clean了一下代码
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@ -11,15 +11,7 @@
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#include "sam_io.h"
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#include "sort_args.h"
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#include "global_vars.h"
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#define PROGRAM_NAME "FastSort"
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#define BAM_COMPRESS_RATIAO 5 // 大概5倍压缩比，用来粗略估计解压后需要多少内存空间
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namespace nsgv {
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// 全局变量 for bamsort
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extern SortArg gSortArg; // 参数
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extern HeaderBuf gInHdr; // 输入文件的header
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extern bool gIsBigEndian;
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}; // namespace nsgv
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@ -1,10 +0,0 @@
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/*
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Description: 压缩相关的函数
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Copyright : All right reserved by ICT
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Author : Zhang Zhonghai
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Date : 2026/02/08
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*/
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#pragma once
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@ -1,10 +0,0 @@
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/*
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Description: 解压相关的函数
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Copyright : All right reserved by ICT
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Author : Zhang Zhonghai
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Date : 2026/02/08
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*/
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#pragma once
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@ -1,5 +1,8 @@
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#include "global_vars.h"
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// 全局参数
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namespace nsgv {
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};
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SortArg gSortArg; // 参数
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HeaderBuf gInHdr; // 输入文件的header
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bool gIsBigEndian;
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}; // namespace nsgv
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@ -32,44 +32,33 @@ std::string getFileNameWithoutExt(const std::string& filepath) {
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return filepath.substr(nameStart);
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}
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void phase1Pipeline() {
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std::string getFilePathWithoutExt(const std::string& filepath) {
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// 1. 找到最后一个路径分隔符
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size_t sep = filepath.find_last_of("/\\");
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size_t nameStart = (sep == std::string::npos) ? 0 : sep + 1;
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#if 1
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/* set up*/
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Phase1PipelineArg phase1Arg;
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phase1Arg.numThread = nsgv::gSortArg.NUM_THREADS;
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const size_t kReadBufSize = 4L * 1024 * 1024 * phase1Arg.numThread; // 平均每线程4M缓冲区，累加起来，用来读入文件（BAM/SAM）（相对解压之后的缓冲区，大小可以忽略）
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// 2. 找到最后一个点（作为扩展名的分隔符）
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size_t dot = filepath.find_last_of('.');
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phase1Arg.midFileNamePrefix = getFileNameWithoutExt(nsgv::gSortArg.OUTPUT_FILE) + "_sort_mid.";
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phase1Arg.maxMemBytes = nsgv::gSortArg.MAX_MEM;
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phase1Arg.uncompressBufBytes = nsgv::gSortArg.MAX_MEM; // 比最大内存参数小点
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for (int i = 0; i<phase1Arg.UNCOMPRESS_BUF_NUM; ++i) {
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phase1Arg.threadUncompressWrap[i].Resize(phase1Arg.numThread); // 每个线程的解压block数组初始大小，后续如果不够用会自动扩容
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// 3. 仅当点位于文件名起始之后时，才认为是扩展名
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if (dot != std::string::npos && dot > nameStart) {
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return filepath.substr(0, dot);
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}
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phase1Arg.singleThreadMemBytes = kReadBufSize * BAM_COMPRESS_RATIAO;
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spdlog::info("max mem: {}, uncompress mem: {}, single thread mem: {}", nsgv::gSortArg.MAX_MEM, phase1Arg.uncompressBufBytes, phase1Arg.singleThreadMemBytes);
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for (int i = 0; i < phase1Arg.READ_BUF_NUM; ++i) {
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phase1Arg.readData[i].Resize(kReadBufSize);
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};
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return filepath;
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}
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// 根据最大内存参数，计算初始化开辟的空间
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phase1Arg.uncompressData.Resize(phase1Arg.uncompressBufBytes);
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void phase1Pipeline(Phase1PipelineArg& p) {
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PROF_G_BEG(mid_all);
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/* create threads */
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pthread_t tidArr[3]; // 2-stage pipeline
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pthread_create(&tidArr[0], NULL, phase1ReadFile, &phase1Arg);
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pthread_create(&tidArr[1], NULL, phase1Uncompress, &phase1Arg);
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pthread_create(&tidArr[2], NULL, phase1MemCopy, &phase1Arg);
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pthread_create(&tidArr[0], NULL, phase1ReadFile, &p);
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pthread_create(&tidArr[1], NULL, phase1Uncompress, &p);
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pthread_create(&tidArr[2], NULL, phase1MemCopy, &p);
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for (int i = 0; i < 3; ++i) pthread_join(tidArr[i], NULL);
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spdlog::info("all bams num: {}", phase1Arg.bamNum);
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spdlog::info("all bams num: {}", p.bamNum);
