Ejemplo n.º 1
0
int main (int argc, const char *argv[])
{
    BaseCallerSalute();

    time_t analysis_start_time;
    time(&analysis_start_time);

    Json::Value basecaller_json(Json::objectValue);
    DumpStartingStateOfProgram (argc,argv,analysis_start_time, basecaller_json["BaseCaller"]);

    //
    // Step 1. Process Command Line Options & Initialize Modules
    //

    BaseCallerParameters bc_params;
    OptArgs opts, null_opts;
    opts.ParseCmdLine(argc, argv);

    if (opts.GetFirstBoolean('h', "help", false) or argc == 1)
    	bc_params.PrintHelp();
    if (opts.GetFirstBoolean('v', "version", false)) {
        fprintf (stdout, "%s", IonVersion::GetFullVersion ("BaseCaller").c_str());
        exit (EXIT_SUCCESS);
    }

    // Command line processing *** Main directories and file locations first
    bc_params.InitializeFilesFromOptArgs(opts);
    bc_params.InitContextVarsFromOptArgs(opts);

    // Command line processing *** Options that have default values retrieved from wells or mask files
    RawWells wells ("", bc_params.GetFiles().filename_wells.c_str());
    if (!wells.OpenMetaData()) {
        fprintf (stderr, "Failed to retrieve metadata from %s\n", bc_params.GetFiles().filename_wells.c_str());
        exit (EXIT_FAILURE);
    }
    Mask mask (1, 1);
    if (mask.SetMask (bc_params.GetFiles().filename_mask.c_str()))
        exit (EXIT_FAILURE);

    string chip_type = "unknown";
    if (wells.KeyExists("ChipType"))
        wells.GetValue("ChipType", chip_type);

    // Command line processing *** Various general option and opts to classify and sample wells
    BaseCallerContext bc;
    bc.mask = &mask;
    bc.SetKeyAndFlowOrder(opts, wells.FlowOrder(), wells.NumFlows());
    bc.chip_subset.InitializeChipSubsetFromOptArgs(opts, mask.W(), mask.H());

    // Sampling options may reset command line arguments & change context
    bc_params.InitializeSamplingFromOptArgs(opts, bc.chip_subset.NumWells());
    bc_params.SetBaseCallerContextVars(bc);
    ClassifyAndSampleWells(bc, bc_params.GetSamplingOpts());


    // *** Setup for different datasets
    BarcodeDatasets datasets_calibration(bc.run_id, bc_params.GetFiles().calibration_panel_file);
    datasets_calibration.SetIonControl(bc.run_id);
    datasets_calibration.GenerateFilenames("IonControl","basecaller_bam",".basecaller.bam",bc_params.GetFiles().output_directory);

    BarcodeDatasets datasets(bc.run_id, bc_params.GetFiles().lib_datasets_file);
    // Check if any of the template barcodes is equal to a control barcode
    if (datasets_calibration.DatasetInUse())
      datasets.RemoveControlBarcodes(datasets_calibration.json());
    datasets.GenerateFilenames("Library","basecaller_bam",".basecaller.bam",bc_params.GetFiles().output_directory);

    BarcodeDatasets datasets_tf(bc.run_id);
    datasets_tf.SetTF(bc.process_tfs);
    datasets_tf.GenerateFilenames("TF","basecaller_bam",".basecaller.bam",bc_params.GetFiles().output_directory);

    BarcodeDatasets datasets_unfiltered_untrimmed(datasets);
    BarcodeDatasets datasets_unfiltered_trimmed(datasets);


    // *** Initialize remaining modules of BaseCallerContext
    vector<string> bam_comments;
    BaseCallerFilters filters(opts, bam_comments, bc.run_id, bc.flow_order, bc.keys, mask);
    bc.filters = &filters;

    BaseCallerMetricSaver metric_saver(opts, bc.chip_subset.GetChipSizeX(), bc.chip_subset.GetChipSizeY(), bc.flow_order.num_flows(),
                                bc.chip_subset.GetRegionSizeX(), bc.chip_subset.GetRegionSizeY(), bc_params.GetFiles().output_directory);
    bc.metric_saver = &metric_saver;

    // Calibration modules
    bc.recalibration.Initialize(opts, bc.flow_order);
    bc.recalModel.Initialize(opts, bam_comments, bc.run_id, bc.chip_subset);
    // initialize the per base quality score generator - dependent on calibration
    bc.quality_generator.Init(opts, chip_type, bc_params.GetFiles().input_directory, bc_params.GetFiles().output_directory, bc.recalibration.is_enabled());

    // Phase estimator
    bc.estimator.InitializeFromOptArgs(opts, bc.chip_subset, bc.keynormalizer);
    // Barcode classification
    BarcodeClassifier barcodes(opts, datasets, bc.flow_order, bc.keys, bc_params.GetFiles().output_directory,
    		                   bc.chip_subset.GetChipSizeX(), bc.chip_subset.GetChipSizeY());
    bc.barcodes = &barcodes;
    // Make sure calibration barcodes are initialized with default parameters
    BarcodeClassifier calibration_barcodes(null_opts, datasets_calibration, bc.flow_order, bc.keys,
                          bc_params.GetFiles().output_directory, bc.chip_subset.GetChipSizeX(), bc.chip_subset.GetChipSizeY());
    bc.calibration_barcodes = &calibration_barcodes;

    // Command line parsing officially over. Detect unknown options.
    opts.CheckNoLeftovers();

