diff --git a/BEDTools-double-parenthesis.patch b/BEDTools-double-parenthesis.patch
new file mode 100644
index 0000000..d91ecb0
--- /dev/null
+++ b/BEDTools-double-parenthesis.patch
@@ -0,0 +1,711 @@
+diff -ur bedtools2/src/annotateBed/Makefile bedtools2.new/src/annotateBed/Makefile
+--- bedtools2/src/annotateBed/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/annotateBed/Makefile	2016-08-06 07:49:57.388330540 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/bamToBed/Makefile bedtools2.new/src/bamToBed/Makefile
+--- bedtools2/src/bamToBed/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/bamToBed/Makefile	2016-08-06 07:49:57.286339582 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/bamToFastq/Makefile bedtools2.new/src/bamToFastq/Makefile
+--- bedtools2/src/bamToFastq/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/bamToFastq/Makefile	2016-08-06 07:49:57.362332845 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/bed12ToBed6/Makefile bedtools2.new/src/bed12ToBed6/Makefile
+--- bedtools2/src/bed12ToBed6/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/bed12ToBed6/Makefile	2016-08-06 07:49:57.243343394 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/bedpeToBam/Makefile bedtools2.new/src/bedpeToBam/Makefile
+--- bedtools2/src/bedpeToBam/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/bedpeToBam/Makefile	2016-08-06 07:49:57.288339405 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/bedToBam/Makefile bedtools2.new/src/bedToBam/Makefile
+--- bedtools2/src/bedToBam/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/bedToBam/Makefile	2016-08-06 07:49:57.369332224 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/bedToIgv/Makefile bedtools2.new/src/bedToIgv/Makefile
+--- bedtools2/src/bedToIgv/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/bedToIgv/Makefile	2016-08-06 07:49:57.282339937 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/closestFile/Makefile bedtools2.new/src/closestFile/Makefile
+--- bedtools2/src/closestFile/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/closestFile/Makefile	2016-08-06 07:49:57.379331338 +0100
+@@ -1,7 +1,7 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+-TOOL_DIR = ../../src/
++TOOL_DIR = ../../src
+ 
+ # -------------------
+ # define our includes
+diff -ur bedtools2/src/clusterBed/Makefile bedtools2.new/src/clusterBed/Makefile
+--- bedtools2/src/clusterBed/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/clusterBed/Makefile	2016-08-06 07:49:57.247343039 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/complementFile/Makefile bedtools2.new/src/complementFile/Makefile
+--- bedtools2/src/complementFile/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/complementFile/Makefile	2016-08-06 07:49:57.280340114 +0100
+@@ -1,7 +1,7 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+-TOOL_DIR = ../../src/
++TOOL_DIR = ../../src
+ 
+ # -------------------
+ # define our includes
+diff -ur bedtools2/src/coverageFile/Makefile bedtools2.new/src/coverageFile/Makefile
+--- bedtools2/src/coverageFile/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/coverageFile/Makefile	2016-08-06 07:49:57.259341976 +0100
+@@ -1,7 +1,7 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+-TOOL_DIR = ../../src/
++TOOL_DIR = ../../src
+ 
+ INCLUDES = -I$(UTILITIES_DIR)/Contexts/ \
+ 			-I$(UTILITIES_DIR)/general/ \
+diff -ur bedtools2/src/expand/Makefile bedtools2.new/src/expand/Makefile
+--- bedtools2/src/expand/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/expand/Makefile	2016-08-06 07:49:57.270341000 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/fastaFromBed/Makefile bedtools2.new/src/fastaFromBed/Makefile
+--- bedtools2/src/fastaFromBed/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/fastaFromBed/Makefile	2016-08-06 07:49:57.367332401 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/fisher/Makefile bedtools2.new/src/fisher/Makefile
+--- bedtools2/src/fisher/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/fisher/Makefile	2016-08-06 07:49:57.291339139 +0100
+@@ -1,7 +1,7 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+-TOOL_DIR = ../../src/
++TOOL_DIR = ../../src
+ 
+ # -------------------
+ # define our includes
+diff -ur bedtools2/src/flankBed/Makefile bedtools2.new/src/flankBed/Makefile
+--- bedtools2/src/flankBed/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/flankBed/Makefile	2016-08-06 07:49:57.358333199 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/genomeCoverageBed/Makefile bedtools2.new/src/genomeCoverageBed/Makefile
+--- bedtools2/src/genomeCoverageBed/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/genomeCoverageBed/Makefile	2016-08-06 07:49:57.277340380 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/getOverlap/Makefile bedtools2.new/src/getOverlap/Makefile
