src/htslib/htslib.mk 7df6e18265341f87a69fba808aa1f92f8ebca841

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 <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/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