diff --git a/playground/java/src/org/broadinstitute/sting/utils/AlleleFrequencyEstimate.java b/playground/java/src/org/broadinstitute/sting/utils/AlleleFrequencyEstimate.java index bd010e1d2..f370cffa9 100755 --- a/playground/java/src/org/broadinstitute/sting/utils/AlleleFrequencyEstimate.java +++ b/playground/java/src/org/broadinstitute/sting/utils/AlleleFrequencyEstimate.java @@ -4,29 +4,29 @@ import org.broadinstitute.sting.gatk.walkers.AlleleFrequencyWalker; public class AlleleFrequencyEstimate { //AlleleFrequencyEstimate(); - char ref; - char alt; - int N; - double qhat; - double qstar; - double logOddsVarRef; + public char ref; + public char alt; + public int N; + public double qhat; + public double qstar; + public double LOD; public double getQstar() { return qstar; } - public double getLogOddsVarRef() { - return logOddsVarRef; + public double getLOD() { + return LOD; } - public AlleleFrequencyEstimate(char ref, char alt, int N, double qhat, double qstar, double logOddsVarRef) { + public AlleleFrequencyEstimate(char ref, char alt, int N, double qhat, double qstar, double LOD) { this.ref = ref; this.alt = alt; this.N = N; this.qhat = qhat; this.qstar = qstar; - this.logOddsVarRef = logOddsVarRef; + this.LOD = LOD; } public String asString() { @@ -39,4 +39,4 @@ public class AlleleFrequencyEstimate { long numRefBases = N - numNonrefBases; return AlleleFrequencyWalker.repeat(ref, numRefBases) + AlleleFrequencyWalker.repeat(alt, numNonrefBases); } -} \ No newline at end of file +}