E:/git/nvbio/sw-benchmark/ssw.h Source File - NVlabs

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• sw-benchmark

ssw.h Go to the documentation of this file. 1 /* 2  * ssw.h 3  * 4  * Created by Mengyao Zhao on 6/22/10. 5  * Copyright 2010 Boston College. All rights reserved. 6  * Version 0.1.4 7  * Last revision by Mengyao Zhao on 01/30/13. 8  * 9  */ 10  11 #ifndef SSW_H 12 #define SSW_H 13  14 #include <stdio.h> 15 #include <string.h> 16 #include <emmintrin.h> 17  18 #if defined(WIN32) 19 typedef char int8_t; 20 typedef unsigned char uint8_t; 21 typedef short int16_t; 22 typedef unsigned short uint16_t; 23 typedef int int32_t; 24 typedef unsigned int uint32_t; 25 #else 26 #include <stdint.h> 27 #endif 28  30 struct _profile; 31 typedef struct _profile s_profile; 32  47 typedef struct { 48  uint16_t score1; 49  uint16_t score2; 50  int32_t ref_begin1; 51  int32_t ref_end1; 52  int32_t read_begin1; 53  int32_t read_end1; 54  int32_t ref_end2; 55  uint32_t* cigar; 56  int32_t cigarLen; 57 } s_align; 58  59 #ifdef __cplusplus 60 extern "C" { 61 #endif // __cplusplus 62  81 s_profile* ssw_init (const int8_t* read, const int32_t readLen, const int8_t* mat, const int32_t n, const int8_t score_size); 82  86 void init_destroy (s_profile* p); 87  88 // @function ssw alignment. 121 s_align* ssw_align (const s_profile* prof, 122  const int8_t* ref, 123  int32_t refLen, 124  const uint8_t weight_gapO, 125  const uint8_t weight_gapE, 126  const uint8_t flag, 127  const uint16_t filters, 128  const int32_t filterd, 129  const int32_t maskLen); 130  134 void align_destroy (s_align* a); 135  136 #ifdef __cplusplus 137 } 138 #endif // __cplusplus 139  140 #endif // SSW_H Generated on Wed Feb 25 2015 08:33:07 for NVBIO by   1.8.4