diff --git a/public/java/src/org/broadinstitute/sting/gatk/downsampling/PerSampleDownsamplingReadsIterator.java b/public/java/src/org/broadinstitute/sting/gatk/downsampling/PerSampleDownsamplingReadsIterator.java
index 5275c471e..b4161b06e 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/downsampling/PerSampleDownsamplingReadsIterator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/downsampling/PerSampleDownsamplingReadsIterator.java
@@ -104,6 +104,56 @@ public class PerSampleDownsamplingReadsIterator implements StingSAMIterator {
                readComparator.compare(orderedDownsampledReadsCache.peek(), earliestPendingRead) <= 0;
     }
 
+    private boolean fillDownsampledReadsCache() {
+        SAMRecord prevRead = null;
+        int numPositionalChanges = 0;
+
+        // Continue submitting reads to the per-sample downsamplers until the read at the top of the priority queue
+        // can be released without violating global sort order
+        while ( nestedSAMIterator.hasNext() && ! readyToReleaseReads() ) {
+            SAMRecord read = nestedSAMIterator.next();
+            String sampleName = read.getReadGroup() != null ? read.getReadGroup().getSample() : null;
+
+            ReadsDownsampler<SAMRecord> thisSampleDownsampler = perSampleDownsamplers.get(sampleName);
+            if ( thisSampleDownsampler == null ) {
+                thisSampleDownsampler = downsamplerFactory.newInstance();
+                perSampleDownsamplers.put(sampleName, thisSampleDownsampler);
+            }
+
+            thisSampleDownsampler.submit(read);
+            processFinalizedAndPendingItems(thisSampleDownsampler);
+
+            if ( prevRead != null && prevRead.getAlignmentStart() != read.getAlignmentStart() ) {
+                numPositionalChanges++;
+            }
+
+            // Periodically inform all downsamplers of the current position in the read stream. This is
+            // to prevent downsamplers for samples with sparser reads than others from getting stuck too
+            // long in a pending state.
+            if ( numPositionalChanges > 0 && numPositionalChanges % DOWNSAMPLER_POSITIONAL_UPDATE_INTERVAL == 0 ) {
+                for ( ReadsDownsampler<SAMRecord> perSampleDownsampler : perSampleDownsamplers.values() ) {
+                    perSampleDownsampler.signalNoMoreReadsBefore(read);
+                    processFinalizedAndPendingItems(perSampleDownsampler);
+                }
+            }
+
+            prevRead = read;
+        }
+
+        if ( ! nestedSAMIterator.hasNext() ) {
+            for ( ReadsDownsampler<SAMRecord> perSampleDownsampler : perSampleDownsamplers.values() ) {
+                perSampleDownsampler.signalEndOfInput();
+                if ( perSampleDownsampler.hasFinalizedItems() ) {
+                    orderedDownsampledReadsCache.addAll(perSampleDownsampler.consumeFinalizedItems());
+                }
+            }
+            earliestPendingRead = null;
+            earliestPendingDownsampler = null;
+        }
+
+        return readyToReleaseReads();
+    }
+
     private void updateEarliestPendingRead( ReadsDownsampler<SAMRecord> currentDownsampler ) {
         // If there is no recorded earliest pending read and this downsampler has pending items,
         // then this downsampler's first pending item becomes the new earliest pending read:
@@ -135,57 +185,11 @@ public class PerSampleDownsamplingReadsIterator implements StingSAMIterator {
         }
     }
 
-    private boolean fillDownsampledReadsCache() {
-        SAMRecord prevRead = null;
-        int numPositionalChanges = 0;
-
-        // Continue submitting reads to the per-sample downsamplers until the read at the top of the priority queue
-        // can be released without violating global sort order
-        while ( nestedSAMIterator.hasNext() && ! readyToReleaseReads() ) {
-            SAMRecord read = nestedSAMIterator.next();
-            String sampleName = read.getReadGroup() != null ? read.getReadGroup().getSample() : null;
-
-            ReadsDownsampler<SAMRecord> thisSampleDownsampler = perSampleDownsamplers.get(sampleName);
-            if ( thisSampleDownsampler == null ) {
-                thisSampleDownsampler = downsamplerFactory.newInstance();
-                perSampleDownsamplers.put(sampleName, thisSampleDownsampler);
-            }
-
-            thisSampleDownsampler.submit(read);
-            updateEarliestPendingRead(thisSampleDownsampler);
-
-            if ( prevRead != null && prevRead.getAlignmentStart() != read.getAlignmentStart() ) {
-                numPositionalChanges++;
-            }
-
-            // Periodically inform all downsamplers of the current position in the read stream. This is
-            // to prevent downsamplers for samples with sparser reads than others from getting stuck too
-            // long in a pending state.
-            if ( numPositionalChanges > 0 && numPositionalChanges % DOWNSAMPLER_POSITIONAL_UPDATE_INTERVAL == 0 ) {
-                for ( ReadsDownsampler<SAMRecord> perSampleDownsampler : perSampleDownsamplers.values() ) {
-                    perSampleDownsampler.signalNoMoreReadsBefore(read);
-                    updateEarliestPendingRead(perSampleDownsampler);
-                }
-            }
-
-            prevRead = read;
+    private void processFinalizedAndPendingItems( ReadsDownsampler<SAMRecord> currentDownsampler ) {
+        if ( currentDownsampler.hasFinalizedItems() ) {
+            orderedDownsampledReadsCache.addAll(currentDownsampler.consumeFinalizedItems());
         }
-
-        if ( ! nestedSAMIterator.hasNext() ) {
-            for ( ReadsDownsampler<SAMRecord> perSampleDownsampler : perSampleDownsamplers.values() ) {
-                perSampleDownsampler.signalEndOfInput();
-            }
-            earliestPendingRead = null;
-            earliestPendingDownsampler = null;
-        }
-
-        for ( ReadsDownsampler<SAMRecord> perSampleDownsampler : perSampleDownsamplers.values() ) {
-            if ( perSampleDownsampler.hasFinalizedItems() ) {
-                orderedDownsampledReadsCache.addAll(perSampleDownsampler.consumeFinalizedItems());
-            }
-        }
-
-        return readyToReleaseReads();
+        updateEarliestPendingRead(currentDownsampler);
     }
 
     public void remove() {