c_cpp/lib/htslib/Makefile

   1 # Makefile for htslib, a C library for high-throughput sequencing data formats.
   2 #
   3 #    Copyright (C) 2013-2017 Genome Research Ltd.
   4 #
   5 #    Author: John Marshall <jm18@sanger.ac.uk>
   6 #
   7 # Permission is hereby granted, free of charge, to any person obtaining a copy
   8 # of this software and associated documentation files (the "Software"), to deal
   9 # in the Software without restriction, including without limitation the rights
  10 # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
  11 # copies of the Software, and to permit persons to whom the Software is
  12 # furnished to do so, subject to the following conditions:
  13 #
  14 # The above copyright notice and this permission notice shall be included in
  15 # all copies or substantial portions of the Software.
  16 #
  17 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
  18 # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  19 # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
  20 # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
  21 # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
  22 # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
  23 # DEALINGS IN THE SOFTWARE.
  24
  25 CC     = gcc
  26 AR     = ar
  27 RANLIB = ranlib
  28
  29 # Default libraries to link if configure is not used
  30 htslib_default_libs = -lz -lm -lbz2 -llzma
  31
  32 CPPFLAGS =
  33 # TODO: probably update cram code to make it compile cleanly with -Wc++-compat
  34 # For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
  35 #CFLAGS   = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__
  36 CFLAGS   = -g -Wall -O2
  37 EXTRA_CFLAGS_PIC = -fpic
  38 LDFLAGS  =
  39 LIBS     = $(htslib_default_libs)
  40
  41 prefix      = /usr/local
  42 exec_prefix = $(prefix)
  43 bindir      = $(exec_prefix)/bin
  44 includedir  = $(prefix)/include
  45 libdir      = $(exec_prefix)/lib
  46 libexecdir  = $(exec_prefix)/libexec
  47 datarootdir = $(prefix)/share
  48 mandir      = $(datarootdir)/man
  49 man1dir     = $(mandir)/man1
  50 man5dir     = $(mandir)/man5
  51 pkgconfigdir= $(libdir)/pkgconfig
  52
  53 MKDIR_P = mkdir -p
  54 INSTALL = install -p
  55 INSTALL_DATA    = $(INSTALL) -m 644
  56 INSTALL_DIR     = $(MKDIR_P) -m 755
  57 INSTALL_LIB     = $(INSTALL_DATA)
  58 INSTALL_MAN     = $(INSTALL_DATA)
  59 INSTALL_PROGRAM = $(INSTALL)
  60
  61 # Set by config.mk if plugins are enabled
  62 plugindir =
  63
  64 BUILT_PROGRAMS = \
  65         bgzip \
  66         htsfile \
  67         tabix
  68
  69 BUILT_TEST_PROGRAMS = \
  70         test/hts_endian \
  71         test/fieldarith \
  72         test/hfile \
  73         test/sam \
  74         test/test_bgzf \
  75         test/test-regidx \
  76         test/test_view \
  77         test/test-vcf-api \
  78         test/test-vcf-sweep \
  79         test/test-bcf-sr
  80
  81 BUILT_THRASH_PROGRAMS = \
  82         test/thrash_threads1 \
  83         test/thrash_threads2 \
  84         test/thrash_threads3 \
  85         test/thrash_threads4 \
  86         test/thrash_threads5 \
  87         test/thrash_threads6
  88
  89 all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS)
  90
  91 HTSPREFIX =
  92 include htslib_vars.mk
  93
  94
  95 PACKAGE_VERSION = 1.5
  96 LIBHTS_SOVERSION = 2
  97
  98
  99 # $(NUMERIC_VERSION) is for items that must have a numeric X.Y.Z string
 100 # even if this is a dirty or untagged Git working tree.
 101 NUMERIC_VERSION = $(PACKAGE_VERSION)
 102
 103 # If building from a Git repository, replace $(PACKAGE_VERSION) with the Git
 104 # description of the working tree: either a release tag with the same value
 105 # as $(PACKAGE_VERSION) above, or an exact description likely based on a tag.