+--- bedtools2/src/getOverlap/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/getOverlap/Makefile	2016-08-06 07:49:57.254342419 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/groupBy/Makefile bedtools2.new/src/groupBy/Makefile
+--- bedtools2/src/groupBy/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/groupBy/Makefile	2016-08-06 07:49:57.266341355 +0100
+@@ -1,7 +1,7 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+-TOOL_DIR = ../../src/
++TOOL_DIR = ../../src
+ 
+ # -------------------
+ # define our includes
+diff -ur bedtools2/src/intersectFile/Makefile bedtools2.new/src/intersectFile/Makefile
+--- bedtools2/src/intersectFile/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/intersectFile/Makefile	2016-08-06 07:49:57.353333643 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/jaccard/Makefile bedtools2.new/src/jaccard/Makefile
+--- bedtools2/src/jaccard/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/jaccard/Makefile	2016-08-06 07:49:57.377331515 +0100
+@@ -1,7 +1,7 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+-TOOL_DIR = ../../src/
++TOOL_DIR = ../../src
+ 
+ # -------------------
+ # define our includes
+diff -ur bedtools2/src/linksBed/Makefile bedtools2.new/src/linksBed/Makefile
+--- bedtools2/src/linksBed/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/linksBed/Makefile	2016-08-06 07:49:57.261341798 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/mapFile/Makefile bedtools2.new/src/mapFile/Makefile
+--- bedtools2/src/mapFile/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/mapFile/Makefile	2016-08-06 07:49:57.383330983 +0100
+@@ -1,7 +1,7 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+-TOOL_DIR = ../../src/
++TOOL_DIR = ../../src
+ 
+ INCLUDES = -I$(UTILITIES_DIR)/Contexts/ \
+ 			-I$(UTILITIES_DIR)/general/ \
+diff -ur bedtools2/src/maskFastaFromBed/Makefile bedtools2.new/src/maskFastaFromBed/Makefile
+--- bedtools2/src/maskFastaFromBed/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/maskFastaFromBed/Makefile	2016-08-06 07:49:57.360333022 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/mergeFile/Makefile bedtools2.new/src/mergeFile/Makefile
+--- bedtools2/src/mergeFile/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/mergeFile/Makefile	2016-08-06 07:49:57.374331781 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/multiBamCov/Makefile bedtools2.new/src/multiBamCov/Makefile
+--- bedtools2/src/multiBamCov/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/multiBamCov/Makefile	2016-08-06 07:49:57.238343837 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/multiIntersectBed/Makefile bedtools2.new/src/multiIntersectBed/Makefile
+--- bedtools2/src/multiIntersectBed/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/multiIntersectBed/Makefile	2016-08-06 07:49:57.233344280 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/nekSandbox1/Makefile bedtools2.new/src/nekSandbox1/Makefile
+--- bedtools2/src/nekSandbox1/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/nekSandbox1/Makefile	2016-08-06 07:49:57.386330717 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/nucBed/Makefile bedtools2.new/src/nucBed/Makefile
+--- bedtools2/src/nucBed/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/nucBed/Makefile	2016-08-06 07:49:57.293338961 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/pairToBed/Makefile bedtools2.new/src/pairToBed/Makefile
+--- bedtools2/src/pairToBed/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/pairToBed/Makefile	2016-08-06 07:49:57.245343217 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/pairToPair/Makefile bedtools2.new/src/pairToPair/Makefile
+--- bedtools2/src/pairToPair/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/pairToPair/Makefile	2016-08-06 07:49:57.273340734 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/randomBed/Makefile bedtools2.new/src/randomBed/Makefile
+--- bedtools2/src/randomBed/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/randomBed/Makefile	2016-08-06 07:49:57.268341178 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/regressTest/Makefile bedtools2.new/src/regressTest/Makefile
+--- bedtools2/src/regressTest/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/regressTest/Makefile	2016-08-06 07:49:57.376331604 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/reldist/Makefile bedtools2.new/src/reldist/Makefile
+--- bedtools2/src/reldist/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/reldist/Makefile	2016-08-06 07:49:57.384330894 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/sampleFile/Makefile bedtools2.new/src/sampleFile/Makefile
+--- bedtools2/src/sampleFile/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/sampleFile/Makefile	2016-08-06 07:49:57.257342153 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/shiftBed/Makefile bedtools2.new/src/shiftBed/Makefile
