diff --git a/recipes/recipes_emscripten/bioconductor-rhtslib/LICENSE b/recipes/recipes_emscripten/bioconductor-rhtslib/LICENSE
new file mode 100644
index 00000000000..3e52e834420
--- /dev/null
+++ b/recipes/recipes_emscripten/bioconductor-rhtslib/LICENSE
@@ -0,0 +1,120 @@
+GNU LIBRARY GENERAL PUBLIC LICENSE
+
+Version 2, June 1991
+
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+51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA
+
+Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
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diff --git a/recipes/recipes_emscripten/bioconductor-rhtslib/Makefile.Rhtslib b/recipes/recipes_emscripten/bioconductor-rhtslib/Makefile.Rhtslib
new file mode 100644
index 00000000000..d619c3c8105
--- /dev/null
+++ b/recipes/recipes_emscripten/bioconductor-rhtslib/Makefile.Rhtslib
@@ -0,0 +1,932 @@
+# This is Makefile.Rhtslib, a minimally modified version of Makefile used
+# to build htslib in the context of 'R CMD INSTALL Rhtslib' on Linux and Mac.
+# Author of original Makefile: John Marshall (see Copyright below)
+# Modified by: Hervé Pagès (October 2023)
+# ----------------------------------------------------------------------------
+# Makefile for htslib, a C library for high-throughput sequencing data formats.
+#
+#    Copyright (C) 2013-2023 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.
+
+# Get CC, AR, RANLIB, CFLAGS, CPPFLAGS, and LDFLAGS values from
+# ${R_HOME}/etc/Makeconf or from a customized Makevars file (site-wide
+# or user-specified).
+CC       := $(shell ${R_HOME}/bin/R CMD config CC)
+AR       := $(shell ${R_HOME}/bin/R CMD config AR)
+RANLIB   := $(shell ${R_HOME}/bin/R CMD config RANLIB)
+CFLAGS   := $(shell ${R_HOME}/bin/R CMD config CFLAGS)
+CPPFLAGS := $(shell ${R_HOME}/bin/R CMD config CPPFLAGS)
+LDFLAGS  := $(shell ${R_HOME}/bin/R CMD config LDFLAGS)
+
+# Default libraries to link if configure is not used
+htslib_default_libs = -lz -lm -lbz2 -llzma #-lcurl
+
+CPPFLAGS += -D_FILE_OFFSET_BITS=64
+# TODO: make the 64-bit support for VCF optional via configure, for now add -DVCF_ALLOW_INT64
+#       to CFLAGS manually, here or in config.mk if the latter exists.
+# TODO: probably update cram code to make it compile cleanly with -Wc++-compat
+# For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
+#CFLAGS   = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600
+CFLAGS += -fpic -fvisibility=hidden
+EXTRA_CFLAGS_PIC =
+TARGET_CFLAGS =
+LDFLAGS += -fvisibility=hidden
+VERSION_SCRIPT_LDFLAGS = -Wl,-version-script,$(srcprefix)htslib.map
+LIBS     = $(htslib_default_libs)
+
+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
+man7dir     = $(mandir)/man7
+pkgconfigdir= $(libdir)/pkgconfig
+
+MKDIR_P = mkdir -p
+INSTALL = install -p
+INSTALL_DATA    = $(INSTALL) -m 644
+INSTALL_DIR     = $(MKDIR_P) -m 755
+LIB_PERM        = 644
+INSTALL_LIB     = $(INSTALL) -m $(LIB_PERM)
+INSTALL_MAN     = $(INSTALL_DATA)
+INSTALL_PROGRAM = $(INSTALL)
+
+# Set by config.mk if plugins are enabled
+plugindir =
+
+all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS) \
+     htslib_static.mk htslib-uninstalled.pc
+
+ALL_CPPFLAGS = -I. $(CPPFLAGS)
+
+# Usually htscodecs.mk is generated by running configure or config.status,
+# but if those aren't used create a default here.
+htscodecs.mk:
+	echo '# Default htscodecs.mk generated by Makefile' > $@
+	echo 'include $$(HTSPREFIX)htscodecs_bundled.mk' >> $@
+	$(srcdir)/hts_probe_cc.sh '$(CC)' '$(CFLAGS) $(CPPFLAGS)' '$(LDFLAGS)' >> $@
+
+srcdir = .
+srcprefix =
+HTSPREFIX =
+
+# Flags for SIMD code
+HTS_CFLAGS_AVX2 =
+HTS_CFLAGS_AVX512 =
+HTS_CFLAGS_SSE4 =
+
+# Control building of SIMD code.  Not used if configure has been run.
+HTS_BUILD_AVX2 =
+HTS_BUILD_AVX512 =
+HTS_BUILD_SSSE3 =
+HTS_BUILD_POPCNT =
+HTS_BUILD_SSE4_1 =
+
+include htslib_vars.mk
+include htscodecs_bundled.mk
+
+# If not using GNU make, you need to copy the version number from version.sh
+# into here.
