/*
     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);

extern int mem_sort_dedup_patch(const mem_opt_t* opt, const bntseq_t* bns, const uint8_t* pac, uint8_t* query, int n, mem_alnreg_t* a);

extern void mem_reg2sam(const mem_opt_t* opt, const bntseq_t* bns, const uint8_t* pac, bseq1_t* s, mem_alnreg_v* a, int extra_flag,
                        const mem_aln_t* m, seq_sam_t* ss);

extern void mem_aln2sam(const mem_opt_t* opt, const bntseq_t* bns, kstring_t* str, bseq1_t* s, int n, const mem_aln_t* list, int which,
                        const mem_aln_t* m);

extern int mem_mark_primary_se(const mem_opt_t* opt, int n, mem_alnreg_t* a, int64_t id);
extern int mem_approx_mapq_se(const mem_opt_t* opt, const mem_alnreg_t* a);

extern char** mem_gen_alt(const mem_opt_t* opt, const bntseq_t* bns, const uint8_t* pac, const mem_alnreg_v* a, int l_query, const char* query);

extern void mem_reorder_primary5(int T, mem_alnreg_v* a);

extern int mem_pair(const mem_opt_t* opt, const bntseq_t* bns, const uint8_t* pac, const mem_pestat_t pes[4], bseq1_t s[2], mem_alnreg_v a[2], int id,
             int* sub, int* n_sub, int z[2], int n_pri[2]);