Examples with PrimitivI com.milaboratory.primitivio.PrimitivI used on opensource projects

Example 1 with PrimitivI

use of com.milaboratory.primitivio.PrimitivI in project mixcr by milaboratory.

the class ActionAssembleContigs method go.

@Override
public void go(ActionHelper helper) throws Exception {
    // TODO FIX!!!!!!!!!!!!!
    if (parameters.threads > 1)
        throw new ParameterException("Multithreaded processing is not supported yet.");
    long beginTimestamp = System.currentTimeMillis();
    FullSeqAssemblerParameters p = FullSeqAssemblerParameters.getByName("default");
    if (!parameters.overrides.isEmpty()) {
        // Perform parameters overriding
        p = JsonOverrider.override(p, FullSeqAssemblerParameters.class, parameters.overrides);
        if (p == null)
            throw new ProcessException("Failed to override some parameter.");
    }
    final FullSeqAssemblerReport report = new FullSeqAssemblerReport();
    FullSeqAssemblerParameters assemblerParameters = p;
    int totalClonesCount = 0;
    List<VDJCGene> genes;
    VDJCAlignerParameters alignerParameters;
    CloneAssemblerParameters cloneAssemblerParameters;
    try (ClnAReader reader = new ClnAReader(parameters.getInputFileName(), VDJCLibraryRegistry.getDefault());
        PrimitivO tmpOut = new PrimitivO(new BufferedOutputStream(new FileOutputStream(parameters.getOutputFileName())))) {
        final CloneFactory cloneFactory = new CloneFactory(reader.getAssemblerParameters().getCloneFactoryParameters(), reader.getAssemblingFeatures(), reader.getGenes(), reader.getAlignerParameters().getFeaturesToAlignMap());
        alignerParameters = reader.getAlignerParameters();
        cloneAssemblerParameters = reader.getAssemblerParameters();
        genes = reader.getGenes();
        IOUtil.registerGeneReferences(tmpOut, genes, alignerParameters);
        ClnAReader.CloneAlignmentsPort cloneAlignmentsPort = reader.clonesAndAlignments();
        SmartProgressReporter.startProgressReport("Assembling", cloneAlignmentsPort);
        OutputPort<Clone[]> parallelProcessor = new ParallelProcessor<>(cloneAlignmentsPort, cloneAlignments -> {
            FullSeqAssembler fullSeqAssembler = new FullSeqAssembler(cloneFactory, assemblerParameters, cloneAlignments.clone, alignerParameters);
            fullSeqAssembler.setReport(report);
            FullSeqAssembler.RawVariantsData rawVariantsData = fullSeqAssembler.calculateRawData(() -> {
                try {
                    return cloneAlignments.alignments();
                } catch (IOException e) {
                    throw new RuntimeException(e);
                }
            });
            return fullSeqAssembler.callVariants(rawVariantsData);
        }, parameters.threads);
        for (Clone[] clones : CUtils.it(parallelProcessor)) {
            totalClonesCount += clones.length;
            for (Clone cl : clones) tmpOut.writeObject(cl);
        }
        assert report.getInitialCloneCount() == reader.numberOfClones();
    }
    assert report.getFinalCloneCount() == totalClonesCount;
    assert report.getFinalCloneCount() >= report.getInitialCloneCount();
    Clone[] clones = new Clone[totalClonesCount];
    try (PrimitivI tmpIn = new PrimitivI(new BufferedInputStream(new FileInputStream(parameters.getOutputFileName())))) {
        IOUtil.registerGeneReferences(tmpIn, genes, alignerParameters);
        int i = 0;
        for (Clone clone : CUtils.it(new PipeDataInputReader<>(Clone.class, tmpIn, totalClonesCount))) clones[i++] = clone;
    }
    Arrays.sort(clones, Comparator.comparingDouble(c -> -c.getCount()));
    for (int i = 0; i < clones.length; i++) clones[i] = clones[i].setId(i);
    CloneSet cloneSet = new CloneSet(Arrays.asList(clones), genes, alignerParameters.getFeaturesToAlignMap(), alignerParameters, cloneAssemblerParameters);
    try (CloneSetIO.CloneSetWriter writer = new CloneSetIO.CloneSetWriter(cloneSet, parameters.getOutputFileName())) {
        SmartProgressReporter.startProgressReport(writer);
        writer.write();
    }
    ReportWrapper reportWrapper = new ReportWrapper(command(), report);
    reportWrapper.setStartMillis(beginTimestamp);
    reportWrapper.setInputFiles(parameters.getInputFileName());
    reportWrapper.setOutputFiles(parameters.getOutputFileName());
    reportWrapper.setCommandLine(helper.getCommandLineArguments());
    reportWrapper.setFinishMillis(System.currentTimeMillis());
    // Writing report to stout
    System.out.println("============= Report ==============");
    Util.writeReportToStdout(report);
    if (parameters.report != null)
        Util.writeReport(parameters.report, reportWrapper);
    if (parameters.jsonReport != null)
        Util.writeJsonReport(parameters.jsonReport, reportWrapper);
}

