rpms / BEDTools

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  1.   f24
  2.   bedtools-debugedit.patch
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diff -ur bedtools2-2.20.1/src/annotateBed/Makefile bedtools2-2.20.1.new/src/annotateBed/Makefile
--- bedtools2-2.20.1/src/annotateBed/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/annotateBed/Makefile	2014-08-25 09:10:49.597164885 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/bamToBed/Makefile bedtools2-2.20.1.new/src/bamToBed/Makefile
--- bedtools2-2.20.1/src/bamToBed/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/bamToBed/Makefile	2014-08-25 09:10:50.217223275 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/bamToFastq/Makefile bedtools2-2.20.1.new/src/bamToFastq/Makefile
--- bedtools2-2.20.1/src/bamToFastq/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/bamToFastq/Makefile	2014-08-25 09:10:50.349235706 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/bed12ToBed6/Makefile bedtools2-2.20.1.new/src/bed12ToBed6/Makefile
--- bedtools2-2.20.1/src/bed12ToBed6/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/bed12ToBed6/Makefile	2014-08-25 09:10:50.325233446 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/bedpeToBam/Makefile bedtools2-2.20.1.new/src/bedpeToBam/Makefile
--- bedtools2-2.20.1/src/bedpeToBam/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/bedpeToBam/Makefile	2014-08-25 09:10:50.250226383 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/bedToBam/Makefile bedtools2-2.20.1.new/src/bedToBam/Makefile
--- bedtools2-2.20.1/src/bedToBam/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/bedToBam/Makefile	2014-08-25 09:10:50.337234576 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/bedToIgv/Makefile bedtools2-2.20.1.new/src/bedToIgv/Makefile
--- bedtools2-2.20.1/src/bedToIgv/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/bedToIgv/Makefile	2014-08-25 09:10:50.212222804 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/clusterBed/Makefile bedtools2-2.20.1.new/src/clusterBed/Makefile
--- bedtools2-2.20.1/src/clusterBed/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/clusterBed/Makefile	2014-08-25 09:10:50.256226948 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/complementBed/Makefile bedtools2-2.20.1.new/src/complementBed/Makefile
--- bedtools2-2.20.1/src/complementBed/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/complementBed/Makefile	2014-08-25 09:10:50.263227607 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/coverageBed/Makefile bedtools2-2.20.1.new/src/coverageBed/Makefile
--- bedtools2-2.20.1/src/coverageBed/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/coverageBed/Makefile	2014-08-25 09:10:50.289230056 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/expand/Makefile bedtools2-2.20.1.new/src/expand/Makefile
--- bedtools2-2.20.1/src/expand/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/expand/Makefile	2014-08-25 09:10:49.606165733 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 
 # -------------------
diff -ur bedtools2-2.20.1/src/fastaFromBed/Makefile bedtools2-2.20.1.new/src/fastaFromBed/Makefile
--- bedtools2-2.20.1/src/fastaFromBed/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/fastaFromBed/Makefile	2014-08-25 09:10:50.241225535 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/flankBed/Makefile bedtools2-2.20.1.new/src/flankBed/Makefile
--- bedtools2-2.20.1/src/flankBed/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/flankBed/Makefile	2014-08-25 09:10:50.410241451 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/genomeCoverageBed/Makefile bedtools2-2.20.1.new/src/genomeCoverageBed/Makefile
--- bedtools2-2.20.1/src/genomeCoverageBed/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/genomeCoverageBed/Makefile	2014-08-25 09:10:50.308231845 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/getOverlap/Makefile bedtools2-2.20.1.new/src/getOverlap/Makefile
--- bedtools2-2.20.1/src/getOverlap/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/getOverlap/Makefile	2014-08-25 09:10:49.592164414 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 
 # -------------------
diff -ur bedtools2-2.20.1/src/groupBy/Makefile bedtools2-2.20.1.new/src/groupBy/Makefile
--- bedtools2-2.20.1/src/groupBy/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/groupBy/Makefile	2014-08-25 09:10:49.580163284 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 
 # -------------------
diff -ur bedtools2-2.20.1/src/intersectFile/Makefile bedtools2-2.20.1.new/src/intersectFile/Makefile
--- bedtools2-2.20.1/src/intersectFile/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/intersectFile/Makefile	2014-08-25 09:10:50.329233823 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/jaccard/Makefile bedtools2-2.20.1.new/src/jaccard/Makefile
--- bedtools2-2.20.1/src/jaccard/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/jaccard/Makefile	2014-08-25 09:10:50.357236460 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/linksBed/Makefile bedtools2-2.20.1.new/src/linksBed/Makefile
--- bedtools2-2.20.1/src/linksBed/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/linksBed/Makefile	2014-08-25 09:10:50.176219414 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/mapFile/Makefile bedtools2-2.20.1.new/src/mapFile/Makefile
