Examples with MultiAllelicResultFilter org.molgenis.data.annotation.core.filter.MultiAllelicResultFilter used on opensource projects

Example 1 with MultiAllelicResultFilter

use of org.molgenis.data.annotation.core.filter.MultiAllelicResultFilter in project molgenis by molgenis.

the class MultiAllelicResultFilterTest method filterResultsTest9.

@Test
public void filterResultsTest9() {
    MultiAllelicResultFilter filter = new MultiAllelicResultFilter(Collections.singletonList(attributeFactory.create().setName("annotation").setDataType(STRING)), vcfAttributes);
    Optional<Entity> result = filter.filterResults(Collections.singletonList(resultEntity7), entity7, false);
    assertEquals(Lists.newArrayList(result.asSet()).get(0).getString("annotation"), "13");
}

Example 2 with MultiAllelicResultFilter

use of org.molgenis.data.annotation.core.filter.MultiAllelicResultFilter in project molgenis by molgenis.

the class MultiAllelicResultFilterTest method filterResultsTest10.

@Test
public void filterResultsTest10() {
    MultiAllelicResultFilter filter = new MultiAllelicResultFilter(Collections.singletonList(attributeFactory.create().setName("annotation").setDataType(STRING)), vcfAttributes);
    Optional<Entity> result = filter.filterResults(Collections.singletonList(resultEntity8), entity8, false);
    assertEquals(Lists.newArrayList(result.asSet()).get(0).getString("annotation"), "15");
}

Example 3 with MultiAllelicResultFilter

use of org.molgenis.data.annotation.core.filter.MultiAllelicResultFilter in project molgenis by molgenis.

the class MultiAllelicResultFilterTest method filterResultsTest6.

@Test
public void filterResultsTest6() {
    MultiAllelicResultFilter filter = new MultiAllelicResultFilter(Collections.singletonList(attributeFactory.create().setName("annotation").setDataType(STRING)), vcfAttributes);
    Optional<Entity> result6 = filter.filterResults(Collections.singletonList(resultEntity2), entity2, false);
    assertEquals(Lists.newArrayList(result6.asSet()).get(0).getString("annotation"), ".,2");
}

Example 4 with MultiAllelicResultFilter

use of org.molgenis.data.annotation.core.filter.MultiAllelicResultFilter in project molgenis by molgenis.

the class MultiAllelicResultFilterTest method filterResultsMergeMultilineMismatchPos.

@Test
public void filterResultsMergeMultilineMismatchPos() {
    MultiAllelicResultFilter filter = new MultiAllelicResultFilter(Collections.singletonList(attributeFactory.create().setName("annotation").setDataType(STRING)), true, vcfAttributes);
    try {
        filter.filterResults(Arrays.asList(entityMismatchPos, resultEntity10), entity10, false);
        Assert.fail("Should throw exception for mismatching positions");
    } catch (MolgenisDataException actual) {
        assertEquals(actual.getMessage(), "Mismatch in location! Location{chrom=1, pos=101} vs Location{chrom=1, pos=100}");
    }
}

Example 5 with MultiAllelicResultFilter

use of org.molgenis.data.annotation.core.filter.MultiAllelicResultFilter in project molgenis by molgenis.

the class MultiAllelicResultFilterTest method filterResultsTest5.

@Test
public void filterResultsTest5() {
    MultiAllelicResultFilter filter = new MultiAllelicResultFilter(Collections.singletonList(attributeFactory.create().setName("annotation").setDataType(STRING)), vcfAttributes);
    Optional<Entity> result5 = filter.filterResults(Collections.singletonList(resultEntity5), entity3, false);
    assertEquals(Lists.newArrayList(result5.asSet()).get(0).getString("annotation"), "8,9,7");
}