1. Don't print out values in filter field of the VCF.

2. Fix ratio printouts (for params file)
3. Rename ratio filter's get counts method to avoid confusion; more changes on the way this week.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1616 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/filters/RatioFilter.java

@@ -37,7 +37,7 @@ public abstract class RatioFilter implements VariantExclusionCriterion {
         highThreshold = threshold;
     }
 
-    protected abstract Pair<Integer, Integer> scoreVariant(char ref, ReadBackedPileup pileup, RodGeliText variant);
+    protected abstract Pair<Integer, Integer> getRatioCounts(char ref, ReadBackedPileup pileup, RodGeliText variant);
     protected abstract boolean excludeHetsOnly();
 
     public boolean useZeroQualityReads() { return false; }
@@ -48,7 +48,7 @@ public abstract class RatioFilter implements VariantExclusionCriterion {
         char ref = context.getReferenceContext().getBase();
 
         ReadBackedPileup pileup = new ReadBackedPileup(ref, context.getAlignmentContext(useZeroQualityReads()));
-        Pair<Integer, Integer> counts = scoreVariant(ref, pileup, variant);
+        Pair<Integer, Integer> counts = getRatioCounts(ref, pileup, variant);
 
         boolean highGenotypeConfidence = variant.getConsensusConfidence() > minGenotypeConfidenceToTest;
         boolean excludable = !excludeHetsOnly() || GenotypeUtils.isHet((AllelicVariant)variant);
@@ -68,10 +68,10 @@ public abstract class RatioFilter implements VariantExclusionCriterion {
 
     // TODO - this whole calculation needs to be redone correctly
     private boolean pointEstimateExclude(Pair<Integer, Integer> counts) {
-        if ( counts.first + counts.second < minDepthOfCoverage )
+        int n = counts.first + counts.second;
+        if ( n < minDepthOfCoverage )
             return false;
 
-        int n = counts.first + counts.second;
         double ratio = counts.first.doubleValue() / (double)n;
         return !passesThreshold(ratio);
     }

java/src/org/broadinstitute/sting/gatk/walkers/filters/VECAlleleBalance.java

@@ -31,7 +31,7 @@ public class VECAlleleBalance extends RatioFilter {
      * Return the count of bases matching the major (first) and minor (second) alleles as a pair.
      *
      */
-    protected Pair<Integer, Integer> scoreVariant(char ref, ReadBackedPileup pileup, RodGeliText variant) {
+    protected Pair<Integer, Integer> getRatioCounts(char ref, ReadBackedPileup pileup, RodGeliText variant) {
         final String genotype = variant.getBestGenotype();
         final String bases = pileup.getBases();
 
@@ -47,7 +47,7 @@ public class VECAlleleBalance extends RatioFilter {
         int refCount = a == ref ? aCount : bCount;
         int altCount = a == ref ? bCount : aCount;
 
-        ratio = (double)refCount / (double)altCount;
+        ratio = (double)refCount / (double)(refCount + altCount);
         return new Pair<Integer, Integer>(refCount, altCount);
     }
 
@@ -69,7 +69,7 @@ public class VECAlleleBalance extends RatioFilter {
     }
 
     public String getVCFFilterString() {
-        return "AlleleBalance" + ratio;
+        return "AlleleBalance";
     }
 
 }

java/src/org/broadinstitute/sting/gatk/walkers/filters/VECDepthOfCoverage.java

@@ -47,7 +47,7 @@ public class VECDepthOfCoverage implements VariantExclusionCriterion {
     }
 
     public String getVCFFilterString() {
-        return "DoC" + depth;
+        return "DoC";
     }
 
     public boolean useZeroQualityReads() { return false; }

java/src/org/broadinstitute/sting/gatk/walkers/filters/VECFisherStrand.java

@@ -48,7 +48,7 @@ public class VECFisherStrand implements VariantExclusionCriterion {
     }
 
     public String getVCFFilterString() {
-        return "strand" + pValue;
+        return "strand";
     }
 
     public boolean useZeroQualityReads() { return false; }

java/src/org/broadinstitute/sting/gatk/walkers/filters/VECLodThreshold.java

@@ -36,6 +36,6 @@ public class VECLodThreshold implements VariantExclusionCriterion {
     }
 
     public String getVCFFilterString() {
-        return "LOD" + lod;
+        return "LOD";
     }
 }

java/src/org/broadinstitute/sting/gatk/walkers/filters/VECMappingQuality.java

@@ -42,7 +42,7 @@ public class VECMappingQuality implements VariantExclusionCriterion {
     }
 
     public String getVCFFilterString() {
-        return "MQ" + rms;
+        return "MQ";
     }
 
     public boolean useZeroQualityReads() { return true; }

java/src/org/broadinstitute/sting/gatk/walkers/filters/VECMappingQualityZero.java

@@ -42,7 +42,7 @@ public class VECMappingQualityZero implements VariantExclusionCriterion {
     }
 
     public String getVCFFilterString() {
-        return "MQzero" + mq0Count;
+        return "MQzero";
     }
 
     public boolean useZeroQualityReads() { return true; }

java/src/org/broadinstitute/sting/gatk/walkers/filters/VECOnOffGenotypeRatio.java

@@ -26,7 +26,7 @@ public class VECOnOffGenotypeRatio extends RatioFilter {
      * best genotype).  On are in the first field, off in the second.
      *
     */
-    protected Pair<Integer, Integer> scoreVariant(char ref, ReadBackedPileup pileup, RodGeliText variant) {
+    protected Pair<Integer, Integer> getRatioCounts(char ref, ReadBackedPileup pileup, RodGeliText variant) {
         final String genotype = variant.getBestGenotype().toUpperCase();
         final String bases = pileup.getBases();
 
@@ -44,7 +44,7 @@ public class VECOnOffGenotypeRatio extends RatioFilter {
             //System.out.printf("count = %d, on=%d, off=%d for %c in %s%n", count, on, off, base, genotype);            
         }
 
-        ratio = (double)on / (double)off;
+        ratio = (double)on / (double)(on + off);
         return new Pair<Integer, Integer>(on, off);
     }
 
@@ -65,6 +65,6 @@ public class VECOnOffGenotypeRatio extends RatioFilter {
     }
 
     public String getVCFFilterString() {
-        return "onOffGenotype" + ratio;
+        return "onOffGenotype";
     }
 }