Examples with VDJCAlignmentResult com.milaboratory.mixcr.vdjaligners.VDJCAlignmentResult used on opensource projects

Example 1 with VDJCAlignmentResult

use of com.milaboratory.mixcr.vdjaligners.VDJCAlignmentResult in project mixcr by milaboratory.

the class ActionAlign method go.

@Override
@SuppressWarnings("unchecked")
public void go(ActionHelper helper) throws Exception {
    // FIXME remove in 2.2
    if (actionParameters.printNonFunctionalWarnings())
        System.out.println("WARNING: -wf / --non-functional-warnings option is deprecated, will be removed in 2.2 " + "release. Use --verbose instead.");
    // Saving initial timestamp
    long beginTimestamp = System.currentTimeMillis();
    // Getting aligner parameters
    VDJCAlignerParameters alignerParameters = actionParameters.getAlignerParameters();
    // FIXME remove in 2.3
    if (actionParameters.getSaveOriginalReads()) {
        System.out.println("WARNING: -g / --save-reads option is deprecated, will be removed in 2.3 " + "release. Use -OsaveOriginalReads=true.");
        alignerParameters.setSaveOriginalReads(true);
    }
    // FIXME remove in 2.3
    if (actionParameters.getSaveReadDescription()) {
        System.out.println("WARNING: -a / --save-description option is deprecated, will be removed in 2.3 " + "release. Use -OsaveOriginalReads=true.");
        alignerParameters.setSaveOriginalReads(true);
    }
    if (!actionParameters.overrides.isEmpty()) {
        // Perform parameters overriding
        alignerParameters = JsonOverrider.override(alignerParameters, VDJCAlignerParameters.class, actionParameters.overrides);
        if (alignerParameters == null)
            throw new ProcessException("Failed to override some parameter.");
    }
    // FIXME remove in 2.2
    if (actionParameters.allowDifferentVJLoci != null && actionParameters.allowDifferentVJLoci) {
        System.out.println("Warning: usage of --diff-loci is deprecated. Use -OallowChimeras=true instead.");
        alignerParameters.setAllowChimeras(true);
    }
    // Creating aligner
    VDJCAligner aligner = VDJCAligner.createAligner(alignerParameters, actionParameters.isInputPaired(), !actionParameters.getNoMerge());
    // Detect if automatic featureToAlign correction is required
    int totalV = 0, totalVErrors = 0, hasVRegion = 0;
    GeneFeature correctingFeature = alignerParameters.getVAlignerParameters().getGeneFeatureToAlign().hasReversedRegions() ? GeneFeature.VRegionWithP : GeneFeature.VRegion;
    VDJCLibrary library = VDJCLibraryRegistry.getDefault().getLibrary(actionParameters.library, actionParameters.species);
    System.out.println("Reference library: " + library.getLibraryId());
    // Printing library level warnings, if specified for the library
    if (!library.getWarnings().isEmpty()) {
        System.out.println("Library warnings:");
        for (String l : library.getWarnings()) System.out.println(l);
    }
    // Printing citation notice, if specified for the library
    if (!library.getCitations().isEmpty()) {
        System.out.println("Please cite:");
        for (String l : library.getCitations()) System.out.println(l);
    }
    for (VDJCGene gene : library.getGenes(actionParameters.getChains())) {
        if (gene.getGeneType() == GeneType.Variable) {
            totalV++;
            if (!alignerParameters.containsRequiredFeature(gene)) {
                totalVErrors++;
                if (gene.getPartitioning().isAvailable(correctingFeature))
                    hasVRegion++;
            }
        }
    }
    // Performing V featureToAlign correction if needed
    if (totalVErrors > totalV * 0.9 && hasVRegion > totalVErrors * 0.8) {
        System.out.println("WARNING: forcing -OvParameters.geneFeatureToAlign=" + GeneFeature.encode(correctingFeature) + " since current gene feature (" + GeneFeature.encode(alignerParameters.getVAlignerParameters().getGeneFeatureToAlign()) + ") is absent in " + Util.PERCENT_FORMAT.format(100.0 * totalVErrors / totalV) + "% of V genes.");
        alignerParameters.getVAlignerParameters().setGeneFeatureToAlign(correctingFeature);
    }
    int numberOfExcludedNFGenes = 0;
    int numberOfExcludedFGenes = 0;
    for (VDJCGene gene : library.getGenes(actionParameters.getChains())) {
        NucleotideSequence featureSequence = alignerParameters.extractFeatureToAlign(gene);
        // exclusionReason is null ==> gene is not excluded
        String exclusionReason = null;
        if (featureSequence == null)
            exclusionReason = "absent " + GeneFeature.encode(alignerParameters.getFeatureToAlign(gene.getGeneType()));
        else if (featureSequence.containsWildcards())
            exclusionReason = "wildcard symbols in " + GeneFeature.encode(alignerParameters.getFeatureToAlign(gene.getGeneType()));
        if (exclusionReason == null)
            // If there are no reasons to exclude the gene, adding it to aligner
            aligner.addGene(gene);
        else {
            if (gene.isFunctional()) {
                ++numberOfExcludedFGenes;
                if (actionParameters.verbose())
                    System.out.println("WARNING: Functional gene " + gene.getName() + " excluded due to " + exclusionReason);
            } else
                ++numberOfExcludedNFGenes;
        }
    }
    if (actionParameters.printWarnings() && numberOfExcludedFGenes > 0)
        System.out.println("WARNING: " + numberOfExcludedFGenes + " functional genes were excluded, re-run " + "with --verbose option to see the list of excluded genes and exclusion reason.");
    if (actionParameters.verbose() && numberOfExcludedNFGenes > 0)
        System.out.println("WARNING: " + numberOfExcludedNFGenes + " non-functional genes excluded.");
    if (aligner.getVGenesToAlign().isEmpty())
        throw new ProcessException("No V genes to align. Aborting execution. See warnings for more info " + "(turn on verbose warnings by adding --verbose option).");
    if (aligner.getJGenesToAlign().isEmpty())
        throw new ProcessException("No J genes to align. Aborting execution. See warnings for more info " + "(turn on verbose warnings by adding --verbose option).");
    AlignerReport report = new AlignerReport();
    report.setStartMillis(beginTimestamp);
    report.setInputFiles(actionParameters.getInputsForReport());
    report.setOutputFiles(actionParameters.getOutputsForReport());
    report.setCommandLine(helper.getCommandLineArguments());
    // Attaching report to aligner
    aligner.setEventsListener(report);
    try (SequenceReaderCloseable<? extends SequenceRead> reader = actionParameters.createReader();
        VDJCAlignmentsWriter writer = actionParameters.getOutputName().equals(".") ? null : new VDJCAlignmentsWriter(actionParameters.getOutputName());
        SequenceWriter notAlignedWriter = actionParameters.failedReadsR1 == null ? null : (actionParameters.isInputPaired() ? new PairedFastqWriter(actionParameters.failedReadsR1, actionParameters.failedReadsR2) : new SingleFastqWriter(actionParameters.failedReadsR1))) {
        if (writer != null)
            writer.header(aligner);
        OutputPort<? extends SequenceRead> sReads = reader;
        CanReportProgress progress = (CanReportProgress) reader;
        if (actionParameters.limit != 0) {
            sReads = new CountLimitingOutputPort<>(sReads, actionParameters.limit);
            progress = SmartProgressReporter.extractProgress((CountLimitingOutputPort<?>) sReads);
        }
        final boolean writeAllResults = actionParameters.getWriteAllResults();
        EnumMap<GeneType, VDJCHit[]> emptyHits = new EnumMap<>(GeneType.class);
        for (GeneType gt : GeneType.values()) if (alignerParameters.getGeneAlignerParameters(gt) != null)
            emptyHits.put(gt, new VDJCHit[0]);
        final PairedEndReadsLayout readsLayout = alignerParameters.getReadsLayout();
        SmartProgressReporter.startProgressReport("Alignment", progress);
        OutputPort<Chunk<? extends SequenceRead>> mainInputReads = CUtils.buffered((OutputPort) chunked(sReads, 64), 16);
        OutputPort<VDJCAlignmentResult> alignments = unchunked(new ParallelProcessor(mainInputReads, chunked(aligner), actionParameters.threads));
        for (VDJCAlignmentResult result : CUtils.it(new OrderedOutputPort<>(alignments, new Indexer<VDJCAlignmentResult>() {

