/// <summary>
/// http://www.broadinstitute.org/gsa/wiki/index.php/Understanding_the_Unified_Genotyper%27s_VCF_files
/// See section on Strand Bias
/// </summary>
// From GATK source:
//double forwardLod = forwardLog10PofF + reverseLog10PofNull - overallLog10PofF;
//double reverseLod = reverseLog10PofF + forwardLog10PofNull - overallLog10PofF;
//
//// strand score is max bias between forward and reverse strands
//double strandScore = Math.max(forwardLod, reverseLod);
//
//// rescale by a factor of 10
//strandScore *= 10.0;
//
//attributes.put("SB", strandScore);
private static double[] AssignBiasScore(StrandBiasStats overallStats, StrandBiasStats fwdStats, StrandBiasStats rvsStats)
{
var forwardBias = (fwdStats.ChanceVarFreqGreaterThanZero * rvsStats.ChanceFalsePos) /
overallStats.ChanceVarFreqGreaterThanZero;
var reverseBias = (rvsStats.ChanceVarFreqGreaterThanZero * fwdStats.ChanceFalsePos) /
overallStats.ChanceVarFreqGreaterThanZero;
var p = Math.Max(forwardBias, reverseBias);
return(new[] { p, MathOperations.PtoGATKBiasScale(p) });
}
