Examples with AssemblyRegion org.broadinstitute.hellbender.engine.AssemblyRegion used on opensource projects

Example 11 with AssemblyRegion

use of org.broadinstitute.hellbender.engine.AssemblyRegion in project gatk by broadinstitute.

the class AssemblyResultSetUnitTest method testTrimTo.

@Test(dataProvider = "trimmingData")
public void testTrimTo(final Map<Haplotype, AssemblyResult> haplotypesAndResultSets, final AssemblyRegion original) {
    final AssemblyResultSet subject = new AssemblyResultSet();
    for (final Map.Entry<Haplotype, AssemblyResult> entry : haplotypesAndResultSets.entrySet()) subject.add(entry.getKey(), entry.getValue());
    subject.setRegionForGenotyping(original);
    final SimpleInterval originalLocation = original.getExtendedSpan();
    final int length = originalLocation.size();
    final SimpleInterval newLocation = new SimpleInterval(originalLocation.getContig(), originalLocation.getStart() + length / 2, originalLocation.getEnd() - length / 2);
    final AssemblyRegion newRegion = original.trim(newLocation);
    final Map<Haplotype, Haplotype> originalHaplotypesByTrimmed = new HashMap<>(haplotypesAndResultSets.size());
    for (final Haplotype h : haplotypesAndResultSets.keySet()) originalHaplotypesByTrimmed.put(h.trim(newRegion.getExtendedSpan()), h);
    final AssemblyResultSet trimmed = subject.trimTo(newRegion);
    Assert.assertFalse(subject.wasTrimmed());
    Assert.assertTrue(trimmed.wasTrimmed());
    for (final Haplotype h : trimmed.getHaplotypeList()) {
        Assert.assertEquals(h.getGenomeLocation(), newLocation);
        Assert.assertEquals(h.getBases().length, newLocation.size());
    }
}

Example 12 with AssemblyRegion

use of org.broadinstitute.hellbender.engine.AssemblyRegion in project gatk by broadinstitute.

the class ReadThreadingAssemblerUnitTest method assemble.

private List<Haplotype> assemble(final ReadThreadingAssembler assembler, final byte[] refBases, final SimpleInterval loc, final List<GATKRead> reads) {
    final Haplotype refHaplotype = new Haplotype(refBases, true);
    final Cigar c = new Cigar();
    c.add(new CigarElement(refHaplotype.getBases().length, CigarOperator.M));
    refHaplotype.setCigar(c);
    final AssemblyRegion activeRegion = new AssemblyRegion(loc, null, true, 0, header);
    activeRegion.addAll(reads);
    //        logger.warn("Assembling " + activeRegion + " with " + engine);
    final AssemblyResultSet assemblyResultSet = assembler.runLocalAssembly(activeRegion, refHaplotype, refBases, loc, Collections.<VariantContext>emptyList(), null, header);
    return assemblyResultSet.getHaplotypeList();
}

Example 13 with AssemblyRegion

use of org.broadinstitute.hellbender.engine.AssemblyRegion in project gatk-protected by broadinstitute.

the class AssemblyBasedCallerUtils method assemblyRegionWithWellMappedReads.

// create the assembly using just high quality reads (eg Q20 or higher).  We may want to use lower
// quality reads in the PairHMM downstream, so we can't use a ReadFilter
public static AssemblyRegion assemblyRegionWithWellMappedReads(final AssemblyRegion originalAssemblyRegion, final int minMappingQuality, final SAMFileHeader readsHeader) {
    final AssemblyRegion result = new AssemblyRegion(originalAssemblyRegion.getSpan(), originalAssemblyRegion.getSupportingStates(), originalAssemblyRegion.isActive(), originalAssemblyRegion.getExtension(), readsHeader);
    originalAssemblyRegion.getReads().stream().filter(rec -> rec.getMappingQuality() >= minMappingQuality).forEach(result::add);
    return result;
}