diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java
index 9e1c12186..fd1ee9859 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java
@@ -6,6 +6,7 @@ import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
 import org.broadinstitute.sting.gatk.iterators.StingSAMIteratorAdapter;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.*;
 
@@ -140,6 +141,9 @@ public class ReadShard extends Shard {
             String contig = null;
 
             for ( final SAMRecord read : reads ) {
+                if ( contig != null && ! read.getReferenceName().equals(contig) )
+                    throw new ReviewedStingException("ReadShard contains reads spanning contig boundaries, which is no longer allowed. "
+                            + "First contig is " + contig + " next read was " + read.getReferenceName() );
                 contig = read.getReferenceName();
                 if ( read.getAlignmentStart() < start ) start = read.getAlignmentStart();
                 if ( read.getAlignmentEnd() > stop ) stop = read.getAlignmentEnd();
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
index 7f0a0c4c0..c8b654f81 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
@@ -486,9 +486,15 @@ public class SAMDataSource {
 
         CloseableIterator<SAMRecord> iterator = getIterator(readers,shard,sortOrder == SAMFileHeader.SortOrder.coordinate);
         while(!shard.isBufferFull() && iterator.hasNext()) {
-            read = iterator.next();
-            shard.addRead(read);
-            noteFilePositionUpdate(positionUpdates,read);
+            final SAMRecord nextRead = iterator.next();
+            if ( read == null || (nextRead.getReferenceIndex().equals(read.getReferenceIndex())) ) {
+                // only add reads to the shard if they are on the same contig
+                read = nextRead;
+                shard.addRead(read);
+                noteFilePositionUpdate(positionUpdates,read);
+            } else {
+                break;
+            }
         }
 
         // If the reads are sorted in queryname order, ensure that all reads
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsIntegrationTest.java
index 057cf1cf9..717d9d953 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsIntegrationTest.java
@@ -38,7 +38,8 @@ public class PrintReadsIntegrationTest extends WalkerTest {
                 {new PRTest(b37KGReference, "unmappedFlagReadsInLastLinearBin.bam", " -L 1", "6e920b8505e7e95d67634b0905237dbc")},
                 {new PRTest(b37KGReference, "unmappedFlagReadsInLastLinearBin.bam", " -L unmapped", "13bb9a91b1d4dd2425f73302b8a1ac1c")},
                 {new PRTest(b37KGReference, "unmappedFlagReadsInLastLinearBin.bam", " -L 1 -L unmapped", "6e920b8505e7e95d67634b0905237dbc")},
-                {new PRTest(b37KGReference, "oneReadAllInsertion.bam", "",  "6caec4f8a25befb6aba562955401af93")}
+                {new PRTest(b37KGReference, "oneReadAllInsertion.bam", "",  "6caec4f8a25befb6aba562955401af93")},
+                {new PRTest(b37KGReference, "NA12878.1_10mb_2_10mb.bam", "",  "c43380ac39b98853af457b90e52f8427")}
         };
     }