Examples with SingleRead com.milaboratory.core.io.sequence.SingleRead used on opensource projects

Example 1 with SingleRead

use of com.milaboratory.core.io.sequence.SingleRead in project mixcr by milaboratory.

the class VDJCAlignerSTest method test2.

@Test
@Ignore
public void test2() throws Exception {
    // @
    // GCTGTGTATTACTGTGCAAGAGGGCCCCAAGAAAATAGTGGTTATTACTACGGGTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGCCTCCACCAAGGGCCCATCGGTCTTCCCCCTGGCGCC
    // +
    // CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
    VDJCAlignerParameters parameters = VDJCParametersPresets.getByName("default");
    VDJCAlignerS aligner = new VDJCAlignerS(parameters);
    for (VDJCGene gene : VDJCLibraryRegistry.getDefault().getLibrary("default", "hs").getGenes(Chains.IGH)) if (parameters.containsRequiredFeature(gene))
        aligner.addGene(gene);
    SingleReadImpl read = new SingleReadImpl(0, new NSequenceWithQuality(new NucleotideSequence("GCTGTGTATTACTGTGCAAGAGGGCCCCAAGAAAATAGTGGTTATTACTACGGGTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGCCTCCACCAAGGGCCCATCGGTCTTCCCCCTGGCGCC"), SequenceQuality.GOOD_QUALITY_VALUE), "");
    RandomUtil.getThreadLocalRandom().setSeed(29);
    VDJCAlignmentResult<SingleRead> result = aligner.process0(read);
}

Example 2 with SingleRead

use of com.milaboratory.core.io.sequence.SingleRead in project mixcr by milaboratory.

the class VDJCAlignerSTest method testSerialization1.

@Test
public void testSerialization1() throws Exception {
    VDJCAlignerParameters parameters = VDJCParametersPresets.getByName("default");
    // LociLibrary ll = LociLibraryManager.getDefault().getLibrary("mi");
    ByteArrayOutputStream bos = new ByteArrayOutputStream();
    List<VDJCAlignments> alignemntsList = new ArrayList<>();
    int header;
    try (SingleFastqReader reader = new SingleFastqReader(VDJCAlignerSTest.class.getClassLoader().getResourceAsStream("sequences/sample_IGH_R1.fastq"), true)) {
        VDJCAlignerS aligner = new VDJCAlignerS(parameters);
        for (VDJCGene gene : VDJCLibraryRegistry.getDefault().getLibrary("default", "hs").getGenes(Chains.IGH)) if (parameters.containsRequiredFeature(gene))
            aligner.addGene(gene);
        try (VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(bos)) {
            writer.header(aligner);
            header = bos.size();
            for (SingleRead read : CUtils.it(reader)) {
                VDJCAlignmentResult<SingleRead> result = aligner.process(read);
                if (result.alignment != null) {
                    writer.write(result.alignment);
                    alignemntsList.add(result.alignment);
                }
            }
        }
    }
    Assert.assertTrue(alignemntsList.size() > 10);
    System.out.println("Bytes per alignment: " + (bos.size() - header) / alignemntsList.size());
    try (VDJCAlignmentsReader reader = new VDJCAlignmentsReader(new ByteArrayInputStream(bos.toByteArray()))) {
        int i = 0;
        for (VDJCAlignments alignments : CUtils.it(reader)) Assert.assertEquals(alignemntsList.get(i++), alignments);
    }
}

Example 3 with SingleRead

use of com.milaboratory.core.io.sequence.SingleRead in project mixcr by milaboratory.

the class VDJCAlignerPVFirst method process0.