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PROF_G_END(mid_all);
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#endif
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}
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@ -202,6 +202,8 @@ struct Phase1PipelineArg {
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// 排序第一阶段，并行流水线执行程序
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void phase1Pipeline();
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void phase1Pipeline(Phase1PipelineArg &p);
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std::string getFileNameWithoutExt(const std::string& filepath);
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std::string getFilePathWithoutExt(const std::string& filepath);
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@ -0,0 +1,14 @@
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/*
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Description: 排序过程的第二阶段
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Copyright : All right reserved by ICT
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Author : Zhang Zhonghai
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Date : 2026/02/08
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*/
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#include "phase_2.h"
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void phase2Pipeline(Phase2PipelineArg& p) {
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}
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@ -13,6 +13,8 @@
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*/
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#pragma once
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#include <stdio.h>
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struct Phase2File {
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FILE* fp;
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@ -21,3 +23,22 @@ struct Phase2File {
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// ReadBuffer
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};
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// 循环缓冲区
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struct CircularBuffer {
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};
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// 循环数组
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struct CircularArray {
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};
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/* 第二阶段的多线程流水线参数 */
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struct Phase2PipelineArg {
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};
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void phase2Pipeline(Phase2PipelineArg &p);
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@ -1,10 +0,0 @@
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/*
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Description: 处理bam/sam文件的header，可能需要解压
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Copyright : All right reserved by ICT
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Author : Zhang Zhonghai
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Date : 2026/02/08
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*/
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#pragma once
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@ -16,647 +16,65 @@
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#include <algorithm>
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#include <string>
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#include "common_data.h"
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#include "const_val.h"
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#include "global_vars.h"
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#include "phase_1.h"
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#include "phase_1_read.h"
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#include "phase_1_uncompress.h"
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#include "phase_1_write.h"
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#include "phase_2.h"
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#include "sam_io.h"
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#include "sort_args.h"
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#include "sort_impl.h"
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#include "util/profiling.h"
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#include "util/yarn.h"
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#include "process_header.h"
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#include "phase_1.h"
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#include "phase_2.h"
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#include "compress.h"
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#include "decompress.h"
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using std::string;
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#define BAM_BLOCK_SIZE 16L * 1024 * 1024
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#define PARAM_BLOCK_SIZE 16L * 1024 * 1024
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namespace nsgv {
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SortArg gSortArg; // 参数
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HeaderBuf gInHdr; // 输入文件的header
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bool gIsBigEndian;
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DataBuffer gMarginBuf; // 用于存放跨两个gz block的解压数据
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}; // namespace nsgv
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struct BamSortData {
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uint16_t flag;
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uint16_t qnameLen;
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uint16_t bamLen;
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int32_t tid;
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int64_t pos;
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uint8_t *uDataPos;
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char *qname; // pointer to qname
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};
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/* 将bam文件内容读取到buf，解析buf中的gz block长度信息 */
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static size_t doFirstPipeReadFile(FirstPipeArg &p, DataBuffer &halfBlock, FILE *fpr) {
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ReadBuffer &readData = p.readData[p.readOrder % p.READ_BUF_NUM];
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size_t readState = 0;
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size_t curReadPos = 0;
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int blockLen = 0;
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int maxBlockLen = 0;
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readState = fread(readData.dataBuf, 1, readData.readBufSize, fpr);
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if (readState == 0) { return 0; }
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readData.startAddrArr.clear();
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/* 处理上一个不完整的block */ // 需要一个额外的空间来保存上一个不完整的block数据，因为readbuffer里的data和block都会用来解析，而且解析之后都会清空。
