From 2fa88f335025407514d4503d2766d1b52d7763ee Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E2=80=9Carq5x=E2=80=9D?= <“aaronquinlan@gmail.com”>
Date: Tue, 5 May 2009 11:29:05 -0400
Subject: [PATCH] Added version.h to simplify versioning

---
 bin/closestBed                               | Bin 78336 -> 78336 bytes
 bin/complementBed                            | Bin 74896 -> 74896 bytes
 bin/coverageBed                              | Bin 74168 -> 74168 bytes
 bin/fastaFromBed                             | Bin 79348 -> 79348 bytes
 bin/genomeCoverageBed                        | Bin 94712 -> 94712 bytes
 bin/intersectBed                             | Bin 82324 -> 82324 bytes
 bin/linksBed                                 | Bin 78776 -> 78776 bytes
 bin/mergeBed                                 | Bin 77932 -> 77932 bytes
 bin/peIntersectBed                           | Bin 91120 -> 91120 bytes
 bin/sortBed                                  | Bin 70332 -> 70332 bytes
 bin/subtractBed                              | Bin 73936 -> 73936 bytes
 bin/windowBed                                | Bin 73944 -> 73944 bytes
 obj/closestMain.o                            | Bin 6848 -> 6848 bytes
 obj/complementMain.o                         | Bin 6252 -> 6252 bytes
 obj/coverageMain.o                           | Bin 5796 -> 5796 bytes
 obj/fastaFromBedMain.o                       | Bin 7120 -> 7120 bytes
 obj/genomeCoverageMain.o                     | Bin 8268 -> 8268 bytes
 obj/intersectMain.o                          | Bin 10156 -> 10156 bytes
 obj/linksMain.o                              | Bin 8904 -> 8904 bytes
 obj/mergeMain.o                              | Bin 7120 -> 7120 bytes
 obj/peIntersectMain.o                        | Bin 11236 -> 11236 bytes
 obj/sortMain.o                               | Bin 8772 -> 8772 bytes
 obj/subtractMain.o                           | Bin 7284 -> 7284 bytes
 obj/windowMain.o                             | Bin 11244 -> 11244 bytes
 src/closestBed/Makefile                      |   2 +-
 src/closestBed/closestMain.cpp               |   4 +---
 src/complementBed/Makefile                   |   2 +-
 src/complementBed/complementMain.cpp         |   3 +--
 src/coverageBed/Makefile                     |   2 +-
 src/coverageBed/coverageMain.cpp             |   6 ++----
 src/fastaFromBed/Makefile                    |   2 +-
 src/fastaFromBed/fastaFromBedMain.cpp        |   3 +--
 src/genomeCoverageBed/Makefile               |   2 +-
 src/genomeCoverageBed/genomeCoverageMain.cpp |   3 +--
 src/intersectBed/Makefile                    |   2 +-
 src/intersectBed/intersectMain.cpp           |   3 +--
 src/linksBed/Makefile                        |   2 +-
 src/linksBed/linksMain.cpp                   |   3 +--
 src/mergeBed/Makefile                        |   2 +-
 src/mergeBed/mergeMain.cpp                   |   3 +--
 src/peIntersectBed/Makefile                  |   2 +-
 src/peIntersectBed/peIntersectBed.cpp        |   2 +-
 src/peIntersectBed/peIntersectMain.cpp       |   4 +---
 src/sortBed/Makefile                         |   2 +-
 src/sortBed/sortMain.cpp                     |   3 +--
 src/subtractBed/Makefile                     |   2 +-
 src/subtractBed/subtractMain.cpp             |   3 +--
 src/utils/version/version.h                  |   7 +++++++
 src/windowBed/Makefile                       |   2 +-
 src/windowBed/windowMain.cpp                 |   5 ++---
 50 files changed, 34 insertions(+), 42 deletions(-)
 create mode 100644 src/utils/version/version.h

