- Cleaned up annotation code some more

- Use QualityUtils when phred-scaling now



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2217 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java

@@ -11,7 +11,7 @@ import java.util.ArrayList;
 
 public class AlleleBalance extends StandardVariantAnnotation {
 
-    public Pair<String, String> annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes) {
+    public String annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes) {
 
         if ( genotypes.size() == 0 )
             return null;
@@ -40,7 +40,7 @@ public class AlleleBalance extends StandardVariantAnnotation {
             ratio = computeSingleBalance(ref.getBase(), genotypeStr, bases);
         }
 
-        return new Pair<String, String>(getKeyName(), String.format("%.2f", ratio));
+        return String.format("%.2f", ratio);
     }
 
     public String getKeyName() { return "AB"; }

java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java

@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.Pair;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.genotype.Genotype;
 import org.broadinstitute.sting.utils.genotype.Variation;
@@ -11,9 +10,9 @@ import java.util.List;
 
 public class DepthOfCoverage extends StandardVariantAnnotation {
 
-    public Pair<String, String> annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes) {
+    public String annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes) {
         int depth = pileup.getReads().size();
-        return new Pair<String, String>(getKeyName(), String.format("%d", depth));
+        return String.format("%d", depth);
     }
 
     public String getKeyName() { return "DP"; }

java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java

@@ -1,8 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.Pair;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.genotype.Genotype;
 import org.broadinstitute.sting.utils.genotype.Variation;
@@ -14,7 +13,7 @@ import java.util.List;
 
 public class FisherStrand implements VariantAnnotation {
 
-    public Pair<String, String> annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes) {
+    public String annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes) {
 
         // this test doesn't make sense for homs
         Genotype genotype = VariantAnnotator.getFirstHetVariant(genotypes);
@@ -33,7 +32,7 @@ public class FisherStrand implements VariantAnnotation {
             return null;
 
         // use Math.abs to prevent -0's
-        return new Pair<String, String>(getKeyName(), String.format("%.1f", Math.abs(10.0 * Math.log10(pvalue))));
+        return String.format("%.1f", Math.abs(QualityUtils.phredScaleErrorRate(pvalue)));
     }
 
     public String getKeyName() { return "FisherStrand"; }

java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java

@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.Pair;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.genotype.Genotype;
@@ -12,13 +11,13 @@ import java.util.List;
 
 public class HomopolymerRun extends StandardVariantAnnotation {
 
-    public Pair<String, String> annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes) {
+    public String annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes) {
 
         if ( !variation.isBiallelic() || !variation.isSNP() )
             return null;
 
         int run = computeHomopolymerRun(variation.getAlternativeBaseForSNP(), ref);
-        return new Pair<String, String>(getKeyName(), String.format("%d", run));
+        return String.format("%d", run);
     }
 
     public String getKeyName() { return "HRun"; }

java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java

@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.Pair;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.genotype.Genotype;
 import org.broadinstitute.sting.utils.genotype.Variation;
@@ -12,14 +11,14 @@ import java.util.List;
 
 public class MappingQualityZero extends StandardVariantAnnotation {
 
-    public Pair<String, String> annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes) {
+    public String annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes) {
         List<SAMRecord> reads = pileup.getReads();
         int MQ0Count = 0;
         for (int i=0; i < reads.size(); i++) {
             if ( reads.get(i).getMappingQuality() == 0 )
                 MQ0Count++;
         }
-        return new Pair<String, String>(getKeyName(), String.format("%d", MQ0Count));
+        return String.format("%d", MQ0Count);
     }
 
     public String getKeyName() { return "MQ0"; }

java/src/org/broadinstitute/sting/gatk/walkers/annotator/PrimaryBaseSecondaryBaseSymmetry.java

@@ -28,7 +28,7 @@ public class PrimaryBaseSecondaryBaseSymmetry implements VariantAnnotation{
 
     public boolean useZeroQualityReads() { return USE_ZERO_MAPQ_READS; }
 
-    public Pair<String,String> annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes) {
+    public String annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes) {
         // todo -- this code doesn't work, should't be called
         if ( true )
             return null;
@@ -42,8 +42,7 @@ public class PrimaryBaseSecondaryBaseSymmetry implements VariantAnnotation{
                 } else {
                     //System.out.printf("refSecondBasePair = %s, nonrefPrimaryBasePair = %s%n", refSecondBasePair, nonrefPrimaryBasePair);
                     double primary_secondary_stat = refSecondBasePair.second - nonrefPrimaryBasePair.second;
-                    String annotation = String.format("%f", primary_secondary_stat);
+                    return String.format("%f", primary_secondary_stat);
-                    return new Pair<String,String>(KEY_NAME, annotation);
                 }
             } else {
                 return null;