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if (halfBlock.readPos > 0) { // 上一轮有剩余
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if (halfBlock.readPos < BLOCK_HEADER_LENGTH) { // 上一轮剩余数据不满足解析block长度信息
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memcpy(&halfBlock.data[halfBlock.readPos], readData.dataBuf, BLOCK_HEADER_LENGTH - halfBlock.readPos);
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halfBlock.curLen = unpackInt16(&halfBlock.data[16]) + 1; // 更新一下剩余block的真正长度
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// spdlog::info("last remain, blocklen: {}, last load: {}", halfBlock.curLen, halfBlock.readPos);
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}
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memcpy(readData.blockBuf, halfBlock.data, halfBlock.readPos);
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curReadPos = halfBlock.curLen - halfBlock.readPos; // curlen保存上一个block的长度，readPos保存上一个block在上一次读取中的长度
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memcpy(&readData.blockBuf[halfBlock.readPos], readData.dataBuf, curReadPos); // 将不完整的block剩余数据拷贝到curBlock
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readData.startAddrArr.push_back(readData.blockBuf);
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}
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/* 解析读入buf中的文件数据，计算包含的每个block的长度信息和起始地址 */
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while (curReadPos + BLOCK_HEADER_LENGTH <= readState) { /* 确保能解析block长度 */
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blockLen = unpackInt16(&readData.dataBuf[curReadPos + 16]) + 1;
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if (blockLen > maxBlockLen) { maxBlockLen = blockLen; }
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if (curReadPos + blockLen <= readState) { /* 完整的block数据在buf里 */
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readData.startAddrArr.push_back(&readData.dataBuf[curReadPos]);
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curReadPos += blockLen;
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} else {
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break; /* 当前block数据不完整，一部分在还没读入的file数据里 */
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}
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}
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/* 如果buf中包含不完整的block数据，先保存一下，放到下一轮里去处理 */
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halfBlock.readPos = readState - curReadPos;
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halfBlock.curLen = blockLen;
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if (halfBlock.readPos > 0) {
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memcpy(halfBlock.data, &readData.dataBuf[curReadPos], halfBlock.readPos); // 将不完整的block拷贝到halfBlock
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}
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// spdlog::info("block num-1: {}", readData.startAddrArr.size());
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//spdlog::info("read order: {}, max block len: {}", p.readOrder, maxBlockLen);
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return readState;
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}
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/* FirstPipe step-1 读取文件线程 */
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static void *firstPipeReadFile(void *data) {
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FirstPipeArg &p = *(FirstPipeArg *)data;
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/* 1. set up */
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FILE *fpr = fopen(nsgv::gSortArg.INPUT_FILE.c_str(), "rb");
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parseSamHeader(fpr, nsgv::gInHdr);
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size_t fileSize = 0;
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DataBuffer halfBlock(SINGLE_BLOCK_SIZE);
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/* 2. do the work */
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while (true) {
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// self dependency
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yarn::DEPENDENCY_NOT_TO_BE(p.readSig, p.READ_BUF_NUM);
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PROF_G_BEG(read);
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size_t readState = doFirstPipeReadFile(p, halfBlock, fpr);
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PROF_G_END(read);
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if (readState == 0) {
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yarn::SIGNAL_FINISH(p.readSig, p.readFinish);
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break;
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}
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// update self status
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yarn::UPDATE_SIG_ORDER(p.readSig, p.readOrder);
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fileSize += readState;
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}
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spdlog::info("read file order: {}, file size: {}", p.readOrder, fileSize);
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/* 3. clean up */
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fclose(fpr);
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return nullptr;
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}
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static int parseBam(uint8_t* addr, bam1_t* b) {
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bam1_core_t* c = &b->core;
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int32_t block_len, ret, i;
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uint32_t new_l_data;
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uint8_t tmp[32], *x;
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b->l_data = 0;
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memcpy(&block_len, addr, 4);
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if (nsgv::gIsBigEndian)
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ed_swap_4p(&block_len);
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if (block_len < 32)
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return -4; // block_len includes core data
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x = addr + 4;
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c->tid = le_to_u32(x);
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c->pos = le_to_i32(x + 4);
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uint32_t x2 = le_to_u32(x + 8);
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c->bin = x2 >> 16;
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c->qual = x2 >> 8 & 0xff;
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c->l_qname = x2 & 0xff;
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c->l_extranul = (c->l_qname % 4 != 0) ? (4 - c->l_qname % 4) : 0;
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uint32_t x3 = le_to_u32(x + 12);
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c->flag = x3 >> 16;
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c->n_cigar = x3 & 0xffff;
