Examples with SeqVertex org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SeqVertex used on opensource projects

Example 1 with SeqVertex

use of org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SeqVertex in project gatk-protected by broadinstitute.

the class ReadThreadingAssemblerUnitTest method testMismatchInFirstKmer.

@Test
public void testMismatchInFirstKmer() {
    final TestAssembler assembler = new TestAssembler(3);
    final String ref = "ACAACTGA";
    final String alt = "AGCTGA";
    assembler.addSequence(ref.getBytes(), true);
    assembler.addSequence(alt.getBytes(), false);
    final SeqGraph graph = assembler.assemble();
    graph.simplifyGraph();
    graph.removeSingletonOrphanVertices();
    final Set<SeqVertex> sources = graph.getSources();
    final Set<SeqVertex> sinks = graph.getSinks();
    Assert.assertEquals(sources.size(), 1);
    Assert.assertEquals(sinks.size(), 1);
    Assert.assertNotNull(graph.getReferenceSourceVertex());
    Assert.assertNotNull(graph.getReferenceSinkVertex());
    final List<KBestHaplotype> paths = new KBestHaplotypeFinder(graph);
    Assert.assertEquals(paths.size(), 1);
}

Example 2 with SeqVertex

use of org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SeqVertex in project gatk by broadinstitute.

the class ReadThreadingAssemblerUnitTest method testMismatchInFirstKmer.

@Test
public void testMismatchInFirstKmer() {
    final TestAssembler assembler = new TestAssembler(3);
    final String ref = "ACAACTGA";
    final String alt = "AGCTGA";
    assembler.addSequence(ref.getBytes(), true);
    assembler.addSequence(alt.getBytes(), false);
    final SeqGraph graph = assembler.assemble();
    graph.simplifyGraph();
    graph.removeSingletonOrphanVertices();
    final Set<SeqVertex> sources = graph.getSources();
    final Set<SeqVertex> sinks = graph.getSinks();
    Assert.assertEquals(sources.size(), 1);
    Assert.assertEquals(sinks.size(), 1);
    Assert.assertNotNull(graph.getReferenceSourceVertex());
    Assert.assertNotNull(graph.getReferenceSinkVertex());
    final List<KBestHaplotype> paths = new KBestHaplotypeFinder(graph);
    Assert.assertEquals(paths.size(), 1);
}