+--- bedtools2/src/shiftBed/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/shiftBed/Makefile	2016-08-06 07:49:57.252342596 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/shuffleBed/Makefile bedtools2.new/src/shuffleBed/Makefile
+--- bedtools2/src/shuffleBed/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/shuffleBed/Makefile	2016-08-06 07:49:57.364332667 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/slopBed/Makefile bedtools2.new/src/slopBed/Makefile
+--- bedtools2/src/slopBed/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/slopBed/Makefile	2016-08-06 07:49:57.275340557 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/sortBed/Makefile bedtools2.new/src/sortBed/Makefile
+--- bedtools2/src/sortBed/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/sortBed/Makefile	2016-08-06 07:49:57.250342773 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/spacingFile/Makefile bedtools2.new/src/spacingFile/Makefile
+--- bedtools2/src/spacingFile/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/spacingFile/Makefile	2016-08-06 07:49:57.356333377 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/split/Makefile bedtools2.new/src/split/Makefile
+--- bedtools2/src/split/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/split/Makefile	2016-08-06 07:49:57.263341621 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/subtractFile/Makefile bedtools2.new/src/subtractFile/Makefile
+--- bedtools2/src/subtractFile/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/subtractFile/Makefile	2016-08-06 07:49:57.236344014 +0100
+@@ -1,7 +1,7 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+-TOOL_DIR = ../../src/
++TOOL_DIR = ../../src
+ 
+ # -------------------
+ # define our includes
+diff -ur bedtools2/src/tagBam/Makefile bedtools2.new/src/tagBam/Makefile
+--- bedtools2/src/tagBam/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/tagBam/Makefile	2016-08-06 07:49:57.295338784 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/unionBedGraphs/Makefile bedtools2.new/src/unionBedGraphs/Makefile
+--- bedtools2/src/unionBedGraphs/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/unionBedGraphs/Makefile	2016-08-06 07:49:57.381331160 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/utils/BamTools-Ancillary/Makefile bedtools2.new/src/utils/BamTools-Ancillary/Makefile
+--- bedtools2/src/utils/BamTools-Ancillary/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/utils/BamTools-Ancillary/Makefile	2016-08-06 07:49:57.349333997 +0100
+@@ -1,6 +1,6 @@
+ OBJ_DIR = ../../../obj/
+ BIN_DIR = ../../../bin/
+-UTILITIES_DIR = ../
++UTILITIES_DIR = ..
+ 
+ INCLUDES = -I$(UTILITIES_DIR)/BamTools/include \
+            -I$(UTILITIES_DIR)/bedFile/ \
+diff -ur bedtools2/src/utils/bedFile/Makefile bedtools2.new/src/utils/bedFile/Makefile
+--- bedtools2/src/utils/bedFile/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/utils/bedFile/Makefile	2016-08-06 07:49:57.317336834 +0100
+@@ -1,6 +1,6 @@
+ OBJ_DIR = ../../../obj/
+ BIN_DIR = ../../../bin/
+-UTILITIES_DIR = ../../utils/
++UTILITIES_DIR = ../../utils
+ # -------------------
+ # define our includes
+ # -------------------
+diff -ur bedtools2/src/utils/bedFilePE/Makefile bedtools2.new/src/utils/bedFilePE/Makefile
+--- bedtools2/src/utils/bedFilePE/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/utils/bedFilePE/Makefile	2016-08-06 07:49:57.334335327 +0100
+@@ -1,6 +1,6 @@
+ OBJ_DIR = ../../../obj/
+ BIN_DIR = ../../../bin/
+-UTILITIES_DIR = ../../utils/
++UTILITIES_DIR = ../../utils
+ # -------------------
+ # define our includes
+ # -------------------
+diff -ur bedtools2/src/utils/bedGraphFile/Makefile bedtools2.new/src/utils/bedGraphFile/Makefile
+--- bedtools2/src/utils/bedGraphFile/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/utils/bedGraphFile/Makefile	2016-08-06 07:49:57.332335504 +0100
+@@ -1,6 +1,6 @@
+ OBJ_DIR = ../../../obj/
+ BIN_DIR = ../../../bin/
+-UTILITIES_DIR = ../../utils/
++UTILITIES_DIR = ../../utils
+ # -------------------
+ # define our includes
+ # -------------------
+diff -ur bedtools2/src/utils/BinTree/Makefile bedtools2.new/src/utils/BinTree/Makefile
+--- bedtools2/src/utils/BinTree/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/utils/BinTree/Makefile	2016-08-06 07:49:57.330335681 +0100
+@@ -1,6 +1,6 @@
+ OBJ_DIR = ../../../obj/
+ BIN_DIR = ../../../bin/
+-UTILITIES_DIR = ../../utils/
++UTILITIES_DIR = ../../utils
+ # -------------------
+ # define our includes
+ # -------------------
+diff -ur bedtools2/src/utils/BlockedIntervals/Makefile bedtools2.new/src/utils/BlockedIntervals/Makefile
+--- bedtools2/src/utils/BlockedIntervals/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/utils/BlockedIntervals/Makefile	2016-08-06 07:49:57.321336479 +0100
+@@ -1,6 +1,6 @@
+ OBJ_DIR = ../../../obj/
+ BIN_DIR = ../../../bin/
+-UTILITIES_DIR = ../
++UTILITIES_DIR = ..
