From 982947d32833c654fa573167ef0ac06bb0fa7d9f Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 18 Jul 2010 02:56:37 +0000
Subject: [PATCH] update to deal with partial indels (I/D with no bases) in the
 HM records

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3820 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/refdata/VariantContextAdaptors.java              | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
index 4c44cc758..0c362b15e 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
@@ -520,7 +520,7 @@ public class VariantContextAdaptors {
             Map<String, Genotype> genotypes = new HashMap<String, Genotype>(samples.length);
             for ( int i = 0; i < samples.length; i++ ) {
                 // ignore bad genotypes
-                if ( genotypeStrings[i].contains("N") )
+                if ( genotypeStrings[i].contains("N") || genotypeStrings[i].contains("I") || genotypeStrings[i].contains("D") )
                     continue;
 
                 String a1 = genotypeStrings[i].substring(0,1);