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While this fix worked for the evaluator module, it could potentially have bad effects in the phasing walkers. Special-case nocalls in the PhasingEvaluator and return AllelePair to previous state.

This commit is contained in:
Christopher Hartl 2012-01-26 13:06:36 -05:00
parent 9c6fda7e15
commit 673ceadd11
2 changed files with 2 additions and 6 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
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@ -35,10 +35,6 @@ public class AllelePair {
private Allele bottom;
public AllelePair(Genotype gt) {
if ( gt.isNoCall() ) {
// do nothing
return;
}
if (gt.getPloidy() != 2)
throw new ReviewedStingException("AllelePair must have ploidy of 2! incoming gt was"+gt.toBriefString());

4
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java
View File

@ -119,7 +119,7 @@ public class GenotypePhasingEvaluator extends VariantEvaluator {
if (evalSampGenotypes != null)
evalSampGt = evalSampGenotypes.get(samp);
if (compSampGt == null || evalSampGt == null) { // Since either comp or eval (or both) are missing the site, the best we can do is hope to preserve phase [if the non-missing one preserves phase]
if (compSampGt == null || evalSampGt == null || compSampGt.isNoCall() || evalSampGt.isNoCall()) { // Since either comp or eval (or both) are missing the site, the best we can do is hope to preserve phase [if the non-missing one preserves phase]
// Having an unphased site breaks the phasing for the sample [does NOT permit "transitive phasing"] - hence, must reset phasing knowledge for both comp and eval [put a null CompEvalGenotypes]:
if (isNonNullButUnphased(compSampGt) || isNonNullButUnphased(evalSampGt))
samplePrevGenotypes.put(samp, null);
@ -209,7 +209,7 @@ public class GenotypePhasingEvaluator extends VariantEvaluator {
}
public boolean isNonNullButUnphased(Genotype gt) {
return (gt != null && !genotypesArePhasedAboveThreshold(gt));
return (gt != null && !gt.isNoCall() && !genotypesArePhasedAboveThreshold(gt));
}
public boolean genotypesArePhasedAboveThreshold(Genotype gt) {