+ 
+ INCLUDES = -I$(UTILITIES_DIR)/BamTools/include \
+            -I$(UTILITIES_DIR)/bedFile/ \
+diff -ur bedtools2/src/utils/chromsweep/Makefile bedtools2.new/src/utils/chromsweep/Makefile
+--- bedtools2/src/utils/chromsweep/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/utils/chromsweep/Makefile	2016-08-06 07:49:57.351333820 +0100
+@@ -1,6 +1,6 @@
+ OBJ_DIR = ../../../obj/
+ BIN_DIR = ../../../bin/
+-UTILITIES_DIR = ../../utils/
++UTILITIES_DIR = ../../utils
+ # -------------------
+ # define our includes
+ # -------------------
+diff -ur bedtools2/src/utils/Contexts/Makefile bedtools2.new/src/utils/Contexts/Makefile
+--- bedtools2/src/utils/Contexts/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/utils/Contexts/Makefile	2016-08-06 07:49:57.319336657 +0100
+@@ -1,6 +1,6 @@
+ OBJ_DIR = ../../../obj/
+ BIN_DIR = ../../../bin/
+-UTILITIES_DIR = ../../utils/
++UTILITIES_DIR = ../../utils
+ # -------------------
+ # define our includes
+ # -------------------
+diff -ur bedtools2/src/utils/driver/Makefile bedtools2.new/src/utils/driver/Makefile
+--- bedtools2/src/utils/driver/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/utils/driver/Makefile	2016-08-06 07:49:57.308337632 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../../utils/
++UTILITIES_DIR = ../../utils
+ TOOLS_DIR = ../../../src/
+ OBJ_DIR = ../../../obj/
+ BIN_DIR = ../../../bin/
+diff -ur bedtools2/src/utils/Fasta/Makefile bedtools2.new/src/utils/Fasta/Makefile
+--- bedtools2/src/utils/Fasta/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/utils/Fasta/Makefile	2016-08-06 07:49:57.323336302 +0100
+@@ -1,6 +1,6 @@
+ OBJ_DIR = ../../../obj/
+ BIN_DIR = ../../../bin/
+-UTILITIES_DIR = ../../utils/
++UTILITIES_DIR = ../../utils
+ # -------------------
+ # define our includes
+ # -------------------
+diff -ur bedtools2/src/utils/FileRecordTools/FileReaders/Makefile bedtools2.new/src/utils/FileRecordTools/FileReaders/Makefile
+--- bedtools2/src/utils/FileRecordTools/FileReaders/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/utils/FileRecordTools/FileReaders/Makefile	2016-08-06 07:49:57.345334352 +0100
+@@ -1,6 +1,6 @@
+ OBJ_DIR = ../../../../obj/
+ BIN_DIR = ../../../../bin/
+-UTILITIES_DIR = ../../../utils/
++UTILITIES_DIR = ../../../utils
+ # -------------------
+ # define our includes
+ # -------------------
+diff -ur bedtools2/src/utils/FileRecordTools/Makefile bedtools2.new/src/utils/FileRecordTools/Makefile
+--- bedtools2/src/utils/FileRecordTools/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/utils/FileRecordTools/Makefile	2016-08-06 07:49:57.340334795 +0100
+@@ -1,6 +1,6 @@
+ OBJ_DIR = ../../../obj/
+ BIN_DIR = ../../../bin/
+-UTILITIES_DIR = ../../utils/
++UTILITIES_DIR = ../../utils
+ # -------------------
+ # define our includes
+ # -------------------
+diff -ur bedtools2/src/utils/FileRecordTools/Records/Makefile bedtools2.new/src/utils/FileRecordTools/Records/Makefile
+--- bedtools2/src/utils/FileRecordTools/Records/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/utils/FileRecordTools/Records/Makefile	2016-08-06 07:49:57.343334529 +0100
+@@ -1,6 +1,6 @@
+ OBJ_DIR = ../../../../obj/
