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Fix integration test affected by non-calling all-zero PL samples, and add a more complicated multi-sample integration test from a phase 1 case, GBR with mixed technologies and complex input alleles

This commit is contained in:
Guillermo del Angel 2011-09-09 20:44:47 -04:00
parent e95d484757
commit b399424a9c
1 changed files with 9 additions and 1 deletions
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10
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
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@ -18,6 +18,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER -glm BOTH --dbsnp " + b36dbSNP129;
private final static String baseCommandIndels = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER -glm INDEL --dbsnp " + b36dbSNP129;
private final static String baseCommandIndelsb37 = "-T UnifiedGenotyper -R " + b37KGReference + " -NO_HEADER -glm INDEL --dbsnp " + b37dbSNP132;
// --------------------------------------------------------------------------------------------------------------
//
@ -28,7 +29,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSamplePilot1() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1,
Arrays.asList("149e6ad9b3fd23551254a691286a96b3"));
Arrays.asList("4bd3e874d071c4df250dce32cf441aab"));
executeTest("test MultiSample Pilot1", spec);
}
@ -276,7 +277,14 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
Arrays.asList("e66b7321e2ac91742ad3ef91040daafd"));
executeTest("test MultiSample Pilot2 indels with complicated records", spec3);
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("b6c3f771e8844a64681187ebb2b620f1"));
executeTest("test MultiSample 1000G Phase1 indels with complicated records emitting all sites", spec4);
}
}