diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountPairsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountPairsWalker.java
deleted file mode 100644
index e770418c1..000000000
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountPairsWalker.java
+++ /dev/null
@@ -1,140 +0,0 @@
-/*
- * Copyright (c) 2010.
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.gatk.walkers.qc;
-
-import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.gatk.walkers.ReadPairWalker;
-import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
-
-import java.io.PrintStream;
-import java.util.Collection;
-import java.util.List;
-
-/**
- * Counts the number of read pairs encountered in a file sorted in
- * query name order.  Breaks counts down by total pairs and number
- * of paired reads.
- *
- *
- * <h2>Input</h2>
- * <p>
- * One or more bam files.
- * </p>
- *
- * <h2>Output</h2>
- * <p>
- * Number of pairs seen.
- * </p>
- *
- * <h2>Examples</h2>
- * <pre>
- * java -Xmx2g -jar GenomeAnalysisTK.jar \
- *   -R ref.fasta \
- *   -T CountPairs \
- *   -o output.txt \
- *   -I input.bam
- * </pre>
- *
- * @author mhanna
- */
-public class CountPairsWalker extends ReadPairWalker<Integer,Long> {
-    @Output
-    private PrintStream out;
-
-    /**
-     * How many reads are the first in a pair, based on flag 0x0040 from the SAM spec.
-     */
-    private long firstOfPair = 0;
-
-    /**
-     * How many reads are the second in a pair, based on flag 0x0080 from the SAM spec.
-     */
-    private long secondOfPair = 0;
-
-    /**
-     * A breakdown of the total number of reads seen with exactly the same read name.
-     */
-    private List<Long> pairCountsByType = new ExpandingArrayList<Long>();
-
-    /**
-     * Maps a read pair to a given reduce of type MapType.  Semantics determined by subclasser.
-     * @param reads Collection of reads having the same name.
-     * @return Semantics defined by implementer.
-     */
-    @Override
-    public Integer map(Collection<SAMRecord> reads) {
-        if(pairCountsByType.get(reads.size()) != null)
-            pairCountsByType.set(reads.size(),pairCountsByType.get(reads.size())+1);
-        else
-            pairCountsByType.set(reads.size(),1L);
-
-        for(SAMRecord read: reads) {
-            if(read.getFirstOfPairFlag()) firstOfPair++;
-            if(read.getSecondOfPairFlag()) secondOfPair++;
-        }
-
-        return 1;
-    }
-
-    /**
-     * No pairs at the beginning of a traversal.
-     * @return 0 always.
-     */
-    @Override
-    public Long reduceInit() {
-        return 0L;
-    }
-
-    /**
-     * Combine number of pairs seen in this iteration (always 1) with total number of pairs
-     * seen in previous iterations. 
-     * @param value Pairs in this iteration (1), from the map function.
-     * @param sum Count of all pairs in prior iterations.
-     * @return All pairs encountered in previous iterations + all pairs encountered in this iteration (sum + 1).
-     */
-    @Override
-    public Long reduce(Integer value, Long sum) {
-        return value + sum;    
-    }
-
-    /**
-     * Print summary statistics over the entire traversal.
-     * @param sum A count of all read pairs viewed.
-     */
-    @Override
-    public void onTraversalDone(Long sum) {
-        out.printf("Total number of pairs               : %d%n",sum);
-        out.printf("Total number of first reads in pair : %d%n",firstOfPair);
-        out.printf("Total number of second reads in pair: %d%n",secondOfPair);
-        for(int i = 1; i < pairCountsByType.size(); i++) {
-            if(pairCountsByType.get(i) == null)
-                continue;
-            out.printf("Pairs of size %d: %d%n",i,pairCountsByType.get(i));
-        }
-    }
-
-}