From 9c0dba69798a9ddbd6bbe3472f31d1aece63c8b2 Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 23 Jun 2009 13:40:13 +0000
Subject: [PATCH] Some quick documentation and typo changes

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1076 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/duplicates/CountDuplicatesWalker.java   | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/duplicates/CountDuplicatesWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/duplicates/CountDuplicatesWalker.java
index 91a68992f..78340f7b6 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/duplicates/CountDuplicatesWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/duplicates/CountDuplicatesWalker.java
@@ -33,12 +33,12 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import java.util.List;
 
 /**
- * a class to store the duplicates information we pass around
+ * a class to store the traversal information we pass around
  */
 class DuplicateCount  {
-        public int count = 0;
-        public int undupDepth = 0;
-        public int depth = 0;
+        public int count = 0; // the count of sites we were given
+        public int undupDepth = 0; // the unique read count
+        public int depth = 0; // the dupplicate read depth
     }
 
 /**
@@ -96,11 +96,10 @@ public class CountDuplicatesWalker extends DuplicateWalker<DuplicateCount, Dupli
      */
     public void onTraversalDone(DuplicateCount result) {
         out.println("[REDUCE RESULT] Traversal result is: ");
-        out.println("duplicate count = " + result.count);
+        out.println("traversal iterations = " + result.count);
         out.println("average depth = " + (double)result.depth / (double)result.count);
         out.println("duplicates seen = " + result.depth);
-        out.println("average unique depth = " + (double)result.undupDepth / (double)result.undupDepth);
         out.println("unique read count = " + result.undupDepth);
-
+        out.println("average unique read depth = " + (double)result.undupDepth / (double)result.count);
     }
 }