diff --git a/bin/closestBed b/bin/closestBed
index 38828d57841498707bfa4e2b4100a552ddeb7379..d40f5ed0385a496d725414e187e900042fb6094f 100755
GIT binary patch
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delta 18
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diff --git a/bin/complementBed b/bin/complementBed
index d2d85c9bf399072c69f9f17193661013ee117094..c1a7c6654833eab43772c9ab45b876c00ab3c768 100755
GIT binary patch
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diff --git a/bin/coverageBed b/bin/coverageBed
index 37b6808c6bc90e0a044c2c62ed0fa6801dafccd0..dae26ad1341da08355f45f40a01a35e727ff30b2 100755
GIT binary patch
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diff --git a/bin/fastaFromBed b/bin/fastaFromBed
index b4ba0479184cfd753b82f2bd5dcb497cfedf253e..470987951012070135550a48b76eb18f631ed04f 100755
GIT binary patch
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diff --git a/bin/genomeCoverageBed b/bin/genomeCoverageBed
index fa91bf3ac714a6834d32e11e9ac6a0daf62c3602..36424f979729f495a8e41a1ebf15e0bf07b85726 100755
GIT binary patch
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diff --git a/bin/intersectBed b/bin/intersectBed
index 52dee09c309c25f7742a18bbac963cf4c0cb5c8b..9fc2522cfd56bd7eb6c416556811894cf82cee49 100755
GIT binary patch
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diff --git a/bin/linksBed b/bin/linksBed
index 604f04f714e4abcddb0e0783cc12b275b9de54ed..beff05fa4612f5b1b7e8e564aef0ec52e143c7a6 100755
GIT binary patch
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delta 18
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diff --git a/bin/mergeBed b/bin/mergeBed
index bac48035f4d71ed3502f051a79be5841b7abb32e..31bfacd9569c7d588d2e245fe143c11a57ebc938 100755
GIT binary patch
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delta 18
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diff --git a/bin/peIntersectBed b/bin/peIntersectBed
index d206b4f971d84816e93d18b87d1084cb6449edbc..bbdf206a050d24d793fdda3517073c455929138a 100755
GIT binary patch
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diff --git a/bin/sortBed b/bin/sortBed
index 4e17557463da0f0b4839b3c6546cdef24307f838..2951603d77aa5514f93fd7ece20de40b00f5ad68 100755
GIT binary patch
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diff --git a/bin/subtractBed b/bin/subtractBed
index 9d0b9295965c22d51ad9561fa4b03698a2570cff..5e1658d43563f48d608b3d721344a3ae160ead84 100755
GIT binary patch
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delta 18
acmca`kmbTbmJO}@nGN-fHh1jzNCW^?00>q9

diff --git a/bin/windowBed b/bin/windowBed
index c2a78a47a34f32e142c57ab1735c5c89d13fc18e..7b4159aab992f275f926ef4d70a3ade5abe64e06 100755
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diff --git a/obj/closestMain.o b/obj/closestMain.o
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GIT binary patch
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diff --git a/obj/complementMain.o b/obj/complementMain.o
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GIT binary patch
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diff --git a/obj/coverageMain.o b/obj/coverageMain.o
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GIT binary patch
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diff --git a/obj/fastaFromBedMain.o b/obj/fastaFromBedMain.o
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diff --git a/obj/genomeCoverageMain.o b/obj/genomeCoverageMain.o
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diff --git a/obj/intersectMain.o b/obj/intersectMain.o
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diff --git a/obj/linksMain.o b/obj/linksMain.o
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diff --git a/obj/mergeMain.o b/obj/mergeMain.o
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diff --git a/obj/peIntersectMain.o b/obj/peIntersectMain.o
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diff --git a/obj/sortMain.o b/obj/sortMain.o
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diff --git a/obj/subtractMain.o b/obj/subtractMain.o
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diff --git a/obj/windowMain.o b/obj/windowMain.o
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GIT binary patch
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diff --git a/src/closestBed/Makefile b/src/closestBed/Makefile
index 56a35336..b5b5c051 100755
--- a/src/closestBed/Makefile
+++ b/src/closestBed/Makefile
@@ -9,7 +9,7 @@ BIN_DIR = ../../bin/
 # -------------------
 # define our includes
 # -------------------
-INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/
+INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/
 
 # ----------------------------------
 # define our source and object files
diff --git a/src/closestBed/closestMain.cpp b/src/closestBed/closestMain.cpp
index 529a64f8..4886a188 100755
--- a/src/closestBed/closestMain.cpp
+++ b/src/closestBed/closestMain.cpp
@@ -1,13 +1,11 @@
 #include "closestBed.h"
+#include "version.h"
 
 using namespace std;
 
