//double overallLog10PofNull = AFresult.log10AlleleFrequencyPosteriors[0];
final double overallLog10PofF = AFresult.getLog10LikelihoodOfAFGT0();
//if ( DEBUG_SLOD ) System.out.println("overallLog10PofF=" + overallLog10PofF);
// the forward lod
final AFCalculationResult forwardAFresult = getDirectionalAfCalcResult(AlignmentContextUtils.ReadOrientation.FORWARD,stratifiedContexts, tracker, refContext, allAllelesToUse, model, perReadAlleleLikelihoodMap);
final double forwardLog10PofNull = forwardAFresult.getLog10LikelihoodOfAFEq0();
final double forwardLog10PofF = forwardAFresult.getLog10LikelihoodOfAFGT0();
//if ( DEBUG_SLOD ) System.out.println("forwardLog10PofNull=" + forwardLog10PofNull + ", forwardLog10PofF=" + forwardLog10PofF);
// the reverse lod
final AFCalculationResult reverseAFresult = getDirectionalAfCalcResult(AlignmentContextUtils.ReadOrientation.REVERSE,stratifiedContexts, tracker, refContext, allAllelesToUse, model, perReadAlleleLikelihoodMap);
final double reverseLog10PofNull = reverseAFresult.getLog10LikelihoodOfAFEq0();
final double reverseLog10PofF = reverseAFresult.getLog10LikelihoodOfAFGT0();
//if ( DEBUG_SLOD ) System.out.println("reverseLog10PofNull=" + reverseLog10PofNull + ", reverseLog10PofF=" + reverseLog10PofF);
final double forwardLod = forwardLog10PofF + reverseLog10PofNull - overallLog10PofF;
final double reverseLod = reverseLog10PofF + forwardLog10PofNull - overallLog10PofF;
//if ( DEBUG_SLOD ) System.out.println("forward lod=" + forwardLod + ", reverse lod=" + reverseLod);