diff --git a/bin/pairToBed b/bin/pairToBed
index c8c5b1b6c2608e59bc9bcd156a1456188443dea3..03ecc492fe6482163515691a6d154a2f7fb089f2 100755
Binary files a/bin/pairToBed and b/bin/pairToBed differ
diff --git a/obj/pairToBed.o b/obj/pairToBed.o
index 6f74692e22a1d1c67dfc0df2477c289eae570f36..190a90c024f40c5f1dda758cdbd85122454bd976 100644
Binary files a/obj/pairToBed.o and b/obj/pairToBed.o differ
diff --git a/src/complementBed/complementBed.cpp b/src/complementBed/complementBed.cpp
index 7c4194a83265af5f6537d0bcba59bd5bcb8ee44a..465bac607cf84f34999c6e08228ef03e470feffb 100755
--- a/src/complementBed/complementBed.cpp
+++ b/src/complementBed/complementBed.cpp
@@ -93,6 +93,7 @@ void BedComplement::ComplementBed() {
 				while ((chromMasks[i] == 0) && (i < chromMasks.size())) {
 					i++;
 				}
+				
 				if (start > 0) {
 					cout << currChrom << "\t" << start << "\t" << i << endl;
 				}
diff --git a/src/intersectBed/intersectBed.cpp b/src/intersectBed/intersectBed.cpp
index d5eaf4e05f4d093779a46f6baec3ab5b811ef266..5091596c4e8f8cb1a39b7bdac322791dd914d0e1 100755
--- a/src/intersectBed/intersectBed.cpp
+++ b/src/intersectBed/intersectBed.cpp
@@ -241,8 +241,12 @@ void BedIntersect::IntersectBam(string bamFile) {
 		a.chrom = refs.at(bamAlignment.RefID).RefName;
 		a.start = bamAlignment.Position;
 		a.end = bamAlignment.Position + bamAlignment.Length;
+
 		a.name = bamAlignment.Name;
-		a.score = "1";
+		if (bamAlignment.IsFirstMate()) a.name += "/1";
+		if (bamAlignment.IsSecondMate()) a.name += "/2";
+
+		a.score = ToString(bamAlignment.MapQuality);
 		a.strand = "+"; if (bamAlignment.IsReverseStrand()) a.strand = "-"; 
 	
 		if (this->bamOutput == true) {
diff --git a/src/intersectBed/test.bam b/src/intersectBed/test.bam
new file mode 100644
index 0000000000000000000000000000000000000000..a31b09e338f7869fd2f9bd7dc3ce597f5c74a0f4
Binary files /dev/null and b/src/intersectBed/test.bam differ
diff --git a/src/intersectBed/test.v.bam b/src/intersectBed/test.v.bam
new file mode 100644
index 0000000000000000000000000000000000000000..1f3d1e727561f35868d53b88bd5d172a15fc930a
Binary files /dev/null and b/src/intersectBed/test.v.bam differ
diff --git a/src/pairToBed/pairToBed.h b/src/pairToBed/pairToBed.h
index 582ea480969c6d9ca0c47ceb311c27e6f142d92e..9742574bff58c117aa0848dea9fe1133d4b95590 100755
--- a/src/pairToBed/pairToBed.h
+++ b/src/pairToBed/pairToBed.h
@@ -75,7 +75,7 @@ private:
 		a.start2 = bam.MatePosition;
 		a.end2 = bam.MatePosition + bam.Length;
 		a.name = bam.Name;
-		a.score = "1";
+		a.score = ToString(bam.MapQuality);
 		a.strand1 = "+"; if (bam.IsReverseStrand()) a.strand1 = "-";
 		a.strand2 = "+"; if (bam.IsMateReverseStrand()) a.strand2 = "-";
 	};