Examples with VariantContextDirectedBreakpoint au.edu.wehi.idsv.VariantContextDirectedBreakpoint used on opensource projects

Example 6 with VariantContextDirectedBreakpoint

use of au.edu.wehi.idsv.VariantContextDirectedBreakpoint in project gridss by PapenfussLab.

the class VcfTransformCommandLineProgram method getAllCalls.

public Iterator<IdsvVariantContext> getAllCalls(File file, CloseableIterator<VariantContextDirectedBreakpoint> breakpointCalls) {
    VCFFileReader vcfReader = new VCFFileReader(file, false);
    CloseableIterator<VariantContext> it = vcfReader.iterator();
    Iterator<IdsvVariantContext> idsvIt = Iterators.transform(it, variant -> IdsvVariantContext.create(getContext(), null, variant));
    Iterator<IdsvVariantContext> nonbpIt = Iterators.filter(idsvIt, variant -> !(variant instanceof VariantContextDirectedBreakpoint));
    // sort back to nominal VCF position
    Iterator<VariantContextDirectedBreakpoint> bpit = new VariantContextWindowedSortingIterator<>(getContext(), SAMEvidenceSource.maximumWindowSize(getContext(), getSamEvidenceSources(), getAssemblySource()), breakpointCalls);
    Iterator<IdsvVariantContext> mergedIt = Iterators.mergeSorted(ImmutableList.of(bpit, nonbpIt), IdsvVariantContext.ByLocationStart);
    return new AutoClosingIterator<>(mergedIt, vcfReader, it);
}

Example 7 with VariantContextDirectedBreakpoint

use of au.edu.wehi.idsv.VariantContextDirectedBreakpoint in project gridss by PapenfussLab.

the class AllocateEvidence method annotate.

private VariantContextDirectedBreakpoint annotate(VariantEvidenceSupport ves) {
    VariantCallingConfiguration vc = getContext().getConfig().getVariantCalling();
    StructuralVariationCallBuilder builder = new StructuralVariationCallBuilder(getContext(), ves.variant);
    for (DirectedEvidence e : ves.support) {
        boolean shouldExclude = false;
        if (!shouldExclude) {
            builder.addEvidence(e);
        }
    }
    VariantContextDirectedBreakpoint bp = (VariantContextDirectedBreakpoint) builder.make();
    if (!vc.writeFiltered) {
        if (bp.getBreakpointQual() < vc.minScore)
            return null;
        if (bp.getBreakpointEvidenceCount() < vc.minReads)
            return null;
        if (bp.isFiltered())
            return null;
    }
    bp = (VariantContextDirectedBreakpoint) vc.applyConfidenceFilter(getContext(), bp);
    return bp;
}

Example 8 with VariantContextDirectedBreakpoint

use of au.edu.wehi.idsv.VariantContextDirectedBreakpoint in project gridss by PapenfussLab.

the class AnnotateReferenceCoverage method iterator.

@Override
public CloseableIterator<VariantContextDirectedBreakpoint> iterator(CloseableIterator<VariantContextDirectedBreakpoint> calls, ExecutorService threadpool) {
    ProcessingContext context = getContext();
    List<SAMEvidenceSource> sources = getSamEvidenceSources();
    AssemblyEvidenceSource asm = getAssemblySource();
    int windowSize = SAMEvidenceSource.maximumWindowSize(context, sources, asm);
    return new SequentialCoverageAnnotator<VariantContextDirectedBreakpoint>(context, sources, calls, 2 * windowSize + WINDOW_SIZE_SAFETY_MARGIN, threadpool);
}

Example 9 with VariantContextDirectedBreakpoint

use of au.edu.wehi.idsv.VariantContextDirectedBreakpoint in project gridss by PapenfussLab.

the class VcfTransformCommandLineProgram method getBreakpoints.

public CloseableIterator<VariantContextDirectedBreakpoint> getBreakpoints(File file) {
    VCFFileReader vcfReader = new VCFFileReader(file, false);
    CloseableIterator<VariantContext> it = vcfReader.iterator();
    Iterator<IdsvVariantContext> idsvIt = Iterators.transform(it, variant -> IdsvVariantContext.create(getContext(), null, variant));
    Iterator<VariantContextDirectedBreakpoint> bpit = Iterators.filter(idsvIt, VariantContextDirectedBreakpoint.class);
    // resort by evidence start
    bpit = new DirectEvidenceWindowedSortingIterator<>(getContext(), SAMEvidenceSource.maximumWindowSize(getContext(), getSamEvidenceSources(), getAssemblySource()), bpit);
    return new AutoClosingIterator<VariantContextDirectedBreakpoint>(bpit, it, vcfReader);
}

Example 10 with VariantContextDirectedBreakpoint

use of au.edu.wehi.idsv.VariantContextDirectedBreakpoint in project gridss by PapenfussLab.

the class AllocateEvidenceTest method should_uniquely_assign.

