完善了统计时间
This commit is contained in:
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95c4a16151
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745963831d
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@ -5,5 +5,5 @@ set(CMAKE_CXX_STANDARD_REQUIRED ON)
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# set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread")
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# set(CMAKE_BUILD_TYPE Debug)
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# set(CMAKE_BUILD_TYPE Release)
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add_definitions(-DSHOW_PERF=1)
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# add_definitions(-DSHOW_PERF=1)
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add_subdirectory(src)
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@ -153,8 +153,10 @@ int SerialBQSR(AuxVar &aux) {
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++round;
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// 一. 读取bam数据
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size_t readNum = 0;
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PROF_START(GP_read);
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if (inBamBuf.ReadStat() >= 0)
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readNum = inBamBuf.ReadBam();
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PROF_GP_END(GP_read);
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if (readNum < 1) {
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break;
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}
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@ -176,7 +178,7 @@ int SerialBQSR(AuxVar &aux) {
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if (sd.read_len <= 0)
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continue;
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PROF_START(clip_read);
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PROF_START(GP_clip_read);
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// 4. 对read的两端进行检测，去除（hardclip）adapter
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ReadTransformer::hardClipAdaptorSequence(bw, sd);
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if (sd.read_len <= 0)
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@ -187,7 +189,7 @@ int SerialBQSR(AuxVar &aux) {
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continue;
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// 应用所有的变换，计算samdata的相关信息
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sd.applyTransformations();
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PROF_END(gprof[GP_clip_read], clip_read);
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PROF_GP_END(GP_clip_read);
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//const char* qname = bam_get_qname(sd.bw->b);
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// fprintf(gf[4], "%ld %d %d %d\n", sd.rid, sd.read_len, 1 + BamWrap::bam_pos(sd.start_pos), 1 + BamWrap::bam_pos(sd.end_pos));
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@ -195,7 +197,7 @@ int SerialBQSR(AuxVar &aux) {
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// 6. 更新每个read的platform信息，好像没啥用，暂时忽略
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// 这里计算snp和indel有点问题，snp和del结果不对，白天调试一下
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const int nErrors = RecalFuncs::calculateIsSNPOrIndel(aux, sd, isSNP, isIns, isDel);
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const int nErrors = RecalFuncs::calculateIsSNPOrIndel(aux, sd, isSNP, isIns, isDel, 0);
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// fprintf(gf[4], "%s %d %ld ", bam_get_qname(sd.bw->b), sd.bw->b->core.flag, sd.rid);
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// for (int ii = 0; ii < sd.read_len; ++ii) fprintf(gf[4], "%d ", skips[ii] ? 1 : 0);
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@ -224,9 +226,9 @@ int SerialBQSR(AuxVar &aux) {
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// 到这里，基本的数据都准备好了，后续就是进行bqsr的统计了
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// 8. 计算这条read对应的协变量
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PROF_START(covariate);
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CovariateUtils::ComputeCovariates(sd, aux.header, readCovariates, true);
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PROF_END(gprof[GP_covariate], covariate);
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PROF_START(GP_covariate);
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CovariateUtils::ComputeCovariates(sd, aux.header, readCovariates, true, 0);
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PROF_GP_END(GP_covariate);
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// fprintf(gf[4], "%ld %d\n", sd.rid, sd.read_len);
