Examples with InMemoryReferenceSequenceFile au.edu.wehi.idsv.picard.InMemoryReferenceSequenceFile used on opensource projects

Example 6 with InMemoryReferenceSequenceFile

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

the class SAMRecordUtilTest method unclipExactReferenceMatches_should_unclip_entire_read.

@Test
public void unclipExactReferenceMatches_should_unclip_entire_read() {
    String refStr = "TAAATTGGAACACTATACCAAAACATTAACCAGCATAGCAGTATATAAGGTTAAACATTAAATAACCCCTGGCTTAACTAACTCTCCAATTGCACTTTCTATAAGTAATTGTTGTTTAGACTTTATTAATTCAGATGTTTCAGACATGTCTTATATACACAAGAGAATTTCATTTCTCTTT";
    String readStr = "AAATTGGAACACTATACCAAAACATTAACCAGCATAGCAGTATATAAGGTTAAACATTAAATAACCCCTGGCTTAACTAACTCTCCAATTGCACTTTCTATAAGTAATTGTTGTTTAGACTTTATTAATTC";
    InMemoryReferenceSequenceFile ref = new InMemoryReferenceSequenceFile(new String[] { "Contig" }, new byte[][] { B(refStr) });
    SAMRecord r = new SAMRecord(new SAMFileHeader());
    r.getHeader().setSequenceDictionary(ref.getSequenceDictionary());
    r.setReferenceIndex(0);
    r.setCigarString("97M34S");
    r.setAlignmentStart(2);
    r.setReadNegativeStrandFlag(false);
    r.setReadBases(B(readStr));
    SAMRecordUtil.unclipExactReferenceMatches(ref, r);
    assertEquals("131M", r.getCigarString());
}

Example 7 with InMemoryReferenceSequenceFile

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

the class AssemblyEvidenceSourceTest method should_realign_very_poor_matches_to_the_reference.

@Test
// TODO: should we even do this? How much of this is covered by SingleReadEvidence.isReference()?
@Ignore("Enhancement")
public void should_realign_very_poor_matches_to_the_reference() {
    String refStr = "TAAATTGGAACACTATACCAAAACATTAACCAGCATAGCAGTATATAAGGTTAAACATTAAATAACCCCTGGCTTAACTAACTCTCCAATTGCACTTTCTATAAGTAATTGTTGTTTAGACTTTATTAATTCAGATGTTTCAGACATGTCTTATATACACAAGAGAATTTCATTTCTCTTT";
    String readStr = "AAATTGGAACACTATACCAAAACATTAACCAGCATAGCAGTATATAAGGTTAAACATTAAATAACCCCTGGCTTAACTAACTCTCCAATTGCACTTTCTATAAGTAATTGTTGTTTAGACTTTATTAATTC";
    // 1234567890123456
    // MMMMMSSSSSSSSSS
    // sssssMMMMMMMMMM
    InMemoryReferenceSequenceFile ref = new InMemoryReferenceSequenceFile(new String[] { "Contig" }, new byte[][] { B(refStr) });
    SAMRecord r = new SAMRecord(new SAMFileHeader());
    r.getHeader().setSequenceDictionary(ref.getSequenceDictionary());
    r.setReferenceIndex(0);
    r.setCigarString("97M34S");
    r.setAlignmentStart(1);
    r.setReadNegativeStrandFlag(false);
    r.setReadBases(B(readStr));
    r.setBaseQualities(B(refStr));
    ProcessingContext pc = new ProcessingContext(new FileSystemContext(testFolder.getRoot(), 500000), reference, ref, Lists.newArrayList(), getConfig(testFolder.getRoot()));
    AssemblyEvidenceSource aes = new AssemblyEvidenceSource(pc, ImmutableList.of(SES(pc)), assemblyFile);
    SAMRecord ra = aes.transformAssembly(r);
    assertEquals(2, ra.getAlignmentStart());
    assertEquals("131M", ra.getCigarString());
}

Example 8 with InMemoryReferenceSequenceFile

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

the class SingleReadEvidenceTest method microhomology_match_bb.

public void microhomology_match_bb() {
    // 1         2         3         4
    // 1234567890123456789012345678901234567890123456789
    // AAAACCGGGCCCCAAAAAAAAAGGGGCCCGGAAAAA
    // <<<<           <<<<<<<<<
    String contig = "AAAACCGGGCCCCAAAAAAAAAGGGGCCCGGAAAAA";
    InMemoryReferenceSequenceFile ref = new InMemoryReferenceSequenceFile(new String[] { "Contig" }, new byte[][] { B(contig) });
    SAMRecord r = new SAMRecord(new SAMFileHeader());
    r.getHeader().setSequenceDictionary(getSequenceDictionary());
    r.setReferenceIndex(0);
    r.setCigarString("9S4M");
    r.setAlignmentStart(11);
    r.setReadNegativeStrandFlag(true);
    r.setReadBases(B("TTCCGGGCCCCA"));
    r.setAttribute("SA", "Contig,36,+,4S9M,0,0");
    SplitReadEvidence e = (SplitReadEvidence) asAssemblyEvidence(new MockSAMEvidenceSource(getContext(ref)), r);
    assertEquals("CCGGGCCCC", e.getHomologySequence());
    assertEquals(3, e.getHomologyAnchoredBaseCount());
    assertEquals(11, e.getBreakendSummary().nominal);
    assertEquals(26, e.getBreakendSummary().nominal2);
    assertEquals(5, e.getBreakendSummary().start);
    assertEquals(14, e.getBreakendSummary().end);
    assertEquals(23, e.getBreakendSummary().start2);
    assertEquals(32, e.getBreakendSummary().end2);
}

Example 9 with InMemoryReferenceSequenceFile

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

the class VcfBreakendSummaryTest method should_allow_colon_in_breakpoint_contig_name.

@Test
public void should_allow_colon_in_breakpoint_contig_name() {
    InMemoryReferenceSequenceFile ref = new InMemoryReferenceSequenceFile(new String[] { "HLA-A*01:04N:1-HLA-A*02:95:3388" }, new byte[][] { B("ACGT") });
    ProcessingContext pc = new ProcessingContext(getFSContext(), null, ref, new ArrayList<Header>(), getConfig());
    IdsvVariantContextBuilder builder = new IdsvVariantContextBuilder(pc);
    builder.chr("HLA-A*01:04N:1-HLA-A*02:95:3388").start(1).stop(1).alleles("A", "A.");
    builder.breakpoint(new BreakpointSummary(0, FWD, 1, 1, 1, 0, BWD, 2, 2, 2), "");
    IdsvVariantContext vc = builder.make();
    VcfBreakendSummary summary = new VcfBreakendSummary(pc, vc);
    Assert.assertEquals(0, summary.location.referenceIndex);
}

Example 10 with InMemoryReferenceSequenceFile

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

the class BreakpointHomologyTest method should_report_homology_on_both_sides.

@Test
public void should_report_homology_on_both_sides() {
    InMemoryReferenceSequenceFile ref = new InMemoryReferenceSequenceFile(new String[] { "0", "1" }, new byte[][] { B("CCCAATGGGCCC"), B("TTTAATGGGAAA") });
    // 123456789012
    // >
    // <
    BreakpointHomology bh = BreakpointHomology.calculate(ref, new BreakpointSummary(0, FWD, 6, 1, BWD, 7), "", 100, 0);
    assertEquals(6, bh.getRemoteHomologyLength() + bh.getLocalHomologyLength());
    assertEquals(3, bh.getLocalHomologyLength());
    assertEquals(3, bh.getRemoteHomologyLength());
}