    // Save some run info into our handy json file
    bc_params.SaveParamsToJson(basecaller_json, bc, chip_type);
    SaveBaseCallerProgress(0, bc_params.GetFiles().output_directory);

    MemUsage("RawWellsBasecalling");


    //
    // Step 2. Filter training and phase estimation
    //

    // Find distribution of clonal reads for use in read filtering:
    filters.TrainClonalFilter(bc_params.GetFiles().output_directory, wells, mask, bc.polyclonal_filter);
    MemUsage("ClonalPopulation");
    ReportState(analysis_start_time,"Polyclonal Filter Training Complete");

    // Library phasing parameter estimation
    MemUsage("BeforePhaseEstimation");
    if (not bc.estimator.HaveEstimates()) {
      wells.OpenForIncrementalRead();
      bc.estimator.DoPhaseEstimation(&wells, &mask, bc.flow_order, bc.keys, (bc_params.NumThreads() == 1));
      wells.Close();
    }
    bc.estimator.ExportResultsToJson(basecaller_json["Phasing"]);
    bc.estimator.ExportTrainSubsetToJson(basecaller_json["TrainSubset"]);

    SaveJson(basecaller_json, bc_params.GetFiles().filename_json);
    SaveBaseCallerProgress(10, bc_params.GetFiles().output_directory);  // Phase estimation assumed to be 10% of the work

    // Initialize Barcode Classifier(s) - dependent on phase estimates
    bc.barcodes->BuildPredictedSignals(bc.estimator.GetAverageCF(), bc.estimator.GetAverageIE(), bc.estimator.GetAverageDR());
    bc.calibration_barcodes->BuildPredictedSignals(bc.estimator.GetAverageCF(), bc.estimator.GetAverageIE(), bc.estimator.GetAverageDR());

    MemUsage("AfterPhaseEstimation");
    ReportState(analysis_start_time,"Phase Parameter Estimation Complete");
    MemUsage("BeforeBasecalling");


    //
    // Step 3. Open wells and output BAM files & initialize writers
    //

    // Library data set writer - always
    bc.lib_writer.Open(bc_params.GetFiles().output_directory, datasets, 0, bc.chip_subset.NumRegions(),
                 bc.flow_order, bc.keys[0].bases(), filters.GetLibBeadAdapters(),
                 bc_params.NumBamWriterThreads(), basecaller_json, bam_comments);

    // Calibration reads data set writer - if applicable
    if (bc.have_calibration_panel)
      bc.calib_writer.Open(bc_params.GetFiles().output_directory, datasets_calibration, 0, bc.chip_subset.NumRegions(),
                     bc.flow_order, bc.keys[0].bases(), filters.GetLibBeadAdapters(),
                     bc_params.NumBamWriterThreads(), basecaller_json, bam_comments);

    // Test fragments data set writer - if applicable
    if (bc.process_tfs)
      bc.tf_writer.Open(bc_params.GetFiles().output_directory, datasets_tf, 1, bc.chip_subset.NumRegions(),
                  bc.flow_order, bc.keys[1].bases(), filters.GetTFBeadAdapters(),
                  bc_params.NumBamWriterThreads(), basecaller_json, bam_comments);

    // Unfiltered / unfiltered untrimmed data set writers - if applicable
    if (!bc.unfiltered_set.empty()) {
    	bc.unfiltered_writer.Open(bc_params.GetFiles().unfiltered_untrimmed_directory, datasets_unfiltered_untrimmed, -1,
                      bc.chip_subset.NumRegions(), bc.flow_order, bc.keys[0].bases(), filters.GetLibBeadAdapters(),
                      bc_params.NumBamWriterThreads(), basecaller_json, bam_comments);

        bc.unfiltered_trimmed_writer.Open(bc_params.GetFiles().unfiltered_trimmed_directory, datasets_unfiltered_trimmed, -1,
                              bc.chip_subset.NumRegions(), bc.flow_order, bc.keys[0].bases(), filters.GetLibBeadAdapters(),
                              bc_params.NumBamWriterThreads(), basecaller_json, bam_comments);
    }

    //
    // Step 4. Execute threaded basecalling
    //

    time_t basecall_start_time;
    time(&basecall_start_time);

    pthread_mutex_init(&bc.mutex, NULL);

    pthread_t worker_id[bc_params.NumThreads()];
    for (int worker = 0; worker < bc_params.NumThreads(); worker++)
        if (pthread_create(&worker_id[worker], NULL, BasecallerWorker, &bc)) {
            printf("*Error* - problem starting thread\n");
            exit (EXIT_FAILURE);
        }

    for (int worker = 0; worker < bc_params.NumThreads(); worker++)
        pthread_join(worker_id[worker], NULL);

    pthread_mutex_destroy(&bc.mutex);

    time_t basecall_end_time;
    time(&basecall_end_time);


