Makefile

# Makefile for htslib, a C library for high-throughput sequencing data formats.
#
#    Copyright (C) 2013-2014 Genome Research Ltd.
#
#    Author: John Marshall <jm18@sanger.ac.uk>

CC     = gcc
AR     = ar
RANLIB = ranlib

# TODO: edit cram code to remove need for -DSAMTOOLS
CPPFLAGS = -I. -DSAMTOOLS=1
# TODO: probably update cram code to make it compile cleanly with -Wc++-compat
CFLAGS   = -g -Wall -O2
EXTRA_CFLAGS_PIC = -fpic
LDFLAGS  =
LDLIBS   =

prefix      = /usr/local
exec_prefix = $(prefix)
includedir  = $(prefix)/include
libdir      = $(exec_prefix)/lib
bindir      = $(exec_prefix)/bin
mandir      = $(prefix)/share/man
man5dir     = $(mandir)/man5

INSTALL = install -p
INSTALL_PROGRAM = $(INSTALL)
INSTALL_DATA    = $(INSTALL) -m 644

PROGRAMS = \
    bgzip \
    tabix

BUILT_TEST_PROGRAMS = \
	test/fieldarith \
	test/hfile \
	test/sam \
	test/test_view \
	test/test-vcf-api \
	test/test-vcf-sweep

all: lib-static lib-shared $(PROGRAMS) $(BUILT_TEST_PROGRAMS)

HTSPREFIX =
include htslib_vars.mk

lib-static: libhts.a

# $(shell), :=, and ifeq/.../endif are GNU Make-specific.  If you don't have
# GNU Make, comment out the parts of this conditional that don't apply.
PLATFORM := $(shell uname -s)
ifeq "$(PLATFORM)" "Darwin"
SHLIB_FLAVOUR = dylib
lib-shared: libhts.dylib
else
SHLIB_FLAVOUR = so
lib-shared: libhts.so
endif


PACKAGE_VERSION  = 0.0.1
LIBHTS_SOVERSION = 0


# $(NUMERIC_VERSION) is for items that must have a numeric X.Y.Z string
# even if this is a dirty or untagged Git working tree.
NUMERIC_VERSION = $(PACKAGE_VERSION)

# If building from a Git repository, replace $(PACKAGE_VERSION) with the Git
# description of the working tree: either a release tag with the same value
# as $(PACKAGE_VERSION) above, or an exact description likely based on a tag.
# Much of this is also GNU Make-specific.  If you don't have GNU Make and/or
# are not building from a Git repository, comment out this conditional.
ifneq "$(wildcard .git)" ""
original_version := $(PACKAGE_VERSION)
PACKAGE_VERSION := $(shell git describe --always --dirty)

# Unless the Git description matches /\d*\.\d*(\.\d*)?/, i.e., is exactly a tag
# with a numeric name, revert $(NUMERIC_VERSION) to the original version number
# written above, but with the patchlevel field bumped to 255.
ifneq "$(subst ..,.,$(subst 0,,$(subst 1,,$(subst 2,,$(subst 3,,$(subst 4,,$(subst 5,,$(subst 6,,$(subst 7,,$(subst 8,,$(subst 9,,$(PACKAGE_VERSION))))))))))))" "."
empty :=
NUMERIC_VERSION := $(subst $(empty) ,.,$(wordlist 1,2,$(subst ., ,$(original_version))) 255)
endif

