diff --git a/src/utils/BamTools-Ancillary/BamAncillary.cpp b/src/utils/BamTools-Ancillary/BamAncillary.cpp
index 54e89f1a47c8e4d809eac3f0b373b18f828162c8..09891e96c00694f366f23ead6d902a8a8b797ec5 100644
--- a/src/utils/BamTools-Ancillary/BamAncillary.cpp
+++ b/src/utils/BamTools-Ancillary/BamAncillary.cpp
@@ -47,11 +47,14 @@ namespace BamTools {
                 if (breakOnDeletionOps == false)
                     currPosition += cigItr->Length;
                 else {
+                    blocksFound = true;
                     currPosition += cigItr->Length;
                     blockStart    = currPosition;
                 }
             }
             else if (cigItr->Type == 'N') {
+                blocks.push_back( BED(chrom, blockStart, currPosition, name, score, strand) );
+                blocksFound = true;
                 currPosition += cigItr->Length;
                 blockStart    = currPosition;
             }