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Merge pull request #1197 from broadinstitute/ts_ve_nullPointer 

Prevent null pointer exception in PrintMissingComp module
This commit is contained in:
ldgauthier 2015-11-02 14:42:50 -05:00
parent 54ab65a340 33462c7b50
commit 3d1dc303b3
2 changed files with 22 additions and 4 deletions
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18
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalIntegrationTest.java
View File

@ -701,4 +701,22 @@ public class VariantEvalIntegrationTest extends WalkerTest {
tests.add(new Object[]{"genotypes/genotypes", evalGenotypes, compGenotypes, "73790b530595fcbd467a88475ea9717f"}); tests.add(new Object[]{"genotypes/genotypes", evalGenotypes, compGenotypes, "73790b530595fcbd467a88475ea9717f"});
return tests.toArray(new Object[][]{}); return tests.toArray(new Object[][]{});
} }
@Test
public void testPrintMissingComp() {
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-eval " + privateTestDir + "validationReportEval.noGenotypes.vcf",
"--comp " + privateTestDir + "validationReportComp.noGenotypes.vcf",
"-L 20",
"-EV PrintMissingComp"
),
0,
Arrays.asList("d41d8cd98f00b204e9800998ecf8427e")); // sato: make sure it doesn't throw a null pointer exception.
executeTest("testPrintMissingComp", spec);
}
} }

8
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/PrintMissingComp.java
View File

@ -25,6 +25,7 @@
package org.broadinstitute.gatk.tools.walkers.varianteval.evaluators; package org.broadinstitute.gatk.tools.walkers.varianteval.evaluators;
import org.apache.commons.lang.ObjectUtils;
import org.broadinstitute.gatk.utils.contexts.AlignmentContext; import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
import org.broadinstitute.gatk.utils.contexts.ReferenceContext; import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
@ -32,9 +33,9 @@ import org.broadinstitute.gatk.tools.walkers.varianteval.util.Analysis;
import org.broadinstitute.gatk.tools.walkers.varianteval.util.DataPoint; import org.broadinstitute.gatk.tools.walkers.varianteval.util.DataPoint;
import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
@Analysis(name = "PrintMissingComp", description = "the overlap between eval and comp sites") @Analysis(name = "PrintMissingComp", description = "count the number of comp SNP sites that are not in eval")
public class PrintMissingComp extends VariantEvaluator { public class PrintMissingComp extends VariantEvaluator {
@DataPoint(description = "number of eval sites outside of comp sites", format = "%d") @DataPoint(description = "number of comp SNP sites outside of eval sites", format = "%d")
public long nMissing = 0; public long nMissing = 0;
public String getName() { public String getName() {
@ -49,9 +50,8 @@ public class PrintMissingComp extends VariantEvaluator {
final boolean compIsGood = comp != null && comp.isNotFiltered() && comp.isSNP(); final boolean compIsGood = comp != null && comp.isNotFiltered() && comp.isSNP();
final boolean evalIsGood = eval != null && eval.isSNP(); final boolean evalIsGood = eval != null && eval.isSNP();
if ( compIsGood & ! evalIsGood ) { if ( compIsGood && !evalIsGood ) {
nMissing++; nMissing++;
super.getWalker().getLogger().info("MissingFrom" + eval.toString() + " is missing from " + comp.getSource());
} }
} }
} }