rpms / BEDTools

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  1.   859c2749e09ed7581fd0df5ffaa3d836a04f35c0
  2.   bedtools-debuginfo-path.patch
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diff -ur bedtools2-2.20.1/src/utils/BamTools/Makefile bedtools2-2.20.1.new/src/utils/BamTools/Makefile
--- bedtools2-2.20.1/src/utils/BamTools/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/utils/BamTools/Makefile	2014-06-14 08:54:38.206849195 +0100
@@ -1,7 +1,7 @@
 # -------------------
 # define our includes
 # -------------------
-OBJ_DIR = ../../../obj/
+OBJ_DIR = ../../../obj
 INCLUDES = -Isrc/ -Iinclude/
 
 # ----------------------------------
diff -ur bedtools2-2.20.1/src/utils/BamTools-Ancillary/Makefile bedtools2-2.20.1.new/src/utils/BamTools-Ancillary/Makefile
--- bedtools2-2.20.1/src/utils/BamTools-Ancillary/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/utils/BamTools-Ancillary/Makefile	2014-06-14 08:54:00.845394556 +0100
@@ -1,6 +1,6 @@
-OBJ_DIR = ../../../obj/
-BIN_DIR = ../../../bin/
-UTILITIES_DIR = ../
+OBJ_DIR = ../../../obj
+BIN_DIR = ../../../bin
+UTILITIES_DIR = ..
 
 INCLUDES = -I$(UTILITIES_DIR)/BamTools/include \
            -I$(UTILITIES_DIR)/bedFile/ \
@@ -27,4 +27,4 @@
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
diff -ur bedtools2-2.20.1/src/utils/bedFile/Makefile bedtools2-2.20.1.new/src/utils/bedFile/Makefile
--- bedtools2-2.20.1/src/utils/bedFile/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/utils/bedFile/Makefile	2014-06-14 08:53:39.343406368 +0100
@@ -1,6 +1,6 @@
-OBJ_DIR = ../../../obj/
-BIN_DIR = ../../../bin/
-UTILITIES_DIR = ../../utils/
+OBJ_DIR = ../../../obj
+BIN_DIR = ../../../bin
+UTILITIES_DIR = ../../utils
 # -------------------
 # define our includes
 # -------------------
@@ -29,4 +29,4 @@
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
diff -ur bedtools2-2.20.1/src/utils/bedFilePE/Makefile bedtools2-2.20.1.new/src/utils/bedFilePE/Makefile
--- bedtools2-2.20.1/src/utils/bedFilePE/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/utils/bedFilePE/Makefile	2014-06-14 08:53:13.494016197 +0100
@@ -1,6 +1,6 @@
-OBJ_DIR = ../../../obj/
-BIN_DIR = ../../../bin/
-UTILITIES_DIR = ../../utils/
+OBJ_DIR = ../../../obj
+BIN_DIR = ../../../bin
+UTILITIES_DIR = ../../utils
 # -------------------
 # define our includes
 # -------------------
@@ -26,4 +26,4 @@
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
diff -ur bedtools2-2.20.1/src/utils/bedGraphFile/Makefile bedtools2-2.20.1.new/src/utils/bedGraphFile/Makefile
--- bedtools2-2.20.1/src/utils/bedGraphFile/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/utils/bedGraphFile/Makefile	2014-06-14 08:52:50.162858875 +0100
@@ -1,6 +1,6 @@
-OBJ_DIR = ../../../obj/
-BIN_DIR = ../../../bin/
-UTILITIES_DIR = ../../utils/
+OBJ_DIR = ../../../obj
+BIN_DIR = ../../../bin
+UTILITIES_DIR = ../../utils
 # -------------------
 # define our includes
 # -------------------
diff -ur bedtools2-2.20.1/src/utils/BinTree/Makefile bedtools2-2.20.1.new/src/utils/BinTree/Makefile
--- bedtools2-2.20.1/src/utils/BinTree/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/utils/BinTree/Makefile	2014-06-14 08:51:35.924994455 +0100
@@ -1,6 +1,6 @@
-OBJ_DIR = ../../../obj/
-BIN_DIR = ../../../bin/
-UTILITIES_DIR = ../../utils/
+OBJ_DIR = ../../../obj
+BIN_DIR = ../../../bin
+UTILITIES_DIR = ../../utils
 # -------------------
 # define our includes
 # -------------------
@@ -36,4 +36,4 @@
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/BinTree.o
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
diff -ur bedtools2-2.20.1/src/utils/BlockedIntervals/Makefile bedtools2-2.20.1.new/src/utils/BlockedIntervals/Makefile
--- bedtools2-2.20.1/src/utils/BlockedIntervals/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/utils/BlockedIntervals/Makefile	2014-06-14 08:50:30.322928549 +0100
@@ -1,6 +1,6 @@
-OBJ_DIR = ../../../obj/
-BIN_DIR = ../../../bin/
-UTILITIES_DIR = ../
+OBJ_DIR = ../../../obj
+BIN_DIR = ../../../bin
+UTILITIES_DIR = ..
 
