找到并行的问题了，是kt_for的steal策略，会导致处理的数据的idx小于已经处理过的。保留调试信息，并行结果和串行一致了
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84463ede19
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@ -64,6 +64,35 @@ void kt_for(int n_threads, void (*func)(void*,long,int), void *data, long n)
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}
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}
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static void* ktf_worker_no_steal(void* data) {
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ktf_worker_t* w = (ktf_worker_t*)data;
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long i;
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for (;;) {
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i = __sync_fetch_and_add(&w->i, w->t->n_threads);
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if (i >= w->t->n)
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break;
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w->t->func(w->t->data, i, w - w->t->w);
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}
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pthread_exit(0);
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}
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void kt_for_no_steal(int n_threads, void (*func)(void*, long, int), void* data, long n) {
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if (n_threads > 1) {
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int i;
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kt_for_t t;
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pthread_t* tid;
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t.func = func, t.data = data, t.n_threads = n_threads, t.n = n;
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t.w = (ktf_worker_t*)alloca(n_threads * sizeof(ktf_worker_t));
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tid = (pthread_t*)alloca(n_threads * sizeof(pthread_t));
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for (i = 0; i < n_threads; ++i) t.w[i].t = &t, t.w[i].i = i;
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for (i = 0; i < n_threads; ++i) pthread_create(&tid[i], 0, ktf_worker_no_steal, &t.w[i]);
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for (i = 0; i < n_threads; ++i) pthread_join(tid[i], 0);
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} else {
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long j;
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for (j = 0; j < n; ++j) func(data, j, 0);
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}
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}
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/***************************
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* kt_for with thread pool *
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***************************/
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@ -6,6 +6,7 @@ extern "C" {
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#endif
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void kt_for(int n_threads, void (*func)(void*,long,int), void *data, long n);
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void kt_for_no_steal(int n_threads, void (*func)(void*, long, int), void* data, long n);
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void kt_pipeline(int n_threads, void *(*func)(void*, int, void*), void *shared_data, int n_steps);
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void *kt_forpool_init(int n_threads);
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@ -28,7 +28,7 @@ struct AuxVar {
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//const static int REF_CONTEXT_PAD = 3; // 需要做一些填充
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//const static int REFERENCE_HALF_WINDOW_LENGTH = 150; // 需要额外多取出一些ref序列，防止边界效应
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static constexpr int BAM_BLOCK_NUM = 1000; // 每个线程每次处理1k个bam记录
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static constexpr int BAM_BLOCK_NUM = 1; // 每个线程每次处理1k个bam记录
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static int64_t processedReads;
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sam_hdr_t* header = nullptr; // bam header
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@ -36,6 +36,7 @@ struct AuxVar {
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char* ref_seq = nullptr; // reference sequence
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int ref_len = 0; // reference sequence length
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int offset = 0; // 在要求的ref序列两边，多余取出的碱基数量
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int64_t threadProcessedReads = 0; // 该线程已经处理的reads数量
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BamArray *bamArr = nullptr; // bam数据数组
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@ -28,7 +28,7 @@ struct BQSRArg {
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int NUM_THREADS = 1;
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size_t MAX_MEM = ((size_t)1) << 30; // // 1G
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size_t MAX_MEM = ((size_t)1) << 30; // 1G
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bool DUPLEX_IO = true; //
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@ -110,22 +110,48 @@ void roundTableValues(RecalTables& rt) {
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_Foreach4D(rt.cycleTable, val, { _round_val(val); });
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}
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// 打印recal tables，用于调试
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static void printRecalTables(const RecalTables& rt) {
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_Foreach2D(rt.readGroupTable, val, {
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if (val.numObservations > 0) {
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fprintf(gf[0], "%ld %f %f\n", val.numObservations, val.numMismatches, val.reportedQuality);
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}
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});
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_Foreach3D(rt.qualityScoreTable, val, {
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if (val.numObservations > 0) {
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fprintf(gf[1], "%ld %f %f\n", val.numObservations, val.numMismatches, val.reportedQuality);
