Detailed description

template< typename ScoringScheme>
struct nvbio::bowtie2::cuda::TracebackPipelineState< ScoringScheme >

This object encapsulates the state of the pipeline during traceback. As such, it includes references to the following objects:

* the reads for both mates
* the genome iterator
* the CIGAR and MD string arenas
* the temporary DP buffer

Definition at line 243 of file pipeline_states.h.

#include <pipeline_states.h>

Public Types
typedef Aligner::read_batch_type	read_batch_type

typedef Aligner::genome_iterator	genome_iterator

typedef ScoringScheme	scheme_type

Public Methods
	TracebackPipelineState (const read_batch_type _reads1, const read_batch_type _reads2, const uint32 _genome_len, const genome_iterator _genome, const ScoringScheme _scoring_scheme, Aligner &_aligner)

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE const read_batch_type &	get_reads (const uint32 mate) const

Public Members
const read_batch_type	reads
	first mates More...

const read_batch_type	reads_o
	second mates More...

const uint32	genome_length
	genome length More...

const genome_iterator	genome
	genome iterator More...

const ScoringScheme	scoring_scheme
	scoring scheme More...

nvbio::VectorArrayView< io::Cigar >	cigar
	cigar arena More...

uint2 *	cigar_coords
	cigar coords More...

nvbio::VectorArrayView< uint8 >	mds
	mds arena More...

uint8 *	dp_buffer
	DP buffer. More...

uint64	dp_buffer_size
	DP buffer size. More...

Member Typedef Documentation

template<typename ScoringScheme>

typedef Aligner::genome_iterator nvbio::bowtie2::cuda::TracebackPipelineState< ScoringScheme >::genome_iterator

Definition at line 246 of file pipeline_states.h.

template<typename ScoringScheme>

typedef Aligner::read_batch_type nvbio::bowtie2::cuda::TracebackPipelineState< ScoringScheme >::read_batch_type

Definition at line 245 of file pipeline_states.h.

template<typename ScoringScheme>

typedef ScoringScheme nvbio::bowtie2::cuda::TracebackPipelineState< ScoringScheme >::scheme_type

Definition at line 247 of file pipeline_states.h.

Constructor & Destructor Documentation

template<typename ScoringScheme>

nvbio::bowtie2::cuda::TracebackPipelineState< ScoringScheme >::TracebackPipelineState	(	const read_batch_type	_reads1,
		const read_batch_type	_reads2,
		const uint32	_genome_len,
		const genome_iterator	_genome,
		const ScoringScheme	_scoring_scheme,
		Aligner &	_aligner
	)

inline

constructor

Parameters

_reads1	the reads corresponding to mate #1
_reads2	the reads corresponding to mate #2
_genome_len	the length of the genome
_genome	the genome iterator
_aligner	the aligner object

Definition at line 256 of file pipeline_states.h.

Member Function Documentation

template<typename ScoringScheme>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE const read_batch_type& nvbio::bowtie2::cuda::TracebackPipelineState< ScoringScheme >::get_reads ( const uint32 mate) const