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c->l_qseq = le_to_u32(x + 16);
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c->mtid = le_to_u32(x + 20);
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c->mpos = le_to_i32(x + 24);
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c->isize = le_to_i32(x + 28);
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#if 0
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new_l_data = block_len - 32 + c->l_extranul;
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if (new_l_data > INT_MAX || c->l_qseq < 0 || c->l_qname < 1)
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return -4;
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if (((uint64_t)c->n_cigar << 2) + c->l_qname + c->l_extranul + (((uint64_t)c->l_qseq + 1) >> 1) + c->l_qseq > (uint64_t)new_l_data)
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return -4;
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if (realloc_bam_data(b, new_l_data) < 0)
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return -4;
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b->l_data = new_l_data;
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if (bgzf_read_small(fp, b->data, c->l_qname) != c->l_qname)
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return -4;
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if (b->data[c->l_qname - 1] != '\0') { // try to fix missing nul termination
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if (fixup_missing_qname_nul(b) < 0)
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return -4;
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}
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for (i = 0; i < c->l_extranul; ++i) b->data[c->l_qname + i] = '\0';
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c->l_qname += c->l_extranul;
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if (b->l_data < c->l_qname || bgzf_read_small(fp, b->data + c->l_qname, b->l_data - c->l_qname) != b->l_data - c->l_qname)
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return -4;
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if (fp->is_be)
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swap_data(c, b->l_data, b->data, 0);
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if (bam_tag2cigar(b, 0, 0) < 0)
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return -4;
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// TODO: consider making this conditional
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if (c->n_cigar > 0) { // recompute "bin" and check CIGAR-qlen consistency
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hts_pos_t rlen, qlen;
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bam_cigar2rqlens(c->n_cigar, bam_get_cigar(b), &rlen, &qlen);
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if ((b->core.flag & BAM_FUNMAP) || rlen == 0)
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rlen = 1;
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b->core.bin = hts_reg2bin(b->core.pos, b->core.pos + rlen, 14, 5);
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// Sanity check for broken CIGAR alignments
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if (c->l_qseq > 0 && !(c->flag & BAM_FUNMAP) && qlen != c->l_qseq) {
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hts_log_error("CIGAR and query sequence lengths differ for %s", bam_get_qname(b));
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return -4;
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}
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}
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#endif
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return 4 + block_len;
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}
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// multi-thread uncompress bam blocks
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static void mtUncompressBlock(void *data, long idx, int tid) {
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PROF_T_BEG(mem_copy);
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UncompressData& p = *(UncompressData*)data;
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ReadBuffer &readData = *p.readDataPtr;
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auto &blockItemArr = p.blockItemArr[tid];
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auto &bamItemArr = p.bamItemArr[tid];
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auto &blockItem = blockItemArr.add();
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uint8_t *block = readData.startAddrArr[idx];
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size_t dlen = SINGLE_BLOCK_SIZE; // 65535
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int block_length = unpackInt16(&block[16]) + 1;
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uint32_t crc = le_to_u32(block + block_length - 8);
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int ret = bgzfUncompress(blockItem.data, &dlen, (Bytef *)block + BLOCK_HEADER_LENGTH,
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block_length - BLOCK_HEADER_LENGTH, crc);
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if (ret != 0) {
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spdlog::error("uncompress error, block id: {}, len: {}, ret: {}", idx, block_length, ret);
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exit(0);
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}
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blockItem.blockId = idx;
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blockItem.blockLen = dlen;
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uint32_t nextBamStart = 0;
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uint32_t bamLen = 0;
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uint32_t bamNum = 0;
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/* 解析每个bam */
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while (nextBamStart + 4 <= blockItem.blockLen) {
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OneBam& bam = bamItemArr.add();
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//bam.blockThread = &blockItemArr;
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//bam.blockIdx = blockItemArr.curIdx - 1;
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bam.offset = nextBamStart;
|
||||
uint8_t *curAddr = &blockItem.data[nextBamStart];
|
||||
#if 0
|
||||
nextBamStart += parseBam(curAddr, &bam.b);
|
||||
++bamNum;
|
||||
#else
|
||||
memcpy(&bamLen, curAddr, 4);
|
||||
curAddr += 4;
|
||||
if (nsgv::gIsBigEndian) ed_swap_4p(&bamLen);
|
||||
//bam.bamLen = bamLen;
|
||||
bam.tid = le_to_u32(curAddr);
|
||||
bam.pos = le_to_i32(curAddr + 4);
|
||||
uint32_t x2 = le_to_u32(curAddr + 8);
|
||||
bam.qnameLen = x2 & 0xff;
|
||||
|
||||
// spdlog::info("bam len: {}, bam struct len: {}", bamLen, sizeof(OneBam));
|
||||
// spdlog::info("bam name: {}, bam name len: {}", string((char*)(blockItem.data + bam.offset + OneBam::QnameOffset), bam.qnameLen), bam.qnameLen);
|
||||
nextBamStart += 4 + bamLen;
|
||||
++bamNum;
|
||||
#endif
|
||||
}
|
||||
// spdlog::info("bam num: {}", bamNum);
|
||||
if (nextBamStart != blockItem.blockLen) {
|
||||