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}
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});
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_Foreach4D(rt.contextTable, val, {
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if (val.numObservations > 0) {
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fprintf(gf[2], "%ld %f %f\n", val.numObservations, val.numMismatches, val.reportedQuality);
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}
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});
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_Foreach4D(rt.cycleTable, val, {
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if (val.numObservations > 0) {
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fprintf(gf[3], "%ld %f %f\n", val.numObservations, val.numMismatches, val.reportedQuality);
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}
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});
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}
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// 串行bqsr
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int SerialBQSR(AuxVar &aux) {
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int SerialBQSR(AuxVar &aux1) {
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BamBufType inBamBuf(nsgv::gBqsrArg.DUPLEX_IO);
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inBamBuf.Init(nsgv::gInBamFp, nsgv::gInBamHeader, nsgv::gBqsrArg.MAX_MEM, bqsrReadFilterOut);
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int64_t readNumSum = 0;
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int round = 0;
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PerReadCovariateMatrix readCovariates;
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CovariateUtils::InitPerReadCovMat(readCovariates);
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RecalTables& recalTables = aux.recalTables;
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SamData& sd = aux.sd;
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StableArray<int>&isSNP = aux.isSNP, &isIns = aux.isIns, &isDel = aux.isDel; // 该位置是否是SNP, indel位置，0不是，1是
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StableArray<uint8_t> &baqArray = aux.baqArray;
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StableArray<double> &snpErrors = aux.snpErrors, &insErrors = aux.insErrors, &delErrors = aux.delErrors;
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StableArray<uint8_t> &skips = aux.skips; // 该位置是否是已知位点
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// PerReadCovariateMatrix &readCovariates = aux.readCovariates;
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// RecalTables& recalTables = aux.recalTables;
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// SamData& sd = aux.sd;
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// StableArray<int>&isSNP = aux.isSNP, &isIns = aux.isIns, &isDel = aux.isDel; // 该位置是否是SNP, indel位置，0不是，1是
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// StableArray<uint8_t> &baqArray = aux.baqArray;
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// StableArray<double> &snpErrors = aux.snpErrors, &insErrors = aux.insErrors, &delErrors = aux.delErrors;
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// StableArray<uint8_t> &skips = aux.skips; // 该位置是否是已知位点
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int numProcessed = 0;
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int numthreads = 2;
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int BLOCK_NUM = AuxVar::BAM_BLOCK_NUM;
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while (true) {
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++round;
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// 一. 读取bam数据
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@ -138,13 +164,34 @@ int SerialBQSR(AuxVar &aux) {
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auto bams = inBamBuf.GetBamArr();
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spdlog::info("{} reads processed in {} round", readNum, round);
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int numBLocks = (bams.size() + BLOCK_NUM - 1) / BLOCK_NUM;
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int blocksPerThread = (numBLocks + numthreads - 1) / numthreads;
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int spanBlocks = numthreads * BLOCK_NUM;
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// 二. 遍历每个bam（read）记录，进行处理
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for (int i = 0; i < bams.size(); ++i) {
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// 1. 对每个read，需要检查cigar是否合法，即没有两个连续的相同的cigar，而且需要将首尾的deletion处理掉，目前看好像没啥影响，我们忽略这一步
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for (int j = 0; j < numthreads; ++j) { // 模拟多线程
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AuxVar &aux = nsgv::gAuxVars[j];
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PerReadCovariateMatrix& readCovariates = aux.readCovariates;
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RecalTables& recalTables = aux.recalTables;
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SamData& sd = aux.sd;
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StableArray<int>&isSNP = aux.isSNP, &isIns = aux.isIns, &isDel = aux.isDel; // 该位置是否是SNP, indel位置，0不是，1是
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StableArray<uint8_t>& baqArray = aux.baqArray;
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StableArray<double>&snpErrors = aux.snpErrors, &insErrors = aux.insErrors, &delErrors = aux.delErrors;
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StableArray<uint8_t>& skips = aux.skips; // 该位置是否是已知位点
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for (int k = 0; k < blocksPerThread; ++k)
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for (int m = 0; m < BLOCK_NUM; ++m) {
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int i = j * BLOCK_NUM + k * spanBlocks + m;
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if (i >= bams.size()) break;
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++numProcessed;
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// for (int i = 0; i < bams.size(); ++i) {
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// if (i % 100 == 0)
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// spdlog::info("Processing read idx: {}", i);
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// 1.
