Added mate to name and mapqual as score in intersectBed.

	- also added map quality as score in pairToBed

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;
 				}

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) {

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 = "-";
 	};