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#
Makefile rules useful for third-party code using htslib's public API.
#
#
Copyright (C) 2013-2017, 2019 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.
#
The makefile fragment included below provides variables that can be used
#
to express dependencies on headers supplied by an in-development htslib.
#
If your source file foo.c #includes <htslib/hts.h> and <htslib/kstring.h>,
#
you can write the correct prerequisites for foo.o as:
#
#
HTSDIR = <path to htslib top-level directory>
#
include $(HTSDIR)/htslib.mk
#
#
foo.o: foo.c $(htslib_hts_h) $(htslib_kstring_h)
HTSPREFIX
=
$(
HTSDIR
)
/
include
$(
HTSDIR
)
/htslib_vars.mk
#
Rules for rebuilding an in-development htslib's static and shared libraries.
#
If your program foo links with libhts, adding the appropriate prerequisite
#
will cause the library to be rebuilt as necessary:
#
#
foo: foo.o $(HTSDIR)/libhts.a
#
#
or similarly if your target requires any of the tools supplied:
#
#
bar.bed.bgz.tbi: bar.bed.bgz $(HTSDIR)/tabix
#
$(HTSDIR)/tabix -p bed bar.bed.bgz
HTSLIB_PUBLIC_HEADERS
=
\
$(
HTSDIR
)
/htslib/bgzf.h
\
$(
HTSDIR
)
/htslib/cram.h
\
$(
HTSDIR
)
/htslib/faidx.h
\
$(
HTSDIR
)
/htslib/hfile.h
\
$(
HTSDIR
)
/htslib/hts.h
\
$(
HTSDIR
)
/htslib/hts_defs.h
\
$(
HTSDIR
)
/htslib/hts_endian.h
\
$(
HTSDIR
)
/htslib/hts_expr.h
\
$(
HTSDIR
)
/htslib/hts_log.h
\
$(
HTSDIR
)
/htslib/hts_os.h
\
$(
HTSDIR
)
/htslib/kbitset.h
\
$(
HTSDIR
)
/htslib/kfunc.h
\
$(
HTSDIR
)
/htslib/khash.h
\
$(
HTSDIR
)
/htslib/khash_str2int.h
\
$(
HTSDIR
)
/htslib/klist.h
\
$(
HTSDIR
)
/htslib/kseq.h
\
$(
HTSDIR
)
/htslib/ksort.h
\
$(
HTSDIR
)
/htslib/kstring.h
\
$(
HTSDIR
)
/htslib/regidx.h
\
$(
HTSDIR
)
/htslib/sam.h
\
$(
HTSDIR
)
/htslib/synced_bcf_reader.h
\
$(
HTSDIR
)
/htslib/tbx.h
\
$(
HTSDIR
)
/htslib/thread_pool.h
\
$(
HTSDIR
)
/htslib/vcf.h
\
$(
HTSDIR
)
/htslib/vcf_sweep.h
\
$(
HTSDIR
)
/htslib/vcfutils.h
HTSLIB_ALL
=
\
$(
HTSLIB_PUBLIC_HEADERS
)
\
$(
HTSDIR
)
/bcf_sr_sort.c
\
$(
HTSDIR
)
/bcf_sr_sort.h
\
$(
HTSDIR
)
/bgzf.c
\
$(
HTSDIR
)
/config.h
\
$(
HTSDIR
)
/errmod.c
\
$(
HTSDIR
)
/faidx.c
\
$(
HTSDIR
)
/header.c
\
$(
HTSDIR
)
/header.h
\
$(
HTSDIR
)
/hfile_internal.h
\
$(
HTSDIR
)
/hfile.c
\
$(
HTSDIR
)
/hfile_gcs.c
\
$(
HTSDIR
)
/hfile_libcurl.c
\
$(
HTSDIR
)
/hfile_s3.c
\
$(
HTSDIR
)
/hfile_s3_write.c
\
$(
HTSDIR
)
/hts.c
\
$(
HTSDIR
)
/hts_expr.c
\
$(
HTSDIR
)
/hts_internal.h
\
$(
HTSDIR
)
/hts_os.c
\
$(
HTSDIR
)
/kfunc.c
\
$(
HTSDIR
)
/kstring.c
\
$(
HTSDIR
)
/md5.c
\
$(
HTSDIR
)
/multipart.c
\
$(
HTSDIR
)
/plugin.c
\
$(
HTSDIR
)
/probaln.c
\
$(
HTSDIR
)
/realn.c
\
$(
HTSDIR
)
/regidx.c
\
$(
HTSDIR
)
/region.c
\
$(
HTSDIR
)
/sam.c
\
$(
