109 lines
3.7 KiB
C++
109 lines
3.7 KiB
C++
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/*
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Description: 全局参数，所有模块都可能用到的参数
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Copyright : All right reserved by NCIC.ICT
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Author : Zhang Zhonghai
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Date : 2023/10/23
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*/
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#include "global_arg.h"
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#include <cstring>
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#include <vector>
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#include <getopt.h>
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#include <iostream>
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using std::vector;
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/*
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* GlobalArg 类
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*/
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struct option *GlobalArg::GLOBAL_OPT = nullptr;
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// 初始化参数
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void GlobalArg::initGlobalOptions()
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{
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vector<struct option> v;
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v.push_back({"INPUT", required_argument, NULL, ns_ga::GlobalOptEnum::OPT_INPUT}); // 输入文件
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v.push_back({"OUTPUT", required_argument, NULL, ns_ga::GlobalOptEnum::OPT_OUTPUT}); // 输出文件
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v.push_back({"num_threads", required_argument, NULL, ns_ga::GlobalOptEnum::OPT_NUM_THREADS});
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v.push_back({"max_mem", required_argument, NULL, ns_ga::GlobalOptEnum::OPT_MAX_MEM});
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v.push_back({"verbosity", required_argument, NULL, ns_ga::GlobalOptEnum::OPT_LOG_LEVEL});
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v.push_back({"asyncio", required_argument, NULL, ns_ga::GlobalOptEnum::OPT_ASYNCIO});
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v.push_back({"version", no_argument, NULL, ns_ga::GlobalOptEnum::OPT_VERSION});
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v.push_back({"help", no_argument, NULL, ns_ga::GlobalOptEnum::OPT_HELP});
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v.push_back({0, 0, 0, 0});
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GLOBAL_OPT = new struct option[GLOBAL_ARG_CNT];
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memcpy(GLOBAL_OPT, v.data(), v.size() * sizeof(struct option));
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/* 添加帮助信息, 按arg enum顺序进行添加信息 */
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vArgInfo.push_back("--INPUT Input file path (bam, vcf ...)\n");
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vArgInfo.push_back("--OUTPUT Output file path \n");
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vArgInfo.push_back("--num_threads <num_threads> Number of threads to allocate to this analysis [1]\n");
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vArgInfo.push_back("--max_mem <max_mem> Set maximum memory; suffix K/M/G recognized [2G]\n");
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vArgInfo.push_back("--verbosity <log level> Control verbosity of logging. error/warning/info/debug [info]\n");
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vArgInfo.push_back("--asyncio Use async io [true]\n");
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vArgInfo.push_back("--version Output version information\n");
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vArgInfo.push_back("--help Generate the help message\n");
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}
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// 解析参数
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void GlobalArg::parseArgument(int argNum)
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{
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using namespace ns_ga;
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switch (argNum)
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{
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case OPT_INPUT:
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in_fn = optarg;
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break;
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case OPT_OUTPUT:
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out_fn = optarg;
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break;
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case OPT_NUM_THREADS:
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num_threads = std::stoi(optarg);
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break;
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case OPT_MAX_MEM:
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{
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char *q;
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size_t mem_arg = strtol(optarg, &q, 0);
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if (*q == 'k' || *q == 'K')
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mem_arg <<= 10;
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else if (*q == 'm' || *q == 'M')
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mem_arg <<= 20;
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else if (*q == 'g' || *q == 'G')
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mem_arg <<= 30;
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if (mem_arg >= max_mem)
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max_mem = mem_arg;
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else
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{
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std::cerr << "[Warn] Too small mem size, use default" << std::endl;
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}
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break;
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}
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case OPT_LOG_LEVEL:
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{
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if (strcmp("ERROR", optarg) == 0)
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verbosity = ns_ga::ERROR;
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else if (strcmp("WARNING", optarg) == 0)
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verbosity = ns_ga::WARNING;
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else if (strcmp("INFO", optarg) == 0)
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verbosity = ns_ga::INFO;
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else if (strcmp("DEBUG", optarg) == 0)
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verbosity = ns_ga::DEBUG;
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break;
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}
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case OPT_ASYNCIO:
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{
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if (strcmp("true", optarg) == 0)
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use_asyncio = true;
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else if (strcmp("false", optarg) == 0)
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use_asyncio = false;
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break;
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}
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default:
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break;
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}
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}
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