Makefile

OS := $(shell uname)
ARCH := $(shell arch)

PYTHON ?= python3

all : libhts.a longphase libclair3.so
clean : clean_htslib clean_longphase clean_libclair3

SAMVER	=	1.15.1
LPVER	=	1.7.3
GCC	?=	gcc
GXX	?=	g++
PREFIX	?=	${CONDA_PREFIX}
LDFLAGS	=	-L ${PREFIX}/lib
CFLAGS	= -fpic -std=c99 -O3 -I ${PREFIX}/include -L ${PREFIX}/lib
CPPFLAGS	=	-std=c++11 -Wall -O3 -I ${PREFIX}/include -L ${PREFIX}/lib -Wl,-rpath=${PREFIX}/lib


samtools-$(SAMVER)/Makefile:
		curl -L -o samtools-${SAMVER}.tar.bz2 https://github.com/samtools/samtools/releases/download/${SAMVER}/samtools-${SAMVER}.tar.bz2; \
		tar -xjf samtools-${SAMVER}.tar.bz2; \
		rm samtools-${SAMVER}.tar.bz2

libhts.a: samtools-$(SAMVER)/Makefile
	# this is required only to add in -fpic so we can build python module
	@echo "\x1b[1;33mMaking $(@F)\x1b[0m"
	cd samtools-${SAMVER}/htslib-${SAMVER}; CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}" ./configure; make CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}"
	cp samtools-${SAMVER}/htslib-${SAMVER}/$@ $@


longphase:
	curl -L -o longphase-${LPVER}.tar.xz https://github.com/twolinin/longphase/releases/download/v${LPVER}/longphase_linux-x64.tar.xz
	tar -xJf longphase-${LPVER}.tar.xz
	mv longphase_linux-x64 $@
	rm longphase-${LPVER}.tar.xz


libclair3.so: samtools-${SAMVER}/htslib-${SAMVER} libhts.a
	${PYTHON} build.py

src/%.o: src/%.c
	$(GCC) -g -Isrc -Isamtools-${SAMVER}/htslib-${SAMVER} -c -pthread -fstack-protector-strong -D_FORTIFY_SOURCE=2 \
		$(CFLAGS) $^ -o $@

fa_test: src/fa_test.o src/levenshtein.o src/medaka_bamiter.o src/medaka_common.o src/medaka_khcounter.o src/clair3_pileup.o src/clair3_full_alignment.o src/csv.o
	gcc -g -Isrc -L ./ -pthread -fstack-protector-strong -D_FORTIFY_SOURCE=2 \
		$(CFLAGS) $^ \
		-lhts -llzma -lcurl -lcrypto -lz -lm -lbz2 -o $@


.PHONY: clean_htslib
clean_htslib:
	cd samtools-${SAMVER} && make clean || exit 0
	cd samtools-${SAMVER}/htslib-${SAMVER} && make clean || exit 0
	rm libhts.a

.PHONY: clean_longphase
clean_longphase:
	rm longphase

.PHONY: clean_libclair3
clean_libclair3:
	rm libclair3.*