPairedAlignments::m_a1

Definition at line 339 of file alignments.h.

Alignment nvbio::io::BestPairedAlignments::m_a2

Definition at line 340 of file alignments.h.

Alignment nvbio::io::BestPairedAlignments::m_o1

Definition at line 341 of file alignments.h.

Alignment nvbio::io::BestPairedAlignments::m_o2

Definition at line 342 of file alignments.h.

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