java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java

@@ -2,7 +2,6 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
 
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.Pair;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.genotype.Genotype;
 import org.broadinstitute.sting.utils.genotype.Variation;
@@ -13,13 +12,13 @@ import java.util.List;
 
 public class RMSMappingQuality extends StandardVariantAnnotation {
 
-    public Pair<String, String> annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes) {
+    public String annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes) {
         List<SAMRecord> reads = pileup.getReads();
         int[] qualities = new int[reads.size()];
         for (int i=0; i < reads.size(); i++)
             qualities[i] = reads.get(i).getMappingQuality();
         double rms = MathUtils.rms(qualities);
-        return new Pair<String, String>(getKeyName(), String.format("%.2f", rms));
+        return String.format("%.2f", rms);
     }
 
     public String getKeyName() { return "MQ"; }

java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java

@@ -12,7 +12,7 @@ import java.util.ArrayList;
 
 public class RankSumTest implements VariantAnnotation {
 
-    public Pair<String, String> annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes) {
+    public String annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes) {
 
         if ( genotypes.size() == 0 )
             return null;
@@ -40,7 +40,7 @@ public class RankSumTest implements VariantAnnotation {
         if ( MathUtils.compareDoubles(pvalue, 0.0) == 0 )
             return null;
 
-        return new Pair<String, String>(getKeyName(), String.format("%.1f", -10.0 * Math.log10(pvalue)));
+        return String.format("%.1f", QualityUtils.phredScaleErrorRate(pvalue));
     }
 
     public String getKeyName() { return "RankSum"; }

java/src/org/broadinstitute/sting/gatk/walkers/annotator/ResidualQuality.java

@@ -1,6 +1,5 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
-import org.broadinstitute.sting.utils.Pair;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.genotype.Genotype;
@@ -22,7 +21,7 @@ public class ResidualQuality implements VariantAnnotation{
 
     public boolean useZeroQualityReads() { return true; } // for robustness
 
-    public Pair<String,String> annotate( ReferenceContext ref, ReadBackedPileup p, Variation variation, List<Genotype> genotypes) {
+    public String annotate( ReferenceContext ref, ReadBackedPileup p, Variation variation, List<Genotype> genotypes) {
 
         Character snp = getSNPChar(ref, genotypes);
         if ( snp == null ) {
@@ -35,7 +34,7 @@ public class ResidualQuality implements VariantAnnotation{
             return null;
         }
 
-        return new Pair<String,String>(KEY_NAME, String.format("%f", logResidQual ));
+        return String.format("%f", logResidQual);
     }
 
     public String getKeyName() { return KEY_NAME; }

java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java

@@ -30,7 +30,7 @@ public class SecondBaseSkew implements VariantAnnotation {
 
     public String getDescription() { return KEY_NAME + ",1,Float,\"Chi-square Secondary Base Skew\""; }
 
-    public Pair<String, String> annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes) {
+    public String annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes) {
         if ( variation.isSNP() && variation.isBiallelic() ) {
             char snp = variation.getAlternativeBaseForSNP();
 //            try {
@@ -50,7 +50,7 @@ public class SecondBaseSkew implements VariantAnnotation {
                 // System.out.println("p_transformed="+p_transformed+" e_transformed="+expected_transformed+" variantDepth="+depthProp.getFirst());
                 // System.out.println("Proportion variant bases with ref 2bb="+depthProp.getSecond()+" Expected="+proportionExpectations[0]);
                 double chi_square =  Math.signum(depthProp.getSecond() - proportionExpectations[0])*Math.min(Math.pow(p_transformed - expected_transformed, 2), Double.MAX_VALUE);
-                return new Pair<String,String>(KEY_NAME, String.format("%f", chi_square));
+                return String.format("%f", chi_square);
             }
         } else {
             return null;

java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java

@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.Pair;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.genotype.Genotype;
 import org.broadinstitute.sting.utils.genotype.Variation;
@@ -11,9 +10,9 @@ import java.util.List;
 
 public class SpanningDeletions extends StandardVariantAnnotation {
 
-    public Pair<String, String> annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes) {
+    public String annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes) {
         int deletions = pileup.getNumberOfDeletions();
-        return new Pair<String, String>(getKeyName(), String.format("%.2f", (double)deletions/(double)pileup.size()));
+        return String.format("%.2f", (double)deletions/(double)pileup.size());
     }
 
     public String getKeyName() { return "Dels"; }

java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotation.java

@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.Pair;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.genotype.Genotype;
 import org.broadinstitute.sting.utils.genotype.Variation;
@@ -10,9 +9,16 @@ import java.util.List;
 
 public interface VariantAnnotation {
 
-    public Pair<String, String> annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes);
+    // return the annotation for the given locus data (return null for no annotation)
+    public String annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List<Genotype> genotypes);
+
+    // return true if you want to use a context with mapping quality zero reads, false otherwise
     public boolean useZeroQualityReads();
+
+    // return the INFO key
     public String getKeyName();
+
+    // return the description used for the VCF INFO meta field
     public String getDescription();
 
