2023-11-01 10:48:02 +08:00
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/*
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Description: Markduplicate需要用到的一些参数，读取命令行给的参数，并做一些初始化
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Copyright : All right reserved by ICT
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Author : Zhang Zhonghai
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Date : 2023/10/27
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*/
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#include "markdups_arg.h"
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#include "common/global_arg.h"
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#include <cstring>
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#include <vector>
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#include <string>
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#include <sstream>
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#include <getopt.h>
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#include <stddef.h>
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#include <stdio.h>
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#include <iostream>
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using std::cout, std::endl;
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using std::ostringstream;
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using std::stod;
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using std::stoi;
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using std::stol;
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using std::string;
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using std::vector;
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using namespace ns_md;
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/*
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* mutect参数
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*/
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const static struct option kMdOpts[] = {
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{"MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP", required_argument, NULL, MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP},
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{"MAX_FILE_HANDLES_FOR_READ_ENDS_MAP", required_argument, NULL, MAX_FILE_HANDLES_FOR_READ_ENDS_MAP},
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{"SORTING_COLLECTION_SIZE_RATIO", required_argument, NULL, SORTING_COLLECTION_SIZE_RATIO},
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{"BARCODE_TAG", required_argument, NULL, BARCODE_TAG},
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{"READ_ONE_BARCODE_TAG", required_argument, NULL, READ_ONE_BARCODE_TAG},
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{"READ_TWO_BARCODE_TAG", required_argument, NULL, READ_TWO_BARCODE_TAG},
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{"TAG_DUPLICATE_SET_MEMBERS", required_argument, NULL, TAG_DUPLICATE_SET_MEMBERS},
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{"REMOVE_SEQUENCING_DUPLICATES", required_argument, NULL, REMOVE_SEQUENCING_DUPLICATES},
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{"TAGGING_POLICY", required_argument, NULL, TAGGING_POLICY},
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{"CLEAR_DT", required_argument, NULL, CLEAR_DT},
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{"DUPLEX_UMI", required_argument, NULL, DUPLEX_UMI},
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{"MOLECULAR_IDENTIFIER_TAG", required_argument, NULL, MOLECULAR_IDENTIFIER_TAG},
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{"METRICS_FILE", required_argument, NULL, METRICS_FILE},
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{"REMOVE_DUPLICATES", required_argument, NULL, REMOVE_DUPLICATES},
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{"ASSUME_SORTED", required_argument, NULL, ASSUME_SORTED},
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{"ASSUME_SORT_ORDER", required_argument, NULL, ASSUME_SORT_ORDER},
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{"DUPLICATE_SCORING_STRATEGY", required_argument, NULL, DUPLICATE_SCORING_STRATEGY},
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{"PROGRAM_RECORD_ID", required_argument, NULL, PROGRAM_RECORD_ID},
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{"PROGRAM_GROUP_VERSION", required_argument, NULL, PROGRAM_GROUP_VERSION},
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{"PROGRAM_GROUP_COMMAND_LINE", required_argument, NULL, PROGRAM_GROUP_COMMAND_LINE},
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{"PROGRAM_GROUP_NAME", required_argument, NULL, PROGRAM_GROUP_NAME},
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{"COMMENT", required_argument, NULL, COMMENT},
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{"READ_NAME_REGEX", required_argument, NULL, READ_NAME_REGEX},
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{"OPTICAL_DUPLICATE_PIXEL_DISTANCE", required_argument, NULL, OPTICAL_DUPLICATE_PIXEL_DISTANCE},
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{"MAX_OPTICAL_DUPLICATE_SET_SIZE", required_argument, NULL, MAX_OPTICAL_DUPLICATE_SET_SIZE},
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{"QUIET", required_argument, NULL, QUIET},
