Deprecated calls to getSamReader on both the GenomeAnalysisEngine and the TraversalEngine. This call fails in the new style traversals, but it won't disapear until the cut-over to the new traversals is complete.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@671 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java

@@ -293,7 +293,13 @@ public class GenomeAnalysisEngine {
         return outputTracker;
     }
 
-
+    /**
+     * This function is deprecated in the new traversal engines, if you need to get the header
+     * please get the engine and then use the getHeader function
+     *
+     * @return
+     */
+    @Deprecated
     public SAMFileReader getSamReader() {
         return this.engine.getSamReader();
     }

java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java

@@ -590,6 +590,6 @@ public abstract class TraversalEngine {
                 logger.warn(msg);
         }
     }
-
+    @Deprecated
     public SAMFileReader getSamReader() { return this.samReader; }
 }