 // define our program name
 #define PROGRAM_NAME "closestBed"
 
-// define the version
-#define VERSION "1.2.0"
-
 // define our parameter checking macro
 #define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
 
diff --git a/src/complementBed/Makefile b/src/complementBed/Makefile
index 72aee529..c58fa32c 100755
--- a/src/complementBed/Makefile
+++ b/src/complementBed/Makefile
@@ -10,7 +10,7 @@ BIN_DIR = ../../bin/
 # -------------------
 # define our includes
 # -------------------
-INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/
+INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/
 
 # ----------------------------------
 # define our source and object files
diff --git a/src/complementBed/complementMain.cpp b/src/complementBed/complementMain.cpp
index e62871eb..b7eac980 100755
--- a/src/complementBed/complementMain.cpp
+++ b/src/complementBed/complementMain.cpp
@@ -1,13 +1,12 @@
 #include <iostream>	
 #include "complementBed.h"
+#include "version.h"
 
 using namespace std;
 
 // define our program name
 #define PROGRAM_NAME "complementBed"
 
-// define the version
-#define VERSION "1.2.0"
 
 // define our parameter checking macro
 #define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
diff --git a/src/coverageBed/Makefile b/src/coverageBed/Makefile
index fd84f6d5..61415f21 100755
--- a/src/coverageBed/Makefile
+++ b/src/coverageBed/Makefile
@@ -9,7 +9,7 @@ BIN_DIR = ../../bin/
 # -------------------
 # define our includes
 # -------------------
-INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/
+INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/
 
 # ----------------------------------
 # define our source and object files
diff --git a/src/coverageBed/coverageMain.cpp b/src/coverageBed/coverageMain.cpp
index 65c99835..59094e2d 100755
--- a/src/coverageBed/coverageMain.cpp
+++ b/src/coverageBed/coverageMain.cpp
@@ -1,12 +1,10 @@
 #include "coverageBed.h"
+#include "version.h"
 
 using namespace std;
 
-// define our program name
-#define PROGRAM_NAME "coverageBed"
-
 // define the version
-#define VERSION "1.2.0"
+#define PROGRAM_NAME "coverageBed"
 
 // define our parameter checking macro
 #define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
diff --git a/src/fastaFromBed/Makefile b/src/fastaFromBed/Makefile
index b9f32efd..3b703f2d 100755
--- a/src/fastaFromBed/Makefile
+++ b/src/fastaFromBed/Makefile
@@ -9,7 +9,7 @@ BIN_DIR = ../../bin/
 # -------------------
 # define our includes
 # -------------------
-INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/sequenceUtilities/ -I$(UTILITIES_DIR)/lineFileUtilities/
+INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/sequenceUtilities/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/
 
 # ----------------------------------
 # define our source and object files
diff --git a/src/fastaFromBed/fastaFromBedMain.cpp b/src/fastaFromBed/fastaFromBedMain.cpp
index 3ee017e3..e5bd2527 100755
--- a/src/fastaFromBed/fastaFromBedMain.cpp
+++ b/src/fastaFromBed/fastaFromBedMain.cpp
@@ -1,12 +1,11 @@
 #include "fastaFromBed.h"
+#include "version.h"
 
 using namespace std;
 
 // define our program name
 #define PROGRAM_NAME "fastaFromBed"
 
-// define the version
-#define VERSION "1.2.0"
 
 // define our parameter checking macro
 #define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
diff --git a/src/genomeCoverageBed/Makefile b/src/genomeCoverageBed/Makefile
index 1d150650..de644817 100755
--- a/src/genomeCoverageBed/Makefile
+++ b/src/genomeCoverageBed/Makefile
@@ -9,7 +9,7 @@ BIN_DIR = ../../bin/
 # -------------------
 # define our includes
 # -------------------
-INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/
+INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/
 
 # ----------------------------------
 # define our source and object files
diff --git a/src/genomeCoverageBed/genomeCoverageMain.cpp b/src/genomeCoverageBed/genomeCoverageMain.cpp
index 48f7efee..b64cbacf 100755
--- a/src/genomeCoverageBed/genomeCoverageMain.cpp
+++ b/src/genomeCoverageBed/genomeCoverageMain.cpp
@@ -1,13 +1,12 @@
 #include <iostream>	
 #include "genomeCoverageBed.h"
+#include "version.h"
 
 using namespace std;
 