spdlog::error("Block content does not contain integer number of bam records!");
|
||||
exit(0);
|
||||
}
|
||||
blockItem.bamNum = bamNum;
|
||||
blockItemArr.bamNum += bamNum;
|
||||
|
||||
// 判断是否超过内存阈值，只要有一个超过阈值，就转入下一阶段，进行排序和合并，但是也得把这一轮数据解压处理完
|
||||
if (blockItemArr.curIdx * SINGLE_BLOCK_SIZE * BLOCK_MEM_FACTOR >= p.father->singleThreadBytes) {
|
||||
p.father->uncompressBufFull = 1;
|
||||
} else {
|
||||
// spdlog::info("block arr: {}, single thread: {}", blockItemArr.blockArr.size() * SINGLE_BLOCK_SIZE, p.father->singleThreadBytes);
|
||||
}
|
||||
PROF_T_END(tid, mem_copy);
|
||||
}
|
||||
|
||||
// multi-thread uncompress bam blocks
|
||||
static void mtUncompressBlockBatch(void* data, long idx, int tid) {
|
||||
PROF_T_BEG(mem_copy);
|
||||
UncompressData& p = *(UncompressData*)data;
|
||||
ReadBuffer& readData = *p.readDataPtr;
|
||||
|
||||
int startIdx = START_IDX(idx, nsgv::gSortArg.NUM_THREADS, readData.startAddrArr.size());
|
||||
int stopIdx = STOP_IDX(idx, nsgv::gSortArg.NUM_THREADS, readData.startAddrArr.size());
|
||||
|
||||
auto& blockItemArr = p.blockItemArr[tid];
|
||||
auto& bamItemArr = p.bamItemArr[tid];
|
||||
|
||||
blockItemArr.add(stopIdx - startIdx);
|
||||
|
||||
for (int i = startIdx; i < stopIdx; ++i) {
|
||||
auto& blockItem = blockItemArr.blockArr[blockItemArr.curIdx++];
|
||||
|
||||
uint8_t* block = readData.startAddrArr[i];
|
||||
|
||||
size_t dlen = SINGLE_BLOCK_SIZE; // 65535
|
||||
int block_length = unpackInt16(&block[16]) + 1;
|
||||
uint32_t crc = le_to_u32(block + block_length - 8);
|
||||
int ret = bgzfUncompress(blockItem.data, &dlen, (Bytef*)block + BLOCK_HEADER_LENGTH, block_length - BLOCK_HEADER_LENGTH, crc);
|
||||
if (ret != 0) {
|
||||
spdlog::error("uncompress error, block id: {}, len: {}, ret: {}", idx, block_length, ret);
|
||||
exit(0);
|
||||
}
|
||||
blockItem.blockId = i;
|
||||
blockItem.blockLen = dlen;
|
||||
uint32_t nextBamStart = 0;
|
||||
uint32_t bamLen = 0;
|
||||
uint32_t bamNum = 0;
|
||||
|
||||
#if 1
|
||||
/* 解析每个bam */
|
||||
while (nextBamStart + 4 <= blockItem.blockLen) {
|
||||
bamItemArr.bamArr.push_back(OneBam());
|
||||
OneBam& bam = bamItemArr.bamArr.back();
|
||||
|
||||
//bam.addr = &blockItem.data[nextBamStart];
|
||||
uint8_t* curAddr = &blockItem.data[nextBamStart];
|
||||
memcpy(&bamLen, curAddr, 4);
|
||||
curAddr += 4;
|
||||
if (nsgv::gIsBigEndian)
|
||||
ed_swap_4p(&bamLen);
|
||||
// bam.bamLen = bamLen;
|
||||
bam.tid = le_to_u32(curAddr);
|
||||
bam.pos = le_to_i32(curAddr + 4);
|
||||
uint32_t x2 = le_to_u32(curAddr + 8);
|
||||
bam.qnameLen = x2 & 0xff;
|
||||
//bam.qnameAddr = (char*)(curAddr + 32);
|
||||
|
||||
// spdlog::info("bam len: {}, bam struct len: {}", bamLen, sizeof(OneBam));
|
||||
nextBamStart += 4 + bamLen;
|
||||
++bamNum;
|
||||
}
|
||||
if (nextBamStart != blockItem.blockLen) {
|
||||
spdlog::error("Block content does not contain integer number of bam records!");
|
||||
exit(0);
|
||||
}
|
||||
#endif
|
||||
blockItem.bamNum = bamNum;
|
||||
|
||||
}
|
||||
// 判断是否超过内存阈值
|
||||
if (blockItemArr.curIdx * SINGLE_BLOCK_SIZE >= p.father->singleThreadBytes) {
|
||||
p.father->uncompressBufFull = 1;
|
||||
} else {
|
||||
// spdlog::info("block arr: {}, single thread: {}", blockItemArr.blockArr.size() * SINGLE_BLOCK_SIZE, p.father->singleThreadBytes);
|
||||
}
|
||||
PROF_T_END(tid, mem_copy);
|
||||
}
|
||||
|
||||
// 线程内排序
|
||||
static void mtInThreadSort(void* data, long idx, int tid) {
|
||||
UncompressData& p = *(UncompressData*)data;
|
||||
auto& bamItemArr = p.bamItemArr[tid];
|
||||
auto& arr = bamItemArr.bamArr;
|
||||
// 先按照坐标排序
|
||||
|
||||
#if 0
|
||||
if (tid == 0)
|
||||
spdlog::info("Before: {} {} {} {} {} {} {} {} {} {}", arr[0].pos, arr[1].pos, arr[2].pos, arr[3].pos, arr[4].pos, arr[5].pos, arr[6].pos,
|
||||
arr[7].pos, arr[8].pos, arr[9].pos);
|
||||
#endif
|
||||
|
||||
if (nsgv::gSortArg.SORT_COORIDINATE) {
|
||||
std::sort(arr.begin(), arr.begin() + bamItemArr.curIdx, [](const OneBam& b1, const OneBam& b2) { return b1.pos < b2.pos; });
|
||||
} else if (nsgv::gSortArg.QUERY_NAME_TYPE == nsmd::QueryNameType::PICARD) {
|
||||
std::sort(arr.begin(), arr.begin() + bamItemArr.curIdx, [](const OneBam& b1, const OneBam& b2) {
|
||||
int cmp = 0;
|
||||
// strncmp((char*)(b1.blockThread->blockArr[b1.blockIdx].data + b1.offset + OneBam::QnameOffset),
|
||||
// (char*)(b2.blockThread->blockArr[b2.blockIdx].data + b2.offset + OneBam::QnameOffset), std::min(b1.qnameLen, b2.qnameLen));
|
||||
if (cmp == 0)
|
||||
return b1.qnameLen < b2.qnameLen;
|
||||
return cmp < 0;
|
||||
});
|
||||
}
|
||||
|
||||
#if 0
|
||||
if (tid == 0)
|
||||
spdlog::info("After: {} {} {} {} {} {} {} {} {} {}", arr[0].pos, arr[1].pos, arr[2].pos, arr[3].pos, arr[4].pos, arr[5].pos, arr[6].pos,
|
||||
arr[7].pos, arr[8].pos, arr[9].pos);
|
||||
#endif
|
||||
|
||||
}
|
||||
|
||||
// 多线程压缩
|
||||
static void mtCompressBlock(void* data, long idx, int tid) {
|
||||
FirstPipeArg &p = *(FirstPipeArg *)data;
|
||||
auto& barr = p.sortedBamArr;
|
||||
auto& t = p.taskArr[idx];
|
||||
auto& buf = p.threadBuf[tid];
|
||||
|
||||
uint8_t block[SINGLE_BLOCK_SIZE] = {0};
|
||||
uint8_t compressBlock[SINGLE_BLOCK_SIZE] = {0};
|
||||
int curAddr = 0;
|
||||
for (int i = t.idx; i < t.idx + t.num; ++i) {
|
||||
// copy data
|
||||
//memccpy(&block[curAddr], barr[i]->blockThread->blockArr[barr[i]->blockIdx].data + barr[i]->offset, 1, barr[i]->bamLen);
|
||||
//curAddr += barr[i]->bamLen;
|
||||
}
|
||||
|
||||
size_t dlen = BGZF_MAX_BLOCK_SIZE;
|
||||
// spdlog::info("len: {}", curAddr);
|
||||
bgzfCompress(block, &dlen, compressBlock, curAddr, -1);
|
||||
// 先放到自己线程内部的buf里
|
||||
|
||||
// 然后在压缩完成之后，检测当前全局压缩序号，如果当前序号的block在自己线程内，则复制过去
|
||||
|
||||
}
|
||||
|
||||
/* 将gz block进行解压，并进行线程内排序 */
|
||||
static void doFirstPipeUncompress(FirstPipeArg &p, int finish = 0) {
|
||||
// return;
|
||||
PROF_G_BEG(uncompress);
|
||||
ReadBuffer &readData = p.readData[p.uncompressOrder % p.READ_BUF_NUM];
|
||||
UncompressData &uncompressData = p.uncompressData[p.uncompressOrder % p.UNCOMPRESS_BUF_NUM];
|
||||
uncompressData.readDataPtr = &readData;
|
||||
|
||||
#if 1
|
||||
kt_for(p.numThread, mtUncompressBlock, &uncompressData, readData.startAddrArr.size());
|
||||
#else
|
||||
kt_for(p.numThread, mtUncompressBlockBatch, &uncompressData, nsgv::gSortArg.NUM_THREADS);
|
||||
#endif
|
||||
|
||||
PROF_G_END(uncompress);
|
||||
|
||||
// 判断是否超过内存阈值，只要有一个超过阈值，就转入下一阶段，进行排序和合并
|
||||
if (p.uncompressBufFull == 1 || finish) {
|
||||
|
||||
spdlog::info("buf full - {}", p.mergeOrder);
|
||||
|
||||
// spdlog::info("max mem: {}, single thread mem: {}", nsgv::gSortArg.MAX_MEM, p.singleThreadBytes);
|
||||
|
||||
// sort，排序的时候应该线程利用率很高，此时不需要跟其他操作如压缩等进行重叠了
|
||||
PROF_G_BEG(sort);
|
||||
kt_for(p.numThread, mtInThreadSort, &uncompressData, nsgv::gSortArg.NUM_THREADS);
|
||||
PROF_G_END(sort);
|
||||
// merge
|
||||
#if 0
|
||||
auto& bamArr = p.sortedBamArr;
|
||||
BamHeap<BamGreaterThan> heap;
|
||||
heap.Init(&uncompressData.bamItemArr);
|
||||
bamArr.resize(heap.Size());
|
||||
auto& taskArr = p.taskArr;
|
||||
taskArr.clear();
|
||||
|
||||
const OneBam* bam = nullptr;
|
||||
uint64_t posAll = 0;
|
||||
int i = 0;
|
||||
ArrayInterval intv{0, 0};
|
||||
uint64_t blockBytes = 0;
|
||||
PROF_G_BEG(merge);
|
||||
while ((bam = heap.Pop()) != nullptr) {
|
||||
