CC = gcc
AR = ar
RANLIB = ranlib
CPPFLAGS =
CFLAGS = -g -Wall -O2
EXTRA_CFLAGS_PIC = -fpic
LDFLAGS =
LIBS =
prefix = /usr/local
exec_prefix = $(prefix)
bindir = $(exec_prefix)/bin
includedir = $(prefix)/include
libdir = $(exec_prefix)/lib
libexecdir = $(exec_prefix)/libexec
datarootdir = $(prefix)/share
mandir = $(datarootdir)/man
man1dir = $(mandir)/man1
man5dir = $(mandir)/man5
pkgconfigdir= $(libdir)/pkgconfig
MKDIR_P = mkdir -p
INSTALL = install -p
INSTALL_PROGRAM = $(INSTALL)
INSTALL_DATA = $(INSTALL) -m 644
INSTALL_DIR = $(MKDIR_P) -m 755
plugindir =
BUILT_PROGRAMS = \
bgzip \
htsfile \
tabix
BUILT_TEST_PROGRAMS = \
test/fieldarith \
test/hfile \
test/sam \
test/test-regidx \
test/test_view \
test/test-vcf-api \
test/test-vcf-sweep
all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS)
HTSPREFIX =
include htslib_vars.mk
PACKAGE_VERSION = 1.3.1
LIBHTS_SOVERSION = 1
NUMERIC_VERSION = $(PACKAGE_VERSION)
ifneq "$(wildcard .git)" ""
original_version := $(PACKAGE_VERSION)
PACKAGE_VERSION := $(shell git describe --always --dirty)
ifneq "$(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
version.h: $(if $(wildcard version.h),$(if $(findstring "$(PACKAGE_VERSION)",$(shell cat version.h)),,force))
endif
version.h:
echo '#define HTS_VERSION "$(PACKAGE_VERSION)"' > $@
print-version:
@echo $(PACKAGE_VERSION)
.SUFFIXES: .bundle .c .o .pico .so
.c.o:
$(CC) $(CFLAGS) -I. $(CPPFLAGS) -c -o $@ $<
.c.pico:
$(CC) $(CFLAGS) -I. $(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 \
md5.o \
regidx.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_external.o \
cram/cram_index.o \
cram/cram_io.o \
cram/cram_samtools.o \
cram/cram_stats.o \
cram/files.o \
cram/mFILE.o \
cram/open_trace_file.o \
cram/pooled_alloc.o \
cram/rANS_static.o \
cram/sam_header.o \
cram/string_alloc.o \
cram/thread_pool.o \
cram/vlen.o \
cram/zfio.o
PLUGIN_OBJS =
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 $(htslib_cram_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)
hts_internal_h = hts_internal.h $(htslib_hts_h)
-include config.mk
config.h:
echo '/* Empty config.h generated by Makefile */' > $@
lib-static: libhts.a
PLATFORM := $(shell uname -s)
ifeq "$(PLATFORM)" "Darwin"
SHLIB_FLAVOUR = dylib
lib-shared: libhts.dylib
BUILT_PLUGINS = $(PLUGIN_OBJS:.o=.bundle)
else
SHLIB_FLAVOUR = so
lib-shared: libhts.so
BUILT_PLUGINS = $(PLUGIN_OBJS:.o=.so)
endif
plugins: $(BUILT_PLUGINS)
libhts.a: $(LIBHTS_OBJS)
@-rm -f $@
$(AR) -rc $@ $(LIBHTS_OBJS)
-$(RANLIB) $@
libhts.so: $(LIBHTS_OBJS:.o=.pico)
$(CC) -shared -Wl,-soname,libhts.so.$(LIBHTS_SOVERSION) -pthread $(LDFLAGS) -o $@ $(LIBHTS_OBJS:.o=.pico) -lz -lm $(LIBS)
ln -sf $@ libhts.so.$(LIBHTS_SOVERSION)
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) -lz $(LIBS)
ln -sf $@ libhts.$(LIBHTS_SOVERSION).dylib
.pico.so:
$(CC) -shared -Wl,-E -pthread $(LDFLAGS) -o $@ $< $(LIBS)
.o.bundle:
$(CC) -bundle -Wl,-undefined,dynamic_lookup $(LDFLAGS) -o $@ $< $(LIBS)
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 config.h $(htslib_kstring_h)
knetfile.o knetfile.pico: knetfile.c config.h $(htslib_knetfile_h)
hfile.o hfile.pico: hfile.c config.h $(htslib_hfile_h) $(hfile_internal_h) $(hts_internal_h) $(htslib_khash_h)
hfile_irods.o hfile_irods.pico: hfile_irods.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h)
hfile_libcurl.o hfile_libcurl.pico: hfile_libcurl.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h)
hfile_net.o hfile_net.pico: hfile_net.c config.h $(hfile_internal_h) $(htslib_knetfile_h)
hts.o hts.pico: hts.c config.h version.h $(htslib_hts_h) $(htslib_bgzf_h) $(cram_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_ksort_h) $(hts_internal_h)
