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

Example 1 with SoftClipEvidence

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

the class NonReferenceContigAssemblerTest method should_call_simple_bwd_SC.

@Test
public void should_call_simple_bwd_SC() {
    ProcessingContext pc = getContext();
    pc.getAssemblyParameters().k = 4;
    SoftClipEvidence sce = SCE(BWD, withSequence("ACGTGGTCGACC", Read(0, 10, "6S6M")));
    List<SAMRecord> output = go(pc, true, sce);
    assertEquals(1, output.size());
    assertEquals("ACGTGGTCGACC", S(output.get(0).getReadBases()));
    assertEquals("6S6M", output.get(0).getCigarString());
    assertEquals(0, (int) output.get(0).getReferenceIndex());
    assertEquals(10, output.get(0).getAlignmentStart());
}

Example 2 with SoftClipEvidence

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

the class NonReferenceContigAssemblerTest method should_set_assembly_attributes.

@Test
public void should_set_assembly_attributes() {
    ProcessingContext pc = getContext();
    pc.getAssemblyParameters().k = 4;
    SoftClipEvidence sce = SCE(FWD, withSequence("ACGTGGTCGACC", Read(0, 5, "6M6S")));
    List<SAMRecord> output = go(pc, true, sce);
    AssemblyAttributes attr = new AssemblyAttributes(output.get(0));
    assertNotNull(attr);
    assertEquals(1, attr.getAssemblySupportCount());
}

Example 3 with SoftClipEvidence

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

the class NonReferenceContigAssemblerTest method should_call_overlapping_SC.

@Test
public void should_call_overlapping_SC() {
    // 12345678901234567890
    // ACGTGGCTCGACC
    // ------
    // ------
    ProcessingContext pc = getContext();
    pc.getAssemblyParameters().k = 4;
    SoftClipEvidence fwd = SCE(BWD, withSequence("ACGTGGCTCGACC", Read(0, 8, "7S6M")));
    SoftClipEvidence bwd = SCE(FWD, withSequence("ACGTGGCTCGACC", Read(0, 1, "6M7S")));
    List<SAMRecord> output = go(pc, true, fwd, bwd);
    assertEquals(1, output.size());
    assertEquals("6M1I1D6M", output.get(0).getCigarString());
}

Example 4 with SoftClipEvidence

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

the class NonReferenceContigAssemblerTest method should_handle_sc_repeated_kmers.

@Test
public void should_handle_sc_repeated_kmers() {
    ProcessingContext pc = getContext();
    pc.getAssemblyParameters().k = 4;
    SoftClipEvidence sce = SCE(FWD, withSequence("TTTTTTTTTTTT", Read(0, 5, "6M6S")));
    List<SAMRecord> output = go(pc, true, sce);
    assertEquals(1, output.size());
    assertEquals("TTTTTTTTTTTT", S(output.get(0).getReadBases()));
}

Example 5 with SoftClipEvidence

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

the class NonReferenceContigAssemblerTest method should_call_simple_fwd_RP.

@Test
public void should_call_simple_fwd_RP() {
    ProcessingContext pc = getContext();
    pc.getAssemblyParameters().k = 4;
    SAMEvidenceSource ses = SES(100, 200);
    DiscordantReadPair e = (DiscordantReadPair) NRRP(ses, withSequence("ACGTGGTCGACC", DP(0, 50, "12M", true, 1, 1, "12M", false)));
    List<SAMRecord> output = go(pc, true, e);
    assertEquals(1, output.size());
    SoftClipEvidence ass = SoftClipEvidence.create(AES(ses), FWD, output.get(0));
    assertEquals(e.getBreakendSummary().localBreakend(), ass.getBreakendSummary());
    assertEquals("ACGTGGTCGACC", S(ass.getBreakendSequence()));
    assertEquals("", S(ass.getAnchorSequence()));
}