e327f01b1a1919b6441797f4757d55d317bddf1c braney Wed Aug 31 17:17:55 2016 -0700 some small tweaks in htslib to better incorporate it in the build diff --git src/htslib/Makefile src/htslib/Makefile index 9692256..ea5ab04 100644 --- src/htslib/Makefile +++ src/htslib/Makefile @@ -1,427 +1,429 @@ # Makefile for htslib, a C library for high-throughput sequencing data formats. # # Copyright (C) 2013-2015 Genome Research Ltd. # # Author: John Marshall <jm18@sanger.ac.uk> # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal # in the Software without restriction, including without limitation the rights # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell # copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER # DEALINGS IN THE SOFTWARE. -CC = gcc +kentSrc = .. +include ${kentSrc}/inc/common.mk +#CC = gcc -p AR = ar RANLIB = ranlib CPPFLAGS = # TODO: probably update cram code to make it compile cleanly with -Wc++-compat -CFLAGS = -ggdb -Wall -DKNETFILE_HOOKS -DUCSC_CRAM +CFLAGS += -DKNETFILE_HOOKS -DUCSC_CRAM EXTRA_CFLAGS_PIC = -fpic LDFLAGS = LIBS = # For now these don't work too well as samtools also needs to know to # add -lbz2 and -llzma if linking against the static libhts.a library. # TODO This needs configury and adding to htslib.pc.in. # # # Bzip2 support; optionally used by CRAM. # HAVE_LIBBZ2 := $(shell echo -e "\#include <bzlib.h>\012int main(void){return 0;}" > .test.c && $(CC) $(CFLAGS) $(CPPFLAGS) -o .test .test.c -lbz2 2>/dev/null && echo yes) # ifeq "$(HAVE_LIBBZ2)" "yes" # CPPFLAGS += -DHAVE_LIBBZ2 # LIBS += -lbz2 # endif # # # Lzma support; optionally used by CRAM. # HAVE_LIBLZMA := $(shell echo -e "\#include <lzma.h>\012int main(void){return 0;}" > .test.c && $(CC) $(CFLAGS) $(CPPFLAGS) -o .test .test.c -llzma 2>/dev/null && echo yes) # ifeq "$(HAVE_LIBLZMA)" "yes" # CPPFLAGS += -DHAVE_LIBLZMA # LIBS += -llzma # endif 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 # Set by config.mk if plugins are enabled 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) all: lib-static HTSPREFIX = include htslib_vars.mk PACKAGE_VERSION = 1.3 LIBHTS_SOVERSION = 1 # $(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)"' > $@ 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) # To be effective, config.mk needs to appear after most Makefile variables are # set but before most rules appear, so that it can both use previously-set # variables in its own rules' prerequisites and also update variables for use # in later rules' prerequisites. # If your make doesn't accept -include, change this to 'include' if you are # using the configure script or just comment the line out if you are not. -include config.mk # Usually config.h is generated by running configure or config.status, # but if those aren't used create a default config.h here. config.h: echo '/* Empty config.h generated by Makefile */' > $@ 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 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) $@ # 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) -pthread $(LDFLAGS) -o $@ $(LIBHTS_OBJS:.o=.pico) -lz -lm $(LIBS) 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) -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 $(htslib_kstring_h) knetfile.o knetfile.pico: knetfile.c $(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) $(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 $(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) # For tests that might use it, set $REF_PATH explicitly to use only reference # areas within the test suite (or set it to ':' to use no reference areas). 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_view.pl 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 $(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_faidx_h) $(htslib_kstring_h) test/test-regidx.o: test/test-regidx.c $(htslib_regidx_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) $(htslib_kseq_h) test/test-vcf-sweep.o: test/test-vcf-sweep.c $(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 # 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.$(LIBHTS_SOVERSION).dylib # Substitute these pseudo-autoconf variables only at install time # so that "make install prefix=/prefix/path" etc continue to work. install-pkgconfig: installdirs sed -e 's#@includedir@#$(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 # A pkg-config file (suitable for copying to $PKG_CONFIG_PATH) that provides # flags for building against the uninstalled library in this build directory. 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 # We recommend libhts-using programs be built against a separate htslib # installation. However if you feel that you must bundle htslib source # code with your program, this hook enables Automake-style "make dist" # for this subdirectory. If you do bundle an htslib snapshot, please # add identifying information to $(PACKAGE_VERSION) as appropriate. # (The wildcards attempt to omit non-exported files (.git*, README.md, # etc) and other detritus that might be in the top-level directory.) 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