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{"VALIDATION_STRINGENCY", required_argument, NULL, VALIDATION_STRINGENCY},
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{"COMPRESSION_LEVEL", required_argument, NULL, COMPRESSION_LEVEL},
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{"MAX_RECORDS_IN_RAM", required_argument, NULL, MAX_RECORDS_IN_RAM},
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{"CREATE_INDEX", required_argument, NULL, CREATE_INDEX},
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{"CREATE_MD5_FILE", required_argument, NULL, CREATE_MD5_FILE}};
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// 判断bool类型的参数
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void setBoolArg(bool *arg) {
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if (strcmp("true", optarg) == 0)
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*arg = true;
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else if (strcmp("false", optarg) == 0)
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*arg = false;
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}
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// 解析参数
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void MarkDupsArg::parseArgument(int argc,
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char **argv,
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vector<AuxVar> *pvAuxVar,
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GlobalArg *pGArg)
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{
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auto &vAuxVar = *pvAuxVar;
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auto &gArg = *pGArg;
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struct option allOpt[MarkDupsArg::ARG_COUNT + GlobalArg::GLOBAL_ARG_CNT];
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memcpy(allOpt, kMdOpts, MarkDupsArg::ARG_COUNT * sizeof(struct option));
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memcpy(&allOpt[MarkDupsArg::ARG_COUNT], GlobalArg::GLOBAL_OPT, GlobalArg::GLOBAL_ARG_CNT * sizeof(struct option));
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// int cnt = MarkDupsArg::ARG_COUNT + GlobalArg::GLOBAL_ARG_CNT;
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// cout << cnt << endl;
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// for (int i = 0; i < cnt; ++i)
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// {
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// cout << i << '\t' << allOpt[i].name << endl;
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// }
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int c;
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while ((c = getopt_long_only(argc, argv, "", allOpt, NULL)) >= 0)
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{
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gArg.parseArgument(c);
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switch (c)
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{
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case ns_ga::OPT_VERSION:
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PrintVersion();
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exit(0);
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case ns_ga::OPT_HELP:
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PrintHelp();
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exit(0);
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case ns_md::MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP:
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MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP = stoi(optarg);
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break;
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case ns_md::MAX_FILE_HANDLES_FOR_READ_ENDS_MAP:
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MAX_FILE_HANDLES_FOR_READ_ENDS_MAP = stoi(optarg);
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break;
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case ns_md::SORTING_COLLECTION_SIZE_RATIO:
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SORTING_COLLECTION_SIZE_RATIO = stod(optarg);
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break;
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case ns_md::BARCODE_TAG:
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BARCODE_TAG = optarg;
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break;
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case ns_md::READ_ONE_BARCODE_TAG:
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READ_ONE_BARCODE_TAG = optarg;
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break;
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case ns_md::READ_TWO_BARCODE_TAG:
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READ_TWO_BARCODE_TAG = optarg;
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break;
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case ns_md::TAG_DUPLICATE_SET_MEMBERS:
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setBoolArg(&TAG_DUPLICATE_SET_MEMBERS);
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break;
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case ns_md::REMOVE_SEQUENCING_DUPLICATES:
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setBoolArg(&REMOVE_SEQUENCING_DUPLICATES);
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break;
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case ns_md::TAGGING_POLICY:
