From b6bceb39b029ea7bed776e49ae9fdfd3bdfcc6bb Mon Sep 17 00:00:00 2001 From: ebanks Date: Wed, 23 Jun 2010 17:00:17 +0000 Subject: [PATCH] Fixing up output for performance tests git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3619 348d0f76-0448-11de-a6fe-93d51630548a --- .../indels/IndelRealignerPerformanceTest.java | 13 +++---------- .../RecalibrationWalkersPerformanceTest.java | 3 +++ 2 files changed, 6 insertions(+), 10 deletions(-) diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java index 63b154763..31bc87931 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java @@ -21,11 +21,8 @@ public class IndelRealignerPerformanceTest extends WalkerTest { " -targetIntervals " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.realigner.intervals", 0, new ArrayList(0)); - try { - executeTest("testIndelRealignerWholeGenome", spec1); - } catch (RuntimeException e) { - // using /dev/null as an output source causes samtools to fail when it closes the stream, we shouldn't sweat it - } + executeTest("testIndelRealignerWholeGenome", spec1); + WalkerTestSpec spec2 = new WalkerTestSpec( "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" + " -T IndelRealigner" + @@ -38,10 +35,6 @@ public class IndelRealignerPerformanceTest extends WalkerTest { " -targetIntervals " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.realigner.intervals", 0, new ArrayList(0)); - try { - executeTest("testIndelRealignerWholeExome", spec2); - } catch (RuntimeException e) { - // using /dev/null as an output source causes samtools to fail when it closes the stream, we shouldn't sweat it - } + executeTest("testIndelRealignerWholeExome", spec2); } } \ No newline at end of file diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java index 9cf24a5aa..086bd6512 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java @@ -5,6 +5,7 @@ import org.junit.Test; import java.util.ArrayList; + public class RecalibrationWalkersPerformanceTest extends WalkerTest { @Test @@ -52,6 +53,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest { try { executeTest("testTableRecalibratorWholeGenome", spec); } catch (RuntimeException e) { + System.out.println("TODO: this is actually an acceptable/expected exception (trying to close dev/null/), so let's get on Picard to fix it..."); // using /dev/null as an output source causes samtools to fail when it closes the stream, we shouldn't sweat it } } @@ -71,6 +73,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest { try { executeTest("testTableRecalibratorWholeExome", spec); } catch (RuntimeException e) { + System.out.println("TODO: this is actually an acceptable/expected exception (trying to close dev/null/), so let's get on Picard to fix it..."); // using /dev/null as an output source causes samtools to fail when it closes the stream, we shouldn't sweat it } }