Commit 5184b441 authored by Aaron's avatar Aaron
Browse files

tool makefiles not recompile with changes to header

parent cee8949d
......@@ -15,12 +15,9 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= annotateMain.cpp annotateBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
SOURCES= annotateMain.cpp annotateBed.cpp annotateBed.h
OBJECTS= annotateMain.o annotateBed.o
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= annotateBed
all: $(BUILT_OBJECTS)
......@@ -31,14 +28,9 @@ $(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
@$(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)/*
@rm -f $(OBJ_DIR)/annotateMain.o $(OBJ_DIR)/annotateBed.o
.PHONY: clean
......@@ -18,11 +18,8 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
# define our source and object files
# ----------------------------------
SOURCES= bamToBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=BamAncillary.o BlockedIntervals.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
OBJECTS= bamToBed.o
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= bamToBed
all: $(BUILT_OBJECTS)
......@@ -33,12 +30,8 @@ $(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamAncillary/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BlockedIntervals/
clean:
@echo "Cleaning up."
@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
@rm -f $(OBJ_DIR)/bamToBed.o
.PHONY: clean
......@@ -17,11 +17,8 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
# define our source and object files
# ----------------------------------
SOURCES= bed12ToBed6.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o BlockedIntervals.o lineFileUtilities.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
OBJECTS= bed12ToBed6.o
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= bed12ToBed6
all: $(BUILT_OBJECTS)
......@@ -32,15 +29,8 @@ $(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BlockedIntervals/
clean:
@echo "Cleaning up."
@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
@rm -f $(OBJ_DIR)/bed12ToBed6.o
.PHONY: clean
......@@ -19,9 +19,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
# define our source and object files
# ----------------------------------
SOURCES= bedToBam.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
OBJECTS= bedToBam.o
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= bedToBam
......@@ -34,16 +32,8 @@ $(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/
@$(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)/*
@rm -f $(OBJ_DIR)/bedToBam.o
.PHONY: clean
......@@ -17,9 +17,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
# define our source and object files
# ----------------------------------
SOURCES= bedToIgv.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
OBJECTS= bedToIgv.o
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= bedToIgv
......@@ -32,15 +30,8 @@ $(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/
@$(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)/*
@rm -f $(OBJ_DIR)/bedToIgv.o
.PHONY: clean
......@@ -13,12 +13,9 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= closestMain.cpp closestBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
SOURCES= closestMain.cpp closestBed.cpp closestBed.h
OBJECTS= closestMain.o closestBed.o
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= closestBed
all: $(BUILT_OBJECTS)
......@@ -28,14 +25,8 @@ $(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/
clean:
@echo "Cleaning up."
@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
@rm -f $(OBJ_DIR)/closestMain.o $(OBJ_DIR)/closestBed.o
.PHONY: clean
......@@ -14,10 +14,8 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= clusterMain.cpp clusterBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
SOURCES= clusterMain.cpp clusterBed.cpp clusterBed.h
OBJECTS= clusterMain.o clusterBed.o
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
......@@ -29,15 +27,8 @@ $(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/
clean:
@echo "Cleaning up."
@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
@rm -f $(OBJ_DIR)/clusterMain.o $(OBJ_DIR)/clusterBed.o
.PHONY: clean
\ No newline at end of file
......@@ -16,10 +16,8 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= complementMain.cpp complementBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
SOURCES= complementMain.cpp complementBed.cpp complementBed.h
OBJECTS= complementMain.o complementBed.o
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= complementBed
......@@ -32,15 +30,9 @@ $(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/
clean:
@echo "Cleaning up."
@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
@rm -f $(OBJ_DIR)/complementMain.o $(OBJ_DIR)/complementBed.o
.PHONY: clean
......@@ -16,13 +16,9 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= coverageMain.cpp coverageBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
# _EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o BlockedIntervals.o
# EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
SOURCES= coverageMain.cpp coverageBed.cpp coverageBed.h
OBJECTS= coverageMain.o coverageBed.o
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= coverageBed
all: $(BUILT_OBJECTS)
......@@ -32,16 +28,8 @@ $(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
# $(EXT_OBJECTS):
# @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
# @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
# @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/
# @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BlockedIntervals/
# @$(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)/*
@rm -f $(OBJ_DIR)/coverageMain.o $(OBJ_DIR)/coverageBed.o
.PHONY: clean
......@@ -17,12 +17,9 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= fastaFromBedMain.cpp fastaFromBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o sequenceUtils.o lineFileUtilities.o gzstream.o fileType.o Fasta.o split.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
SOURCES= fastaFromBedMain.cpp fastaFromBed.cpp fastaFromBed.h
OBJECTS= fastaFromBedMain.o fastaFromBed.o
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= fastaFromBed
all: $(BUILT_OBJECTS)
......@@ -33,16 +30,8 @@ $(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/sequenceUtilities/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/Fasta/
clean:
@echo "Cleaning up."
