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Commit 3e74755a authored by Aaron's avatar Aaron
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Updated all Makefiles for gzstream support.

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Makefile
+ 2
− 2
View file @ 3e74755a
......@@ -9,9 +9,9 @@ export BIN_DIR = bin
export SRC_DIR = src
# define our source subdirectories
SUBDIRS = $(SRC_DIR)/bamToBed $(SRC_DIR)/closestBed $(SRC_DIR)/complementBed $(SRC_DIR)/coverageBed $(SRC_DIR)/fastaFromBed $(SRC_DIR)/genomeCoverageBed $(SRC_DIR)/intersectBed $(SRC_DIR)/linksBed $(SRC_DIR)/maskFastaFromBed $(SRC_DIR)/mergeBed $(SRC_DIR)/overlap $(SRC_DIR)/pairToBed $(SRC_DIR)/pairToPair $(SRC_DIR)/shuffleBed $(SRC_DIR)/slopBed $(SRC_DIR)/sortBed $(SRC_DIR)/subtractBed $(SRC_DIR)/windowBed
SUBDIRS = $(SRC_DIR)/bamToBed $(SRC_DIR)/bedToBam $(SRC_DIR)/closestBed $(SRC_DIR)/complementBed $(SRC_DIR)/coverageBed $(SRC_DIR)/fastaFromBed $(SRC_DIR)/genomeCoverageBed $(SRC_DIR)/intersectBed $(SRC_DIR)/linksBed $(SRC_DIR)/maskFastaFromBed $(SRC_DIR)/mergeBed $(SRC_DIR)/overlap $(SRC_DIR)/pairToBed $(SRC_DIR)/pairToPair $(SRC_DIR)/shuffleBed $(SRC_DIR)/slopBed $(SRC_DIR)/sortBed $(SRC_DIR)/subtractBed $(SRC_DIR)/windowBed
UTIL_SUBDIRS = $(SRC_DIR)/utils/lineFileUtilities $(SRC_DIR)/utils/bedFile $(SRC_DIR)/utils/genomeFile $(SRC_DIR)/utils/bedFilePE $(SRC_DIR)/utils/sequenceUtilities $(SRC_DIR)/utils/BamTools
UTIL_SUBDIRS = $(SRC_DIR)/utils/lineFileUtilities $(SRC_DIR)/utils/bedFile $(SRC_DIR)/utils/genomeFile $(SRC_DIR)/utils/gzstream $(SRC_DIR)/utils/bedFilePE $(SRC_DIR)/utils/sequenceUtilities $(SRC_DIR)/utils/BamTools
all:
......
src/annotateBed/Makefile 0 → 100755
+ 45
− 0
View file @ 3e74755a
CXX = g++
CXXFLAGS = -O3 -Wall
LDFLAGS =
UTILITIES_DIR = ../utils/
OBJ_DIR = ../../obj/
BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= coverageMain.cpp coverageBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= coverageBed
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 $(UTILITIES_DIR)/bedFile/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
clean:
@echo "Cleaning up."
@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
.PHONY: clean
src/bedToBam/Makefile 0 → 100755
+ 48
− 0
View file @ 3e74755a
CXX= g++
CXXFLAGS= -Wall -O3
LIBS= -lz
UTILITIES_DIR = ../utils/
OBJ_DIR = ../../obj/
BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/BamTools/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= bedToBam.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=BamWriter.o BGZF.o bedFile.o genomeFile.o lineFileUtilities.o gzstream.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= bedToBam
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 $(UTILITIES_DIR)/BamTools/
@$(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/
clean:
@echo "Cleaning up."
@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
.PHONY: clean
src/bedToBam/bedToBam.cpp
+ 3
− 3
View file @ 3e74755a
......@@ -191,7 +191,7 @@ void ProcessBed(istream &bedInput, BedFile *bed, GenomeFile *genome, bool isBED1
RefVector refs;
string bamHeader;
map<string, int, std::less<string> > chromToId;
MakeBamHeader(genome->genomeFile, refs, bamHeader, chromToId);
MakeBamHeader(genome->getGenomeFileName(), refs, bamHeader, chromToId);
// add the reference headers to the BAM file
writer.Open("stdout", bamHeader, refs);
......@@ -265,8 +265,8 @@ void ConvertBedToBam(const BED &bed, BamAlignment &bam, map<string, int, std::le
// extract the relevant BED fields to convert BED12 to BAM
// namely: thickStart, thickEnd, blockCount, blockStarts, blockEnds
unsigned int thickStart = atoi(bed.otherFields[0].c_str());
unsigned int thickEnd = atoi(bed.otherFields[1].c_str());
// unsigned int thickStart = atoi(bed.otherFields[0].c_str());
// unsigned int thickEnd = atoi(bed.otherFields[1].c_str());
unsigned int blockCount = atoi(bed.otherFields[3].c_str());
vector<string> blockSizesString, blockStartsString;
......
src/closestBed/Makefile
+ 5
− 4
View file @ 3e74755a
CXX = g++
CXXFLAGS = -O3 -Wall
LDFLAGS =
LIBS = -lz
UTILITIES_DIR = ../utils/
OBJ_DIR = ../../obj/
BIN_DIR = ../../bin/
......@@ -9,14 +9,14 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= closestMain.cpp closestBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= closestBed
......@@ -34,9 +34,10 @@ $(BUILT_OBJECTS): $(SOURCES)
@$(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/
clean:
@echo "Cleaning up."