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// for (auto &arr1 : readCovariates) {
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@ -248,7 +250,7 @@ int SerialBQSR(AuxVar &aux) {
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// fprintf(gf[3], "\n");
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// 9. 计算这条read需要跳过的位置
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PROF_START(read_vcf);
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PROF_START(GP_read_vcf);
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RecalFuncs::calculateKnownSites(sd, aux.vcfArr, aux.header, skips, 0);
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for (int ii = 0; ii < sd.read_len; ++ii) {
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skips[ii] = skips[ii] || (ContextCovariate::baseIndexMap[sd.bases[ii]] == -1) ||
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@ -257,7 +259,7 @@ int SerialBQSR(AuxVar &aux) {
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//stringstream ss;
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//for (auto s : skips) ss << (int)s << ' ';
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//spdlog::info("{}", ss.str());
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PROF_GP_END(read_vcf);
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PROF_GP_END(GP_read_vcf);
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// fprintf(gf[3], "%s %d %ld ", bam_get_qname(sd.bw->b), sd.bw->b->core.flag, sd.rid);
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// for (int ii = 0; ii < sd.read_len; ++ii) fprintf(gf[3], "%d ", skips[ii] ? 1 : 0);
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@ -268,19 +270,19 @@ int SerialBQSR(AuxVar &aux) {
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// fprintf(gf[0], "\n");
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// 10. 根据BAQ进一步处理snp，indel，得到处理后的数据
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PROF_START(frac_err);
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PROF_START(GP_frac_err);
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RecalFuncs::calculateFractionalErrorArray(isSNP, baqArray, snpErrors);
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RecalFuncs::calculateFractionalErrorArray(isIns, baqArray, insErrors);
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RecalFuncs::calculateFractionalErrorArray(isDel, baqArray, delErrors);
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PROF_GP_END(frac_err);
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PROF_GP_END(GP_frac_err);
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// aggregate all of the info into our info object, and update the data
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// 11. 合并之前计算的数据，得到info，并更新bqsr table数据
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ReadRecalInfo info(sd, readCovariates, skips, snpErrors, insErrors, delErrors);
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PROF_START(update_info);
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PROF_START(GP_update_info);
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RecalUtils::updateRecalTablesForRead(info, recalTables);
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PROF_END(gprof[GP_update_info], update_info);
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PROF_GP_END(GP_update_info);
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}
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readNumSum += readNum;
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inBamBuf.ClearAll(); //
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@ -289,26 +291,32 @@ int SerialBQSR(AuxVar &aux) {
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spdlog::info("read count: {}", readNumSum);
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// 12. 创建总结数据
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PROF_START(GP_collapse_round);
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collapseQualityScoreTableToReadGroupTable(recalTables.readGroupTable, recalTables.qualityScoreTable);
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roundTableValues(recalTables);
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PROF_GP_END(GP_collapse_round);
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#if 0
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printRecalTables(recalTables);
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#endif
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// 13. 量化质量分数
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PROF_START(GP_quantize);
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QuantizationInfo quantInfo(recalTables, nsgv::gBqsrArg.QUANTIZING_LEVELS);
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PROF_GP_END(GP_quantize);
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// 14. 输出结果
