Examples with ChimericAlignment au.edu.wehi.idsv.sam.ChimericAlignment used on opensource projects

Example 11 with ChimericAlignment

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

the class TestHelper method Read.

public static SAMRecord Read(String chimericAlignment) {
    ChimericAlignment ca = new ChimericAlignment(chimericAlignment);
    SAMRecord record = new SAMRecord(getHeader());
    record.setReferenceIndex(record.getHeader().getSequenceIndex(ca.rname));
    record.setAlignmentStart(ca.pos);
    record.setReadUnmappedFlag(false);
    record.setReadPairedFlag(false);
    record.setReadNegativeStrandFlag(ca.isNegativeStrand);
    record.setCigar(ca.cigar);
    record.setMappingQuality(ca.mapq);
    record.setReadName(chimericAlignment);
    clean(record);
    return record;
}

Example 12 with ChimericAlignment

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

the class SplitReadEvidenceTest method should_handle_multiple_overlapping_fragments.

@Test
public void should_handle_multiple_overlapping_fragments() {
    SAMRecord r1 = Read(0, 100, "48M52S");
    SAMRecord r2 = Read(0, 100, "32S48M20S");
    SAMRecord r3 = Read(0, 100, "64S36M");
    r1.setReadName("R");
    r2.setReadName("R");
    r3.setReadName("R");
    r1.setAttribute("SA", new ChimericAlignment(r2).toString() + ";" + new ChimericAlignment(r3).toString());
    r2.setAttribute("SA", new ChimericAlignment(r1).toString() + ";" + new ChimericAlignment(r3).toString());
    r3.setAttribute("SA", new ChimericAlignment(r1).toString() + ";" + new ChimericAlignment(r2).toString());
    List<SplitReadEvidence> e1 = SplitReadEvidence.create(SES(), r1);
    List<SplitReadEvidence> e2 = SplitReadEvidence.create(SES(), r2);
    List<SplitReadEvidence> e3 = SplitReadEvidence.create(SES(), r3);
    Assert.assertEquals(1, e1.size());
    Assert.assertEquals(2, e2.size());
    Assert.assertEquals(1, e3.size());
    Assert.assertEquals(e1.get(0).getEvidenceID(), e2.get(0).getRemoteEvidenceID());
    Assert.assertEquals(e2.get(0).getEvidenceID(), e1.get(0).getRemoteEvidenceID());
    Assert.assertEquals(e2.get(1).getEvidenceID(), e3.get(0).getRemoteEvidenceID());
    Assert.assertEquals(e3.get(0).getEvidenceID(), e2.get(1).getRemoteEvidenceID());
}

Example 13 with ChimericAlignment

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

the class SplitReadEvidenceTest method overaligned_breakpoints_should_be_symmetrical.

@Test
public void overaligned_breakpoints_should_be_symmetrical() {
    // 12345
    // MMMM
    // MMM
    // overlap = 2
    SAMRecord r1 = withSequence("NNNNN", Read(0, 100, "4M1S"))[0];
    SAMRecord r2 = withSequence("NNNNN", Read(0, 200, "2S3M"))[0];
    r1.setAttribute("SA", new ChimericAlignment(r2).toString());
    r2.setAttribute("SA", new ChimericAlignment(r1).toString());
    SplitReadEvidence e1 = (SplitReadEvidence) SingleReadEvidence.createEvidence(SES(), 0, r1).get(0);
    SplitReadEvidence e2 = (SplitReadEvidence) SingleReadEvidence.createEvidence(SES(), 0, r2).get(0);
    Assert.assertEquals(2, e2.getBreakendSummary().end - e2.getBreakendSummary().start);
    Assert.assertEquals(2, e1.getBreakendSummary().end - e1.getBreakendSummary().start);
    Assert.assertEquals(e1.getBreakendSummary(), e2.getBreakendSummary().remoteBreakpoint());
    Assert.assertEquals(e2.getBreakendSummary(), e1.getBreakendSummary().remoteBreakpoint());
}

Example 14 with ChimericAlignment

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

the class SplitReadEvidenceTest method isReference_should_require_entire_aligned_region_to_match.

@Test
public void isReference_should_require_entire_aligned_region_to_match() {
    SAMRecord r1 = withSequence("TAAATAAA", Read(0, 10, "3M5S"))[0];
    SAMRecord r2 = withSequence("TAAATAAA", Read(0, 20, "3S2M3S"))[0];
    r1.setAttribute("SA", new ChimericAlignment(r2).toString());
    r2.setAttribute("SA", new ChimericAlignment(r1).toString());
    SplitReadEvidence e1 = SplitReadEvidence.create(SES(), r1).get(0);
    SplitReadEvidence e2 = SplitReadEvidence.create(SES(), r2).get(0);
    Assert.assertFalse(e2.isReference());
    Assert.assertFalse(e1.isReference());
}

Example 15 with ChimericAlignment

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

the class SplitReadEvidenceTest method score_should_be_symmetrical_even_if_anchors_overlap.

@Test
public void score_should_be_symmetrical_even_if_anchors_overlap() {
    SAMRecord primary = Read(0, 100, "6M4S");
    primary.setReadBases(B("NNNNNNNNNN"));
    primary.setBaseQualities(B("1234567890"));
    primary.setMappingQuality(40);
    SAMRecord supp = Read(0, 200, "3S7M");
    supp.setSupplementaryAlignmentFlag(true);
    supp.setReadBases(B("NNNNNNNNNN"));
    supp.setBaseQualities(B("1234567890"));
    supp.setMappingQuality(20);
    primary.setAttribute("SA", new ChimericAlignment(supp).toString());
    supp.setAttribute("SA", new ChimericAlignment(primary).toString());
    StubSAMEvidenceSource ses = new StubSAMEvidenceSource(getContext(), null, 0, 0, 100);
    SplitReadEvidence ep = SplitReadEvidence.create(ses, primary).get(0);
    SplitReadEvidence es = SplitReadEvidence.create(ses, supp).get(0);
    assertEquals(ep.getBreakpointQual(), es.getBreakpointQual(), 0);
}