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Fixing up output for performance tests 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3619 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-06-23 17:00:17 +00:00
parent 75d4736600
commit b6bceb39b0
2 changed files with 6 additions and 10 deletions
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13
java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java
View File

@ -21,11 +21,8 @@ public class IndelRealignerPerformanceTest extends WalkerTest {
" -targetIntervals " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.realigner.intervals", " -targetIntervals " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.realigner.intervals",
0, 0,
new ArrayList<String>(0)); new ArrayList<String>(0));
try { executeTest("testIndelRealignerWholeGenome", spec1);
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
}
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" +
@ -38,10 +35,6 @@ public class IndelRealignerPerformanceTest extends WalkerTest {
" -targetIntervals " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.realigner.intervals", " -targetIntervals " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.realigner.intervals",
0, 0,
new ArrayList<String>(0)); new ArrayList<String>(0));
try { executeTest("testIndelRealignerWholeExome", spec2);
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
}
} }
} }

3
java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java
View File

@ -5,6 +5,7 @@ import org.junit.Test;
import java.util.ArrayList; import java.util.ArrayList;
public class RecalibrationWalkersPerformanceTest extends WalkerTest { public class RecalibrationWalkersPerformanceTest extends WalkerTest {
@Test @Test
@ -52,6 +53,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
try { try {
executeTest("testTableRecalibratorWholeGenome", spec); executeTest("testTableRecalibratorWholeGenome", spec);
} catch (RuntimeException e) { } 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 // 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 { try {
executeTest("testTableRecalibratorWholeExome", spec); executeTest("testTableRecalibratorWholeExome", spec);
} catch (RuntimeException e) { } 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 // using /dev/null as an output source causes samtools to fail when it closes the stream, we shouldn't sweat it
} }
} }