            @Override
            public long getIndex(VDJCAlignmentResult o) {
                return o.read.getId();
            }
        }))) {
            VDJCAlignments alignment = result.alignment;
            SequenceRead read = result.read;
            if (alignment == null) {
                if (writeAllResults) // Creating empty alignment object if alignment for current read failed
                {
                    Target target = readsLayout.createTargets(read)[0];
                    alignment = new VDJCAlignments(emptyHits, target.targets, SequenceHistory.RawSequence.of(read.getId(), target), alignerParameters.isSaveOriginalReads() ? new SequenceRead[] { read } : null);
                } else {
                    if (notAlignedWriter != null)
                        notAlignedWriter.write(result.read);
                    continue;
                }
            }
            if (alignment.isChimera())
                report.onChimera();
            if (writer != null)
                writer.write(alignment);
        }
        if (writer != null)
            writer.setNumberOfProcessedReads(reader.getNumberOfReads());
    }
    report.setFinishMillis(System.currentTimeMillis());
    // Writing report to stout
    System.out.println("============= Report ==============");
    Util.writeReportToStdout(report);
    if (actionParameters.report != null)
        Util.writeReport(actionParameters.report, report);
    if (actionParameters.jsonReport != null)
        Util.writeJsonReport(actionParameters.jsonReport, report);
}