    //
    // Step 5. Close files and print out some statistics
    //

    printf("\n\nBASECALLING: called %d of %u wells in %1.0lf seconds with %d threads\n\n",
           filters.NumWellsCalled(), bc.chip_subset.NumWells(),
           difftime(basecall_end_time,basecall_start_time), bc_params.NumThreads());

    bc.lib_writer.Close(datasets, "Library");
    if (bc.have_calibration_panel)
    	bc.calib_writer.Close(datasets_calibration, "IonControl");
    if (bc.process_tfs)
        bc.tf_writer.Close(datasets_tf, "Test Fragments");

    filters.TransferFilteringResultsToMask(mask);

    if (!bc.unfiltered_set.empty()) {

        // Must happen after filters transferred to mask
        bc.WriteUnfilteredFilterStatus(bc_params.GetFiles());

        bc.unfiltered_writer.Close(datasets_unfiltered_untrimmed);
        bc.unfiltered_trimmed_writer.Close(datasets_unfiltered_trimmed);

        datasets_unfiltered_untrimmed.SaveJson(bc_params.GetFiles().unfiltered_untrimmed_directory+"/datasets_basecaller.json");
        datasets_unfiltered_trimmed.SaveJson(bc_params.GetFiles().unfiltered_trimmed_directory+"/datasets_basecaller.json");
    }

    metric_saver.Close();
    barcodes.Close(datasets);
    calibration_barcodes.Close(datasets_calibration);
    if (bc.have_calibration_panel) {
      datasets.json()["IonControl"]["datasets"] = datasets_calibration.json()["datasets"];
      datasets.json()["IonControl"]["read_groups"] = datasets_calibration.read_groups();
    }
    datasets.SaveJson(bc_params.GetFiles().output_directory+"/datasets_basecaller.json");
    if (bc.process_tfs)
        datasets_tf.SaveJson(bc_params.GetFiles().output_directory+"/datasets_tf.json");

    // Generate BaseCaller.json

    bc.lib_writer.SaveFilteringStats(basecaller_json, "lib", true);
    if (bc.have_calibration_panel)
      bc.calib_writer.SaveFilteringStats(basecaller_json, "control", false);
    if (bc.process_tfs)
      bc.tf_writer.SaveFilteringStats(basecaller_json, "tf", false);

    time_t analysis_end_time;
    time(&analysis_end_time);

    basecaller_json["BaseCaller"]["end_time"] = get_time_iso_string(analysis_end_time);
    basecaller_json["BaseCaller"]["total_duration"] = (int)difftime(analysis_end_time,analysis_start_time);
    basecaller_json["BaseCaller"]["basecalling_duration"] = (int)difftime(basecall_end_time,basecall_start_time);

    basecaller_json["Filtering"]["qv_histogram"] = Json::arrayValue;
    for (int qv = 0; qv < 50; ++qv)
        basecaller_json["Filtering"]["qv_histogram"][qv] = (Json::UInt64)bc.lib_writer.qv_histogram()[qv];

    SaveJson(basecaller_json, bc_params.GetFiles().filename_json);
    SaveBaseCallerProgress(100, bc_params.GetFiles().output_directory);

    mask.WriteRaw (bc_params.GetFiles().filename_filter_mask.c_str());
    mask.validateMask();

    MemUsage("AfterBasecalling");
    ReportState(analysis_start_time,"Basecalling Complete");

    return EXIT_SUCCESS;
}
Ejemplo n.º 2
0
void * BasecallerWorker(void *input)
{
    BaseCallerContext& bc = *static_cast<BaseCallerContext*>(input);

    RawWells wells ("", bc.filename_wells.c_str());
    pthread_mutex_lock(&bc.mutex);
    wells.OpenForIncrementalRead();
    pthread_mutex_unlock(&bc.mutex);

    vector<float> residual(bc.flow_order.num_flows(), 0);
    vector<float> scaled_residual(bc.flow_order.num_flows(), 0);
    vector<float> wells_measurements(bc.flow_order.num_flows(), 0);
    vector<float> local_noise(bc.flow_order.num_flows(), 0);
    vector<float> minus_noise_overlap(bc.flow_order.num_flows(), 0);
    vector<float> homopolymer_rank(bc.flow_order.num_flows(), 0);
    vector<float> neighborhood_noise(bc.flow_order.num_flows(), 0);
    vector<float> phasing_parameters(3);
    vector<uint16_t>  flowgram(bc.flow_order.num_flows());
    vector<int16_t>   flowgram2(bc.flow_order.num_flows());
    vector<int16_t> filtering_details(13,0);

    vector<char> abParams;
    abParams.reserve(256);

    vector<uint8_t>   quality(3*bc.flow_order.num_flows());
    vector<int>       base_to_flow (3*bc.flow_order.num_flows());             //!< Flow of in-phase incorporation of each base.

    TreephaserSSE treephaser_sse(bc.flow_order, bc.windowSize);
    DPTreephaser  treephaser(bc.flow_order, bc.windowSize);
    treephaser.SetStateProgression(bc.diagonal_state_prog);
    treephaser.SkipRecalDuringNormalization(bc.skip_recal_during_norm);
    treephaser_sse.SkipRecalDuringNormalization(bc.skip_recal_during_norm);


    while (true) {

        //
        // Step 1. Retrieve next unprocessed region
        //

        pthread_mutex_lock(&bc.mutex);

        int current_region, begin_x, begin_y, end_x, end_y;
        if (not bc.chip_subset.GetCurrentRegionAndIncrement(current_region, begin_x, end_x, begin_y, end_y)) {
           wells.Close();
           pthread_mutex_unlock(&bc.mutex);
           return NULL;
        }

        int num_usable_wells = 0;
        for (int y = begin_y; y < end_y; ++y)
            for (int x = begin_x; x < end_x; ++x)
                if (bc.class_map[x + y * bc.chip_subset.GetChipSizeX()] >= 0)
                    num_usable_wells++;

        if      (begin_x == 0)            printf("\n% 5d/% 5d: ", begin_y, bc.chip_subset.GetChipSizeY());
        if      (num_usable_wells ==   0) printf("  ");
        else if (num_usable_wells <  750) printf(". ");
        else if (num_usable_wells < 1500) printf("o ");
        else if (num_usable_wells < 2250) printf("# ");
        else                              printf("##");
        fflush(NULL);

        if (begin_x == 0)
            SaveBaseCallerProgress(10 + (80*begin_y)/bc.chip_subset.GetChipSizeY(), bc.output_directory);

        pthread_mutex_unlock(&bc.mutex);

