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

Example 1 with SequentialIdGenerator

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

the class NonReferenceContigAssemblerTest method create.

private NonReferenceContigAssembler create(ProcessingContext pc, boolean collapse, DirectedEvidence... input) {
    Arrays.sort(input, DirectedEvidence.ByStartEnd);
    AssemblyEvidenceSource aes = new AssemblyEvidenceSource(pc, Arrays.stream(input).map(e -> (SAMEvidenceSource) e.getEvidenceSource()).collect(Collectors.toList()), new File("NonReferenceContigAssemblerTest.bam"));
    int maxEvidenceWidth = aes.getMaxConcordantFragmentSize() - aes.getMinConcordantFragmentSize() + 1;
    int maxReadLength = maxReadLength(input);
    int k = pc.getAssemblyParameters().k;
    int maxPathLength = pc.getAssemblyParameters().positional.maxPathLengthInBases(maxReadLength);
    int maxPathCollapseLength = pc.getAssemblyParameters().errorCorrection.maxPathCollapseLengthInBases(maxReadLength);
    tracker = new EvidenceTracker();
    SupportNodeIterator supportIt = new SupportNodeIterator(k, Arrays.stream(input).iterator(), aes.getMaxConcordantFragmentSize(), tracker, pc.getAssemblyParameters().includePairAnchors, pc.getAssemblyParameters().pairAnchorMismatchIgnoreEndBases);
    AggregateNodeIterator agIt = new AggregateNodeIterator(supportIt);
    Iterator<KmerPathNode> pnIt = new PathNodeIterator(agIt, maxPathLength, k);
    if (collapse) {
        pnIt = new PathCollapseIterator(pnIt, k, maxPathCollapseLength, pc.getAssemblyParameters().errorCorrection.maxBaseMismatchForCollapse, pc.getAssemblyParameters().errorCorrection.collapseBubblesOnly, 0);
        pnIt = new PathSimplificationIterator(pnIt, maxPathLength, maxEvidenceWidth);
    }
    caller = new NonReferenceContigAssembler(pnIt, 0, maxEvidenceWidth + maxReadLength + 2, maxReadLength, k, aes, new SequentialIdGenerator("asm"), tracker, "test");
    return caller;
}

Example 2 with SequentialIdGenerator

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

the class PositionalAssemblerTest method should_assemble_simple_forward_soft_clips.

@Test
public void should_assemble_simple_forward_soft_clips() {
    ProcessingContext pc = getContext();
    pc.getAssemblyParameters().anchorLength = 1;
    AssemblyEvidenceSource aes = AES(pc);
    pc.getAssemblyParameters().k = 4;
    List<DirectedEvidence> input = new ArrayList<DirectedEvidence>();
    // 12345678901234567890
    // ACGTTGGTTA
    // MMMMMSSSSS
    // GCAACGTTGGTTAA
    // MMMMMMMMSSSSSS
    input.add(SCE(FWD, withSequence("ACGTTGGTTA", Read(0, 10, "5M5S"))[0]));
    input.add(SCE(FWD, withSequence("TTTTTGCAACGTTGGTTAA", Read(0, 2, "13M6S"))[0]));
    input.sort(DirectedEvidenceOrder.ByStartEnd);
    List<SingleReadEvidence> r = asAssemblyEvidence(aes, Lists.newArrayList(new PositionalAssembler(pc, aes, new SequentialIdGenerator("asm"), input.iterator())));
    assertEquals(1, r.size());
    assertEquals(new BreakendSummary(0, FWD, 14), r.get(0).getBreakendSummary());
    // anchor length to match breakend length
    assertEquals("AACGTT", S(r.get(0).getAnchorSequence()));
    assertEquals("GGTTAA", S(r.get(0).getBreakendSequence()));
    assertEquals("AACGTTGGTTAA", S(r.get(0).getSAMRecord().getReadBases()));
}

Example 3 with SequentialIdGenerator

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

the class PositionalAssemblerTest method should_assemble_simple_input.

