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Makefile
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#MAC=1
all : kmer_contamination kmer_hash_build kmer_filter
#all : cortex_con_cs solid_converter
#all: solid_converter
ifndef CC
CC = gcc
endif
BIN = bin
LIB = lib
ifeq ($(MAXK),31)
BITFIELDS = 1
endif
ifeq ($(MAXK),63)
BITFIELDS = 2
endif
ifeq ($(MAXK),95)
BITFIELDS = 3
endif
ifeq ($(MAXK),127)
BITFIELDS = 4
endif
ifeq ($(MAXK),160)
BITFIELDS = 5
endif
ifeq ($(MAXK),192)
BITFIELDS = 6
endif
ifeq ($(MAXK),223)
BITFIELDS = 7
endif
ifeq ($(MAXK),255)
BITFIELDS = 8
endif
ifndef BITFIELDS
BITFIELDS = 1
MAXK = 31
endif
# Main program includes
IDIR_BASIC =include/basic
IDIR_UTIL =include/util
IDIR_HASH =include/hash_table
IDIR_CORTEX_CON = include/cortex_con
IDIR_ALIGNMENT = include/alignment
IDIR_STATS = include/stats
# Test code includes
IDIR_BASIC_TESTS =include/test/basic
IDIR_HASH_TABLE_TESTS =include/test/hash_table
IDIR_CORTEX_CON_TESTS=include/test/cortex_con
#Default CUnit installation path in some Linux distributions.
IDIR_CUNIT=/usr/local/include/CUnit/
UNAME := $(shell uname)
ifeq ($(UNAME), Darwin)
MAC=1
endif
# Mac OS X specific. Assuming CUnit is installed with MacPorts
ifdef MAC
#¢-fnested-functions
MACFLAG = -L/opt/local/lib/
IDIR_CUNIT=/opt/local/include/CUnit/
CFLAGS_CUNIT = -L/opt/local/lib/ -lncurses
#LD_CUNIT=
endif
# 64bit architecture by default
ARCH = -m64
ifdef 32_BITS
ARCH =
endif
# Compiler options
OPT = $(ARCH) -Wall -O3 $(MACFLAG) -DNUMBER_OF_BITFIELDS_IN_BINARY_KMER=$(BITFIELDS) -pthread -g
ifdef DEBUG
OPT = $(ARCH) -Wall -O0 $(MACFLAG) -DNUMBER_OF_BITFIELDS_IN_BINARY_KMER=$(BITFIELDS) -g3 -pthread
endif
ifdef ENABLE_READ_PAIR
OPT += -DENABLE_READ_PAIR
endif
ifdef ENABLE_READ_PAIR_OLD
OPT += -DENABLE_READ_PAIR_OLD
endif
ifdef READ_PAIR_DEBUG_GRAPH
OPT += -DREAD_PAIR_DEBUG_GRAPH
endif
ifdef DEBUG_PRINT_LABELS
OPT += -DDEBUG_PRINT_LABELS
endif
kmerinfo: OPT += -DNUMBER_OF_COLOURS=2
kmer_contamination: OPT += -DKMER_CONTAMINATION -DNUMBER_OF_COLOURS=2 -DKMER_TOOLS
kmer_hash_build: OPT += -DKMER_HASH_BUILD -DKMER_TOOLS
kmer_filter: OPT += -DKMER_TOOLS
# Include dirs
CFLAGS_CORTEX_CON = -I$(IDIR_BASIC) -I$(IDIR_HASH) -I$(IDIR_CORTEX_CON) -I$(IDIR_UTIL)
CFLAGS_CORTEX_BUB = -I$(IDIR_BASIC) -I$(IDIR_HASH) -I$(IDIR_CORTEX_CON) -I$(IDIR_UTIL)
CFLAGS_GRAPHOUT = -I$(IDIR_BASIC) -I$(IDIR_CORTEX_CON) -I$(IDIR_HASH) -I$(IDIR_UTIL)
CFLAGS_FILTERREADS = -I$(IDIR_BASIC) -I$(IDIR_CORTEX_CON) -I$(IDIR_HASH) -I$(IDIR_UTIL)