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PROF_START(GP_print_report);
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RecalUtils::outputRecalibrationReport(nsgv::gBqsrArg, quantInfo, recalTables);
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PROF_GP_END(GP_print_report);
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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, int steal) {
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static void thread_worker(void* data, long idx, int thid, int steal) {
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// static void thread_worker(void* data, long idx, int tid) {
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AuxVar& aux = (*(vector<AuxVar>*)data)[tid];
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AuxVar& aux = (*(vector<AuxVar>*)data)[thid];
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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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@ -319,7 +327,6 @@ static void thread_worker(void* data, long idx, int tid, int steal) {
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auto &bams = *aux.bamArr;
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if (steal)
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for (auto& vcf : aux.vcfArr) vcf.knownSites.clear();
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int f = tid * 4;
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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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@ -338,26 +345,16 @@ static void thread_worker(void* data, long idx, int tid, int steal) {
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sd.rid = i + aux.processedReads;
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if (sd.read_len <= 0) continue;
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//PROF_START(clip_read);
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PROF_START(TP_clip_read);
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ReadTransformer::hardClipAdaptorSequence(bw, sd);
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if (sd.read_len <= 0) continue;
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ReadTransformer::hardClipSoftClippedBases(bw, sd);
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if (sd.read_len <= 0) continue;
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sd.applyTransformations();
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// PROF_END(gprof[GP_clip_read], clip_read);
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PROF_TP_END(TP_clip_read);
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const int nErrors = RecalFuncs::calculateIsSNPOrIndel(aux, sd, isSNP, isIns, isDel, thid);
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const int nErrors = RecalFuncs::calculateIsSNPOrIndel(aux, sd, isSNP, isIns, isDel);
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#if 0
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fprintf(gf[f + 0], "%s %d %ld ", bam_get_qname(sd.bw->b), sd.bw->b->core.flag, sd.rid);
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for (int ii = 0; ii < sd.read_len; ++ii) fprintf(gf[f + 0], "%d ", isSNP[ii]);
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fprintf(gf[f + 0], "\n");
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fprintf(gf[f + 1], "%s %d %ld ", bam_get_qname(sd.bw->b), sd.bw->b->core.flag, sd.rid);
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for (int ii = 0; ii < sd.read_len; ++ii) fprintf(gf[f + 1], "%d ", isIns[ii]);
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fprintf(gf[f + 1], "\n");
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fprintf(gf[f + 2], "%s %d %ld ", bam_get_qname(sd.bw->b), sd.bw->b->core.flag, sd.rid);
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for (int ii = 0; ii < sd.read_len; ++ii) fprintf(gf[f + 2], "%d ", isDel[ii]);
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fprintf(gf[f + 2], "\n");
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#endif
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bool baqCalculated = false;
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if (nErrors == 0 || !nsgv::gBqsrArg.enableBAQ) {
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baqCalculated = BAQ::flatBAQArray(sd, baqArray);
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@ -366,44 +363,27 @@ static void thread_worker(void* data, long idx, int tid, int steal) {
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}
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if (!baqCalculated) continue;
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// PROF_START(covariate);
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CovariateUtils::ComputeCovariates(sd, aux.header, readCovariates, true);
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// PROF_END(gprof[GP_covariate], covariate);