+PACKAGE_VERSION := $(shell $(srcdir)/version.sh)
+
+LIBHTS_SOVERSION = 3
+
+# Version numbers for the Mac dynamic library.  Note that the leading 3
+# is not strictly necessary and should be removed the next time
+# LIBHTS_SOVERSION is bumped (see #1144 and
+# https://developer.apple.com/library/archive/documentation/DeveloperTools/Conceptual/DynamicLibraries/100-Articles/DynamicLibraryDesignGuidelines.html#//apple_ref/doc/uid/TP40002013-SW23)
+MACH_O_COMPATIBILITY_VERSION = 3.1.18
+MACH_O_CURRENT_VERSION = 3.1.18
+
+# $(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 := $(shell $(srcdir)/version.sh numeric)
+
+# 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))
+
+version.h:
+	echo '#define HTS_VERSION_TEXT "$(PACKAGE_VERSION)"' > $@
+
+print-version:
+	@echo $(PACKAGE_VERSION)
+
+show-version:
+	@echo PACKAGE_VERSION = $(PACKAGE_VERSION)
+	@echo NUMERIC_VERSION = $(NUMERIC_VERSION)
+
+config_vars.h: override escape=$(subst ',\x27,$(subst ",\",$(subst \,\\,$(1))))
+config_vars.h: override hts_cc_escaped=$(call escape,$(CC))
+config_vars.h: override hts_cppflags_escaped=$(call escape,$(CPPFLAGS))
+config_vars.h: override hts_cflags_escaped=$(call escape,$(CFLAGS))
+config_vars.h: override hts_ldflags_escaped=$(call escape,$(LDFLAGS))
+config_vars.h: override hts_libs_escaped=$(call escape,$(LIBS))
+
+config_vars.h:
+	printf '#define HTS_CC "%s"\n#define HTS_CPPFLAGS "%s"\n#define HTS_CFLAGS "%s"\n#define HTS_LDFLAGS "%s"\n#define HTS_LIBS "%s"\n' \
+	'$(hts_cc_escaped)' \
+	'$(hts_cppflags_escaped)' \
+	'$(hts_cflags_escaped)' \
+	'$(hts_ldflags_escaped)' \
+	'$(hts_libs_escaped)' > $@
+
+.SUFFIXES: .bundle .c .cygdll .dll .o .pico .so
+
+.c.o:
+	$(CC) $(CFLAGS) $(TARGET_CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $<
+
+.c.pico:
+	$(CC) $(CFLAGS) $(TARGET_CFLAGS) $(ALL_CPPFLAGS) $(EXTRA_CFLAGS_PIC) -c -o $@ $<
+
+
+LIBHTS_OBJS = \
+	kfunc.o \
+	kstring.o \
+	bcf_sr_sort.o \
+	bgzf.o \
+	errmod.o \
+	faidx.o \
+	header.o \
+	hfile.o \
+	hts.o \
+	hts_expr.o \
+	hts_os.o\
+	md5.o \
+	multipart.o \
+	probaln.o \
+	realn.o \
+	regidx.o \
+	region.o \
+	sam.o \
+	sam_mods.o \
+	synced_bcf_reader.o \
+	vcf_sweep.o \
+	tbx.o \
+	textutils.o \
+	thread_pool.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_stats.o \
+	cram/mFILE.o \
+	cram/open_trace_file.o \
+	cram/pooled_alloc.o \
+	cram/string_alloc.o \
+	$(HTSCODECS_OBJS) 
+
+
+# Without configure we wish to have a rich set of default figures,
+# but we still need conditional inclusion as we wish to still
+# support ./configure --disable-blah.
+
+
+PLUGIN_EXT  =
+PLUGIN_OBJS =
+
+cram_h = cram/cram.h $(cram_samtools_h) $(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/os.h $(htslib_hts_endian_h)
+cram_samtools_h = cram/cram_samtools.h $(htslib_sam_h)
+cram_structs_h = cram/cram_structs.h $(htslib_thread_pool_h) $(htslib_cram_h) cram/string_alloc.h cram/mFILE.h $(htslib_khash_h)
+cram_open_trace_file_h = cram/open_trace_file.h cram/mFILE.h
+bcf_sr_sort_h = bcf_sr_sort.h $(htslib_synced_bcf_reader_h) $(htslib_kbitset_h)
+header_h = header.h cram/string_alloc.h cram/pooled_alloc.h $(htslib_khash_h) $(htslib_kstring_h) $(htslib_sam_h)
+hfile_internal_h = hfile_internal.h $(htslib_hts_defs_h) $(htslib_hfile_h) $(textutils_internal_h)
+hts_internal_h = hts_internal.h $(htslib_hts_h) $(textutils_internal_h)
+hts_time_funcs_h = hts_time_funcs.h
+sam_internal_h = sam_internal.h $(htslib_sam_h)
+textutils_internal_h = textutils_internal.h $(htslib_kstring_h)
+thread_pool_internal_h = thread_pool_internal.h $(htslib_thread_pool_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 '/* Default config.h generated by Makefile */' > $@
+	echo '#ifndef _XOPEN_SOURCE' >> $@
+	echo '#define _XOPEN_SOURCE 600' >> $@
+	echo '#endif' >> $@
+	echo '#define HAVE_LIBBZ2 1' >> $@
+	echo '#define HAVE_LIBLZMA 1' >> $@
+	echo '#ifndef __APPLE__' >> $@
+	echo '#define HAVE_LZMA_H 1' >> $@
+	echo '#endif' >> $@
+	echo '#define HAVE_LIBCURL 1' >> $@
+	if [ "x$(HTS_BUILD_POPCNT)" != "x" ] && \
+	   [ "x$(HTS_BUILD_SSE4_1)" != "x" ] && \
+	   [ "x$(HTS_BUILD_SSSE3)" != "x" ]; then \
+	    echo '#define HAVE_POPCNT 1' >> $@ ; \
+	    echo '#define HAVE_SSE4_1 1' >> $@ ; \
+	    echo '#define HAVE_SSSE3 1' >> $@ ; \
+	    echo '#if defined(HTS_ALLOW_UNALIGNED) && HTS_ALLOW_UNALIGNED == 0' >> $@ ; \
+	    echo '#define UBSAN 1' >> $@ ; \
+	    echo '#endif' >> $@ ; \
+	fi
+	if [ "x$(HTS_BUILD_AVX2)" != "x" ] ; then \
+	    echo '#define HAVE_AVX2 1' >> $@ ; \
+	fi
+	if [ "x$(HTS_BUILD_AVX512)" != "x" ] ; then \
+	    echo '#define HAVE_AVX512 1' >> $@ ; \
+	fi
+
+# And similarly for htslib.pc.tmp ("pkg-config template").  No dependency
+# on htslib.pc.in listed, as if that file is newer the usual way to regenerate
+# this target is via configure or config.status rather than this rule.
+htslib.pc.tmp:
+	sed -e '/^static_libs=/s/@static_LIBS@/$(htslib_default_libs)/;s#@[^-][^@]*@##g' $(srcprefix)htslib.pc.in > $@
+
+# Create a makefile fragment listing the libraries and LDFLAGS needed for
+# static linking.  This can be included by projects that want to build
+# and link against the htslib source tree instead of an installed library.
+htslib_static.mk: htslib.pc.tmp
+	sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' $< > $@
+
+
+lib-static: libhts.a
+
+# $(shell), :=, and ifeq/.../endif are GNU Make-specific.  If you don't have
+# GNU Make, comment out the parts of these conditionals that don't apply.
