Examples with CloneAssemblerParameters com.milaboratory.mixcr.assembler.CloneAssemblerParameters used on opensource projects

Example 1 with CloneAssemblerParameters

use of com.milaboratory.mixcr.assembler.CloneAssemblerParameters 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 CloneAssemblerParameters

use of com.milaboratory.mixcr.assembler.CloneAssemblerParameters in project mixcr by milaboratory.

the class CloneSetIO method readClns.

public static CloneSet readClns(InputStream inputStream, VDJCLibraryRegistry libraryRegistry) {
    PrimitivI input = new PrimitivI(inputStream);
    // Registering custom serializer
    input.getSerializersManager().registerCustomSerializer(GeneFeature.class, new GeneFeatureSerializer(true));
    byte[] magicBytes = new byte[MAGIC_LENGTH];
    input.readFully(magicBytes);
    String magicString = new String(magicBytes);
    SerializersManager serializersManager = input.getSerializersManager();
    switch(magicString) {
        case MAGIC_V5:
            serializersManager.registerCustomSerializer(Clone.class, new CompatibilityIO.CloneSerializerV5());
            break;
        case MAGIC:
            break;
        default:
            throw new RuntimeException("Unsupported file format; .clns file of version " + magicString + " while you are running MiXCR " + MAGIC);
    }
    String versionInfo = input.readUTF();
    if (!magicString.equals(MAGIC))
        // Dropping this field for v5 files
        input.readObject(GeneFeature[].class);
    VDJCAlignerParameters alignerParameters;
    CloneAssemblerParameters assemblerParameters;
    if (magicString.equals(MAGIC)) {
        alignerParameters = input.readObject(VDJCAlignerParameters.class);
        assemblerParameters = input.readObject(CloneAssemblerParameters.class);
    } else {
        alignerParameters = null;
        assemblerParameters = null;
    }
    EnumMap<GeneType, GeneFeature> alignedFeatures = IO.readGF2GTMap(input);
    List<VDJCGene> genes = IOUtil.readAndRegisterGeneReferences(input, libraryRegistry, new GT2GFAdapter(alignedFeatures));
    int count = input.readInt();
    List<Clone> clones = new ArrayList<>(count);
    for (int i = 0; i < count; i++) clones.add(input.readObject(Clone.class));
    CloneSet cloneSet = new CloneSet(clones, genes, alignedFeatures, alignerParameters, assemblerParameters);
    cloneSet.versionInfo = versionInfo;
    return cloneSet;
}