CFLAGS_BUBBLEPARSE = -I$(IDIR_BASIC) -I$(IDIR_CORTEX_CON) -I$(IDIR_HASH)
CFLAGS_KMERINFO = -I$(IDIR_BASIC) -I$(IDIR_CORTEX_CON) -I$(IDIR_HASH)
CFLAGS_LOGPARSE = -I$(IDIR_BASIC) -I$(IDIR_CORTEX_CON) -I$(IDIR_HASH) -I$(IDIR_UTIL)
CFLAGS_HASH_TABLE_TESTS = -I$(IDIR_CUNIT) $(CFLAGS_CUNIT) -I$(IDIR_BASIC) -I$(IDIR_HASH) -I$(IDIR_CORTEX_CON) -I$(IDIR_HASH_TABLE_TESTS)
CFLAGS_CORTEX_CON_TESTS = -I$(IDIR_CUNIT) $(CFLAGS_CUNIT) -I$(IDIR_BASIC) -I$(IDIR_HASH) -I$(IDIR_CORTEX_CON) -I$(IDIR_CORTEX_CON_TESTS)
CFLAGS_BASIC_TESTS = -I$(IDIR_CUNIT) $(CFLAGS_CUNIT) -I$(IDIR_BASIC) -I$(IDIR_BASIC_TESTS)
CFLAGS_KMER_STATS = -I$(IDIR_BASIC) -I$(IDIR_CORTEX_CON) -I$(IDIR_HASH) -I$(IDIR_UTIL) -I$(IDIR_STATS)
CFLAGS_KMER_HASH_BUILD = -I$(IDIR_BASIC) -I$(IDIR_CORTEX_CON) -I$(IDIR_HASH) -I$(IDIR_UTIL) -I$(IDIR_STATS)
CFLAGS_DEMULTIPLEXER = -I$(IDIR_BASIC) -I$(IDIR_UTIL) -I$(IDIR_STATS)
# Program objects
CORTEX_CON_OBJ = obj/kontaminant/file_format.o obj/kontaminant/flags.o obj/kontaminant/cleaning.o obj/kontaminant/path.o obj/kontaminant/perfect_path.o obj/kontaminant/branches.o obj/kontaminant/y_walk.o obj/kontaminant/cmd_line.o obj/kontaminant/binary_kmer.o obj/kontaminant/seq.o obj/kontaminant/element.o obj/kontaminant/hash_value.o obj/kontaminant/hash_table.o obj/kontaminant/dB_graph.o obj/kontaminant/file_reader.o obj/kontaminant/cortex_con.o obj/kontaminant/logger.o obj/kontaminant/metacortex.o obj/kontaminant/coverage_walk.o obj/util/node_queue.o
ifdef ENABLE_READ_PAIR
CORTEX_CON_OBJ += obj/kontaminant/binary_tree.o obj/kontaminant/read_pair.o
BIN_SUFFIX = $(join rp_,$(MAXK))
else
BIN_SUFFIX = $(MAXK)
endif
cortex_con_rp: CORTEX_CON_OBJ += obj/kontaminant/binary_tree.o obj/kontaminant/read_pair.o
cortex_con_mp: CORTEX_CON_OBJ += obj/kontaminant/mark_pair.o
CORTEX_BUB_OBJ = $(CORTEX_CON_OBJ) obj/kontaminant/bubble_find.o
KMERINFO_OBJ = obj/kontaminant/flags.o obj/kontaminant/path.o obj/kontaminant/binary_kmer.o obj/kontaminant/seq.o obj/kontaminant/element.o obj/kontaminant/hash_table.o obj/kontaminant/file_reader.o obj/util/kmerinfo.o obj/kontaminant/logger.o obj/kontaminant/hash_value.o
KMER_COUNT_OBJ = obj/kontaminant/flags.o obj/kontaminant/binary_kmer.o obj/kontaminant/path.o obj/kontaminant/perfect_path.o obj/kontaminant/seq.o obj/kontaminant/element.o obj/kontaminant/hash_value.o obj/kontaminant/hash_table.o obj/kontaminant/dB_graph.o obj/kontaminant/file_reader.o obj/stats/kmer_stats.o obj/stats/kmer_hash.o obj/kontaminant/logger.o obj/stats/kmer_reader.o obj/kontaminant/file_format.o