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PROF_START(TP_covariate);
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CovariateUtils::ComputeCovariates(sd, aux.header, readCovariates, true, thid);
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PROF_TP_END(TP_covariate);
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// PROF_START(read_vcf);
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RecalFuncs::calculateKnownSites(sd, aux.vcfArr, aux.header, skips, tid);
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RecalFuncs::calculateKnownSites(sd, aux.vcfArr, aux.header, skips, thid);
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for (int ii = 0; ii < sd.read_len; ++ii) {
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skips[ii] =
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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 0
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fprintf(gf[f + 3], "%s %d %ld ", bam_get_qname(sd.bw->b), sd.bw->b->core.flag, sd.rid);
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for (int ii = 0; ii < sd.read_len; ++ii) fprintf(gf[f + 3], "%d ", skips[ii] ? 1 : 0);
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fprintf(gf[f + 3], "\n");
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#endif
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#if 0
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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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PROF_START(TP_frac_err);
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RecalFuncs::calculateFractionalErrorArray(isSNP, baqArray, snpErrors);
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RecalFuncs::calculateFractionalErrorArray(isIns, baqArray, insErrors);
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RecalFuncs::calculateFractionalErrorArray(isDel, baqArray, delErrors);
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// PROF_GP_END(frac_err);
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PROF_TP_END(TP_frac_err);
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ReadRecalInfo info(sd, readCovariates, skips, snpErrors, insErrors, delErrors);
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//PROF_START(update_info);
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PROF_START(TP_update_info);
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RecalUtils::updateRecalTablesForRead(info, recalTables);
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//PROF_END(gprof[GP_update_info], update_info);
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PROF_TP_END(TP_update_info);
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}
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}
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@ -418,7 +398,9 @@ int ParallelBQSR(vector<AuxVar>& auxArr) {
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++round;
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// 一. 读取bam数据
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size_t readNum = 0;
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PROF_START(GP_read);
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if (inBamBuf.ReadStat() >= 0) readNum = inBamBuf.ReadBam();
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PROF_GP_END(GP_read);
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if (readNum < 1) { break; }
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auto bams = inBamBuf.GetBamArr();
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for_each(auxArr.begin(), auxArr.end(), [&](AuxVar& aux) {
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@ -426,11 +408,13 @@ 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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PROF_START(GP_thread_worker);
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#if 1
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kt_for_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_steal(auxArr.size(), thread_worker, &auxArr, auxArr.size());
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#endif
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PROF_GP_END(GP_thread_worker);
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readNumSum += readNum;
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AuxVar::processedReads += readNum;
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inBamBuf.ClearAll(); //
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@ -442,6 +426,8 @@ int ParallelBQSR(vector<AuxVar>& auxArr) {
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// printRecalTables(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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PROF_START(GP_merge_covs);