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// 对每个read，需要检查cigar是否合法，即没有两个连续的相同的cigar，而且需要将首尾的deletion处理掉，目前看好像没啥影响，我们忽略这一步
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// 2. 对质量分数长度跟碱基长度不匹配的read，缺少的质量分数用默认值补齐，先忽略，后边有需要再处理
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// 3. 如果bam文件之前做过bqsr，tag中包含OQ（originnal
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// quality，原始质量分数），检查用户参数里是否指定用原始质量分数进行bqsr，如果是则将质量分数替换为OQ，否则忽略OQ，先忽略 spdlog::info("bam
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// idx: {}", i);
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// quality，原始质量分数），检查用户参数里是否指定用原始质量分数进行bqsr，如果是则将质量分数替换为OQ，否则忽略OQ，先忽略
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// spdlog::info("bam idx: {}", i);
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BamWrap* bw = bams[i];
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sd.init();
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sd.parseBasic(bw);
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@ -228,6 +275,14 @@ int SerialBQSR(AuxVar &aux) {
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sd.base_quals[ii] < nsgv::gBqsrArg.PRESERVE_QSCORES_LESS_THAN;
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}
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PROF_GP_END(read_vcf);
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#if 1
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int fidx = 0;
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if (sd.rid % 2 == 0) fidx = 0;
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else fidx = 1;
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fprintf(gf[fidx], "%ld %d\t", sd.rid, sd.read_len);
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for (int ii = 0; ii < sd.read_len; ++ii) fprintf(gf[fidx], "%d ", skips[ii] ? 1 : 0);
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fprintf(gf[fidx], "\n");
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#endif
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// fprintf(gf[0], "%ld %d\t", sd.rid, sd.read_len);
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// for (int ii = 0; ii < sd.read_len; ++ii) fprintf(gf[0], "%d ", skips[ii] ? 1 : 0);
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// fprintf(gf[0], "\n");
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@ -247,12 +302,37 @@ int SerialBQSR(AuxVar &aux) {
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RecalUtils::updateRecalTablesForRead(info, recalTables);
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PROF_END(gprof[GP_update_info], update_info);
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}
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}
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readNumSum += readNum;
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inBamBuf.ClearAll(); //
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}
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#if 0
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printRecalTables(recalTables);
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#endif
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spdlog::info("read count: {}", readNumSum);
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spdlog::info("processed count: {}", numProcessed);
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auto& auxArr = nsgv::gAuxVars;
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RecalTables& recalTables = auxArr[0].recalTables;
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for (int i = 0; i < numthreads; ++i) spdlog::info("thread {} processed reads {}.", i, auxArr[i].threadProcessedReads);
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for (int i = 1; i < numthreads; ++i) {
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auxArr[0].threadProcessedReads += auxArr[i].threadProcessedReads;
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_Foreach3DK(auxArr[i].recalTables.qualityScoreTable, qualDatum, {
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if (qualDatum.numObservations > 0) {
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recalTables.qualityScoreTable(k1, k2, k3).increment(qualDatum);
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}
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});
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_Foreach4DK(auxArr[i].recalTables.contextTable, contextDatum, {
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if (contextDatum.numObservations > 0) {
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recalTables.contextTable(k1, k2, k3, k4).increment(contextDatum);
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}
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});
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_Foreach4DK(auxArr[i].recalTables.cycleTable, cycleDatum, {
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if (cycleDatum.numObservations > 0) {
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recalTables.cycleTable(k1, k2, k3, k4).increment(cycleDatum);
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}
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});
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}
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// 12. 创建总结数据
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collapseQualityScoreTableToReadGroupTable(recalTables.readGroupTable, recalTables.qualityScoreTable);
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roundTableValues(recalTables);
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@ -266,8 +346,9 @@ int SerialBQSR(AuxVar &aux) {
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return 0;
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}
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// 多线程处理bam数据, tmd是乱序的？
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static void thread_worker(void* data, long idx, int tid) {
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AuxVar& aux = ((AuxVar*)data)[tid];
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AuxVar& aux = (*(vector<AuxVar>*)data)[tid];
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auto& readCovariates = aux.readCovariates;
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RecalTables& recalTables = aux.recalTables;
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SamData& sd = aux.sd;
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@ -276,9 +357,18 @@ static void thread_worker(void* data, long idx, int tid) {
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StableArray<double>&snpErrors = aux.snpErrors, &insErrors = aux.insErrors, &delErrors = aux.delErrors;
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StableArray<uint8_t>& skips = aux.skips; // 该位置是否是已知位点
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auto &bams = *aux.bamArr;
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// for (auto& vcf : aux.vcfArr) vcf.knownSites.clear();
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#if 1
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int startIdx = idx * aux.BAM_BLOCK_NUM;
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int stopIdx = std::min((size_t)(idx + 1) * aux.BAM_BLOCK_NUM, bams.size());
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#else
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int blockReadNums = (bams.size() + nsgv::gAuxVars.size() - 1) / nsgv::gAuxVars.size();
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int startIdx = idx * blockReadNums;
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int stopIdx = std::min((size_t)(idx + 1) * blockReadNums, bams.size());
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#endif
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aux.threadProcessedReads += stopIdx - startIdx;
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for (int i = startIdx; i < stopIdx; ++i) {
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// spdlog::info("Thread {} processing read idx: {}", tid, i);
