defs.h File Reference

#include <nvbio/basic/cuda/arch.h>
#include <nvbio/basic/pod.h>
#include <nvbio/io/sequence/sequence.h>
#include <algorithm>

Go to the source code of this file.

Classes
struct	nvbio::bowtie2::cuda::edit_distance_scoring_tag
struct	nvbio::bowtie2::cuda::smith_waterman_scoring_tag
struct	nvbio::bowtie2::cuda::DebugState
struct	nvbio::bowtie2::cuda::packed_read
struct	nvbio::bowtie2::cuda::packed_seed
struct	nvbio::bowtie2::cuda::pack_read

Namespaces
	nvbio
	Define a vector_view POD type and plain_view() for std::vector.
	nvbio::bowtie2
	nvbio::bowtie2::cuda

Macros
#define	USE_TEX   1
#define	USE_TEX_READS   1
#define	USE_UINT4_PACKING   0
#define	TEX_STATEMENT(x)   x
#define	TEX_SELECTOR(vec, tex)   tex
#define	READ_TEX_STATEMENT(x)   x
#define	READ_TEX_SELECTOR(vec, tex)   tex
#define	USE_WARP_SYNCHRONOUS_QUEUES   1
#define	USE_REVERSE_INDEX   0
#define	DO_OPTIONAL_SYNCHRONIZE   1
#define	DO_DEVICE_TIMING   0
#define	DP_REPORT_MULTIPLE   0

Enumerations
enum	nvbio::bowtie2::cuda::EndType { nvbio::bowtie2::cuda::kSingleEnd = 0u, nvbio::bowtie2::cuda::kPairedEnds = 1u }
enum	{ nvbio::bowtie2::cuda::AVG_READ_LENGTH = 175 }
enum	{ nvbio::bowtie2::cuda::BLOCKDIM = 96 }
enum	{ nvbio::bowtie2::cuda::SCORE_MATE_BLOCKDIM = 128 }
enum	{ nvbio::bowtie2::cuda::MAX_BAND_LEN = 63 }
enum	{ nvbio::bowtie2::cuda::MAXIMUM_READ_LENGTH = 512 }
enum	{ nvbio::bowtie2::cuda::MAXIMUM_INSERT_LENGTH = 1024 }
enum	{ nvbio::bowtie2::cuda::MAXIMUM_BAND_LENGTH = 31 }
enum	{ nvbio::bowtie2::cuda::MAXIMUM_BAND_LEN_MULT = 4 }
enum	{ nvbio::bowtie2::cuda::BANDED_DP_CHECKPOINTS = 16 }
enum	{ nvbio::bowtie2::cuda::FULL_DP_CHECKPOINTS = 64 }
enum	{ nvbio::bowtie2::cuda::LMEM_CACHE_WORDS = 64 }
enum	{   nvbio::bowtie2::cuda::HIT_STATS_RANGES = 0, nvbio::bowtie2::cuda::HIT_STATS_MAX_RANGE = 1, nvbio::bowtie2::cuda::HIT_STATS_TOTAL = 2, nvbio::bowtie2::cuda::HIT_STATS_MAX = 3,   nvbio::bowtie2::cuda::HIT_STATS_TOP = 4, nvbio::bowtie2::cuda::HIT_STATS_TOP_MAX = 5, nvbio::bowtie2::cuda::HIT_STATS_BINS = 6, nvbio::bowtie2::cuda::HIT_STATS_TOP_BINS = 6 + 32 }

Macro Definition Documentation

#define DO_DEVICE_TIMING   0

Definition at line 65 of file defs.h.

#define DO_OPTIONAL_SYNCHRONIZE   1

Definition at line 64 of file defs.h.

#define DP_REPORT_MULTIPLE   0

Definition at line 67 of file defs.h.

#define READ_TEX_SELECTOR	(		vec,
			tex
	)		tex

Definition at line 55 of file defs.h.

#define READ_TEX_STATEMENT

(

x)

x

Definition at line 54 of file defs.h.

#define TEX_SELECTOR	(		vec,
			tex
	)		tex

Definition at line 47 of file defs.h.

#define TEX_STATEMENT

(

x)

x

Definition at line 46 of file defs.h.

#define USE_REVERSE_INDEX   0

Definition at line 62 of file defs.h.

#define USE_TEX   1

Definition at line 41 of file defs.h.

#define USE_TEX_READS   1

Definition at line 42 of file defs.h.

#define USE_UINT4_PACKING   0

Definition at line 43 of file defs.h.

#define USE_WARP_SYNCHRONOUS_QUEUES   1

Definition at line 61 of file defs.h.