/*
     Description: 针对paired数据，计算生成sam步骤的优化

     Copyright : All right reserved by ICT

     Author : Zhang Zhonghai
     Date : 2026/01/08
*/
#pragma once

#include "bwamem.h"

// for avx512
#define SIMD512_WIDTH8 64
#define SIMD512_WIDTH16 32

void gen_paired_sam(mem_worker_t* w);

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],
                      mem_alnreg_v a[2], seq_sam_t ss[2], int tid);

extern void mem_reg2ovlp(const mem_opt_t* opt, const bntseq_t* bns, const uint8_t* pac, bseq1_t* s, mem_alnreg_v* a);

extern void kt_for(int n_threads, void (*func)(void*, int, int), void* data, int n);