diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoarseCoverageWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoarseCoverageWalker.java
deleted file mode 100644
index 405a44c29..000000000
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoarseCoverageWalker.java
+++ /dev/null
@@ -1,118 +0,0 @@
-/*
- * Copyright (c) 2010 The Broad Institute
- *
- * 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.coverage;
-
-import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-
-import java.io.PrintStream;
-
-/**
- * Computes the coverage per every <granularity> bases on the reference, or on the subset of the reference
- * specified by the intervals provided. Moving to the next contig on the reference will always restart the
- * count anew, even if the count of bases in the last chunk on the previous contig did not reach specified <granularity>.
- */
-public class CoarseCoverageWalker extends ReadWalker<Integer,Integer> {
-    @Output
-    public PrintStream out;
-	
-    @Argument(fullName="granularity", shortName="G", doc="Granularity", required=true)
-    public Integer N;
-
-    @Argument(fullName="dontZeroMissingContigs", shortName="Z", doc="If provided, we won't emit 0 counts for all sites on contigs skipped", required=true)
-    public boolean dontZeroMissingContigs;
-
-    private int chunkStart = 1; // start of the current chunk we are counting reads for
-    private int contig = 0; // current contig we are on
-    private int count = 0; // number of reads overlapping with the current chunk
-    private static String zeroString = "0";
-    
-    @Override 
-    public void initialize() {
-    	chunkStart = 1;
-    	contig = 0;
-    	count = 0;
-    }
-    
-	@Override
-	public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
-		
-		if ( read.getReadUnmappedFlag() ||
-			 read.getDuplicateReadFlag() ||
-			 read.getNotPrimaryAlignmentFlag() ||
-			 read.getMappingQuality() == 0 ) return 0;
-		
-		if ( read.getReferenceIndex() != contig ) {
-			// we jumped onto another contig
-			out.printf("%d%n", count); // print old count
-			count = 0;
-			
-			// if we skipped one or more contigs completely, make sure we print 0 counts over all of them:
-            for ( contig++ ; contig < read.getReferenceIndex() ; contig++) {
-                if ( ! dontZeroMissingContigs ) {
-                    int contigSize = read.getHeader().getSequence(contig).getSequenceLength();
-                    for ( int k = 1 ; k < contigSize ;  k+=N ) out.println(zeroString);
-                }
-            }
-            // by now we scrolled to the right contig
-			
-			chunkStart = 1; // reset chunk start
-		}
-		
-		// if our read is past the boundary of the current chunk, print old count(s)
-		// (for the current chunk and all chunks we may have skipped altogether) and reinitialize:
-		while ( chunkStart+N < read.getAlignmentStart() ) {
-			out.printf("%d%n", count); // print old count
-			count = 0;
-			chunkStart += N;
-		}
-		count++;
-		return 1;
-	}
-
-	@Override
-	public Integer reduce(Integer value, Integer sum) {
-		return value+sum;
-	}
-
-	@Override
-	public Integer reduceInit() {
-		return 0;
-	}
-	
-	@Override 
-	public void onTraversalDone(Integer result) {
-		out.printf("%d%n", count); // print count from the last chunk
-		super.onTraversalDone(result);
-		
-	}
-	
-
-}