From 64aad67b5fe0388a31c6acc4e198beeffd5f122f Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 27 Jul 2011 16:13:45 -0400
Subject: [PATCH] Fixing dbSNP adaptor for complex indels (wasn)

---
 .../sting/gatk/refdata/VariantContextAdaptors.java          | 6 ++++--
 .../sting/gatk/refdata/utils/helpers/DbSNPHelper.java       | 6 +++++-
 2 files changed, 9 insertions(+), 3 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 1d622e2c7..dedd2f26e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
@@ -122,14 +122,16 @@ public class VariantContextAdaptors {
 
                 Map<String, Object> attributes = new HashMap<String, Object>();
                 attributes.put(VariantContext.ID_KEY, dbsnp.getRsID());
-                if ( DbSNPHelper.isDeletion(dbsnp) ) {
+
+                boolean vcIsDeletion = DbSNPHelper.isDeletion(dbsnp) || DbSNPHelper.isComplexIndel(dbsnp);
+                if ( vcIsDeletion ) {
                     int index = dbsnp.getStart() - ref.getWindow().getStart() - 1;
                     if ( index < 0 )
                         return null; // we weren't given enough reference context to create the VariantContext
                     attributes.put(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY, new Byte(ref.getBases()[index]));
                 }
                 Collection<Genotype> genotypes = null;
-                VariantContext vc = new VariantContext(name, dbsnp.getChr(),dbsnp.getStart() - (DbSNPHelper.isDeletion(dbsnp) ? 1 : 0),dbsnp.getEnd(), alleles, genotypes, VariantContext.NO_NEG_LOG_10PERROR, null, attributes);
+                VariantContext vc = new VariantContext(name, dbsnp.getChr(), dbsnp.getStart() - (vcIsDeletion ? 1 : 0),dbsnp.getEnd(), alleles, genotypes, VariantContext.NO_NEG_LOG_10PERROR, null, attributes);
                 return vc;
             } else
                 return null; // can't handle anything else
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/helpers/DbSNPHelper.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/helpers/DbSNPHelper.java
index 3201769e0..35b0f73c6 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/helpers/DbSNPHelper.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/helpers/DbSNPHelper.java
@@ -117,7 +117,11 @@ public class DbSNPHelper {
     }
 
     public static boolean isIndel(DbSNPFeature feature) {
-        return DbSNPHelper.isInsertion(feature) || DbSNPHelper.isDeletion(feature) || feature.getVariantType().contains("in-del");
+        return DbSNPHelper.isInsertion(feature) || DbSNPHelper.isDeletion(feature) || DbSNPHelper.isComplexIndel(feature);
+    }
+
+    public static boolean isComplexIndel(DbSNPFeature feature) {
+        return feature.getVariantType().contains("in-del");
     }
 
     public static boolean isHapmap(DbSNPFeature feature) {