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 5275c471ee..b4161b06e7 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/downsampling/PerSampleDownsamplingReadsIterator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/downsampling/PerSampleDownsamplingReadsIterator.java
@@ -104,37 +104,6 @@ private boolean readyToReleaseReads() {
                readComparator.compare(orderedDownsampledReadsCache.peek(), earliestPendingRead) <= 0;
     }
 
-    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:
-        if ( earliestPendingRead == null && currentDownsampler.hasPendingItems() ) {
-            earliestPendingRead = currentDownsampler.peekPending();
-            earliestPendingDownsampler = currentDownsampler;
-        }
-        // In all other cases, we only need to update the earliest pending read when the downsampler
-        // associated with it experiences a change in its pending reads, since by assuming a sorted
-        // read stream we're assured that each downsampler's earliest pending read will only increase
-        // in genomic position over time.
-        //
-        // TODO: An occasional O(samples) linear search seems like a better option than keeping the downsamplers
-        // TODO: sorted by earliest pending read, which would cost at least O(total_reads * (samples + log(samples))),
-        // TODO: but need to verify this empirically.
-        else if ( currentDownsampler == earliestPendingDownsampler &&
-                  (! currentDownsampler.hasPendingItems() || readComparator.compare(currentDownsampler.peekPending(), earliestPendingRead) != 0) ) {
-
-            earliestPendingRead = null;
-            earliestPendingDownsampler = null;
-            for ( ReadsDownsampler<SAMRecord> perSampleDownsampler : perSampleDownsamplers.values() ) {
-                if ( perSampleDownsampler.hasPendingItems() &&
-                     (earliestPendingRead == null || readComparator.compare(perSampleDownsampler.peekPending(), earliestPendingRead) < 0) ) {
-
-                    earliestPendingRead = perSampleDownsampler.peekPending();
-                    earliestPendingDownsampler = perSampleDownsampler;
-                }
-            }
-        }
-    }
-
     private boolean fillDownsampledReadsCache() {
         SAMRecord prevRead = null;
         int numPositionalChanges = 0;
@@ -152,7 +121,7 @@ private boolean fillDownsampledReadsCache() {
             }
 
             thisSampleDownsampler.submit(read);
-            updateEarliestPendingRead(thisSampleDownsampler);
+            processFinalizedAndPendingItems(thisSampleDownsampler);
 
             if ( prevRead != null && prevRead.getAlignmentStart() != read.getAlignmentStart() ) {
                 numPositionalChanges++;
@@ -164,7 +133,7 @@ private boolean fillDownsampledReadsCache() {
             if ( numPositionalChanges > 0 && numPositionalChanges % DOWNSAMPLER_POSITIONAL_UPDATE_INTERVAL == 0 ) {
                 for ( ReadsDownsampler<SAMRecord> perSampleDownsampler : perSampleDownsamplers.values() ) {
                     perSampleDownsampler.signalNoMoreReadsBefore(read);
-                    updateEarliestPendingRead(perSampleDownsampler);
+                    processFinalizedAndPendingItems(perSampleDownsampler);
                 }
             }
 
@@ -174,18 +143,53 @@ private boolean fillDownsampledReadsCache() {
         if ( ! nestedSAMIterator.hasNext() ) {
             for ( ReadsDownsampler<SAMRecord> perSampleDownsampler : perSampleDownsamplers.values() ) {
                 perSampleDownsampler.signalEndOfInput();
+                if ( perSampleDownsampler.hasFinalizedItems() ) {
+                    orderedDownsampledReadsCache.addAll(perSampleDownsampler.consumeFinalizedItems());
+                }
             }
             earliestPendingRead = null;
             earliestPendingDownsampler = null;
         }
 
-        for ( ReadsDownsampler<SAMRecord> perSampleDownsampler : perSampleDownsamplers.values() ) {
-            if ( perSampleDownsampler.hasFinalizedItems() ) {
-                orderedDownsampledReadsCache.addAll(perSampleDownsampler.consumeFinalizedItems());
+        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:
+        if ( earliestPendingRead == null && currentDownsampler.hasPendingItems() ) {
+            earliestPendingRead = currentDownsampler.peekPending();
+            earliestPendingDownsampler = currentDownsampler;
+        }
+        // In all other cases, we only need to update the earliest pending read when the downsampler
+        // associated with it experiences a change in its pending reads, since by assuming a sorted
+        // read stream we're assured that each downsampler's earliest pending read will only increase
+        // in genomic position over time.
+        //
+        // TODO: An occasional O(samples) linear search seems like a better option than keeping the downsamplers
+        // TODO: sorted by earliest pending read, which would cost at least O(total_reads * (samples + log(samples))),
+        // TODO: but need to verify this empirically.
+        else if ( currentDownsampler == earliestPendingDownsampler &&
+                  (! currentDownsampler.hasPendingItems() || readComparator.compare(currentDownsampler.peekPending(), earliestPendingRead) != 0) ) {
+
+            earliestPendingRead = null;
+            earliestPendingDownsampler = null;
+            for ( ReadsDownsampler<SAMRecord> perSampleDownsampler : perSampleDownsamplers.values() ) {
+                if ( perSampleDownsampler.hasPendingItems() &&
+                     (earliestPendingRead == null || readComparator.compare(perSampleDownsampler.peekPending(), earliestPendingRead) < 0) ) {
+
+                    earliestPendingRead = perSampleDownsampler.peekPending();
+                    earliestPendingDownsampler = perSampleDownsampler;
+                }
             }
         }
+    }
 
-        return readyToReleaseReads();
+    private void processFinalizedAndPendingItems( ReadsDownsampler<SAMRecord> currentDownsampler ) {
+        if ( currentDownsampler.hasFinalizedItems() ) {
+            orderedDownsampledReadsCache.addAll(currentDownsampler.consumeFinalizedItems());
+        }
+        updateEarliestPendingRead(currentDownsampler);
     }
 
     public void remove() {