Removed -m64 from Makefiles.

src/bamToBed/Makefile

 CXX=		g++
-CXXFLAGS=	-Wall -O3 -m64
+CXXFLAGS=	-Wall -O3
 LIBS=		-lz
 UTILITIES_DIR = ../utils/
 OBJ_DIR = ../../obj/

src/closestBed/Makefile

 CXX = g++
-CXXFLAGS = -O3 -Wall -m64
+CXXFLAGS = -O3 -Wall
 LDFLAGS = 
 
 UTILITIES_DIR = ../utils/

src/complementBed/Makefile

 CXX = g++
-CXXFLAGS = -O3  -Wall -m64
+CXXFLAGS = -O3  -Wall
 LDFLAGS = 
 LIBFLAGS = -lc
 

src/coverageBed/Makefile

 CXX = g++
-CXXFLAGS = -O3  -Wall -m64
+CXXFLAGS = -O3  -Wall
 LDFLAGS =
 
 UTILITIES_DIR = ../utils/

src/fastaFromBed/Makefile

 CXX = g++
-CXXFLAGS = -O3  -Wall -m64
+CXXFLAGS = -O3  -Wall
 LDFLAGS = 
 
 UTILITIES_DIR = ../utils/

src/genomeCoverageBed/Makefile

 CXX = g++
-CXXFLAGS = -O3  -Wall -m64
+CXXFLAGS = -O3  -Wall
 LDFLAGS =  
 
 UTILITIES_DIR = ../utils/

src/intersectBed/Makefile

 CXX=		g++
-CXXFLAGS=	-Wall -O3 -m64
+CXXFLAGS=	-Wall -O3
 LIBS=		-lz
 UTILITIES_DIR = ../utils/
 OBJ_DIR = ../../obj/

src/linksBed/Makefile

 CXX = g++
-CXXFLAGS = -O3  -Wall -m64
+CXXFLAGS = -O3  -Wall
 LDFLAGS = 
 
 UTILITIES_DIR = ../utils/

src/maskFastaFromBed/Makefile

 CXX = g++
-CXXFLAGS = -O3  -Wall -m64
+CXXFLAGS = -O3  -Wall
 LDFLAGS = 
 
 UTILITIES_DIR = ../utils/

src/mergeBed/Makefile

 CXX = g++
-CXXFLAGS = -O3  -Wall -m64
+CXXFLAGS = -O3  -Wall
 LDFLAGS = 
 
 UTILITIES_DIR = ../utils/

src/pairToBed/Makefile

 CXX = g++
-CXXFLAGS = -O3  -Wall -m64
+CXXFLAGS = -O3  -Wall
 LDFLAGS = 
 LIBS=	-lz
 

src/pairToBed/pairToBed.cpp

@@ -194,7 +194,7 @@ bool BedIntersectPE::FindOneOrMoreOverlaps(BEDPE &a, vector<BED> &hits1, vector<
 
 		// is there enough overlap relative to the user's request? (default ~ 1bp)
 		if ( ( (float) overlapBases / (float) aLength ) >= this->overlapFraction ) {
-			numOverlapsEnd1++;
+			numOverlapsEnd2++;
 				
 			if (type == "either") return true;
 			else {
@@ -205,7 +205,7 @@ bool BedIntersectPE::FindOneOrMoreOverlaps(BEDPE &a, vector<BED> &hits1, vector<
 		
 	// Now report the hits depending on what the user has requested.
 	if (type == "neither") {
-		if ( (numOverlapsEnd1 == 0) && (numOverlapsEnd2 == 0) ) return false;
+		if ( (numOverlapsEnd1 == 0) && (numOverlapsEnd2 == 0) ) return true;
 	}
 	else if (type == "xor") {
 		if ( (numOverlapsEnd1 > 0) && (numOverlapsEnd2 == 0) ) return true;
@@ -441,7 +441,7 @@ void BedIntersectPE::IntersectBamPE(string bamFile) {
 		else if (this->searchType == "neither") {
 			if (this->bamOutput == true) {
 				overlapsFound = FindOneOrMoreOverlaps(a, hits1, hits2, this->searchType);
-				if (overlapsFound == false) {		// write to BAM if not hits found
+				if (overlapsFound == true) {		// write to BAM if not hits found
 					writer.SaveAlignment(bam);
 				}
 			}

src/pairToPair/Makefile

 CXX = g++
-CXXFLAGS = -O3  -Wall -m64
+CXXFLAGS = -O3  -Wall
 LDFLAGS = 
 
 UTILITIES_DIR = ../utils/