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Merge pull request #458 from broadinstitute/eb_dont_fail_when_using_incompatible_annotation 

Don't fail in annotations if the wrong tools are calling them, just silently skip them.
This commit is contained in:
Eric Banks 2013-12-31 21:22:26 -08:00
parent 050ca8ae09 9665f75ad4
commit 9355598129
1 changed files with 4 additions and 4 deletions
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8
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/StrandBiasBySample.java
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@ -80,12 +80,9 @@ public class StrandBiasBySample extends GenotypeAnnotation implements Experiment
final Genotype g,
final GenotypeBuilder gb,
final PerReadAlleleLikelihoodMap alleleLikelihoodMap) {
if ( g == null || !g.isCalled() || ( stratifiedContext == null && alleleLikelihoodMap == null) )
if ( ! isAppropriateInput(alleleLikelihoodMap, g) )
return;
if (alleleLikelihoodMap == null )
throw new IllegalStateException("StrandBiasBySample can only be used with likelihood based annotations in the HaplotypeCaller");
final int[][] table = FisherStrand.getContingencyTable(Collections.singletonMap(g.getSampleName(), alleleLikelihoodMap), vc);
gb.attribute(STRAND_BIAS_BY_SAMPLE_KEY_NAME, FisherStrand.getContingencyArray(table));
@ -97,4 +94,7 @@ public class StrandBiasBySample extends GenotypeAnnotation implements Experiment
@Override
public List<VCFFormatHeaderLine> getDescriptions() { return Collections.singletonList(new VCFFormatHeaderLine(getKeyNames().get(0), 4, VCFHeaderLineType.Integer, "Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.")); }
private boolean isAppropriateInput(final PerReadAlleleLikelihoodMap map, final Genotype g) {
return ! (map == null || g == null || !g.isCalled());
}
}