diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
index b7846399f..a5d1370ba 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
@@ -56,7 +56,8 @@ public class LinearMicroScheduler extends MicroScheduler {
             traversalEngine.startTimersIfNecessary();
             if(shard.getShardType() == Shard.ShardType.LOCUS) {
                 LocusWalker lWalker = (LocusWalker)walker;
-                WindowMaker windowMaker = new WindowMaker(shard, engine.getGenomeLocParser(), getReadIterator(shard), shard.getGenomeLocs(), engine.getSampleDB());
+                WindowMaker windowMaker = new WindowMaker(shard, engine.getGenomeLocParser(),
+                        getReadIterator(shard), shard.getGenomeLocs(), engine.getSampleDB().getSampleNames());
                 for(WindowMaker.WindowMakerIterator iterator: windowMaker) {
                     ShardDataProvider dataProvider = new LocusShardDataProvider(shard,iterator.getSourceInfo(),engine.getGenomeLocParser(),iterator.getLocus(),iterator,reference,rods);
                     Object result = traversalEngine.traverse(walker, dataProvider, accumulator.getReduceInit());
diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java b/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
index 428813b71..11e51d99b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
@@ -62,7 +62,10 @@ public class ShardTraverser implements Callable {
 
             Object accumulator = walker.reduceInit();
             LocusWalker lWalker = (LocusWalker)walker;
-            WindowMaker windowMaker = new WindowMaker(shard,microScheduler.getEngine().getGenomeLocParser(),microScheduler.getReadIterator(shard),shard.getGenomeLocs(), microScheduler.engine.getSampleDB()); // todo: microScheduler.engine is protected - is it okay to user it here?
+            WindowMaker windowMaker = new WindowMaker(shard,microScheduler.getEngine().getGenomeLocParser(),
+                    microScheduler.getReadIterator(shard),
+                    shard.getGenomeLocs(),
+                    microScheduler.engine.getSampleDB().getSampleNames()); // todo: microScheduler.engine is protected - is it okay to user it here?
             ShardDataProvider dataProvider = null;
 
             for(WindowMaker.WindowMakerIterator iterator: windowMaker) {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java b/public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java
index fb207087f..825a81e64 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java
@@ -12,6 +12,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
+import java.util.Collection;
 import java.util.Iterator;
 import java.util.List;
 import java.util.NoSuchElementException;
@@ -63,17 +64,20 @@ public class WindowMaker implements Iterable<WindowMaker.WindowMakerIterator>, I
      * the given intervals.
      * @param iterator The data source for this window.
      * @param intervals The set of intervals over which to traverse.
-     * @param sampleData SampleDataSource that we can reference reads with
+     * @param sampleNames The complete set of sample names in the reads in shard
      */
 
-    public WindowMaker(Shard shard, GenomeLocParser genomeLocParser, StingSAMIterator iterator, List<GenomeLoc> intervals, SampleDataSource sampleData ) {
+    public WindowMaker(Shard shard, GenomeLocParser genomeLocParser, StingSAMIterator iterator, List<GenomeLoc> intervals, Collection<String> sampleNames) {
         this.sourceInfo = shard.getReadProperties();
         this.readIterator = iterator;
-
-        this.sourceIterator = new PeekableIterator<AlignmentContext>(new LocusIteratorByState(iterator,sourceInfo,genomeLocParser,sampleData.getSampleNames()));
+        this.sourceIterator = new PeekableIterator<AlignmentContext>(new LocusIteratorByState(iterator,sourceInfo,genomeLocParser, sampleNames));
         this.intervalIterator = intervals.size()>0 ? new PeekableIterator<GenomeLoc>(intervals.iterator()) : null;
     }
 
+    public WindowMaker(Shard shard, GenomeLocParser genomeLocParser, StingSAMIterator iterator, List<GenomeLoc> intervals ) {
+        this(shard, genomeLocParser, iterator, intervals, LocusIteratorByState.sampleListForSAMWithoutReadGroups());
+    }
+
     public Iterator<WindowMakerIterator> iterator() {
         return this;
     }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java b/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
index 9a468f482..d16502b1d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
@@ -284,6 +284,16 @@ public class LocusIteratorByState extends LocusIterator {
             throw new IllegalArgumentException("samples list must not be empty");
     }
 
+    /**
+     * For testing only.  Assumes that the incoming SAMRecords have no read groups, so creates a dummy sample list
+     * for the system.
+     */
+    public final static Collection<String> sampleListForSAMWithoutReadGroups() {
+        List<String> samples = new ArrayList<String>();
+        samples.add(null);
+        return samples;
+    }
+
     public Iterator<AlignmentContext> iterator() {
         return this;
     }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusViewTemplate.java b/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusViewTemplate.java
index d962f7dc8..8b226101a 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusViewTemplate.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusViewTemplate.java
@@ -50,7 +50,7 @@ public abstract class LocusViewTemplate extends BaseTest {
 
         GenomeLoc shardBounds = genomeLocParser.createGenomeLoc("chr1", 1, 5);
         Shard shard = new LocusShard(genomeLocParser, new SAMDataSource(Collections.<SAMReaderID>emptyList(),genomeLocParser),Collections.singletonList(shardBounds),Collections.<SAMReaderID,SAMFileSpan>emptyMap());
-        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs(), new SampleDataSource());
+        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
         WindowMaker.WindowMakerIterator window = windowMaker.next();
         LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, null, genomeLocParser, window.getLocus(), window, null, null);
 