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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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@ -460,19 +446,26 @@ int ParallelBQSR(vector<AuxVar>& auxArr) {
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}
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});
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}
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PROF_GP_END(GP_merge_covs);
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spdlog::info("All processed reads {}.", auxArr[0].threadProcessedReads);
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// 创建总结数据
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PROF_START(GP_collapse_round);
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collapseQualityScoreTableToReadGroupTable(recalTables.readGroupTable, recalTables.qualityScoreTable);
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roundTableValues(recalTables);
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PROF_GP_END(GP_collapse_round);
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// printRecalTables(recalTables);
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// 量化质量分数
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PROF_START(GP_quantize);
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QuantizationInfo quantInfo(recalTables, nsgv::gBqsrArg.QUANTIZING_LEVELS);
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PROF_GP_END(GP_quantize);
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// 输出结果
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PROF_START(GP_print_report);
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RecalUtils::outputRecalibrationReport(nsgv::gBqsrArg, quantInfo, recalTables);
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PROF_GP_END(GP_print_report);
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return 0;
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}
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@ -562,7 +555,7 @@ static void globalDestroy() {
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int BaseRecalibrator() {
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int ret = 0;
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PROF_START(whole_process);
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PROF_START(GP_whole_process);
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globalInit();
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if (nsgv::gBqsrArg.NUM_THREADS == 1)
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ret = SerialBQSR(nsgv::gAuxVars[0]); // 串行处理数据，生成recal table
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@ -570,7 +563,7 @@ int BaseRecalibrator() {
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ret = ParallelBQSR(nsgv::gAuxVars); // 并行处理数据，生成recal table
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globalDestroy();
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sam_close(nsgv::gInBamFp);
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PROF_END(gprof[GP_whole_process], whole_process);
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PROF_GP_END(GP_whole_process);
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return ret;
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}
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@ -1,4 +1,5 @@
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#include "covariate.h"
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#include "util/profiling.h"
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// for EventType
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EventTypeValue EventType::BASE_SUBSTITUTION = {0, 'M', "Base Substitution"};
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@ -24,11 +25,19 @@ int CycleCovariate::MAXIMUM_CYCLE_VALUE;
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// for CovariateUtils
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// 对一条read计算协变量（该协变量被上一个read用过）
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void CovariateUtils::ComputeCovariates(SamData& sd, sam_hdr_t* header, PerReadCovariateMatrix& values,
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bool recordIndelValues) {
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bool recordIndelValues, int thid) {
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PROF_START(TP_readgroup);
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ReadGroupCovariate::RecordValues(sd, header, values, recordIndelValues);
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PROF_TP_END(TP_readgroup);
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PROF_START(TP_qualityscore);
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BaseQualityCovariate::RecordValues(sd, header, values, recordIndelValues);
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PROF_TP_END(TP_qualityscore);