 INCLUDES = -I$(UTILITIES_DIR)/BamTools/include \
            -I$(UTILITIES_DIR)/bedFile/ \
diff -ur bedtools2-2.20.1/src/utils/chromsweep/Makefile bedtools2-2.20.1.new/src/utils/chromsweep/Makefile
--- bedtools2-2.20.1/src/utils/chromsweep/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/utils/chromsweep/Makefile	2014-06-14 08:49:28.158180480 +0100
@@ -1,6 +1,6 @@
-OBJ_DIR = ../../../obj/
-BIN_DIR = ../../../bin/
-UTILITIES_DIR = ../../utils/
+OBJ_DIR = ../../../obj
+BIN_DIR = ../../../bin
+UTILITIES_DIR = ../../utils
 # -------------------
 # define our includes
 # -------------------
@@ -29,4 +29,4 @@
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
diff -ur bedtools2-2.20.1/src/utils/Contexts/Makefile bedtools2-2.20.1.new/src/utils/Contexts/Makefile
--- bedtools2-2.20.1/src/utils/Contexts/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/utils/Contexts/Makefile	2014-06-14 08:50:03.671464219 +0100
@@ -1,6 +1,6 @@
-OBJ_DIR = ../../../obj/
-BIN_DIR = ../../../bin/
-UTILITIES_DIR = ../../utils/
+OBJ_DIR = ../../../obj
+BIN_DIR = ../../../bin
+UTILITIES_DIR = ../../utils
 # -------------------
 # define our includes
 # -------------------
@@ -43,4 +43,4 @@
 	       $(OBJ_DIR)/ContextMerge.o \
 	       $(OBJ_DIR)/ContextJaccard.o \
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
diff -ur bedtools2-2.20.1/src/utils/Fasta/Makefile bedtools2-2.20.1.new/src/utils/Fasta/Makefile
--- bedtools2-2.20.1/src/utils/Fasta/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/utils/Fasta/Makefile	2014-06-14 08:54:53.325247123 +0100
@@ -1,6 +1,6 @@
-OBJ_DIR = ../../../obj/
-BIN_DIR = ../../../bin/
-UTILITIES_DIR = ../../utils/
+OBJ_DIR = ../../../obj
+BIN_DIR = ../../../bin
+UTILITIES_DIR = ../../utils
 # -------------------
 # define our includes
 # -------------------
diff -ur bedtools2-2.20.1/src/utils/FileRecordTools/Makefile bedtools2-2.20.1.new/src/utils/FileRecordTools/Makefile
--- bedtools2-2.20.1/src/utils/FileRecordTools/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/utils/FileRecordTools/Makefile	2014-06-14 08:56:04.393818506 +0100
@@ -1,6 +1,6 @@
-OBJ_DIR = ../../../obj/
-BIN_DIR = ../../../bin/
-UTILITIES_DIR = ../../utils/
+OBJ_DIR = ../../../obj
+BIN_DIR = ../../../bin
+UTILITIES_DIR = ../../utils
 # -------------------
 # define our includes
 # -------------------
@@ -48,4 +48,4 @@
 	@rm -f $(OBJ_DIR)/FileRecordMergeMgr.o
 	