+ BIN_DIR = ../../../../bin/
+-UTILITIES_DIR = ../../../utils/
++UTILITIES_DIR = ../../../utils
+ # -------------------
+ # define our includes
+ # -------------------
+diff -ur bedtools2/src/utils/fileType/Makefile bedtools2.new/src/utils/fileType/Makefile
+--- bedtools2/src/utils/fileType/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/utils/fileType/Makefile	2016-08-06 07:49:57.299338430 +0100
+@@ -1,6 +1,6 @@
+ OBJ_DIR = ../../../obj/
+ BIN_DIR = ../../../bin/
+-UTILITIES_DIR = ../../utils/
++UTILITIES_DIR = ../../utils
+ # -------------------
+ # define our includes
+ # -------------------
+diff -ur bedtools2/src/utils/general/Makefile bedtools2.new/src/utils/general/Makefile
+--- bedtools2/src/utils/general/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/utils/general/Makefile	2016-08-06 07:49:57.297338607 +0100
+@@ -1,6 +1,6 @@
+ OBJ_DIR = ../../../obj/
+ BIN_DIR = ../../../bin/
+-UTILITIES_DIR = ../../utils/
++UTILITIES_DIR = ../../utils
+ # -------------------
+ # define our includes
+ # -------------------
+diff -ur bedtools2/src/utils/GenomeFile/Makefile bedtools2.new/src/utils/GenomeFile/Makefile
+--- bedtools2/src/utils/GenomeFile/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/utils/GenomeFile/Makefile	2016-08-06 07:49:57.310337454 +0100
+@@ -1,6 +1,6 @@
+ OBJ_DIR = ../../../obj/
+ BIN_DIR = ../../../bin/
+-UTILITIES_DIR = ../
++UTILITIES_DIR = ..
+ # -------------------
+ # define our includes
+ # -------------------
+diff -ur bedtools2/src/utils/gzstream/Makefile bedtools2.new/src/utils/gzstream/Makefile
+--- bedtools2/src/utils/gzstream/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/utils/gzstream/Makefile	2016-08-06 07:49:57.313337189 +0100
+@@ -35,7 +35,7 @@
+ INCLUDES = -I.
+ OBJ_DIR = ../../../obj/
+ BIN_DIR = ../../../bin/
+-UTILITIES_DIR = ../../utils/
++UTILITIES_DIR = ../../utils
+ 	
+ ${OBJ_DIR}/gzstream.o : gzstream.C gzstream.h
+ 	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c -o $(OBJ_DIR)/gzstream.o gzstream.C $(INCLUDES)
+diff -ur bedtools2/src/utils/KeyListOps/Makefile bedtools2.new/src/utils/KeyListOps/Makefile
+--- bedtools2/src/utils/KeyListOps/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/utils/KeyListOps/Makefile	2016-08-06 07:49:57.338334972 +0100
+@@ -1,6 +1,6 @@
+ OBJ_DIR = ../../../obj/
+ BIN_DIR = ../../../bin/
+-UTILITIES_DIR = ../../utils/
++UTILITIES_DIR = ../../utils
+ # -------------------
+ # define our includes
+ # -------------------
+diff -ur bedtools2/src/utils/NewChromsweep/Makefile bedtools2.new/src/utils/NewChromsweep/Makefile
+--- bedtools2/src/utils/NewChromsweep/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/utils/NewChromsweep/Makefile	2016-08-06 07:49:57.304337986 +0100
+@@ -1,6 +1,6 @@
+ OBJ_DIR = ../../../obj/
+ BIN_DIR = ../../../bin/
+-UTILITIES_DIR = ../../utils/
++UTILITIES_DIR = ../../utils
+ # -------------------
+ # define our includes
+ # -------------------
+diff -ur bedtools2/src/utils/RecordOutputMgr/Makefile bedtools2.new/src/utils/RecordOutputMgr/Makefile
+--- bedtools2/src/utils/RecordOutputMgr/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/utils/RecordOutputMgr/Makefile	2016-08-06 07:49:57.347334174 +0100