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PROF_START(TP_context);
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ContextCovariate::RecordValues(sd, header, values, recordIndelValues);
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PROF_TP_END(TP_context);
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PROF_START(TP_cycle);
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CycleCovariate::RecordValues(sd, header, values, recordIndelValues);
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PROF_TP_END(TP_cycle);
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}
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/*
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@ -316,5 +316,5 @@ struct CovariateUtils {
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}
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// 对一条read计算协变量（该协变量被上一个read用过）
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static void ComputeCovariates(SamData& ad, sam_hdr_t* header, PerReadCovariateMatrix& values, bool recordIndelValues);
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static void ComputeCovariates(SamData& ad, sam_hdr_t* header, PerReadCovariateMatrix& values, bool recordIndelValues, int thid);
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};
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@ -29,19 +29,19 @@ struct RecalFuncs {
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}
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// 计算该read的每个碱基位置是否是SNP或Indel
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static int calculateIsSNPOrIndel(AuxVar& aux, SamData& sd, StableArray<int>& isSNP, StableArray<int>& isIns, StableArray<int>& isDel) {
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static int calculateIsSNPOrIndel(AuxVar& aux, SamData& sd, StableArray<int>& isSNP, StableArray<int>& isIns, StableArray<int>& isDel, int thid) {
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isSNP.resize_fill(sd.read_len, 0);
|
||||
isIns.resize_fill(sd.read_len, 0);
|
||||
isDel.resize_fill(sd.read_len, 0);
|
||||
// 1. 读取参考基因组，先看看串行运行性能，稍后可以将读入ref和vcf合并起来做成一个并行流水线步骤
|
||||
Interval interval{sd.start_pos, sd.end_pos}; // 闭区间
|
||||
PROF_START(read_ref);
|
||||
PROF_START(TP_read_ref);
|
||||
read_ref_base(aux, interval.left, interval);
|
||||
PROF_GP_END(read_ref);
|
||||
PROF_TP_END(TP_read_ref);
|
||||
const char *refBases = aux.ref_seq;
|
||||
|
||||
// 2. 遍历cigar，计算每个碱基是否是SNP或Indel
|
||||
PROF_START(calc_snp);
|
||||
PROF_START(TP_calc_snp);
|
||||
int readPos = 0, refPos = 0, nEvents = 0;
|
||||
for (int i = 0; i < sd.cigars.size(); ++i) {
|
||||
const char c = sd.cigars[i].op;
|
||||
|
|
@ -77,7 +77,7 @@ struct RecalFuncs {
|
|||
}
|
||||
}
|
||||
nEvents += std::accumulate(isIns.begin(), isIns.end(), 0) + std::accumulate(isDel.begin(), isDel.end(), 0);
|
||||
PROF_GP_END(calc_snp);
|
||||
PROF_TP_END(TP_calc_snp);
|
||||
return nEvents;
|
||||
}
|
||||
|
||||
|
|
@ -114,6 +114,7 @@ struct RecalFuncs {
|
|||
|
||||
// update vcfs
|
||||
// int idx = 0;
|
||||
PROF_START(TP_read_vcf);
|
||||
for (auto& vcf : vcfs) {
|
||||
// 为啥多线程环境会出现，deque的front和[0]不一样？好像是调试的时候的问题，实际运行时没再出现
|
||||
// if (vcf.knownSites.front().left != vcf.knownSites[0].left || vcf.knownSites.front().right != vcf.knownSites[0].right)
|
||||
|
|
@ -166,7 +167,9 @@ struct RecalFuncs {
|
|||
}
|
||||
}
|
||||
}
|
||||
PROF_TP_END(TP_read_vcf);
|
||||
// fprintf(gf[0], "%s %d %ld ", bam_get_qname(sd.bw->b), sd.bw->b->core.flag, sd.rid);
|
||||
PROF_START(TP_calc_skips);
|
||||
for (auto& vcf : vcfs) {
|
||||
for (auto& intv : vcf.knownSites) {
|
||||
// knownSite is outside clipping window for the read, ignore
|
||||
|
|
@ -198,6 +201,7 @@ struct RecalFuncs {
|
|||
}
|
||||
//idx += 1;
|
||||
}
|
||||
PROF_TP_END(TP_calc_skips);
|
||||
//fprintf(gf[0], "\n");
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -143,7 +143,7 @@ int main_BaseRecalibrator(int argc, char *argv[]) {
|
|||
BaseRecalibrator();
|
||||
spdlog::info("fast base recalibration phase-1 end");
|
||||
|
||||
DisplayProfiling(1);
|
||||
DisplayProfiling(nsgv::gBqsrArg.NUM_THREADS);
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -36,50 +36,49 @@ static int CalcThreadTime(uint64_t *a, int len, double *max, double *min, double
|
|||
}
|
||||
|
||||
#define PRINT_GP(gpname) \
|
||||
fprintf(stderr, "time G %-15s: %0.2lfs\n", #gpname, gprof[GP_##gpname] * 1.0 / proc_freq);
|
||||
fprintf(stderr, "time %-15s: %0.2lfs\n", #gpname, gprof[gpname] * 1.0 / proc_freq);
|
||||
|
||||
#define PRINT_TP(tpname, nthread) \
|
||||
{ \
|
||||
double maxTime, minTime, avgTime; \
|
||||
CalcThreadTime(tprof[TP_##tpname], nthread, &maxTime, &minTime, &avgTime); \
|
||||
fprintf(stderr, "time T %-15s: avg %0.2lfs min %0.2lfs max %0.2lfs\n", #tpname, avgTime, minTime, maxTime); \
|
||||
#define PRINT_TP(tpname) \
|
||||
{ \
|
||||
