From 35139cf990d3e95213e9f84f650ea0d2ed1c2fa6 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Fri, 8 Feb 2013 15:13:34 -0500
Subject: [PATCH] HaplotypeScore only annotates SNPs

-- The new HMM new edge conditions the likelihoods are offset by log10(n possible starts) so the results don't really mean "fits the haplotype well" any longer.  This results in grossly inflated HaplotypeScores for indels and with the HaplotypeCaller.  So I'm simply not going to emit this annotation value any longer for indels and for the HC
---
 .../walkers/annotator/HaplotypeScore.java     | 60 -------------------
 1 file changed, 60 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
index c4a0480ef..0455290e3 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
@@ -91,8 +91,6 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
                                         final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
         if (vc.isSNP() && stratifiedContexts != null)
             return annotatePileup(ref, stratifiedContexts, vc);
-        else if (stratifiedPerReadAlleleLikelihoodMap != null && vc.isVariant())
-            return annotateWithLikelihoods(stratifiedPerReadAlleleLikelihoodMap, vc);
         else
             return null;
     }
@@ -133,31 +131,6 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
         return map;
     }
 
-    private Map<String, Object> annotateWithLikelihoods(final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap,
-                                                        final VariantContext vc) {
-
-        final MathUtils.RunningAverage scoreRA = new MathUtils.RunningAverage();
-        for (final Genotype genotype : vc.getGenotypes()) {
-            final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = stratifiedPerReadAlleleLikelihoodMap.get(genotype.getSampleName());
-            if (perReadAlleleLikelihoodMap == null)
-                continue;
-
-            Double d = scoreIndelsAgainstHaplotypes(perReadAlleleLikelihoodMap);
-            if (d == null)
-                continue;
-           scoreRA.add(d); // Taking the simple average of all sample's score since the score can be negative and the RMS doesn't make sense
-        }
-
- //       if (scoreRA.observationCount() == 0)
- //           return null;
-
-        // annotate the score in the info field
-        final Map<String, Object> map = new HashMap<String, Object>();
-        map.put(getKeyNames().get(0), String.format("%.4f", scoreRA.mean()));
-        return map;
-
-    }
-
     private static class HaplotypeComparator implements Comparator<Haplotype>, Serializable {
 
         public int compare(Haplotype a, Haplotype b) {
@@ -412,39 +385,6 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
         return mismatches - expected;
     }
 
-
-    private Double scoreIndelsAgainstHaplotypes(final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap) {
-        final ArrayList<double[]> haplotypeScores = new ArrayList<double[]>();
-
-        if (perReadAlleleLikelihoodMap.isEmpty())
-            return null;
-
-        for (Map<Allele,Double> el : perReadAlleleLikelihoodMap.getLikelihoodMapValues()) {
-
-            // retrieve likelihood information corresponding to this read
-            // Score all the reads in the pileup, even the filtered ones
-            final double[] scores = new double[el.size()];
-            int i = 0;
-            for (Map.Entry<Allele, Double> a : el.entrySet()) {
-                scores[i++] = -a.getValue();
-                if (DEBUG) {
-                    System.out.printf("  vs. haplotype %d = %f%n", i - 1, scores[i - 1]);
-                }
-            }
-
-            haplotypeScores.add(scores);
-        }
-
-        // indel likelihoods are strict log-probs, not phred scored
-        double overallScore = 0.0;
-        for (final double[] readHaplotypeScores : haplotypeScores) {
-            overallScore += MathUtils.arrayMin(readHaplotypeScores);
-        }
-
-        return overallScore;
-
-    }
-
     public List<String> getKeyNames() {
         return Arrays.asList("HaplotypeScore");
     }