HTSDIR
)
/sam_internal.h
\
$(
HTSDIR
)
/synced_bcf_reader.c
\
$(
HTSDIR
)
/tbx.c
\
$(
HTSDIR
)
/textutils.c
\
$(
HTSDIR
)
/textutils_internal.h
\
$(
HTSDIR
)
/thread_pool.c
\
$(
HTSDIR
)
/thread_pool_internal.h
\
$(
HTSDIR
)
/vcf.c
\
$(
HTSDIR
)
/vcf_sweep.c
\
$(
HTSDIR
)
/vcfutils.c
\
$(
HTSDIR
)
/cram/cram.h
\
$(
HTSDIR
)
/cram/cram_codecs.c
\
$(
HTSDIR
)
/cram/cram_codecs.h
\
$(
HTSDIR
)
/cram/cram_decode.c
\
$(
HTSDIR
)
/cram/cram_decode.h
\
$(
HTSDIR
)
/cram/cram_encode.c
\
$(
HTSDIR
)
/cram/cram_encode.h
\
$(
HTSDIR
)
/cram/cram_external.c
\
$(
HTSDIR
)
/cram/cram_index.c
\
$(
HTSDIR
)
/cram/cram_index.h
\
$(
HTSDIR
)
/cram/cram_io.c
\
$(
HTSDIR
)
/cram/cram_io.h
\
$(
HTSDIR
)
/cram/cram_samtools.h
\
$(
HTSDIR
)
/cram/cram_stats.c
\
$(
HTSDIR
)
/cram/cram_stats.h
\
$(
HTSDIR
)
/cram/cram_structs.h
\
$(
HTSDIR
)
/cram/mFILE.c
\
$(
HTSDIR
)
/cram/mFILE.h
\
$(
HTSDIR
)
/cram/misc.h
\
$(
HTSDIR
)
/cram/open_trace_file.c
\
$(
HTSDIR
)
/cram/open_trace_file.h
\
$(
HTSDIR
)
/cram/os.h
\
$(
HTSDIR
)
/cram/pooled_alloc.c
\
$(
HTSDIR
)
/cram/pooled_alloc.h
\
$(
HTSDIR
)
/cram/rANS_byte.h
\
$(
HTSDIR
)
/cram/rANS_static.c
\
$(
HTSDIR
)
/cram/rANS_static.h
\
$(
HTSDIR
)
/cram/string_alloc.c
\
$(
HTSDIR
)
/cram/string_alloc.h
\
$(
HTSDIR
)
/os/lzma_stub.h
\
$(
HTSDIR
)
/os/rand.c
$(
HTSDIR
)
/config.h
:
+cd
$(
HTSDIR
)
&&
$(
MAKE
)
config.h
$(
HTSDIR
)
/hts-object-files
:
$(
HTSLIB_ALL
)
+cd
$(
HTSDIR
)
&&
$(
MAKE
)
hts-object-files
$(
HTSDIR
)
/libhts.a
:
$(
HTSDIR
)
/hts-object-files
+cd
$(
HTSDIR
)
&&
$(
MAKE
)
lib-static
$(
HTSDIR
)
/libhts.so
:
$(
HTSLIB_ALL
)
+cd
$(
HTSDIR
)
&&
$(
MAKE
)
lib-shared
$(
HTSDIR
)
/libhts.dylib
$(
HTSDIR
)
/libhts.dll.a
$(
HTSDIR
)
/hts.dll.a
:
$(
HTSDIR
)
/hts-object-files
+cd
$(
HTSDIR
)
&&
$(
MAKE
)
lib-shared
$(
HTSDIR
)
/bgzip
:
$(
HTSDIR
)
/bgzip.c
$(
HTSLIB_PUBLIC_HEADERS
)
$(
HTSDIR
)
/libhts.a
+cd
$(
HTSDIR
)
&&
$(
MAKE
)
bgzip
$(
HTSDIR
)
/htsfile
:
$(
HTSDIR
)
/htsfile.c
$(
HTSLIB_PUBLIC_HEADERS
)
$(
HTSDIR
)
/libhts.a
+cd $(HTSDIR) && $(MAKE) htsfile
$(
HTSDIR
)
/tabix
:
$(
HTSDIR
)
/tabix.c
$(
HTSLIB_PUBLIC_HEADERS
)
$(
HTSDIR
)
/libhts.a
+cd $(HTSDIR) && $(MAKE) tabix
$(
HTSDIR
)
/htslib_static.mk
:
$(
HTSDIR
)
/htslib.pc.tmp
+cd
$(
HTSDIR
)
&&
$(
MAKE
)
htslib_static.mk
$(
HTSDIR
)
/htslib.pc.tmp
:
+cd
$(
HTSDIR
)
&&
$(
MAKE
)
htslib.pc.tmp
#
Rules for phony targets. You may wish to have your corresponding phony
#
targets invoke these in addition to their own recipes:
#
#
clean: clean-htslib
all-htslib
clean-htslib
install-htslib
plugins-htslib
:
+cd
$(
HTSDIR
)
&&
$(
MAKE
)
$(
@:-htslib=
)
.PHONY
: all-htslib clean-htslib install-htslib plugins-htslib
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