From 82b4798913e29f3c77570751981d85513d76a228 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Mon, 23 Apr 2012 17:24:22 -0400
Subject: [PATCH] CountBasesWalker -- a quick QC walker.

---
 .../gatk/walkers/qc/CountBasesWalker.java     | 51 +++++++++++++++++++
 1 file changed, 51 insertions(+)
 create mode 100755 public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountBasesWalker.java

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountBasesWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountBasesWalker.java
new file mode 100755
index 000000000..b846ce6b0
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountBasesWalker.java
@@ -0,0 +1,51 @@
+package org.broadinstitute.sting.gatk.walkers.qc;
+
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.DataSource;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.walkers.Requires;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+
+/**
+ * Walks over the input data set, calculating the number of reads seen for diagnostic purposes.
+ *
+ * <p>
+ * Can also count the number of reads matching a given criterion using read filters (see the
+ * --read-filter command line argument).  Simplest example of a read-backed analysis.
+ *
+ *
+ * <h2>Input</h2>
+ * <p>
+ * One or more BAM files.
+ * </p>
+ *
+ * <h2>Output</h2>
+ * <p>
+ * Number of reads seen.
+ * </p>
+ *
+ * <h2>Examples</h2>
+ * <pre>
+ * java -Xmx2g -jar GenomeAnalysisTK.jar \
+ *   -R ref.fasta \
+ *   -T CountReads \
+ *   -o output.txt \
+ *   -I input.bam \
+ *   [-L input.intervals]
+ * </pre>
+ *
+ */
+@Requires({DataSource.READS, DataSource.REFERENCE})
+public class CountBasesWalker extends ReadWalker<Integer, Long> {
+    public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) {
+
+        return read.getReadLength();
+    }
+
+    public Long reduceInit() { return 0L; }
+
+    public Long reduce(Integer value, Long sum) {
+        return (long) value + sum;
+    }
+}