zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Better error message for Petr's null pointer exception. Also added an exception integration test because I'm certain this used to work. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4319 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-09-21 13:44:40 +00:00
parent 8719dde59d
commit 547763b230
2 changed files with 31 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModel.java
View File

@ -426,7 +426,7 @@ public final class VariantGaussianMixtureModel extends VariantOptimizationModel
} else {
try {
value = Double.parseDouble( (String)vc.getAttribute( annotationKey ) );
} catch( NumberFormatException e ) {
} catch( Exception e ) {
throw new UserException.MalformedFile(vc.getName(), "No double value detected for annotation = " + annotationKey + " in variant at " + VariantContextUtils.getLocation(vc) + ", reported annotation value = " + vc.getAttribute( annotationKey ), e );
}
}

30
java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
View File

@ -1,6 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
import org.broadinstitute.sting.WalkerTest;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.junit.Test;
import java.util.*;
@ -109,4 +110,33 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
}
}
}
@Test
public void testFailWithBadAnnotation() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "lowpass.N3.chr1.raw.vcf", "" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String vcf = entry.getKey();
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
" -NO_HEADER" +
" --DBSNP " + GATKDataLocation + "dbsnp_129_b36.rod" +
" -B:hapmap,VCF " + comparisonDataLocation + "Validated/HapMap/3.2/genotypes_r27_nr.b36_fwd.vcf" +
" -weightDBSNP 0.2 -weightHapMap 1.0" +
" -T GenerateVariantClusters" +
" -B:input,VCF " + vcf +
" -L 1:50,000,000-200,000,000" +
" -qual 50.0" +
" --ignore_filter GATK_STANDARD" +
" -an QD -an HRun -an ThisAnnotationIsBAD" + // There is a bad annotation here
" -clusterFile %s",
1, // just one output file
UserException.MalformedFile.class);
executeTest("testFailWithBadAnnotation", spec);
}
}
}