diff --git a/bin/complementBed b/bin/complementBed
index 07dec1d70376bb11889587bac959087c8ee4cb51..c09cd465e028589621860700e1029c75410e0e8b 100755
Binary files a/bin/complementBed and b/bin/complementBed differ
diff --git a/obj/complementBed.o b/obj/complementBed.o
index 9682f0a77c63043360dde3eb765221e3c976ca2a..2e02c87204bdec7ec8f09308f510f6ae8dd30b58 100644
Binary files a/obj/complementBed.o and b/obj/complementBed.o differ
diff --git a/src/complementBed/complementBed.cpp b/src/complementBed/complementBed.cpp
index e540178c1486be19b33f3d52ebbffb0abd7663f2..7c4194a83265af5f6537d0bcba59bd5bcb8ee44a 100755
--- a/src/complementBed/complementBed.cpp
+++ b/src/complementBed/complementBed.cpp
@@ -80,7 +80,7 @@ void BedComplement::ComplementBed() {
 			}
 			
 			// mask all of the positions spanned by this BED entry.
-			for (int b = bIt->start; b <= bIt->end; b++) {
+			for (int b = bIt->start; b < bIt->end; b++) {
 				chromMasks[b] = 1;
 			}
 		}
@@ -94,7 +94,7 @@ void BedComplement::ComplementBed() {
 					i++;
 				}
 				if (start > 0) {
-					cout << currChrom << "\t" << start -1 << "\t" << i << endl;
+					cout << currChrom << "\t" << start << "\t" << i << endl;
 				}
 				else {
 					cout << currChrom << "\t" << 0 << "\t" << i << endl;