        // Process the data
        deque<ProcessedRead> lib_reads;                // Collection of template library reads
        deque<ProcessedRead> tf_reads;                 // Collection of test fragment reads
        deque<ProcessedRead> calib_reads;              // Collection of calibration library reads
        deque<ProcessedRead> unfiltered_reads;         // Random subset of lib_reads
        deque<ProcessedRead> unfiltered_trimmed_reads; // Random subset of lib_reads

        if (num_usable_wells == 0) { // There is nothing in this region. Don't even bother reading it
            bc.lib_writer.WriteRegion(current_region, lib_reads);
            if (bc.have_calibration_panel)
                bc.calib_writer.WriteRegion(current_region, calib_reads);
            if (bc.process_tfs)
                bc.tf_writer.WriteRegion(current_region, tf_reads);
            if (!bc.unfiltered_set.empty()) {
                bc.unfiltered_writer.WriteRegion(current_region,unfiltered_reads);
                bc.unfiltered_trimmed_writer.WriteRegion(current_region,unfiltered_trimmed_reads);
            }
            continue;
        }

        wells.SetChunk(begin_y, end_y-begin_y, begin_x, end_x-begin_x, 0, bc.flow_order.num_flows());
        wells.ReadWells();

        for (int y = begin_y; y < end_y; ++y)
            for (int x = begin_x; x < end_x; ++x) {   // Loop over wells within current region

                //
                // Step 2. Retrieve additional information needed to process this read
                //

                unsigned int read_index = x + y * bc.chip_subset.GetChipSizeX();
                int read_class = bc.class_map[read_index];
                if (read_class < 0)
                    continue;
                bool is_random_calibration_read = false;
                if (read_class == 2){
                  is_random_calibration_read = true;
                  read_class = 0; // Calibration reads are library beads;
                }
                bool is_random_unfiltered  = bc.unfiltered_set.count(read_index) > 0;

                if (not is_random_unfiltered and bc.only_process_unfiltered_set)
                  continue;

                bc.filters->SetValid(read_index); // Presume valid until some filter proves otherwise

                if (read_class == 0)
                    lib_reads.push_back(ProcessedRead(bc.barcodes->NoBarcodeReadGroup()));
                else
                    tf_reads.push_back(ProcessedRead(0));
                ProcessedRead& processed_read = (read_class==0) ? lib_reads.back() : tf_reads.back();

                // Respect filter decisions from Background Model
                if (bc.mask->Match(read_index, MaskFilteredBadResidual))
                    bc.filters->SetBkgmodelHighPPF(read_index, processed_read.filter);

                if (bc.mask->Match(read_index, MaskFilteredBadPPF))
                    bc.filters->SetBkgmodelPolyclonal(read_index, processed_read.filter);

                if (bc.mask->Match(read_index, MaskFilteredBadKey))
                    bc.filters->SetBkgmodelFailedKeypass(read_index, processed_read.filter);

                if (!is_random_unfiltered and !bc.filters->IsValid(read_index)) // No reason to waste more time
                    continue;

                float cf = bc.estimator.GetWellCF(x,y);
                float ie = bc.estimator.GetWellIE(x,y);
                float dr = bc.estimator.GetWellDR(x,y);

                for (int flow = 0; flow < bc.flow_order.num_flows(); ++flow)
                    wells_measurements[flow] = wells.At(y,x,flow);

                // Sanity check. If there are NaNs in this read, print warning
                vector<int> nanflow;
                for (int flow = 0; flow < bc.flow_order.num_flows(); ++flow) {
                    if (!isnan(wells_measurements[flow]))
                        continue;
                    wells_measurements[flow] = 0;
                    nanflow.push_back(flow);
                }
                if (nanflow.size() > 0) {
                    fprintf(stderr, "ERROR: BaseCaller read NaNs from wells file, x=%d y=%d flow=%d", x, y, nanflow[0]);
                    for (unsigned int flow=1; flow < nanflow.size(); flow++) {
                        fprintf(stderr, ",%d", nanflow[flow]);
                    }
                    fprintf(stderr, "\n");
                    fflush(stderr);
                }

                //
                // Step 3. Perform base calling and quality value calculation
                //

                BasecallerRead read;
                bool key_pass = true;
                if (bc.keynormalizer == "keynorm-new") {
                  key_pass = read.SetDataAndKeyNormalizeNew(&wells_measurements[0], wells_measurements.size(), bc.keys[read_class].flows(), bc.keys[read_class].flows_length() - 1, false);
                } else { // if (bc.keynormalizer == "keynorm-old") {
                  key_pass = read.SetDataAndKeyNormalize(&wells_measurements[0], wells_measurements.size(), bc.keys[read_class].flows(), bc.keys[read_class].flows_length() - 1);
                }

                // Get rid of outliers quickly
                bc.filters->FilterHighPPFAndPolyclonal (read_index, read_class, processed_read.filter, read.raw_measurements, bc.polyclonal_filter);
                if (not key_pass)
                  bc.filters->FilterFailedKeypass (read_index, read_class, processed_read.filter, read.sequence);
                if (!is_random_unfiltered and !bc.filters->IsValid(read_index)) // No reason to waste more time
                  continue;

