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In AlleleCount stratification, check to make sure the AC (or MLEAC) is valid (i.e. not higher than number of chromosomes) and throw a User Error if it isn't. Added a test for bad AC.

This commit is contained in:
Eric Banks 2012-08-14 15:02:30 -04:00
parent 8e3774fb0e
commit 87e41c83c5
2 changed files with 19 additions and 0 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
View File

@ -51,6 +51,10 @@ public class AlleleCount extends VariantStratifier {
AC = Math.max(AC, eval.getCalledChrCount(allele));
}
// make sure that the AC isn't invalid
if ( AC > eval.getCalledChrCount() )
throw new UserException.MalformedVCF(String.format("The AC or MLEAC value (%d) at position %s:%d is larger than the possible called chromosome count (%d)", AC, eval.getChr(), eval.getStart(), eval.getCalledChrCount()));
return Collections.singletonList((Object) AC);
} else {
return Collections.emptyList();

15
public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
View File

@ -585,6 +585,21 @@ public class VariantEvalIntegrationTest extends WalkerTest {
executeTest("testStandardIndelEval", spec);
}
@Test
public void testBadACValue() {
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-eval " + privateTestDir + "vcfexample.withBadAC.vcf",
"-noST -ST AlleleCount",
"-noEV -EV VariantSummary"
),
0,
UserException.class);
executeTest("testBadACValue", spec);
}
@Test()
public void testIncompatibleEvalAndStrat() {