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

Example 21 with DirectedEvidence

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

the class PositionalAssemblerTest method should_assemble_each_read_alignment_only_once.

@Test
public void should_assemble_each_read_alignment_only_once() {
    ProcessingContext pc = getContext();
    AssemblyEvidenceSource aes = AES(pc);
    pc.getAssemblyParameters().k = 4;
    String seq = "AACCGGTTAA";
    List<DirectedEvidence> input = new ArrayList<DirectedEvidence>();
    input.add(SCE(FWD, withSequence(seq, Read(0, 10, "5M5S"))[0]));
    input.add(SCE(FWD, withSequence(seq, Read(0, 10, "5M5S"))[0]));
    input.add(SCE(FWD, withSequence(seq, Read(0, 10, "5M5S"))[0]));
    input.add(IE(withSequence(seq, Read(0, 10, "5M100D5M"))[0]));
    input.add(IE(withSequence(seq, Read(0, 10, "5M100D5M"))[0]));
    input.add(IE(withSequence(seq, Read(0, 10, "5M100D5M"))[0]));
    input.sort(DirectedEvidenceOrder.ByStartEnd);
    ArrayList<SAMRecord> r = Lists.newArrayList(new PositionalAssembler(pc, aes, new SequentialIdGenerator("asm"), input.iterator()));
    assertEquals(2, ((int[]) r.get(0).getAttribute("sc"))[0]);
}

Example 22 with DirectedEvidence

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

the class SupportNodeIteratorTest method scrp.

public static List<DirectedEvidence> scrp(int k, String sequence, int minFragSize, int maxFragSize) {
    SAMEvidenceSource ses = SES(minFragSize, maxFragSize);
    byte[] qual = new byte[sequence.length()];
    for (int i = 0; i < qual.length; i++) {
        qual[i] = (byte) i;
    }
    List<DirectedEvidence> input = new ArrayList<DirectedEvidence>();
    for (int i = 1; i <= 100; i++) {
        input.add(SCE(FWD, ses, withQual(qual, withSequence(sequence, Read(0, i, "1S4M6S")))));
        input.add(SCE(BWD, ses, withQual(qual, withSequence(sequence, Read(0, i, "1S4M6S")))));
        input.add(NRRP(ses, withQual(qual, withSequence(sequence, DP(0, i, "1S9M1S", false, 1, 1, "11M", true)))));
        input.add(NRRP(ses, withQual(qual, withSequence(sequence, DP(0, i, "1S9M1S", false, 1, 1, "11M", false)))));
    }
    Collections.sort(input, DirectedEvidence.ByStartEnd);
    return input;
}