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BamWrap* bw = bams[i];
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sd.init();
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sd.parseBasic(bw);
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@ -314,6 +404,14 @@ static void thread_worker(void* data, long idx, int tid) {
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skips[ii] || (ContextCovariate::baseIndexMap[sd.bases[ii]] == -1) || sd.base_quals[ii] < nsgv::gBqsrArg.PRESERVE_QSCORES_LESS_THAN;
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}
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// PROF_GP_END(read_vcf);
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#if 1
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int fidx = 0 + 2 * tid;
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//if (sd.rid % 2 == 0) fidx = 0 + 2 * tid;
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//else fidx = 1 + 2 * tid;
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fprintf(gf[fidx], "%ld %d\t", sd.rid, sd.read_len);
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for (int ii = 0; ii < sd.read_len; ++ii) fprintf(gf[fidx], "%d ", skips[ii] ? 1 : 0);
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fprintf(gf[fidx], "\n");
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#endif
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// PROF_START(frac_err);
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RecalFuncs::calculateFractionalErrorArray(isSNP, baqArray, snpErrors);
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@ -348,24 +446,54 @@ int ParallelBQSR(vector<AuxVar>& auxArr) {
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});
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spdlog::info("{} reads processed in {} round", readNum, round);
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kt_for(nsgv::gBqsrArg.NUM_THREADS, thread_worker, auxArr.data(), (readNum + AuxVar::BAM_BLOCK_NUM - 1) / AuxVar::BAM_BLOCK_NUM);
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#if 1
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kt_for_no_steal(auxArr.size(), thread_worker, &auxArr, (readNum + AuxVar::BAM_BLOCK_NUM - 1) / AuxVar::BAM_BLOCK_NUM);
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#else
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kt_for(auxArr.size(), thread_worker, &auxArr, auxArr.size());
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#endif
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readNumSum += readNum;
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AuxVar::processedReads += readNum;
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inBamBuf.ClearAll(); //
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}
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spdlog::info("read count: {}", readNumSum);
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// // 12. 创建总结数据
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// collapseQualityScoreTableToReadGroupTable(recalTables.readGroupTable, recalTables.qualityScoreTable);
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// roundTableValues(recalTables);
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//
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// // 13. 量化质量分数
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// QuantizationInfo quantInfo(recalTables, nsgv::gBqsrArg.QUANTIZING_LEVELS);
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//
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// // 14. 输出结果
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// RecalUtils::outputRecalibrationReport(nsgv::gBqsrArg, quantInfo, recalTables);
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//
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// 合并各个线程的结果
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RecalTables& recalTables = auxArr[0].recalTables;
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for (int i = 0; i < auxArr.size(); ++i)
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spdlog::info("thread {} processed reads {}.", i, auxArr[i].threadProcessedReads);
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for (int i = 1; i < auxArr.size(); ++i) {
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auxArr[0].threadProcessedReads += auxArr[i].threadProcessedReads;
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_Foreach3DK(auxArr[i].recalTables.qualityScoreTable, qualDatum, {
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if (qualDatum.numObservations > 0) {
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recalTables.qualityScoreTable(k1, k2, k3).increment(qualDatum);
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}
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});
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_Foreach4DK(auxArr[i].recalTables.contextTable, contextDatum, {
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if (contextDatum.numObservations > 0) {
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recalTables.contextTable(k1, k2, k3, k4).increment(contextDatum);
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}
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});
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_Foreach4DK(auxArr[i].recalTables.cycleTable, cycleDatum, {
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if (cycleDatum.numObservations > 0) {
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recalTables.cycleTable(k1, k2, k3, k4).increment(cycleDatum);
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}
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});
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}
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spdlog::info("All processed reads {}.", auxArr[0].threadProcessedReads);
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// printRecalTables(recalTables);
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// 创建总结数据
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collapseQualityScoreTableToReadGroupTable(recalTables.readGroupTable, recalTables.qualityScoreTable);
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roundTableValues(recalTables);
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// 量化质量分数
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QuantizationInfo quantInfo(recalTables, nsgv::gBqsrArg.QUANTIZING_LEVELS);
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// 输出结果
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RecalUtils::outputRecalibrationReport(nsgv::gBqsrArg, quantInfo, recalTables);
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return 0;
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}
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@ -455,8 +583,10 @@ int BaseRecalibrator() {
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PROF_START(whole_process);
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||||
globalInit();
|
||||
//if (nsgv::gBqsrArg.NUM_THREADS == 1)
|
||||
// ret = SerialBQSR(nsgv::gAuxVars[0]); // 串行处理数据，生成recal table
|
||||
ret = ParallelBQSR(nsgv::gAuxVars); // 串行处理数据，生成recal table
|
||||
//else
|
||||
ret = ParallelBQSR(nsgv::gAuxVars); // 并行处理数据，生成recal table
|
||||
globalDestroy();
|
||||
sam_close(nsgv::gInBamFp);
|
||||
PROF_END(gprof[GP_whole_process], whole_process);
|
||||
|
|
|
|||
|
|
@ -110,6 +110,13 @@ struct RecalDatum {
|
|||
empiricalQuality = UNINITIALIZED_EMPIRICAL_QUALITY;
|
||||
}
|
||||
|
||||
inline void increment(const RecalDatum& other) {
|
||||
numObservations += other.numObservations;
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||||
numMismatches += other.numMismatches;
|
||||
reportedQuality = other.reportedQuality;
|
||||
empiricalQuality = UNINITIALIZED_EMPIRICAL_QUALITY;
|
||||
}
|
||||
|
||||
/**
|
||||
* Add in all of the data from other into this object, updating the reported quality from the expected
|
||||
* error rate implied by the two reported qualities.