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
diff -ur bedtools2-2.20.1/src/utils/fileType/Makefile bedtools2-2.20.1.new/src/utils/fileType/Makefile
--- bedtools2-2.20.1/src/utils/fileType/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/utils/fileType/Makefile	2014-06-14 08:56:38.004926372 +0100
@@ -1,6 +1,6 @@
-OBJ_DIR = ../../../obj/
-BIN_DIR = ../../../bin/
-UTILITIES_DIR = ../../utils/
+OBJ_DIR = ../../../obj
+BIN_DIR = ../../../bin
+UTILITIES_DIR = ../../utils
 # -------------------
 # define our includes
 # -------------------
@@ -28,4 +28,4 @@
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/fileType.o $(OBJ_DIR)/FileRecordTypeChecker.o
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
diff -ur bedtools2-2.20.1/src/utils/general/Makefile bedtools2-2.20.1.new/src/utils/general/Makefile
--- bedtools2-2.20.1/src/utils/general/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/utils/general/Makefile	2014-06-14 08:56:59.510914933 +0100
@@ -1,6 +1,6 @@
-OBJ_DIR = ../../../obj/
-BIN_DIR = ../../../bin/
-UTILITIES_DIR = ../../utils/
+OBJ_DIR = ../../../obj
+BIN_DIR = ../../../bin
+UTILITIES_DIR = ../../utils
 # -------------------
 # define our includes
 # -------------------
diff -ur bedtools2-2.20.1/src/utils/GenomeFile/Makefile bedtools2-2.20.1.new/src/utils/GenomeFile/Makefile
--- bedtools2-2.20.1/src/utils/GenomeFile/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/utils/GenomeFile/Makefile	2014-06-14 08:57:15.329377595 +0100
@@ -1,6 +1,6 @@
-OBJ_DIR = ../../../obj/
-BIN_DIR = ../../../bin/
-UTILITIES_DIR = ../
+OBJ_DIR = ../../../obj
+BIN_DIR = ../../../bin
+UTILITIES_DIR = ..
 # -------------------
 # define our includes
 # -------------------
diff -ur bedtools2-2.20.1/src/utils/gzstream/Makefile bedtools2-2.20.1.new/src/utils/gzstream/Makefile
--- bedtools2-2.20.1/src/utils/gzstream/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/utils/gzstream/Makefile	2014-06-14 08:57:51.588730334 +0100
@@ -33,9 +33,9 @@
 # ----------------------------------------------------------------------------
 
 INCLUDES = -I.
-OBJ_DIR = ../../../obj/
-BIN_DIR = ../../../bin/
-UTILITIES_DIR = ../../utils/
+OBJ_DIR = ../../../obj
+BIN_DIR = ../../../bin
+UTILITIES_DIR = ../../utils
 	