// posAll += bam->pos;
|
||||
//spdlog::info("pos: {}", bam->pos);
|
||||
bamArr[i++] = bam;
|
||||
blockBytes += bam->bamLen;
|
||||
if (blockBytes >= SINGLE_BLOCK_SIZE) {
|
||||
intv.num = i - 1 - intv.idx;
|
||||
taskArr.push_back(intv);
|
||||
intv.idx = i - 1;
|
||||
blockBytes = bam->bamLen;
|
||||
}
|
||||
}
|
||||
PROF_G_END(merge);
|
||||
spdlog::info("task size: {} {}", taskArr.size(), bamArr.size());
|
||||
if (i - 1 > intv.idx) {
|
||||
intv.num = i - 1 - intv.idx;
|
||||
taskArr.push_back(intv);
|
||||
}
|
||||
|
||||
// spdlog::info("pos all: {}", posAll);
|
||||
#endif
|
||||
// compress，此时并行压缩的多线程利用率应该很高了
|
||||
PROF_G_BEG(compress);
|
||||
#if 0
|
||||
kt_for(p.numThread, mtCompressBlock, &p, taskArr.size());
|
||||
#endif
|
||||
|
||||
for (auto &blockItemArr : uncompressData.blockItemArr) {
|
||||
p.bamNum += blockItemArr.bamNum;
|
||||
}
|
||||
|
||||
uncompressData.ResetBlockArr();
|
||||
uncompressData.ResetBamArr();
|
||||
p.uncompressBufFull = 0;
|
||||
p.mergeOrder++;
|
||||
for(auto &buf : p.threadBuf) {
|
||||
buf.curLen = 0;
|
||||
}
|
||||
PROF_G_END(compress);
|
||||
|
||||
// 压缩完之后应该写入中间文件，这个应该可以overlap
|
||||
}
|
||||
// 等处理完这些数据之后，进入新一轮的解压和归并排序压缩输出中间文件。
|
||||
|
||||
// auto &bam = uncompressData.bamItemArr[0].bamArr.back();
|
||||
// string qname(bam.qnameAddr, bam.qnameLen);
|
||||
// spdlog::info("bam name:{}", qname);
|
||||
}
|
||||
|
||||
/* FirstPipe step-2 并行解压gz blocks*/
|
||||
static void *firstPipeUncompress(void *data) {
|
||||
FirstPipeArg &p = *(FirstPipeArg *)data;
|
||||
|
||||
/* 2. do the work */
|
||||
while (true) {
|
||||
// previous dependency
|
||||
yarn::DEPENDENCY_NOT_TO_BE(p.readSig, 0);
|
||||
// self dependency
|
||||
yarn::DEPENDENCY_NOT_TO_BE(p.uncompressSig, p.UNCOMPRESS_BUF_NUM);
|
||||
|
||||
if (p.readFinish) {
|
||||
while (p.uncompressOrder < p.readOrder) {
|
||||
yarn::DEPENDENCY_NOT_TO_BE(p.uncompressSig, p.UNCOMPRESS_BUF_NUM);
|
||||
doFirstPipeUncompress(p, 1);
|
||||
yarn::UPDATE_SIG_ORDER(p.uncompressSig, p.uncompressOrder);
|
||||
}
|
||||
yarn::SIGNAL_FINISH(p.uncompressSig, p.uncompressFinish);
|
||||
break;
|
||||
}
|
||||
|
||||
doFirstPipeUncompress(p);
|
||||
|
||||
// update status
|
||||
yarn::CONSUME_SIGNAL(p.readSig);
|
||||
yarn::UPDATE_SIG_ORDER(p.uncompressSig, p.uncompressOrder);
|
||||
}
|
||||
|
||||
spdlog::info("uncompress order: {}", p.uncompressOrder);
|
||||
return nullptr;
|
||||
}
|
||||
|
||||
/* 将并行解压的数据放到一起，解析，到容量阈值后，进行排序并输出到中间文件 */
|
||||
void dofirstPipeWrite(FirstPipeArg &p) {
|
||||
PROF_G_BEG(sort);
|
||||
UncompressData &uncompressData = p.uncompressData[p.writeOrder % p.UNCOMPRESS_BUF_NUM];
|
||||
|
||||
size_t blockNum = 0;
|
||||
for (int i = 0; i < p.numThread; ++i) {
|
||||
blockNum += uncompressData.blockItemArr[i].curIdx;
|
||||
}
|
||||
size_t bamNum = blockNum * 256;
|
||||
|
||||
size_t curBlockBamMemSize = blockNum * SINGLE_BLOCK_SIZE + bamNum * 32;
|
||||
/* 内存使用量达到阈值后，进行排序 */
|
||||
if (curBlockBamMemSize > nsgv::gSortArg.MAX_MEM / 2) {
|
||||
//uncompressData.ResetBlockArr();
|
||||
//uncompressData.ResetBamArr();
|
||||
}
|
||||
|
||||
//spdlog::info("block num: {}, bam num: {}, block size: {}, bam size: {}", blockNum, bamNum, blockBytes, bamNum * 32);
|
||||
// spdlog::info("block num: {}, bam num: {}, block size: {}, bam size: {}", blockNum, bamNum, blockNum * SINGLE_BLOCK_SIZE, bamNum * 32);
|
||||
PROF_G_END(sort);
|
||||
}
|
||||
|
||||
/* FirstPipe step-3 串行写入中间文件（已经压缩好） */
|
||||
static void *firstPipeWrite(void *data) {
|
||||
FirstPipeArg &p = *(FirstPipeArg *)data;
|
||||
|
||||
while (true) {
|
||||
yarn::DEPENDENCY_NOT_TO_BE(p.uncompressSig, 0);
|
||||
|
||||
if (p.uncompressFinish) {
|
||||
spdlog::info("uncompress finish, cur sort order: {}", p.writeOrder);
|
||||
while (p.writeOrder < p.uncompressOrder) {
|
||||
dofirstPipeWrite(p);
|
||||
p.writeOrder += 1;
|
||||
}
|
||||
/* 需要检测一下buf中是否还有数据，如果还有，则需要进行排序，可以不输出到中间文件，直接进行second-pipe的归并排序 */
|
||||
break;
|
||||
}
|
||||
|
||||
dofirstPipeWrite(p);
|
||||
|
||||
p.writeOrder += 1;
|
||||
|
||||
// update status
|
||||
yarn::CONSUME_SIGNAL(p.uncompressSig);
|
||||
}
|
||||
|
||||
spdlog::info("merge sort order: {}", p.writeOrder);
|
||||
return nullptr;
|
||||
}
|
||||
|
||||
/* 对bam文件进行排序第一阶段，线程内排序，线程间merge，输入到中间bam文件 */
|
||||
static void bamSortFirstPipe() {
|
||||
/* set up*/
|
||||
FirstPipeArg firstPipeArg;
|
||||
firstPipeArg.numThread = nsgv::gSortArg.NUM_THREADS;
|
||||
firstPipeArg.singleThreadBytes = nsgv::gSortArg.MAX_MEM / firstPipeArg.numThread;
|
||||
spdlog::info("max mem: {}, single thread mem: {}", nsgv::gSortArg.MAX_MEM, firstPipeArg.singleThreadBytes);
|
||||
const size_t kReadBufSize = 1L * 1024 * 1024 * firstPipeArg.numThread; // 平均每线程1M缓冲区，累加起来，用来读入文件（BAM/SAM）（相对解压之后的缓冲区，大小可以忽略）
|
||||
for (int i = 0; i<firstPipeArg.READ_BUF_NUM; ++i) {
|
||||
firstPipeArg.readData[i].Resize(kReadBufSize);
|
||||
}
|
||||
|
||||
// 根据最大内存参数，计算初始化开辟的空间
|
||||
int blockInitNum = nsgv::gSortArg.MAX_MEM / nsgv::gSortArg.NUM_THREADS / SINGLE_BLOCK_SIZE / BLOCK_MEM_FACTOR;
|
||||
spdlog::info("Init block num: {}", blockInitNum);
|
||||
for (int i = 0; i < firstPipeArg.UNCOMPRESS_BUF_NUM; ++i) {
|
||||
firstPipeArg.uncompressData[i].Resize(firstPipeArg.numThread, blockInitNum);
|
||||
}
|
||||
|
||||
PROF_G_BEG(mid_all);
|
||||
/* create threads */
|
||||
pthread_t pipeThreadIdArr[3]; // 3-stage pipeline
|
||||
pthread_create(&pipeThreadIdArr[0], NULL, firstPipeReadFile, &firstPipeArg);
|
||||
pthread_create(&pipeThreadIdArr[1], NULL, firstPipeUncompress, &firstPipeArg);
|
||||
pthread_create(&pipeThreadIdArr[2], NULL, firstPipeWrite, &firstPipeArg);
|
||||
|
||||
for (int i = 0; i < 3; ++i) pthread_join(pipeThreadIdArr[i], NULL);
|
||||
|
||||
spdlog::info("all bams num: {}", firstPipeArg.bamNum);
|
||||
|
||||
PROF_G_END(mid_all);
|
||||
}
|
||||
|
||||
/* IO同步的方式进行排序 */
|
||||
static void bamSortSerialFirstPipe() {
|
||||
/* set up*/
|
||||
FirstPipeArg firstPipeArg;
|
||||
firstPipeArg.numThread = nsgv::gSortArg.NUM_THREADS;
|
||||
const size_t kReadBufSize = 1L * 1024 * 1024 * firstPipeArg.numThread;
|
||||
for (int i = 0; i < firstPipeArg.READ_BUF_NUM; ++i) {
|
||||
firstPipeArg.readData[i].Resize(kReadBufSize);
|
||||
}
|
||||
for (int i = 0; i < firstPipeArg.UNCOMPRESS_BUF_NUM; ++i) {
|
||||
firstPipeArg.uncompressData[i].Resize(firstPipeArg.numThread, 128);
|
||||
}
|
||||
|
||||
/* 1. read file */
|
||||
FILE *fpr = fopen(nsgv::gSortArg.INPUT_FILE.c_str(), "rb");
|
||||
parseSamHeader(fpr, nsgv::gInHdr);
|
||||
size_t fileSize = 0;
|
||||
DataBuffer halfBlock(SINGLE_BLOCK_SIZE);
|
||||
|
||||
/* 2. do the work */
|
||||
while (true) {
|
||||
size_t readState = doFirstPipeReadFile(firstPipeArg, halfBlock, fpr);
|
||||
doFirstPipeUncompress(firstPipeArg);
|
||||
dofirstPipeWrite(firstPipeArg);
|
||||
if (readState == 0) break;
|
||||
fileSize += readState;
|
||||
}
|
||||
|
||||
/* 3. clean up */
|
||||
fclose(fpr);
|
||||
}
|
||||
|
||||
/* 对sam文件进行排序 */
|
||||
static void samSortFirstPipe() {
|
||||
|
||||
}
|
||||
|
||||
static void bamSortPipeline() {
|
||||
/* set up phase 1 parameters */
|
||||
Phase1PipelineArg p1;
|
||||
p1.numThread = nsgv::gSortArg.NUM_THREADS;
|
||||
// 平均每线程4M缓冲区，累加起来，用来读入文件（BAM/SAM）（相对解压之后的缓冲区，大小可以忽略）
|
||||
const size_t kReadBufSize = 4L * 1024 * 1024 * p1.numThread;
|
||||
