diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index 07b2f0566..ec62c4bfd 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -257,34 +257,40 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { } @Test - public void testWithIndelAllelesPassedIn() { + public void testWithIndelAllelesPassedIn1() { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1, Arrays.asList("408d3aba4d094c067fc00a43992c2292")); executeTest("test MultiSample Pilot2 indels with alleles passed in", spec1); + } + @Test + public void testWithIndelAllelesPassedIn2() { WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1, - Arrays.asList("94977d6e42e764280e9deaf4e3ac8c80")); + Arrays.asList("5e4e09354410b76fc0d822050d84132a")); executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec2); + } + + @Test + public void testWithIndelAllelesPassedIn3() { WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec( baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "ALL.wgs.union_v2.20101123.indels.sites.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,080,000", 1, - Arrays.asList("e66b7321e2ac91742ad3ef91040daafd")); + Arrays.asList("c599eedbeb422713b8a28529e805e4ae")); executeTest("test MultiSample Pilot2 indels with complicated records", spec3); + } + @Test + public void testWithIndelAllelesPassedIn4() { WalkerTest.WalkerTestSpec spec4 = new WalkerTest.WalkerTestSpec( baseCommandIndelsb37 + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "ALL.wgs.union_v2_chr20_100_110K.20101123.indels.sites.vcf -I " + validationDataLocation + "phase1_GBR_realigned.chr20.100K-110K.bam -o %s -L 20:100,000-110,000", 1, - Arrays.asList("37e891bf1ac40caec9ea228f39c27e44")); + Arrays.asList("37d908a682ac269f8f19dec939ff5b01")); executeTest("test MultiSample 1000G Phase1 indels with complicated records emitting all sites", spec4); - } - - - }