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if (strcmp("DontTag", optarg) == 0)
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TAGGING_POLICY = ns_md::DuplicateTaggingPolicy::DontTag;
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else if (strcmp("OpticalOnly", optarg) == 0)
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TAGGING_POLICY = ns_md::DuplicateTaggingPolicy::OpticalOnly;
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else if (strcmp("All", optarg) == 0)
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TAGGING_POLICY = ns_md::DuplicateTaggingPolicy::All;
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break;
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case ns_md::CLEAR_DT:
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setBoolArg(&CLEAR_DT);
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break;
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case ns_md::DUPLEX_UMI:
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setBoolArg(&DUPLEX_UMI);
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break;
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case ns_md::MOLECULAR_IDENTIFIER_TAG:
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MOLECULAR_IDENTIFIER_TAG = optarg;
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break;
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case ns_md::METRICS_FILE:
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METRICS_FILE = optarg;
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break;
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case ns_md::REMOVE_DUPLICATES:
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setBoolArg(&REMOVE_DUPLICATES);
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break;
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case ns_md::ASSUME_SORTED:
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setBoolArg(&ASSUME_SORTED);
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break;
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case ns_md::ASSUME_SORT_ORDER:
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if (strcmp("unsorted", optarg) == 0)
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ASSUME_SORT_ORDER = ns_md::SortOrder::unsorted;
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else if (strcmp("queryname", optarg) == 0)
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ASSUME_SORT_ORDER = ns_md::SortOrder::queryname;
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else if (strcmp("coordinate", optarg) == 0)
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ASSUME_SORT_ORDER = ns_md::SortOrder::coordinate;
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else if (strcmp("duplicate", optarg) == 0)
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ASSUME_SORT_ORDER = ns_md::SortOrder::duplicate;
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else if (strcmp("unknown", optarg) == 0)
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ASSUME_SORT_ORDER = ns_md::SortOrder::unknown;
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break;
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case ns_md::DUPLICATE_SCORING_STRATEGY:
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if (strcmp("SUM_OF_BASE_QUALITIES", optarg) == 0)
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DUPLICATE_SCORING_STRATEGY = ns_md::ScoringStrategy::SUM_OF_BASE_QUALITIES;
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else if (strcmp("TOTAL_MAPPED_REFERENCE_LENGTH", optarg) == 0)
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DUPLICATE_SCORING_STRATEGY = ns_md::ScoringStrategy::TOTAL_MAPPED_REFERENCE_LENGTH;
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else if (strcmp("RANDOM", optarg) == 0)
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DUPLICATE_SCORING_STRATEGY = ns_md::ScoringStrategy::RANDOM;
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break;
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case ns_md::PROGRAM_RECORD_ID:
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PROGRAM_RECORD_ID = optarg;
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break;
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case ns_md::PROGRAM_GROUP_VERSION:
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PROGRAM_GROUP_VERSION = optarg;
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break;
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case ns_md::PROGRAM_GROUP_COMMAND_LINE:
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PROGRAM_GROUP_COMMAND_LINE = optarg;
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break;
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case ns_md::PROGRAM_GROUP_NAME:
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PROGRAM_GROUP_NAME = optarg;
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break;
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case ns_md::COMMENT:
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COMMENT.push_back(optarg);
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break;
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case ns_md::READ_NAME_REGEX:
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READ_NAME_REGEX = optarg;
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break;
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case ns_md::OPTICAL_DUPLICATE_PIXEL_DISTANCE:
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OPTICAL_DUPLICATE_PIXEL_DISTANCE = stoi(optarg);
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break;
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case ns_md::MAX_OPTICAL_DUPLICATE_SET_SIZE:
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MAX_OPTICAL_DUPLICATE_SET_SIZE = stol(optarg);
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break;
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case ns_md::QUIET:
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setBoolArg(&QUIET);
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break;
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case ns_md::VALIDATION_STRINGENCY:
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if (strcmp("STRICT", optarg) == 0)
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VALIDATION_STRINGENCY = ns_md::ValidationStringency::STRICT;
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else if (strcmp("LENIENT", optarg) == 0)
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VALIDATION_STRINGENCY = ns_md::ValidationStringency::LENIENT;
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else if (strcmp("SILENT", optarg) == 0)
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VALIDATION_STRINGENCY = ns_md::ValidationStringency::SILENT;
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break;
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case ns_md::COMPRESSION_LEVEL:
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COMPRESSION_LEVEL = stoi(optarg);
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break;
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case ns_md::MAX_RECORDS_IN_RAM:
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MAX_RECORDS_IN_RAM = stoi(optarg);
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break;
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case ns_md::CREATE_INDEX:
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setBoolArg(&CREATE_INDEX);
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break;
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case ns_md::CREATE_MD5_FILE:
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setBoolArg(&CREATE_MD5_FILE);
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break;
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default:
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break;
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}
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}
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gArg.printArgValue();
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}
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// 打印版本信息
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void MarkDupsArg::PrintVersion()
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{
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fprintf(stdout, "\n MarkDuplicate Version: %s\n", MARKDUPLICATE_VERSION);
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}
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// 释放资源，关闭文件等
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void MarkDupsArg::Finalize(MarkDupsArg *pMdArg,
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vector<AuxVar> *pvAuxVar,
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GlobalArg *pGArg)
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{
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}
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// 打印帮助信息
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void MarkDupsArg::PrintHelp()
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{
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FILE *fp = stdout;
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fprintf(fp,
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"Usage: MarkDuplicates [arguments]\n"
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"\n"
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"Example:\n"
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" ./picard_cpp MarkDuplicates --num_thread 4 --INPUT input.bam --OUTPUT marked_duplicates.bam --METRICS_FILE marked_dup_metrics.txt\n"
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"\n"
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"Required Arguments:\n"
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"\n"
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"--INPUT,-I <String> One or more input SAM, BAM or CRAM files to analyze. Must be coordinate sorted. This\n"
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|
|
|
" argument must be specified at least once.Required.\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--METRICS_FILE,-M <File> File to write duplication metrics to Required.\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--OUTPUT,-O <File> The output file to write marked records to Required.\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"Optional Arguments:\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--ADD_PG_TAG_TO_READS <Boolean>\n"
|
|
|
|
|
|
" Add PG tag to each read in a SAM or BAM Default value: true. Possible values: {true,\n"
|
|
|
|
|
|
" false}\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--arguments_file <File> read one or more arguments files and add them to the command line This argument may be\n"
|
|
|
|
|
|