|
||||
|
|
|
|||
|
|
@ -110,9 +110,11 @@ struct RecalFuncs {
|
|||
int64_t startPos = bw->start_pos(); // 闭区间
|
||||
int64_t endPos = bw->end_pos(); // 闭区间
|
||||
knownSites.resize_fill(sd.read_len, 0);
|
||||
// return;
|
||||
|
||||
// update vcfs
|
||||
for (auto& vcf : vcfs) {
|
||||
#if 1
|
||||
// 清理旧的interval
|
||||
while (!vcf.knownSites.empty()) {
|
||||
auto& intv = vcf.knownSites.front();
|
||||
|
|
@ -122,9 +124,11 @@ struct RecalFuncs {
|
|||
else
|
||||
break;
|
||||
}
|
||||
if (!vcf.knownSites.empty() && vcf.knownSites.back().left > endPos)
|
||||
// #endif
|
||||
if (!vcf.knownSites.empty() && vcf.knownSites.back().left > endPos) // 此时vcf的区域包含bam，不需要读取
|
||||
continue;
|
||||
|
||||
#endif
|
||||
vcf.knownSites.clear();
|
||||
// 读取新的interval
|
||||
int64_t fpos, flen;
|
||||
endPos = std::max(startPos + MAX_SITES_INTERVAL, endPos);
|
||||
|
|
@ -151,7 +155,7 @@ struct RecalFuncs {
|
|||
tid = sam_hdr_name2tid(samHdr, stid.c_str());
|
||||
int64_t varStart = BamWrap::bam_global_pos(tid, pos);
|
||||
Interval varIntv(varStart, varStart + ref.size() - 1);
|
||||
if (readIntv.overlaps(varIntv)) {
|
||||
if (varIntv.right >= readIntv.left) {
|
||||
vcf.knownSites.push_back(Interval(tid, pos - 1, pos - 1 + ref.size() - 1)); // 闭区间
|
||||
}
|
||||
get_line_from_buf(buf, flen, &cur, &line);
|
||||
|
|
|
|||
|
|
@ -118,6 +118,10 @@ int main_BaseRecalibrator(int argc, char *argv[]) {
|
|||
nsgv::gBqsrArg.INPUT_FILE = program.get("--input");
|
||||
nsgv::gBqsrArg.OUTPUT_FILE = program.get("--output");
|
||||
nsgv::gBqsrArg.NUM_THREADS = program.get<int>("--num-threads");
|
||||
if (nsgv::gBqsrArg.NUM_THREADS < 1) {
|
||||
spdlog::error("num-threads must be positive.");
|
||||
exit(1);
|
||||
}
|
||||
nsgv::gBqsrArg.CREATE_INDEX = program.get<bool>("--create-index");
|
||||
nsgv::gBqsrArg.REFERENCE_FILE = program.get<string>("--reference");
|
||||
nsgv::gBqsrArg.KNOWN_SITES_VCFS = program.get<std::vector<string>>("--known-sites");
|
||||
|
|
|
|||
|
|
@ -29,7 +29,7 @@ typedef std::vector<Interval> IntervalArr;
|
|||
*/
|
||||
struct Interval {
|
||||
// const常量
|
||||
const static int CONTIG_SHIFT = 40;
|
||||
const static int CONTIG_SHIFT = BamWrap::MAX_CONTIG_LEN_SHIFT;
|
||||
const static uint64_t POS_MASK = (1LL << CONTIG_SHIFT) - 1;
|
||||
|
||||
// 类变量
|
||||
|
|
|
|||
Loading…
Reference in New Issue