+ifneq "$(origin PLATFORM)" "file"
+PLATFORM := $(shell uname -s)
+endif
+ifeq "$(PLATFORM)" "Darwin"
+SHLIB_FLAVOUR = dylib
+lib-shared: libhts.dylib
+else ifeq "$(findstring CYGWIN,$(PLATFORM))" "CYGWIN"
+SHLIB_FLAVOUR = cygdll
+lib-shared: cyghts-$(LIBHTS_SOVERSION).dll
+else ifeq "$(findstring MSYS,$(PLATFORM))" "MSYS"
+SHLIB_FLAVOUR = dll
+lib-shared: hts-$(LIBHTS_SOVERSION).dll hts-$(LIBHTS_SOVERSION).def hts-$(LIBHTS_SOVERSION).lib
+else ifeq "$(findstring MINGW,$(PLATFORM))" "MINGW"
+SHLIB_FLAVOUR = dll
+lib-shared: hts-$(LIBHTS_SOVERSION).dll hts-$(LIBHTS_SOVERSION).def hts-$(LIBHTS_SOVERSION).lib
+else
+SHLIB_FLAVOUR = so
+lib-shared: libhts.so
+endif
+
+BUILT_PLUGINS = $(PLUGIN_OBJS:.o=$(PLUGIN_EXT))
+
+ifneq "$(BUILT_PLUGINS)" ""
+plugins: lib-shared
+endif
+plugins: $(BUILT_PLUGINS)
+
+
+libhts.a: $(LIBHTS_OBJS)
+	@-rm -f $@
+	$(AR) -rc $@ $(LIBHTS_OBJS)
+	-$(RANLIB) $@
+
+print-config:
+	@echo HTS_CFLAGS_AVX2 = $(HTS_CFLAGS_AVX2)
+	@echo HTS_CFLAGS_AVX512 = $(HTS_CFLAGS_AVX512)
+	@echo HTS_CFLAGS_SSE4 = $(HTS_CFLAGS_SSE4)
+	@echo HTS_HAVE_NEON = $(HTS_HAVE_NEON)
+	@echo LDFLAGS = $(LDFLAGS)
+	@echo LIBHTS_OBJS = $(LIBHTS_OBJS)
+	@echo LIBS = $(LIBS)
+	@echo PLATFORM = $(PLATFORM)
+
+# 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) $(VERSION_SCRIPT_LDFLAGS) $(LDFLAGS) -o $@ $(LIBHTS_OBJS:.o=.pico) $(LIBS) -lpthread
+	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 $(MACH_O_CURRENT_VERSION) -compatibility_version $(MACH_O_COMPATIBILITY_VERSION) $(LDFLAGS) -o $@ $(LIBHTS_OBJS) $(LIBS)
+	ln -sf $@ libhts.$(LIBHTS_SOVERSION).dylib
+
+cyghts-$(LIBHTS_SOVERSION).dll libhts.dll.a: $(LIBHTS_OBJS)
+	$(CC) -shared -Wl,--out-implib=libhts.dll.a -Wl,--enable-auto-import $(LDFLAGS) -o $@ -Wl,--whole-archive $(LIBHTS_OBJS) -Wl,--no-whole-archive $(LIBS) -lpthread
+
+hts-$(LIBHTS_SOVERSION).dll hts.dll.a: $(LIBHTS_OBJS)
+	$(CC) -shared -Wl,--out-implib=hts.dll.a -Wl,--enable-auto-import -Wl,--exclude-all-symbols $(LDFLAGS) -o $@ -Wl,--whole-archive $(LIBHTS_OBJS) -Wl,--no-whole-archive $(LIBS) -lpthread
+
+hts-$(LIBHTS_SOVERSION).def: hts-$(LIBHTS_SOVERSION).dll
+	gendef hts-$(LIBHTS_SOVERSION).dll
+
+hts-$(LIBHTS_SOVERSION).lib: hts-$(LIBHTS_SOVERSION).def
+	dlltool -m i386:x86-64 -d hts-$(LIBHTS_SOVERSION).def -l hts-$(LIBHTS_SOVERSION).lib
+
+# Bundling libraries, binaries, dll dependencies, and licenses into a
+# single directory.  NB: This is not needed for end-users, but a test bed
+# for maintainers building binary distributions.
+#
+# NOTE: only tested on the supported MSYS2/MINGW64 environment.
+dist-windows: DESTDIR=
+dist-windows: prefix=dist-windows
+dist-windows: install
+	cp hts-$(LIBHTS_SOVERSION).def hts-$(LIBHTS_SOVERSION).lib dist-windows/lib
+	cp `ldd hts-$(LIBHTS_SOVERSION).dll| awk '/mingw64/ {print $$3}'` dist-windows/bin
+	mkdir -p dist-windows/share/licenses/htslib
+	-cp -r /mingw64/share/licenses/mingw-w64-libraries \
+	      /mingw64/share/licenses/brotli \
+	      /mingw64/share/licenses/bzip2 \
+	      /mingw64/share/licenses/gcc-libs \
+	      /mingw64/share/licenses/libdeflate \
+	      /mingw64/share/licenses/libpsl \
+	      /mingw64/share/licenses/libtre \
+	      /mingw64/share/licenses/libwinpthread \
+	      /mingw64/share/licenses/openssl \
+	      /mingw64/share/licenses/xz \
+	      /mingw64/share/licenses/zlib \
+	      /mingw64/share/licenses/zstd \
+	      dist-windows/share/licenses/
+	-cp -r /usr/share/licenses/curl \
+	      dist-windows/share/licenses/
+	cp LICENSE dist-windows/share/licenses/htslib/
+
+
+# Target to allow htslib.mk to build all the object files before it
+# links the shared and static libraries.
+hts-object-files: $(LIBHTS_OBJS)
+	touch $@
+
+# On Unix dlopen("libhts.so.NN", RTLD_LAZY) may default to RTLD_LOCAL.
+# Hence plugins need to link to (shared) libhts.so.NN themselves, as they
+# may not be able to access libhts symbols via the main program's libhts
+# if that was dynamically loaded without an explicit RTLD_GLOBAL.
+%.so: %.pico libhts.so
+	$(CC) -shared -Wl,-E $(LDFLAGS) -o $@ $< libhts.so $(LIBS) -lpthread
+
+# For programs *statically* linked to libhts.a, on macOS loading a plugin
+# linked to a shared libhts.NN.dylib would lead to conflicting duplicate
+# symbols.  Fortunately macOS dlopen() defaults to RTLD_GLOBAL so there
+# is less need for plugins to link back to libhts themselves.