                // Check if this read is either from the calibration panel or from the random calibration set
                if(bc.calibration_training and bc.have_calibration_panel) {
                  if (!is_random_calibration_read and !bc.calibration_barcodes->MatchesBarcodeSignal(read)) {
                	bc.filters->SetFiltered(read_index, read_class, processed_read.filter); // Set as filtered
                    continue;  // And move on along
                  }
                }

                // Equal recalibration opportunity for everybody! (except TFs!)
                const vector<vector<vector<float> > > * aPtr = 0;
                const vector<vector<vector<float> > > * bPtr = 0;
                if (bc.recalModel.is_enabled() && read_class == 0) { //do not recalibrate TF read bc.chip_subset.GetChipSizeX()
                  aPtr = bc.recalModel.getAs(x+bc.chip_subset.GetColOffset(), y+bc.chip_subset.GetRowOffset());
                  bPtr = bc.recalModel.getBs(x+bc.chip_subset.GetColOffset(), y+bc.chip_subset.GetRowOffset());
                }

                // Execute the iterative solving-normalization routine - switch by specified algorithm
                if (bc.dephaser == "treephaser-sse") {
                  treephaser_sse.SetAsBs(aPtr, bPtr);  // Set/delete recalibration model for this read
                  treephaser_sse.SetModelParameters(cf, ie); // sse version has no hookup for droop.
                  treephaser_sse.NormalizeAndSolve(read);
                  treephaser.SetModelParameters(cf, ie); // Adapter trimming uses the cpp treephaser

                } else { // Setup cpp treephaser
                  if (bc.skip_droop)
                    treephaser.SetModelParameters(cf, ie);
                  else
                    treephaser.SetModelParameters(cf, ie, dr);
                  treephaser.SetAsBs(aPtr, bPtr); // Set/delete recalibration model for this read

                  if (bc.dephaser == "dp-treephaser") {
                    // Single parameter gain estimation
                    treephaser.NormalizeAndSolve_GainNorm(read, bc.flow_order.num_flows());
                  } else if (bc.dephaser == "treephaser-adaptive") {
                    // Adaptive nortmalization - resolving read from start in each iteration
                    treephaser.NormalizeAndSolve_Adaptive(read, bc.flow_order.num_flows());
                  } else { //if (bc.dephaser == "treephaser-swan") {
                    // Default corresponding to (approximately) what the sse version is doing
                	// Adaptive normalization - sliding window without resolving start
                	treephaser.NormalizeAndSolve_SWnorm(read, bc.flow_order.num_flows());
                  }

                  // Need this function to calculate inphase population for cpp version
                  treephaser.ComputeQVmetrics(read);
                }

                // If recalibration is enabled, generate adjusted sequence and normalized_measurements, and recompute QV metrics
                bool calibrate_read = (bc.recalibration.is_enabled() && read_class == 0); //do not recalibrate TF read
                if (calibrate_read) {
                	// Change base sequence for low hps
                    bc.recalibration.CalibrateRead(x+bc.chip_subset.GetColOffset(),y+bc.chip_subset.GetRowOffset(),read.sequence, read.normalized_measurements, read.prediction, read.state_inphase);
                    if (bc.dephaser == "treephaser-sse")
                      treephaser_sse.ComputeQVmetrics(read);
                    else
                      treephaser.ComputeQVmetrics(read);
                } else if (bc.dephaser == "treephaser-sse") {
                  // in case we didn't calibrate low hps, still want to have QV metrics for sse output
                  treephaser_sse.ComputeQVmetrics(read);
                }

                // Misc data management: Generate residual, scaled_residual
                for (int flow = 0; flow < bc.flow_order.num_flows(); ++flow) {
                    residual[flow] = read.normalized_measurements[flow] - read.prediction[flow];
                    scaled_residual[flow] = residual[flow] / read.state_inphase[flow];
                }

                // Misc data management: Put base calls in proper string form
                processed_read.filter.n_bases = read.sequence.size();
                processed_read.filter.is_called = true;

                // Misc data management: Generate base_to_flow

                base_to_flow.clear();
                base_to_flow.reserve(processed_read.filter.n_bases);
                for (int base = 0, flow = 0; base < processed_read.filter.n_bases; ++base) {
                    while (flow < bc.flow_order.num_flows() and read.sequence[base] != bc.flow_order[flow])
                        flow++;
                    base_to_flow.push_back(flow);
                }


                // Misc data management: Populate some trivial read properties

                char read_name[256];
                sprintf(read_name, "%s:%05d:%05d", bc.run_id.c_str(), bc.chip_subset.GetRowOffset() + y, bc.chip_subset.GetColOffset() + x);
                processed_read.bam.Name = read_name;
                processed_read.bam.SetIsMapped(false);

                phasing_parameters[0] = cf;
                phasing_parameters[1] = ie;
                phasing_parameters[2] = dr;
                processed_read.bam.AddTag("ZP", phasing_parameters);


                // Calculation of quality values
                // Predictor 1 - Treephaser residual penalty
                // Predictor 2 - Local noise/flowalign - 'noise' in the input base's measured val.  Noise is max[abs(val - round(val))] within +-1 BASES
                // Predictor 3 - Read Noise/Overlap - mean & stdev of the 0-mers & 1-mers in the read
                // Predictor 3 (new) - Beverly Events
                // Predictor 4 - Transformed homopolymer length
                // Predictor 5 - Treephaser: Penalty indicating deletion after the called base
                // Predictor 6 - Neighborhood noise - mean of 'noise' +-5 BASES around a base.  Noise is mean{abs(val - round(val))}

                int num_predictor_bases = min(bc.flow_order.num_flows(), processed_read.filter.n_bases);