Example 2 with VDJCAlignmentResult

use of com.milaboratory.mixcr.vdjaligners.VDJCAlignmentResult in project mixcr by milaboratory.

the class PartialAlignmentsAssemblerAligner method process0.

@Override
@SuppressWarnings("unchecked")
protected VDJCAlignmentResult<VDJCMultiRead> process0(VDJCMultiRead input) {
    final int nReads = input.numberOfReads();
    EnumMap<GeneType, VDJCHit[]> vdjcHits = new EnumMap<>(GeneType.class);
    NSequenceWithQuality[] targets = new NSequenceWithQuality[nReads];
    Chains currentChains = Chains.ALL;
    // Across all gene types
    int lastAlignedTarget = 0;
    int firstJTarget = -1;
    int lastVTarget = -1;
    for (int g = 0; g < GeneType.VJC_REFERENCE.length; g++) {
        GeneType gt = GeneType.VJC_REFERENCE[g];
        AlignmentHit<NucleotideSequence, VDJCGene>[][] alignmentHits = new AlignmentHit[nReads][];
        Arrays.fill(alignmentHits, new AlignmentHit[0]);
        for (int targetId = lastAlignedTarget; targetId < nReads; targetId++) {
            targets[targetId] = input.getRead(targetId).getData();
            final NucleotideSequence sequence = input.getRead(targetId).getData().getSequence();
            AlignmentResult<AlignmentHit<NucleotideSequence, VDJCGene>> als;
            final BatchAlignerWithBaseWithFilter<NucleotideSequence, VDJCGene, AlignmentHit<NucleotideSequence, VDJCGene>> aligner = getAligner(gt);
            if (aligner != null) {
                int pointer = 0;
                if (g != 0) {
                    // Not V gene
                    VDJCHit[] vdjcHits1 = vdjcHits.get(GeneType.VJC_REFERENCE[g - 1]);
                    Alignment<NucleotideSequence> alignment;
                    if (vdjcHits1.length != 0 && (alignment = vdjcHits1[0].getAlignment(targetId)) != null)
                        pointer = alignment.getSequence2Range().getTo();
                }
                als = aligner.align(sequence, pointer, sequence.size(), getFilter(gt, currentChains));
                if (als != null && als.hasHits()) {
                    lastAlignedTarget = targetId;
                    if (// V
                    g == 0)
                        lastVTarget = targetId;
                    if (// J
                    g == 1)
                        firstJTarget = targetId;
                    alignmentHits[targetId] = als.getHits().toArray(new AlignmentHit[als.getHits().size()]);
                }
            }
        }
        Chains chains = Chains.EMPTY;
        for (AlignmentHit<NucleotideSequence, VDJCGene>[] alignmentHit0 : alignmentHits) if (alignmentHit0 != null)
            for (AlignmentHit<NucleotideSequence, VDJCGene> hit : alignmentHit0) chains = chains.merge(hit.getRecordPayload().getChains());
        currentChains = currentChains.intersection(chains);
        vdjcHits.put(gt, combine(parameters.getFeatureToAlign(gt), alignmentHits));
    }
    boolean fineVAlignmentPerformed = false, fineJAlignmentPerformed = false;
    // Additional (fine) alignment step for V gene
    VDJCHit[] vHits = vdjcHits.get(GeneType.Variable);
    final AlignmentScoring<NucleotideSequence> vScoring = parameters.getVAlignerParameters().getParameters().getScoring();
    if (// TODO implement AffineGapAlignmentScoring
    vHits != null && vHits.length > 0 && !(vScoring instanceof AffineGapAlignmentScoring) && vdjcHits.get(GeneType.Joining) != null && vdjcHits.get(GeneType.Joining).length > 0) {
        int minimalVSpace = getAbsoluteMinScore(parameters.getVAlignerParameters().getParameters()) / vScoring.getMaximalMatchScore();
        // Assert
        if (firstJTarget == -1)
            throw new AssertionError();
        for (int targetId = 1; targetId <= firstJTarget; targetId++) {
            int vSpace;
            final NucleotideSequence sequence2 = targets[targetId].getSequence();
            if (vdjcHits.get(GeneType.Joining)[0].getAlignment(targetId) != null && (vSpace = vdjcHits.get(GeneType.Joining)[0].getAlignment(targetId).getSequence2Range().getFrom()) >= minimalVSpace) {
                for (int vHitIndex = 0; vHitIndex < vHits.length; vHitIndex++) {
                    VDJCHit vHit = vHits[vHitIndex];
                    // Perform fine alignment only if target is not already aligned by fast aligner
                    if (vHit.getAlignment(targetId) != null)
                        continue;
                    Alignment<NucleotideSequence> leftAlignment = vHit.getAlignment(targetId - 1);
                    if (leftAlignment == null)
                        continue;
                    final NucleotideSequence sequence1 = leftAlignment.getSequence1();
                    final int beginFR3 = vHit.getGene().getPartitioning().getRelativePosition(parameters.getFeatureToAlign(GeneType.Variable), ReferencePoint.FR3Begin);
