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

Example 1 with VariantContextDirectedBreakpoint

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

the class VariantCallingConfigurationTest method V.

public VariantContextDirectedBreakpoint V(BreakpointSummary bs, String untemplated) {
    IdsvVariantContextBuilder builder = new IdsvVariantContextBuilder(getContext());
    builder.breakpoint(bs, untemplated);
    return (VariantContextDirectedBreakpoint) builder.make();
}

Example 2 with VariantContextDirectedBreakpoint

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

the class AllocateEvidenceTest method should_annotate_reads.

@Test
public void should_annotate_reads() throws IOException {
    final ProcessingContext pc = getCommandlineContext();
    pc.getVariantCallingParameters().minScore = 0;
    pc.getVariantCallingParameters().minSize = 0;
    createInput(RP(0, 1, 10), DP(0, 1, "5M5S", true, 1, 10, "5M", true), DP(0, 2, "5M5S", true, 1, 10, "5M", true));
    SAMEvidenceSource ses = new SAMEvidenceSource(getContext(), input, null, 0);
    ses.ensureMetrics();
    File assemblyFile = new File(testFolder.getRoot(), "assembly.bam");
    AssemblyEvidenceSource aes = new AssemblyEvidenceSource(pc, ImmutableList.of(ses), assemblyFile);
    aes.assembleBreakends(null);
    aes.ensureExtracted();
    VariantCaller caller = new VariantCaller(pc, ImmutableList.of(ses), aes);
    caller.callBreakends(output, MoreExecutors.newDirectExecutorService());
    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");
    List<VariantContextDirectedBreakpoint> vcfs = Lists.newArrayList(Iterables.filter(getVcf(output, null), VariantContextDirectedBreakpoint.class));
    // both breakends
    assertEquals(2 * 1, vcfs.size());
    assertSymmetrical(vcfs);
    List<VariantContextDirectedBreakpoint> results = Lists.newArrayList(cmd.iterator(new AutoClosingIterator<>(vcfs.iterator()), MoreExecutors.newDirectExecutorService()));
    assertSymmetrical(results);
    assertEquals(vcfs.size(), results.size());
    VariantContextDirectedBreakpoint e = results.get(0);
    assertEquals(2, e.getBreakpointEvidenceCount());
    assertEquals(2, e.getBreakendEvidenceCountSoftClip());
}

Example 3 with VariantContextDirectedBreakpoint

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

the class AllocateEvidenceTest method should_apply_filters.

@Test
public void should_apply_filters() throws IOException {
    final ProcessingContext pc = getCommandlineContext();
    pc.getVariantCallingParameters().minScore = 0;
    pc.getVariantCallingParameters().minSize = 0;
    createInput(RP(0, 1, 10), DP(0, 1, "5M5S", true, 1, 10, "5M", true));
    SAMEvidenceSource ses = new SAMEvidenceSource(getContext(), input, null, 0);
    ses.ensureMetrics();
    File assemblyFile = new File(testFolder.getRoot(), "assembly.bam");
    AssemblyEvidenceSource aes = new AssemblyEvidenceSource(pc, ImmutableList.of(ses), assemblyFile);
    aes.assembleBreakends(null);
    aes.ensureExtracted();
    VariantCaller caller = new VariantCaller(pc, ImmutableList.of(ses), aes);
    caller.callBreakends(output, MoreExecutors.newDirectExecutorService());
    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");
    List<VariantContextDirectedBreakpoint> vcfs = Lists.newArrayList(Iterables.filter(getVcf(output, null), VariantContextDirectedBreakpoint.class));
    // both breakends
    assertEquals(2 * 1, vcfs.size());
    assertSymmetrical(vcfs);
    List<VariantContextDirectedBreakpoint> results = Lists.newArrayList(cmd.iterator(new AutoClosingIterator<>(vcfs.iterator()), MoreExecutors.newDirectExecutorService()));
    assertSymmetrical(results);
    // single read support
    assertEquals(0, results.size());
}

