Makefile

PROG= PISA

all: $(PROG)

HTSDIR = third_party/htslib-1.10.2
include $(HTSDIR)/htslib.mk
HTSLIB = $(HTSDIR)/libhts.a
HTSVERSION = $(HTSDIR)/version.h

#FMLDIR = third_party/fermi-lite
#include $(FMLDIR)/fermi.mk
#FMLLIB = $(FMLDIR)/libfml.a

LIBA = src/liba.a

ZLIBDIR= third_party/zlib-1.2.11
include $(ZLIBDIR)/zlib.mk
LIBZ = $(ZLIBDIR)/libz.a

CC       = gcc
BUILD_TYPE ?= release
ifeq ($(BUILD_TYPE),debug)
CFLAGS   = -Wall -O0 -g -D_FILE_OFFSET_BITS=64 -fopenmp
else
CFLAGS   = -Wall -O3 -D_FILE_OFFSET_BITS=64 -fopenmp
endif
DFLAGS   =
INCLUDES = -Isrc -I$(HTSDIR)/ -I. -I$(ZLIBDIR)
LIBS = -pthread -lm
# Optional deps: auto-detected (override with: make USE_BZ2=0 etc.)
USE_BZ2   ?= $(shell echo 'int main(){return 0;}' | $(CC) -include bzlib.h -x c - -lbz2 -o /dev/null 2>/dev/null && echo 1 || echo 0)
USE_LZMA  ?= $(shell echo 'int main(){return 0;}' | $(CC) -include lzma.h -x c - -llzma -o /dev/null 2>/dev/null && echo 1 || echo 0)
USE_CURL  ?= $(shell echo 'int main(){return 0;}' | $(CC) -include curl/curl.h -x c - -lcurl -o /dev/null 2>/dev/null && echo 1 || echo 0)
ifeq ($(USE_BZ2),1)
  LIBS += -lbz2
endif
ifeq ($(USE_LZMA),1)
  LIBS += -llzma
endif
ifeq ($(USE_CURL),1)
  LIBS += -lcurl
endif

#all:$(PROG)

# See htslib/Makefile
PACKAGE_VERSION := $(shell git describe --tags)

.SUFFIXES:.c .o

.PHONY:all debug clean clean-all distclean install lib tags test testclean 

debug:
	@$(MAKE) BUILD_TYPE=debug clean all

force:

.c.o:
	@printf "Compiling $<...                               \r"
	@$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@

LIB_OBJ = src/barcode_list.o \
	src/bam_anno_vcf.o \
	src/bed.o \
	src/number.o \
	src/fastq.o \
	src/kson.o \
	src/json_config.o \
	src/gtf.o \
	src/region_index.o \
	src/dict.o \
	src/ksa.o \
	src/bam_pool.o \
	src/umi_corr.o \
	src/read_tags.o \
	src/sim_search.o \
	src/fragment.o \
	src/compactDNA.o \
	src/bam_region.o \
	src/dna_pool.o \
	src/bam_files.o \
	src/biostring.o \
	src/read_anno.o \
	src/kthread.o \
	src/coverage.o

AOBJ = src/main.o \
	src/bam_anno.o \
	src/bam_count.o \
	src/bam_pick.o \
	src/sam2bam.o \
	src/bam_attr_count.o \
	src/fastq_sort.o \
	src/fastq_parse_barcode.o \
	src/bam_tag_corr.o \
	src/bam2fq.o \
	src/bam_extract_tags.o \
	src/bam_rmdup.o\
	src/gene_fusion.o \
	src/bam_depth.o \
	src/usage.o \
	src/addtags.o \
	src/fragment_count.o \
	src/fastq_stream.o \
	src/fastq_parse2.o \
	src/gtf_format.o \
	src/callept.o \
	src/genomecov.o \
	src/bed_merge.o \
	src/bed_anno.o \
	src/gtf2bed.o \
	src/bed_flatten.o \
	src/bam_cov.o \
	src/pisa_history.o

liba.a: $(LIB_OBJ)
	@-rm -f src/$@
	$(AR) -rcs src/$@ $(LIB_OBJ)

test: $(HTSLIB) $(HTSVERSION)

PISA: $(HTSLIB) $(LIBZ) liba.a $(AOBJ)
	$(CC) $(CFLAGS) $(INCLUDES) -o $@ $(AOBJ) src/liba.a $(HTSLIB) $(LIBS) $(LIBZ)

prefix ?= /usr/local
bindir ?= $(prefix)/bin

install: $(PROG)
	install -d $(bindir)
	install -m 755 $(PROG) $(bindir)

git:
	@-echo '#define PISA_VERSION "$(PACKAGE_VERSION)"' > pisa_version.h
	@-git push

src/gtf_format.o: src/gtf_format.c
src/fastq_parse2.o: src/fastq_parse2.c
src/fastq_stream.o: src/fastq_stream.c
src/read_anno.o: src/read_anno.c
src/sim_search.o: src/sim_search.c
src/bam_depth.o: src/bam_depth.c
src/bam2fq.o: src/bam2fq.c
src/bam_anno.o: src/bam_anno.c
src/bam_count.o: src/bam_count.c 
src/bam_pick.o: src/bam_pick.c
src/bam_anno_vcf.o: src/bam_anno_vcf.c
src/bam_tag_corr.o: src/bam_tag_corr.c
src/umi_corr.o: src/umi_corr.c
src/fastq_parse_barcode.o: src/fastq_parse_barcode.c
src/fastq_sort.o: src/fastq_sort.c
src/dict.o: src/dict.c
src/sam2bam.o: src/sam2bam.c
src/barcode_list.o: src/barcode_list.c
src/bed.o: src/bed.c
src/number.o: src/number.c
src/gtf.o: src/gtf.c
src/region_index.o: src/region_index.c
src/fastq.o: src/fastq.c
src/json_config.o: src/json_config.c
src/kson.o: src/kson.c
src/bam_attr_count.o: src/bam_attr_count.c
src/read_tags.o: src/read_tags.c
src/ksa.o: src/ksa.c
src/bam_pool.o: src/bam_pool.c
src/bam_extract_tags.o: src/bam_extract_tags.c
src/usage.o:src/usage.c
src/bam_rmdup.o:src/bam_rmdup.c
src/dna_pool.o:src/dna_pool.c
src/gene_fusion.o:src/gene_fusion.c
src/bam_files.o:src/bam_files.c
src/biostring.o:src/biostring.c
src/kthread.o:src/kthread.c
src/addtags.o:src/addtags.c
src/fragment.o:src/fragment.c
src/fragment_count.o:src/fragment_count.c
src/callept.o:src/callept.c
src/genomecov.o:src/genomecov.c
src/main.o:src/main.c
src/coverage.o:src/coverage.c
src/compactDNA.o:src/compactDNA.c
src/bam_region.o:src/bam_region.c
src/bed_merge.o:src/bed_merge.c
src/bed_flatten.o:src/bed_flatten.c
src/bam_cov.o:src/bam_cov.c
src/pisa_history.o:src/pisa_history.c
src/gtf2bed.o:src/gtf2bed.c

clean: testclean
	-rm -f gmon.out *.o *~ $(PROG) 
	-rm -rf *.dSYM plugins/*.dSYM test/*.dSYM
	-rm src/*.o src/liba.a

testclean:
	-rm -f test/*.o test/*~ $(TEST_PROG)

distclean: clean
	-rm -f TAGS

clean-all: clean clean-htslib

tags:
	ctags -f TAGS src/*.[ch] $(HTSDIR)/*.c