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Merge pull request #1557 from broadinstitute/rhl_ggvcfs_input_prior_1532 

Total ploidy does not have to equal to the number of priors
This commit is contained in:
Ron Levine 2017-02-20 22:21:25 -05:00 committed by GitHub
parent c55c77ab27 3c347c1385
commit b9a43cc35e
2 changed files with 10 additions and 2 deletions
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2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/CustomAFPriorProvider.java
View File

@ -86,8 +86,6 @@ public class CustomAFPriorProvider extends AFPriorProvider {
@Override @Override
protected double[] buildPriors(final int totalPloidy) { protected double[] buildPriors(final int totalPloidy) {
if (totalPloidy != priors.length - 1)
throw new IllegalStateException("requesting an invalid prior total ploidy " + totalPloidy + " != " + (priors.length - 1));
return priors; return priors;
} }
} }

10
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
View File

@ -700,4 +700,14 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
spec.disableShadowBCF(); spec.disableShadowBCF();
executeTest("testHomRefHighMQ", spec); executeTest("testHomRefHighMQ", spec);
} }
@Test
public void testInputPrior() {
final WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -V " + privateTestDir + "gvcfExample1.vcf -V " + privateTestDir + "gvcfExample2.vcf " +
"-L 1:69485-69791 -inputPrior 0.2 -inputPrior 0.2 -inputPrior 0.2 -inputPrior 0.2", b37KGReference),
Collections.singletonList("860d133262160bbc75ce5849e5fa491f"));
spec.disableShadowBCF();
executeTest("testInputPrior", spec);
}
} }