 106 # Much of this is also GNU Make-specific.  If you don't have GNU Make and/or
 107 # are not building from a Git repository, comment out this conditional.
 108 ifneq "$(wildcard .git)" ""
 109 original_version := $(PACKAGE_VERSION)
 110 PACKAGE_VERSION := $(shell git describe --always --dirty)
 111
 112 # Unless the Git description matches /\d*\.\d*(\.\d*)?/, i.e., is exactly a tag
 113 # with a numeric name, revert $(NUMERIC_VERSION) to the original version number
 114 # written above, but with the patchlevel field bumped to 255.
 115 ifneq "$(subst ..,.,$(subst 0,,$(subst 1,,$(subst 2,,$(subst 3,,$(subst 4,,$(subst 5,,$(subst 6,,$(subst 7,,$(subst 8,,$(subst 9,,$(PACKAGE_VERSION))))))))))))" "."
 116 empty :=
 117 NUMERIC_VERSION := $(subst $(empty) ,.,$(wordlist 1,2,$(subst ., ,$(original_version))) 255)
 118 endif
 119
 120 # Force version.h to be remade if $(PACKAGE_VERSION) has changed.
 121 version.h: $(if $(wildcard version.h),$(if $(findstring "$(PACKAGE_VERSION)",$(shell cat version.h)),,force))
 122 endif
 123
 124 version.h:
 125         echo '#define HTS_VERSION "$(PACKAGE_VERSION)"' > $@
 126
 127 print-version:
 128         @echo $(PACKAGE_VERSION)
 129
 130
 131 .SUFFIXES: .bundle .c .cygdll .dll .o .pico .so
 132
 133 .c.o:
 134         $(CC) $(CFLAGS) -I. $(CPPFLAGS) -c -o $@ $<
 135
 136 .c.pico:
 137         $(CC) $(CFLAGS) -I. $(CPPFLAGS) $(EXTRA_CFLAGS_PIC) -c -o $@ $<
 138
 139
 140 LIBHTS_OBJS = \
 141         kfunc.o \
 142         knetfile.o \
 143         kstring.o \
 144         bcf_sr_sort.o \
 145         bgzf.o \
 146         errmod.o \
 147         faidx.o \
 148         hfile.o \
 149         hfile_net.o \
 150         hts.o \
 151         md5.o \
 152         multipart.o \
 153         probaln.o \
 154         realn.o \
 155         regidx.o \
 156         sam.o \
 157         synced_bcf_reader.o \
 158         vcf_sweep.o \
 159         tbx.o \
 160         textutils.o \
 161         thread_pool.o \
 162         vcf.o \
 163         vcfutils.o \
 164         cram/cram_codecs.o \
 165         cram/cram_decode.o \
 166         cram/cram_encode.o \
 167         cram/cram_external.o \
 168         cram/cram_index.o \
 169         cram/cram_io.o \
 170         cram/cram_samtools.o \
 171         cram/cram_stats.o \
 172         cram/files.o \
 173         cram/mFILE.o \
 174         cram/open_trace_file.o \
 175         cram/pooled_alloc.o \
 176         cram/rANS_static.o \
 177         cram/sam_header.o \
 178         cram/string_alloc.o
 179
 180 PLUGIN_EXT  =
 181 PLUGIN_OBJS =
 182
 183 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)
 184 cram_io_h = cram/cram_io.h $(cram_misc_h)
 185 cram_misc_h = cram/misc.h $(cram_os_h)
 186 cram_os_h = cram/os.h $(htslib_hts_endian_h)
 187 cram_sam_header_h = cram/sam_header.h cram/string_alloc.h cram/pooled_alloc.h $(htslib_khash_h) $(htslib_kstring_h)
 188 cram_samtools_h = cram/cram_samtools.h $(htslib_sam_h) $(cram_sam_header_h)
 189 cram_structs_h = cram/cram_structs.h $(htslib_thread_pool_h) cram/string_alloc.h $(htslib_khash_h)
 190 cram_open_trace_file_h = cram/open_trace_file.h cram/mFILE.h
 191 hfile_internal_h = hfile_internal.h $(htslib_hfile_h)
 192 hts_internal_h = hts_internal.h $(htslib_hts_h)
 193 thread_pool_internal_h = thread_pool_internal.h $(htslib_thread_pool_h)
 194
 195
 196 # To be effective, config.mk needs to appear after most Makefile variables are
 197 # set but before most rules appear, so that it can both use previously-set
 198 # variables in its own rules' prerequisites and also update variables for use
 199 # in later rules' prerequisites.
