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

Example 11 with VariantContextDirectedBreakpoint

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

the class AllocateEvidenceTest method should_filter_if_insufficient_reads.

@Test
public void should_filter_if_insufficient_reads() throws IOException {
    final ProcessingContext pc = getCommandlineContext();
    pc.getVariantCallingParameters().minScore = 0;
    pc.getVariantCallingParameters().minSize = 0;
    pc.getVariantCallingParameters().minReads = 3;
    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));
    List<VariantContextDirectedBreakpoint> results = Lists.newArrayList(cmd.iterator(new AutoClosingIterator<>(vcfs.iterator()), MoreExecutors.newDirectExecutorService()));
    assertEquals(2, vcfs.size());
    assertEquals(0, results.size());
}

Example 12 with VariantContextDirectedBreakpoint

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

the class AllocateEvidenceTest method should_filter_if_insufficient_quality.

@Test
public void should_filter_if_insufficient_quality() throws IOException {
    final ProcessingContext pc = getCommandlineContext();
    pc.getVariantCallingParameters().minScore = 1000;
    pc.getVariantCallingParameters().minSize = 0;
    pc.getVariantCallingParameters().minReads = 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));
    List<VariantContextDirectedBreakpoint> results = Lists.newArrayList(cmd.iterator(new AutoClosingIterator<>(vcfs.iterator()), MoreExecutors.newDirectExecutorService()));
    assertEquals(0, results.size());
}

Example 13 with VariantContextDirectedBreakpoint

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

the class AnnotateInexactHomologyTest method should_calculate_inexact_homology.

@Test
public void should_calculate_inexact_homology() {
    ProcessingContext pc = getContext();
    StructuralVariationCallBuilder builder = new StructuralVariationCallBuilder(pc, (VariantContextDirectedEvidence) new IdsvVariantContextBuilder(getContext()) {

        {
            breakpoint(new BreakpointSummary(2, FWD, 78, 6, BWD, 79), "");
            phredScore(50);
        }
    }.make());
    builder.addEvidence(SR(Read(2, 78, "1M1S"), Read(6, 79, "1M")));
    VariantContextDirectedBreakpoint e = (VariantContextDirectedBreakpoint) builder.make();
    AnnotateInexactHomology aih = new AnnotateInexactHomology();
    aih.setContext(pc);
    ExecutorService threadpool = Executors.newSingleThreadExecutor();
    e = aih.iterator(new AutoClosingIterator<>(ImmutableList.of(e).iterator()), threadpool).next();
    assertEquals(-78, ((int[]) e.getAttribute(VcfInfoAttributes.INEXACT_HOMPOS.attribute()))[0]);
    assertEquals(300, ((int[]) e.getAttribute(VcfInfoAttributes.INEXACT_HOMPOS.attribute()))[1]);
    threadpool.shutdown();
}