# Force version.h to be remade if $(PACKAGE_VERSION) has changed.
version.h: $(if $(wildcard version.h),$(if $(findstring "$(PACKAGE_VERSION)",$(shell cat version.h)),,force))
endif

version.h:
	echo '#define HTS_VERSION "$(PACKAGE_VERSION)"' > $@


.SUFFIXES: .c .o .pico

.c.o:
	$(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ $<

.c.pico:
	$(CC) $(CFLAGS) $(CPPFLAGS) $(EXTRA_CFLAGS_PIC) -c -o $@ $<


LIBHTS_OBJS = \
	kfunc.o \
	knetfile.o \
	kstring.o \
	bgzf.o \
	faidx.o \
	hfile.o \
	hfile_net.o \
	hts.o \
	sam.o \
	synced_bcf_reader.o \
	vcf_sweep.o \
	tbx.o \
	vcf.o \
	vcfutils.o \
	cram/cram_codecs.o \
	cram/cram_decode.o \
	cram/cram_encode.o \
	cram/cram_index.o \
	cram/cram_io.o \
	cram/cram_samtools.o \
	cram/cram_stats.o \
	cram/files.o \
	cram/mFILE.o \
	cram/md5.o \
	cram/open_trace_file.o \
	cram/pooled_alloc.o \
	cram/sam_header.o \
	cram/string_alloc.o \
	cram/thread_pool.o \
	cram/vlen.o \
	cram/zfio.o


libhts.a: $(LIBHTS_OBJS)
	@-rm -f $@
	$(AR) -rc $@ $(LIBHTS_OBJS)
	-$(RANLIB) $@


# The target here is libhts.so, as that is the built file that other rules
# depend upon and that is used when -lhts appears in other program's recipes.
# As a byproduct invisible to make, libhts.so.NN is also created, as it is the
# file used at runtime (when $LD_LIBRARY_PATH includes the build directory).

libhts.so: $(LIBHTS_OBJS:.o=.pico)
	$(CC) -shared -Wl,-soname,libhts.so.$(LIBHTS_SOVERSION) $(LDFLAGS) -o $@ $(LIBHTS_OBJS:.o=.pico) $(LDLIBS) -lz
	ln -sf $@ libhts.so.$(LIBHTS_SOVERSION)

# Similarly this also creates libhts.NN.dylib as a byproduct, so that programs
# when run can find this uninstalled shared library (when $DYLD_LIBRARY_PATH
# includes this project's build directory).

libhts.dylib: $(LIBHTS_OBJS)
	$(CC) -dynamiclib -install_name $(libdir)/libhts.$(LIBHTS_SOVERSION).dylib -current_version $(NUMERIC_VERSION) -compatibility_version $(LIBHTS_SOVERSION) $(LDFLAGS) -o $@ $(LIBHTS_OBJS) $(LDLIBS) -lz
	ln -sf $@ libhts.$(LIBHTS_SOVERSION).dylib


cram_h = cram/cram.h $(cram_samtools_h) $(cram_sam_header_h) $(cram_structs_h) $(cram_io_h) cram/cram_encode.h cram/cram_decode.h cram/cram_stats.h cram/cram_codecs.h cram/cram_index.h
cram_io_h = cram/cram_io.h $(cram_misc_h)
cram_misc_h = cram/misc.h cram/os.h
cram_sam_header_h = cram/sam_header.h cram/string_alloc.h cram/pooled_alloc.h htslib/khash.h htslib/kstring.h
cram_samtools_h = cram/cram_samtools.h $(htslib_sam_h) $(cram_sam_header_h)
cram_structs_h = cram/cram_structs.h cram/thread_pool.h cram/string_alloc.h htslib/khash.h
cram_open_trace_file_h = cram/open_trace_file.h cram/mFILE.h
hfile_internal_h = hfile_internal.h $(htslib_hfile_h)