 200
 201 # If your make doesn't accept -include, change this to 'include' if you are
 202 # using the configure script or just comment the line out if you are not.
 203 -include config.mk
 204
 205 # Usually config.h is generated by running configure or config.status,
 206 # but if those aren't used create a default config.h here.
 207 config.h:
 208         echo '/* Default config.h generated by Makefile */' > $@
 209         echo '#define HAVE_LIBBZ2 1' >> $@
 210         echo '#define HAVE_LIBLZMA 1' >> $@
 211
 212 # And similarly for htslib.pc.tmp ("pkg-config template").  No dependency
 213 # on htslib.pc.in listed, as if that file is newer the usual way to regenerate
 214 # this target is via configure or config.status rather than this rule.
 215 htslib.pc.tmp:
 216         sed -e '/^static_libs=/s/@static_LIBS@/$(htslib_default_libs)/;s#@[^-][^@]*@##g' htslib.pc.in > $@
 217
 218 # Create a makefile fragment listing the libraries and LDFLAGS needed for
 219 # static linking.  This can be included by projects that want to build
 220 # and link against the htslib source tree instead of an installed library.
 221 htslib_static.mk: htslib.pc.tmp
 222         sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' $< > $@
 223
 224
 225 lib-static: libhts.a
 226
 227 # $(shell), :=, and ifeq/.../endif are GNU Make-specific.  If you don't have
 228 # GNU Make, comment out the parts of these conditionals that don't apply.
 229 ifneq "$(origin PLATFORM)" "file"
 230 PLATFORM := $(shell uname -s)
 231 endif
 232 ifeq "$(PLATFORM)" "Darwin"
 233 SHLIB_FLAVOUR = dylib
 234 lib-shared: libhts.dylib
 235 else ifeq "$(findstring CYGWIN,$(PLATFORM))" "CYGWIN"
 236 SHLIB_FLAVOUR = cygdll
 237 lib-shared: cyghts-$(LIBHTS_SOVERSION).dll
 238 else
 239 SHLIB_FLAVOUR = so
 240 lib-shared: libhts.so
 241 endif
 242
 243 BUILT_PLUGINS = $(PLUGIN_OBJS:.o=$(PLUGIN_EXT))
 244
 245 plugins: $(BUILT_PLUGINS)
 246
 247
 248 libhts.a: $(LIBHTS_OBJS)
 249         @-rm -f $@
 250         $(AR) -rc $@ $(LIBHTS_OBJS)
 251         -$(RANLIB) $@
 252
 253 print-config:
 254         @echo LDFLAGS = $(LDFLAGS)
 255         @echo LIBHTS_OBJS = $(LIBHTS_OBJS)
 256         @echo LIBS = $(LIBS)
 257         @echo PLATFORM = $(PLATFORM)
 258
 259 # The target here is libhts.so, as that is the built file that other rules
 260 # depend upon and that is used when -lhts appears in other program's recipes.
 261 # As a byproduct invisible to make, libhts.so.NN is also created, as it is the
 262 # file used at runtime (when $LD_LIBRARY_PATH includes the build directory).
