diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/tools/JavaIOSpeedTest.java b/java/src/org/broadinstitute/sting/oneoffprojects/tools/JavaIOSpeedTest.java
new file mode 100755
index 000000000..2d16bc33f
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/tools/JavaIOSpeedTest.java
@@ -0,0 +1,72 @@
+package org.broadinstitute.sting.oneoffprojects.tools;
+
+import java.io.BufferedInputStream;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileReader;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.util.Date;
+import java.util.zip.GZIPInputStream;
+
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.CommandLineProgram;
+
+/**
+ * Used to test how long it takes to read through a text files and gzipped files.
+ * If the passed-in filename ends with .gz, it will be read using GZIPInputStream.
+ * Otherwise, its read using FileReader.
+ */
+public class JavaIOSpeedTest extends CommandLineProgram {
+
+    @Argument(fullName = "input", shortName = "i", doc = "file to read", required = true) public String filename;
+    @Argument(fullName = "buffer_size", shortName = "s", doc = "read buffer size", required=false) public int bufferSize = -1;
+
+    @Override
+    protected int execute() {
+        System.out.println("Filename: " + filename);
+        try {
+            final File file = new File(filename);
+            final Reader reader;
+            if(filename.endsWith(".gz")) {
+                reader = new InputStreamReader(new GZIPInputStream(new BufferedInputStream(new FileInputStream(file))));
+            } else {
+                reader = new FileReader(file);
+            }
+
+            final BufferedReader br;
+            if(bufferSize != -1) {
+                br = new BufferedReader(reader, bufferSize);
+            } else {
+                br = new BufferedReader(reader);
+            }
+
+            System.out.println("Reading...");
+            int incr = 10000000;
+            int next = incr;
+            int counter = 0;
+            while(br.ready()) {
+                br.readLine();
+                if(++counter == next) {
+                    next += incr;
+                    System.err.println(new Date() + ": " + filename + " - read " + counter + " lines...");
+                }
+            }
+
+            System.out.println("Read " + counter + " lines from " + filename);
+
+        } catch(Exception e) {
+            System.err.println("ERROR: " + e);
+            e.printStackTrace();
+        }
+
+        return 0;
+    }
+
+    public static void main(String args[])
+    {
+        CommandLineProgram.start(new JavaIOSpeedTest(), args);
+    }
+
+}