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Work around for GSA-513: ClassCastException in VariantEval

This commit is contained in:
Mark DePristo 2012-08-23 18:14:10 -04:00
parent f1166d6d00
commit 1999b95754
1 changed files with 16 additions and 6 deletions
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22
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
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@ -45,12 +45,22 @@ public class AlleleCount extends VariantStratifier {
if (eval != null) { if (eval != null) {
int AC = 0; // by default, the site is considered monomorphic int AC = 0; // by default, the site is considered monomorphic
if ( eval.hasAttribute(VCFConstants.MLE_ALLELE_COUNT_KEY) && eval.isBiallelic() ) { try {
// the MLEAC is allowed to be larger than the AN (e.g. in the case of all PLs being 0, the GT is ./. but the exact model may arbitrarily choose an AC>1) if ( eval.isBiallelic() ) {
AC = Math.min(eval.getAttributeAsInt(VCFConstants.MLE_ALLELE_COUNT_KEY, 0), nchrom); if ( eval.hasAttribute(VCFConstants.MLE_ALLELE_COUNT_KEY) ) {
} else if ( eval.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) && eval.isBiallelic() ) { // the MLEAC is allowed to be larger than the AN (e.g. in the case of all PLs being 0, the GT is ./. but the exact model may arbitrarily choose an AC>1)
AC = eval.getAttributeAsInt(VCFConstants.ALLELE_COUNT_KEY, 0); AC = Math.min(eval.getAttributeAsInt(VCFConstants.MLE_ALLELE_COUNT_KEY, 0), nchrom);
} else if ( eval.isVariant() ) { } else if ( eval.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) ) {
AC = eval.getAttributeAsInt(VCFConstants.ALLELE_COUNT_KEY, 0);
}
}
} catch ( ClassCastException e ) {
// protect ourselves from bad inputs
// TODO -- fully decode VC
}
if ( AC == 0 && eval.isVariant() ) {
// fall back to the direct calculation
for (Allele allele : eval.getAlternateAlleles()) for (Allele allele : eval.getAlternateAlleles())
AC = Math.max(AC, eval.getCalledChrCount(allele)); AC = Math.max(AC, eval.getCalledChrCount(allele));
} }