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

Example 1 with DirectedEvidence

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

the class NonReferenceContigAssemblerTest method should_call_suboptimal_contigs_if_graph_size_limit_exceeded.

@Test
public void should_call_suboptimal_contigs_if_graph_size_limit_exceeded() {
    ProcessingContext pc = getContext();
    MockSAMEvidenceSource ses = SES(10, 10);
    pc.getAssemblyParameters().k = 4;
    pc.getAssemblyParameters().maxExpectedBreakendLengthMultiple = 1;
    pc.getAssemblyParameters().positional.retainWidthMultiple = 1;
    pc.getAssemblyParameters().positional.flushWidthMultiple = 2;
    List<DirectedEvidence> e = new ArrayList<>();
    for (int i = 0; i < 100; i++) {
        for (int j = 0; j < i + 1; j++) {
            e.add(SCE(FWD, ses, withReadName(String.format("%d-%d", i, j), withSequence("AACCGGTT", Read(0, i, "4M4S")))[0]));
        }
    }
    List<SAMRecord> output = go(pc, false, e.toArray(new DirectedEvidence[0]));
    assertEquals(100, output.size());
    // unbounded execution would call high->low thus call the last contig first
    // bounded execution will force the early calls to be made first
    List<Integer> startPos = output.stream().map(x -> x.getAlignmentStart()).collect(Collectors.toList());
    assertFalse(Ordering.natural().reverse().isOrdered(startPos));
}

Example 2 with DirectedEvidence

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

the class NonReferenceContigAssemblerTest method should_not_remove_misassembled_partial_paths_when_could_be_collapsed_with_adjacent_read.

@Test
public void should_not_remove_misassembled_partial_paths_when_could_be_collapsed_with_adjacent_read() {
    ProcessingContext pc = getContext();
    MockSAMEvidenceSource ses = SES(10, 10);
    pc.getAssemblyParameters().k = 2;
    pc.getAssemblyParameters().maxExpectedBreakendLengthMultiple = 5;
    pc.getAssemblyParameters().removeMisassembledPartialContigsDuringAssembly = true;
    pc.getAssemblyParameters().positional.flushWidthMultiple = 100000;
    pc.getAssemblyParameters().positional.maxPathLengthMultiple = 4;
    List<DirectedEvidence> e = new ArrayList<>();
    for (int i = 1; i < 1000; i += 1) {
        SAMRecord[] rp = OEA(0, i, "2M", true);
        rp[0].setReadBases(B("GG"));
        // expect reverse comp of read sequence
        rp[1].setReadBases(B("AA"));
        e.add(NRRP(ses, rp));
    }
    go(pc, true, e.toArray(new DirectedEvidence[0]));
}

Example 3 with DirectedEvidence

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

the class NonReferenceContigAssemblerTest method should_remove_fully_reference_evidence_before_end.

@Test
public void should_remove_fully_reference_evidence_before_end() {
    ProcessingContext pc = getContext();
    pc.getAssemblyParameters().k = 4;
    int n = 8;
    DirectedEvidence[] input = new DirectedEvidence[2 * n];
    for (int i = 0; i < n; i++) {
        input[2 * i] = SCE(FWD, withSequence("ACGTGGTCGACC", Read(0, 1000 * i, "6M6S")));
        input[2 * i + 1] = SCE(FWD, withSequence("AACGTGG", Read(0, 1000 * i - 1, "6M1S")));
    }
    NonReferenceContigAssembler caller = create(pc, true, input);
    for (int i = 0; i < n / 2; i++) {
        caller.next();
    }
    assertTrue(caller.tracking_activeNodes() <= 3);
}

Example 4 with DirectedEvidence

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

the class AggregateNodeIteratorTest method should_aggregate_kmer_weights.

@Test
public void should_aggregate_kmer_weights() {
    int k = 4;
    SAMEvidenceSource ses = SES(30, 60);
    List<DirectedEvidence> input = new ArrayList<DirectedEvidence>();
    input.add(NRRP(ses, withQual(new byte[] { 1, 1, 1, 1, 1 }, withSequence("ACGTT", DP(0, 1, "5M", false, 1, 1, "5M", false)))));
    input.add(NRRP(ses, withQual(new byte[] { 1, 1, 1, 1, 1 }, withSequence("ACGTT", DP(0, 2, "5M", false, 1, 1, "5M", false)))));
    Collections.sort(input, DirectedEvidence.ByStartEnd);
    List<KmerSupportNode> snList = Lists.newArrayList(new SupportNodeIterator(k, input.iterator(), ses.getMaxConcordantFragmentSize(), null, false, 0));
    List<KmerNode> anList = Lists.newArrayList(new AggregateNodeIterator(snList.iterator()));
    assertTrue(KmerNodeUtil.ByLastStart.isOrdered(anList));
    assertEquals(4, snList.size());
    assertEquals(6, anList.size());
}

Example 5 with DirectedEvidence

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

the class CallVariantsTest method test_sr_rp_assembly.

@Test
public void test_sr_rp_assembly() throws IOException {
    List<DirectedEvidence> in = new ArrayList<DirectedEvidence>();
    in.add(SCE(FWD, withSequence("AACCGGTTCTA", Read(0, 15, "5M6S"))));
    in.add(SCE(FWD, withSequence("AACCGGTTCTA", Read(0, 15, "6M5S"))));
    in.add(NRRP(withSequence("AACCGGTTCTA", DP(0, 1, "11M", true, 1, 100, "11M", false))));
    in.add(NRRP(withSequence("AACCGGTTCTA", DP(0, 2, "11M", true, 1, 100, "11M", false))));
    List<SAMRecord> insam = in.stream().flatMap(de -> {
        if (de instanceof SoftClipEvidence)
            return ImmutableList.<SAMRecord>of(((SoftClipEvidence) de).getSAMRecord()).stream();
        if (de instanceof NonReferenceReadPair)
            return ImmutableList.<SAMRecord>of(((NonReferenceReadPair) de).getNonReferenceRead(), ((NonReferenceReadPair) de).getLocalledMappedRead()).stream();
        throw new RuntimeException("NYI");
    }).collect(Collectors.toList());
    insam.addAll(Lists.newArrayList(RP(0, 1, 100, 10)));
    createInput(insam);
    File propfile = testFolder.newFile("custom.properties");
    try (BufferedWriter writer = new BufferedWriter(new FileWriter(propfile))) {
        writer.write("assembly.k=5\n");
        writer.write("softclip.minLength=1\n");
        writer.write("minAnchorShannonEntropy=0\n");
        writer.write("softclip.minAnchorIdentity=0\n");
        writer.write("softclip.minAverageQual=0\n");
        writer.write("realignment.aligner=\n");
    }
    File assembly = new File(testFolder.getRoot(), "assembly.bam");
    String[] args = new String[] { "INPUT=" + input.toString(), "ASSEMBLY=" + assembly.toString(), "REFERENCE_SEQUENCE=" + reference.toString(), "OUTPUT=" + output.toString(), "TMP_DIR=" + super.testFolder.getRoot().toString(), "WORKING_DIR=" + super.testFolder.getRoot().toString(), "CONFIGURATION_FILE=" + propfile.toString(), "INPUT_MIN_FRAGMENT_SIZE=10", "INPUT_MAX_FRAGMENT_SIZE=100" };
    assertEquals(0, new CallVariants().instanceMain(args));
    List<SAMRecord> breakendAssemblies = getRecords(assembly);
    assertEquals(1, breakendAssemblies.size());
    assembly.delete();
}