Examples with FittedRegion com.hartwig.hmftools.common.purple.region.FittedRegion used on opensource projects

Example 21 with FittedRegion

use of com.hartwig.hmftools.common.purple.region.FittedRegion in project hmftools by hartwigmedical.

the class CombinedRegionTest method testObservedTumorRatioCountSummationOnlyAppliesToSomatic.

@Test
public void testObservedTumorRatioCountSummationOnlyAppliesToSomatic() {
    final FittedRegion somaticRegion = PurpleDatamodelTest.createDefaultFittedRegion("1", 2001, 3000).observedTumorRatioCount(2).status(GermlineStatus.DIPLOID).build();
    final CombinedRegion region = new CombinedRegion(true, somaticRegion);
    assertEquals(2, region.region().observedTumorRatioCount());
    final FittedRegion amplificationRegion = PurpleDatamodelTest.createDefaultFittedRegion("1", 1, 1000).observedTumorRatioCount(2).status(GermlineStatus.AMPLIFICATION).build();
    region.extend(amplificationRegion);
    assertEquals(2, region.region().observedTumorRatioCount());
    final FittedRegion germlineRegion = PurpleDatamodelTest.createDefaultFittedRegion("1", 1001, 2000).observedTumorRatioCount(2).status(GermlineStatus.AMPLIFICATION).build();
    region.extend(germlineRegion);
    assertEquals(2, region.region().observedTumorRatioCount());
}

Example 22 with FittedRegion

use of com.hartwig.hmftools.common.purple.region.FittedRegion in project hmftools by hartwigmedical.

the class CombinedRegionTest method doNotIncludeZeroCopyNumber.

@Test
public void doNotIncludeZeroCopyNumber() {
    final FittedRegion startRegion = create(1, 100, 200, 0.5, 0);
    CombinedRegion builder = new CombinedRegion(true, startRegion);
    assertAverages(builder, 0.5, 0);
    builder.extendWithBAFWeightedAverage(create(201, 300, 200, 1, 2));
    assertAverages(builder, 0.75, 2);
}

Example 23 with FittedRegion

use of com.hartwig.hmftools.common.purple.region.FittedRegion in project hmftools by hartwigmedical.

the class ExtendDiploidTest method testFavourTumorRatioCountOverLength.

@Test
public void testFavourTumorRatioCountOverLength() {
    final FittedRegion dubious1 = createDubiousRegion(1, 50000, 2, 10, 0);
    final FittedRegion dubious2 = createDubiousRegion(50001, 60000, 3, 20, 0);
    final List<CombinedRegion> result = PURE_VICTIM.extendDiploid(Lists.newArrayList(dubious1, dubious2));
    assertEquals(1, result.size());
    assertRegion(1, 60000, 3, result.get(0));
}

Example 24 with FittedRegion

use of com.hartwig.hmftools.common.purple.region.FittedRegion in project hmftools by hartwigmedical.

the class ExtendDiploidTest method testDubiousRegionGetsExcludedBecauseOfSV.

@Test
public void testDubiousRegionGetsExcludedBecauseOfSV() {
    final FittedRegion somaticLeft = createValidSomatic(1, 10000, 3.0, 50, SegmentSupport.BND);
    final FittedRegion dubious = createDubiousRegion(10001, 20000, 2.0, 10);
    final FittedRegion somaticRight = createValidSomatic(20001, 30000, 3.0, 40, SegmentSupport.BND);
    final List<CombinedRegion> result = PURE_VICTIM.extendDiploid(Lists.newArrayList(somaticLeft, dubious, somaticRight));
    assertEquals(3, result.size());
}

Example 25 with FittedRegion

use of com.hartwig.hmftools.common.purple.region.FittedRegion in project hmftools by hartwigmedical.

the class ExtendDiploidTest method testDubiousRegionGetsExcludedBecauseOfTooManyConsecutiveRatioCounts.

@Test
public void testDubiousRegionGetsExcludedBecauseOfTooManyConsecutiveRatioCounts() {
    final FittedRegion somaticLeft = createValidSomatic(1, 10000, 3.0, 50, SegmentSupport.BND);
    final FittedRegion dubious1 = createDubiousRegion(10001, 11000, 2.0, 20);
    final FittedRegion dubious2 = createDubiousRegion(11001, 12000, 2.0, 10);
    final FittedRegion dubious3 = createDubiousRegion(12001, 20000, 2.0, 20);
    final FittedRegion somaticRight = createValidSomatic(20001, 30000, 3.0, 40, SegmentSupport.NONE);
    final List<CombinedRegion> result = PURE_VICTIM.extendDiploid(Lists.newArrayList(somaticLeft, dubious1, dubious2, dubious3, somaticRight));
    assertEquals(3, result.size());
    assertRegion(1, 10000, 3, result.get(0));
    assertRegion(10001, 20000, 2, result.get(1));
    assertRegion(20001, 30000, 3, result.get(2));
}