From 5406e779d2036112dc1cf44d87723cc297fa6129 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 14 Mar 2011 15:51:19 +0000
Subject: [PATCH] Ryan noticed that I accidentally killed a public interface
 method for getting tag information. Reinstated.  Proper unit test to follow.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5434 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/GenomeAnalysisEngine.java               | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index 74868e61b..1b504fcff 100755
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -34,6 +34,7 @@ import org.broadinstitute.sting.commandline.ArgumentSource;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.CommandLineUtils;
 import org.broadinstitute.sting.commandline.ParsingEngine;
+import org.broadinstitute.sting.commandline.Tags;
 import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
@@ -653,6 +654,15 @@ public class GenomeAnalysisEngine {
         outputs.add(stub);
     }
 
+    /**
+     * Returns the tag associated with a given command-line argument.
+     * @param key Object for which to inspect the tag.
+     * @return Tags object associated with the given key, or an empty Tag structure if none are present. 
+     */
+    public Tags getTags(Object key)  {
+        return parsingEngine.getTags(key);
+    }
+
     protected void initializeDataSources() {
         logger.info("Strictness is " + argCollection.strictnessLevel);