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

Example 21 with SoftClipEvidence

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

the class PathNodeIteratorTest method should_handle_repeated_kmers.

@Test
public void should_handle_repeated_kmers() {
    SoftClipEvidence sce = SCE(FWD, withSequence("TTTTTTTTTTTTTTTT", Read(0, 5, "6M10S")));
    DirectedEvidence rp = NRRP(SES(10, 200), withSequence("CCCCCCCCCC", DP(0, 25, "10M", true, 1, 1, "10M", false)));
    List<KmerPathNode> result = asCheckedKPN(4, 100, sce, rp);
    assertCompleteGraph(result, 4);
    // SC: ref repeat; nonref repeat
    // RP: single width starting kmer <-> repeat cycle <-> single width ending kmer
    assertEquals(5, result.size());
}

Example 22 with SoftClipEvidence

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

the class PathNodeIteratorTest method should_assemble_adjacent_sc_rp.

@Test
public void should_assemble_adjacent_sc_rp() {
    SoftClipEvidence sc = SCE(FWD, withSequence("GTGGTCGACC", Read(0, 50, "4M6S")));
    DiscordantReadPair rp = (DiscordantReadPair) NRRP(SES(10, 200), withSequence("GACCT", DP(0, 25, "5M", true, 1, 1, "5M", false)));
    List<KmerPathNode> result = asCheckedKPN(5, 1000, sc, rp);
    assertCompleteGraph(result, 5);
    assertEquals(2, result.size());
    assertEquals(1, result.stream().mapToInt(n -> n.next().size()).sum());
    assertEquals(1, result.stream().mapToInt(n -> n.prev().size()).sum());
}