diff --git a/bin/intersectBed b/bin/intersectBed
index c789efb3f822f49b93965e8890a3c0694496396e..3c29e610ee3b2f43568cd6c77c8e6b5d6b82d161 100755
Binary files a/bin/intersectBed and b/bin/intersectBed differ
diff --git a/bin/mergeBed b/bin/mergeBed
index b47e7ac5d71d9ce6568582b656a36d7560e6ff5d..33908712f42621acf42104df090642ccc4f17f23 100755
Binary files a/bin/mergeBed and b/bin/mergeBed differ
diff --git a/bin/pairToBed b/bin/pairToBed
index 03ecc492fe6482163515691a6d154a2f7fb089f2..8f5050c783234a8ff2d615b95457d5c3ab2077d9 100755
Binary files a/bin/pairToBed and b/bin/pairToBed differ
diff --git a/obj/intersectBed.o b/obj/intersectBed.o
index 669d0ba809b1c057b67ee2cbc3c0c935514194b1..852904d4179a6a1e3862cc564dd5254a5e28ea58 100644
Binary files a/obj/intersectBed.o and b/obj/intersectBed.o differ
diff --git a/obj/mergeBed.o b/obj/mergeBed.o
index f4f880b301e4bafdef02c1cce60d82c8c5254962..3c5ded85ab4c08180e20fbe9d8c910191ef69c06 100644
Binary files a/obj/mergeBed.o and b/obj/mergeBed.o differ
diff --git a/obj/pairToBed.o b/obj/pairToBed.o
index 190a90c024f40c5f1dda758cdbd85122454bd976..01264d9ed6894ec9cdfa9be9998202e33f96573e 100644
Binary files a/obj/pairToBed.o and b/obj/pairToBed.o differ
diff --git a/src/bamToBed/Makefile b/src/bamToBed/Makefile
index 671e8b8c73a760d044126bb74bae84aaa814eef1..263bebc58713c2d9c0cd3e30079830bc0ce9a2c8 100755
--- a/src/bamToBed/Makefile
+++ b/src/bamToBed/Makefile
@@ -1,5 +1,5 @@
CXX= g++
-CXXFLAGS= -Wall -O3 -m64
+CXXFLAGS= -Wall -O3
LIBS= -lz
UTILITIES_DIR = ../utils/
OBJ_DIR = ../../obj/
diff --git a/src/closestBed/Makefile b/src/closestBed/Makefile
index 9f9b75a45bc49a822c57e750dcba0f784ad04061..12bd9e4bf10f0a42ec6be92535113a721d084d29 100755
--- a/src/closestBed/Makefile
+++ b/src/closestBed/Makefile
@@ -1,5 +1,5 @@
CXX = g++
-CXXFLAGS = -O3 -Wall -m64
+CXXFLAGS = -O3 -Wall
LDFLAGS =
UTILITIES_DIR = ../utils/
diff --git a/src/complementBed/Makefile b/src/complementBed/Makefile
index 6e13bcb63475176a39dfc18a823ed9d1489c2bf4..c58fa32cd0168724f0f6e8871a96bb7797e4e4de 100755
--- a/src/complementBed/Makefile
+++ b/src/complementBed/Makefile
@@ -1,5 +1,5 @@
CXX = g++
-CXXFLAGS = -O3 -Wall -m64
+CXXFLAGS = -O3 -Wall
LDFLAGS =
LIBFLAGS = -lc
diff --git a/src/coverageBed/Makefile b/src/coverageBed/Makefile
index 1a2babc83d748c3799594e7ea42ec5d6d84779a7..4de568d74ced3c675edd25fea38cfb7d59c8c5e8 100755
--- a/src/coverageBed/Makefile
+++ b/src/coverageBed/Makefile
@@ -1,5 +1,5 @@
CXX = g++
-CXXFLAGS = -O3 -Wall -m64
+CXXFLAGS = -O3 -Wall
LDFLAGS =
UTILITIES_DIR = ../utils/
diff --git a/src/fastaFromBed/Makefile b/src/fastaFromBed/Makefile
index bb196aed6542ba382077bf07a7008dd821886f25..30c07eb8899b1bba37b49eed5b69dd7ae7726415 100755
--- a/src/fastaFromBed/Makefile
+++ b/src/fastaFromBed/Makefile
@@ -1,5 +1,5 @@
CXX = g++
-CXXFLAGS = -O3 -Wall -m64
