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

Example 46 with IntegrationTestSpec

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

the class ValidateVariantsIntegrationTest method testGoodFile2.

@Test
public void testGoodFile2() throws IOException {
    IntegrationTestSpec spec = new IntegrationTestSpec(baseTestString(true, hg19_chr1_1M_exampleVCF, false, ALL), Collections.emptyList());
    spec.executeTest("test good file", this);
}

Example 47 with IntegrationTestSpec

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

the class ValidateVariantsIntegrationTest method testBadChrCount2.

@Test
public void testBadChrCount2() throws IOException {
    IntegrationTestSpec spec = new IntegrationTestSpec(baseTestString(false, "validationExampleBad2.vcf", false, CHR_COUNTS), 0, UserException.FailsStrictValidation.class);
    spec.executeTest("test bad chr counts #2", this);
}

Example 48 with IntegrationTestSpec

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

the class ValidateVariantsIntegrationTest method testComplexEvents.

@Test
public void testComplexEvents() throws IOException {
    IntegrationTestSpec spec = new IntegrationTestSpec(baseTestString(false, "complexEvents.vcf", false, ALL), Collections.emptyList());
    spec.executeTest("test validating complex events", this);
}

Example 49 with IntegrationTestSpec

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

the class ValidateVariantsIntegrationTest method testBadID2_okIfIDnotInDBSNP_withoutDbDNParg.

@Test
public void testBadID2_okIfIDnotInDBSNP_withoutDbDNParg() throws IOException {
    final IntegrationTestSpec spec = new IntegrationTestSpec(baseTestString(false, "validationExampleRSIDonPositionNotInDBSNP.vcf", false, IDS), Collections.emptyList());
    spec.executeTest("test bad RS ID is OK when not in dbSNP when no dbsnp arg", this);
}

Example 50 with IntegrationTestSpec

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

the class ValidateVariantsIntegrationTest method testUnusedAlleleError.

//The problem was that a gvcf contained a variant with <NON_REF> alt and no sample had that genotype.
// This is not allowed in the vcf spec but OK in gvcf. The fix is to not fail when ALLELES is not checked.
@Test(description = "Checks '''bug''' reported in story https://www.pivotaltracker.com/story/show/68725164")
public void testUnusedAlleleError() throws IOException {
    IntegrationTestSpec spec = new IntegrationTestSpec(baseTestString(false, "validationUnusedAllelesBugFix.vcf", false, ALLELES, "1:1-739000", hg19_chr1_1M_Reference), 0, UserException.FailsStrictValidation.class);
    spec.executeTest("test unused allele bug fix", this);
}