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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_tksw_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
sizeNumber of bytes used to store a score; valid valures are 1 or 2
qlenLength of the query sequence
queryQuery sequence
mSize of the alphabet
matScoring 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.