" specified 0 or more times. Default value: null.\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--ASSUME_SORT_ORDER,-ASO <SortOrder>\n"
|
|
|
|
|
|
" If not null, assume that the input file has this order even if the header says otherwise.\n"
|
|
|
|
|
|
" Default value: null. Possible values: {unsorted, queryname, coordinate, duplicate,\n"
|
|
|
|
|
|
" unknown} Cannot be used in conjunction with argument(s) ASSUME_SORTED (AS)\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--ASSUME_SORTED,-AS <Boolean> If true, assume that the input file is coordinate sorted even if the header says\n"
|
|
|
|
|
|
" otherwise. Deprecated, used ASSUME_SORT_ORDER=coordinate instead. Default value: false.\n"
|
|
|
|
|
|
" Possible values: {true, false} Cannot be used in conjunction with argument(s)\n"
|
|
|
|
|
|
" ASSUME_SORT_ORDER (ASO)\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--BARCODE_TAG <String> Barcode SAM tag (ex. BC for 10X Genomics) Default value: null.\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--CLEAR_DT <Boolean> Clear DT tag from input SAM records. Should be set to false if input SAM doesn't have this\n"
|
|
|
|
|
|
" tag. Default true Default value: true. Possible values: {true, false}\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--COMMENT,-CO <String> Comment(s) to include in the output file's header. This argument may be specified 0 or\n"
|
|
|
|
|
|
" more times. Default value: null.\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--COMPRESSION_LEVEL <Integer> Compression level for all compressed files created (e.g. BAM and VCF). Default value: 5.\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--CREATE_INDEX <Boolean> Whether to create an index when writing VCF or coordinate sorted BAM output. Default\n"
|
|
|
|
|
|
" value: false. Possible values: {true, false}\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--CREATE_MD5_FILE <Boolean> Whether to create an MD5 digest for any BAM or FASTQ files created. Default value:\n"
|
|
|
|
|
|
" false. Possible values: {true, false}\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--DUPLEX_UMI <Boolean> Treat UMIs as being duplex stranded. This option requires that the UMI consist of two\n"
|
|
|
|
|
|
" equal length strings that are separated by a hyphen (e.g. 'ATC-GTC'). Reads are considered\n"
|
|
|
|
|
|
" duplicates if, in addition to standard definition, have identical normalized UMIs. A UMI\n"
|
|
|
|
|
|
" from the 'bottom' strand is normalized by swapping its content around the hyphen (eg.\n"
|
|
|
|
|
|
" ATC-GTC becomes GTC-ATC). A UMI from the 'top' strand is already normalized as it is.\n"
|
|
|
|
|
|
" Both reads from a read pair considered top strand if the read 1 unclipped 5' coordinate is\n"
|
|
|
|
|
|
" less than the read 2 unclipped 5' coordinate. All chimeric reads and read fragments are\n"
|
|
|
|
|
|
" treated as having come from the top strand. With this option is it required that the\n"
|
|
|
|
|
|
" BARCODE_TAG hold non-normalized UMIs. Default false. Default value: false. Possible\n"
|
|
|
|
|
|
" values: {true, false}\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--DUPLICATE_SCORING_STRATEGY,-DS <ScoringStrategy>\n"
|
|
|
|
|
|
" The scoring strategy for choosing the non-duplicate among candidates. Default value:\n"
|
|
|
|
|
|
" SUM_OF_BASE_QUALITIES. Possible values: {SUM_OF_BASE_QUALITIES,\n"
|
|
|
|
|
|
" TOTAL_MAPPED_REFERENCE_LENGTH, RANDOM}\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--FLOW_EFFECTIVE_QUALITY_THRESHOLD <Integer>\n"
|
|
|
|
|
|
" Threshold for considering a quality value high enough to be included when calculating\n"
|
|
|
|
|
|
" FLOW_QUALITY_SUM_STRATEGY calculation. Default value: 15.\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--FLOW_MODE <Boolean> enable parameters and behavior specific to flow based reads. Default value: false.\n"
|
|
|
|
|
|
" Possible values: {true, false}\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--FLOW_Q_IS_KNOWN_END <Boolean>\n"
|
|
|
|
|
|
" Treat position of read trimming based on quality as the known end (relevant for flow based\n"
|
|
|
|
|
|
" reads). Default false - if the read is trimmed on quality its end is not defined and the\n"
|
|
|
|
|
|
" read is duplicate of any read starting at the same place. Default value: false. Possible\n"
|
|
|
|
|
|
" values: {true, false}\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--FLOW_QUALITY_SUM_STRATEGY <Boolean>\n"
|
|
|
|
|
|
" Use specific quality summing strategy for flow based reads. The strategy ensures that the\n"
|
|
|
|
|
|
" same (and correct) quality value is used for all bases of the same homopolymer. Default\n"
|
|
|
|
|
|
" value: false. Possible values: {true, false}\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--FLOW_SKIP_FIRST_N_FLOWS <Integer>\n"
|
|
|
|
|
|
" Skip first N flows, starting from the read's start, when considering duplicates. Useful\n"
|
|
|
|
|
|
" for flow based reads where sometimes there is noise in the first flows (for this argument,\n"
|
|
|
|
|
|
" \" read start \" means 5' end). Default value: 0.\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--help,-h <Boolean> display the help message Default value: false. Possible values: {true, false}\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--MAX_FILE_HANDLES_FOR_READ_ENDS_MAP,-MAX_FILE_HANDLES <Integer>\n"
|
|
|
|
|
|
" Maximum number of file handles to keep open when spilling read ends to disk. Set this\n"
|
|
|
|
|
|
