2024-12-14 12:24:19 +08:00
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/*
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Description:
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标记bam文件中的冗余信息，只处理按照坐标排序后的bam，且bam为单一样本数据
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Copyright : All right reserved by ICT
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Author : Zhang Zhonghai
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Date : 2023/10/23
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*/
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2024-12-15 03:20:35 +08:00
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#include <htslib/sam.h>
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#include <htslib/thread_pool.h>
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#include <spdlog/spdlog.h>
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2024-12-14 12:24:19 +08:00
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2024-12-15 03:20:35 +08:00
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#include <vector>
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#include "dup_metrics.h"
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#include "md_args.h"
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#include "md_funcs.h"
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#include "pipeline_md.h"
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#include "read_name_parser.h"
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#include "util/profiling.h"
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#include "version.h"
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#define BAM_BLOCK_SIZE 16L * 1024 * 1024
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namespace nsgv {
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MarkDupsArg gMdArg; // 用来测试性能
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std::vector<ReadNameParser> gNameParsers; // 每个线程一个read name parser
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samFile *gInBamFp; // 输入的bam文件
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sam_hdr_t *gInBamHeader; // 输入的bam文件头信息
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samFile *gOutBamFp; // 输出文件, sam或者bam格式
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sam_hdr_t *gOutBamHeader; // 输出文件的header
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DuplicationMetrics gMetrics; // 统计信息
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PipelineArg gPipe;
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};
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/*
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* 获取文件名后缀
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*/
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static string getFileExtension(const string &filename) {
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auto last_dot = filename.find_last_of('.');
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if (last_dot == string::npos) {
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return "";
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}
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return filename.substr(last_dot + 1);
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}
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// entrance of mark duplicates
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int MarkDuplicates() {
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/* 初始化一些参数和变量*/
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nsgv::gNameParsers.resize(nsgv::gMdArg.NUM_THREADS);
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for (auto &parser : nsgv::gNameParsers)
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parser.SetReadNameRegex(nsgv::gMdArg.READ_NAME_REGEX); // 用来解析read name中的tile，x，y信息
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/* 打开输入bam文件 */
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nsgv::gInBamFp = sam_open_format(nsgv::gMdArg.INPUT_FILE.c_str(), "r", nullptr);
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if (!nsgv::gInBamFp) {
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spdlog::error("[{}] load sam/bam file failed.\n", __func__);
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return -1;
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}
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hts_set_opt(nsgv::gInBamFp, HTS_OPT_BLOCK_SIZE, BAM_BLOCK_SIZE);
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nsgv::gInBamHeader = sam_hdr_read(nsgv::gInBamFp); // 读取header
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// 获取样本名称(libraryId)
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nsgv::gMetrics.LIBRARY = sam_hdr_line_name(nsgv::gInBamHeader, "RG", 0);
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/* 利用线程池对输入输出文件进行读写 */
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htsThreadPool htsPoolRead = {NULL, 0}; // 多线程读取，创建线程池
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htsThreadPool htsPoolWrite = {NULL, 0}; // 读写用不同的线程池
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htsPoolRead.pool = hts_tpool_init(nsgv::gMdArg.NUM_THREADS);
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htsPoolWrite.pool = hts_tpool_init(nsgv::gMdArg.NUM_THREADS);
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// htsPoolRead.pool = hts_tpool_init(8);
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// htsPoolWrite.pool = hts_tpool_init(32);
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if (!htsPoolRead.pool || !htsPoolWrite.pool) {
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spdlog::error("[{}] failed to set up thread pool", __LINE__);
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sam_close(nsgv::gInBamFp);
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return -1;
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}
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hts_set_opt(nsgv::gInBamFp, HTS_OPT_THREAD_POOL, &htsPoolRead);
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// 测试读写速度
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#if 1
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bam1_t *bamp = bam_init1();
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while (sam_read1(nsgv::gInBamFp, nsgv::gInBamHeader, bamp) >= 0);
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DisplayProfiling(nsgv::gMdArg.NUM_THREADS);
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exit(0);
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#endif
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return 0;
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}
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