                PerBaseQual::PredictorLocalNoise(local_noise, num_predictor_bases, base_to_flow, read.normalized_measurements, read.prediction);
                PerBaseQual::PredictorNeighborhoodNoise(neighborhood_noise, num_predictor_bases, base_to_flow, read.normalized_measurements, read.prediction);
                //PerBaseQual::PredictorNoiseOverlap(minus_noise_overlap, num_predictor_bases, read.normalized_measurements, read.prediction);
                PerBaseQual::PredictorBeverlyEvents(minus_noise_overlap, num_predictor_bases, base_to_flow, scaled_residual);
                PerBaseQual::PredictorHomopolymerRank(homopolymer_rank, num_predictor_bases, read.sequence);

                quality.clear();
                bc.quality_generator.GenerateBaseQualities(processed_read.bam.Name, processed_read.filter.n_bases, bc.flow_order.num_flows(),
                        read.penalty_residual, local_noise, minus_noise_overlap, // <- predictors 1,2,3
                        homopolymer_rank, read.penalty_mismatch, neighborhood_noise, // <- predictors 4,5,6
                        base_to_flow, quality,
                        read.additive_correction,
                        read.multiplicative_correction,
                        read.state_inphase);

                //
                // Step 4a. Barcode classification of library reads
                //

                if (processed_read.filter.n_bases_filtered == -1)
                    processed_read.filter.n_bases_filtered = processed_read.filter.n_bases;

                processed_read.filter.n_bases_key = min(bc.keys[read_class].bases_length(), processed_read.filter.n_bases);
                processed_read.filter.n_bases_prefix = processed_read.filter.n_bases_key;

                processed_read.barcode_n_errors = 0;
                if (read_class == 0)
                {   // Library beads - first separate out calibration barcodes
                	processed_read.read_group_index = -1;
                	if (bc.have_calibration_panel){
                	  bc.calibration_barcodes->ClassifyAndTrimBarcode(read_index, processed_read, read, base_to_flow);
                	  processed_read.is_control_barcode = (processed_read.read_group_index >= 0);
                	}
                    if (processed_read.read_group_index < 0)
                      bc.barcodes->ClassifyAndTrimBarcode(read_index, processed_read, read, base_to_flow);
                }

                //
                // Step 4b. Custom mod: Trim extra bases after key and barcode. Make it look like barcode trimming.
                //

                if (bc.extra_trim_left > 0)
                    processed_read.filter.n_bases_prefix = min(processed_read.filter.n_bases_prefix + bc.extra_trim_left, processed_read.filter.n_bases);


                //
                // Step 4. Calculate/save read metrics and apply filters
                //

                bc.filters->FilterZeroBases     (read_index, read_class, processed_read.filter);
                bc.filters->FilterShortRead     (read_index, read_class, processed_read.filter);
                bc.filters->FilterFailedKeypass (read_index, read_class, processed_read.filter, read.sequence);
                bc.filters->FilterHighResidual  (read_index, read_class, processed_read.filter, residual);
                bc.filters->FilterBeverly       (read_index, read_class, processed_read.filter, scaled_residual, base_to_flow);
                bc.filters->FilterQuality       (read_index, read_class, processed_read.filter, quality);
                bc.filters->TrimAdapter         (read_index, read_class, processed_read, scaled_residual, base_to_flow, treephaser, read);
                bc.filters->TrimQuality         (read_index, read_class, processed_read.filter, quality);
                bc.filters->TrimAvalanche       (read_index, read_class, processed_read.filter, quality);

                //! New mechanism for dumping potentially useful metrics.
                if (bc.metric_saver->save_anything() and (is_random_unfiltered or !bc.metric_saver->save_subset_only())) {
                    pthread_mutex_lock(&bc.mutex);

                    bc.metric_saver->SaveRawMeasurements          (y,x,read.raw_measurements);
                    bc.metric_saver->SaveAdditiveCorrection       (y,x,read.additive_correction);
                    bc.metric_saver->SaveMultiplicativeCorrection (y,x,read.multiplicative_correction);
                    bc.metric_saver->SaveNormalizedMeasurements   (y,x,read.normalized_measurements);
                    bc.metric_saver->SavePrediction               (y,x,read.prediction);
                    bc.metric_saver->SaveStateInphase             (y,x,read.state_inphase);
                    bc.metric_saver->SaveStateTotal               (y,x,read.state_total);
                    bc.metric_saver->SavePenaltyResidual          (y,x,read.penalty_residual);
                    bc.metric_saver->SavePenaltyMismatch          (y,x,read.penalty_mismatch);
                    bc.metric_saver->SaveLocalNoise               (y,x,local_noise);
                    bc.metric_saver->SaveNoiseOverlap             (y,x,minus_noise_overlap);
                    bc.metric_saver->SaveHomopolymerRank          (y,x,homopolymer_rank);
                    bc.metric_saver->SaveNeighborhoodNoise        (y,x,neighborhood_noise);

                    pthread_mutex_unlock(&bc.mutex);
                }


                //
                // Step 4b. Add flow signal information to ZM tag in BAM record.
                //

                flowgram2.clear();
                int max_flow = min(bc.flow_order.num_flows(),16);
                if (processed_read.filter.n_bases_filtered > 0)
                    max_flow = min(bc.flow_order.num_flows(), base_to_flow[processed_read.filter.n_bases_filtered-1] + 16);

