[BEDTools] Update debugedit patch

verdurin verdurin at fedoraproject.org
Mon Aug 25 08:16:41 UTC 2014 

commit 0617f7d450a1afd2784603d76e974a791a71354a
Author: Adam Huffman <verdurin at fedoraproject.org>
Date:   Mon Aug 25 09:16:20 2014 +0100

    Update debugedit patch

 BEDTools.spec            |   12 +-
 bedtools-debugedit.patch |  533 ++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 542 insertions(+), 3 deletions(-)
---
diff --git a/BEDTools.spec b/BEDTools.spec
index 49d7270..ffa0baf 100644
--- a/BEDTools.spec
+++ b/BEDTools.spec
@@ -1,6 +1,6 @@
 Name:		BEDTools
 Version:	2.20.1
-Release:	3%{?dist}
+Release:	4%{?dist}
 Summary:	A flexible suite of utilities for comparing genomic features
 
 Group:		Applications/Engineering
@@ -10,7 +10,8 @@ URL:		https://github.com/arq5x/bedtools
 Source0:	https://github.com/arq5x/bedtools2/releases/download/v%{version}/bedtools-%{version}.tar.gz
 #Source1:	http://bedtools.googlecode.com/files/%{name}-User-Manual.v4.pdf
 #Fix debuginfo canonicalization error
-Patch0:		bedtools-debuginfo-path.patch
+Patch0:		bedtools-debugedit.patch
+Patch1:		bedtools-gzstream-path.patch
 BuildRoot:	%{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
 
 BuildRequires:	  zlib-devel
@@ -38,7 +39,8 @@ together.
 
 %prep
 %setup -q -n bedtools2-%{version}
-%patch0 -p1 -b .BEDTools.debuginfo
+%patch0 -p1 -b .BEDTools.debugedit
+%patch1 -p1 -b .BEDTools.gzstream
 
 # remove bundled curl library
 rm -rf src/utils/curl
@@ -130,6 +132,10 @@ rm -rf %{buildroot}
 #%doc %{name}-User-Manual.v4.pdf
 
 %changelog
+* Mon Aug 25 2014 Adam Huffman <bloch at verdurin.com> - 2.20.1-4
+- Update debugedit patch
+- Reinstate gzstream patch
+
 * Fri Aug 15 2014 Fedora Release Engineering <rel-eng at lists.fedoraproject.org> - 2.20.1-3
 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild
 
diff --git a/bedtools-debugedit.patch b/bedtools-debugedit.patch
new file mode 100644
index 0000000..b576cb5
--- /dev/null
+++ b/bedtools-debugedit.patch
@@ -0,0 +1,533 @@
+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/closestBed/Makefile bedtools2-2.20.1.new/src/closestBed/Makefile
+--- bedtools2-2.20.1/src/closestBed/Makefile	2014-05-24 02:35:47.000000000 +0100
++++ bedtools2-2.20.1.new/src/closestBed/Makefile	2014-08-25 09:10:50.383238908 +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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