@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
@rm -f $(OBJ_DIR)/fastaFromBedMain.o $(OBJ_DIR)/fastaFromBed.o
.PHONY: clean
\ No newline at end of file
......@@ -16,13 +16,9 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= flankBedMain.cpp flankBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
SOURCES= flankBedMain.cpp flankBed.cpp flankBed.h
OBJECTS= flankBedMain.o flankBed.o
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= flankBed
all: $(BUILT_OBJECTS)
......@@ -31,16 +27,9 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/
@$(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)/*
@rm -f $(OBJ_DIR)/flankBedMain.o $(OBJ_DIR)/flankBed.o
.PHONY: clean
......@@ -16,12 +16,9 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= genomeCoverageMain.cpp genomeCoverageBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o BamAncillary.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
SOURCES= genomeCoverageMain.cpp genomeCoverageBed.cpp genomeCoverageBed.h
OBJECTS= genomeCoverageMain.o genomeCoverageBed.o
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= genomeCoverageBed
all: $(BUILT_OBJECTS)
......@@ -32,17 +29,8 @@ $(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BlockedIntervals/
@$(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)/*
@rm -f $(OBJ_DIR)/genomeCoverageMain.o $(OBJ_DIR)/genomeCoverageBed.o
.PHONY: clean
......@@ -16,11 +16,8 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
# define our source and object files
# ----------------------------------
SOURCES= getOverlap.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
OBJECTS= getOverlap.o
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= getOverlap
all: $(BUILT_OBJECTS)
......@@ -31,16 +28,9 @@ $(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
@$(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)/*
@rm -f $(OBJ_DIR)/getOverlap.o
.PHONY: clean
......@@ -17,9 +17,7 @@ INCLUDES = -I$(UTILITIES_DIR)/tabFile/ \
# define our source and object files
# ----------------------------------
SOURCES= groupBy.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=tabFile.o gzstream.o fileType.o VectorOps.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
OBJECTS= groupBy.o
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
all: $(BUILT_OBJECTS)
......@@ -30,15 +28,9 @@ all: $(BUILT_OBJECTS)
$(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 $(UTILITIES_DIR)/gzstream/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/
clean:
@echo "Cleaning up."
@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
@rm -f $(OBJ_DIR)/groupBy.o
.PHONY: clean
......@@ -19,10 +19,8 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= intersectMain.cpp intersectBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o BlockedIntervals.o BamAncillary.o gzstream.o fileType.o chromsweep.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
SOURCES= intersectMain.cpp intersectBed.cpp intersectBed.h
OBJECTS= intersectMain.o intersectBed.o
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= intersectBed
......@@ -33,19 +31,9 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BlockedIntervals/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools-Ancillary/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/chromsweep/
clean:
@echo "Cleaning up."
@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
@rm -f $(OBJ_DIR)/intersectMain.o $(OBJ_DIR)/intersectBed.o
.PHONY: clean
......@@ -14,12 +14,9 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= linksMain.cpp linksBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
SOURCES= linksMain.cpp linksBed.cpp linksBed.h
OBJECTS= linksMain.o linksBed.o
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= linksBed
all: $(BUILT_OBJECTS)
......@@ -30,14 +27,8 @@ $(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
@$(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)/*
@rm -f $(OBJ_DIR)/linksMain.o $(OBJ_DIR)/linksBed.o
.PHONY: clean
\ No newline at end of file
......@@ -19,12 +19,9 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= mapMain.cpp mapBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o BamAncillary.o gzstream.o fileType.o VectorOps.o chromsweep.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
SOURCES= mapMain.cpp mapBed.cpp mapBed.h
OBJECTS= mapMain.o mapBed.o
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= mapBed
all: $(BUILT_OBJECTS)
......@@ -34,18 +31,8 @@ $(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools-Ancillary/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/VectorOps/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/chromsweep/
clean:
@echo "Cleaning up."
@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
@rm -f $(OBJ_DIR)/mapMain.o $(OBJ_DIR)/mapBed.o
.PHONY: clean
......@@ -15,12 +15,9 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= maskFastaFromBedMain.cpp maskFastaFromBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o sequenceUtils.o lineFileUtilities.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
SOURCES= maskFastaFromBedMain.cpp maskFastaFromBed.cpp maskFastaFromBed.h
OBJECTS= maskFastaFromBedMain.o maskFastaFromBed.o
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= maskFastaFromBed
all: $(BUILT_OBJECTS)
......@@ -30,15 +27,8 @@ $(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/sequenceUtilities/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
@$(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)/*
@rm -f $(OBJ_DIR)/maskFastaFromBedMain.o $(OBJ_DIR)/maskFastaFromBed.o
.PHONY: clean
\ No newline at end of file
......@@ -14,12 +14,9 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= mergeMain.cpp mergeBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
SOURCES= mergeMain.cpp mergeBed.cpp mergeBed.h
OBJECTS= mergeMain.o mergeBed.o
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= mergeBed
all: $(BUILT_OBJECTS)
......@@ -30,15 +27,8 @@ $(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/
clean:
@echo "Cleaning up."
@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
@rm -f $(OBJ_DIR)/mergeMain.o $(OBJ_DIR)/mergeBed.o
.PHONY: clean
\ No newline at end of file
......@@ -15,12 +15,9 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= multiBamCovMain.cpp multiBamCov.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
SOURCES= multiBamCovMain.cpp multiBamCov.cpp multiBamCov.h
OBJECTS= multiBamCovMain.o multiBamCov.o
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= multiBamCov
all: $(BUILT_OBJECTS)
......@@ -30,15 +27,8 @@ $(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/