From 3c347c138587c98c344bd303112e8ef970da7367 Mon Sep 17 00:00:00 2001 From: Ron Levine Date: Mon, 20 Feb 2017 20:28:41 -0500 Subject: [PATCH] Total ploidy does not have to equal to the number of priors --- .../tools/walkers/genotyper/CustomAFPriorProvider.java | 2 -- .../variantutils/GenotypeGVCFsIntegrationTest.java | 10 ++++++++++ 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/CustomAFPriorProvider.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/CustomAFPriorProvider.java index c43106eec..90bb95b5b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/CustomAFPriorProvider.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/CustomAFPriorProvider.java @@ -86,8 +86,6 @@ public class CustomAFPriorProvider extends AFPriorProvider { @Override 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; } } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java index 8ddfe3123..00f08851c 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java @@ -700,4 +700,14 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { spec.disableShadowBCF(); 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); + } } \ No newline at end of file