 }

java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java

@@ -191,10 +191,9 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
         HashMap<String, String> results = new HashMap<String, String>();
 
         for ( VariantAnnotation annotator : annotations) {
-            Pair<String, String> annot = annotator.annotate(ref, (annotator.useZeroQualityReads() ? fullPileup : MQ0freePileup), variation, genotypes);
+            String annot = annotator.annotate(ref, (annotator.useZeroQualityReads() ? fullPileup : MQ0freePileup), variation, genotypes);
             if ( annot != null ) {
-                // System.out.println("Annotating: First="+annot.getFirst()+" Second="+annot.getSecond());
+                results.put(annotator.getKeyName(), annot);
-                results.put(annot.first, annot.second);
             }
         }
 

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/EMGenotypeCalculationModel.java

@@ -37,9 +37,9 @@ public abstract class EMGenotypeCalculationModel extends GenotypeCalculationMode
         double phredScaledConfidence;
         boolean bestIsRef = false;
         if ( PofD > PofNull ) {
-            phredScaledConfidence = -10.0 * Math.log10(PofNull / sum);
+            phredScaledConfidence = QualityUtils.phredScaleErrorRate(PofNull / sum);
         } else {
-            phredScaledConfidence = -10.0 * Math.log10(PofD / sum);
+            phredScaledConfidence = QualityUtils.phredScaleErrorRate(PofD / sum);
             bestIsRef = true;
         }
 

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java

@@ -280,7 +280,7 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
                 char base = Character.toLowerCase(altAllele);
                 int baseIndex = BaseUtils.simpleBaseToBaseIndex(altAllele);
                 if ( MathUtils.compareDoubles(PofFs[baseIndex], 0.0) != 0 ) {
-                    double phredScaledConfidence = -10.0 * Math.log10(alleleFrequencyPosteriors[baseIndex][0]);
+                    double phredScaledConfidence = QualityUtils.phredScaleErrorRate(alleleFrequencyPosteriors[baseIndex][0]);
                     if ( Double.isInfinite(phredScaledConfidence) ) {
                         phredScaledConfidence = -10.0 * log10PofDgivenAFi[baseIndex][0];
                         verboseWriter.println("P(f>0)_" + base + " = 1");
@@ -288,7 +288,7 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
                         verboseWriter.println("LOD_" + base + " = " + phredScaledConfidence);
                     } else {
                         verboseWriter.println("P(f>0)_" + base + " = " + Math.log10(PofFs[baseIndex]));
-                        verboseWriter.println("Qscore_" + base + " = " + (-10.0 * Math.log10(alleleFrequencyPosteriors[baseIndex][0])));
+                        verboseWriter.println("Qscore_" + base + " = " + (QualityUtils.phredScaleErrorRate(alleleFrequencyPosteriors[baseIndex][0])));
                         verboseWriter.println("LOD_" + base + " = " + (Math.log10(PofFs[baseIndex]) - Math.log10(alleleFrequencyPosteriors[baseIndex][0])));
                     }
                 }
@@ -306,7 +306,7 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
         // only need to look at the most likely alternate allele
         int indexOfMax = BaseUtils.simpleBaseToBaseIndex(bestAlternateAllele);
 
-        double phredScaledConfidence = -10.0 * Math.log10(alleleFrequencyPosteriors[indexOfMax][0]);
+        double phredScaledConfidence = QualityUtils.phredScaleErrorRate(alleleFrequencyPosteriors[indexOfMax][0]);
         if ( Double.isInfinite(phredScaledConfidence) )
             phredScaledConfidence = -10.0 * log10PofDgivenAFi[indexOfMax][0];
         int bestAFguess = Utils.findIndexOfMaxEntry(alleleFrequencyPosteriors[indexOfMax]);

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PointEstimateGenotypeCalculationModel.java

@@ -58,12 +58,12 @@ public class PointEstimateGenotypeCalculationModel extends EMGenotypeCalculation
             // calculate the phred-scaled confidence score
             double phredScaledConfidence;
             if ( GENOTYPE_MODE ) {
-                phredScaledConfidence = -10.0 * Math.log10(1.0 - posteriors[bestIndex]);
+                phredScaledConfidence = QualityUtils.phredScaleErrorRate(1.0 - posteriors[bestIndex]);
             } else {
                 int refIndex = DiploidGenotype.createHomGenotype(ref).ordinal();
                 bestIsRef = (refIndex == bestIndex);
                 double pError = (bestIsRef ? 1.0 - posteriors[refIndex] : posteriors[refIndex]);
-                phredScaledConfidence = -10.0 * Math.log10(pError);
+                phredScaledConfidence = QualityUtils.phredScaleErrorRate(pError);
             }
 
             // are we above the lod threshold for emitting calls (and not in all-bases mode)?