From 824c2bbac07b0dc76f59e132e164389e9e07196d Mon Sep 17 00:00:00 2001 From: ebanks Date: Tue, 22 Jun 2010 17:21:38 +0000 Subject: [PATCH] Finishing previous checkin git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3608 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/TrioGenotyperWalker.java | 2 +- .../UnifiedGenotyperIntegrationTest.java | 20 ------------------- 2 files changed, 1 insertion(+), 21 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/TrioGenotyperWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/TrioGenotyperWalker.java index 16ca66dfc..13a55d176 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/TrioGenotyperWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/TrioGenotyperWalker.java @@ -81,7 +81,7 @@ public class TrioGenotyperWalker extends RefWalker{ private VCFWriter writer = null; public void initialize() { - UGEngine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, null, null); + UGEngine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, null); // initialize the header FAMILY_MEMBERS = Arrays.asList(mom, dad, kid); diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index 03e8d6c76..ad8b43641 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -112,26 +112,6 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { executeTest("testConfidence2", spec2); } - // -------------------------------------------------------------------------------------------------------------- - // - // testing beagle output - // - // -------------------------------------------------------------------------------------------------------------- - @Test - public void testOtherOutput() { - WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T UnifiedGenotyper" + - " -R " + oneKGLocation + "reference/human_b36_both.fasta" + - " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam" + - " -varout /dev/null" + - " -beagle %s" + - " -L 1:10,023,400-10,024,000", - 1, - Arrays.asList("0a6f06f1900c2b965a1d0ac413df8151")); - - executeTest(String.format("testOtherOutput"), spec); - } - // -------------------------------------------------------------------------------------------------------------- // // testing other output formats