Move getSamplesForSamFile to SampleUtils

-- A nearly identical piece of code already lived in SampleUtils.  Now there are two functions, one taking a regular header and another grabbing the merged header from the GATK engine itself.  Much cleaner

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

@@ -1041,13 +1041,6 @@ public class GenomeAnalysisEngine {
         return this.sampleDataSource;
     }
 
-    /**
-     * Returns all samples that were referenced in the SAM file
-     */
-    public Set<Sample> getSAMFileSamples() {
-        return sampleDataSource.getSamples(SampleUtils.getSAMFileSamples(getSAMFileHeader()));
-    }
-
     public Map<String,String> getApproximateCommandLineArguments(Object... argumentProviders) {
         return CommandLineUtils.getApproximateCommandLineArguments(parsingEngine,argumentProviders);
     }

public/java/src/org/broadinstitute/sting/utils/SampleUtils.java

@@ -69,6 +69,18 @@ public class SampleUtils {
         return samples;
     }
 
+
+    /**
+     * Same as @link getSAMFileSamples but gets all of the samples
+     * in the SAM files loaded by the engine
+     *
+     * @param engine
+     * @return
+     */
+    public final static Set<String> getSAMFileSamples(GenomeAnalysisEngine engine) {
+        return SampleUtils.getSAMFileSamples(engine.getSAMFileHeader());
+    }
+
     /**
      * Gets all of the unique sample names from all VCF rods input by the user
      *