+@@ -1,6 +1,6 @@
+ OBJ_DIR = ../../../obj/
+ BIN_DIR = ../../../bin/
+-UTILITIES_DIR = ../../utils/
++UTILITIES_DIR = ../../utils
+ # -------------------
+ # define our includes
+ # -------------------
+diff -ur bedtools2/src/utils/sequenceUtilities/Makefile bedtools2.new/src/utils/sequenceUtilities/Makefile
+--- bedtools2/src/utils/sequenceUtilities/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/utils/sequenceUtilities/Makefile	2016-08-06 07:49:57.315337011 +0100
+@@ -1,6 +1,6 @@
+ OBJ_DIR = ../../../obj/
+ BIN_DIR = ../../../bin/
+-UTILITIES_DIR = ../../utils/
++UTILITIES_DIR = ../../utils
+ # -------------------
+ # define our includes
+ # -------------------
+diff -ur bedtools2/src/utils/tabFile/Makefile bedtools2.new/src/utils/tabFile/Makefile
+--- bedtools2/src/utils/tabFile/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/utils/tabFile/Makefile	2016-08-06 07:49:57.336335150 +0100
+@@ -1,6 +1,6 @@
+ OBJ_DIR = ../../../obj/
+ BIN_DIR = ../../../bin/
+-UTILITIES_DIR = ../../utils/
++UTILITIES_DIR = ../../utils
+ # -------------------
+ # define our includes
+ # -------------------
+diff -ur bedtools2/src/utils/ToolBase/Makefile bedtools2.new/src/utils/ToolBase/Makefile
+--- bedtools2/src/utils/ToolBase/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/utils/ToolBase/Makefile	2016-08-06 07:49:57.306337809 +0100
+@@ -1,6 +1,6 @@
+ OBJ_DIR = ../../../obj/
+ BIN_DIR = ../../../bin/
+-UTILITIES_DIR = ../../utils/
++UTILITIES_DIR = ../../utils
+ # -------------------
+ # define our includes
+ # -------------------
+diff -ur bedtools2/src/utils/VectorOps/Makefile bedtools2.new/src/utils/VectorOps/Makefile
+--- bedtools2/src/utils/VectorOps/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/utils/VectorOps/Makefile	2016-08-06 07:49:57.325336125 +0100
+@@ -1,6 +1,6 @@
+ OBJ_DIR = ../../../obj/
+ BIN_DIR = ../../../bin/
+-UTILITIES_DIR = ../../utils/
++UTILITIES_DIR = ../../utils
+ 
+ # ----------------------------------
+ # define our source and object files
+diff -ur bedtools2/src/utils/version/Makefile bedtools2.new/src/utils/version/Makefile
+--- bedtools2/src/utils/version/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/utils/version/Makefile	2016-08-06 07:49:57.301338252 +0100
+@@ -1,6 +1,6 @@
+ OBJ_DIR = ../../../obj/
+ BIN_DIR = ../../../bin/
+-UTILITIES_DIR = ../../utils/
++UTILITIES_DIR = ../../utils
+ # -------------------
+ # define our includes
+ # -------------------
+diff -ur bedtools2/src/windowBed/Makefile bedtools2.new/src/windowBed/Makefile
+--- bedtools2/src/windowBed/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/windowBed/Makefile	2016-08-06 07:49:57.284339759 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+ 
+diff -ur bedtools2/src/windowMaker/Makefile bedtools2.new/src/windowMaker/Makefile
+--- bedtools2/src/windowMaker/Makefile	2016-07-06 23:25:44.000000000 +0100
++++ bedtools2.new/src/windowMaker/Makefile	2016-08-06 07:49:57.241343571 +0100
+@@ -1,4 +1,4 @@
+-UTILITIES_DIR = ../utils/
++UTILITIES_DIR = ../utils
+ OBJ_DIR = ../../obj/
+ BIN_DIR = ../../bin/
+