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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
This commit is contained in:
ebanks 2010-04-19 14:28:12 +00:00
parent abf48cee05
commit c44f63c846
2 changed files with 6 additions and 16 deletions
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5
java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java
View File

@ -1,6 +1,5 @@
package org.broadinstitute.sting.gatk.walkers.indels; package org.broadinstitute.sting.gatk.walkers.indels;
import net.sf.samtools.util.RuntimeIOException;
import org.broadinstitute.sting.WalkerTest; import org.broadinstitute.sting.WalkerTest;
import org.junit.Test; import org.junit.Test;
@ -27,7 +26,7 @@ public class IndelRealignerPerformanceTest extends WalkerTest {
new ArrayList<String>(0)); new ArrayList<String>(0));
try { try {
executeTest("testRealignerTargetCreatorWholeGenome", spec1); 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 // 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( WalkerTestSpec spec2 = new WalkerTestSpec(
@ -47,7 +46,7 @@ public class IndelRealignerPerformanceTest extends WalkerTest {
new ArrayList<String>(0)); new ArrayList<String>(0));
try { try {
executeTest("testRealignerTargetCreatorWholeExome", spec2); 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 // using /dev/null as an output source causes samtools to fail when it closes the stream, we shouldn't sweat it
} }
} }

17
java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java
View File

@ -1,6 +1,5 @@
package org.broadinstitute.sting.gatk.walkers.recalibration; package org.broadinstitute.sting.gatk.walkers.recalibration;
import net.sf.samtools.util.RuntimeIOException;
import org.broadinstitute.sting.WalkerTest; import org.broadinstitute.sting.WalkerTest;
import org.junit.Test; import org.junit.Test;
@ -20,11 +19,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
" -recalFile /dev/null", " -recalFile /dev/null",
0, 0,
new ArrayList<String>(0)); new ArrayList<String>(0));
try { executeTest("testCountCovariatesWholeGenome", spec);
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
}
} }
@Test @Test
@ -39,11 +34,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
" -recalFile /dev/null", " -recalFile /dev/null",
0, 0,
new ArrayList<String>(0)); new ArrayList<String>(0));
try { executeTest("testCountCovariatesWholeExome", spec);
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
}
} }
@Test @Test
@ -60,7 +51,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
new ArrayList<String>(0)); new ArrayList<String>(0));
try { try {
executeTest("testTableRecalibratorWholeGenome", spec); 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 // 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)); new ArrayList<String>(0));
try { try {
executeTest("testTableRecalibratorWholeExome", spec); 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 // using /dev/null as an output source causes samtools to fail when it closes the stream, we shouldn't sweat it
} }
} }