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made all data members public. 

switched logOddsVarRef to LOD.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@118 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2009-03-20 16:44:17 +00:00
parent 9b5e5e06f9
commit 1161c261ac
1 changed files with 11 additions and 11 deletions
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22
playground/java/src/org/broadinstitute/sting/utils/AlleleFrequencyEstimate.java
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@ -4,29 +4,29 @@ import org.broadinstitute.sting.gatk.walkers.AlleleFrequencyWalker;
public class AlleleFrequencyEstimate { public class AlleleFrequencyEstimate {
//AlleleFrequencyEstimate(); //AlleleFrequencyEstimate();
char ref; public char ref;
char alt; public char alt;
int N; public int N;
double qhat; public double qhat;
double qstar; public double qstar;
double logOddsVarRef; public double LOD;
public double getQstar() { public double getQstar() {
return qstar; return qstar;
} }
public double getLogOddsVarRef() { public double getLOD() {
return logOddsVarRef; 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.ref = ref;
this.alt = alt; this.alt = alt;
this.N = N; this.N = N;
this.qhat = qhat; this.qhat = qhat;
this.qstar = qstar; this.qstar = qstar;
this.logOddsVarRef = logOddsVarRef; this.LOD = LOD;
} }
public String asString() { public String asString() {
@ -39,4 +39,4 @@ public class AlleleFrequencyEstimate {
long numRefBases = N - numNonrefBases; long numRefBases = N - numNonrefBases;
return AlleleFrequencyWalker.repeat(ref, numRefBases) + AlleleFrequencyWalker.repeat(alt, numNonrefBases); return AlleleFrequencyWalker.repeat(ref, numRefBases) + AlleleFrequencyWalker.repeat(alt, numNonrefBases);
} }
} }