vcf.o vcf.pico: vcf.c config.h $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(htslib_hfile_h) $(hts_internal_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_kstring_h) $(htslib_khash_str2int_h)
sam.o sam.pico: sam.c config.h $(htslib_sam_h) $(htslib_bgzf_h) $(cram_h) $(hts_internal_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_kstring_h)
tbx.o tbx.pico: tbx.c config.h $(htslib_tbx_h) $(htslib_bgzf_h) $(htslib_khash_h)
faidx.o faidx.pico: faidx.c config.h $(htslib_bgzf_h) $(htslib_faidx_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kstring_h)
synced_bcf_reader.o synced_bcf_reader.pico: synced_bcf_reader.c config.h $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_bgzf_h)
vcf_sweep.o vcf_sweep.pico: vcf_sweep.c config.h $(htslib_vcf_sweep_h) $(htslib_bgzf_h)
vcfutils.o vcfutils.pico: vcfutils.c config.h $(htslib_vcfutils_h) $(htslib_kbitset_h)
kfunc.o kfunc.pico: kfunc.c config.h $(htslib_kfunc_h)
regidx.o regidx.pico: regidx.c config.h $(htslib_hts_h) $(htslib_kstring_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_regidx_h)
md5.o md5.pico: md5.c config.h $(htslib_hts_h)
plugin.o plugin.pico: plugin.c config.h $(hts_internal_h) $(htslib_kstring_h)
cram/cram_codecs.o cram/cram_codecs.pico: cram/cram_codecs.c config.h $(cram_h)
cram/cram_decode.o cram/cram_decode.pico: cram/cram_decode.c config.h $(cram_h) cram/os.h $(htslib_hts_h)
cram/cram_encode.o cram/cram_encode.pico: cram/cram_encode.c config.h $(cram_h) cram/os.h $(htslib_hts_h)
cram/cram_external.o cram/cram_external.pico: cram/cram_external.c config.h $(htslib_hfile_h) $(cram_h)
cram/cram_index.o cram/cram_index.pico: cram/cram_index.c config.h $(htslib_hfile_h) $(cram_h) cram/os.h cram/zfio.h $(hts_internal_h)
cram/cram_io.o cram/cram_io.pico: cram/cram_io.c config.h $(cram_h) cram/os.h $(htslib_hts_h) $(cram_open_trace_file_h) cram/rANS_static.h $(htslib_hfile_h) $(htslib_bgzf_h) $(htslib_faidx_h)
cram/cram_samtools.o cram/cram_samtools.pico: cram/cram_samtools.c config.h $(cram_h) $(htslib_sam_h)
cram/cram_stats.o cram/cram_stats.pico: cram/cram_stats.c config.h $(cram_h) cram/os.h
cram/files.o cram/files.pico: cram/files.c config.h $(cram_misc_h)
cram/mFILE.o cram/mFILE.pico: cram/mFILE.c config.h cram/os.h cram/mFILE.h cram/vlen.h
cram/open_trace_file.o cram/open_trace_file.pico: cram/open_trace_file.c config.h cram/os.h $(cram_open_trace_file_h) $(cram_misc_h) $(htslib_hfile_h)
cram/pooled_alloc.o cram/pooled_alloc.pico: cram/pooled_alloc.c config.h cram/pooled_alloc.h
cram/rANS_static.o cram/rANS_static.pico: cram/rANS_static.c config.h cram/rANS_static.h cram/rANS_byte.h
cram/sam_header.o cram/sam_header.pico: cram/sam_header.c config.h $(cram_sam_header_h) cram/string_alloc.h
cram/string_alloc.o cram/string_alloc.pico: cram/string_alloc.c config.h cram/string_alloc.h
cram/thread_pool.o cram/thread_pool.pico: cram/thread_pool.c config.h cram/thread_pool.h
cram/vlen.o cram/vlen.pico: cram/vlen.c config.h cram/vlen.h cram/os.h
cram/zfio.o cram/zfio.pico: cram/zfio.c config.h cram/os.h cram/zfio.h
bgzip: bgzip.o libhts.a
$(CC) -pthread $(LDFLAGS) -o $@ bgzip.o libhts.a -lz $(LIBS)
htsfile: htsfile.o libhts.a
$(CC) -pthread $(LDFLAGS) -o $@ htsfile.o libhts.a -lz $(LIBS)
tabix: tabix.o libhts.a
$(CC) -pthread $(LDFLAGS) -o $@ tabix.o libhts.a -lz $(LIBS)
bgzip.o: bgzip.c config.h $(htslib_bgzf_h) $(htslib_hts_h)
htsfile.o: htsfile.c config.h $(htslib_hfile_h) $(htslib_hts_h) $(htslib_sam_h) $(htslib_vcf_h)
tabix.o: tabix.c config.h $(htslib_tbx_h) $(htslib_sam_h) $(htslib_vcf_h) $(htslib_kseq_h) $(htslib_bgzf_h) $(htslib_hts_h) $(htslib_regidx_h)
check test: htsfile $(BUILT_TEST_PROGRAMS)
