From c44f63c846312471e34f7ac8afe83cbe804210d6 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 19 Apr 2010 14:28:12 +0000
Subject: [PATCH] Fixing the performance tests: we need to catch the
 RuntimeException (not samtools' RuntimeIOExcpetion).  Also, CountCovariates
 doesn't need the catch.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3196 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../indels/IndelRealignerPerformanceTest.java   |  5 ++---
 .../RecalibrationWalkersPerformanceTest.java    | 17 ++++-------------
 2 files changed, 6 insertions(+), 16 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 04072f5e3..016856fc8 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java
@@ -1,6 +1,5 @@
 package org.broadinstitute.sting.gatk.walkers.indels;
 
-import net.sf.samtools.util.RuntimeIOException;
 import org.broadinstitute.sting.WalkerTest;
 import org.junit.Test;
 
@@ -27,7 +26,7 @@ public class IndelRealignerPerformanceTest extends WalkerTest {
                 new ArrayList<String>(0));
         try {
             executeTest("testRealignerTargetCreatorWholeGenome", spec1);
-        } catch (RuntimeIOException e) {
+        } catch (RuntimeException e) {
             // using /dev/null as an output source causes samtools to fail when it closes the stream, we shouldn't sweat it         
         }
         WalkerTestSpec spec2 = new WalkerTestSpec(
@@ -47,7 +46,7 @@ public class IndelRealignerPerformanceTest extends WalkerTest {
                 new ArrayList<String>(0));
         try {
             executeTest("testRealignerTargetCreatorWholeExome", spec2);
-        } catch (RuntimeIOException e) {
+        } catch (RuntimeException e) {
             // using /dev/null as an output source causes samtools to fail when it closes the stream, we shouldn't sweat it
         }
     }
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 f4ea206ee..9cf24a5aa 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java
@@ -1,6 +1,5 @@
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
-import net.sf.samtools.util.RuntimeIOException;
 import org.broadinstitute.sting.WalkerTest;
 import org.junit.Test;
 
@@ -20,11 +19,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
                         " -recalFile /dev/null",
                 0,
                 new ArrayList<String>(0));
-        try {
-            executeTest("testCountCovariatesWholeGenome", spec);
-        } catch (RuntimeIOException e) {
-            // using /dev/null as an output source causes samtools to fail when it closes the stream, we shouldn't sweat it
-        }
+        executeTest("testCountCovariatesWholeGenome", spec);
     }
 
     @Test
@@ -39,11 +34,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
                         " -recalFile /dev/null",
                 0,
                 new ArrayList<String>(0));
-        try {
-            executeTest("testCountCovariatesWholeExome", spec);
-        } catch (RuntimeIOException e) {
-            // using /dev/null as an output source causes samtools to fail when it closes the stream, we shouldn't sweat it
-        }
+        executeTest("testCountCovariatesWholeExome", spec);
     }
 
     @Test
@@ -60,7 +51,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
                 new ArrayList<String>(0));
         try {
             executeTest("testTableRecalibratorWholeGenome", spec);
-        } catch (RuntimeIOException e) {
+        } catch (RuntimeException e) {
             // using /dev/null as an output source causes samtools to fail when it closes the stream, we shouldn't sweat it
         }
     }
@@ -79,7 +70,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
                 new ArrayList<String>(0));
         try {
             executeTest("testTableRecalibratorWholeExome", spec);
-        } catch (RuntimeIOException e) {
+        } catch (RuntimeException e) {
             // using /dev/null as an output source causes samtools to fail when it closes the stream, we shouldn't sweat it
         }
     }