bgzf.o bgzf.pico: bgzf.c config.h $(htslib_hts_h) $(htslib_bgzf_h) $(htslib_hfile_h) htslib/khash.h
kstring.o kstring.pico: kstring.c htslib/kstring.h
knetfile.o knetfile.pico: knetfile.c htslib/knetfile.h
hfile.o hfile.pico: hfile.c $(htslib_hfile_h) $(hfile_internal_h)
hfile_net.o hfile_net.pico: hfile_net.c $(hfile_internal_h) htslib/knetfile.h
hts.o hts.pico: hts.c version.h $(htslib_hts_h) $(htslib_bgzf_h) $(cram_h) $(htslib_hfile_h) htslib/khash.h htslib/kseq.h htslib/ksort.h
vcf.o vcf.pico: vcf.c $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(htslib_hfile_h) htslib/khash.h htslib/kseq.h htslib/kstring.h
sam.o sam.pico: sam.c $(htslib_sam_h) $(htslib_bgzf_h) $(cram_h) $(htslib_hfile_h) htslib/khash.h htslib/kseq.h htslib/kstring.h
tbx.o tbx.pico: tbx.c $(htslib_tbx_h) $(htslib_bgzf_h) htslib/khash.h
faidx.o faidx.pico: faidx.c config.h $(htslib_bgzf_h) $(htslib_faidx_h) htslib/khash.h htslib/knetfile.h
razf.o razf.pico: razf.c $(htslib_razf_h)
synced_bcf_reader.o synced_bcf_reader.pico: synced_bcf_reader.c $(htslib_synced_bcf_reader_h) htslib/kseq.h htslib/khash_str2int.h
vcf_sweep.o vcf_sweep.pico: vcf_sweep.c $(htslib_vcf_sweep_h) $(htslib_bgzf_h)
vcfutils.o vcfutils.pico: vcfutils.c $(htslib_vcfutils_h)
kfunc.o kfunc.pico: kfunc.c htslib/kfunc.h

cram/cram_codecs.o cram/cram_codecs.pico: cram/cram_codecs.c $(cram_h)
cram/cram_decode.o cram/cram_decode.pico: cram/cram_decode.c $(cram_h) cram/os.h cram/md5.h
cram/cram_encode.o cram/cram_encode.pico: cram/cram_encode.c $(cram_h) cram/os.h cram/md5.h
cram/cram_index.o cram/cram_index.pico: cram/cram_index.c $(htslib_hfile_h) $(cram_h) cram/os.h cram/zfio.h
cram/cram_io.o cram/cram_io.pico: cram/cram_io.c $(cram_h) cram/os.h cram/md5.h $(cram_open_trace_file_h) $(htslib_hfile_h)
cram/cram_samtools.o cram/cram_samtools.pico: cram/cram_samtools.c $(cram_h) $(htslib_sam_h)
cram/cram_stats.o cram/cram_stats.pico: cram/cram_stats.c $(cram_h) cram/os.h
cram/files.o cram/files.pico: cram/files.c $(cram_misc_h)
cram/mFILE.o cram/mFILE.pico: cram/mFILE.c cram/os.h cram/mFILE.h cram/vlen.h
cram/md5.o cram/md5.pico: cram/md5.c cram/md5.h
cram/open_trace_file.o cram/open_trace_file.pico: cram/open_trace_file.c $(cram_open_trace_file_h) $(cram_misc_h)
cram/pooled_alloc.o cram/pooled_alloc.pico: cram/pooled_alloc.c cram/pooled_alloc.h
cram/sam_header.o cram/sam_header.pico: cram/sam_header.c $(cram_sam_header_h) cram/string_alloc.h
cram/string_alloc.o cram/string_alloc.pico: cram/string_alloc.c cram/string_alloc.h
cram/thread_pool.o cram/thread_pool.pico: cram/thread_pool.c cram/thread_pool.h
cram/vlen.o cram/vlen.pico: cram/vlen.c cram/vlen.h cram/os.h
cram/zfio.o cram/zfio.pico: cram/zfio.c cram/os.h cram/zfio.h


check test: $(BUILT_TEST_PROGRAMS)
	test/fieldarith test/fieldarith.sam
	test/hfile
	test/sam
	cd test && ./test_view.pl
	cd test && ./test.pl

test/fieldarith: test/fieldarith.o libhts.a
	$(CC) -pthread $(LDFLAGS) -o $@ test/fieldarith.o libhts.a $(LDLIBS) -lz