double maxTime, minTime, avgTime; \
|
||||
CalcThreadTime(tprof[tpname], nthread, &maxTime, &minTime, &avgTime); \
|
||||
fprintf(stderr, "time %-15s: avg %0.2lfs min %0.2lfs max %0.2lfs\n", #tpname, avgTime, minTime, maxTime); \
|
||||
}
|
||||
|
||||
int DisplayProfiling(int nthread) {
|
||||
|
||||
#ifdef SHOW_PERF
|
||||
fprintf(stderr, "\n");
|
||||
// PRINT_GP(read_wait);
|
||||
// PRINT_GP(gen_wait);
|
||||
// PRINT_GP(sort_wait);
|
||||
// PRINT_GP(markdup_wait);
|
||||
// PRINT_GP(intersect_wait);
|
||||
PRINT_GP(clip_read);
|
||||
PRINT_GP(read_ref);
|
||||
PRINT_GP(calc_snp);
|
||||
PRINT_GP(read_vcf);
|
||||
PRINT_GP(covariate);
|
||||
PRINT_GP(frac_err);
|
||||
PRINT_GP(update_info);
|
||||
//PRINT_GP(markdup);
|
||||
//PRINT_GP(intersect);
|
||||
// PRINT_GP(merge_result);
|
||||
// PRINT_GP(sort_pair);
|
||||
// PRINT_GP(sort_frag);
|
||||
// PRINT_GP(markdup_pair);
|
||||
// PRINT_GP(markdup_frag);
|
||||
// PRINT_GP(merge_match);
|
||||
// PRINT_GP(merge_markdup);
|
||||
// PRINT_GP(merge_update);
|
||||
// PRINT_GP(merge_add);
|
||||
//PRINT_GP(markdup_all);
|
||||
// PRINT_GP(final_read);
|
||||
//PRINT_GP(write);
|
||||
// PRINT_GP(whole_process);
|
||||
|
||||
// PRINT_TP(gen, nthread);
|
||||
// PRINT_TP(sort_frag, nthread);
|
||||
// PRINT_TP(sort_pair, nthread);
|
||||
PRINT_GP(GP_read);
|
||||
if (nthread == 1) {
|
||||
PRINT_GP(GP_clip_read);
|
||||
PRINT_GP(GP_read_ref);
|
||||
PRINT_GP(GP_calc_snp);
|
||||
PRINT_GP(GP_read_vcf);
|
||||
PRINT_TP(TP_read_vcf);
|
||||
PRINT_TP(TP_calc_skips);
|
||||
PRINT_GP(GP_covariate);
|
||||
PRINT_TP(TP_readgroup);
|
||||
PRINT_TP(TP_qualityscore);
|
||||
PRINT_TP(TP_context);
|
||||
PRINT_TP(TP_cycle);
|
||||
PRINT_GP(GP_frac_err);
|
||||
PRINT_GP(GP_update_info);
|
||||
} else {
|
||||
PRINT_TP(TP_clip_read);
|
||||
PRINT_TP(TP_read_ref);
|
||||
PRINT_TP(TP_calc_snp);
|
||||
PRINT_TP(TP_read_vcf);
|
||||
PRINT_TP(TP_calc_skips);
|
||||
PRINT_TP(TP_covariate);
|
||||
PRINT_TP(TP_readgroup);
|
||||
PRINT_TP(TP_qualityscore);
|
||||
PRINT_TP(TP_context);
|
||||
PRINT_TP(TP_cycle);
|
||||
PRINT_TP(TP_frac_err);
|
||||
PRINT_TP(TP_update_info);
|
||||
}
|
||||
PRINT_GP(GP_whole_process);
|
||||
|
||||
fprintf(stderr, "\n");
|
||||
#endif
|
||||
|
|
|
|||
|
|
@ -25,7 +25,8 @@ extern uint64_t gprof[LIM_GLOBAL_PROF_TYPE];
|
|||
#define PROF_START(tmp_time) uint64_t prof_tmp_##tmp_time = RealtimeMsec()
|
||||
#define PROF_START_AGAIN(tmp_time) prof_tmp_##tmp_time = RealtimeMsec()
|
||||
#define PROF_END(result, tmp_time) result += RealtimeMsec() - prof_tmp_##tmp_time
|
||||
#define PROF_GP_END(tmp_time) gprof[GP_##tmp_time] += RealtimeMsec() - prof_tmp_##tmp_time
|
||||
#define PROF_GP_END(tmp_time) gprof[tmp_time] += RealtimeMsec() - prof_tmp_##tmp_time
|
||||
#define PROF_TP_END(tmp_time) tprof[tmp_time][thid] += RealtimeMsec() - prof_tmp_##tmp_time
|
||||
#define PROF_PRINT_START(tmp_time) uint64_t tmp_time = RealtimeMsec()
|
||||
#define PROF_PRINT_END(tmp_time) \
|
||||
tmp_time = RealtimeMsec() - tmp_time; \
|
||||
|
|
@ -34,6 +35,7 @@ extern uint64_t gprof[LIM_GLOBAL_PROF_TYPE];
|
|||
#define PROF_START(tmp_time)
|
||||
#define PROF_END(result, tmp_time)
|
||||
#define PROF_GP_END(tmp_time)
|
||||
#define PROF_TP_END(tmp_time)
|
||||
#define PROF_PRINT_START(tmp_time)
|
||||
#define PROF_PRINT_END(tmp_time)
|
||||
#endif
|
||||
|
|
@ -41,40 +43,39 @@ extern uint64_t gprof[LIM_GLOBAL_PROF_TYPE];
|
|||
// GLOBAL
|
||||
enum { GP_0 = 0, GP_1, GP_2, GP_3, GP_4, GP_5, GP_6, GP_7, GP_8, GP_9, GP_10 };
|
||||
enum {
|
||||
GP_read_wait = 11,
|
||||
GP_clip_read,
|
||||
GP_clip_read = 11,
|
||||
GP_calc_snp,
|
||||
GP_covariate,
|
||||
GP_read_ref,
|
||||
GP_read_vcf,
|
||||
GP_frac_err,
|
||||
GP_update_info,
|
||||
GP_gen_wait,
|
||||
GP_sort_wait,
|
||||
GP_markdup_wait,
|
||||
GP_intersect_wait,
|
||||
GP_merge_covs,
|
||||
GP_collapse_round,
|
||||
GP_quantize,
|
||||
GP_print_report,
|
||||
GP_read,
|
||||
GP_gen,
|
||||
GP_sort,
|
||||
GP_markdup,
|
||||
GP_intersect,
|
||||
GP_merge_result,
|
||||
GP_markdup_pair,
|
||||
GP_markdup_frag,
|
||||
GP_sort_pair,
|
||||
GP_sort_frag,
|
||||
GP_merge_match,
|
||||
GP_merge_markdup,
|
||||
GP_merge_update,
|
||||
GP_merge_add,
|
||||
GP_markdup_all,
|
||||
GP_final_read,
|
||||
GP_write,
|
||||
GP_thread_worker,
|
||||
GP_whole_process
|
||||
};
|
||||
// THREAD
|
||||
enum { TP_0 = 0, TP_1, TP_2, TP_3, TP_4, TP_5, TP_6, TP_7, TP_8, TP_9, TP_10 };
|
||||
enum { TP_gen = 11, TP_sort, TP_sort_frag, TP_sort_pair};
|
||||
enum {
|
||||
TP_clip_read = 11,
|
||||
TP_calc_snp,
|
||||
TP_covariate,
|
||||
TP_read_ref,
|
||||
TP_read_vcf,
|
||||
TP_calc_skips,
|
||||
TP_frac_err,
|
||||
TP_readgroup,
|
||||
TP_qualityscore,
|
||||
TP_context,
|
||||
TP_cycle,
|
||||
TP_update_info,
|
||||
TP_whole_process
|
||||
};
|
||||
|
||||
uint64_t RealtimeMsec(void);
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue