73 lines
2.5 KiB
C
73 lines
2.5 KiB
C
#pragma once
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#include <emmintrin.h>
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#include <immintrin.h>
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#include <stdint.h>
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#include "ksw.h"
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#define AMBIG_ 4 // ambiguous base
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// for 16 bit
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#define DUMMY1_ 4
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#define DUMMY2_ 5
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#define DUMMY3 26
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#define AMBR16 15
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#define AMBQ16 16
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// for 8-bit
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#define DUMMY8 8
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#define DUMMY5 5
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#define AMBRQ 0xFF
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#define AMBR 4
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#define AMBQ 8
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#define min_(x, y) ((x) > (y) ? (y) : (x))
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#define max_(x, y) ((x) > (y) ? (x) : (y))
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typedef struct {
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int score; // best score
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int te, qe; // target end and query end
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int score2, te2; // second best score and ending position on the target
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int tb, qb; // target start and query start
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} kswr_avx_t;
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typedef struct {
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int seq_len;
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int ref_len;
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uint8_t* H0;
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uint8_t* H1;
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uint8_t* Hmax;
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uint8_t* F;
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uint8_t* rowMax;
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uint8_t* seqArr;
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uint8_t* refArr;
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} matesw_buf_t; // inter-query算法的mate sw计算过程需要用到的缓存空间
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#ifdef __cplusplus
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extern "C" {
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#endif
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void ksw_align_avx2_u8(int qlen, uint8_t* query, int tlen, uint8_t* target, int m, const int8_t* mat, int gapo, int gape, int xtra, kswq_t** qry);
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void ksw_align_avx2_i16(int qlen, uint8_t* query, int tlen, uint8_t* target, int m, const int8_t* mat, int gapo, int gape, int xtra, kswq_t** qry);
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void ksw_align_avx512_u8(int8_t w_match, // match分数，正数
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int8_t w_mismatch, // 错配罚分，负数
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int8_t o_ins, // 开始一个insert罚分，正数
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int8_t e_ins, // 延续一个insert罚分，正数
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int8_t o_del, // 开始一个delete罚分，正数
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int8_t e_del, // 延续一个delete罚分，正数
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matesw_buf_t* cache, // 计算用到的一些数据
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uint8_t* seq1SoA, // ref序列，已经pack好了
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uint8_t* seq2SoA, // seq序列
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int16_t nrow, // 最长的行数，对应ref长度
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int16_t ncol, // 最长的列数，对应seq长度
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int* xtras, // 每个seq对应一个xtra
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int* rlenA, // ref真实长度
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kswr_avx_t* alns, // 存放结果
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int phase); // 正向阶段0，反向阶段1
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void ksw_align_avx512_i16(int qlen, uint8_t* query, int tlen, uint8_t* target, int m, const int8_t* mat, int gapo, int gape, int xtra, kswq_t** qry);
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#ifdef __cplusplus
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}
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#endif |