From f392d330c3ba13a0ed8bb83f7b99f4d2a2cde522 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Sat, 19 Nov 2011 22:09:56 -0500
Subject: [PATCH] Proper use of builder.  Previous conversion attempt was
 flawed

---
 .../walkers/phasing/ReadBackedPhasingWalker.java   | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
index dc0acfb6a..9470ce2f4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
@@ -1122,7 +1122,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
         private int start;
         private int stop;
         private Collection<Allele> alleles;
-        private GenotypesContext genotypes;
+        private Map<String,Genotype> genotypes;
         private double log10PError;
         private Set<String> filters;
         private Map<String, Object> attributes;
@@ -1135,15 +1135,21 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
             this.start = vc.getStart();
             this.stop = vc.getEnd();
             this.alleles = vc.getAlleles();
-            this.genotypes = GenotypesContext.copy(vc.getGenotypes()); // since vc.getGenotypes() is unmodifiable
+
+            this.genotypes = new HashMap<String, Genotype>();
+            for ( final Genotype g : vc.getGenotypes() ) {
+                this.genotypes.put(g.getSampleName(), g);
+            }
+
             this.log10PError = vc.getLog10PError();
             this.filters = vc.filtersWereApplied() ? vc.getFilters() : null;
             this.attributes = new HashMap<String, Object>(vc.getAttributes());
         }
 
         public VariantContext toVariantContext() {
+            GenotypesContext gc = GenotypesContext.copy(this.genotypes.values());
             return new VariantContextBuilder(name, contig, start, stop, alleles).id(id)
-                    .genotypes(genotypes).log10PError(log10PError).filters(filters).attributes(attributes).make();
+                    .genotypes(gc).log10PError(log10PError).filters(filters).attributes(attributes).make();
         }
 
         public GenomeLoc getLocation() {
@@ -1155,7 +1161,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
         }
 
         public void setGenotype(String sample, Genotype newGt) {
-            genotypes.add(newGt);
+            this.genotypes.put(sample, newGt);
         }
 
         public void setPhasingInconsistent() {