From e2f7f33ce7419fc3255bbaa14a414f0bb18105e2 Mon Sep 17 00:00:00 2001
From: fromer <fromer@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 17 Nov 2010 16:33:07 +0000
Subject: [PATCH] Added getIntegerAttribute()

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4697 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../variantcontext/VariantContextUtils.java         | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
index ff3a51c92..449c58479 100755
--- a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
@@ -982,6 +982,19 @@ public class VariantContextUtils {
         }
     }
 
+    public static Integer getIntegerAttribute(Map<String, Object> attribs, String attribName) {
+        Object val = attribs.get(attribName);
+        if (val == null || val.equals(VCFConstants.MISSING_VALUE_v4))
+            return null;
+
+        try {
+            return new Integer(val.toString());
+        }
+        catch (Exception e) {// IGNORE unparseable data
+            return null;
+        }
+    }
+
     private static boolean mergeIntoMNPvalidationCheck(GenomeLocParser genomeLocParser,VariantContext vc1, VariantContext vc2) {
         GenomeLoc loc1 = VariantContextUtils.getLocation(genomeLocParser,vc1);
         GenomeLoc loc2 = VariantContextUtils.getLocation(genomeLocParser,vc2);