From f97e7d2fb4d8af03bdb08d67ff2159d6769eafe0 Mon Sep 17 00:00:00 2001
From: carneiro <carneiro@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 29 Apr 2011 19:19:39 +0000
Subject: [PATCH] Walker that calculates the percentage of bases that are
 covered to at least 20x. Very useful! In oneoffs until someone else thinks
 it's as useful as I think it is ;)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5714 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/Percent20xCoverage.java           | 59 +++++++++++++++++++
 1 file changed, 59 insertions(+)
 create mode 100755 java/src/org/broadinstitute/sting/oneoffprojects/walkers/Percent20xCoverage.java

diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/Percent20xCoverage.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/Percent20xCoverage.java
new file mode 100755
index 000000000..d8fbf041c
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/Percent20xCoverage.java
@@ -0,0 +1,59 @@
+package org.broadinstitute.sting.oneoffprojects.walkers;
+
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.gatk.walkers.TreeReducible;
+
+import java.io.PrintStream;
+
+/**
+ * Walks over the input data set, calculating the total number of covered loci for diagnostic purposes.
+ * Simplest example of a locus walker.
+ */
+public class Percent20xCoverage extends LocusWalker<Integer, Long> implements TreeReducible<Long> {
+    @Output(doc="Write count to this file instead of STDOUT")
+    PrintStream out;
+
+    @Argument(fullName="target_coverage", shortName="coverage", doc="Set the target coverage", required=false)
+    private int targetCoverage = 20;
+
+
+    private long totalLoci;
+    private long totalCoverage;
+
+    public void initialize () {
+        totalLoci = 0;
+        totalCoverage = 0;
+    }
+
+    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        totalLoci++;
+        int coverage = context.getBasePileup().size();
+        totalCoverage += coverage;
+        if (coverage >= targetCoverage)
+            return 1;
+        return 0;
+    }
+
+    public Long reduceInit() { return 0l; }
+
+    public Long reduce(Integer value, Long sum) {
+        return value + sum;
+    }
+
+    /**
+     * Reduces two subtrees together.  In this case, the implementation of the tree reduce
+     * is exactly the same as the implementation of the single reduce.
+     */
+    public Long treeReduce(Long lhs, Long rhs) {
+        return lhs + rhs;
+    }
+
+    public void onTraversalDone( Long c ) {
+        out.println(Math.floor(totalCoverage/totalLoci) + "\t" + (double) c/totalLoci);
+    }
+}