 263
 264 libhts.so: $(LIBHTS_OBJS:.o=.pico)
 265         $(CC) -shared -Wl,-soname,libhts.so.$(LIBHTS_SOVERSION) $(LDFLAGS) -o $@ $(LIBHTS_OBJS:.o=.pico) $(LIBS) -lpthread
 266         ln -sf $@ libhts.so.$(LIBHTS_SOVERSION)
 267
 268 # Similarly this also creates libhts.NN.dylib as a byproduct, so that programs
 269 # when run can find this uninstalled shared library (when $DYLD_LIBRARY_PATH
 270 # includes this project's build directory).
 271
 272 libhts.dylib: $(LIBHTS_OBJS)
 273         $(CC) -dynamiclib -install_name $(libdir)/libhts.$(LIBHTS_SOVERSION).dylib -current_version $(NUMERIC_VERSION) -compatibility_version $(LIBHTS_SOVERSION) $(LDFLAGS) -o $@ $(LIBHTS_OBJS) $(LIBS)
 274         ln -sf $@ libhts.$(LIBHTS_SOVERSION).dylib
 275
 276 cyghts-$(LIBHTS_SOVERSION).dll: $(LIBHTS_OBJS)
 277         $(CC) -shared -Wl,--out-implib=libhts.dll.a -Wl,--export-all-symbols -Wl,--enable-auto-import $(LDFLAGS) -o $@ -Wl,--whole-archive $(LIBHTS_OBJS) -Wl,--no-whole-archive $(LIBS) -lpthread
 278
 279
 280 .pico.so:
 281         $(CC) -shared -Wl,-E $(LDFLAGS) -o $@ $< $(LIBS) -lpthread
 282
 283 .o.bundle:
 284         $(CC) -bundle -Wl,-undefined,dynamic_lookup $(LDFLAGS) -o $@ $< $(LIBS)
 285
 286 .o.cygdll:
 287         $(CC) -shared $(LDFLAGS) -o $@ $< libhts.dll.a $(LIBS)
 288
 289
 290 bgzf.o bgzf.pico: bgzf.c config.h $(htslib_hts_h) $(htslib_bgzf_h) $(htslib_hfile_h) $(htslib_thread_pool_h) cram/pooled_alloc.h $(htslib_khash_h)
 291 errmod.o errmod.pico: errmod.c config.h $(htslib_hts_h) $(htslib_ksort_h)
 292 kstring.o kstring.pico: kstring.c config.h $(htslib_kstring_h)
 293 knetfile.o knetfile.pico: knetfile.c config.h $(htslib_hts_log_h) $(htslib_knetfile_h)
 294 hfile.o hfile.pico: hfile.c config.h $(htslib_hfile_h) $(hfile_internal_h) $(hts_internal_h) $(htslib_khash_h)
 295 hfile_gcs.o hfile_gcs.pico: hfile_gcs.c config.h $(htslib_hts_h) $(htslib_kstring_h) $(hfile_internal_h)
 296 hfile_libcurl.o hfile_libcurl.pico: hfile_libcurl.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h)
 297 hfile_net.o hfile_net.pico: hfile_net.c config.h $(hfile_internal_h) $(htslib_knetfile_h)
 298 hfile_s3.o hfile_s3.pico: hfile_s3.c config.h $(hts_internal_h) $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h)
 299 hts.o hts.pico: hts.c config.h $(htslib_hts_h) $(htslib_bgzf_h) $(cram_h) $(hfile_internal_h) $(htslib_hfile_h) version.h $(hts_internal_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_ksort_h)
 300 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_str2int_h) $(htslib_kstring_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_hts_endian_h)
 301 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) $(htslib_hts_endian_h)
 302 tbx.o tbx.pico: tbx.c config.h $(htslib_tbx_h) $(htslib_bgzf_h) $(hts_internal_h) $(htslib_khash_h)
 303 faidx.o faidx.pico: faidx.c config.h $(htslib_bgzf_h) $(htslib_faidx_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kstring_h) $(hts_internal_h)
 304 bcf_sr_sort.o bcf_sr_sort.pico: bcf_sr_sort.c config.h bcf_sr_sort.h $(htslib_kseq_h) $(htslib_khash_str2int_h)
 305 synced_bcf_reader.o synced_bcf_reader.pico: synced_bcf_reader.c config.h bcf_sr_sort.h $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_bgzf_h) $(htslib_thread_pool_h)