// p1.midFileNamePrefix = getFileNameWithoutExt(nsgv::gSortArg.OUTPUT_FILE) + "_sort_mid.";
|
||||
p1.midFileNamePrefix = getFilePathWithoutExt(nsgv::gSortArg.OUTPUT_FILE) + "_sort_mid."; // 跟输出文件路径相同
|
||||
spdlog::info("prefix: {}", p1.midFileNamePrefix);
|
||||
p1.maxMemBytes = nsgv::gSortArg.MAX_MEM;
|
||||
p1.uncompressBufBytes = nsgv::gSortArg.MAX_MEM; // 可以再考虑一下
|
||||
for (int i = 0; i < p1.UNCOMPRESS_BUF_NUM; ++i) {
|
||||
p1.threadUncompressWrap[i].Resize(p1.numThread); // 每个线程的解压block数组初始大小，后续如果不够用会自动扩容
|
||||
}
|
||||
// 每个线程解压数据的内存上限，平均每线程4M读入数据，解压后大概5倍，留点余量，所以乘以5，除以线程数
|
||||
p1.singleThreadMemBytes = kReadBufSize * BAM_COMPRESS_RATIAO / p1.numThread;
|
||||
spdlog::info("max mem: {}, uncompress mem: {}, single thread mem: {}", nsgv::gSortArg.MAX_MEM, p1.uncompressBufBytes,
|
||||
p1.singleThreadMemBytes);
|
||||
for (int i = 0; i < p1.READ_BUF_NUM; ++i) {
|
||||
p1.readData[i].Resize(kReadBufSize);
|
||||
};
|
||||
// 根据最大内存参数，计算初始化开辟的空间
|
||||
p1.uncompressData.Resize(p1.uncompressBufBytes);
|
||||
|
||||
// 运行第一阶段
|
||||
phase1Pipeline(p1);
|
||||
|
||||
/////////////////////////////////////////////////////
|
||||
|
||||
// 第二阶段参数初始化
|
||||
Phase2PipelineArg p2;
|
||||
|
||||
// 运行第二阶段
|
||||
phase2Pipeline(p2);
|
||||
|
||||
}
|
||||
|
||||
// 排序的入口函数，entry function
|
||||
int doSort() {
|
||||
|
|
@ -670,13 +88,11 @@ int doSort() {
|
|||
|
||||
#if 1
|
||||
nsgv::gIsBigEndian = ed_is_big();
|
||||
// 第一轮排序，外排到多个中间文件
|
||||
//bamSortFirstPipe();
|
||||
|
||||
phase1Pipeline();
|
||||
// 并行流水线排序bam文件
|
||||
bamSortPipeline();
|
||||
|
||||
spdlog::info("OneBam size: {}", sizeof(OneBam));
|
||||
// bamSortSerialFirstPipe();
|
||||
#else
|
||||
|
||||
/* 打开输入bam文件 */
|
||||
|
|
@ -685,7 +101,7 @@ int doSort() {
|
|||
spdlog::error("[{}] load sam/bam file failed.\n", __func__);
|
||||
return -1;
|
||||
}
|
||||
hts_set_opt(inBamFp, HTS_OPT_BLOCK_SIZE, BAM_BLOCK_SIZE);
|
||||
hts_set_opt(inBamFp, HTS_OPT_BLOCK_SIZE, PARAM_BLOCK_SIZE);
|
||||
sam_hdr_t *inBamHdr = sam_hdr_read(inBamFp); // 读取header
|
||||
|
||||
htsThreadPool htsPoolRead = {NULL, 0}; // 多线程读取，创建线程池
|
||||
|
|
|
|||
316
src/sort/sort.h
316
src/sort/sort.h
|
|
@ -101,12 +101,10 @@ struct FastVector {
|
|||
#endif
|
||||
}
|
||||
}
|
||||
|
||||
void Add(const T& item) {
|
||||
T &newItem = Add();
|
||||
newItem = item;
|
||||
}
|
||||
|
||||
void AddSize(size_t num) {
|
||||
if (curIdx + num > arr.size()) {
|
||||
arr.resize(curIdx + num);
|
||||
|
|
@ -122,19 +120,8 @@ struct FastVector {
|
|||
void Clear() { curIdx = 0; }
|
||||
};
|
||||
|
||||
/* */
|
||||
|
||||
|
||||
|
||||
class ThreadBlockArr;
|
||||
/* for step-2 parallel uncompress gz blocks，还有缓存满了之后的线程内排序，用来排序的*/
|
||||
struct OneBam {
|
||||
// uint16_t bamLen = 0;
|
||||
// uint16_t qnameLen = 0;
|
||||
// uint32_t tid = 0;
|
||||
// char *qnameAddr = 0; // qname的地址
|
||||
// uint64_t pos = 0; // mapping 位置
|
||||
// uint8_t *addr = 0; // 地址
|
||||
static constexpr int QnameOffset = 36; // 距离该sam记录开头地址的偏移量，包含了4字节bam长度，32字节的bam core信息，后面紧跟着qname字符串
|
||||
uint32_t qnameLen; // 序列名字长度
|
||||
uint32_t wholeBamLen = 0; // 包含4字节bam长度的所有bam内容长度，uint16只适合二代
|
||||
|
|
@ -143,308 +130,5 @@ struct OneBam {
|
|||
uint64_t offset = 0; // 距离首地址的偏移量
|
||||
};
|
||||
|
||||
|
||||
|
||||
struct ThreadBamArr {
|
||||
vector<OneBam> bamArr;
|
||||
int curIdx = 0; //
|
||||
OneBam &add() {
|
||||
if (curIdx < bamArr.size())
|
||||
return bamArr[curIdx++];
|
||||
else {
|
||||
#if 0
|
||||
bamArr.resize((bamArr.size() + 1) << 1);
|
||||
return bamArr[curIdx++];
|
||||
|
||||
#else
|
||||
bamArr.push_back(OneBam());
|
||||
curIdx++;
|
||||
return bamArr.back();
|
||||
#endif
|
||||
}
|
||||
}
|
||||
void clear() { curIdx = 0; }
|
||||
};
|
||||
|
||||
// 解压后的一个block数据
|
||||
struct OneBlock {
|
||||
uint8_t data[SINGLE_BLOCK_SIZE];
|
||||
uint32_t blockLen = 0; // 解压后的数据长度
|
||||
uint64_t blockId = 0; // 按照顺序排列的block ID
|
||||
uint64_t bamNum = 0; // 解压后的bam数量
|
||||
};
|
||||
|
||||
struct BlockIdIdx {
|
||||
uint64_t blockId = 0;
|
||||
int blockArrIdx = 0; // 在block数组里的索引
|
||||
// 方法一：重载 operator> 供 std::greater<Task> 使用
|
||||
bool operator>(const BlockIdIdx& other) const {
|
||||
return blockId > other.blockId; // blockId 小的优先级高（最小堆）
|
||||
}
|
||||
};
|
||||
// 每个线程一个解压block数组
|
||||
struct ThreadBlockArr {
|
||||
vector<OneBlock> blockArr; // 解压后的数据
|
||||
int curIdx = 0; // 当前解压数据对应的vector的索引
|
||||
uint64_t bamNum = 0; // 解压后的bam数量
|
||||
|
||||
OneBlock& add() {
|
||||
if (curIdx < blockArr.size())
|
||||
return blockArr[curIdx++];
|
||||
else {
|
||||
#if 0
|
||||
blockArr.resize((blockArr.size() + 1) << 1);
|
||||
return blockArr[curIdx++];
|
||||
|
||||
#else
|
||||
blockArr.push_back(OneBlock());
|
||||
curIdx++;
|
||||
return blockArr.back();
|
||||
#endif
|
||||
}
|
||||
}
|
||||
void add(int num) {
|
||||
if (curIdx + num > blockArr.size()) {
|
||||
blockArr.resize(curIdx + num);
|
||||
}
|
||||
}
|
||||
|
||||
void clear() {
|
||||
curIdx = 0;
|
||||
bamNum = 0;
|
||||
}
|
||||
};
|
||||
|
||||
class FirstPipeArg;
|
||||
|
||||
// 第一阶段的解压、排序、归并、压缩
|
||||
struct UncompressData {
|
||||
vector<ThreadBlockArr> blockItemArr; // 每个thread一个，用来保存解压后的block数据
|
||||
vector<ThreadBamArr> bamItemArr; // 每个thread一个，用来保存解压后的bam数据
|
||||
|
||||
ReadBuffer *readDataPtr = nullptr; // 读取数据的指针
|
||||
FirstPipeArg* father = nullptr; // 保存父参数的指针，可能更新一些状态
|
||||
|
||||
UncompressData() { }
|
||||
UncompressData(int numThread) { Resize(numThread); }
|
||||
UncompressData(int numThread, int vecInitSize) { Resize(numThread, vecInitSize); }
|
||||
void Resize(int numThread) {
|
||||
Resize(numThread, 128);
|
||||
}
|
||||
void Resize(int numThread, int vecInitSize) {
|
||||
blockItemArr.resize(numThread);
|
||||
bamItemArr.resize(numThread);
|
||||
for (int i = 0; i < numThread; ++i) {
|
||||
blockItemArr[i].blockArr.reserve(vecInitSize);
|
||||
bamItemArr[i].bamArr.reserve(vecInitSize * 192); // 192是每个block平均包含的bam数量，单线程解压一个block的数据，平均会得到192条bam记录，应该作为一个参数或者宏定义
|
||||
}
|
||||
}
|
||||
void ResetBlockArr() {
|
||||
for (int i = 0; i < blockItemArr.size(); ++i) {
|
||||
blockItemArr[i].clear();
|
||||
}
|
||||
}
|
||||
void ResetBamArr() {
|
||||
for (int i = 0; i < bamItemArr.size(); ++i) {
|
||||
bamItemArr[i].clear();
|
||||
}
|
||||
}
|
||||
};
|
||||
/* block 排序堆 */
|
||||
struct BlockArrIdIdx {
|
||||
int arrId = 0;
|
||||
size_t arrIdx = 0; // 下一个待读入数据的idx
|
||||
const OneBlock *block = nullptr;
|
||||
};
|
||||
|
||||
struct BlockGreaterThan{
|
||||
bool operator()(const BlockArrIdIdx &a, const BlockArrIdIdx &b) const {
|
||||
return a.block->blockId > b.block->blockId;
|
||||
}
|
||||
};
|
||||
|
||||
/* 用来排序 */
|
||||
struct BlockHeap {
|
||||
vector<ThreadBlockArr> *arr2d;
|
||||
priority_queue<BlockArrIdIdx, vector<BlockArrIdIdx>, BlockGreaterThan> minHeap;
|
||||
size_t popNum = 0;
|
||||
|
||||
int Init(vector<ThreadBlockArr> *_arr2d) {
|
||||
arr2d = _arr2d;
|
||||
if (arr2d == nullptr) {
|
||||
return -1;
|
||||
}
|
||||
for (int i = 0; i < arr2d->size(); ++i) {
|
||||
auto &v = (*arr2d)[i];
|
||||
if (v.curIdx > 0) {
|
||||
minHeap.push({i, 1, &v.blockArr[0]});
|
||||
}
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
const OneBlock *Pop() {
|
||||
const OneBlock *ret = nullptr;
|
||||
if (!minHeap.empty()) {
|
||||
auto minVal = minHeap.top();
|
||||
minHeap.pop();
|
||||
++popNum;
|
||||