                vector<int> out_of_boud_flows;
                for (int flow = 0; flow < max_flow; ++flow){
                    float temp_flowgram = 128*read.normalized_measurements[flow];
                    if (temp_flowgram < -16383.0f or temp_flowgram > 16383.0f) {
                        out_of_boud_flows.push_back(flow);
                        temp_flowgram = min(max(-16383.0f,temp_flowgram), 16383.0f);
                    }
                    //flowgram2.push_back(2*(int16_t)(128*read.normalized_measurements[flow]));
                    flowgram2.push_back(2*(int16_t)temp_flowgram);
                }
                // Do not spam stderr
                /*if (out_of_boud_flows.size() > 0) {
                  cerr << "BaseCaller WARNING: Normalized signal out of bounds in well y="
                       << y << ", x=" << x << ", in flows ";
                  for (unsigned int flow = 0; flow < out_of_boud_flows.size()-1; ++flow)
                    cerr << out_of_boud_flows.at(flow) << ',';
                  cerr << out_of_boud_flows.at(out_of_boud_flows.size()-1) << endl;
                } */
                processed_read.bam.AddTag("ZM", flowgram2);
                //flowgram2.push_back(1*(int16_t)(256*read.normalized_measurements[flow]));
                //flowgram2.push_back(2*(int16_t)(128*read.normalized_measurements[flow]));
                //flowgram2.push_back(4*(int16_t)(64*read.normalized_measurements[flow]));
                //flowgram2.push_back(8*(int16_t)(32*read.normalized_measurements[flow]));

                //
                // Step 4c. Populate FZ tag in BAM record.
                //

                flowgram.clear();
                if (bc.flow_signals_type == "wells") {
                    for (int flow = 0; flow < bc.flow_order.num_flows(); ++flow)
                        flowgram.push_back(max(0,(int)(100.0*wells_measurements[flow]+0.5)));
                    processed_read.bam.AddTag("FZ", flowgram); // Will be phased out soon

                } else if (bc.flow_signals_type == "key-normalized") {
                    for (int flow = 0; flow < bc.flow_order.num_flows(); ++flow)
                        flowgram.push_back(max(0,(int)(100.0*read.raw_measurements[flow]+0.5)));
                    processed_read.bam.AddTag("FZ", flowgram); // Will be phased out soon

                } else if (bc.flow_signals_type == "adaptive-normalized") {
                    for (int flow = 0; flow < bc.flow_order.num_flows(); ++flow)
                        flowgram.push_back(max(0,(int)(100.0*read.normalized_measurements[flow]+0.5)));
                    processed_read.bam.AddTag("FZ", flowgram); // Will be phased out soon

                } else if (bc.flow_signals_type == "residual") {
                    for (int flow = 0; flow < bc.flow_order.num_flows(); ++flow)
                        flowgram.push_back(max(0,(int)(1000 + 100*residual[flow])));
                    processed_read.bam.AddTag("FZ", flowgram); // Will be phased out soon

                } else if (bc.flow_signals_type == "scaled-residual") { // This settings is necessary part of calibration training
                    for (int flow = 0; flow < bc.flow_order.num_flows(); ++flow) {
                        //between 0 and 98
                        float adjustment = min(0.49f, max(-0.49f, scaled_residual[flow]));
                        flowgram.push_back(max(0,(int)(49.5 + 100*adjustment)));
                    }
                    processed_read.bam.AddTag("FZ", flowgram);
                }

                //
                // Step 5. Pass basecalled reads to appropriate writers
                //

                // Create BAM entries
                if (processed_read.filter.n_bases > 0) {
                    processed_read.bam.QueryBases.reserve(processed_read.filter.n_bases);
                    processed_read.bam.Qualities.reserve(processed_read.filter.n_bases);
                    for (int base = processed_read.filter.n_bases_prefix; base < processed_read.filter.n_bases_filtered; ++base) {
                        processed_read.bam.QueryBases.push_back(read.sequence[base]);
                        processed_read.bam.Qualities.push_back(quality[base] + 33);
                    }
                    processed_read.bam.AddTag("ZF","i", base_to_flow[processed_read.filter.n_bases_prefix]);
                } else
                    processed_read.bam.AddTag("ZF","i", 0);

                // Randomly selected library beads - excluding calibration reads
                if (is_random_unfiltered and (not processed_read.is_control_barcode)) {
                    unfiltered_trimmed_reads.push_back(processed_read);
                    unfiltered_reads.push_back(processed_read);

                    ProcessedRead& untrimmed_read = unfiltered_reads.back();

                    processed_read.filter.GenerateZDVector(filtering_details);
                    untrimmed_read.bam.AddTag("ZD", filtering_details);

                    if (processed_read.filter.n_bases > 0) {
                        untrimmed_read.bam.QueryBases.reserve(processed_read.filter.n_bases);
                        untrimmed_read.bam.Qualities.reserve(processed_read.filter.n_bases);
                        for (int base = max(processed_read.filter.n_bases_filtered,processed_read.filter.n_bases_prefix); base < processed_read.filter.n_bases; ++base) {
                            untrimmed_read.bam.QueryBases.push_back(read.sequence[base]);
                            untrimmed_read.bam.Qualities.push_back(quality[base] + 33);
                        }
                    }

