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

Example 6 with DirectedEvidence

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

the class PositionalAssemblerTest method should_assemble_simple_forward_soft_clips.

@Test
public void should_assemble_simple_forward_soft_clips() {
    ProcessingContext pc = getContext();
    pc.getAssemblyParameters().anchorLength = 1;
    AssemblyEvidenceSource aes = AES(pc);
    pc.getAssemblyParameters().k = 4;
    List<DirectedEvidence> input = new ArrayList<DirectedEvidence>();
    // 12345678901234567890
    // ACGTTGGTTA
    // MMMMMSSSSS
    // GCAACGTTGGTTAA
    // MMMMMMMMSSSSSS
    input.add(SCE(FWD, withSequence("ACGTTGGTTA", Read(0, 10, "5M5S"))[0]));
    input.add(SCE(FWD, withSequence("TTTTTGCAACGTTGGTTAA", Read(0, 2, "13M6S"))[0]));
    input.sort(DirectedEvidenceOrder.ByStartEnd);
    List<SingleReadEvidence> r = asAssemblyEvidence(aes, Lists.newArrayList(new PositionalAssembler(pc, aes, new SequentialIdGenerator("asm"), input.iterator())));
    assertEquals(1, r.size());
    assertEquals(new BreakendSummary(0, FWD, 14), r.get(0).getBreakendSummary());
    // anchor length to match breakend length
    assertEquals("AACGTT", S(r.get(0).getAnchorSequence()));
    assertEquals("GGTTAA", S(r.get(0).getBreakendSequence()));
    assertEquals("AACGTTGGTTAA", S(r.get(0).getSAMRecord().getReadBases()));
}

Example 7 with DirectedEvidence

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

the class PositionalAssemblerTest method should_assemble_simple_input.

@Test
public void should_assemble_simple_input() {
    ProcessingContext pc = getContext();
    AssemblyEvidenceSource aes = AES(pc);
    pc.getAssemblyParameters().k = 4;
    List<DirectedEvidence> input = new ArrayList<DirectedEvidence>();
    input.add(SCE(BWD, Read(0, 10, "5S5M")));
    input.add(SCE(FWD, Read(0, 10, "5M5S")));
    input.add(SCE(BWD, Read(0, 100, "5S5M")));
    input.add(SCE(FWD, Read(0, 100, "5M5S")));
    input.sort(DirectedEvidenceOrder.ByStartEnd);
    ArrayList<SAMRecord> r = Lists.newArrayList(new PositionalAssembler(pc, aes, new SequentialIdGenerator("asm"), input.iterator()));
    assertEquals(4, r.size());
}

Example 8 with DirectedEvidence

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

the class PositionalAssemblerTest method rp_anchor_should_set_non_reference_bases_as_anchoring.

@Test
public void rp_anchor_should_set_non_reference_bases_as_anchoring() {
    ProcessingContext pc = getContext();
    pc.getAssemblyParameters().anchorLength = 1;
    AssemblyEvidenceSource aes = AES(pc);
    pc.getAssemblyParameters().k = 4;
    List<DirectedEvidence> input = new ArrayList<DirectedEvidence>();
    // 12345678901234567890
    // ACGTTGGTTA
    // MMMMMSSSSS
    // GCAACGTTGGTTAA
    // MMMMMMMMSSSSSS
    // TTTTTGCAACGTTGGTTAA
    input.add(SCE(FWD, withSequence("ACGTTGGTTA", Read(0, 10, "5M5S"))[0]));
    input.add(SCE(FWD, withSequence("TTTTTGCAACGTTGGTTAA", Read(0, 2, "13M6S"))[0]));
    input.add(NRRP(withSequence("TTTTTGCAACGTTGGTTAA", DP(0, 2, "13M6S", true, 1, 1, "19M", false))));
    input.sort(DirectedEvidenceOrder.ByStartEnd);
    List<SingleReadEvidence> r = asAssemblyEvidence(aes, Lists.newArrayList(new PositionalAssembler(pc, aes, new SequentialIdGenerator("asm"), input.iterator())));
    assertEquals(2, r.size());
    // race condition w.r.t which assembly returns first
    assertEquals(new BreakendSummary(0, FWD, 14), r.get(0).getBreakendSummary());
    // anchor length to match breakend length
    assertEquals("AACGTT", S(r.get(0).getAnchorSequence()));
    assertEquals("GGTTAA", S(r.get(0).getBreakendSequence()));
    assertEquals("AACGTTGGTTAA", S(r.get(0).getSAMRecord().getReadBases()));
}

Example 9 with DirectedEvidence

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

the class AnnotateVariants method writeAssemblyBreakends.

public static void writeAssemblyBreakends(File file, AssemblyEvidenceSource assemblyEvidence) throws IOException {
    log.info("Writing breakend assembly support.");
    File tmp = gridss.Defaults.OUTPUT_TO_TEMP_FILE ? FileSystemContext.getWorkingFileFor(file) : file;
    try (BufferedOutputStream writer = new BufferedOutputStream(new FileOutputStream(tmp))) {
        try (CloseableIterator<DirectedEvidence> it = assemblyEvidence.iterator()) {
            while (it.hasNext()) {
                SingleReadEvidence ass = (SingleReadEvidence) it.next();
                if (!ass.getSAMRecord().isSecondaryOrSupplementary()) {
                    writer.write('>');
                    writer.write(ass.getEvidenceID().getBytes(StandardCharsets.US_ASCII));
                    writer.write('\n');
                    if (ass.getBreakendSummary().direction == BreakendDirection.Forward) {
                        writer.write(ass.getAnchorSequence(), 0, ass.getAnchorSequence().length);
                        writer.write(ass.getBreakendSequence(), 0, ass.getBreakendSequence().length);
                    } else {
                        writer.write(ass.getBreakendSequence(), 0, ass.getBreakendSequence().length);
                        writer.write(ass.getAnchorSequence(), 0, ass.getAnchorSequence().length);
                    }
                    writer.write('\n');
                }
            }
        }
    }
    if (tmp != file) {
        Files.move(tmp, file);
    }
    log.info("Writing breakend assembly support complete.");
}

Example 10 with DirectedEvidence

use of au.edu.wehi.idsv.DirectedEvidence 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;
}