From 3896cc8f1744b74fffd1c70eb1f097b75c72e481 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 31 Mar 2009 05:02:33 +0000
Subject: [PATCH] Moved avg depth of coverage functionality into the core depth
 of coverage walker.  Used new command line args for walkers.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@234 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/DepthOfCoverageWalker.java   | 25 ++++++++++++-----
 .../walkers/AvgDepthOfCoverageWalker.java     | 28 -------------------
 2 files changed, 18 insertions(+), 35 deletions(-)
 delete mode 100644 java/src/org/broadinstitute/sting/playground/gatk/walkers/AvgDepthOfCoverageWalker.java

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java
index 4643f4ecf..488a85da0 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java
@@ -2,7 +2,8 @@ package org.broadinstitute.sting.gatk.walkers;
 
 import org.broadinstitute.sting.gatk.LocusContext;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
-
+import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.utils.Pair;
 import java.util.List;
 
 /**
@@ -12,15 +13,25 @@ import java.util.List;
  * Time: 3:22:14 PM
  * To change this template use File | Settings | File Templates.
  */
-public class DepthOfCoverageWalker extends LocusWalker<Integer, Integer> {
+public class DepthOfCoverageWalker extends LocusWalker<Integer, Pair<Long, Long>> {
+    @Argument(fullName="printall",required=false,defaultValue="true")
+    public String printAllLoci;  // booleans don't work
+
     public Integer map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
-        out.printf("%s: %d%n", context.getLocation(), context.getReads().size() );
-        return 1;
+        if (printAllLoci.equals("true"))
+            out.printf("%s: %d%n", context.getLocation(), context.getReads().size() );
+        return context.getReads().size();
     }
 
-    public Integer reduceInit() { return 0; }
+    public Pair<Long, Long> reduceInit() { return new Pair<Long, Long>((long)0,(long)0); }
 
-    public Integer reduce(Integer value, Integer sum) {
-        return value + sum;
+    public Pair<Long, Long> reduce(Integer value, Pair<Long, Long> sum) {
+        long left = new Long(value.longValue() + sum.getFirst().longValue());
+        long right = new Long(sum.getSecond().longValue() + 1);
+        return new Pair<Long, Long>(left, right);
+    }
+
+    public void onTraversalDone(Pair<Long, Long> result) {
+        out.println("Average depth of coverage is: " + ((double)result.getFirst() / (double)result.getSecond()));
     }
 }
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/AvgDepthOfCoverageWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AvgDepthOfCoverageWalker.java
deleted file mode 100644
index 83c6f5434..000000000
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/AvgDepthOfCoverageWalker.java
+++ /dev/null
@@ -1,28 +0,0 @@
-package org.broadinstitute.sting.playground.gatk.walkers;
-
-import org.broadinstitute.sting.utils.Pair;
-import org.broadinstitute.sting.gatk.LocusContext;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
-import org.broadinstitute.sting.gatk.walkers.LocusWalker;
-import org.broadinstitute.sting.gatk.walkers.WalkerName;
-import java.util.List;
-
-@WalkerName("Average_Depth_Of_Coverage")
-public class AvgDepthOfCoverageWalker extends LocusWalker<Integer, Pair<Long, Long>> {
-
-    public Integer map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
-        return context.getReads().size();
-    }
-
-    public Pair<Long, Long> reduceInit() { return new Pair<Long, Long>((long)0,(long)0); }
-
-    public Pair<Long, Long> reduce(Integer value, Pair<Long, Long> sum) {
-        long left = new Long(value.longValue() + sum.getFirst().longValue());
-        long right = new Long(sum.getSecond().longValue() + 1);
-        return new Pair<Long, Long>(left, right);
-    }
-
-    public void onTraversalDone(Pair<Long, Long> result) {
-        System.out.println("Average depth of coverage is: " + ((double)result.getFirst() / (double)result.getSecond()));
-    }
-}