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

Example 6 with SoftClipEvidence

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

the class PathNodeIteratorTest method should_overlapping_adjacent_sc_rp.

@Test
public void should_overlapping_adjacent_sc_rp() {
    SoftClipEvidence sc = SCE(FWD, withSequence("ACGTGGTCGACC", Read(0, 50, "6M6S")));
    DiscordantReadPair rp = (DiscordantReadPair) NRRP(SES(13, 200), withSequence("TCGACCTCCGGAA", DP(0, 25, "13M", true, 1, 1, "13M", false)));
    List<KmerPathNode> result = asCheckedKPN(5, 1000, sc, rp);
    assertCompleteGraph(result, 5);
    assertEquals(5, result.size());
    assertEquals(4, result.stream().mapToInt(n -> n.next().size()).sum());
    assertEquals(4, result.stream().mapToInt(n -> n.prev().size()).sum());
}

Example 7 with SoftClipEvidence

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

the class ContigCallerTest method should_assemble_overlapping_sc_rp.

@Test
public void should_assemble_overlapping_sc_rp() {
    SoftClipEvidence sc = SCE(FWD, withSequence("ACGTGGTCGACC", Read(0, 50, "6M6S")));
    DiscordantReadPair rp = (DiscordantReadPair) NRRP(SES(10, 200), withSequence("GACCTCCGGAA", DP(0, 25, "11M", true, 1, 1, "11M", false)));
    ArrayList<KmerPathNode> in = Lists.newArrayList(asKPN(4, 1000, sc, rp));
    String result = S(getCaller(in, 1000).bestContig(Integer.MAX_VALUE), 4);
    // assertEquals(3, result.size()); // SC+RP, RP starting before SC, RP starting after SC
    assertEquals("TGGTCGACCTCCGGAA", result);
// assertEquals("GACCTCCGGAA", result.get(1));
// assertEquals("GACCTCCGGAA", result.get(2));
}

Example 8 with SoftClipEvidence

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

the class ContigCallerTest method should_preference_anchored_paths.

@Test
public void should_preference_anchored_paths() {
    // both sides anchored
    SoftClipEvidence spanf = SCE(FWD, withSequence("TGTTAATTGT", Read(0, 1, "4M6S")));
    SoftClipEvidence spanb = SCE(BWD, withSequence("TGTTAATTGT", Read(0, 7, "6S4M")));
    // start anchored
    SoftClipEvidence scf = SCE(FWD, withSequence("ACGTGGTCGACC", Read(0, 5, "6M6S")));
    // end anchored (but less support)
    SoftClipEvidence scb = SCE(BWD, withSequence("GTCAGTC", Read(0, 5, "3S4M")));
    // unanchored
    DiscordantReadPair e = (DiscordantReadPair) NRRP(SES(20, 30), withSequence("GACCTCTACT", DP(0, 25, "10M", true, 1, 1, "10M", false)));
    String result = S(getCaller(Lists.newArrayList(asKPN(4, 100, spanf, spanb, scf, scb, e)), 100).bestContig(Integer.MAX_VALUE), 4);
    // assertEquals(4, result.size());
    // only returns the unanchored kmers
    assertEquals("GTTAATTG", result);
// assertEquals("TGGTCGACC", result.get(1));
// assertEquals("GTCAGT", result.get(2));
// assertEquals("GACCTCTACT", result.get(3));
}

Example 9 with SoftClipEvidence

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

the class KmerEvidenceTest method fwd_softclip.

@Test
public void fwd_softclip() {
    SoftClipEvidence sce = SCE(FWD, withQual(new byte[] { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 }, withSequence("ACGTTATACCG", Read(0, 2, "1S4M6S"))));
    KmerEvidence e = KmerEvidence.create(4, sce);
    // int startsclength = 1;
    assertEquals(2, e.startPosition());
    assertEquals(2, e.endPosition());
    assertEquals(11 - 1 - (4 - 1), e.length());
    assertEquals(2, e.weight(0));
    assertEquals(3, e.weight(1));
    assertEquals(4, e.weight(2));
    assertEquals(5, e.weight(3));
    assertEquals(6, e.weight(4));
    assertEquals(7, e.weight(5));
    assertEquals(8, e.weight(6));
    assertEquals("CGTT", K(4, e.kmer(0)));
    assertEquals("GTTA", K(4, e.kmer(1)));
    assertEquals("TTAT", K(4, e.kmer(2)));
    assertEquals("TATA", K(4, e.kmer(3)));
    assertEquals("ATAC", K(4, e.kmer(4)));
    assertEquals("TACC", K(4, e.kmer(5)));
    assertEquals("ACCG", K(4, e.kmer(6)));
    assertTrue(e.isAnchored(0));
    assertFalse(e.isAnchored(1));
    assertFalse(e.isAnchored(2));
    assertFalse(e.isAnchored(3));
    assertFalse(e.isAnchored(4));
    assertFalse(e.isAnchored(5));
    assertFalse(e.isAnchored(6));
    assertEquals(sce.getEvidenceID(), e.evidence().getEvidenceID());
    for (int i = 0; i < e.length(); i++) {
        assertEquals(2 + i, e.node(i).lastStart());
        assertEquals(2 + i, e.node(i).lastEnd());
        assertEquals(e.isAnchored(i), e.node(i).isReference());
        assertEquals(e.kmer(i), e.node(i).lastKmer());
        assertEquals(e.weight(i), e.node(i).weight());
        assertEquals(e, e.node(i).evidence());
    }
}

Example 10 with SoftClipEvidence

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

the class KmerEvidenceTest method bwd_softclip.

@Test
public void bwd_softclip() {
    SoftClipEvidence sce = SCE(BWD, withQual(new byte[] { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 }, withSequence("ACGTTATACCG", Read(0, 2, "1S4M6S"))));
    KmerEvidence e = KmerEvidence.create(4, sce);
    assertEquals(1, e.startPosition());
    assertEquals(1, e.endPosition());
    assertEquals(11 - 6 - (4 - 1), e.length());
    assertEquals(1, e.weight(0));
    assertEquals(2, e.weight(1));
    assertEquals("ACGT", K(4, e.kmer(0)));
    assertEquals("CGTT", K(4, e.kmer(1)));
    assertFalse(e.isAnchored(0));
    assertTrue(e.isAnchored(1));
    assertEquals(sce.getEvidenceID(), e.evidence().getEvidenceID());
    for (int i = 0; i < e.length(); i++) {
        assertEquals(1 + i, e.node(i).lastStart());
        assertEquals(1 + i, e.node(i).lastEnd());
        assertEquals(e.isAnchored(i), e.node(i).isReference());
        assertEquals(e.kmer(i), e.node(i).lastKmer());
        assertEquals(e.weight(i), e.node(i).weight());
        assertEquals(e, e.node(i).evidence());
    }
}