 ${OBJ_DIR}/gzstream.o : gzstream.C gzstream.h
 	${CXX} ${CXXFLAGS} -c -o ${OBJ_DIR}/gzstream.o gzstream.C $(INCLUDES)
diff -ur bedtools2-2.20.1/src/utils/KeyListOps/Makefile bedtools2-2.20.1.new/src/utils/KeyListOps/Makefile
--- bedtools2-2.20.1/src/utils/KeyListOps/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/utils/KeyListOps/Makefile	2014-06-14 08:58:07.554206590 +0100
@@ -1,6 +1,6 @@
-OBJ_DIR = ../../../obj/
-BIN_DIR = ../../../bin/
-UTILITIES_DIR = ../../utils/
+OBJ_DIR = ../../../obj
+BIN_DIR = ../../../bin
+UTILITIES_DIR = ../../utils
 # -------------------
 # define our includes
 # -------------------
@@ -40,4 +40,4 @@
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/KeyListOps.o $(OBJ_DIR)/KeyListOpsMethods.o
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
diff -ur bedtools2-2.20.1/src/utils/NewChromsweep/Makefile bedtools2-2.20.1.new/src/utils/NewChromsweep/Makefile
--- bedtools2-2.20.1/src/utils/NewChromsweep/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/utils/NewChromsweep/Makefile	2014-06-14 08:58:36.332867624 +0100
@@ -1,6 +1,6 @@
-OBJ_DIR = ../../../obj/
-BIN_DIR = ../../../bin/
-UTILITIES_DIR = ../../utils/
+OBJ_DIR = ../../../obj
+BIN_DIR = ../../../bin
+UTILITIES_DIR = ../../utils
 # -------------------
 # define our includes
 # -------------------
@@ -37,4 +37,4 @@
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/NewChromsweep.o $(BIN_DIR)/NewChromsweep.o
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
diff -ur bedtools2-2.20.1/src/utils/RecordOutputMgr/Makefile bedtools2-2.20.1.new/src/utils/RecordOutputMgr/Makefile
--- bedtools2-2.20.1/src/utils/RecordOutputMgr/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/utils/RecordOutputMgr/Makefile	2014-06-14 08:59:04.656486583 +0100
@@ -1,6 +1,6 @@
-OBJ_DIR = ../../../obj/
-BIN_DIR = ../../../bin/
-UTILITIES_DIR = ../../utils/
+OBJ_DIR = ../../../obj
+BIN_DIR = ../../../bin
+UTILITIES_DIR = ../../utils
 # -------------------
 # define our includes
 # -------------------
@@ -37,4 +37,4 @@
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/RecordOutputMgr.o 
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
diff -ur bedtools2-2.20.1/src/utils/sequenceUtilities/Makefile bedtools2-2.20.1.new/src/utils/sequenceUtilities/Makefile
--- bedtools2-2.20.1/src/utils/sequenceUtilities/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/utils/sequenceUtilities/Makefile	2014-06-14 08:59:21.389033768 +0100
@@ -1,6 +1,6 @@
-OBJ_DIR = ../../../obj/
-BIN_DIR = ../../../bin/
-UTILITIES_DIR = ../../utils/
+OBJ_DIR = ../../../obj
+BIN_DIR = ../../../bin
+UTILITIES_DIR = ../../utils
 # -------------------
 # define our includes
 # -------------------
@@ -26,4 +26,4 @@
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
diff -ur bedtools2-2.20.1/src/utils/tabFile/Makefile bedtools2-2.20.1.new/src/utils/tabFile/Makefile
--- bedtools2-2.20.1/src/utils/tabFile/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/utils/tabFile/Makefile	2014-06-14 08:59:43.699096681 +0100
@@ -1,6 +1,6 @@
-OBJ_DIR = ../../../obj/
-BIN_DIR = ../../../bin/
-UTILITIES_DIR = ../../utils/
+OBJ_DIR = ../../../obj
+BIN_DIR = ../../../bin
+UTILITIES_DIR = ../../utils
 # -------------------
 # define our includes
 # -------------------
@@ -28,4 +28,4 @@
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
diff -ur bedtools2-2.20.1/src/utils/VectorOps/Makefile bedtools2-2.20.1.new/src/utils/VectorOps/Makefile
--- bedtools2-2.20.1/src/utils/VectorOps/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/utils/VectorOps/Makefile	2014-06-14 09:00:01.820772313 +0100
@@ -1,6 +1,6 @@
-OBJ_DIR = ../../../obj/
-BIN_DIR = ../../../bin/
-UTILITIES_DIR = ../../utils/
+OBJ_DIR = ../../../obj
+BIN_DIR = ../../../bin
+UTILITIES_DIR = ../../utils
 
 # ----------------------------------
 # define our source and object files
@@ -17,4 +17,4 @@
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
diff -ur bedtools2-2.20.1/src/utils/version/Makefile bedtools2-2.20.1.new/src/utils/version/Makefile
--- bedtools2-2.20.1/src/utils/version/Makefile	2014-05-24 02:35:47.000000000 +0100
+++ bedtools2-2.20.1.new/src/utils/version/Makefile	2014-06-14 09:00:15.809065749 +0100
@@ -1,6 +1,6 @@
-OBJ_DIR = ../../../obj/
-BIN_DIR = ../../../bin/
-UTILITIES_DIR = ../../utils/
+OBJ_DIR = ../../../obj
+BIN_DIR = ../../../bin
+UTILITIES_DIR = ../../utils
 # -------------------
 # define our includes
 # -------------------
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