diff --git a/src/intersectBed/intersectBed.cpp b/src/intersectBed/intersectBed.cpp
index d6ec2c28db2f5e622e382a93c72085a9a8777702..53222ebc1a04c349c1ae48de6c2736c6c4cfd47e 100644
--- a/src/intersectBed/intersectBed.cpp
+++ b/src/intersectBed/intersectBed.cpp
@@ -278,6 +278,10 @@ void BedIntersect::IntersectBam(string bamFile) {
                 bool overlapsFound = false;
                 // treat the BAM alignment as a single "block"
                 if (_obeySplits == false) {
+                    // Toying with adding tags.  Need new version of FindOverlaps.
+                    // FindOverlaps(a, hits);
+                    // bam.AddTag("YB", "i", static_cast<int>(hits.size()));
+                    // hits.clear();
                     overlapsFound = FindOneOrMoreOverlap(a);
                 }
                 // split the BAM alignment into discrete blocks and
@@ -327,6 +331,10 @@ void BedIntersect::IntersectBam(string bamFile) {
                 }
             }
         }
+        // BAM IsMapped() is false
+        else if (_noHit == true) {
+            writer.SaveAlignment(bam);
+        }
     }
 
     // close the relevant BAM files.
diff --git a/src/windowBed/windowBed.cpp b/src/windowBed/windowBed.cpp
index 6b0336128d153363d466bf9b2aebafc508772557..b961f02c2049076a0da11b6faa744c583206a38a 100644
--- a/src/windowBed/windowBed.cpp
+++ b/src/windowBed/windowBed.cpp
@@ -204,6 +204,10 @@ void BedWindow::WindowIntersectBam(string bamFile) {
                 hits.clear();
             }
         }
+        // BAM IsMapped() is false
+        else if (_noHit == true) {
+            writer.SaveAlignment(bam);
+        }
     }
 
     // close the relevant BAM files.