@@ -66,7 +66,7 @@ public abstract class LocusViewTemplate extends BaseTest {
 
         GenomeLoc shardBounds = genomeLocParser.createGenomeLoc("chr1", 1, 5);
         Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(shardBounds));
-        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs(), new SampleDataSource());
+        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
         WindowMaker.WindowMakerIterator window = windowMaker.next();
         LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
 
@@ -81,7 +81,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecordIterator iterator = new SAMRecordIterator(read);
 
         Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 1, 10)));
-        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs(),new SampleDataSource());
+        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
         WindowMaker.WindowMakerIterator window = windowMaker.next();
         LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
         LocusView view = createView(dataProvider);
@@ -95,7 +95,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecordIterator iterator = new SAMRecordIterator(read);
 
         Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 1, 10)));
-        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs(), new SampleDataSource());
+        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
         WindowMaker.WindowMakerIterator window = windowMaker.next();
         LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
         LocusView view = createView(dataProvider);
@@ -109,7 +109,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecordIterator iterator = new SAMRecordIterator(read);
 
         Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 1, 10)));
-        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs(), new SampleDataSource());
+        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
         WindowMaker.WindowMakerIterator window = windowMaker.next();
         LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
         LocusView view = createView(dataProvider);
@@ -123,7 +123,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecordIterator iterator = new SAMRecordIterator(read);
 
         Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 5, 5)));
-        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs(),new SampleDataSource());
+        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
         WindowMaker.WindowMakerIterator window = windowMaker.next();
         LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
         LocusView view = createView(dataProvider);
@@ -137,7 +137,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecordIterator iterator = new SAMRecordIterator(read);
 
         Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 6, 15)));
-        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs(), new SampleDataSource());
+        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
         WindowMaker.WindowMakerIterator window = windowMaker.next();
         LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
         LocusView view = createView(dataProvider);
@@ -151,7 +151,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecordIterator iterator = new SAMRecordIterator(read);
 
         Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 1, 10)));
-        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs(),new SampleDataSource());
+        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
         WindowMaker.WindowMakerIterator window = windowMaker.next();
         LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
         LocusView view = createView(dataProvider);
@@ -166,7 +166,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecordIterator iterator = new SAMRecordIterator(read1, read2);
 
         Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 1, 10)));
-        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs(),new SampleDataSource());
+        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
         WindowMaker.WindowMakerIterator window = windowMaker.next();
         LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
         LocusView view = createView(dataProvider);
@@ -185,7 +185,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecordIterator iterator = new SAMRecordIterator(read1, read2, read3, read4);
 
         Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 1, 10)));
-        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs(),new SampleDataSource());
+        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
         WindowMaker.WindowMakerIterator window = windowMaker.next();
         LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
         LocusView view = createView(dataProvider);
@@ -204,7 +204,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecordIterator iterator = new SAMRecordIterator(read1, read2, read3, read4);
 
         Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 1, 10)));
-        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs(),new SampleDataSource());
+        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
         WindowMaker.WindowMakerIterator window = windowMaker.next();
         LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
         LocusView view = createView(dataProvider);
@@ -225,7 +225,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecordIterator iterator = new SAMRecordIterator(read1, read2, read3, read4, read5, read6);
 
         Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 1, 10)));
-        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs(), new SampleDataSource());
+        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
         WindowMaker.WindowMakerIterator window = windowMaker.next();
         LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
         LocusView view = createView(dataProvider);
@@ -253,7 +253,7 @@ public abstract class LocusViewTemplate extends BaseTest {
                                                            read07, read08, read09, read10, read11, read12);
 
         Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chr1", 6, 15)));
-        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs(), new SampleDataSource());
+        WindowMaker windowMaker = new WindowMaker(shard,genomeLocParser,iterator,shard.getGenomeLocs());
         WindowMaker.WindowMakerIterator window = windowMaker.next();
         LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, window.getSourceInfo(), genomeLocParser, window.getLocus(), window, null, null);
         LocusView view = createView(dataProvider);
diff --git a/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/DownsamplerBenchmark.java b/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/DownsamplerBenchmark.java
index 0e1f4253a..41d7a23c6 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/DownsamplerBenchmark.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/DownsamplerBenchmark.java
@@ -89,7 +89,7 @@ public class DownsamplerBenchmark extends ReadProcessingBenchmark {
 
             // Filter unmapped reads.  TODO: is this always strictly necessary?  Who in the GATK normally filters these out?
             Iterator<SAMRecord> readIterator = new FilteringIterator(reader.iterator(),new UnmappedReadFilter());
-            LocusIteratorByState locusIteratorByState = new LocusIteratorByState(readIterator,readProperties,genomeLocParser,sampleDataSource.getSampleNames());
+            LocusIteratorByState locusIteratorByState = new LocusIteratorByState(readIterator,readProperties,genomeLocParser, LocusIteratorByState.sampleListForSAMWithoutReadGroups());
             while(locusIteratorByState.hasNext()) {
                 locusIteratorByState.next().getLocation();
             }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java
index dc43b4968..297a8501a 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java
@@ -11,7 +11,6 @@ import org.testng.Assert;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.gatk.ReadProperties;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
-import org.broadinstitute.sting.gatk.samples.SampleDataSource;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.utils.GenomeLocParser;
@@ -39,11 +38,8 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
     }
 
     private final LocusIteratorByState makeLTBS(List<SAMRecord> reads, ReadProperties readAttributes) {
-        List<String> samples = new ArrayList<String>();
-        samples.add(null);
-
         return new LocusIteratorByState(new FakeCloseableIterator<SAMRecord>(reads.iterator()),
-                readAttributes,genomeLocParser, samples);
+                readAttributes, genomeLocParser, LocusIteratorByState.sampleListForSAMWithoutReadGroups());
     }
 
     @Test