--- bedtools2-2.20.1/src/mapFile/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/mapFile/Makefile	2014-08-25 09:10:50.341234953 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/maskFastaFromBed/Makefile bedtools2-2.20.1.new/src/maskFastaFromBed/Makefile
--- bedtools2-2.20.1/src/maskFastaFromBed/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/maskFastaFromBed/Makefile	2014-08-25 09:10:49.628167805 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/mergeFile/Makefile bedtools2-2.20.1.new/src/mergeFile/Makefile
--- bedtools2-2.20.1/src/mergeFile/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/mergeFile/Makefile	2014-08-25 09:10:50.283229491 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/multiBamCov/Makefile bedtools2-2.20.1.new/src/multiBamCov/Makefile
--- bedtools2-2.20.1/src/multiBamCov/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/multiBamCov/Makefile	2014-08-25 09:10:50.317232693 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/multiIntersectBed/Makefile bedtools2-2.20.1.new/src/multiIntersectBed/Makefile
--- bedtools2-2.20.1/src/multiIntersectBed/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/multiIntersectBed/Makefile	2014-08-25 09:10:50.193221015 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/nekSandbox1/Makefile bedtools2-2.20.1.new/src/nekSandbox1/Makefile
--- bedtools2-2.20.1/src/nekSandbox1/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/nekSandbox1/Makefile	2014-08-25 09:10:50.417242110 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/nucBed/Makefile bedtools2-2.20.1.new/src/nucBed/Makefile
--- bedtools2-2.20.1/src/nucBed/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/nucBed/Makefile	2014-08-25 09:10:50.201221768 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/pairToBed/Makefile bedtools2-2.20.1.new/src/pairToBed/Makefile
--- bedtools2-2.20.1/src/pairToBed/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/pairToBed/Makefile	2014-08-25 09:10:50.404240886 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/pairToPair/Makefile bedtools2-2.20.1.new/src/pairToPair/Makefile
--- bedtools2-2.20.1/src/pairToPair/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/pairToPair/Makefile	2014-08-25 09:10:50.300231092 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/randomBed/Makefile bedtools2-2.20.1.new/src/randomBed/Makefile
--- bedtools2-2.20.1/src/randomBed/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/randomBed/Makefile	2014-08-25 09:10:50.367237401 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/regressTest/Makefile bedtools2-2.20.1.new/src/regressTest/Makefile
--- bedtools2-2.20.1/src/regressTest/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/regressTest/Makefile	2014-08-25 09:10:49.610166110 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/reldist/Makefile bedtools2-2.20.1.new/src/reldist/Makefile
--- bedtools2-2.20.1/src/reldist/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/reldist/Makefile	2014-08-25 09:10:50.167218566 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/sampleFile/Makefile bedtools2-2.20.1.new/src/sampleFile/Makefile
--- bedtools2-2.20.1/src/sampleFile/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/sampleFile/Makefile	2014-08-25 09:10:49.584163661 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/shuffleBed/Makefile bedtools2-2.20.1.new/src/shuffleBed/Makefile
--- bedtools2-2.20.1/src/shuffleBed/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/shuffleBed/Makefile	2014-08-25 09:10:50.222223746 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/slopBed/Makefile bedtools2-2.20.1.new/src/slopBed/Makefile
--- bedtools2-2.20.1/src/slopBed/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/slopBed/Makefile	2014-08-25 09:10:50.183220073 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/sortBed/Makefile bedtools2-2.20.1.new/src/sortBed/Makefile
--- bedtools2-2.20.1/src/sortBed/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/sortBed/Makefile	2014-08-25 09:10:50.271228360 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/subtractBed/Makefile bedtools2-2.20.1.new/src/subtractBed/Makefile
--- bedtools2-2.20.1/src/subtractBed/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/subtractBed/Makefile	2014-08-25 09:10:49.619166957 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/tagBam/Makefile bedtools2-2.20.1.new/src/tagBam/Makefile
--- bedtools2-2.20.1/src/tagBam/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/tagBam/Makefile	2014-08-25 09:10:50.374238061 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/unionBedGraphs/Makefile bedtools2-2.20.1.new/src/unionBedGraphs/Makefile
--- bedtools2-2.20.1/src/unionBedGraphs/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/unionBedGraphs/Makefile	2014-08-25 09:10:50.394239944 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/windowBed/Makefile bedtools2-2.20.1.new/src/windowBed/Makefile
--- bedtools2-2.20.1/src/windowBed/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/windowBed/Makefile	2014-08-25 09:10:50.155217436 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
diff -ur bedtools2-2.20.1/src/windowMaker/Makefile bedtools2-2.20.1.new/src/windowMaker/Makefile
--- bedtools2-2.20.1/src/windowMaker/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/windowMaker/Makefile	2014-08-25 09:10:50.231224593 +0100
@@ -1,6 +1,6 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
+UTILITIES_DIR = ../utils
+OBJ_DIR = ../../obj
+BIN_DIR = ../../bin
 
 # -------------------
 # define our includes
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