Added a constructor in which the lod threshold can be set.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@501 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/playground/utils/AlleleMetrics.java

@@ -47,6 +47,23 @@ public class AlleleMetrics {
         }
     }
 
+    public AlleleMetrics(String MetricsOutputFile, double lodThreshold) {
+        LOD_cutoff = lodThreshold;
+
+        try
+        {
+            /*if ( MetricsOutputFile.equals("-") )
+                this.out = out;
+            else*/
+            this.out = new PrintStream(MetricsOutputFile);
+        }
+        catch (Exception e)
+        {
+            e.printStackTrace();
+            System.exit(-1);
+        }
+    }
+
     public void nextPosition(AlleleFrequencyEstimate alleleFreq, RefMetaDataTracker tracker) {
         num_loci_total += 1;