+%.bundle: %.o
+	$(CC) -bundle -Wl,-undefined,dynamic_lookup $(LDFLAGS) -o $@ $< $(LIBS)
+
+%.cygdll: %.o libhts.dll.a
+	$(CC) -shared $(LDFLAGS) -o $@ $< libhts.dll.a $(LIBS)
+
+%.dll: %.o hts.dll.a
+	$(CC) -shared $(LDFLAGS) -o $@ $< hts.dll.a $(LIBS)
+
+
+bgzf.o bgzf.pico: bgzf.c config.h $(htslib_hts_h) $(htslib_bgzf_h) $(htslib_hfile_h) $(htslib_thread_pool_h) $(htslib_hts_endian_h) cram/pooled_alloc.h $(hts_internal_h) $(htslib_khash_h)
+errmod.o errmod.pico: errmod.c config.h $(htslib_hts_h) $(htslib_ksort_h) $(htslib_hts_os_h)
+kstring.o kstring.pico: kstring.c config.h $(htslib_kstring_h)
+header.o header.pico: header.c config.h $(textutils_internal_h) $(header_h)
+hfile.o hfile.pico: hfile.c config.h $(htslib_hfile_h) $(hfile_internal_h) $(htslib_kstring_h) $(hts_internal_h) $(htslib_khash_h)
+hfile_gcs.o hfile_gcs.pico: hfile_gcs.c config.h $(htslib_hts_h) $(htslib_kstring_h) $(hfile_internal_h)
+# hfile_libcurl.o hfile_libcurl.pico: hfile_libcurl.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h) $(htslib_khash_h)
+# hfile_s3_write.o hfile_s3_write.pico: hfile_s3_write.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h) $(htslib_khash_h)
+# hfile_s3.o hfile_s3.pico: hfile_s3.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h) $(hts_time_funcs_h)
+hts.o hts.pico: hts.c config.h os/lzma_stub.h $(htslib_hts_h) $(htslib_bgzf_h) $(cram_h) $(htslib_hfile_h) $(htslib_hts_endian_h) version.h config_vars.h $(hts_internal_h) $(hfile_internal_h) $(sam_internal_h) $(htslib_hts_expr_h) $(htslib_hts_os_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_ksort_h) $(htslib_tbx_h) $(htscodecs_htscodecs_h)
+hts_expr.o hts_expr.pico: hts_expr.c config.h $(htslib_hts_expr_h) $(htslib_hts_log_h) $(textutils_internal_h)
+hts_os.o hts_os.pico: hts_os.c config.h $(htslib_hts_defs_h) os/rand.c
+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_sam_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_hts_endian_h)
+sam.o sam.pico: sam.c config.h $(htslib_hts_defs_h) $(htslib_sam_h) $(htslib_bgzf_h) $(cram_h) $(hts_internal_h) $(sam_internal_h) $(htslib_hfile_h) $(htslib_hts_endian_h) $(htslib_hts_expr_h) $(header_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_kstring_h)
+sam_mods.o sam_mods.pico: sam_mods.c config.h $(htslib_sam_h) $(textutils_internal_h)
+tbx.o tbx.pico: tbx.c config.h $(htslib_tbx_h) $(htslib_bgzf_h) $(htslib_hts_endian_h) $(hts_internal_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) $(hts_internal_h)
+bcf_sr_sort.o bcf_sr_sort.pico: bcf_sr_sort.c config.h $(bcf_sr_sort_h) $(htslib_khash_str2int_h) $(htslib_kbitset_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) $(htslib_thread_pool_h) $(bcf_sr_sort_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 config.h $(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) $(hts_internal_h)
+region.o region.pico: region.c config.h $(htslib_hts_h) $(htslib_khash_h)
+md5.o md5.pico: md5.c config.h $(htslib_hts_h) $(htslib_hts_endian_h)
+multipart.o multipart.pico: multipart.c config.h $(htslib_kstring_h) $(hts_internal_h) $(hfile_internal_h)
+plugin.o plugin.pico: plugin.c config.h $(hts_internal_h) $(htslib_kstring_h)
+probaln.o probaln.pico: probaln.c config.h $(htslib_hts_h)
+realn.o realn.pico: realn.c config.h $(htslib_hts_h) $(htslib_sam_h)
+textutils.o textutils.pico: textutils.c config.h $(htslib_hfile_h) $(htslib_kstring_h) $(htslib_sam_h) $(hts_internal_h)
+
+cram/cram_codecs.o cram/cram_codecs.pico: cram/cram_codecs.c config.h $(htslib_hts_endian_h) $(htscodecs_varint_h) $(htscodecs_pack_h) $(htscodecs_rle_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) $(sam_internal_h) $(htslib_hts_h) $(htslib_hts_endian_h) $(textutils_internal_h)
+cram/cram_external.o cram/cram_external.pico: cram/cram_external.c config.h $(htscodecs_rANS_static4x16_h) $(htslib_hfile_h) $(cram_h)
+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)
+cram/cram_io.o cram/cram_io.pico: cram/cram_io.c config.h os/lzma_stub.h $(cram_h) $(cram_os_h) $(htslib_hts_h) $(cram_open_trace_file_h) $(htscodecs_rANS_static_h) $(htscodecs_rANS_static4x16_h) $(htscodecs_arith_dynamic_h) $(htscodecs_tokenise_name3_h) $(htscodecs_fqzcomp_qual_h) $(htscodecs_varint_h) $(htslib_hfile_h) $(htslib_bgzf_h) $(htslib_faidx_h) $(hts_internal_h)
+cram/cram_stats.o cram/cram_stats.pico: cram/cram_stats.c config.h $(cram_h) $(cram_os_h)
+cram/mFILE.o cram/mFILE.pico: cram/mFILE.c config.h $(htslib_hts_log_h) $(cram_os_h) cram/mFILE.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) $(htslib_hts_log_h) $(htslib_hts_h)
+cram/pooled_alloc.o cram/pooled_alloc.pico: cram/pooled_alloc.c config.h cram/pooled_alloc.h $(cram_misc_h)
+cram/string_alloc.o cram/string_alloc.pico: cram/string_alloc.c config.h cram/string_alloc.h
+thread_pool.o thread_pool.pico: thread_pool.c config.h $(thread_pool_internal_h) $(htslib_hts_log_h)
+
+htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.pico: htscodecs/htscodecs/arith_dynamic.c config.h $(htscodecs_arith_dynamic_h) $(htscodecs_varint_h) $(htscodecs_pack_h) $(htscodecs_utils_h) $(htscodecs_c_simple_model_h)
+htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.pico: htscodecs/htscodecs/fqzcomp_qual.c config.h $(htscodecs_fqzcomp_qual_h) $(htscodecs_varint_h) $(htscodecs_utils_h) $(htscodecs_c_simple_model_h)
+htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.pico: htscodecs/htscodecs/htscodecs.c $(htscodecs_htscodecs_h) $(htscodecs_version_h)
+htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.pico: htscodecs/htscodecs/pack.c config.h $(htscodecs_pack_h)
+htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.pico: htscodecs/htscodecs/rANS_static32x16pr.c config.h $(htscodecs_rANS_word_h) $(htscodecs_rANS_static4x16_h) $(htscodecs_rANS_static16_int_h) $(htscodecs_varint_h) $(htscodecs_utils_h)
+htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.pico: htscodecs/htscodecs/rANS_static32x16pr_avx2.c config.h $(htscodecs_rANS_word_h) $(htscodecs_rANS_static4x16_h) $(htscodecs_rANS_static16_int_h) $(htscodecs_varint_h) $(htscodecs_utils_h) $(htscodecs_permute_h)
+htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.pico: htscodecs/htscodecs/rANS_static32x16pr_avx512.c config.h $(htscodecs_rANS_word_h) $(htscodecs_rANS_static4x16_h) $(htscodecs_rANS_static16_int_h) $(htscodecs_varint_h) $(htscodecs_utils_h)
+htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.pico: htscodecs/htscodecs/rANS_static32x16pr_neon.c config.h $(htscodecs_rANS_word_h) $(htscodecs_rANS_static4x16_h) $(htscodecs_rANS_static16_int_h) $(htscodecs_varint_h) $(htscodecs_utils_h)
+htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.pico: htscodecs/htscodecs/rANS_static32x16pr_sse4.c config.h $(htscodecs_rANS_word_h) $(htscodecs_rANS_static4x16_h) $(htscodecs_rANS_static16_int_h) $(htscodecs_varint_h) $(htscodecs_utils_h)
+htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.pico: htscodecs/htscodecs/rANS_static4x16pr.c config.h $(htscodecs_rANS_word_h) $(htscodecs_rANS_static4x16_h) $(htscodecs_rANS_static16_int_h) $(htscodecs_pack_h) $(htscodecs_rle_h) $(htscodecs_utils_h) $(htscodecs_rANS_static32x16pr_h)
+htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.pico: htscodecs/htscodecs/rANS_static.c config.h $(htscodecs_rANS_byte_h) $(htscodecs_utils_h) $(htscodecs_rANS_static_h)
+htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.pico: htscodecs/htscodecs/rle.c config.h $(htscodecs_varint_h) $(htscodecs_rle_h)
+htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.pico: htscodecs/htscodecs/tokenise_name3.c config.h $(htscodecs_pooled_alloc_h) $(htscodecs_arith_dynamic_h) $(htscodecs_rANS_static4x16_h) $(htscodecs_tokenise_name3_h) $(htscodecs_varint_h) $(htscodecs_utils_h)
+htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.pico: htscodecs/htscodecs/utils.c config.h $(htscodecs_utils_h)
+
+# Extra CFLAGS for specific files
+htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.pico: TARGET_CFLAGS = $(HTS_CFLAGS_AVX2)
+htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.pico: TARGET_CFLAGS = $(HTS_CFLAGS_AVX512)
+htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.pico: TARGET_CFLAGS = $(HTS_CFLAGS_SSE4)
+
+bgzip: bgzip.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ bgzip.o libhts.a $(LIBS) -lpthread
+
+htsfile: htsfile.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ htsfile.o libhts.a $(LIBS) -lpthread
+
+tabix: tabix.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ tabix.o libhts.a $(LIBS) -lpthread
+
+bgzip.o: bgzip.c config.h $(htslib_bgzf_h) $(htslib_hts_h) $(htslib_hfile_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) $(htslib_hts_defs_h) $(htslib_hts_log_h)
+
+# Runes to check that the htscodecs submodule is present
+ifdef HTSCODECS_SOURCES
+htscodecs/htscodecs/%.c: | htscodecs/htscodecs
+	@if test -e htscodecs/.git && test ! -e "$@" ; then \
+	  echo "Missing file '$@'" ; \
+	  echo "  - Do you need to update the htscodecs submodule?" ; \
+	  false ; \
+	fi
+
+htscodecs/htscodecs/%.h: | htscodecs/htscodecs
+	@if test -e htscodecs/.git && test ! -e "$@" ; then \
+	  echo "Missing file '$@'" ; \
+	  echo "  - Do you need to update the htscodecs submodule?" ; \
+	  false ; \
+	fi
+
+htscodecs/htscodecs:
+	@if test -e .git ; then \
+	printf "\\n\\nError: htscodecs submodule files not present for htslib.\\n\
+	Try running: \\n\
+	    git submodule update --init --recursive\\n\
+	in the top-level htslib directory and then re-run make.\\n\\n\\n" ; \
+	else \
+	  printf "\\n\\nError: htscodecs submodule files not present and this is not a git checkout.\\n\
+	  You have an incomplete distribution.  Please try downloading one of the\\n\
+	  official releases from https://www.htslib.org/\\n" ; \
+	fi
+	@false
+
+# Build the htscodecs/htscodecs/version.h file if necessary
+htscodecs/htscodecs/version.h: force
+	@if test -e $(srcdir)/htscodecs/.git && test -e $(srcdir)/htscodecs/configure.ac ; then \
+	  vers=`cd $(srcdir)/htscodecs && git describe --always --dirty --match 'v[0-9]\.[0-9]*'` && \
+	  case "$$vers" in \
+	    v*) vers=$${vers#v} ;; \
+	    *) iv=`awk '/^AC_INIT/ { match($$0, /^AC_INIT\(htscodecs, *([0-9](\.[0-9])*)\)/, m); print substr($$0, m[1, "start"], m[1, "length"]) }' $(srcdir)/htscodecs/configure.ac` ; vers="$$iv$${vers:+-g$$vers}" ;; \
+	  esac ; \
+	  if ! grep -s -q '"'"$$vers"'"' $@ ; then \
+	    echo 'Updating $@ : #define HTSCODECS_VERSION_TEXT "'"$$vers"'"' ; \
+	    echo '#define HTSCODECS_VERSION_TEXT "'"$$vers"'"' > $@ ; \
+	  fi ; \
+	fi
+endif
+
+# Maintainer source code checks
+# - copyright boilerplate presence
+# - tab and trailing space detection
+maintainer-check:
+	test/maintainer/check_copyright.pl .
+	test/maintainer/check_spaces.pl .
+
+# Look for untracked files in the git repository.
+check-untracked:
+	@if test -e .git && git status --porcelain | grep '^\?'; then \
+	    echo 'Untracked files detected (see above). Please either clean up, add to .gitignore, or for test output files consider naming them to match *.tmp or *.tmp.*' ; \
+	    false ; \
+	fi
+
+# Create a shorthand. We use $(SRC) or $(srcprefix) rather than $(srcdir)/
+# for brevity in test and install rules, and so that build logs do not have
+# ./ sprinkled throughout.