" number a little lower than the per-process maximum number of file that may be open. This\n"
|
|
|
|
|
|
" number can be found by executing the 'ulimit -n' command on a Unix system. Default value:\n"
|
|
|
|
|
|
" 8000.\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--MAX_OPTICAL_DUPLICATE_SET_SIZE <Long>\n"
|
|
|
|
|
|
" This number is the maximum size of a set of duplicate reads for which we will attempt to\n"
|
|
|
|
|
|
" determine which are optical duplicates. Please be aware that if you raise this value too\n"
|
|
|
|
|
|
" high and do encounter a very large set of duplicate reads, it will severely affect the\n"
|
|
|
|
|
|
" runtime of this tool. To completely disable this check, set the value to -1. Default\n"
|
|
|
|
|
|
" value: 300000.\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--MAX_RECORDS_IN_RAM <Integer>When writing files that need to be sorted, this will specify the number of records stored\n"
|
|
|
|
|
|
" in RAM before spilling to disk. Increasing this number reduces the number of file handles\n"
|
|
|
|
|
|
" needed to sort the file, and increases the amount of RAM needed. Default value: 500000.\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP,-MAX_SEQS <Integer>\n"
|
|
|
|
|
|
" This option is obsolete. ReadEnds will always be spilled to disk. Default value: 50000.\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--MOLECULAR_IDENTIFIER_TAG <String>\n"
|
|
|
|
|
|
" SAM tag to uniquely identify the molecule from which a read was derived. Use of this\n"
|
|
|
|
|
|
" option requires that the BARCODE_TAG option be set to a non null value. Default null.\n"
|
|
|
|
|
|
" Default value: null.\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--OPTICAL_DUPLICATE_PIXEL_DISTANCE <Integer>\n"
|
|
|
|
|
|
" The maximum offset between two duplicate clusters in order to consider them optical\n"
|
|
|
|
|
|
" duplicates. The default is appropriate for unpatterned versions of the Illumina platform.\n"
|
|
|
|
|
|
" For the patterned flowcell models, 2500 is moreappropriate. For other platforms and\n"
|
|
|
|
|
|
" models, users should experiment to find what works best. Default value: 100.\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--PROGRAM_GROUP_COMMAND_LINE,-PG_COMMAND <String>\n"
|
|
|
|
|
|
" Value of CL tag of PG record to be created. If not supplied the command line will be\n"
|
|
|
|
|
|
" detected automatically. Default value: null.\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--PROGRAM_GROUP_NAME,-PG_NAME <String>\n"
|
|
|
|
|
|
" Value of PN tag of PG record to be created. Default value: MarkDuplicates.\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--PROGRAM_GROUP_VERSION,-PG_VERSION <String>\n"
|
|
|
|
|
|
" Value of VN tag of PG record to be created. If not specified, the version will be detected\n"
|
|
|
|
|
|
" automatically. Default value: null.\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--PROGRAM_RECORD_ID,-PG <String>\n"
|
|
|
|
|
|
" The program record ID for the @PG record(s) created by this program. Set to null to\n"
|
|
|
|
|
|
" disable PG record creation. This string may have a suffix appended to avoid collision\n"
|
|
|
|
|
|
" with other program record IDs. Default value: MarkDuplicates.\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--QUIET <Boolean> Whether to suppress job-summary info on System.err. Default value: false. Possible\n"
|
|
|
|
|
|
" values: {true, false}\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--READ_NAME_REGEX <String> MarkDuplicates can use the tile and cluster positions to estimate the rate of optical\n"
|
|
|
|
|
|
" duplication in addition to the dominant source of duplication, PCR, to provide a more\n"
|
|
|
|
|
|
" accurate estimation of library size. By default (with no READ_NAME_REGEX specified),\n"
|
|
|
|
|
|
" MarkDuplicates will attempt to extract coordinates using a split on ':' (see Note below).\n"
|
|
|
|
|
|
" Set READ_NAME_REGEX to 'null' to disable optical duplicate detection. Note that without\n"
|
|
|
|
|
|
" optical duplicate counts, library size estimation will be less accurate. If the read name\n"
|
|
|
|
|
|
" does not follow a standard Illumina colon-separation convention, but does contain tile and\n"
|
|
|
|
|
|
" x,y coordinates, a regular expression can be specified to extract three variables:\n"
|
|
|
|
|
|
" tile/region, x coordinate and y coordinate from a read name. The regular expression must\n"
|
|
|
|
|
|
" contain three capture groups for the three variables, in order. It must match the entire\n"
|
|
|
|
|
|
" read name. e.g. if field names were separated by semi-colon (';') this example regex\n"
|
|
|
|
|
|
" could be specified (?:.*;)?([0-9]+)[^;]*;([0-9]+)[^;]*;([0-9]+)[^;]*$ Note that if no\n"
|
|
|
|
|
|
" READ_NAME_REGEX is specified, the read name is split on ':'. For 5 element names, the\n"
|
|
|
|
|
|
" 3rd, 4th and 5th elements are assumed to be tile, x and y values. For 7 element names\n"
|
|
|
|
|
|
" (CASAVA 1.8), the 5th, 6th, and 7th elements are assumed to be tile, x and y values.\n"
|
|
|
|
|
|
" Default value: <optimized capture of last three ':' separated fields as numeric values>.\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--READ_ONE_BARCODE_TAG <String>\n"
|
|
|
|
|
|
" Read one barcode SAM tag (ex. BX for 10X Genomics) Default value: null.\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--READ_TWO_BARCODE_TAG <String>\n"
|
|
|
|
|
|