 // define our program name
 #define PROGRAM_NAME "coverageBed"
 
-// define the version
-#define VERSION "1.2.0"
 
 // define our parameter checking macro
 #define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
diff --git a/src/intersectBed/Makefile b/src/intersectBed/Makefile
index b039979e..3bdc6fcf 100755
--- a/src/intersectBed/Makefile
+++ b/src/intersectBed/Makefile
@@ -9,7 +9,7 @@ BIN_DIR = ../../bin/
 # -------------------
 # define our includes
 # -------------------
-INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/
+INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/
 
 # ----------------------------------
 # define our source and object files
diff --git a/src/intersectBed/intersectMain.cpp b/src/intersectBed/intersectMain.cpp
index 17fe0c9e..a6fe61b9 100755
--- a/src/intersectBed/intersectMain.cpp
+++ b/src/intersectBed/intersectMain.cpp
@@ -1,12 +1,11 @@
 #include "intersectBed.h"
+#include "version.h"
 
 using namespace std;
 
 // define our program name
 #define PROGRAM_NAME "intersectBed"
 
-// define the version
-#define VERSION "1.2.0"
 
 // define our parameter checking macro
 #define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
diff --git a/src/linksBed/Makefile b/src/linksBed/Makefile
index 2fa4c671..dc3f45ad 100755
--- a/src/linksBed/Makefile
+++ b/src/linksBed/Makefile
@@ -9,7 +9,7 @@ BIN_DIR = ../../bin/
 # -------------------
 # define our includes
 # -------------------
-INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/
+INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/
 
 # ----------------------------------
 # define our source and object files
diff --git a/src/linksBed/linksMain.cpp b/src/linksBed/linksMain.cpp
index 50056773..a5383a3d 100755
--- a/src/linksBed/linksMain.cpp
+++ b/src/linksBed/linksMain.cpp
@@ -1,13 +1,12 @@
 #include <iostream>	
 #include "linksBed.h"
+#include "version.h"
 
 using namespace std;
 
 // define our program name
 #define PROGRAM_NAME "linksBed"
 
-// define the version
-#define VERSION "1.2.0"
 
 // define our parameter checking macro
 #define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
diff --git a/src/mergeBed/Makefile b/src/mergeBed/Makefile
index 0bffbdf0..219e6546 100755
--- a/src/mergeBed/Makefile
+++ b/src/mergeBed/Makefile
@@ -9,7 +9,7 @@ BIN_DIR = ../../bin/
 # -------------------
 # define our includes
 # -------------------
-INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/
+INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/
 
 # ----------------------------------
 # define our source and object files
diff --git a/src/mergeBed/mergeMain.cpp b/src/mergeBed/mergeMain.cpp
index 19df09f5..a9ecd37b 100755
--- a/src/mergeBed/mergeMain.cpp
+++ b/src/mergeBed/mergeMain.cpp
@@ -1,13 +1,12 @@
 #include <iostream>	
 #include "mergeBed.h"
+#include "version.h"
 
 using namespace std;
 
 // define our program name
 #define PROGRAM_NAME "mergeBed"
 
-// define the version
-#define VERSION "1.2.0"
 
 // define our parameter checking macro
 #define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
diff --git a/src/peIntersectBed/Makefile b/src/peIntersectBed/Makefile
index 9dc7bc5d..3d7eda6c 100755
--- a/src/peIntersectBed/Makefile
+++ b/src/peIntersectBed/Makefile
@@ -9,7 +9,7 @@ BIN_DIR = ../../bin/
 # -------------------
 # define our includes
 # -------------------
-INCLUDES = -I$(UTILITIES_DIR)/bedFilePE/ -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/
+INCLUDES = -I$(UTILITIES_DIR)/bedFilePE/ -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/
 
