Examples with SegmentedGenome org.broadinstitute.hellbender.tools.exome.SegmentedGenome used on opensource projects

Example 6 with SegmentedGenome

use of org.broadinstitute.hellbender.tools.exome.SegmentedGenome in project gatk-protected by broadinstitute.

the class AlleleFractionDataUnitTest method testData.

@Test
public void testData() {
    final List<AllelicCount> ac = new ArrayList<>();
    final List<SimpleInterval> segments = new ArrayList<>();
    // segment 0: hets 0-2
    segments.add(new SimpleInterval("chr", 1, 5));
    ac.add(new AllelicCount(new SimpleInterval("chr", 1, 1), 0, 5));
    ac.add(new AllelicCount(new SimpleInterval("chr", 2, 2), 5, 0));
    ac.add(new AllelicCount(new SimpleInterval("chr", 3, 3), 5, 5));
    // segment 1: hets 3-4
    segments.add(new SimpleInterval("chr", 10, 15));
    ac.add(new AllelicCount(new SimpleInterval("chr", 10, 10), 1, 1));
    ac.add(new AllelicCount(new SimpleInterval("chr", 11, 11), 2, 2));
    final Genome genome = new Genome(AlleleFractionSimulatedData.TRIVIAL_TARGETS, ac);
    final SegmentedGenome segmentedGenome = new SegmentedGenome(segments, genome);
    final AlleleFractionData dc = new AlleleFractionData(segmentedGenome);
    Assert.assertEquals(dc.getNumSegments(), 2);
    Assert.assertEquals(dc.getRefCount(0), 0);
    Assert.assertEquals(dc.getAltCount(0), 5);
    Assert.assertEquals(dc.getReadCount(2), 10);
    Assert.assertEquals(dc.getReadCount(3), 2);
    Assert.assertEquals(dc.getRefCount(4), 2);
    Assert.assertEquals(dc.getAltCount(4), 2);
    Assert.assertEquals(dc.getAllelicCount(0).getAltReadCount(), 5);
    Assert.assertEquals(dc.getAllelicCount(1).getAltReadCount(), 0);
    Assert.assertEquals(dc.getAllelicCount(3).getRefReadCount(), 1);
    Assert.assertEquals(dc.getAllelicCount(4).getRefReadCount(), 2);
    Assert.assertEquals(dc.getCountsInSegment(0).get(1).getRefReadCount(), 5);
    Assert.assertEquals(dc.getCountsInSegment(0).get(1).getAltReadCount(), 0);
    final List<Integer> hetsInSegment0 = dc.getHetsInSegment(0);
    Assert.assertEquals(hetsInSegment0.size(), 3);
    Assert.assertEquals((int) hetsInSegment0.get(0), 0);
    Assert.assertEquals((int) hetsInSegment0.get(2), 2);
    final List<Integer> hetsInSegment1 = dc.getHetsInSegment(1);
    Assert.assertEquals(hetsInSegment1.size(), 2);
    Assert.assertEquals((int) hetsInSegment1.get(0), 3);
    Assert.assertEquals((int) hetsInSegment1.get(1), 4);
}