Example 2 with PrimitivI

use of com.milaboratory.primitivio.PrimitivI in project mixcr by milaboratory.

the class ClnAReader method readCloneSet.

/**
 * Read clone set completely
 */
public CloneSet readCloneSet() throws IOException {
    PrimitivI input = new PrimitivI(new InputDataStream(firstClonePosition, index[0]));
    // Initializing PrimitivI object
    // (see big comment block in ClnAWriter.writeClones())
    IOUtil.registerGeneReferences(input, genes, alignedFeatures);
    // Reading clones
    int count = numberOfClones();
    List<Clone> clones = new ArrayList<>(count);
    for (int i = 0; i < count; i++) clones.add(input.readObject(Clone.class));
    return new CloneSet(clones, genes, alignedFeatures.map, alignerParameters, assemblerParameters);
}

Example 3 with PrimitivI

use of com.milaboratory.primitivio.PrimitivI in project mixcr by milaboratory.

the class ClnAReader method readClones.

/**
 * Constructs output port to read clones one by one as a stream
 */
public OutputPort<Clone> readClones() throws IOException {
    PrimitivI input = new PrimitivI(new InputDataStream(firstClonePosition, index[0]));
    IOUtil.registerGeneReferences(input, genes, alignedFeatures);
    return new PipeDataInputReader<>(Clone.class, input, numberOfClones());
}

Example 4 with PrimitivI

use of com.milaboratory.primitivio.PrimitivI in project mixcr by milaboratory.

the class ClnAReader method readAllAlignments.

/**
 * Constructs output port to read all alignments form the file. Alignments are sorted by cloneIndex.
 */
public OutputPort<VDJCAlignments> readAllAlignments() throws IOException {
    PrimitivI input = new PrimitivI(new InputDataStream(index[0], index[index.length - 1]));
    IOUtil.registerGeneReferences(input, genes, alignedFeatures);
    return new PipeDataInputReader<>(VDJCAlignments.class, input, totalAlignmentsCount);
}

Example 5 with PrimitivI

use of com.milaboratory.primitivio.PrimitivI in project mixcr by milaboratory.

the class ClnAReader method readAlignmentsOfClone.

/**
 * Constructs output port to read alignments for a specific clone, or read unassembled alignments block
 *
 * @param cloneIndex index of clone; -1 to read unassembled alignments
 */
public OutputPort<VDJCAlignments> readAlignmentsOfClone(int cloneIndex) throws IOException {
    PrimitivI input = new PrimitivI(new InputDataStream(index[cloneIndex + 1], index[cloneIndex + 2]));
    IOUtil.registerGeneReferences(input, genes, alignedFeatures);
    return new PipeDataInputReader<>(VDJCAlignments.class, input, counts[cloneIndex + 1]);
}