@Test
public void should_assemble_simple_input() {
    ProcessingContext pc = getContext();
    AssemblyEvidenceSource aes = AES(pc);
    pc.getAssemblyParameters().k = 4;
    List<DirectedEvidence> input = new ArrayList<DirectedEvidence>();
    input.add(SCE(BWD, Read(0, 10, "5S5M")));
    input.add(SCE(FWD, Read(0, 10, "5M5S")));
    input.add(SCE(BWD, Read(0, 100, "5S5M")));
    input.add(SCE(FWD, Read(0, 100, "5M5S")));
    input.sort(DirectedEvidenceOrder.ByStartEnd);
    ArrayList<SAMRecord> r = Lists.newArrayList(new PositionalAssembler(pc, aes, new SequentialIdGenerator("asm"), input.iterator()));
    assertEquals(4, r.size());
}

Example 4 with SequentialIdGenerator

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

the class PositionalAssemblerTest method rp_anchor_should_set_non_reference_bases_as_anchoring.

@Test
public void rp_anchor_should_set_non_reference_bases_as_anchoring() {
    ProcessingContext pc = getContext();
    pc.getAssemblyParameters().anchorLength = 1;
    AssemblyEvidenceSource aes = AES(pc);
    pc.getAssemblyParameters().k = 4;
    List<DirectedEvidence> input = new ArrayList<DirectedEvidence>();
    // 12345678901234567890
    // ACGTTGGTTA
    // MMMMMSSSSS
    // GCAACGTTGGTTAA
    // MMMMMMMMSSSSSS
    // TTTTTGCAACGTTGGTTAA
    input.add(SCE(FWD, withSequence("ACGTTGGTTA", Read(0, 10, "5M5S"))[0]));
    input.add(SCE(FWD, withSequence("TTTTTGCAACGTTGGTTAA", Read(0, 2, "13M6S"))[0]));
    input.add(NRRP(withSequence("TTTTTGCAACGTTGGTTAA", DP(0, 2, "13M6S", true, 1, 1, "19M", false))));
    input.sort(DirectedEvidenceOrder.ByStartEnd);
    List<SingleReadEvidence> r = asAssemblyEvidence(aes, Lists.newArrayList(new PositionalAssembler(pc, aes, new SequentialIdGenerator("asm"), input.iterator())));
    assertEquals(2, r.size());
    // race condition w.r.t which assembly returns first
    assertEquals(new BreakendSummary(0, FWD, 14), r.get(0).getBreakendSummary());
    // anchor length to match breakend length
    assertEquals("AACGTT", S(r.get(0).getAnchorSequence()));
    assertEquals("GGTTAA", S(r.get(0).getBreakendSequence()));
    assertEquals("AACGTTGGTTAA", S(r.get(0).getSAMRecord().getReadBases()));
}

Example 5 with SequentialIdGenerator

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

the class PositionalAssemblerTest method should_set_assembly_direction.

@Test
public void should_set_assembly_direction() {
    ProcessingContext pc = getContext();
    pc.getAssemblyParameters().k = 4;
    pc.getAssemblyParameters().maxExpectedBreakendLengthMultiple = 10;
    List<DirectedEvidence> e = new ArrayList<>();
    // ACGTACGTACGTACGTACGT
    // 12345678901234567890
    // MMMM----MMMM
    // MMMM>>>>
    e.add(SCE(FWD, withSequence("ACGTCCGGACGG", Read(1, 1, "4M8S"))[0]));
    e.add(SCE(FWD, withSequence("ACGGTTGT", Read(1, 9, "4M4S"))[0]));
    e.sort(DirectedEvidenceOrder.ByStartEnd);
    ArrayList<SAMRecord> output = Lists.newArrayList(new PositionalAssembler(pc, AES(pc), new SequentialIdGenerator("asm"), e.iterator(), BreakendDirection.Forward));
    for (SAMRecord r : output) {
        assertEquals(BreakendDirection.Forward, new AssemblyAttributes(r).getAssemblyDirection());
    }
}