 306 vcf_sweep.o vcf_sweep.pico: vcf_sweep.c config.h $(htslib_vcf_sweep_h) $(htslib_bgzf_h)
 307 vcfutils.o vcfutils.pico: vcfutils.c config.h $(htslib_vcfutils_h) $(htslib_kbitset_h)
 308 kfunc.o kfunc.pico: kfunc.c config.h $(htslib_kfunc_h)
 309 regidx.o regidx.pico: regidx.c config.h $(htslib_hts_h) $(htslib_kstring_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_regidx_h) $(hts_internal_h)
 310 md5.o md5.pico: md5.c config.h $(htslib_hts_h) $(htslib_hts_endian_h)
 311 multipart.o multipart.pico: multipart.c config.h $(htslib_kstring_h) $(hts_internal_h) $(hfile_internal_h)
 312 plugin.o plugin.pico: plugin.c config.h $(hts_internal_h) $(htslib_kstring_h)
 313 probaln.o probaln.pico: probaln.c config.h $(htslib_hts_h)
 314 realn.o realn.pico: realn.c config.h $(htslib_hts_h) $(htslib_sam_h)
 315 textutils.o textutils.pico: textutils.c config.h $(htslib_hfile_h) $(htslib_kstring_h) $(hts_internal_h)
 316
 317 cram/cram_codecs.o cram/cram_codecs.pico: cram/cram_codecs.c config.h $(cram_h)
 318 cram/cram_decode.o cram/cram_decode.pico: cram/cram_decode.c config.h $(cram_h) $(cram_os_h) $(htslib_hts_h)
 319 cram/cram_encode.o cram/cram_encode.pico: cram/cram_encode.c config.h $(cram_h) $(cram_os_h) $(htslib_hts_h) $(htslib_hts_endian_h)
 320 cram/cram_external.o cram/cram_external.pico: cram/cram_external.c config.h $(htslib_hfile_h) $(cram_h)
 321 cram/cram_index.o cram/cram_index.pico: cram/cram_index.c config.h $(htslib_bgzf_h) $(htslib_hfile_h) $(hts_internal_h) $(cram_h) $(cram_os_h)
 322 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) $(hts_internal_h)
 323 cram/cram_samtools.o cram/cram_samtools.pico: cram/cram_samtools.c config.h $(cram_h) $(htslib_sam_h)
 324 cram/cram_stats.o cram/cram_stats.pico: cram/cram_stats.c config.h $(cram_h) $(cram_os_h)
 325 cram/files.o cram/files.pico: cram/files.c config.h $(cram_misc_h)
 326 cram/mFILE.o cram/mFILE.pico: cram/mFILE.c config.h $(cram_os_h) cram/mFILE.h
 327 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)
 328 cram/pooled_alloc.o cram/pooled_alloc.pico: cram/pooled_alloc.c config.h cram/pooled_alloc.h $(cram_misc_h)
 329 cram/rANS_static.o cram/rANS_static.pico: cram/rANS_static.c config.h cram/rANS_static.h cram/rANS_byte.h
 330 cram/sam_header.o cram/sam_header.pico: cram/sam_header.c config.h $(cram_sam_header_h) cram/string_alloc.h
 331 cram/string_alloc.o cram/string_alloc.pico: cram/string_alloc.c config.h cram/string_alloc.h
 332 thread_pool.o thread_pool.pico: thread_pool.c config.h $(thread_pool_internal_h)
 333
 334
 335 bgzip: bgzip.o libhts.a
 336         $(CC) $(LDFLAGS) -o $@ bgzip.o libhts.a $(LIBS) -lpthread
 337
 338 htsfile: htsfile.o libhts.a
 339         $(CC) $(LDFLAGS) -o $@ htsfile.o libhts.a $(LIBS) -lpthread
 340
 341 tabix: tabix.o libhts.a
 342         $(CC) $(LDFLAGS) -o $@ tabix.o libhts.a $(LIBS) -lpthread
 343
 344 bgzip.o: bgzip.c config.h $(htslib_bgzf_h) $(htslib_hts_h)
 345 htsfile.o: htsfile.c config.h $(htslib_hfile_h) $(htslib_hts_h) $(htslib_sam_h) $(htslib_vcf_h)
 346 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)
 347
 348
 349 # For tests that might use it, set $REF_PATH explicitly to use only reference
 350 # areas within the test suite (or set it to ':' to use no reference areas).
