24 lines
726 B
C
24 lines
726 B
C
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/*
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Description: 针对paired数据，计算生成sam步骤的优化
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Copyright : All right reserved by ICT
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Author : Zhang Zhonghai
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Date : 2026/01/08
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*/
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#pragma once
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#include "bwamem.h"
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// for avx512
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#define SIMD512_WIDTH8 64
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#define SIMD512_WIDTH16 32
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void gen_paired_sam(mem_worker_t* w);
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extern int mem_sam_pe(const mem_opt_t* opt, const bntseq_t* bns, const uint8_t* pac, const mem_pestat_t pes[4], uint64_t id, bseq1_t s[2],
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mem_alnreg_v a[2], seq_sam_t ss[2], int tid);
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extern void mem_reg2ovlp(const mem_opt_t* opt, const bntseq_t* bns, const uint8_t* pac, bseq1_t* s, mem_alnreg_v* a);
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extern void kt_for(int n_threads, void (*func)(void*, int, int), void* data, int n);
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