                    if (beginFR3 == -1)
                        continue;
                    final Alignment alignment = AlignerCustom.alignLinearSemiLocalLeft0((LinearGapAlignmentScoring<NucleotideSequence>) vScoring, sequence1, sequence2, beginFR3, sequence1.size() - beginFR3, 0, vSpace, false, true, NucleotideSequence.ALPHABET, linearMatrixCache.get());
                    if (alignment.getScore() < getAbsoluteMinScore(parameters.getVAlignerParameters().getParameters()))
                        continue;
                    fineVAlignmentPerformed = true;
                    vHits[vHitIndex] = vHit.setAlignment(targetId, alignment);
                }
            }
        }
    }
    Arrays.sort(vHits);
    vdjcHits.put(GeneType.Variable, cutRelativeScore(vHits, parameters.getVAlignerParameters().getRelativeMinScore(), parameters.getVAlignerParameters().getParameters().getMaxHits()));
    // Additional (fine) alignment step for J gene
    VDJCHit[] jHits = vdjcHits.get(GeneType.Joining);
    final AlignmentScoring<NucleotideSequence> jScoring = parameters.getJAlignerParameters().getParameters().getScoring();
    if (// TODO implement AffineGapAlignmentScoring
    jHits != null && jHits.length > 0 && !(jScoring instanceof AffineGapAlignmentScoring) && vdjcHits.get(GeneType.Variable) != null && vdjcHits.get(GeneType.Variable).length > 0) {
        int minimalJSpace = getAbsoluteMinScore(parameters.getJAlignerParameters().getParameters()) / jScoring.getMaximalMatchScore();
        // Assert
        if (lastVTarget == -1)
            throw new AssertionError();
        for (int targetId = lastVTarget; targetId < nReads - 1; targetId++) {
            int jSpaceBegin;
            final NucleotideSequence sequence2 = targets[targetId].getSequence();
            if (vdjcHits.get(GeneType.Variable)[0].getAlignment(targetId) != null && (sequence2.size() - (jSpaceBegin = vdjcHits.get(GeneType.Variable)[0].getAlignment(targetId).getSequence2Range().getTo())) >= minimalJSpace) {
                for (int jHitIndex = 0; jHitIndex < jHits.length; jHitIndex++) {
                    VDJCHit jHit = jHits[jHitIndex];
                    // Perform fine alignment only if target is not already aligned by fast aligner
                    if (jHit.getAlignment(targetId) != null)
                        continue;
                    Alignment<NucleotideSequence> rightAlignment = jHit.getAlignment(targetId + 1);
                    if (rightAlignment == null)
                        continue;
                    final NucleotideSequence sequence1 = rightAlignment.getSequence1();
                    final Alignment alignment = AlignerCustom.alignLinearSemiLocalRight0((LinearGapAlignmentScoring) jScoring, sequence1, sequence2, 0, sequence1.size(), jSpaceBegin, sequence2.size() - jSpaceBegin, false, true, NucleotideSequence.ALPHABET, linearMatrixCache.get());
                    if (alignment.getScore() < getAbsoluteMinScore(parameters.getJAlignerParameters().getParameters()))
                        continue;
                    fineJAlignmentPerformed = true;
                    jHits[jHitIndex] = jHit.setAlignment(targetId, alignment);
                }
            }
        }
    }
    Arrays.sort(jHits);
    vdjcHits.put(GeneType.Joining, cutRelativeScore(jHits, parameters.getJAlignerParameters().getRelativeMinScore(), parameters.getJAlignerParameters().getParameters().getMaxHits()));
    int dGeneTarget = -1;
    VDJCHit[] vResult = vdjcHits.get(GeneType.Variable);
    VDJCHit[] jResult = vdjcHits.get(GeneType.Joining);
    if (vResult.length != 0 && jResult.length != 0)
        for (int i = 0; i < nReads; i++) if (vResult[0].getAlignment(i) != null && jResult[0].getAlignment(i) != null) {
            dGeneTarget = i;
            break;
        }
    // if (fineVAlignmentPerformed && fineJAlignmentPerformed)
    // System.out.println("sd");
    VDJCHit[] dResult;
    if (dGeneTarget == -1)
        dResult = new VDJCHit[0];
    else {
        final Alignment<NucleotideSequence> vAl = vResult[0].getAlignment(dGeneTarget);
        final Alignment<NucleotideSequence> jAl = jResult[0].getAlignment(dGeneTarget);
        if (vAl == null || jAl == null || singleDAligner == null)
            dResult = new VDJCHit[0];
        else
            dResult = singleDAligner.align(targets[dGeneTarget].getSequence(), getPossibleDLoci(vResult, jResult), vAl.getSequence2Range().getTo(), jAl.getSequence2Range().getFrom(), dGeneTarget, nReads);
    }
    final VDJCAlignments alignment = new VDJCAlignments(vResult, dResult, jResult, cutRelativeScore(vdjcHits.get(GeneType.Constant), parameters.getCAlignerParameters().getRelativeMinScore(), parameters.getMaxHits()), targets, input.getHistory(), input.getOriginalReads());
    return new VDJCAlignmentResult<>(input, alignment);
}

