7df6e18265341f87a69fba808aa1f92f8ebca841 markd Wed Apr 15 13:39:42 2026 -0700 move copy of htslib diff --git src/htslib/htslib.mk src/htslib/htslib.mk deleted file mode 100644 index 48b9552c745..00000000000 --- src/htslib/htslib.mk +++ /dev/null @@ -1,163 +0,0 @@ -# Makefile rules useful for third-party code using htslib's public API. -# -# Copyright (C) 2013-2015 Genome Research Ltd. -# -# Author: John Marshall -# -# 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 and , -# you can write the correct prerequisites for foo.o as: -# -# HTSDIR = -# 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/kbitset.h \ - $(HTSDIR)/htslib/kfunc.h \ - $(HTSDIR)/htslib/khash.h \ - $(HTSDIR)/htslib/khash_str2int.h \ - $(HTSDIR)/htslib/klist.h \ - $(HTSDIR)/htslib/knetfile.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/vcf.h \ - $(HTSDIR)/htslib/vcf_sweep.h \ - $(HTSDIR)/htslib/vcfutils.h - -HTSLIB_ALL = \ - $(HTSLIB_PUBLIC_HEADERS) \ - $(HTSDIR)/bgzf.c \ - $(HTSDIR)/config.h \ - $(HTSDIR)/faidx.c \ - $(HTSDIR)/hfile_internal.h \ - $(HTSDIR)/hfile.c \ - $(HTSDIR)/hfile_irods.c \ - $(HTSDIR)/hfile_libcurl.c \ - $(HTSDIR)/hfile_net.c \ - $(HTSDIR)/hts.c \ - $(HTSDIR)/hts_internal.h \ - $(HTSDIR)/kfunc.c \ - $(HTSDIR)/knetfile.c \ - $(HTSDIR)/kstring.c \ - $(HTSDIR)/md5.c \ - $(HTSDIR)/plugin.c \ - $(HTSDIR)/regidx.c \ - $(HTSDIR)/sam.c \ - $(HTSDIR)/synced_bcf_reader.c \ - $(HTSDIR)/tbx.c \ - $(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.c \ - $(HTSDIR)/cram/cram_samtools.h \ - $(HTSDIR)/cram/cram_stats.c \ - $(HTSDIR)/cram/cram_stats.h \ - $(HTSDIR)/cram/cram_structs.h \ - $(HTSDIR)/cram/files.c \ - $(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/sam_header.c \ - $(HTSDIR)/cram/sam_header.h \ - $(HTSDIR)/cram/string_alloc.c \ - $(HTSDIR)/cram/string_alloc.h \ - $(HTSDIR)/cram/thread_pool.c \ - $(HTSDIR)/cram/thread_pool.h \ - $(HTSDIR)/cram/vlen.c \ - $(HTSDIR)/cram/vlen.h \ - $(HTSDIR)/cram/zfio.c \ - $(HTSDIR)/cram/zfio.h - -$(HTSDIR)/config.h: - +cd $(HTSDIR) && $(MAKE) config.h - -$(HTSDIR)/libhts.a: $(HTSLIB_ALL) - +cd $(HTSDIR) && $(MAKE) lib-static - -$(HTSDIR)/libhts.so $(HTSDIR)/libhts.dylib: $(HTSLIB_ALL) - +cd $(HTSDIR) && $(MAKE) lib-shared - -$(HTSDIR)/bgzip: $(HTSDIR)/bgzip.c $(HTSLIB_PUBLIC_HEADERS) - +cd $(HTSDIR) && $(MAKE) bgzip - -$(HTSDIR)/htsfile: $(HTSDIR)/htsfile.c $(HTSLIB_PUBLIC_HEADERS) - +cd $(HTSDIR) && $(MAKE) htsfile - -$(HTSDIR)/tabix: $(HTSDIR)/tabix.c $(HTSLIB_PUBLIC_HEADERS) - +cd $(HTSDIR) && $(MAKE) tabix - -# 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