@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
......
src/complementBed/Makefile
+ 4
− 3
View file @ 3e74755a
CXX = g++
CXXFLAGS = -O3 -Wall
LDFLAGS =
LIBS=
LIBS= -lz
UTILITIES_DIR = ../utils/
OBJ_DIR = ../../obj/
......@@ -10,14 +10,14 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= complementMain.cpp complementBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o
_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= complementBed
......@@ -38,6 +38,7 @@ $(BUILT_OBJECTS): $(SOURCES)
$(EXT_OBJECTS):
@$(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 $(UTILITIES_DIR)/genomeFile/
clean:
......
src/coverageBed/Makefile
+ 4
− 3
View file @ 3e74755a
......@@ -10,14 +10,14 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/BamTools/
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/BamTools/ -I$(UTILITIES_DIR)/gzstream/
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= coverageMain.cpp coverageBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o BamReader.o BGZF.o
_EXT_OBJECTS=bedFile.o lineFileUtilities.o BamReader.o BGZF.o gzstream.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= coverageBed
......@@ -39,7 +39,8 @@ $(EXT_OBJECTS):
@$(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)/gzstream/
clean:
@echo "Cleaning up."
@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
......
src/fastaFromBed/Makefile
+ 5
− 4
View file @ 3e74755a
CXX = g++
CXXFLAGS = -O3 -Wall
LDFLAGS =
LIBS = -lz
UTILITIES_DIR = ../utils/
OBJ_DIR = ../../obj/
BIN_DIR = ../../bin/
......@@ -9,14 +9,14 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/sequenceUtilities/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/sequenceUtilities/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= fastaFromBedMain.cpp fastaFromBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o sequenceUtils.o lineFileUtilities.o
_EXT_OBJECTS=bedFile.o sequenceUtils.o lineFileUtilities.o gzstream.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= fastaFromBed
......@@ -38,7 +38,8 @@ $(EXT_OBJECTS):
@$(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/
clean:
@echo "Cleaning up."
@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
......
src/genomeCoverageBed/Makefile
+ 4
− 3
View file @ 3e74755a
......@@ -10,14 +10,14 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/BamTools/
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/BamTools/ -I$(UTILITIES_DIR)/gzstream/
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= genomeCoverageMain.cpp genomeCoverageBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o BamReader.o BGZF.o
_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o BamReader.o BGZF.o gzstream.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= genomeCoverageBed
......@@ -40,7 +40,8 @@ $(EXT_OBJECTS):
@$(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)/gzstream/
clean:
@echo "Cleaning up."
@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
......
src/intersectBed/Makefile
+ 4
− 3
View file @ 3e74755a
......@@ -10,14 +10,14 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/BamTools/
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/BamTools/ -I$(UTILITIES_DIR)/gzstream/
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= intersectMain.cpp intersectBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o BamReader.o BamWriter.o BGZF.o
_EXT_OBJECTS=bedFile.o lineFileUtilities.o BamReader.o BamWriter.o BGZF.o gzstream.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= intersectBed
......@@ -37,7 +37,8 @@ $(BUILT_OBJECTS): $(SOURCES)
$(EXT_OBJECTS):
@$(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 $(UTILITIES_DIR)/BamTools/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
clean:
@echo "Cleaning up."
......
src/intersectBed/intersectBed.cpp
+ 1
− 0
View file @ 3e74755a
......@@ -307,6 +307,7 @@ void BedIntersect::DetermineBedInput() {
// it's BED or GFF
if (_bamInput == false) {
IntersectBed();
}
// it's BAM
else {
IntersectBam("stdin");
......
src/linksBed/Makefile
+ 6
− 4
View file @ 3e74755a
CXX = g++
CXXFLAGS = -O3 -Wall
LDFLAGS =
LDFLAGS =
LIBS = -lz
UTILITIES_DIR = ../utils/
OBJ_DIR = ../../obj/
......@@ -9,14 +10,14 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= linksMain.cpp linksBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= linksBed
......@@ -37,7 +38,8 @@ $(BUILT_OBJECTS): $(SOURCES)
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
clean:
@echo "Cleaning up."
