2024-08-22 02:28:36 +08:00
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#pragma once
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#include <common/utils/timer.h>
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#include <common/utils/util.h>
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#include <htslib/sam.h>
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#include <htslib/thread_pool.h>
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#include <sam/utils/read_ends.h>
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#include <sam/utils/read_name_parser.h>
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2024-11-11 18:10:17 +08:00
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//#include "md_types.h"
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2024-08-28 12:00:23 +08:00
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#include <set>
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using std::set;
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2024-08-22 02:28:36 +08:00
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2024-11-21 22:46:50 +08:00
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extern Timer tm_arr[50]; // 用来测试性能
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2024-08-22 02:28:36 +08:00
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/* 全局本地变量 */
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extern vector<ReadNameParser> g_vRnParser; // 每个线程一个read name parser
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extern samFile *g_inBamFp; // 输入的bam文件
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extern sam_hdr_t *g_inBamHeader; // 输入的bam文件头信息
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extern samFile *g_outBamFp; // 输出文件, sam或者bam格式
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extern sam_hdr_t *g_outBamHeader; // 输出文件的header
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/* 参数对象作为全局对象，免得多次作为参数传入函数中 */
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class GlobalArg;
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2024-11-11 18:10:17 +08:00
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extern GlobalArg &g_gArg; // 全局参数
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2024-08-22 02:28:36 +08:00
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class MarkDupsArg;
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2024-11-11 18:10:17 +08:00
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extern MarkDupsArg &g_mdArg; // markduplicate程序相关的参数
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// 上边加下划线表示所有模块共享，不加下划线表示markduplicate计算时候内部使用
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2024-11-26 23:51:16 +08:00
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class PipelineArg;
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extern PipelineArg &gPipe; // 计算冗余过程中保存在全局的数据
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2024-08-22 02:28:36 +08:00
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class DuplicationMetrics;
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2024-11-11 18:10:17 +08:00
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extern DuplicationMetrics &gMetrics; // 用来计算统计信息
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2024-08-28 12:00:23 +08:00
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extern int zzhtestnum;
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2024-11-11 18:10:17 +08:00
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extern int64_t bam_num1, bam_num2;
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