picard_cpp/src/sam/markdups/markdups.cpp

/*
Description: 标记bam文件中的冗余信息

Copyright : All right reserved by ICT

Author : Zhang Zhonghai
Date : 2023/10/23
*/
#include "markdups_arg.h"
#include <common/global_arg.h>

#include <iostream>

using namespace std;

/*
 * mark duplicate 入口
 */
int MarkDuplicates(int argc, char *argv[])
{
    // cout << argc << endl;
    // for (int i = 0; i < argc; ++i) {
    //     cout << argv[i] << '\t';
    // }
    // cout << endl;

    GlobalArg &gArg = GlobalArg::Instance();
    MarkDupsArg mdArg;
    vector<AuxVar> vAuxVar;
    mdArg.parseArgument(argc, argv, &vAuxVar, &gArg);

    // cout << ns_md::ValidationStringency::DEFAULT_STRINGENCY << '\t' << ns_md::ValidationStringency::SILENT << endl;

    return 0;
}