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

Example 16 with SoftClipEvidence

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

the class NonReferenceContigAssemblerTest method should_call_overlapping_sc_rp.

@Test
public void should_call_overlapping_sc_rp() {
    ProcessingContext pc = getContext();
    pc.getAssemblyParameters().k = 4;
    SoftClipEvidence sce = SCE(FWD, withSequence("ACGTGGTCGACC", Read(0, 50, "6M6S")));
    DiscordantReadPair e = (DiscordantReadPair) NRRP(SES(10, 200), withSequence("GACCTCTACT", DP(0, 25, "10M", true, 1, 1, "10M", false)));
    List<SAMRecord> output = go(pc, true, sce, e);
    assertEquals(1, output.size());
    assertEquals("ACGTGGTCGACCTCTACT", S(output.get(0).getReadBases()));
}

Example 17 with SoftClipEvidence

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

the class NonReferenceContigAssemblerTest method should_call_simple_fwd_SC.

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

Example 18 with SoftClipEvidence

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

the class NonReferenceContigAssemblerTest method should_truncate_anchored_polyA_expansion_fwd.

@Test
public void should_truncate_anchored_polyA_expansion_fwd() {
    ProcessingContext pc = getContext();
    pc.getAssemblyParameters().k = 4;
    SoftClipEvidence sce = SCE(FWD, withSequence("GTACAAAA", Read(0, 10, "4M4S")));
    DiscordantReadPair dp = (DiscordantReadPair) NRRP(SES(11, 100), withSequence("CAAAAT", DP(0, 1, "6M", true, 1, 1, "6M", false)));
    List<SAMRecord> output = go(pc, true, sce, dp);
    assertEquals(1, output.size());
    assertEquals("GTACAAAA", S(output.get(0).getReadBases()));
}

Example 19 with SoftClipEvidence

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

the class NonReferenceContigAssemblerTest method should_call_simple_bwd_RP.

@Test
public void should_call_simple_bwd_RP() {
    ProcessingContext pc = getContext();
    pc.getAssemblyParameters().k = 4;
    MockSAMEvidenceSource ses = SES(100, 200);
    DiscordantReadPair e = (DiscordantReadPair) NRRP(ses, withSequence("ACGTGGTCGACC", DP(0, 450, "12M", false, 1, 1, "12M", true)));
    List<SAMRecord> output = go(pc, true, e);
    assertEquals(1, output.size());
    SoftClipEvidence ass = SoftClipEvidence.create(AES(ses), BWD, output.get(0));
    assertEquals(e.getBreakendSummary().localBreakend(), ass.getBreakendSummary());
    assertEquals("ACGTGGTCGACC", S(ass.getBreakendSequence()));
    assertEquals("", S(ass.getAnchorSequence()));
}

Example 20 with SoftClipEvidence

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

the class NonReferenceContigAssemblerTest method should_call_multiple_nonoverlapping_contigs.

@Test
public void should_call_multiple_nonoverlapping_contigs() {
    ProcessingContext pc = getContext();
    pc.getAssemblyParameters().k = 4;
    SoftClipEvidence sce = SCE(FWD, withSequence("ACGTGGTCGACC", Read(0, 5, "6M6S")));
    DiscordantReadPair e = (DiscordantReadPair) NRRP(SES(100, 200), withSequence("GACCTCTACT", DP(0, 25, "10M", true, 1, 1, "10M", false)));
    List<SAMRecord> output = go(pc, true, sce, e);
    assertEquals(2, output.size());
    assertEquals("ACGTGGTCGACC", S(output.get(0).getReadBases()));
    assertEquals("NN" + "GACCTCTACT", S(output.get(1).getReadBases()));
}