Example 3 with VDJCAlignmentResult

use of com.milaboratory.mixcr.vdjaligners.VDJCAlignmentResult in project mixcr by milaboratory.

the class RunMiXCR method align.

public static AlignResult align(RunMiXCRAnalysis parameters) throws Exception {
    VDJCAlignerParameters alignerParameters = parameters.alignerParameters;
    VDJCAligner aligner = VDJCAligner.createAligner(alignerParameters, parameters.isInputPaired(), alignerParameters.getMergerParameters() != null);
    List<VDJCGene> genes = new ArrayList<>();
    for (VDJCGene gene : VDJCLibraryRegistry.getDefault().getLibrary(parameters.library, parameters.species).getGenes(parameters.chains)) if (alignerParameters.containsRequiredFeature(gene) && (gene.isFunctional() || !parameters.isFunctionalOnly)) {
        genes.add(gene);
        aligner.addGene(gene);
    }
    AlignerReport report = new AlignerReport();
    aligner.setEventsListener(report);
    try (SequenceReaderCloseable<? extends SequenceRead> reader = parameters.getReader()) {
        // start progress reporting
        if (reader instanceof CanReportProgress)
            SmartProgressReporter.startProgressReport("align", (CanReportProgress) reader);
        OutputPort<Chunk<SequenceRead>> mainInputReads = CUtils.buffered((OutputPort) chunked(reader, 64), 16);
        OutputPort<VDJCAlignmentResult> alignments = unchunked(new ParallelProcessor(mainInputReads, chunked(aligner), parameters.threads));
        List<VDJCAlignments> als = new ArrayList<>();
        int ind = 0;
        for (VDJCAlignmentResult t : CUtils.it(new OrderedOutputPort<>(alignments, new Indexer<VDJCAlignmentResult>() {

            @Override
            public long getIndex(VDJCAlignmentResult r) {
                return r.read.getId();
            }
        }))) {
            if (t.alignment != null) {
                t.alignment.setAlignmentsIndex(ind++);
                als.add(t.alignment);
            }
        }
        return new AlignResult(parameters, reader.getNumberOfReads(), report, als, genes, aligner);
    }
}