+SRC = $(srcprefix)
+
+# For tests that might use it, set $REF_PATH explicitly to use only reference
+# areas within the test suite (or set it to ':' to use no reference areas).
+#
+# If using MSYS, avoid poor shell expansion via:
+#    MSYS2_ARG_CONV_EXCL="*" make check
+check test: all $(HTSCODECS_TEST_TARGETS)
+	test/hts_endian
+	test/test_expr
+	test/test_kfunc
+	test/test_kstring
+	test/test_str2int
+	test/test_time_funcs
+	test/fieldarith test/fieldarith.sam
+	test/hfile
+	if test "x$(BUILT_PLUGINS)" != "x"; then \
+	    HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.$(SHLIB_FLAVOUR); \
+	fi
+	if test "x$(BUILT_PLUGINS)" != "x"; then \
+	  HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -l ./libhts.$(SHLIB_FLAVOUR); \
+	fi
+	test/test_bgzf test/bgziptest.txt
+	test/test-parse-reg -t test/colons.bam
+	cd test/faidx && ./test-faidx.sh faidx.tst
+	cd test/sam_filter && ./filter.sh filter.tst
+	cd test/tabix && ./test-tabix.sh tabix.tst
+	cd test/mpileup && ./test-pileup.sh mpileup.tst
+	cd test/fastq && ./test-fastq.sh
+	cd test/base_mods && ./base-mods.sh base-mods.tst
+	REF_PATH=: test/sam test/ce.fa test/faidx/faidx.fa test/faidx/fastqs.fq
+	test/test-regidx
+	cd test && REF_PATH=: ./test.pl $${TEST_OPTS:-}
+
+test/hts_endian: test/hts_endian.o
+	$(CC) $(LDFLAGS) -o $@ test/hts_endian.o $(LIBS)
+
+test/fuzz/hts_open_fuzzer: test/fuzz/hts_open_fuzzer.o
+	$(CC) $(LDFLAGS) -o $@ test/fuzz/hts_open_fuzzer.o libhts.a $(LIBS) -lpthread
+
+test/fieldarith: test/fieldarith.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/fieldarith.o libhts.a $(LIBS) -lpthread
+
+test/hfile: test/hfile.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/hfile.o libhts.a $(LIBS) -lpthread
+
+test/pileup: test/pileup.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/pileup.o libhts.a $(LIBS) -lpthread
+
+test/pileup_mod: test/pileup_mod.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/pileup_mod.o libhts.a $(LIBS) -lpthread
+
+test/plugins-dlhts: test/plugins-dlhts.o
+	$(CC) $(LDFLAGS) -o $@ test/plugins-dlhts.o $(LIBS)
+
+test/sam: test/sam.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/sam.o libhts.a $(LIBS) -lpthread
+
+test/test_bgzf: test/test_bgzf.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/test_bgzf.o libhts.a -lz $(LIBS) -lpthread
+
+test/test_expr: test/test_expr.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/test_expr.o libhts.a -lz $(LIBS) -lpthread
+
+test/test_faidx: test/test_faidx.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/test_faidx.o libhts.a -lz $(LIBS) -lpthread
+
+test/test_kfunc: test/test_kfunc.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/test_kfunc.o libhts.a -lz $(LIBS) -lpthread
+
+test/test_kstring: test/test_kstring.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/test_kstring.o libhts.a -lz $(LIBS) -lpthread
+
+test/test_mod: test/test_mod.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/test_mod.o libhts.a $(LIBS) -lpthread
+
+test/test_realn: test/test_realn.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/test_realn.o libhts.a $(LIBS) -lpthread
+
+test/test-regidx: test/test-regidx.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/test-regidx.o libhts.a $(LIBS) -lpthread
+
+test/test-parse-reg: test/test-parse-reg.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/test-parse-reg.o libhts.a $(LIBS) -lpthread
+
+test/test_str2int: test/test_str2int.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/test_str2int.o libhts.a $(LIBS) -lpthread
+
+test/test_time_funcs: test/test_time_funcs.o
+	$(CC) $(LDFLAGS) -o $@ test/test_time_funcs.o
+
+test/test_view: test/test_view.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/test_view.o libhts.a $(LIBS) -lpthread
+
+test/test_index: test/test_index.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/test_index.o libhts.a $(LIBS) -lpthread
+
+test/test-vcf-api: test/test-vcf-api.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/test-vcf-api.o libhts.a $(LIBS) -lpthread
+
+test/test-vcf-sweep: test/test-vcf-sweep.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/test-vcf-sweep.o libhts.a $(LIBS) -lpthread
+
+test/test-bcf-sr: test/test-bcf-sr.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/test-bcf-sr.o libhts.a -lz $(LIBS) -lpthread
+
+test/test-bcf-translate: test/test-bcf-translate.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/test-bcf-translate.o libhts.a -lz $(LIBS) -lpthread
+
+test/test_introspection: test/test_introspection.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/test_introspection.o libhts.a $(LIBS) -lpthread
+
+test/test-bcf_set_variant_type: test/test-bcf_set_variant_type.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/test-bcf_set_variant_type.o libhts.a $(LIBS) -lpthread
+
+# Extra tests for bundled htscodecs
+test_htscodecs_rans4x8: htscodecs/tests/rans4x8
+	cd htscodecs/tests && srcdir=. && export srcdir && ./rans4x8.test
+
+test_htscodecs_rans4x16: htscodecs/tests/rans4x16pr
+	cd htscodecs/tests && srcdir=. && export srcdir && ./rans4x16.test
+
+test_htscodecs_arith: htscodecs/tests/arith_dynamic
+	cd htscodecs/tests && srcdir=. && export srcdir && ./arith.test
+
+test_htscodecs_tok3: htscodecs/tests/tokenise_name3
+	cd htscodecs/tests && srcdir=. && export srcdir && ./tok3.test
+
+test_htscodecs_fqzcomp: htscodecs/tests/fqzcomp_qual
+	cd htscodecs/tests && srcdir=. && export srcdir && ./fqzcomp.test
+
+test_htscodecs_varint: htscodecs/tests/varint
+	cd htscodecs/tests && ./varint
+