test/fieldarith test/fieldarith.sam
test/hfile
test/sam test/ce.fa test/faidx.fa
test/test-regidx
cd test && REF_PATH=: ./test.pl
test/fieldarith: test/fieldarith.o libhts.a
$(CC) -pthread $(LDFLAGS) -o $@ test/fieldarith.o libhts.a -lz $(LIBS)
test/hfile: test/hfile.o libhts.a
$(CC) -pthread $(LDFLAGS) -o $@ test/hfile.o libhts.a -lz $(LIBS)
test/sam: test/sam.o libhts.a
$(CC) -pthread $(LDFLAGS) -o $@ test/sam.o libhts.a -lz $(LIBS)
test/test-regidx: test/test-regidx.o libhts.a
$(CC) -pthread $(LDFLAGS) -o $@ test/test-regidx.o libhts.a -lz $(LIBS)
test/test_view: test/test_view.o libhts.a
$(CC) -pthread $(LDFLAGS) -o $@ test/test_view.o libhts.a -lz $(LIBS)
test/test-vcf-api: test/test-vcf-api.o libhts.a
$(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-api.o libhts.a -lz $(LIBS)
test/test-vcf-sweep: test/test-vcf-sweep.o libhts.a
$(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-sweep.o libhts.a -lz $(LIBS)
test/fieldarith.o: test/fieldarith.c config.h $(htslib_sam_h)
test/hfile.o: test/hfile.c config.h $(htslib_hfile_h) $(htslib_hts_defs_h)
test/sam.o: test/sam.c config.h $(htslib_hts_defs_h) $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h)
test/test-regidx.o: test/test-regidx.c config.h $(htslib_regidx_h)
test/test_view.o: test/test_view.c config.h $(cram_h) $(htslib_sam_h)
test/test-vcf-api.o: test/test-vcf-api.c config.h $(htslib_hts_h) $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_kseq_h)
test/test-vcf-sweep.o: test/test-vcf-sweep.c config.h $(htslib_vcf_sweep_h)
install: libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) installdirs install-$(SHLIB_FLAVOUR) install-pkgconfig
$(INSTALL_PROGRAM) $(BUILT_PROGRAMS) $(DESTDIR)$(bindir)
if test -n "$(BUILT_PLUGINS)"; then $(INSTALL_PROGRAM) $(BUILT_PLUGINS) $(DESTDIR)$(plugindir); fi
$(INSTALL_DATA) htslib/*.h $(DESTDIR)$(includedir)/htslib
$(INSTALL_DATA) libhts.a $(DESTDIR)$(libdir)/libhts.a
$(INSTALL_DATA) htsfile.1 tabix.1 $(DESTDIR)$(man1dir)
$(INSTALL_DATA) faidx.5 sam.5 vcf.5 $(DESTDIR)$(man5dir)
installdirs:
$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(includedir) $(DESTDIR)$(includedir)/htslib $(DESTDIR)$(libdir) $(DESTDIR)$(man1dir) $(DESTDIR)$(man5dir) $(DESTDIR)$(pkgconfigdir)
if test -n "$(plugindir)"; then $(INSTALL_DIR) $(DESTDIR)$(plugindir); fi
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.$(LIBHTS_SOVERSION).dylib
install-pkgconfig: installdirs
sed -e 's#@includedir@#$(includedir)#g;s#@libdir@#$(libdir)#g;s#@PACKAGE_VERSION@#$(PACKAGE_VERSION)#g' htslib.pc.in > $(DESTDIR)$(pkgconfigdir)/htslib.pc
chmod 644 $(DESTDIR)$(pkgconfigdir)/htslib.pc
htslib-uninstalled.pc: htslib.pc.in
sed -e 's#@includedir@#'`pwd`'#g;s#@libdir@#'`pwd`'#g' htslib.pc.in > $@
testclean:
-rm -f test/*.tmp test/*.tmp.*
mostlyclean: testclean
-rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM version.h
clean: mostlyclean clean-$(SHLIB_FLAVOUR)
-rm -f libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) $(BUILT_TEST_PROGRAMS)
distclean maintainer-clean: clean
-rm -f config.cache config.h config.log config.mk config.status
-rm -f TAGS *-uninstalled.pc
clean-so:
-rm -f libhts.so libhts.so.*
clean-dylib:
-rm -f libhts.dylib libhts.*.dylib
tags TAGS:
ctags -f TAGS *.[ch] cram/*.[ch] htslib/*.h
distdir:
tar -c *.[ch15] [ILMNRcht]*[ELSbcekmnt] | (cd $(distdir) && tar -x)
+cd $(distdir) && $(MAKE) distclean
force:
.PHONY: all check clean distclean distdir force
.PHONY: install install-pkgconfig installdirs lib-shared lib-static
.PHONY: maintainer-clean mostlyclean plugins print-version tags test testclean
.PHONY: clean-so install-so
.PHONY: clean-dylib install-dylib