+CXXFLAGS = -O3 -Wall
LDFLAGS =
UTILITIES_DIR = ../utils/
diff --git a/src/genomeCoverageBed/Makefile b/src/genomeCoverageBed/Makefile
index d7368c04ba99a193dfef4f4b7e47ba0a3f2a59ef..59c4a5dfd34e223e29ed94290e58ce3e785d8f52 100755
--- a/src/genomeCoverageBed/Makefile
+++ b/src/genomeCoverageBed/Makefile
@@ -1,5 +1,5 @@
CXX = g++
-CXXFLAGS = -O3 -Wall -m64
+CXXFLAGS = -O3 -Wall
LDFLAGS =
UTILITIES_DIR = ../utils/
diff --git a/src/intersectBed/Makefile b/src/intersectBed/Makefile
index 923e1bc4328cc0f4efa5175f81f5c71db9327dc6..bdb5bd907aef7d1bde76dc44e2ffbc30216d1275 100755
--- a/src/intersectBed/Makefile
+++ b/src/intersectBed/Makefile
@@ -1,5 +1,5 @@
CXX= g++
-CXXFLAGS= -Wall -O3 -m64
+CXXFLAGS= -Wall -O3
LIBS= -lz
UTILITIES_DIR = ../utils/
OBJ_DIR = ../../obj/
diff --git a/src/linksBed/Makefile b/src/linksBed/Makefile
index 94812c5017c1c2caf70611816e1947ccb6c8df62..b4a2550ef0e5fbc4c33f57d8ff3e6f1a9204a777 100755
--- a/src/linksBed/Makefile
+++ b/src/linksBed/Makefile
@@ -1,5 +1,5 @@
CXX = g++
-CXXFLAGS = -O3 -Wall -m64
+CXXFLAGS = -O3 -Wall
LDFLAGS =
UTILITIES_DIR = ../utils/
diff --git a/src/maskFastaFromBed/Makefile b/src/maskFastaFromBed/Makefile
index 4a4472212975969439ed7ea9ac5ad71f5e92bcf3..650577a1379591918c287044e2721932a14dadf4 100755
--- a/src/maskFastaFromBed/Makefile
+++ b/src/maskFastaFromBed/Makefile
@@ -1,5 +1,5 @@
CXX = g++
-CXXFLAGS = -O3 -Wall -m64
+CXXFLAGS = -O3 -Wall
LDFLAGS =
UTILITIES_DIR = ../utils/
diff --git a/src/mergeBed/Makefile b/src/mergeBed/Makefile
index 87c4c70ac6ea6f4ada5a88389cb607a889790253..57231bbb9161d425488cde93cdcba6ed679017ea 100755
--- a/src/mergeBed/Makefile
+++ b/src/mergeBed/Makefile
@@ -1,5 +1,5 @@
CXX = g++
-CXXFLAGS = -O3 -Wall -m64
+CXXFLAGS = -O3 -Wall
LDFLAGS =
UTILITIES_DIR = ../utils/
diff --git a/src/pairToBed/Makefile b/src/pairToBed/Makefile
index 791f5b5e21d00fd19b7ac079198d89653ee058a5..8207271e69e39965acf17235d1300af0ca09975c 100755
--- a/src/pairToBed/Makefile
+++ b/src/pairToBed/Makefile
@@ -1,5 +1,5 @@
CXX = g++
-CXXFLAGS = -O3 -Wall -m64
+CXXFLAGS = -O3 -Wall
LDFLAGS =
LIBS= -lz
diff --git a/src/pairToBed/pairToBed.cpp b/src/pairToBed/pairToBed.cpp
index 8aa598e7b18bfd268b7db46ef466e1b9d199afe5..d696052af1bde04c0f00c345ef3ffb977a8ebf58 100755
--- a/src/pairToBed/pairToBed.cpp
+++ b/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);
}
}
diff --git a/src/pairToBed/test.bam b/src/pairToBed/test.bam
index 7415237a133dfedf9e1f5895a6de417cbf9941f9..a407e780e9d92f7576c9a7f59f812422cfd2ff8d 100644
Binary files a/src/pairToBed/test.bam and b/src/pairToBed/test.bam differ
diff --git a/src/pairToPair/Makefile b/src/pairToPair/Makefile
index 4693693ddd7a140469fd17183c6ae72bc84da428..0472ee36fee21d42447096e03a046a983b661829 100755
--- a/src/pairToPair/Makefile
+++ b/src/pairToPair/Makefile
@@ -1,5 +1,5 @@
CXX = g++
