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add sample_name to constructor, misc bug fixes 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@665 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2009-05-12 15:10:17 +00:00
parent 0267ccae7f
commit add7b6cf65
1 changed files with 12 additions and 2 deletions
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14
java/src/org/broadinstitute/sting/playground/utils/AlleleFrequencyEstimate.java
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@ -34,17 +34,19 @@ public class AlleleFrequencyEstimate {
public String bases; public String bases;
public double[][] quals; public double[][] quals;
public double[] posteriors; public double[] posteriors;
public String sample_name;
GenomeLoc l; GenomeLoc l;
public AlleleFrequencyEstimate(GenomeLoc location, char ref, char alt, int N, double qhat, double qstar, double lodVsRef, double lodVsNextBest, double pBest, double pRef, int depth, String bases, double[][] quals, double[] posteriors)
public AlleleFrequencyEstimate(GenomeLoc location, char ref, char alt, int N, double qhat, double qstar, double lodVsRef, double lodVsNextBest, double pBest, double pRef, int depth, String bases, double[][] quals, double[] posteriors, String sample_name)
{ {
if( Double.isNaN(lodVsRef)) { System.out.printf("%s: lodVsRef is NaN\n", location.toString()); } if( Double.isNaN(lodVsRef)) { System.out.printf("%s: lodVsRef is NaN\n", location.toString()); }
if( Double.isNaN(lodVsNextBest)) { System.out.printf("lodVsNextBest is NaN\n"); } if( Double.isNaN(lodVsNextBest)) { System.out.printf("lodVsNextBest is NaN\n"); }
if( Double.isNaN(qhat)) { System.out.printf("qhat is NaN\n"); } if( Double.isNaN(qhat)) { System.out.printf("qhat is NaN\n"); }
if( Double.isNaN(qstar)) { System.out.printf("qstar is NaN\n"); } if( Double.isNaN(qstar)) { System.out.printf("qstar is NaN\n"); }
if( Double.isNaN(pBest)) { System.out.printf("pBest is NaN\n"); } if( Double.isNaN(pBest)) { System.out.printf("pBest is NaN\n"); }
if( Double.isNaN(pRef)) { System.out.printf("pRef is NaN\n"); } if( Double.isNaN(pRef)) { System.out.printf("pRef is NaN (%c %s)\n", ref, bases); }
if( Double.isInfinite(lodVsRef)) if( Double.isInfinite(lodVsRef))
{ {
@ -82,13 +84,19 @@ public class AlleleFrequencyEstimate {
this.qstar = qstar; this.qstar = qstar;
this.lodVsRef = lodVsRef; this.lodVsRef = lodVsRef;
this.lodVsNextBest = lodVsNextBest; this.lodVsNextBest = lodVsNextBest;
this.pBest = pBest;
this.pRef = pRef;
this.depth = depth; this.depth = depth;
this.notes = ""; this.notes = "";
this.bases = bases; this.bases = bases;
this.quals = quals; this.quals = quals;
this.posteriors = posteriors; this.posteriors = posteriors;
this.sample_name = sample_name;
} }
public boolean isREF() { return (this.lodVsRef <= -5.0); }
public boolean isSNP() { return (this.lodVsRef >= 5.0); }
/** Return the most likely genotype. */ /** Return the most likely genotype. */
public String genotype() public String genotype()
{ {
@ -120,9 +128,11 @@ public class AlleleFrequencyEstimate {
location.getStart(), location.getStart(),
location.getStart(), location.getStart(),
lodVsRef); lodVsRef);
s += String.format("\t;\tSAMPLE %s", sample_name);
s += String.format("\t;\tREF %c", ref); s += String.format("\t;\tREF %c", ref);
s += String.format("\t;\tALT %c", alt); s += String.format("\t;\tALT %c", alt);
s += String.format("\t;\tFREQ %f", qstar); s += String.format("\t;\tFREQ %f", qstar);
s += String.format("\t;\tGENOTYPE %s", this.genotype());
s += String.format("\t;\tDEPTH %d", depth); s += String.format("\t;\tDEPTH %d", depth);
s += String.format("\t;\tLODvsREF %f", lodVsRef); s += String.format("\t;\tLODvsREF %f", lodVsRef);
s += String.format("\t;\tLODvsNEXTBEST %f", lodVsNextBest); s += String.format("\t;\tLODvsNEXTBEST %f", lodVsNextBest);