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adding a catch for the exception thrown by samtools when it attempts to close /dev/null in the performance tests. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3186 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-04-16 17:41:48 +00:00
parent bbb83859cd
commit be7cbf948b
2 changed files with 33 additions and 8 deletions
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16
java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java
View File

@ -1,5 +1,6 @@
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;
@ -8,8 +9,8 @@ import java.util.ArrayList;
public class IndelRealignerPerformanceTest extends WalkerTest { public class IndelRealignerPerformanceTest extends WalkerTest {
@Test @Test
public void testRealigner() { public void testRealigner() {
WalkerTestSpec spec1 = new WalkerTestSpec( WalkerTestSpec spec1 = new WalkerTestSpec(
"-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" + "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" +
" -T IndelRealigner" + " -T IndelRealigner" +
" -LOD 5" + " -LOD 5" +
@ -24,8 +25,11 @@ public class IndelRealignerPerformanceTest extends WalkerTest {
" -O /dev/null", " -O /dev/null",
0, 0,
new ArrayList<String>(0)); new ArrayList<String>(0));
executeTest("testRealignerTargetCreatorWholeGenome", spec1); try {
executeTest("testRealignerTargetCreatorWholeGenome", spec1);
} catch (RuntimeIOException 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( WalkerTestSpec spec2 = new WalkerTestSpec(
"-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" + "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" +
" -T IndelRealigner" + " -T IndelRealigner" +
@ -41,6 +45,10 @@ public class IndelRealignerPerformanceTest extends WalkerTest {
" -O /dev/null", " -O /dev/null",
0, 0,
new ArrayList<String>(0)); new ArrayList<String>(0));
executeTest("testRealignerTargetCreatorWholeExome", spec2); try {
executeTest("testRealignerTargetCreatorWholeExome", spec2);
} catch (RuntimeIOException e) {
// using /dev/null as an output source causes samtools to fail when it closes the stream, we shouldn't sweat it
}
} }
} }

25
java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java
View File

@ -1,5 +1,6 @@
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;
@ -19,7 +20,11 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
" -recalFile /dev/null", " -recalFile /dev/null",
0, 0,
new ArrayList<String>(0)); new ArrayList<String>(0));
executeTest("testCountCovariatesWholeGenome", spec); 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
}
} }
@Test @Test
@ -34,7 +39,11 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
" -recalFile /dev/null", " -recalFile /dev/null",
0, 0,
new ArrayList<String>(0)); new ArrayList<String>(0));
executeTest("testCountCovariatesWholeExome", spec); 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
}
} }
@Test @Test
@ -49,7 +58,11 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
" -outputBam /dev/null", " -outputBam /dev/null",
0, 0,
new ArrayList<String>(0)); new ArrayList<String>(0));
executeTest("testTableRecalibratorWholeGenome", spec); try {
executeTest("testTableRecalibratorWholeGenome", 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
@ -64,6 +77,10 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
" -outputBam /dev/null", " -outputBam /dev/null",
0, 0,
new ArrayList<String>(0)); new ArrayList<String>(0));
executeTest("testTableRecalibratorWholeExome", spec); try {
executeTest("testTableRecalibratorWholeExome", 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
}
} }
} }