@Override
protected VDJCAlignmentResult<PairedRead> process0(final PairedRead input) {
    Target[] targets = getTargets(input);
    // Creates helper classes for each PTarget
    PAlignmentHelper[] helpers = createInitialHelpers(targets);
    VDJCAlignmentResult<PairedRead> result = parameters.getAllowPartialAlignments() ? processPartial(input, helpers) : processStrict(input, helpers);
    // if sAligner == null (which means --no-merge option), no merge will be performed
    if (result.alignment != null && sAligner != null) {
        final VDJCAlignments alignment = result.alignment;
        final TargetMerger.TargetMergingResult mergeResult = alignmentsMerger.merge(new AlignedTarget(alignment, 0), new AlignedTarget(alignment, 1), false);
        if (mergeResult.failedDueInconsistentAlignments()) {
            GeneType geneType = mergeResult.getFailedMergedGeneType();
            int removeId = alignment.getBestHit(geneType).getAlignment(0).getScore() > alignment.getBestHit(geneType).getAlignment(1).getScore() ? 1 : 0;
            if (listener != null)
                listener.onTopHitSequenceConflict(input, alignment, geneType);
            return new VDJCAlignmentResult<>(input, alignment.removeBestHitAlignment(geneType, removeId));
        } else if (mergeResult.isSuccessful()) {
            assert mergeResult.isUsingAlignments();
            NSequenceWithQuality alignedTarget = mergeResult.getResult().getTarget();
            SingleRead sRead = new SingleReadImpl(input.getId(), alignedTarget, "");
            VDJCAlignmentResult<SingleRead> sResult = sAligner.process0(sRead);
            if (sResult.alignment == null)
                return result;
            VDJCAlignments sAlignment = sResult.alignment.setHistory(new SequenceHistory[] { new SequenceHistory.Merge(SequenceHistory.OverlapType.AlignmentOverlap, result.alignment.getHistory(0), result.alignment.getHistory(1), mergeResult.getOffset(), mergeResult.getMismatched()) }, new SequenceRead[] { input });
            if (listener != null)
                listener.onSuccessfulAlignmentOverlap(input, sAlignment);
            return new VDJCAlignmentResult<>(input, sAlignment);
        }
    }
    return result;
}

Example 4 with SingleRead

use of com.milaboratory.core.io.sequence.SingleRead in project mixcr by milaboratory.

the class IOTest method testSerialization1.

@Test
public void testSerialization1() throws Exception {
    VDJCAlignerParameters parameters = VDJCParametersPresets.getByName("default");
    ByteArrayOutputStream bos = new ByteArrayOutputStream();
    List<VDJCAlignments> alignemntsList = new ArrayList<>();
    int header;
    long numberOfReads;
    try (SingleFastqReader reader = new SingleFastqReader(IOTest.class.getClassLoader().getResourceAsStream("sequences/sample_IGH_R1.fastq"), true)) {
        VDJCAlignerS aligner = new VDJCAlignerS(parameters);
        for (VDJCGene gene : VDJCLibraryRegistry.getDefault().getLibrary("default", "hs").getGenes(Chains.IGH)) {
            if (parameters.containsRequiredFeature(gene))
                aligner.addGene(gene);
        }
        try (VDJCAlignmentsWriter writer = new VDJCAlignmentsWriter(bos)) {
            writer.header(aligner);
            header = bos.size();
            for (SingleRead read : CUtils.it(reader)) {
                VDJCAlignmentResult<SingleRead> result = aligner.process(read);
                if (result.alignment != null) {
                    writer.write(result.alignment);
                    alignemntsList.add(result.alignment);
                }
            }
            writer.setNumberOfProcessedReads(numberOfReads = reader.getNumberOfReads());
        }
    }
    assertTrue(alignemntsList.size() > 10);
    assertTrue(numberOfReads > 10);
    System.out.println("Bytes per alignment: " + (bos.size() - header) / alignemntsList.size());
    try (VDJCAlignmentsReader reader = new VDJCAlignmentsReader(new ByteArrayInputStream(bos.toByteArray()))) {
        int i = 0;
        for (VDJCAlignments alignments : CUtils.it(reader)) assertEquals(alignemntsList.get(i++), alignments);
        Assert.assertEquals(numberOfReads, reader.getNumberOfReads());
    }
}

Example 5 with SingleRead

use of com.milaboratory.core.io.sequence.SingleRead in project mixcr by milaboratory.

the class VDJCAligner method hash.

private static <R extends SequenceRead> long hash(R input) {
    long hash = 1;
    for (int i = 0; i < input.numberOfReads(); i++) {
        final SingleRead r = input.getRead(i);
        hash = 31 * hash + r.getData().getSequence().hashCode();
        if (r.getDescription() != null)
            hash = 31 * hash + r.getDescription().hashCode();
        else
            hash = 31 * hash + HashFunctions.JenkinWang64shift(input.getId());
    }
    return hash;
}