From ac99437eec6da551b0de03b02c0a5ce5500e44d0 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Mon, 29 Oct 2012 01:45:33 -0400
Subject: [PATCH] Bug fixes to hapmap conversion in VariantsToVCF

---
 .../sting/gatk/refdata/VariantContextAdaptors.java              | 2 +-
 .../sting/gatk/walkers/variantutils/VariantsToVCF.java          | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
index 2b46414a8..5c7da82d0 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
@@ -364,7 +364,7 @@ public class VariantContextAdaptors {
 
             long end = hapmap.getEnd();
             if ( deletionLength > 0 )
-                end += deletionLength;
+                end += (deletionLength - 1);
             VariantContext vc = new VariantContextBuilder(name, hapmap.getChr(), hapmap.getStart(), end, alleles).id(hapmap.getName()).genotypes(genotypes).make();
             return vc;
        }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
index 5f80f77a4..059e9c5fb 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
@@ -160,7 +160,7 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
 
                         Map<String, Allele> alleleMap = new HashMap<String, Allele>(2);
                         alleleMap.put(RawHapMapFeature.DELETION, Allele.create(ref.getBase(), dbsnpVC.isSimpleInsertion()));
-                        alleleMap.put(RawHapMapFeature.INSERTION, Allele.create(ref.getBase() + ((RawHapMapFeature)record).getAlleles()[1], !dbsnpVC.isSimpleInsertion()));
+                        alleleMap.put(RawHapMapFeature.INSERTION, Allele.create((char)ref.getBase() + ((RawHapMapFeature)record).getAlleles()[1], !dbsnpVC.isSimpleInsertion()));
                         hapmap.setActualAlleles(alleleMap);
 
                         // also, use the correct positioning for insertions