" Read two barcode SAM tag (ex. BX for 10X Genomics) Default value: null.\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--REFERENCE_SEQUENCE,-R <File>Reference sequence file. Default value: null.\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--REMOVE_DUPLICATES <Boolean> If true do not write duplicates to the output file instead of writing them with\n"
|
|
|
|
|
|
" appropriate flags set. Default value: false. Possible values: {true, false}\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--REMOVE_SEQUENCING_DUPLICATES <Boolean>\n"
|
|
|
|
|
|
" If true remove 'optical' duplicates and other duplicates that appear to have arisen from\n"
|
|
|
|
|
|
" the sequencing process instead of the library preparation process, even if\n"
|
|
|
|
|
|
" REMOVE_DUPLICATES is false. If REMOVE_DUPLICATES is true, all duplicates are removed and\n"
|
|
|
|
|
|
" this option is ignored. Default value: false. Possible values: {true, false}\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--SORTING_COLLECTION_SIZE_RATIO <Double>\n"
|
|
|
|
|
|
" This number, plus the maximum RAM available to the JVM, determine the memory footprint\n"
|
|
|
|
|
|
" used by some of the sorting collections. If you are running out of memory, try reducing\n"
|
|
|
|
|
|
" this number. Default value: 0.25.\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--TAG_DUPLICATE_SET_MEMBERS <Boolean>\n"
|
|
|
|
|
|
" If a read appears in a duplicate set, add two tags. The first tag, DUPLICATE_SET_SIZE_TAG\n"
|
|
|
|
|
|
" (DS), indicates the size of the duplicate set. The smallest possible DS value is 2 which\n"
|
|
|
|
|
|
" occurs when two reads map to the same portion of the reference only one of which is marked\n"
|
|
|
|
|
|
" as duplicate. The second tag, DUPLICATE_SET_INDEX_TAG (DI), represents a unique identifier\n"
|
|
|
|
|
|
" for the duplicate set to which the record belongs. This identifier is the index-in-file of\n"
|
|
|
|
|
|
" the representative read that was selected out of the duplicate set. Default value: false.\n"
|
|
|
|
|
|
" Possible values: {true, false}\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--TAGGING_POLICY <DuplicateTaggingPolicy>\n"
|
|
|
|
|
|
" Determines how duplicate types are recorded in the DT optional attribute. Default value:\n"
|
|
|
|
|
|
" DontTag. Possible values: {DontTag, OpticalOnly, All}\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--TMP_DIR <File> One or more directories with space available to be used by this program for temporary\n"
|
|
|
|
|
|
" storage of working files This argument may be specified 0 or more times. Default value:\n"
|
|
|
|
|
|
" null.\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--UNPAIRED_END_UNCERTAINTY <Integer>\n"
|
|
|
|
|
|
" Maximal difference of the read end position that counted as equal. Useful for flow based\n"
|
|
|
|
|
|
" reads where the end position might vary due to sequencing errors. (for this argument,\n"
|
|
|
|
|
|
" \" read end \" means 3' end) Default value: 0.\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--USE_END_IN_UNPAIRED_READS <Boolean>\n"
|
|
|
|
|
|
" Make the end location of single end read be significant when considering duplicates, in\n"
|
|
|
|
|
|
" addition to the start location, which is always significant (i.e. require single-ended\n"
|
|
|
|
|
|
" reads to start andend on the same position to be considered duplicate) (for this argument,\n"
|
|
|
|
|
|
" \" read end \" means 3' end). Default value: false. Possible values: {true, false}\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--USE_JDK_DEFLATER,-use_jdk_deflater <Boolean>\n"
|
|
|
|
|
|
" Use the JDK Deflater instead of the Intel Deflater for writing compressed output Default\n"
|
|
|
|
|
|
" value: false. Possible values: {true, false}\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--USE_JDK_INFLATER,-use_jdk_inflater <Boolean>\n"
|
|
|
|
|
|
" Use the JDK Inflater instead of the Intel Inflater for reading compressed input Default\n"
|
|
|
|
|
|
" value: false. Possible values: {true, false}\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--USE_UNPAIRED_CLIPPED_END <Boolean>\n"
|
|
|
|
|
|
" Use position of the clipping as the end position, when considering duplicates (or use the\n"
|
|
|
|
|
|
" unclipped end position) (for this argument, \" read end \" means 3' end). Default value:\n"
|
|
|
|
|
|
" false. Possible values: {true, false}\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--VALIDATION_STRINGENCY <ValidationStringency>\n"
|
|
|
|
|
|
" Validation stringency for all SAM files read by this program. Setting stringency to\n"
|
|
|
|
|
|
" SILENT can improve performance when processing a BAM file in which variable-length data\n"
|
|
|
|
|
|
" (read, qualities, tags) do not otherwise need to be decoded. Default value: STRICT.\n"
|
|
|
|
|
|
" Possible values: {STRICT, LENIENT, SILENT}\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
|
"--VERBOSITY <LogLevel> Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING,\n"
|
|
|
|
|
|
" INFO, DEBUG}\n"
|
|
|
|
|
|
"\n"
|
|
|
|
|
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"--version <Boolean> display the version number for this tool Default value: false. Possible values: {true,\n"
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" false}\n"
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"\n");
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}
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