-CXXFLAGS = -O3 -Wall -m64
+CXXFLAGS = -O3 -Wall
LDFLAGS =
UTILITIES_DIR = ../utils/
diff --git a/src/shuffleBed/Makefile b/src/shuffleBed/Makefile
index c21d2011e9ebc930692071653b0b0b609557e884..369f97d9aea26b268afb21649d8d5e48b3f5c03b 100755
--- a/src/shuffleBed/Makefile
+++ b/src/shuffleBed/Makefile
@@ -1,5 +1,5 @@
CXX = g++
-CXXFLAGS = -O3 -Wall -m64
+CXXFLAGS = -O3 -Wall
LDFLAGS =
UTILITIES_DIR = ../utils/
diff --git a/src/slopBed/Makefile b/src/slopBed/Makefile
index 3e6677eedabac0b10b6bb43f396830753a98b2b1..f5c1c618d7f6cd553f49f3be94dd7cb9f12c25fc 100755
--- a/src/slopBed/Makefile
+++ b/src/slopBed/Makefile
@@ -1,5 +1,5 @@
CXX = g++
-CXXFLAGS = -O3 -Wall -m64
+CXXFLAGS = -O3 -Wall
LDFLAGS =
UTILITIES_DIR = ../utils/
diff --git a/src/sortBed/Makefile b/src/sortBed/Makefile
index 12134ca5f16f4095ff8a11ef7e9d43be448e24c3..904ea7ec19dd111a5d52022c7c50b9e9784ae86f 100755
--- a/src/sortBed/Makefile
+++ b/src/sortBed/Makefile
@@ -1,5 +1,5 @@
CXX = g++
-CXXFLAGS = -O3 -Wall -m64
+CXXFLAGS = -O3 -Wall
LDFLAGS =
UTILITIES_DIR = ../utils/
diff --git a/src/subtractBed/Makefile b/src/subtractBed/Makefile
index 0e3928f60edc6079c76e05c2326bfde5fb5d0ace..43a956e743a621a56860af3b2abf928e6519af75 100755
--- a/src/subtractBed/Makefile
+++ b/src/subtractBed/Makefile
@@ -1,5 +1,5 @@
CXX = g++
-CXXFLAGS = -O3 -Wall -m64
+CXXFLAGS = -O3 -Wall
LDFLAGS =
UTILITIES_DIR = ../utils/
diff --git a/src/utils/BamTools/Makefile b/src/utils/BamTools/Makefile
index 91c24ef353e61da13a8193f1a42bb5a8623f43c5..20a4193233453cbe6a29cd9515802cc7f1633f83 100644
--- a/src/utils/BamTools/Makefile
+++ b/src/utils/BamTools/Makefile
@@ -1,5 +1,5 @@
CXX = g++
-CXXFLAGS = -O3 -Wall -m64
+CXXFLAGS = -O3 -Wall
LDFLAGS =
OBJ_DIR = ../../../obj/
BIN_DIR = ../../../bin/
diff --git a/src/utils/bedFile/Makefile b/src/utils/bedFile/Makefile
index 5bb6b0de4c22633cc759fc46ebaef1cc88cf2df5..41a166865a358cbe0e3d07fc8bdd01620d8ad548 100755
--- a/src/utils/bedFile/Makefile
+++ b/src/utils/bedFile/Makefile
@@ -1,5 +1,5 @@
CXX = g++ -c
-CXXFLAGS = -O3 -Wall -m64
+CXXFLAGS = -O3 -Wall
LDFLAGS =
OBJ_DIR = ../../../obj/
BIN_DIR = ../../../bin/
diff --git a/src/utils/bedFilePE/Makefile b/src/utils/bedFilePE/Makefile
index fc15078cd4a64e3403b25f37ca53114780a52e0e..f3853d54ce6f93d53de24711103e276a8e70dae8 100755
--- a/src/utils/bedFilePE/Makefile
+++ b/src/utils/bedFilePE/Makefile
@@ -1,5 +1,5 @@
CXX = g++ -c
-CXXFLAGS = -O3 -Wall -m64
+CXXFLAGS = -O3 -Wall
LDFLAGS =
OBJ_DIR = ../../../obj/
BIN_DIR = ../../../bin/
diff --git a/src/windowBed/Makefile b/src/windowBed/Makefile
index 35f27f47992dd03890a5540c1053a44f49ac248e..3e81b17050c326f3108affe5acc97696aa73364a 100755
--- a/src/windowBed/Makefile
+++ b/src/windowBed/Makefile
@@ -1,5 +1,5 @@
CXX = g++
-CXXFLAGS = -O3 -Wall -m64
+CXXFLAGS = -O3 -Wall
LDFLAGS =
UTILITIES_DIR = ../utils/