test/hfile: test/hfile.o libhts.a
	$(CC) $(LDFLAGS) -o $@ test/hfile.o libhts.a $(LDLIBS) -lz

test/sam: test/sam.o libhts.a
	$(CC) -pthread $(LDFLAGS) -o $@ test/sam.o libhts.a $(LDLIBS) -lz

test/test_view: test/test_view.o libhts.a
	$(CC) -pthread $(LDFLAGS) -o $@ test/test_view.o libhts.a $(LDLIBS) -lz

test/test-vcf-api: test/test-vcf-api.o libhts.a
	$(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-api.o libhts.a $(LDLIBS) -lz

test/test-vcf-sweep: test/test-vcf-sweep.o libhts.a
	$(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-sweep.o libhts.a $(LDLIBS) -lz

test/fieldarith.o: test/fieldarith.c $(htslib_sam_h)
test/hfile.o: test/hfile.c $(htslib_hfile_h) $(htslib_hts_defs_h)
test/sam.o: test/sam.c $(htslib_sam_h) htslib/kstring.h
test/test_view.o: test/test_view.c $(cram_h) $(htslib_sam_h)
test/test-vcf-api.o: test/test-vcf-api.c $(htslib_hts_h) $(htslib_vcf_h) htslib/kstring.h
test/test-vcf-sweep.o: test/test-vcf-sweep.c $(htslib_vcf_sweep_h)

bgzip: bgzip.o libhts.a 
	$(CC) $(CFLAGS) -o bgzip bgzip.o libhts.a -lpthread -lz -lm -ldl

tabix: tabix.o libhts.a 
	$(CC) $(CFLAGS) -o tabix tabix.o libhts.a -lpthread -lz -lm -ldl

install: installdirs install-$(SHLIB_FLAVOUR)
	$(INSTALL_DATA) htslib/*.h $(DESTDIR)$(includedir)/htslib
	$(INSTALL_DATA) libhts.a $(DESTDIR)$(libdir)/libhts.a
	$(INSTALL_DATA) *.5 $(DESTDIR)$(man5dir)
	$(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir)

installdirs:
	mkdir -p $(DESTDIR)$(includedir)/htslib $(DESTDIR)$(libdir) $(DESTDIR)$(man5dir) $(DESTDIR)$(bindir)

# After installation, the real file in $(libdir) will be libhts.so.X.Y.Z,
# with symlinks libhts.so (used via -lhts during linking of client programs)
# and libhts.so.NN (used by client executables at runtime).

install-so: libhts.so installdirs
	$(INSTALL_DATA) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION)
	ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so
	ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so.$(LIBHTS_SOVERSION)

install-dylib: libhts.dylib installdirs
	$(INSTALL_PROGRAM) libhts.dylib $(DESTDIR)$(libdir)/libhts.$(PACKAGE_VERSION).dylib
	ln -sf libhts.$(PACKAGE_VERSION).dylib $(DESTDIR)$(libdir)/libhts.dylib
	ln -sf libhts.$(PACKAGE_VERSION).dylib $(DESTDIR)$(libdir)/libhts.$(LIBHTS_SOVERSION).dylib


testclean:
	-rm -f test/*.tmp test/*.tmp.*

mostlyclean: testclean
	-rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM version.h

clean: mostlyclean clean-$(SHLIB_FLAVOUR)
	-rm -f libhts.a $(BUILT_TEST_PROGRAMS) $(PROGRAMS)

distclean: clean
	-rm -f TAGS

clean-so:
	-rm -f libhts.so libhts.so.*

clean-dylib:
	-rm -f libhts.dylib libhts.*.dylib


tags:
	ctags -f TAGS *.[ch] cram/*.[ch] htslib/*.h


force:


.PHONY: all check clean distclean force install installdirs
.PHONY: lib-shared lib-static mostlyclean tags test testclean
.PHONY: clean-so install-so
.PHONY: clean-dylib install-dylib