Example 4 with VariantContextDirectedBreakpoint

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

the class BreakpointHomology method annotate.

public static VariantContextDirectedBreakpoint annotate(ProcessingContext context, VariantContextDirectedBreakpoint bp) {
    if (!bp.isBreakendExact())
        return bp;
    IdsvVariantContextBuilder builder = new IdsvVariantContextBuilder(context, bp);
    BreakpointHomology bh = BreakpointHomology.calculate(context.getReference(), bp.getBreakendSummary().getNominalPosition(), bp.getUntemplatedSequence(), context.getVariantCallingParameters().maxBreakendHomologyLength, context.getVariantCallingParameters().breakendHomologyAlignmentMargin);
    int[] bounds;
    if (bp.getBreakendSummary().direction == BreakendDirection.Forward) {
        bounds = new int[] { -bh.getLocalHomologyLength(), bh.getRemoteHomologyLength() };
    } else {
        bounds = new int[] { -bh.getRemoteHomologyLength(), bh.getLocalHomologyLength() };
    }
    builder.attribute(VcfInfoAttributes.INEXACT_HOMPOS, bounds);
    return (VariantContextDirectedBreakpoint) builder.make();
}

Example 5 with VariantContextDirectedBreakpoint

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

the class BreakpointFilterTracker method isValidBreakpoint.

private boolean isValidBreakpoint(T be1, T be2) {
    String be1value = "";
    String be2value = "";
    if (!be1.getFilters().equals(be2.getFilters())) {
        be1value += " {" + be1.getFilters().toString() + "}";
        be2value += " {" + be2.getFilters().toString() + "}";
    }
    if (!breakendsMatchs(be1, be2)) {
        be1value += be1.getBreakendSummary().toString();
        be2value += be2.getBreakendSummary().toString();
    }
    if (Math.abs(be1.getPhredScaledQual() - be2.getPhredScaledQual()) > 0.01) {
        be1value += " Q:" + be1.getPhredScaledQual();
        be2value += " Q:" + be2.getPhredScaledQual();
    }
    if (be1 instanceof VariantContextDirectedBreakpoint && be2 instanceof VariantContextDirectedBreakpoint) {
        VariantContextDirectedBreakpoint bp1 = (VariantContextDirectedBreakpoint) be1;
        VariantContextDirectedBreakpoint bp2 = (VariantContextDirectedBreakpoint) be2;
        if (bp1.getBreakpointEvidenceCountAssembly() != bp2.getBreakpointEvidenceCountAssembly()) {
            be1value += " AS:" + bp1.getBreakpointEvidenceCountLocalAssembly() + " RAS:" + bp1.getBreakpointEvidenceCountRemoteAssembly();
            be2value += " AS:" + bp2.getBreakpointEvidenceCountLocalAssembly() + " RAS:" + bp2.getBreakpointEvidenceCountRemoteAssembly();
        }
        if (bp1.getBreakpointEvidenceCountSoftClip() != bp2.getBreakpointEvidenceCountSoftClip()) {
            be1value += " SC:" + bp1.getBreakpointEvidenceCountSoftClip();
            be2value += " SC:" + bp2.getBreakpointEvidenceCountSoftClip();
        }
        if (bp1.getBreakpointEvidenceCountReadPair() != bp2.getBreakpointEvidenceCountReadPair()) {
            be1value += " RP:" + bp1.getBreakpointEvidenceCountReadPair();
            be2value += " RP:" + bp2.getBreakpointEvidenceCountReadPair();
        }
        if (bp1.getHomologySequence().length() != bp2.getHomologySequence().length()) {
            be1value += " HOMSEQ:" + bp1.getHomologySequence();
            be2value += " HOMSEQ:" + bp2.getHomologySequence();
        }
    }
    if (be1value.length() > 0) {
        String msg = String.format("Breakend mismatch between %s %s and %s %s", be1.getID(), be1value, be2.getID(), be2value);
        log.error(msg);
        return !doAssert;
    }
    return true;
}