#pragma once

#include <common/utils/timer.h>
#include <common/utils/util.h>
#include <htslib/sam.h>
#include <htslib/thread_pool.h>
#include <sam/utils/read_ends.h>
#include <sam/utils/read_name_parser.h>
#include <set>
using std::set;

extern Timer tm_arr[20];  // 用来测试性能
/* 全局本地变量 */
extern vector<ReadNameParser> g_vRnParser;  // 每个线程一个read name parser
extern samFile *g_inBamFp;                  // 输入的bam文件
extern sam_hdr_t *g_inBamHeader;            // 输入的bam文件头信息
extern samFile *g_outBamFp;       // 输出文件, sam或者bam格式
extern sam_hdr_t *g_outBamHeader;           // 输出文件的header

/* 参数对象作为全局对象，免得多次作为参数传入函数中 */
class GlobalArg;
extern GlobalArg &g_gArg;
class MarkDupsArg;
extern MarkDupsArg &g_mdArg;
class GlobalDataArg;
extern GlobalDataArg &gData;
class DuplicationMetrics;
extern DuplicationMetrics &gMetrics;

extern int zzhtestnum;
extern set<int64_t> zzhopticalSet;
extern vector<int64_t> zzhopticalArr;