Examples with VariantEvidenceSupport au.edu.wehi.idsv.SequentialEvidenceAllocator.VariantEvidenceSupport used on opensource projects

Example 1 with VariantEvidenceSupport

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

the class SequentialEvidenceAllocatorTest 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 = getContext();
    pc.getVariantCallingParameters().writeFiltered = true;
    pc.getVariantCallingParameters().minScore = 0;
    pc.getVariantCallingParameters().breakendMargin = 0;
    StubSAMEvidenceSource ses = new StubSAMEvidenceSource(pc, null, 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]);
        }
    }
    ses.evidence.sort(DirectedEvidenceOrder.ByNatural);
    AggregateEvidenceSource es = new AggregateEvidenceSource(pc, ImmutableList.of(ses), null);
    VariantCallIterator processor = new VariantCallIterator(es);
    ArrayList<VariantContextDirectedEvidence> calls = Lists.newArrayList(processor);
    calls.sort(VariantContextDirectedEvidence.ByBreakendStartEnd);
    SequentialEvidenceAllocator allocator = new SequentialEvidenceAllocator(pc, calls.iterator(), ses.evidence.iterator(), 4, true);
    ArrayList<VariantEvidenceSupport> result = Lists.newArrayList(allocator);
    assertEquals(ses.evidence.size(), result.stream().mapToInt(ves -> ves.support.size()).sum());
    for (VariantEvidenceSupport ves : result) {
        for (DirectedEvidence evidence : ves.support) {
            // check the assignment is valid
            assertTrue(ves.variant.getBreakendSummary().overlaps(evidence.getBreakendSummary()));
            // check the assignment is to the best option
            assertEquals(ves.variant.getPhredScaledQual(), calls.stream().filter(v -> v.getBreakendSummary().overlaps(evidence.getBreakendSummary())).mapToDouble(v -> v.getPhredScaledQual()).max().getAsDouble(), 0);
        }
    }
}

Example 2 with VariantEvidenceSupport

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

the class SequentialEvidenceAllocatorTest method RemoteOverlap_localLookup_should_split_on_referenceIndex_and_direction.

@Test
public void RemoteOverlap_localLookup_should_split_on_referenceIndex_and_direction() {
    final ProcessingContext pc = getContext();
    pc.getVariantCallingParameters().writeFiltered = true;
    pc.getVariantCallingParameters().minScore = 0;
    pc.getVariantCallingParameters().breakendMargin = 0;
    StubSAMEvidenceSource ses = new StubSAMEvidenceSource(pc, null, 0, 0, 100);
    ses.evidence.add(SCE(FWD, Read(0, 1, "1S1M1S")));
    ses.evidence.add(SCE(BWD, Read(0, 1, "1S1M1S")));
    // ses.evidence.add(SCE(BWD, Read(1, 1, "1S1M1S")));
    // ses.evidence.add(SCE(FWD, Read(1, 1, "1S1M1S")));
    SequentialEvidenceAllocator allocator = new SequentialEvidenceAllocator(pc, ImmutableList.of((VariantContextDirectedBreakpoint) TestHelper.minimalVariant().breakpoint(new BreakpointSummary(1, FWD, 1, 1, 1, 0, FWD, 1, 1, 1), "").phredScore(1).id("call").make()).iterator(), ses.evidence.iterator(), Integer.MAX_VALUE, true);
    // shouldn't crash
    VariantEvidenceSupport ves = allocator.next();
    Assert.assertTrue(ves.support.stream().allMatch(e -> ves.variant.getBreakendSummary().overlaps(e.getBreakendSummary())));
}