+htscodecs/tests/arith_dynamic: htscodecs/tests/arith_dynamic_test.o $(HTSCODECS_OBJS)
+	$(CC) $(LDFLAGS) -o $@ $^ $(LIBS) -lm -lpthread
+
+htscodecs/tests/fqzcomp_qual: htscodecs/tests/fqzcomp_qual_test.o $(HTSCODECS_OBJS)
+	$(CC) $(LDFLAGS) -o $@ $^ $(LIBS) -lm -lpthread
+
+htscodecs/tests/rans4x16pr: htscodecs/tests/rANS_static4x16pr_test.o $(HTSCODECS_OBJS)
+	$(CC) $(LDFLAGS) -o $@ $^ $(LIBS) -lm -lpthread
+
+htscodecs/tests/rans4x8: htscodecs/tests/rANS_static_test.o $(HTSCODECS_OBJS)
+	$(CC) $(LDFLAGS) -o $@ $^ $(LIBS) -lm -lpthread
+
+htscodecs/tests/tokenise_name3: htscodecs/tests/tokenise_name3_test.o $(HTSCODECS_OBJS)
+	$(CC) $(LDFLAGS) -o $@ $^ $(LIBS) -lm -lpthread
+
+htscodecs/tests/varint: htscodecs/tests/varint_test.o $(HTSCODECS_OBJS)
+	$(CC) $(LDFLAGS) -o $@ $^ $(LIBS) -lm -lpthread
+
+htscodecs/tests/arith_dynamic_test.o: CPPFLAGS += -Ihtscodecs
+htscodecs/tests/arith_dynamic_test.o: htscodecs/tests/arith_dynamic_test.c config.h $(htscodecs_arith_dynamic_h)
+htscodecs/tests/fqzcomp_qual_test.o: CPPFLAGS += -Ihtscodecs
+htscodecs/tests/fqzcomp_qual_test.o: htscodecs/tests/fqzcomp_qual_test.c config.h $(htscodecs_fqzcomp_qual_h) $(htscodecs_varint_h)
+htscodecs/tests/rANS_static4x16pr_test.o: CPPFLAGS += -Ihtscodecs
+htscodecs/tests/rANS_static4x16pr_test.o: htscodecs/tests/rANS_static4x16pr_test.c config.h $(htscodecs_rANS_static4x16_h)
+htscodecs/tests/rANS_static_test.o: CPPFLAGS += -Ihtscodecs
+htscodecs/tests/rANS_static_test.o: htscodecs/tests/rANS_static_test.c config.h $(htscodecs_rANS_static_h)
+htscodecs/tests/tokenise_name3_test.o: CPPFLAGS += -Ihtscodecs
+htscodecs/tests/tokenise_name3_test.o: htscodecs/tests/tokenise_name3_test.c config.h $(htscodecs_tokenise_name3_h)
+htscodecs/tests/varint_test.o: CPPFLAGS += -Ihtscodecs
+htscodecs/tests/varint_test.o: htscodecs/tests/varint_test.c config.h $(htscodecs_varint_h)
+
+test/hts_endian.o: test/hts_endian.c config.h $(htslib_hts_endian_h)
+test/fuzz/hts_open_fuzzer.o: test/fuzz/hts_open_fuzzer.c config.h $(htslib_hfile_h) $(htslib_hts_h) $(htslib_sam_h) $(htslib_vcf_h)
+test/fieldarith.o: test/fieldarith.c config.h $(htslib_sam_h)
+test/hfile.o: test/hfile.c config.h $(htslib_hfile_h) $(htslib_hts_defs_h) $(htslib_kstring_h)
+test/pileup.o: test/pileup.c config.h $(htslib_sam_h) $(htslib_kstring_h)
+test/pileup_mod.o: test/pileup_mod.c config.h $(htslib_sam_h)
+test/plugins-dlhts.o: test/plugins-dlhts.c config.h
+test/sam.o: test/sam.c config.h $(htslib_hts_defs_h) $(htslib_sam_h) $(htslib_faidx_h) $(htslib_khash_h) $(htslib_hts_log_h)
+test/test_bgzf.o: test/test_bgzf.c config.h $(htslib_bgzf_h) $(htslib_hfile_h) $(htslib_hts_log_h) $(hfile_internal_h)
+test/test_expr.o: test/test_expr.c config.h $(htslib_hts_expr_h)
+test/test_kfunc.o: test/test_kfunc.c config.h $(htslib_kfunc_h)
+test/test_kstring.o: test/test_kstring.c config.h $(htslib_kstring_h)
+test/test_mod.o: test/test_mod.c config.h $(htslib_sam_h)
+test/test-parse-reg.o: test/test-parse-reg.c config.h $(htslib_hts_h) $(htslib_sam_h)
+test/test_realn.o: test/test_realn.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h)
+test/test-regidx.o: test/test-regidx.c config.h $(htslib_kstring_h) $(htslib_regidx_h) $(htslib_hts_defs_h) $(textutils_internal_h)
+test/test_str2int.o: test/test_str2int.c config.h $(textutils_internal_h)
+test/test_time_funcs.o: test/test_time_funcs.c config.h $(hts_time_funcs_h)
+test/test_view.o: test/test_view.c config.h $(cram_h) $(htslib_sam_h) $(htslib_vcf_h) $(htslib_hts_log_h)
+test/test_faidx.o: test/test_faidx.c config.h $(htslib_faidx_h)
+test/test_index.o: test/test_index.c config.h $(htslib_sam_h) $(htslib_vcf_h)
+test/test-vcf-api.o: test/test-vcf-api.c config.h $(htslib_hts_h) $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_kseq_h)
+test/test-vcf-sweep.o: test/test-vcf-sweep.c config.h $(htslib_vcf_sweep_h)
+test/test-bcf-sr.o: test/test-bcf-sr.c config.h $(htslib_synced_bcf_reader_h) $(htslib_hts_h) $(htslib_vcf_h)
+test/test-bcf-translate.o: test/test-bcf-translate.c config.h $(htslib_vcf_h)
+test/test_introspection.o: test/test_introspection.c config.h $(htslib_hts_h) $(htslib_hfile_h)
+test/test-bcf_set_variant_type.o: test/test-bcf_set_variant_type.c config.h $(htslib_hts_h) vcf.c
+
+
+test/thrash_threads1: test/thrash_threads1.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/thrash_threads1.o libhts.a -lz $(LIBS) -lpthread
+
+test/thrash_threads2: test/thrash_threads2.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/thrash_threads2.o libhts.a -lz $(LIBS) -lpthread
+
+test/thrash_threads3: test/thrash_threads3.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/thrash_threads3.o libhts.a -lz $(LIBS) -lpthread
+
+test/thrash_threads4: test/thrash_threads4.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/thrash_threads4.o libhts.a -lz $(LIBS) -lpthread
+
+test/thrash_threads5: test/thrash_threads5.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/thrash_threads5.o libhts.a -lz $(LIBS) -lpthread
+
+test/thrash_threads6: test/thrash_threads6.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/thrash_threads6.o libhts.a -lz $(LIBS) -lpthread
+
+test/thrash_threads7: test/thrash_threads7.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/thrash_threads7.o libhts.a -lz $(LIBS) -lpthread
+
+test_thrash: $(BUILT_THRASH_PROGRAMS)
+
+# Test to ensure the functions in the header files are exported by the shared
+# library.  This currently works by comparing the output from ctags on
+# the headers with the list of functions exported by the shared library.
