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Updating integration tests to deal with the new GL framework. Now multi-allelic indel calls are correct.

This commit is contained in:
Eric Banks 2012-03-16 12:50:39 -04:00
parent dce6b91f7d
commit 7424041a17
1 changed files with 9 additions and 3 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

12
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
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@ -60,7 +60,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultipleSNPAlleles() { public void testMultipleSNPAlleles() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl -NO_HEADER -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + validationDataLocation + "multiallelic.snps.bam -o %s -L " + validationDataLocation + "multiallelic.snps.intervals", 1, "-T UnifiedGenotyper -R " + b37KGReference + " -nosl -NO_HEADER -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + validationDataLocation + "multiallelic.snps.bam -o %s -L " + validationDataLocation + "multiallelic.snps.intervals", 1,
Arrays.asList("5af005255240a2186f04cb50851b8b6f")); Arrays.asList("0de4aeed6a52f08ed86a7642c812478b"));
executeTest("test Multiple SNP alleles", spec); executeTest("test Multiple SNP alleles", spec);
} }
@ -300,7 +300,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "ALL.wgs.union_v2.20101123.indels.sites.vcf -I " + validationDataLocation + 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, "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,080,000", 1,
Arrays.asList("2609675a356f2dfc86f8a1d911210978")); Arrays.asList("0d226004e283291e60436fda8e305b8d"));
executeTest("test MultiSample Pilot2 indels with complicated records", spec3); executeTest("test MultiSample Pilot2 indels with complicated records", spec3);
} }
@ -309,10 +309,16 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec4 = new WalkerTest.WalkerTestSpec( 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 + 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, "phase1_GBR_realigned.chr20.100K-110K.bam -o %s -L 20:100,000-110,000", 1,
Arrays.asList("4fdd8da77167881b71b3547da5c13f94")); Arrays.asList("372f26842c77680aaf9ee2ab64334742"));
executeTest("test MultiSample Phase1 indels with complicated records", spec4); executeTest("test MultiSample Phase1 indels with complicated records", spec4);
} }
// --------------------------------------------------------------------------------------------------------------
//
// testing SnpEff
//
// --------------------------------------------------------------------------------------------------------------
@Test @Test
public void testSnpEffAnnotationRequestedWithoutRodBinding() { public void testSnpEffAnnotationRequestedWithoutRodBinding() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(