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

Example 16 with ProcessingContext

use of au.edu.wehi.idsv.ProcessingContext 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 17 with ProcessingContext

use of au.edu.wehi.idsv.ProcessingContext 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 18 with ProcessingContext

use of au.edu.wehi.idsv.ProcessingContext 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 19 with ProcessingContext

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

the class StaticDeBruijnPathGraphGexfExporterTest method positional_should_export_dot.

@Test
@Category(Hg19Tests.class)
public void positional_should_export_dot() throws IOException {
    File output = new File(super.testFolder.getRoot(), "chr12-244000.vcf");
    setReference(Hg19Tests.findHg19Reference("chr12.fa"));
    createInput(new File("src/test/resources/chr12-244000.tagged.bam"));
    BuildBamIndex bbi = new BuildBamIndex();
    bbi.instanceMain(new String[] { "I=" + input.getAbsolutePath() });
    ProcessingContext pc = getCommandlineContext();
    SAMEvidenceSource ses = new SAMEvidenceSource(pc, input, null, 0);
    AssemblyEvidenceSource aes = new AssemblyEvidenceSource(pc, ImmutableList.of(ses), output);
    aes.assembleBreakends(null);
    File dir = new File(super.testFolder.getRoot(), "visualisation");
    File[] export = dir.listFiles((FileFilter) new WildcardFileFilter("*.dot"));
    // TODO: change graph write timing
    assertTrue(export != null && export.length > 0);
}

Example 20 with ProcessingContext

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

the class AssembleBreakends method doWork.

@Override
public int doWork(ExecutorService threadpool) throws IOException {
    IOUtil.assertFileIsWritable(OUTPUT);
    ProcessingContext pc = getContext();
    List<SAMEvidenceSource> sources = getSamEvidenceSources();
    AssemblyEvidenceSource assembler = new AssemblyEvidenceSource(pc, sources, OUTPUT);
    assembler.assembleBreakends(threadpool);
    return 0;
}