 351 check test: $(BUILT_PROGRAMS) $(BUILT_TEST_PROGRAMS)
 352         test/hts_endian
 353         test/fieldarith test/fieldarith.sam
 354         test/hfile
 355         test/test_bgzf test/bgziptest.txt
 356         cd test/tabix && ./test-tabix.sh tabix.tst
 357         REF_PATH=: test/sam test/ce.fa test/faidx.fa
 358         test/test-regidx
 359         cd test && REF_PATH=: ./test.pl
 360
 361 test/hts_endian: test/hts_endian.o
 362         $(CC) $(LDFLAGS) -o $@ test/hts_endian.o $(LIBS)
 363
 364 test/fieldarith: test/fieldarith.o libhts.a
 365         $(CC) $(LDFLAGS) -o $@ test/fieldarith.o libhts.a $(LIBS) -lpthread
 366
 367 test/hfile: test/hfile.o libhts.a
 368         $(CC) $(LDFLAGS) -o $@ test/hfile.o libhts.a $(LIBS) -lpthread
 369
 370 test/sam: test/sam.o libhts.a
 371         $(CC) $(LDFLAGS) -o $@ test/sam.o libhts.a $(LIBS) -lpthread
 372
 373 test/test_bgzf: test/test_bgzf.o libhts.a
 374         $(CC) $(LDFLAGS) -o $@ test/test_bgzf.o libhts.a -lz $(LIBS) -lpthread
 375
 376 test/test-regidx: test/test-regidx.o libhts.a
 377         $(CC) $(LDFLAGS) -o $@ test/test-regidx.o libhts.a $(LIBS) -lpthread
 378
 379 test/test_view: test/test_view.o libhts.a
 380         $(CC) $(LDFLAGS) -o $@ test/test_view.o libhts.a $(LIBS) -lpthread
 381
 382 test/test-vcf-api: test/test-vcf-api.o libhts.a
 383         $(CC) $(LDFLAGS) -o $@ test/test-vcf-api.o libhts.a $(LIBS) -lpthread
 384
 385 test/test-vcf-sweep: test/test-vcf-sweep.o libhts.a
 386         $(CC) $(LDFLAGS) -o $@ test/test-vcf-sweep.o libhts.a $(LIBS) -lpthread
 387
 388 test/test-bcf-sr: test/test-bcf-sr.o libhts.a
 389         $(CC) $(LDFLAGS) -o $@ test/test-bcf-sr.o libhts.a -lz $(LIBS) -lpthread
 390
 391 test/hts_endian.o: test/hts_endian.c $(htslib_hts_endian_h)
 392 test/fieldarith.o: test/fieldarith.c config.h $(htslib_sam_h)
 393 test/hfile.o: test/hfile.c config.h $(htslib_hfile_h) $(htslib_hts_defs_h)
 394 test/sam.o: test/sam.c config.h $(htslib_hts_defs_h) $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h)
 395 test/test_bgzf.o: test/test_bgzf.c $(htslib_bgzf_h) $(htslib_hfile_h)
 396 test/test-regidx.o: test/test-regidx.c config.h $(htslib_regidx_h) $(hts_internal_h)
 397 test/test_view.o: test/test_view.c config.h $(cram_h) $(htslib_sam_h)
