diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MarkIntervals.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MarkIntervals.java
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+/*
+ * 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
+ * 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.oneoffprojects.walkers;
+
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.commandline.Input;
+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.refdata.utils.GATKFeature;
+import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.gatk.walkers.RefWalker;
+import org.broadinstitute.sting.gatk.walkers.RodWalker;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.text.XReadLines;
+import org.broadinstitute.sting.utils.collections.Pair;
+import org.broad.tribble.util.variantcontext.VariantContext;
+
+import java.util.List;
+import java.util.Collection;
+import java.util.ArrayList;
+import java.io.PrintStream;
+import java.io.InputStream;
+import java.io.File;
+import java.io.FileNotFoundException;
+
+import net.sf.picard.util.IntervalList;
+import net.sf.picard.util.Interval;
+
+/**
+ * Counts the number of contiguous regions the walker traverses over. Slower than it needs to be, but
+ * very useful since overlapping intervals get merged, so you can count the number of intervals the GATK merges down to.
+ * This was its very first use.
+ */
+public class MarkIntervals extends RodWalker<Long, Long> {
+    @Output
+    File out;
+
+    @Input(doc="List of bad SNP sites", required=true)
+    File locs;
+
+    List<GenomeLoc> badSites = new ArrayList<GenomeLoc>();
+    IntervalList intervalList;
+
+    @Argument(doc="Should we match intervals or just the sites?", required=false)
+    boolean matchJustSites = false;
+
+    public void initialize() {
+        if ( this.getToolkit().getArguments().intervals.size() != 1 )
+            throw new UserException("This walker only works with a single -L argument provided, sorry");
+
+        File intervalFile = new File(this.getToolkit().getArguments().intervals.get(0));
+        try {
+            intervalList = IntervalList.fromFile(intervalFile);
+        } catch ( Exception ex ) {
+            throw new UserException.MalformedFile(intervalFile, "Couldn't read interval file", ex);
+        }
+
+        try {
+            for ( String line : new XReadLines(locs, true) ) {
+                String parts[] = line.split(":");
+                badSites.add(GenomeLocParser.createGenomeLoc(parts[0], Long.valueOf(parts[1])));
+            }
+        } catch ( FileNotFoundException e ) {
+            throw new UserException.CouldNotReadInputFile(locs, e);
+        }
+    }
+
+    public Long reduceInit() {
+        return 0l;
+    }
+
+    public boolean isReduceByInterval() { return true; }
+
+    public Long map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        if ( tracker == null ) {
+            return null;
+        }
+
+        return 0L;
+    }
+
+    public Long reduce(Long loc, Long prev) {
+        return 0L;
+    }
+
+    public void onTraversalDone(List<Pair<GenomeLoc,Long>> finalReduce) {
+        long nBadIntervals = 0;
+        long nBadBases = 0;
+
+        IntervalList badIntervals = new IntervalList(intervalList.getHeader());
+
+        if ( matchJustSites ) {
+            for ( GenomeLoc loc : badSites ) {
+                nBadIntervals++;
+                nBadBases += loc.size();
+                badIntervals.add(new Interval(loc.getContig(), (int)loc.getStart(), (int)loc.getStop(), false, "nBadSites_" + 1));
+            }
+        } else {
+            for ( Pair<GenomeLoc,Long> g : finalReduce ) {
+                int overlaps = 0;
+                GenomeLoc interval = g.getFirst();
+                for ( GenomeLoc loc : badSites ) {
+                    if ( interval.overlapsP(loc) ) {
+                        logger.info(String.format("Overlapping %s with bad site %s", interval, loc));
+                        overlaps++;
+                    }
+                }
+
+                if ( overlaps > 0 ) {
+                    nBadIntervals++;
+                    nBadBases += interval.size();
+                    badIntervals.add(new Interval(interval.getContig(), (int)interval.getStart(), (int)interval.getStop(), false, "nBadSites_" + overlaps));
+                    //out.printf("%s %d%n", interval, overlaps);
+                }
+            }
+        }
+
+        logger.info("No. intervals marked as bad: " + nBadIntervals);
+        logger.info("No.     bases marked as bad: " + nBadBases);
+        badIntervals.write(out);
+    }
+}
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