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

Example 1 with SingleReadEvidence

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

the class SupportNodeIterator method addSupport.

private boolean addSupport(List<KmerSupportNode> supportNodes, DirectedEvidence de, KmerEvidence e) {
    boolean hasNonReference = false;
    if (e != null) {
        for (int i = 0; i < e.length(); i++) {
            KmerSupportNode support = e.node(i);
            if (support != null) {
                // make sure that we are actually able to resort into kmer order
                if (support.firstStart() < de.getBreakendSummary().start - maxSupportStartPositionOffset) {
                    SAMRecord read = null;
                    if (de instanceof SingleReadEvidence) {
                        read = ((SingleReadEvidence) de).getSAMRecord();
                    } else if (de instanceof NonReferenceReadPair) {
                        read = ((NonReferenceReadPair) de).getLocalledMappedRead();
                    }
                    String readString = "";
                    if (read != null) {
                        readString = read.getReadName();
                        if (!read.getReadUnmappedFlag()) {
                            readString += String.format(" (%s:%d %s)", read.getReferenceName(), read.getStart(), read.getCigarString());
                        }
                    }
                    String msg = String.format("Error: kmer in evidence %s of read %s out of bounds." + " Kmer support starts at %d which is more than %d before the breakpoint start position at %s", de.getEvidenceID(), readString, support.firstStart(), maxSupportStartPositionOffset, de.getBreakendSummary());
                    log.error(msg);
                // Try to continue
                // throw new RuntimeException(msg);
                } else if (support.weight() <= 0) {
                    String msg = String.format("Invalid support weight of %d for evidence %s", support.weight(), de.getEvidenceID());
                    log.error(msg);
                    throw new RuntimeException(msg);
                } else {
                    supportNodes.add(support);
                    hasNonReference |= !support.isReference();
                }
            }
        }
    }
    return hasNonReference;
}

Example 2 with SingleReadEvidence

use of au.edu.wehi.idsv.SingleReadEvidence 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 3 with SingleReadEvidence

use of au.edu.wehi.idsv.SingleReadEvidence 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 4 with SingleReadEvidence

use of au.edu.wehi.idsv.SingleReadEvidence 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.");
}