 398 test/test-vcf-api.o: test/test-vcf-api.c config.h $(htslib_hts_h) $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_kseq_h)
 399 test/test-vcf-sweep.o: test/test-vcf-sweep.c config.h $(htslib_vcf_sweep_h)
 400 test/test-bcf-sr.o: test/test-bcf-sr.c config.h $(htslib_vcf_sweep_h) bcf_sr_sort.h
 401
 402
 403 test/thrash_threads1: test/thrash_threads1.o libhts.a
 404         $(CC) $(LDFLAGS) -o $@ test/thrash_threads1.o libhts.a -lz $(LIBS) -lpthread
 405
 406 test/thrash_threads2: test/thrash_threads2.o libhts.a
 407         $(CC) $(LDFLAGS) -o $@ test/thrash_threads2.o libhts.a -lz $(LIBS) -lpthread
 408
 409 test/thrash_threads3: test/thrash_threads3.o libhts.a
 410         $(CC) $(LDFLAGS) -o $@ test/thrash_threads3.o libhts.a -lz $(LIBS) -lpthread
 411
 412 test/thrash_threads4: test/thrash_threads4.o libhts.a
 413         $(CC) $(LDFLAGS) -o $@ test/thrash_threads4.o libhts.a -lz $(LIBS) -lpthread
 414
 415 test/thrash_threads5: test/thrash_threads5.o libhts.a
 416         $(CC) $(LDFLAGS) -o $@ test/thrash_threads5.o libhts.a -lz $(LIBS) -lpthread
 417
 418 test/thrash_threads6: test/thrash_threads6.o libhts.a
 419         $(CC) $(LDFLAGS) -o $@ test/thrash_threads6.o libhts.a -lz $(LIBS) -lpthread
 420
 421 test_thrash: $(BUILT_THRASH_PROGRAMS)
 422
 423
 424 install: libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) installdirs install-$(SHLIB_FLAVOUR) install-pkgconfig
 425         $(INSTALL_PROGRAM) $(BUILT_PROGRAMS) $(DESTDIR)$(bindir)
 426         if test -n "$(BUILT_PLUGINS)"; then $(INSTALL_PROGRAM) $(BUILT_PLUGINS) $(DESTDIR)$(plugindir); fi
 427         $(INSTALL_DATA) htslib/*.h $(DESTDIR)$(includedir)/htslib
 428         $(INSTALL_DATA) libhts.a $(DESTDIR)$(libdir)/libhts.a
 429         $(INSTALL_MAN) htsfile.1 tabix.1 $(DESTDIR)$(man1dir)
 430         $(INSTALL_MAN) faidx.5 sam.5 vcf.5 $(DESTDIR)$(man5dir)
 431
 432 installdirs:
 433         $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(includedir) $(DESTDIR)$(includedir)/htslib $(DESTDIR)$(libdir) $(DESTDIR)$(man1dir) $(DESTDIR)$(man5dir) $(DESTDIR)$(pkgconfigdir)
 434         if test -n "$(plugindir)"; then $(INSTALL_DIR) $(DESTDIR)$(plugindir); fi
 435
 436 # After installation, the real file in $(libdir) will be libhts.so.X.Y.Z,
 437 # with symlinks libhts.so (used via -lhts during linking of client programs)
 438 # and libhts.so.NN (used by client executables at runtime).