                    // Temporary workaround: provide fake FZ tag for unfiltered.trimmed and unfiltered.untrimmed sets.
                    if (bc.flow_signals_type == "none") {
                        flowgram.assign(1,0);
                        unfiltered_reads.back().bam.AddTag("FZ", flowgram);
                        unfiltered_trimmed_reads.back().bam.AddTag("FZ", flowgram);
                    }


                    // If this read was supposed to have "early filtering", make sure we emulate that here
                    if (processed_read.filter.n_bases_after_bkgmodel_bad_key >= 0 or
                            processed_read.filter.n_bases_after_bkgmodel_high_ppf >= 0 or
                            processed_read.filter.n_bases_after_bkgmodel_polyclonal >= 0 or
                            processed_read.filter.n_bases_after_high_ppf >= 0 or
                            processed_read.filter.n_bases_after_polyclonal >= 0)
                        processed_read.filter.n_bases = -1;
                }

                // Move read from lib_reads stack to calib_reads if necessary
                // This invalidates the processed_read reference and needs to be at the very end
                if (processed_read.is_control_barcode) {
                  calib_reads.push_back(processed_read);
                  lib_reads.pop_back();
                }
            }

        bc.lib_writer.WriteRegion(current_region, lib_reads);
        if (bc.have_calibration_panel)
            bc.calib_writer.WriteRegion(current_region, calib_reads);
        if (bc.process_tfs)
            bc.tf_writer.WriteRegion(current_region, tf_reads);
        if (!bc.unfiltered_set.empty()) {
            bc.unfiltered_writer.WriteRegion(current_region,unfiltered_reads);
            bc.unfiltered_trimmed_writer.WriteRegion(current_region,unfiltered_trimmed_reads);
        }
    }
}
Ejemplo n.º 3
0
int main (int argc, const char *argv[])
{

  if (argc == 1) {
    printf ("BaseCallerLite - Bare bone basecaller\n");
    printf ("\n");
    printf ("Usage:\n");
    printf ("BaseCallerLite [options]\n");
    printf ("\tOptions:\n");
    printf ("\t\tComing soon\n");
    printf ("\n");
    return 1;
  }

  string libKey = "TCAG";
  string inputDirectory = ".";
  string outputDirectory = ".";
  bool singleCoreCafie = false;

  BaseCallerLite basecaller;
  basecaller.regionXSize = 50;
  basecaller.regionYSize = 50;
  basecaller.runId = "BCLTE";
  basecaller.CF = 0.0;
  basecaller.IE = 0.0;
  basecaller.numWellsCalled = 0;
  basecaller.nextRegionX = 0;
  basecaller.nextRegionY = 0;


  OptArgs opts;
  opts.ParseCmdLine(argc, argv);
  opts.GetOption(basecaller.CF, "0.0", '-',  "cf");
  opts.GetOption(basecaller.IE, "0.0", '-',  "ie");
  opts.GetOption(inputDirectory, ".", '-',  "input-dir");
  opts.GetOption(outputDirectory, ".", '-',  "output-dir");
  opts.GetOption(singleCoreCafie, "false", '-',  "singlecorecafie");

  int numWorkers = 2*numCores();
  if (singleCoreCafie)
    numWorkers = 1;


  Mask mask (1, 1);
  if (mask.SetMask ((inputDirectory + "/bfmask.bin").c_str()))
    exit (EXIT_FAILURE);
  RawWells wells (inputDirectory.c_str(),"1.wells");
  //SetWellsToLiveBeadsOnly(wells,&mask);
  wells.OpenForIncrementalRead();

  basecaller.maskPtr = &mask;
  basecaller.wellsPtr = &wells;
  basecaller.rows = mask.H();
  basecaller.cols = mask.W();
  basecaller.flowOrder.SetFlowOrder(wells.FlowOrder(), wells.NumFlows());
  basecaller.numFlows = wells.NumFlows();


  basecaller.numRegionsX = (basecaller.cols +  basecaller.regionXSize - 1) / basecaller.regionXSize;
  basecaller.numRegionsY = (basecaller.rows +  basecaller.regionYSize - 1) / basecaller.regionYSize;
  basecaller.numRegions = basecaller.numRegionsX * basecaller.numRegionsY;

  basecaller.libKeyFlows.assign(basecaller.numFlows,0);
  basecaller.libNumKeyFlows = basecaller.flowOrder.BasesToFlows(libKey, &basecaller.libKeyFlows[0], basecaller.numFlows);

  basecaller.libSFF.Open(outputDirectory+"/rawlib.sff", basecaller.numRegions,
      basecaller.flowOrder, libKey);


  time_t startBasecall;
  time(&startBasecall);

  pthread_mutex_init(&basecaller.wellsAccessMutex, NULL);

  pthread_t worker_id[numWorkers];
  for (int iWorker = 0; iWorker < numWorkers; iWorker++)
    if (pthread_create(&worker_id[iWorker], NULL, BasecallerWorkerWrapper, &basecaller)) {
      printf("*Error* - problem starting thread\n");
      return 1;
    }

  for (int iWorker = 0; iWorker < numWorkers; iWorker++)
    pthread_join(worker_id[iWorker], NULL);

  pthread_mutex_destroy(&basecaller.wellsAccessMutex);

  time_t endBasecall;
  time(&endBasecall);

  basecaller.libSFF.Close();

  printf("\nBASECALLING: called %d of %d wells in %1.1f seconds with %d threads\n",
      basecaller.numWellsCalled, basecaller.rows*basecaller.cols, difftime(endBasecall,startBasecall), numWorkers);
  printf("Generated library SFF with %d reads\n", basecaller.libSFF.num_reads());

  return 0;
}