cpu.cpp File Reference

#include <nvbio/basic/types.h>
#include <nvbio/basic/numbers.h>
#include <nvbio/basic/timer.h>
#include <emmintrin.h>
#include <stdio.h>
#include <stdlib.h>
#include <vector>

Go to the source code of this file.

Classes
struct	kswr_t
struct	kswq_t

Macros
#define	KSW_XBYTE   0x10000
#define	KSW_XSTOP   0x20000
#define	KSW_XSUBO   0x40000
#define	KSW_XSTART   0x80000
#define	LIKELY(x)   (x)
#define	UNLIKELY(x)   (x)

Typedefs
typedef uint8	uint8_t
typedef uint16	uint16_t
typedef uint32	uint32_t
typedef uint64	uint64_t
typedef int8	int8_t
typedef int16	int16_t
typedef int32	int32_t
typedef int64	int64_t

Functions
__device__ int	__max_16 (__m128i xx)
kswq_t *	ksw_qinit (int size, int qlen, const uint8_t *query, int m, const int8_t *mat)
kswr_t	ksw_u8 (kswq_t *q, int tlen, const uint8_t *target, int _gapo, int _gape, int xtra)
void	cpu_test ()
void	cpu_ksw_test ()

Macro Definition Documentation

#define KSW_XBYTE   0x10000

Definition at line 20 of file cpu.cpp.

#define KSW_XSTART   0x80000

Definition at line 23 of file cpu.cpp.

#define KSW_XSTOP   0x20000

Definition at line 21 of file cpu.cpp.

#define KSW_XSUBO   0x40000

Definition at line 22 of file cpu.cpp.

#define LIKELY

(

x)

(x)

Definition at line 42 of file cpu.cpp.

#define UNLIKELY

(

x)

(x)

Definition at line 43 of file cpu.cpp.

Typedef Documentation

typedef int16 int16_t

Definition at line 16 of file cpu.cpp.

typedef int32 int32_t

Definition at line 17 of file cpu.cpp.

typedef int64 int64_t

Definition at line 18 of file cpu.cpp.

typedef int8 int8_t

Definition at line 15 of file cpu.cpp.

typedef uint16 uint16_t

Definition at line 12 of file cpu.cpp.

typedef uint32 uint32_t

Definition at line 13 of file cpu.cpp.

typedef uint64 uint64_t

Definition at line 14 of file cpu.cpp.

typedef uint8 uint8_t

Definition at line 11 of file cpu.cpp.

Function Documentation

__device__ int __max_16

(

__m128i

xx)

Definition at line 46 of file cpu.cpp.

void cpu_ksw_test

(

)

Definition at line 269 of file cpu.cpp.

void cpu_test

(

)

Definition at line 242 of file cpu.cpp.

kswq_t* ksw_qinit	(	int	size,
		int	qlen,
		const uint8_t *	query,
		int	m,
		const int8_t *	mat
	)

Initialize the query data structure

Parameters

size	Number of bytes used to store a score; valid valures are 1 or 2
qlen	Length of the query sequence
query	Query sequence
m	Size of the alphabet
mat	Scoring matrix in a one-dimension array

Returns

Query data structure

Definition at line 67 of file cpu.cpp.

kswr_t ksw_u8	(	kswq_t *	q,
		int	tlen,
		const uint8_t *	target,
		int	_gapo,
		int	_gape,
		int	xtra
	)

Definition at line 115 of file cpu.cpp.