 439
 440 install-so: libhts.so installdirs
 441         $(INSTALL_LIB) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION)
 442         ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so
 443         ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so.$(LIBHTS_SOVERSION)
 444
 445 install-cygdll: cyghts-$(LIBHTS_SOVERSION).dll installdirs
 446         $(INSTALL_PROGRAM) cyghts-$(LIBHTS_SOVERSION).dll $(DESTDIR)$(bindir)/cyghts-$(LIBHTS_SOVERSION).dll
 447         $(INSTALL_PROGRAM) libhts.dll.a $(DESTDIR)$(libdir)/libhts.dll.a
 448
 449 install-dylib: libhts.dylib installdirs
 450         $(INSTALL_PROGRAM) libhts.dylib $(DESTDIR)$(libdir)/libhts.$(PACKAGE_VERSION).dylib
 451         ln -sf libhts.$(PACKAGE_VERSION).dylib $(DESTDIR)$(libdir)/libhts.dylib
 452         ln -sf libhts.$(PACKAGE_VERSION).dylib $(DESTDIR)$(libdir)/libhts.$(LIBHTS_SOVERSION).dylib
 453
 454 # Substitute these pseudo-autoconf variables only at install time
 455 # so that "make install prefix=/prefix/path" etc continue to work.
 456 install-pkgconfig: htslib.pc.tmp installdirs
 457         sed -e 's#@-includedir@#$(includedir)#g;s#@-libdir@#$(libdir)#g;s#@-PACKAGE_VERSION@#$(PACKAGE_VERSION)#g' htslib.pc.tmp > $(DESTDIR)$(pkgconfigdir)/htslib.pc
 458         chmod 644 $(DESTDIR)$(pkgconfigdir)/htslib.pc
 459
 460 # A pkg-config file (suitable for copying to $PKG_CONFIG_PATH) that provides
 461 # flags for building against the uninstalled library in this build directory.
 462 htslib-uninstalled.pc: htslib.pc.tmp
 463         sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > $@
 464
 465
 466 testclean:
 467         -rm -f test/*.tmp test/*.tmp.* test/tabix/*.tmp.* test/tabix/FAIL*
 468
 469 mostlyclean: testclean
 470         -rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM version.h
 471
 472 clean: mostlyclean clean-$(SHLIB_FLAVOUR)
 473         -rm -f libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) $(BUILT_TEST_PROGRAMS) $(BUILT_THRASH_PROGRAMS)
 474
 475 distclean maintainer-clean: clean
 476         -rm -f config.cache config.h config.log config.mk config.status
 477         -rm -f TAGS *.pc.tmp *-uninstalled.pc htslib_static.mk
 478         -rm -rf autom4te.cache
 479
 480 clean-so:
 481         -rm -f libhts.so libhts.so.*
 482
 483 clean-cygdll:
 484         -rm -f cyghts-*.dll libhts.dll.a
 485
 486 clean-dylib:
 487         -rm -f libhts.dylib libhts.*.dylib
 488
 489
 490 tags TAGS:
 491         ctags -f TAGS *.[ch] cram/*.[ch] htslib/*.h
 492
 493 # We recommend libhts-using programs be built against a separate htslib
 494 # installation.  However if you feel that you must bundle htslib source
 495 # code with your program, this hook enables Automake-style "make dist"
 496 # for this subdirectory.  If you do bundle an htslib snapshot, please
 497 # add identifying information to $(PACKAGE_VERSION) as appropriate.
 498 # (The wildcards attempt to omit non-exported files (.git*, README.md,
 499 # etc) and other detritus that might be in the top-level directory.)
 500 distdir:
 501         tar -c *.[ch15] [ILMNRcht]*[ELSbcekmnt] | (cd $(distdir) && tar -x)
 502         +cd $(distdir) && $(MAKE) distclean
 503
 504 force:
 505
 506
 507 .PHONY: all check clean distclean distdir force
 508 .PHONY: install install-pkgconfig installdirs lib-shared lib-static
 509 .PHONY: maintainer-clean mostlyclean plugins print-config print-version
 510 .PHONY: tags test testclean
 511 .PHONY: clean-so install-so
 512 .PHONY: clean-cygdll install-cygdll
 513 .PHONY: clean-dylib install-dylib