KMER_HASH_BUILD_OBJ = obj/kontaminant/flags.o obj/kontaminant/file_format.o obj/kontaminant/path.o obj/kontaminant/perfect_path.o obj/kontaminant/binary_kmer.o obj/kontaminant/seq.o obj/kontaminant/element.o obj/kontaminant/hash_value.o obj/kontaminant/hash_table.o obj/kontaminant/dB_graph.o obj/kontaminant/file_reader.o obj/stats/kmer_hash.o obj/stats/kmer_hash_build.o obj/stats/kmer_reader.o obj/kontaminant/logger.o
KMER_FILTER_OBJ = obj/kontaminant/seq_io.o obj/kontaminant/flags.o obj/kontaminant/file_format.o obj/kontaminant/path.o obj/kontaminant/perfect_path.o obj/kontaminant/binary_kmer.o obj/kontaminant/seq.o obj/kontaminant/element.o obj/kontaminant/hash_value.o obj/kontaminant/hash_table.o obj/kontaminant/dB_graph.o obj/kontaminant/file_reader.o obj/stats/kmer_hash.o obj/stats/kmer_filter.o obj/stats/kmer_reader.o obj/kontaminant/logger.o
#Library objects
LIBRARY_OBJ = obj/kontaminant/file_format.o obj/kontaminant/analysis.o obj/kontaminant/flags.o obj/kontaminant/cleaning.o obj/kontaminant/path.o obj/kontaminant/perfect_path.o obj/kontaminant/branches.o obj/kontaminant/y_walk.o obj/kontaminant/cmd_line.o obj/kontaminant/binary_kmer.o obj/kontaminant/seq.o obj/kontaminant/element.o obj/kontaminant/hash_value.o obj/kontaminant/hash_table.o obj/kontaminant/dB_graph.o obj/kontaminant/file_reader.o obj/kontaminant/cortex_con.o obj/kontaminant/logger.o obj/kontaminant/metacortex.o obj/kontaminant/coverage_walk.o obj/util/node_queue.o
# Main rules
kmerinfo: remove_objects $(KMERINFO_OBJ)
mkdir -p $(BIN); $(CC) -lm $(OPT) -o $(BIN)/kmerinfo $(KMERINFO_OBJ)
kmer_contamination: remove_objects $(KMER_COUNT_OBJ)
mkdir -p $(BIN); $(CC) -lm $(OPT) -o $(BIN)/kmer_contamination_$(BIN_SUFFIX) $(KMER_COUNT_OBJ)
kmer_hash_build: remove_objects $(KMER_HASH_BUILD_OBJ)
mkdir -p $(BIN); $(CC) -lm $(OPT) -o $(BIN)/kmer_hash_build_$(BIN_SUFFIX) $(KMER_HASH_BUILD_OBJ)
kmer_filter: remove_objects $(KMER_FILTER_OBJ)
mkdir -p $(BIN); $(CC) -lm $(OPT) -o $(BIN)/kmer_filter_$(BIN_SUFFIX) $(KMER_FILTER_OBJ)
tests: remove_objects run_basic_tests run_hash_table_tests run_graph_tests
# Cleaning rules
.PHONY : clean
clean :
rm -rf $(BIN)/*
rm -rf obj
remove_objects:
rm -rf obj
# Pattern rules
# cortex_con
obj/kontaminant/%.o : src/cortex_con/%.c include/cortex_con/%.h
mkdir -p obj/kontaminant; $(CC) $(CFLAGS_CORTEX_CON) $(OPT) -c $< -o $@