@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
......
src/maskFastaFromBed/Makefile
+ 4
− 4
View file @ 3e74755a
CXX = g++
CXXFLAGS = -O3 -Wall
LDFLAGS =
LIBS = -lz
UTILITIES_DIR = ../utils/
OBJ_DIR = ../../obj/
BIN_DIR = ../../bin/
......@@ -9,18 +9,17 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/sequenceUtilities/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/sequenceUtilities/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= maskFastaFromBedMain.cpp maskFastaFromBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o sequenceUtils.o lineFileUtilities.o
_EXT_OBJECTS=bedFile.o sequenceUtils.o lineFileUtilities.o gzstream.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= maskFastaFromBed
LIBS=
all: $(PROGRAM)
......@@ -38,6 +37,7 @@ $(EXT_OBJECTS):
@$(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 $(UTILITIES_DIR)/gzstream/
clean:
@echo "Cleaning up."
......
src/mergeBed/Makefile
+ 5
− 4
View file @ 3e74755a
CXX = g++
CXXFLAGS = -O3 -Wall
LDFLAGS =
LIBS = -lz
UTILITIES_DIR = ../utils/
OBJ_DIR = ../../obj/
BIN_DIR = ../../bin/
......@@ -9,14 +9,14 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= mergeMain.cpp mergeBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= mergeBed
......@@ -37,7 +37,8 @@ $(BUILT_OBJECTS): $(SOURCES)
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
clean:
@echo "Cleaning up."
@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
......
src/overlap/Makefile
+ 5
− 2
View file @ 3e74755a
CXX= g++
CXXFLAGS= -Wall -O3
LDFLAGS =
LIBS= -lz
UTILITIES_DIR = ../utils/
OBJ_DIR = ../../obj/
......@@ -10,14 +11,14 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= overlap.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= overlap
......@@ -39,6 +40,8 @@ $(BUILT_OBJECTS): $(SOURCES)
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
clean:
......
src/pairToBed/Makefile
+ 4
− 3
View file @ 3e74755a
......@@ -10,14 +10,14 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFilePE/ -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/BamTools/
INCLUDES = -I$(UTILITIES_DIR)/bedFilePE/ -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/BamTools/ -I$(UTILITIES_DIR)/gzstream/
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= pairToBedMain.cpp pairToBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFilePE.o bedFile.o lineFileUtilities.o BamReader.o BamWriter.o BGZF.o
_EXT_OBJECTS=bedFilePE.o bedFile.o lineFileUtilities.o BamReader.o BamWriter.o BGZF.o gzstream.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= pairToBed
......@@ -39,7 +39,8 @@ $(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFilePE/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
clean:
@echo "Cleaning up."
@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
......
src/pairToPair/Makefile
+ 4
− 3
View file @ 3e74755a
CXX = g++
CXXFLAGS = -O3 -Wall
LDFLAGS =
LIBS = -lz
UTILITIES_DIR = ../utils/
OBJ_DIR = ../../obj/
BIN_DIR = ../../bin/
......@@ -9,14 +9,14 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFilePE/ -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/
INCLUDES = -I$(UTILITIES_DIR)/bedFilePE/ -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/gzstream/ -I$(UTILITIES_DIR)/version/
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= pairToPairMain.cpp pairToPair.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFilePE.o bedFile.o lineFileUtilities.o
_EXT_OBJECTS=bedFilePE.o bedFile.o lineFileUtilities.o gzstream.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= pairToPair
......@@ -38,6 +38,7 @@ $(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFilePE/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
clean:
@echo "Cleaning up."
......
src/shuffleBed/Makefile
+ 5
− 3
View file @ 3e74755a
CXX = g++
CXXFLAGS = -O3 -Wall
LDFLAGS =
LIBS = -lz
UTILITIES_DIR = ../utils/
OBJ_DIR = ../../obj/
......@@ -9,14 +10,14 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= shuffleBedMain.cpp shuffleBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o
_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= shuffleBed
......@@ -37,7 +38,8 @@ $(BUILT_OBJECTS): $(SOURCES)
$(EXT_OBJECTS):
@$(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 $(UTILITIES_DIR)/genomeFile/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
clean:
@echo "Cleaning up."
......
src/slopBed/Makefile
+ 4
− 2
View file @ 3e74755a
CXX = g++
CXXFLAGS = -O3 -Wall
LDFLAGS =
LIBS = -lz
UTILITIES_DIR = ../utils/
OBJ_DIR = ../../obj/
......@@ -9,14 +10,14 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= slopBedMain.cpp slopBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o
_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o gzstream.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= slopBed
......@@ -38,6 +39,7 @@ $(EXT_OBJECTS):
@$(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 $(UTILITIES_DIR)/gzstream/
clean:
@echo "Cleaning up."
......
src/sortBed/Makefile
+ 4
− 3
View file @ 3e74755a
CXX = g++
CXXFLAGS = -O3 -Wall
LDFLAGS =
LIBS = -lz
UTILITIES_DIR = ../utils/
OBJ_DIR = ../../obj/
BIN_DIR = ../../bin/
......@@ -9,14 +9,14 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= sortMain.cpp sortBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
_EXT_OBJECTS=bedFile.o lineFileUtilities.o
_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= sortBed
......@@ -37,6 +37,7 @@ $(BUILT_OBJECTS): $(SOURCES)
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
clean:
@echo "Cleaning up."
......
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