From 7e30fe230aab4204ff9508105c633fb102705682 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 10 Nov 2009 13:25:18 +0000
Subject: [PATCH] oops, missing file

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2009 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/utils/genotype/vcf/VCFRecord.java   | 25 +++++++++++++++----
 1 file changed, 20 insertions(+), 5 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java
index aa9387ad7..df9675f89 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java
@@ -220,17 +220,21 @@ public class VCFRecord {
     }
 
     public boolean isFiltered() {
-	String[] codes = getFilteringCodes();
-	if ( codes.length > 1 ) return true;
-	else if ( codes[0].equals(".") || codes[0].equals("0") ) return false;
-	else return true;
+        String[] codes = getFilteringCodes();
+        if ( codes.length > 1 ) return true;
+        else if ( codes[0].equals(".") || codes[0].equals("0") ) return false;
+        else return true;
     }
 
     public boolean hasFilteringCodes() {
-	// todo --- currently always returns true
+        // todo --- currently always returns true
         return getFilteringCodes() != null;
     }
 
+    public String getFilterString() {
+        return mFilterString;
+    }
+
     /**
      * get the information key-value pairs as a Map<>
      *
@@ -333,6 +337,17 @@ public class VCFRecord {
         this.mInfoFields.put(key, value);
     }
 
+
+    /**
+     * add an info field to the record
+     *
+     * @param m A map from info keys to info values
+     */
+    public void addInfoFields(Map<String,String> m) {
+        for ( Map.Entry<String, String> e : m.entrySet() )
+            addInfoField(e.getKey(), e.getValue());
+    }
+
     /**
      * the generation of a string representation, which is used by the VCF writer
      *