obj/kontaminant/%.o : src/basic/%.c include/basic/%.h
mkdir -p obj/kontaminant; $(CC) $(CFLAGS_CORTEX_CON) $(OPT) -c $< -o $@
obj/kontaminant/%.o : src/hash_table/hash_key/bob_jenkins/%.c include/hash_table/hash_value.h
mkdir -p obj/kontaminant; $(CC) $(CFLAGS_CORTEX_CON) $(OPT) -c $< -o $@
obj/kontaminant/%.o : src/hash_table/open_hash/%.c include/hash_table/open_hash/%.h
mkdir -p obj/kontaminant; $(CC) $(CFLAGS_CORTEX_CON) $(OPT) -c $< -o $@
obj/kontaminant/%.o : src/kontaminant/%.c
mkdir -p obj/kontaminant; $(CC) $(CFLAGS_CORTEX_CON) $(OPT) -c $? -o $@
# Unit tests
obj/test/%.o : src/test/kontaminant/%.c include/test/kontaminant/%.h
mkdir -p obj/test/; $(CC) $(CFLAGS_CORTEX_CON_TESTS) $(OPT) -c $< -o $@
obj/test/run_dB_graph_tests.o : src/test/kontaminant/run_dB_graph_tests.c
mkdir -p obj/test/; $(CC) $(CFLAGS_CORTEX_CON_TESTS) $(OPT) -c $< -o $@
obj/test/%.o : src/basic/%.c include/basic/%.h
mkdir -p obj/test/; $(CC) $(CFLAGS_BASIC_TESTS) $(OPT) -c $< -o $@
obj/test/%.o : src/test/basic/%.c include/test/basic/%.h
mkdir -p obj/test/; $(CC) $(CFLAGS_BASIC_TESTS) $(OPT) -c $< -o $@
obj/test/%.o : src/test/hash_table/%.c include/test/hash_table/%.h
mkdir -p obj/test/; $(CC) $(CFLAGS_HASH_TABLE_TESTS) $(OPT) -c $< -o $@
# Utils
obj/util/kmerinfo.o : src/util/kmerinfo.c
mkdir -p obj/util; $(CC) $(CFLAGS_GRAPHOUT) $(OPT) -c $? -o $@
# Stats
obj/stats/%.o : src/stats/%.c include/stats/%.h
mkdir -p obj/stats; $(CC) $(CFLAGS_KMER_STATS) $(OPT) -c $< -o $@
obj/stats/kmer_stats.o : src/stats/kmer_stats.c
mkdir -p obj/stats; $(CC) $(CFLAGS_KMER_STATS) $(OPT) -c $< -o $@
obj/stats/demultiplexer.o : src/stats/demultiplexer.c
mkdir -p obj/stats; $(CC) $(CFLAGS_DEMULTIPLEXER) $(OPT) -c $< -o $@
obj/stats/kmer_hash_build.o : src/stats/kmer_hash_build.c
mkdir -p obj/stats; $(CC) $(CFLAGS_KMER_HASH_BUILD) $(OPT) -c $< -o $@
obj/stats/kmer_filter.o : src/stats/kmer_filter.c
mkdir -p obj/stats; $(CC) $(CFLAGS_KMER_HASH_BUILD) $(OPT) -c $< -o $@
libctx.dylib:$(LIBRARY_OBJ)
ld -dylib -dynamic $(LIBRARY_OBJ) -o $(LIB)/libctx_$(BIN_SUFFIX).dylib -lc -lz ;
libctx.so.1:$(LIBRARY_OBJ)
$(CC) -shared -Wl,-soname,libctx.so -o $(LIB)/libctx_$(BIN_SUFFIX).so.1 $(LIBRARY_OBJ) -lc -lz
dylib:
mkdir -p $(BIN);
@$(MAKE) clean; \
case `uname` in \
Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libctx.so.1;; \
Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libctx.dylib;; \
*) echo 'Unknown OS';; \
esac