From 21744e024b3281d76176a27bf3427a671d3bf07e Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 29 Nov 2009 06:51:19 +0000
Subject: [PATCH] Quick walker that determines % of bases covered at (user -
 defined depth)x . I've been maintaining it in my directories alone, but now
 that i've accidentally deleted it twice, into playground it goes

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2174 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/PercentOfBasesCoveredWalker.java  | 64 +++++++++++++++++++
 1 file changed, 64 insertions(+)
 create mode 100644 java/src/org/broadinstitute/sting/playground/gatk/walkers/PercentOfBasesCoveredWalker.java

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PercentOfBasesCoveredWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PercentOfBasesCoveredWalker.java
new file mode 100644
index 000000000..9e77b5f04
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PercentOfBasesCoveredWalker.java
@@ -0,0 +1,64 @@
+package org.broadinstitute.sting.playground.gatk.walkers;
+
+import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.gatk.walkers.TreeReducible;
+import org.broadinstitute.sting.gatk.walkers.DataSource;
+import org.broadinstitute.sting.gatk.walkers.By;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.utils.Pair;
+import org.broadinstitute.sting.utils.cmdLine.Argument;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: Ghost
+ * Date: Nov 25, 2009
+ * Time: 7:54:42 PM
+ * To change this template use File | Settings | File Templates.
+ */
+@By(DataSource.REFERENCE)
+public class PercentOfBasesCoveredWalker extends LocusWalker<Boolean, Pair<Integer,Integer>> implements TreeReducible<Pair<Integer,Integer>> {
+    @Argument(fullName="minimumDepth", shortName="minDepth", doc="Minimum depth beyond which to discount the base as uncovered", required=false)
+    int minDepth = 0;
+    @Argument(fullName="includeName",doc="include this name in the output of this walker (e.g. NAME: percent of bases covered . . .) ", required=false)
+    String name = null;
+    public void initialize() {
+        // do nothing
+    }
+
+    public Pair<Integer,Integer> reduceInit() {
+        return new Pair<Integer,Integer>(0,1); // robust initialization -- seen one base with zero coverage
+    }
+
+    public Boolean map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        return context.numReads() > minDepth;
+    }
+
+    public Pair<Integer,Integer> reduce(Boolean map, Pair<Integer,Integer> prevReduce) {
+        if ( map.booleanValue() ) {
+            return new Pair<Integer,Integer>(prevReduce.first+1,prevReduce.second+1);
+        } else {
+            return new Pair<Integer,Integer>(prevReduce.first,prevReduce.second+1);
+        }
+    }
+
+    public Pair<Integer,Integer> treeReduce( Pair<Integer,Integer> left, Pair<Integer,Integer> right) {
+        right.set(right.first+left.first,right.second+left.second);
+        return right;
+    }
+
+    public void onTraversalDone(Pair<Integer,Integer> reduceFinal) {
+        String msg;
+        if (name == null)
+            msg = "Percent of bases covered at "+minDepth+"x=";
+        else
+            msg = name+": Percent of bases covered at "+minDepth+"x=";
+        
+        out.printf("%s%s",msg,pair2percent(reduceFinal));
+    }
+
+    private String pair2percent(Pair<Integer,Integer> p ) {
+        return String.format("%d%s", (int) Math.floor( ( ( double) p.first*100.0) / p.second ), "%" );
+    }
+}