diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java
index dca4cc771..bcb726607 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java
@@ -256,7 +256,7 @@ public class BAMScheduler implements Iterator<FilePointer> {
             // Naive algorithm: find all elements in current contig for proper schedule creation.
             List<GenomeLoc> lociInContig = new LinkedList<GenomeLoc>();
             for(GenomeLoc locus: loci) {
-                if(dataSource.getHeader().getSequence(locus.getContig()).getSequenceIndex() == lastReferenceSequenceLoaded)
+                if(!GenomeLoc.isUnmapped(locus) && dataSource.getHeader().getSequence(locus.getContig()).getSequenceIndex() == lastReferenceSequenceLoaded)
                     lociInContig.add(locus);
             }
 
diff --git a/public/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java
index 3fb330853..a8364419d 100644
--- a/public/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java
@@ -83,6 +83,28 @@ public class IntervalIntegrationTest extends WalkerTest {
         executeTest("testUnmappedReadInclusion",spec);
     }
 
+    @Test
+    public void testMixedMappedAndUnmapped() {
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-T PrintReads" +
+                        " -I " + validationDataLocation + "MV1994.bam" +
+                        " -R " + validationDataLocation + "Escherichia_coli_K12_MG1655.fasta" +
+                        " -L Escherichia_coli_K12:4630000-4639675" +
+                        " -L unmapped" +
+                        " -U",
+                        0, // two output files
+                        Collections.<String>emptyList());
+
+        // our base file
+        File baseOutputFile = createTempFile("testUnmappedReadInclusion",".bam");
+        spec.setOutputFileLocation(baseOutputFile);
+        spec.addAuxFile("083ef1e9ded868e0d12c05a1354c0319",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
+        spec.addAuxFile("fa90ff91ac0cc689c71a3460a3530b8b", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai"));
+
+        executeTest("testUnmappedReadInclusion",spec);
+    }
+
+
     @Test(enabled = false)
     public void testUnmappedReadExclusion() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(