ret = minVal.block;
|
||||
auto &v = (*arr2d)[minVal.arrId];
|
||||
if (v.curIdx > minVal.arrIdx) {
|
||||
minHeap.push({minVal.arrId, minVal.arrIdx + 1, &v.blockArr[minVal.arrIdx]});
|
||||
}
|
||||
}
|
||||
return ret;
|
||||
}
|
||||
|
||||
size_t AllBlockBytes() {
|
||||
size_t bytes = 0;
|
||||
if (arr2d != nullptr) {
|
||||
for (auto &v : *arr2d) {
|
||||
for (int i = 0; i < v.curIdx; ++i) {
|
||||
bytes += v.blockArr[i].blockLen;
|
||||
}
|
||||
}
|
||||
}
|
||||
return bytes;
|
||||
}
|
||||
|
||||
size_t Size() {
|
||||
size_t len = 0;
|
||||
if (arr2d != nullptr) {
|
||||
for (auto &v : *arr2d) {
|
||||
len += v.curIdx;
|
||||
}
|
||||
}
|
||||
return len - popNum;
|
||||
}
|
||||
};
|
||||
|
||||
/* bam 排序堆 */
|
||||
struct BamArrIdIdx {
|
||||
int arrId = 0;
|
||||
size_t arrIdx = 0; // 下一个待读入数据的idx
|
||||
const OneBam* bam = nullptr;
|
||||
};
|
||||
|
||||
struct BamGreaterThan {
|
||||
bool operator()(const BamArrIdIdx& a, const BamArrIdIdx& b) const { return a.bam->pos > b.bam->pos; }
|
||||
};
|
||||
|
||||
/* 用来排序 bam*/
|
||||
template<class GreaterThan>
|
||||
struct BamHeap {
|
||||
vector<ThreadBamArr>* arr2d;
|
||||
priority_queue<BamArrIdIdx, vector<BamArrIdIdx>, GreaterThan> minHeap;
|
||||
size_t popNum = 0;
|
||||
|
||||
int Init(vector<ThreadBamArr>* _arr2d) {
|
||||
arr2d = _arr2d;
|
||||
if (arr2d == nullptr) {
|
||||
return -1;
|
||||
}
|
||||
for (int i = 0; i < arr2d->size(); ++i) {
|
||||
auto& v = (*arr2d)[i];
|
||||
if (v.curIdx > 0) {
|
||||
minHeap.push({i, 1, &v.bamArr[0]});
|
||||
}
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
const OneBam* Pop() {
|
||||
const OneBam* ret = nullptr;
|
||||
if (!minHeap.empty()) {
|
||||
auto minVal = minHeap.top();
|
||||
minHeap.pop();
|
||||
++popNum;
|
||||
ret = minVal.bam;
|
||||
auto& v = (*arr2d)[minVal.arrId];
|
||||
if (v.curIdx > minVal.arrIdx) {
|
||||
minHeap.push({minVal.arrId, minVal.arrIdx + 1, &v.bamArr[minVal.arrIdx]});
|
||||
}
|
||||
}
|
||||
return ret;
|
||||
}
|
||||
|
||||
size_t Size() {
|
||||
size_t len = 0;
|
||||
if (arr2d != nullptr) {
|
||||
for (auto& v : *arr2d) {
|
||||
len += v.curIdx;
|
||||
}
|
||||
}
|
||||
return len - popNum;
|
||||
}
|
||||
};
|
||||
|
||||
struct ArrayInterval {
|
||||
int idx;
|
||||
int num;
|
||||
};
|
||||
|
||||
/* for step-3 serial merge blocks and sort them */
|
||||
|
||||
struct MergeSortData {
|
||||
DataBuffer bamData; // 用来保存解压后的数据
|
||||
// BamPtrArr bamPtrArr; // 每个bam对应的解压数据，起始地址和长度
|
||||
MergeSortData() {
|
||||
// bamPtrArr.bamArr.reserve(128);
|
||||
}
|
||||
};
|
||||
|
||||
typedef FastVector<OneBam> BamArr;
|
||||
typedef FastVector<const OneBam*> BamPtrArr;
|
||||
typedef FastVector<OneBlock> BlockArr;
|
||||
|
||||
|
||||
/* 第一阶段的多线程流水线参数 */
|
||||
struct FirstPipeArg {
|
||||
static const int READ_BUF_NUM = 2; // 读入的buf数量
|
||||
static const int UNCOMPRESS_BUF_NUM = 1; // 解压的buf数量
|
||||
static const int COMPRESS_BUF_NUM = 2; // merge之后，每个线程缓冲区的数量
|
||||
|
||||
int numThread = 0; // 线程数
|
||||
uint64_t singleThreadBytes = 0; // 单线程开辟的内存字节上限
|
||||
|
||||
// for test
|
||||
uint64_t bamNum = 0; // 解压后的bam数量
|
||||
|
||||
uint64_t readOrder = 0; // 读取文件
|
||||
uint64_t uncompressOrder = 0; // 并行解压gz block, 包含排序（缓冲区满之后排序），以及合并之后的压缩
|
||||
uint64_t writeOrder = 0; // 串行合并解压后的blocks，并解析每个bam的长度，达到内存阈值后，并行排序
|
||||
uint64_t mergeOrder = 0; // 用来给中间文件编号
|
||||
|
||||
volatile int readFinish = 0;
|
||||
volatile int uncompressFinish = 0;
|
||||
volatile int uncompressBufFull = 0;
|
||||
|
||||
yarn::lock_t *readSig;
|
||||
yarn::lock_t *uncompressSig;
|
||||
|
||||
ReadBuffer readData[READ_BUF_NUM]; // 用来读如数据，双缓冲
|
||||
UncompressData uncompressData[UNCOMPRESS_BUF_NUM]; // 每个线程内保留一些自己的数据，比如解压缩的数据
|
||||
UncompressBlockBuffer unCompblockDataBuf; // 所有线程共用一个，串行往这里添加解压后的block数据
|
||||
|
||||
vector<const OneBam*> sortedBamArr;
|
||||
vector<ArrayInterval> taskArr;
|
||||
vector<DataBuffer> threadBuf;
|
||||
|
||||
MergeSortData mergeSortData;
|
||||
|
||||
FirstPipeArg()
|
||||
{
|
||||
readSig = yarn::NEW_LOCK(0);
|
||||
uncompressSig = yarn::NEW_LOCK(0);
|
||||
for (int i = 0; i < UNCOMPRESS_BUF_NUM; ++i) {
|
||||
uncompressData[i].father = this;
|
||||
}
|
||||
}
|
||||
};
|
||||
|
||||
/* 第二阶段的多线程流水线参数 */
|
||||
struct PipeSecondArg
|
||||
{
|
||||
/* data */
|
||||
};
|
||||
|
|
@ -1,41 +0,0 @@
|
|||
#include <htslib/sam.h>
|
||||
#include <spdlog/spdlog.h>
|
||||
#include <stdint.h>
|
||||
#include <stdio.h>
|
||||
|
||||
#include "sort_impl.h"
|
||||
|
||||
int ks_radixsort(size_t n, OneBam* buf, const sam_hdr_t* h, int tid) {
|
||||
if (tid == 0) spdlog::info("sort in thread, {} {}", tid, n);
|
||||
|
||||
int curr = 0, ret = -1;
|
||||
ssize_t i;
|
||||
OneBam *buf_ar2[2], *bam_a, *bam_b;
|
||||
uint64_t max_pos = 1;
|
||||
uint32_t max_tid = 1, tid_bytes = 0, pos_bytes = 0, byte = 0;
|
||||
uint32_t tid_shift_l, tid_shift_r;
|
||||
int nref = sam_hdr_nref(h);
|
||||
|
||||
//if (tid == 0)
|
||||
//spdlog::info("Before: {} {} {} {} {} {} {} {} {} {}", buf[0].pos, buf[1].pos, buf[2].pos, buf[3].pos, buf[4].pos, buf[5].pos, buf[6].pos,
|
||||
//buf[7].pos, buf[8].pos, buf[9].pos);
|
||||
// spdlog::info("name: {}", std::string(buf[0].qnameAddr, buf[0].qnameLen));
|
||||
// spdlog::info("name addr: {}", (uint64_t)buf[0].qnameLen);
|
||||
// std::sort(buf, buf + n, [](const OneBam& b1, const OneBam& b2) { return b1.pos < b2.pos; });
|
||||
std::sort(buf, buf + n, [](const OneBam& b1, const OneBam& b2) {
|
||||
int cmp = 0;
|
||||
// strncmp((char*)(b1.blockThread->blockArr[b1.blockIdx].data + b1.offset + OneBam::QnameOffset),
|
||||
// (char*)(b2.blockThread->blockArr[b2.blockIdx].data + b2.offset + OneBam::QnameOffset), std::min(b1.qnameLen, b2.qnameLen));
|
||||
if (cmp == 0)
|
||||
return b1.qnameLen < b2.qnameLen;
|
||||
return cmp < 0;
|
||||
});
|
||||
if (tid == 0) {
|
||||
//std::string s1 = (char*)(buf[0].blockThread->blockArr[buf[0].blockIdx].data + buf[0].offset + OneBam::QnameOffset);
|
||||
//std::string s2 = (char*)(buf[1].blockThread->blockArr[buf[1].blockIdx].data + buf[1].offset + OneBam::QnameOffset);
|
||||
//spdlog::info("After: {} {} {} {} {} {} {} {} {} {}", s1, s2, buf[2].pos, buf[3].pos, buf[4].pos, buf[5].pos, buf[6].pos, buf[7].pos,
|
||||
//buf[8].pos, buf[9].pos);
|
||||
}
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
|
@ -1,36 +0,0 @@
|
|||
#pragma once
|
||||
|
||||
#include <htslib/sam.h>
|
||||
#include <stdio.h>
|
||||
|
||||
#include "sort.h"
|
||||
|
||||
// 好像不需要用到这些了？
|
||||
|
||||
// Struct which contains the sorting key for TemplateCoordinate sort.
|
||||
struct TemplateCoordinateKey {
|
||||
int tid1;
|
||||
int tid2;
|
||||
hts_pos_t pos1;
|
||||
hts_pos_t pos2;
|
||||
bool neg1;
|
||||
bool neg2;
|
||||
const char *library;
|
||||
char *mid;
|
||||
char *name;
|
||||
bool is_upper_of_pair;
|
||||
};
|
||||
|
||||
// Struct which contains the a record, and the pointer to the sort tag (if any) or
|
||||
// a combined ref / position / strand.
|
||||
// Used to speed up sorts (coordinate, by-tag, and template-coordinate).
|
||||
struct BamSortTag {
|
||||
bam1_t *bam_record;
|
||||
union {
|
||||
const uint8_t *tag;
|
||||
uint8_t pos_tid[12];
|
||||
TemplateCoordinateKey *key;
|
||||
} u;
|
||||
};
|
||||
|
||||
int ks_radixsort(size_t n, OneBam* buf, const sam_hdr_t* h, int tid);
|
||||
Loading…
Reference in New Issue