Examples with IntegrationTestSpec org.broadinstitute.hellbender.utils.test.IntegrationTestSpec used on opensource projects

Example 41 with IntegrationTestSpec

use of org.broadinstitute.hellbender.utils.test.IntegrationTestSpec in project gatk by broadinstitute.

the class ValidateVariantsIntegrationTest method testComplexEventsDictError.

@Test
public void testComplexEventsDictError() throws IOException {
    IntegrationTestSpec spec = new IntegrationTestSpec(baseTestString(false, "complexEvents_incompatibleDict.vcf", false, ALL), 0, UserException.IncompatibleSequenceDictionaries.class);
    spec.executeTest("test validating complex events", this);
}

Example 42 with IntegrationTestSpec

use of org.broadinstitute.hellbender.utils.test.IntegrationTestSpec in project gatk by broadinstitute.

the class ValidateVariantsIntegrationTest method testBadChrCount1.

@Test
public void testBadChrCount1() throws IOException {
    IntegrationTestSpec spec = new IntegrationTestSpec(baseTestString(false, "validationExampleBad.vcf", false, CHR_COUNTS), 0, UserException.FailsStrictValidation.class);
    spec.executeTest("test bad chr counts #1", this);
}

Example 43 with IntegrationTestSpec

use of org.broadinstitute.hellbender.utils.test.IntegrationTestSpec in project gatk by broadinstitute.

the class ValidateVariantsIntegrationTest method testBadID.

@Test
public void testBadID() throws IOException {
    final IntegrationTestSpec spec = new IntegrationTestSpec(baseTestString(false, "validationExampleBadRSID.vcf", false, IDS) + " --dbsnp " + hg19_chr1_1M_dbSNP_modified, 0, UserException.FailsStrictValidation.class);
    spec.executeTest("test bad RS ID", this);
}

Example 44 with IntegrationTestSpec

use of org.broadinstitute.hellbender.utils.test.IntegrationTestSpec in project gatk by broadinstitute.

the class ValidateVariantsIntegrationTest method testBadAllele.

@Test
public void testBadAllele() throws IOException {
    IntegrationTestSpec spec = new IntegrationTestSpec(baseTestString(false, "validationExampleBad.vcf", false, ALLELES), 0, UserException.FailsStrictValidation.class);
    spec.executeTest("test bad alt allele", this);
}

Example 45 with IntegrationTestSpec

use of org.broadinstitute.hellbender.utils.test.IntegrationTestSpec in project gatk by broadinstitute.

the class ValidateVariantsIntegrationTest method testMissingReference.

@Test
public void testMissingReference() throws IOException {
    IntegrationTestSpec spec = new IntegrationTestSpec(baseTestStringWithoutReference(false, "validationExampleBad.vcf", false, REF), 0, UserException.MissingReference.class);
    spec.executeTest("test bad ref base #1", this);
}