Don't fail in annotations if the wrong tools are calling them, just silently skip them.

This is important for cases when users want to use annotation groups (like all experimental annotations).

protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/StrandBiasBySample.java

@@ -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());
+    }
 }