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Merge pull request #1403 from broadinstitute/rhl_ggvcf_max_num_pls 

Add integration test using -maxNumPLValues for GenotypeGVCFs
This commit is contained in:
Ron Levine 2016-06-08 12:54:19 -04:00
parent f0f482c1fe ba2e7be05b
commit 050bcbb06b
1 changed files with 15 additions and 2 deletions
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17
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
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@ -122,7 +122,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
" -L " + privateTestDir + "tetraploid-gvcfs.intervals", b37KGReference),
1,
Arrays.asList("64fa89f20ee25df21ad20ce4ada7e7ad"));
executeTest("combineSingleSamplePipelineGVCF", spec);
executeTest("testTetraploidRun", spec);
}
@Test(enabled= true)
@ -134,7 +134,20 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
" -L " + privateTestDir + "tetraploid-gvcfs.intervals", b37KGReference),
1,
Arrays.asList("b1d93f4cd93093c208be2c9842f38d12"));
executeTest("combineSingleSamplePipelineGVCF", spec);
executeTest("testMixedPloidyRun", spec);
}
@Test(enabled= true)
public void testMixedPloidyMaxNumPLValuesRun() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -V:sample1 " + privateTestDir + "haploid-gvcf-1.vcf" +
" -V:sample2 " + privateTestDir + "tetraploid-gvcf-2.vcf" +
" -V:sample3 " + privateTestDir + "diploid-gvcf-3.vcf" +
" -L " + privateTestDir + "tetraploid-gvcfs.intervals" +
" -maxNumPLValues 3", b37KGReference),
1,
Arrays.asList("c0dcf62fb116c4c0baabe432eceea52c"));
executeTest("testMixedPloidyMaxNumPLValuesRun", spec);
}
@Test(enabled = true)