Removed groupBy from the BEDTools distribution.

It now lives in the "filo" package.

Makefile

@@ -22,8 +22,8 @@ SUBDIRS = $(SRC_DIR)/annotateBed \
 		  $(SRC_DIR)/complementBed \
 		  $(SRC_DIR)/coverageBed \
 		  $(SRC_DIR)/fastaFromBed \
+		  $(SRC_DIR)/fjoin \
 		  $(SRC_DIR)/genomeCoverageBed \
-		  $(SRC_DIR)/groupBy \
 		  $(SRC_DIR)/intersectBed \
 		  $(SRC_DIR)/linksBed \
 		  $(SRC_DIR)/maskFastaFromBed \

src/groupBy/Makefile

-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
-
-
-# -------------------
-# define our includes
-# -------------------
-INCLUDES = -I$(UTILITIES_DIR)/tabFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/fileType/
-
-# ----------------------------------
-# define our source and object files
-# ----------------------------------
-SOURCES= groupBy.cpp
-OBJECTS= $(SOURCES:.cpp=.o)
-_EXT_OBJECTS=tabFile.o lineFileUtilities.o gzstream.o fileType.o
-EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
-BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
-PROGRAM= groupBy
-
-
-all: $(PROGRAM)
-
-.PHONY: all
-
-
-$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
-	@echo "  * linking $(PROGRAM)"
-	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS)
-
-$(BUILT_OBJECTS): $(SOURCES)
-	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
-
-$(EXT_OBJECTS):
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/tabFile/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/	
-	
-
-	
-clean:
-	@echo "Cleaning up."
-	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
-
-.PHONY: clean