 # ----------------------------------
 # define our source and object files
diff --git a/src/peIntersectBed/peIntersectBed.cpp b/src/peIntersectBed/peIntersectBed.cpp
index e6bc0850..da8e022a 100755
--- a/src/peIntersectBed/peIntersectBed.cpp
+++ b/src/peIntersectBed/peIntersectBed.cpp
@@ -223,7 +223,7 @@ void BedIntersectPE::IntersectBedPE() {
 					vector<BED> hits1, hits2;
 					FindOverlaps(a, hits1, hits2, this->searchType);
 				}
-								
+				
 			}
 		}
 	}
diff --git a/src/peIntersectBed/peIntersectMain.cpp b/src/peIntersectBed/peIntersectMain.cpp
index 0e0b16b8..ce185518 100755
--- a/src/peIntersectBed/peIntersectMain.cpp
+++ b/src/peIntersectBed/peIntersectMain.cpp
@@ -1,13 +1,11 @@
 #include "peIntersectBed.h"
+#include "version.h"
 
 using namespace std;
 
 // define our program name
 #define PROGRAM_NAME "peIntersectBed"
 
-// define the version
-#define VERSION "1.2.0"
-
 // define our parameter checking macro
 #define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
 
diff --git a/src/sortBed/Makefile b/src/sortBed/Makefile
index fefca26e..1c631a40 100755
--- a/src/sortBed/Makefile
+++ b/src/sortBed/Makefile
@@ -9,7 +9,7 @@ BIN_DIR = ../../bin/
 # -------------------
 # define our includes
 # -------------------
-INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/
+INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/
 
 # ----------------------------------
 # define our source and object files
diff --git a/src/sortBed/sortMain.cpp b/src/sortBed/sortMain.cpp
index f280aed0..22c9db3c 100755
--- a/src/sortBed/sortMain.cpp
+++ b/src/sortBed/sortMain.cpp
@@ -1,13 +1,12 @@
 #include <iostream>	
 #include "sortBed.h"
+#include "version.h"
 
 using namespace std;
 
 // define our program name
 #define PROGRAM_NAME "sortBed"
 
-// define the version
-#define VERSION "1.2.0"
 
 // define our parameter checking macro
 #define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
diff --git a/src/subtractBed/Makefile b/src/subtractBed/Makefile
index 42e8bd6d..d33935a6 100755
--- a/src/subtractBed/Makefile
+++ b/src/subtractBed/Makefile
@@ -9,7 +9,7 @@ BIN_DIR = ../../bin/
 # -------------------
 # define our includes
 # -------------------
-INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/
+INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/
 
 # ----------------------------------
 # define our source and object files
diff --git a/src/subtractBed/subtractMain.cpp b/src/subtractBed/subtractMain.cpp
index 8121108c..eeb960c0 100755
--- a/src/subtractBed/subtractMain.cpp
+++ b/src/subtractBed/subtractMain.cpp
@@ -1,12 +1,11 @@
 #include "subtractBed.h"
+#include "version.h"
 
 using namespace std;
 
 // define our program name
 #define PROGRAM_NAME "subtractBed"
 
-// define the version
-#define VERSION "1.2.0"
 
 // define our parameter checking macro
 #define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
diff --git a/src/utils/version/version.h b/src/utils/version/version.h
new file mode 100644
index 00000000..cbde5308
--- /dev/null
+++ b/src/utils/version/version.h
@@ -0,0 +1,7 @@
+#ifndef VERSION_H
+#define VERSION_H
+
+// define the version
+#define VERSION "2.0.0"
+
+#endif /* VERSION_H */
\ No newline at end of file
diff --git a/src/windowBed/Makefile b/src/windowBed/Makefile
index 337401e1..9f61b8ab 100755
--- a/src/windowBed/Makefile
+++ b/src/windowBed/Makefile
@@ -9,7 +9,7 @@ BIN_DIR = ../../bin/
 # -------------------
 # define our includes
 # -------------------
-INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/
+INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/
 
 # ----------------------------------
 # define our source and object files
diff --git a/src/windowBed/windowMain.cpp b/src/windowBed/windowMain.cpp
index 0a84e29c..ddf56656 100755
--- a/src/windowBed/windowMain.cpp
+++ b/src/windowBed/windowMain.cpp
@@ -1,12 +1,11 @@
 #include "windowBed.h"
+#include "version.h"
 
 using namespace std;
 
-// define our program name
-#define PROGRAM_NAME "windowBed"
 
 // define the version
-#define VERSION "1.2.0"
+#define PROGRAM_NAME "windowBed"
 
 // define our parameter checking macro
 #define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
-- 
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