@Test
public void should_uniquely_assign() throws IOException, InterruptedException, ExecutionException {
    final int fragSize = 4;
    final int testSize = 64;
    final List<SAMRecord> in = new ArrayList<SAMRecord>();
    final ProcessingContext pc = getCommandlineContext();
    pc.getVariantCallingParameters().writeFiltered = true;
    pc.getVariantCallingParameters().minScore = 0;
    StubSAMEvidenceSource ses = new StubSAMEvidenceSource(pc, input, 0, 0, fragSize);
    for (int i = 1; i < testSize; i++) {
        for (int j = 1; j < testSize; j++) {
            SAMRecord[] dp = withReadName(String.format("read-%d-%d", i, j), DP(0, i, "1M", true, 1, j, "1M", false));
            ses.evidence.add(NonReferenceReadPair.create(dp[0], dp[1], ses));
            ses.evidence.add(NonReferenceReadPair.create(dp[1], dp[0], ses));
            in.add(dp[0]);
            in.add(dp[1]);
        }
    }
    StubAssemblyEvidenceSource aes = new StubAssemblyEvidenceSource(pc);
    aes.fragSize = fragSize;
    Collections.sort(ses.evidence, DirectedEvidenceOrder.ByNatural);
    createInput(in);
    VariantCaller vc = new VariantCaller(pc, ImmutableList.<SAMEvidenceSource>of(ses), aes);
    ExecutorService threadpool = Executors.newSingleThreadExecutor();
    vc.callBreakends(output, threadpool);
    threadpool.shutdown();
    AllocateEvidence cmd = new AllocateEvidence();
    cmd.INPUT_VCF = output;
    cmd.setContext(pc);
    cmd.setAssemblySource(aes);
    cmd.setSamEvidenceSources(ImmutableList.of(ses));
    cmd.OUTPUT_VCF = new File(testFolder.getRoot(), "annotated.vcf");
    cmd.ASSEMBLY = new File(testFolder.getRoot(), "assembly.bam");
    // to shut up the command-line parsing
    createBAM(cmd.ASSEMBLY, SortOrder.coordinate, Collections.emptyList());
    cmd.doWork(null);
    // List<IdsvVariantContext> annotated = getVcf(new File(testFolder.getRoot(), "out.vcf"), null);
    List<IdsvVariantContext> rawcalls = getVcf(output, null);
    List<IdsvVariantContext> calls = getVcf(cmd.OUTPUT_VCF, null);
    assertSymmetrical(rawcalls.stream().map(x -> (VariantContextDirectedBreakpoint) x).collect(Collectors.toList()));
    assertSymmetrical(calls.stream().map(x -> (VariantContextDirectedBreakpoint) x).collect(Collectors.toList()));
    // with no filtering, annotation should not change call set
    double expectedEvidence = 0;
    for (DirectedEvidence e : ses.evidence) {
        DiscordantReadPair bp = (DiscordantReadPair) e;
        expectedEvidence += bp.getBreakpointQual();
    }
    double annotatedEvidence = 0;
    for (IdsvVariantContext e : calls) {
        annotatedEvidence += e.getPhredScaledQual();
    }
    double rawEvidence = rawcalls.stream().mapToDouble(e -> e.getPhredScaledQual()).sum();
    // unique assignment must result in the evidence total being, at most, the same
    assertTrue(annotatedEvidence <= rawEvidence);
    // each piece of evidence should be assigned to a single breakpoint so totals should match
    int rpCalls = calls.stream().mapToInt(v -> ((VariantContextDirectedBreakpoint) v).getBreakpointEvidenceCount()).sum();
    assertEquals(ses.evidence.size(), rpCalls);
    // floating point truncation on VCF is severe!
    assertEquals(expectedEvidence, annotatedEvidence, 20);
}