thisPileup = thisContext.getExtendedEventPileup();
else if (thisContext.hasBasePileup())
thisPileup = thisContext.getBasePileup();
else
thisPileup = null;
<BUG>if (thisPileup != null) {
scoreRA.add( scoreReadsAgainstHaplotypes(haplotypes, thisPileup, contextSize, locus) ); // Taking the simple average of all sample's score since the score can be negative and the RMS doesn't make sense
}</BUG>
}
}

thisPileup = thisContext.getExtendedEventPileup();
else if (thisContext.hasBasePileup())
thisPileup = thisContext.getBasePileup();
else
thisPileup = null;
if (thisPileup != null) {
if (vc.isSNP())
scoreRA.add( scoreReadsAgainstHaplotypes(haplotypes, thisPileup, contextSize, locus) ); // Taking the simple average of all sample's score since the score can be negative and the RMS doesn't make sense
else if (vc.isIndel() || vc.isMixed()) {
Double d = scoreIndelsAgainstHaplotypes(thisPileup);
if (d == null)
return null;
scoreRA.add( d ); // Taking the simple average of all sample's score since the score can be negative and the RMS doesn't make sense
