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Adding integration test to cover errors from my previous commit (GENOTYPE_GIVEN_ALLELE bugs reported by Sara Pulit and Chris Hartl)

This commit is contained in:
Eric Banks 2012-03-13 12:43:40 -04:00
parent 5d7c761784
commit 6e18ecfc9a
1 changed files with 10 additions and 0 deletions
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10
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
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@ -313,6 +313,16 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
executeTest("test MultiSample Phase1 indels with complicated records", spec4);
}
@Test
public void testWithIndelAllelesPassedIn5() {
final String vcf = "small.indel.test.vcf";
WalkerTest.WalkerTestSpec spec4 = new WalkerTest.WalkerTestSpec(
baseCommandIndelsb37 + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + validationDataLocation + vcf + " -I " + validationDataLocation +
"NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam -o %s -L " + validationDataLocation + vcf, 1,
Arrays.asList("7d069596597aee5e0d562964036141eb"));
executeTest("test GENOTYPE_GIVEN_ALLELES with no evidence in reads", spec4);
}
@Test
public void testSnpEffAnnotationRequestedWithoutRodBinding() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(