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

Example 6 with FittedRegion

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

the class ExtendDiploidTest method testDubiousRegionGetsIncludedFromRight.

@Test
public void testDubiousRegionGetsIncludedFromRight() {
    final FittedRegion somaticLeft = createValidSomatic(1, 10000, 3.0, 30, SegmentSupport.BND);
    final FittedRegion dubious = createDubiousRegion(10001, 20000, 2.0, 10);
    final FittedRegion somaticRight = createValidSomatic(20001, 30000, 3.0, 40, SegmentSupport.NONE);
    final List<CombinedRegion> result = PURE_VICTIM.extendDiploid(Lists.newArrayList(somaticLeft, dubious, somaticRight));
    assertEquals(1, result.size());
    assertRegion(1, 30000, 3, result.get(0));
}

Example 7 with FittedRegion

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

the class ExtendDiploidTest method testTowardsCentromere.

@Test
public void testTowardsCentromere() {
    final FittedRegion somaticLeft = createValidSomatic(1, 10000, 3.0, 50, SegmentSupport.BND);
    final FittedRegion dubious1 = createDubiousRegion(10001, 11000, 2.0, 11);
    final FittedRegion dubious2 = createDubiousRegion(11001, 12000, 2.0, 11);
    final FittedRegion dubious3 = createDubiousRegion(12001, 20000, 2.0, 11);
    final FittedRegion somaticRight = createValidSomatic(20001, 30000, 3.0, 40, SegmentSupport.CENTROMERE);
    final List<CombinedRegion> result = PURE_VICTIM.extendDiploid(Lists.newArrayList(somaticLeft, dubious1, dubious2, dubious3, somaticRight));
    assertEquals(2, result.size());
    assertRegion(1, 20000, 3, result.get(0));
    assertRegion(20001, 30000, 3, result.get(1));
}

Example 8 with FittedRegion

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

the class ExtendDiploidTest method testCentromereIsDubious.

@Test
public void testCentromereIsDubious() {
    final FittedRegion valid = createValidSomatic(1, 10000, 1, 1, SegmentSupport.TELOMERE);
    final FittedRegion dubiousCentromere = createRegion(10001, 20000, 2, 2, 0, SegmentSupport.CENTROMERE);
    final FittedRegion dubious1 = createRegion(20001, 30000, 3, 3, 0, SegmentSupport.NONE);
    final FittedRegion dubious2 = createRegion(30001, 40000, 4, 4, 0, SegmentSupport.NONE);
    final List<CombinedRegion> result = PURE_VICTIM.extendDiploid(Lists.newArrayList(valid, dubiousCentromere, dubious1, dubious2));
    assertEquals(2, result.size());
    assertRegion(1, 10000, 1, result.get(0));
    assertRegion(10001, 40000, 4, result.get(1));
}

Example 9 with FittedRegion

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

the class ExtendDiploidTest method testInvalidGermlineIsKeptWithSVSupport.

@Test
public void testInvalidGermlineIsKeptWithSVSupport() {
    final FittedRegion somatic = createFittedRegion(1, 10000, 3.0, GermlineStatus.DIPLOID, SegmentSupport.BND);
    final FittedRegion germline = createFittedRegion(10001, 20000, 4.0, GermlineStatus.AMPLIFICATION, SegmentSupport.BND);
    final List<FittedRegion> regions = Lists.newArrayList(somatic, germline);
    final List<CombinedRegion> result = PURE_VICTIM.extendDiploid(regions);
    assertEquals(2, result.size());
    assertRegion(1, 10000, 3, result.get(0));
    assertRegion(10001, 20000, 4, result.get(1));
}

Example 10 with FittedRegion

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

the class ExtendDiploidTest method testInvalidGermlineGetsIgnored.

@Test
public void testInvalidGermlineGetsIgnored() {
    final FittedRegion somatic = createFittedRegion(1, 10000, 3.0, GermlineStatus.DIPLOID, SegmentSupport.BND);
    final FittedRegion germline = createFittedRegion(10001, 20000, 4, GermlineStatus.AMPLIFICATION, SegmentSupport.NONE);
    final List<FittedRegion> regions = Lists.newArrayList(somatic, germline);
    final List<CombinedRegion> result = PURE_VICTIM.extendDiploid(regions);
    assertEquals(1, result.size());
    assertRegion(1, 20000, 3, result.get(0));
}