use of com.hartwig.hmftools.healthchecker.result.BaseResult in project hmftools by hartwigmedical.
the class AmberCheckerTest method extractDataFromAmberWorksForSomatic.
@Test
public void extractDataFromAmberWorksForSomatic() throws IOException {
final RunContext runContext = TestRunContextFactory.forSomaticTest(BASE_DIRECTORY, REF_SAMPLE, TUMOR_SAMPLE);
final BaseResult result = checker.run(runContext);
assertEquals(CheckType.AMBER, result.checkType());
final HealthCheck check = ((SingleValueResult) result).check();
assertCheck(check, "0.4951");
}
use of com.hartwig.hmftools.healthchecker.result.BaseResult in project hmftools by hartwigmedical.
the class StrelkaCheckerTest method canAnalyseTypicalSomaticVariantVCF.
@Test
public void canAnalyseTypicalSomaticVariantVCF() throws IOException {
final RunContext runContext = TestRunContextFactory.forSomaticTest(RUN_DIRECTORY, REF_SAMPLE, TUMOR_SAMPLE);
final BaseResult result = checker.run(runContext);
final List<HealthCheck> checks = ((MultiValueResult) result).checks();
Assert.assertEquals(CheckType.STRELKA, result.checkType());
assertEquals(EXPECTED_NUM_CHECKS, checks.size());
assertCheck(checks, StrelkaCheck.SOMATIC_SNP_COUNT.toString(), 990);
assertCheck(checks, StrelkaCheck.SOMATIC_SNP_DBSNP_COUNT.toString(), 820);
assertCheck(checks, StrelkaCheck.SOMATIC_INDEL_COUNT.toString(), 67);
assertCheck(checks, StrelkaCheck.SOMATIC_INDEL_DBSNP_COUNT.toString(), 42);
assertCheck(checks, StrelkaCheck.SOMATIC_MNP_COUNT.toString(), 1);
assertCheck(checks, StrelkaCheck.SOMATIC_MNP_DBSNP_COUNT.toString(), 0);
}
use of com.hartwig.hmftools.healthchecker.result.BaseResult in project hmftools by hartwigmedical.
the class PurpleCheckerTest method extractDataFromPurpleWorksForSomatic.
@Test
public void extractDataFromPurpleWorksForSomatic() throws IOException {
final RunContext runContext = TestRunContextFactory.forSomaticTest(BASE_DIRECTORY, REF_SAMPLE, TUMOR_SAMPLE);
final BaseResult result = checker.run(runContext);
Assert.assertEquals(CheckType.PURPLE, result.checkType());
final List<HealthCheck> checks = ((MultiValueResult) result).checks();
assertCheck(checks, PurpleCheck.AMBER_GENDER.toString(), "MALE");
assertCheck(checks, PurpleCheck.COBALT_GENDER.toString(), "FEMALE");
assertCheck(checks, PurpleCheck.PURPLE_SEGMENT_SCORE.toString(), "199");
}
use of com.hartwig.hmftools.healthchecker.result.BaseResult in project hmftools by hartwigmedical.
the class StrelkaCheckerTest method runsCorrectlyForSingleSample.
@Test
public void runsCorrectlyForSingleSample() throws IOException {
final RunContext runContext = TestRunContextFactory.forSingleSampleTest(RUN_DIRECTORY, REF_SAMPLE);
final BaseResult result = checker.run(runContext);
assertTrue(result instanceof NoResult);
}
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