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GSA-488: MLEAC > AN error when running variant eval fixed

This commit is contained in:
Mark DePristo 2012-08-16 13:00:35 -04:00
parent 4e42988c66
commit 132cdfd9c1
1 changed files with 8 additions and 3 deletions
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11
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
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@ -19,6 +19,8 @@ import java.util.*;
* it computes the AC from the genotypes themselves. If no AC can be computed, 0 is used.
*/
public class AlleleCount extends VariantStratifier {
int nchrom;
@Override
public void initialize() {
// we can only work with a single eval VCF, and it must have genotypes
@ -26,7 +28,8 @@ public class AlleleCount extends VariantStratifier {
throw new UserException.BadArgumentValue("AlleleCount", "AlleleCount stratification only works with a single eval vcf");
// There are 2 x n sample chromosomes for diploids
int nchrom = getVariantEvalWalker().getSampleNamesForEvaluation().size() * 2;
// TODO -- generalize to handle multiple ploidy
nchrom = getVariantEvalWalker().getSampleNamesForEvaluation().size() * 2;
if ( nchrom < 2 )
throw new UserException.BadArgumentValue("AlleleCount", "AlleleCount stratification requires an eval vcf with at least one sample");
@ -52,8 +55,10 @@ public class AlleleCount extends VariantStratifier {
}
// 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()));
if ( AC > nchrom )
throw new UserException.MalformedVCF(String.format("The AC or MLEAC value (%d) at position %s:%d " +
"is larger than the number of chromosomes over all samples (%d)", AC,
eval.getChr(), eval.getStart(), nchrom));
return Collections.singletonList((Object) AC);
} else {