the "-genotype" option now acts correctly as a discovery mode caller in SSG

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1359 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java

@@ -135,11 +135,9 @@ public class SingleSampleGenotyper extends LocusWalker<SSGGenotypeCall, Genotype
      */
     public SSGGenotypeCall map(RefMetaDataTracker tracker, char ref, LocusContext context) {
         rationalizeSampleName(context.getReads().get(0));
-        if (context.getLocation().getStart() == 73) {
-            int stop = 1;
-        }
         ReadBackedPileup pileup = new ReadBackedPileup(ref, context);
         GenotypeLikelihoods G = callGenotype(tracker);
+        G.setDiscovery(GENOTYPE); // set it to discovery mode or variant detection mode
         SSGGenotypeCall geno = (SSGGenotypeCall)G.callGenotypes(tracker, ref, pileup);
         if (geno != null) {
             metricsOut.nextPosition(geno, tracker);
@@ -238,8 +236,8 @@ public class SingleSampleGenotyper extends LocusWalker<SSGGenotypeCall, Genotype
      *
      * @return an empty string
      */
-    public GenotypeWriter reduce(org.broadinstitute.sting.utils.genotype.calls.SSGGenotypeCall call, GenotypeWriter sum) {
+    public GenotypeWriter reduce(SSGGenotypeCall call, GenotypeWriter sum) {
-        if (call != null && call.isVariation()) {
+        if (call != null && (GENOTYPE || call.isVariation())) {
             if (call.getConfidenceScore().getScore() > LOD_THRESHOLD)
                 sum.addGenotypeCall(call);
         }

java/src/org/broadinstitute/sting/utils/genotype/calls/SSGGenotypeCall.java

@@ -88,7 +88,7 @@ public class SSGGenotypeCall implements GenotypeCall, GenotypeOutput {
 
         // reset the confidence based on either the discovery mode or the genotype mode
         for (Genotype g : genotypes) {
-            double val = (discoveryMode) ? Math.abs(likelihoods[index] - best) : Math.abs(likelihoods[index] - ref);
+            double val = (discoveryMode) ? Math.abs(likelihoods[index] - next) : Math.abs(likelihoods[index] - ref);
             ((BasicGenotype) g).setConfidenceScore(new BayesianConfidenceScore(val));
             mGenotypes.put(likelihoods[index], g);
             index++;

java/src/org/broadinstitute/sting/utils/genotype/confidence/ConfidenceScore.java

@@ -12,8 +12,11 @@ public abstract class ConfidenceScore implements Comparable<ConfidenceScore> {
     // the general error of a floating point value
     private static final Double EPSILON = 1.0e-15;
 
+    /**
+     * the method we use to generate this confidence
+     */
     public enum SCORE_METHOD {
-        LOD_SCORE, UNKNOWN;
+        LOD_SCORE, CHIP, UNKNOWN;
     }
 
     private Double mScore;

java/src/org/broadinstitute/sting/utils/genotype/variant/Variant.java

@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.utils.genotype.variant;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.genotype.confidence.ConfidenceScore;
 
 /**
  * @author aaron
@@ -12,7 +13,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 public interface Variant {
     // the types of variants we currently allow
     public enum VARIANT_TYPE {
-        SNP, INDEL, DELETION, REFERENCE
+        SNP, INDEL, DELETION, REFERENCE // though reference is not really a variant
     }
 
     /**
@@ -22,6 +23,13 @@ public interface Variant {
      */
     public VariantFrequency getFrequency();
 
+    /**
+     * get the confidence score for this variance
+     *
+     * @return the confidence score
+     */
+    public ConfidenceScore getConfidenceScore();
+
     /** @return the VARIANT_TYPE of the current variant */
     public VARIANT_TYPE getType();
 
@@ -57,7 +65,10 @@ public interface Variant {
      * @return a GenomeLoc
      */
     public GenomeLoc getLocation();
-    
-
 
+    /**
+     * get the reference base(s) at this position
+     * @return the reference base or bases, as a string
+     */
+    public String getReference();
 }