From d406d9b3fc71edde3b43d656877ed0a5c9620554 Mon Sep 17 00:00:00 2001 From: ebanks Date: Mon, 31 Jan 2011 15:05:45 +0000 Subject: [PATCH] There's no reason to special case no-calls if they already have PLs associated with them. Just use the PLs! git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5136 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java | 4 ++-- .../sting/gatk/walkers/beagle/BeagleIntegrationTest.java | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java index 4bf7eb62f..edc3056a8 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java @@ -206,7 +206,7 @@ public class ProduceBeagleInputWalker extends RodWalker { /** * Use likelihoods if: is validation, prior is negative; or: is not validation, has genotype key */ - if ( (isValidation && prior < 0.0) || genotype.isCalled() && genotype.hasLikelihoods()) { + if ( (isValidation && prior < 0.0) || genotype.hasLikelihoods() ) { double[] likeArray = genotype.getLikelihoods().getAsVector(); if( isMaleOnChrX ) { likeArray[1] = -255; @@ -228,7 +228,7 @@ public class ProduceBeagleInputWalker extends RodWalker { } } - if (beagleGenotypesWriter != null) { + if ( beagleGenotypesWriter != null && genotype.isCalled() ) { char a = genotype.getAllele(0).toString().charAt(0); char b = genotype.getAllele(0).toString().charAt(0); diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java index 160a646c9..08ccbb324 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java @@ -50,7 +50,7 @@ public class BeagleIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T ProduceBeagleInput -R " + hg19Reference + " " + "-B:variant,VCF " + beagleValidationDataLocation + "inttestbgl.input.vcf " + - "-o %s", 1, Arrays.asList("c0d30e5dbe903874f8422a0e63a5118e")); + "-o %s", 1, Arrays.asList("a01c704246f3dd1b9c65774007e51e69")); executeTest("test BeagleInput", spec); }