+# Note that functions marked as exported in the .c files and not the public
+# headers will be missed by this test.
+test-shlib-exports: header-exports.txt shlib-exports-$(SHLIB_FLAVOUR).txt
+	@echo "Checking shared library exports"
+	@if test ! -s header-exports.txt ; then echo "Error: header-exports.txt empty" ; false ; fi
+	@if test ! -s shlib-exports-$(SHLIB_FLAVOUR).txt ; then echo "Error: shlib-exports-$(SHLIB_FLAVOUR).txt empty" ; false ; fi
+	@! comm -23 header-exports.txt shlib-exports-$(SHLIB_FLAVOUR).txt | grep . || \
+	( echo "Error: Found unexported symbols (listed above)" ; false )
+
+# Extract symbols that should be exported from public headers using ctags
+# Filter out macros in htslib/hts_defs.h.
+header-exports.txt: test/header_syms.pl htslib/*.h
+	test/header_syms.pl htslib/*.h | sort -u -o $@
+
+shlib-exports-so.txt: libhts.so
+	nm -D -g libhts.so | awk '$$2 == "T" { sub("@.*", "", $$3); print $$3 }' | sort -u -o $@
+
+shlib-exports-dylib.txt: libhts.dylib
+	nm -Ug libhts.dylib | awk '$$2 == "T" { sub("^_", "", $$3); print $$3 }' | sort -u -o $@
+
+shlib-exports-dll.txt: hts.dll.a
+	nm -g hts.dll.a | awk '$$2 == "T" { print $$3 }' | sort -u -o $@
+
+$(srcprefix)htslib.map: libhts.so
+	LC_ALL=C ; export LC_ALL; \
+	curr_vers=`expr 'X$(PACKAGE_VERSION)' : 'X\([0-9]*\.[0-9.]*\)'` ; \
+	last_vers=`awk '/^HTSLIB_[0-9](\.[0-9]+)+/ { lv = $$1 } END { print lv }' htslib.map` ; \
+	if test "x$$curr_vers" = 'x' || test "x$$last_vers" = 'x' ; then \
+	    echo "Version check failed : $$curr_vers / $$las_vers" 1>&2 ; \
+	    exit 1 ; \
+	fi && \
+	if test "HTSLIB_$$curr_vers" = "$$last_vers" ; then \
+	    echo "Refusing to update $@ - HTSlib version not changed" 1>&2 ; \
+	    exit 1 ; \
+	fi && \
+	nm --with-symbol-versions -D -g libhts.so | awk '$$2 ~ /^[DGRT]$$/ && $$3 ~ /@@Base$$/ && $$3 !~ /^(_init|_fini|_edata)@@/ { sub(/@@Base$$/, ";", $$3); print "    " $$3 }' > $@.tmp && \
+	if [ -s $@.tmp ] ; then \
+	    cat $@ > $@.new.tmp && \
+	    printf '\n%s {\n' "HTSLIB_$$curr_vers" >> $@.new.tmp && \
+	    cat $@.tmp >> $@.new.tmp && \
+	    printf '} %s;\n' "$$last_vers" >> $@.new.tmp && \
+	        rm -f $@.tmp && \
+	        mv $@.new.tmp $@ ; \
+	    fi ; \
+	else \
+	    rm -f $@.tmp ; \
+	fi
+
+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) $(SRC)htslib/*.h $(DESTDIR)$(includedir)/htslib
+	$(INSTALL_DATA) libhts.a $(DESTDIR)$(libdir)/libhts.a
+	$(INSTALL_MAN) $(SRC)bgzip.1 $(SRC)htsfile.1 $(SRC)tabix.1 $(DESTDIR)$(man1dir)
+	$(INSTALL_MAN) $(SRC)faidx.5 $(SRC)sam.5 $(SRC)vcf.5 $(DESTDIR)$(man5dir)
+	$(INSTALL_MAN) $(SRC)htslib-s3-plugin.7 $(DESTDIR)$(man7dir)
+
+installdirs:
+	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(includedir) $(DESTDIR)$(includedir)/htslib $(DESTDIR)$(libdir) $(DESTDIR)$(man1dir) $(DESTDIR)$(man5dir) $(DESTDIR)$(man7dir) $(DESTDIR)$(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_LIB) 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.$(LIBHTS_SOVERSION)
+
+install-cygdll: cyghts-$(LIBHTS_SOVERSION).dll installdirs
+	$(INSTALL_PROGRAM) cyghts-$(LIBHTS_SOVERSION).dll $(DESTDIR)$(bindir)/cyghts-$(LIBHTS_SOVERSION).dll
+	$(INSTALL_PROGRAM) libhts.dll.a $(DESTDIR)$(libdir)/libhts.dll.a
+
+install-dll: hts-$(LIBHTS_SOVERSION).dll installdirs
+	$(INSTALL_PROGRAM) hts-$(LIBHTS_SOVERSION).dll $(DESTDIR)$(bindir)/hts-$(LIBHTS_SOVERSION).dll
+	$(INSTALL_PROGRAM) hts.dll.a $(DESTDIR)$(libdir)/hts.dll.a
+
+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.$(LIBHTS_SOVERSION).dylib
+
+# Substitute these pseudo-autoconf variables only at install time
+# so that "make install prefix=/prefix/path" etc continue to work.
+install-pkgconfig: htslib.pc.tmp installdirs
+	sed -e 's#@-includedir@#$(includedir)#g;s#@-libdir@#$(libdir)#g;s#@-PACKAGE_VERSION@#$(PACKAGE_VERSION)#g' htslib.pc.tmp > $(DESTDIR)$(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.tmp
+	sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > $@
+
+
+testclean:
+	-rm -f test/*.tmp test/*.tmp.* test/faidx/*.tmp* test/faidx/FAIL* \
+               test/longrefs/*.tmp.* test/tabix/*.tmp.* test/tabix/FAIL* \
+               header-exports.txt shlib-exports-$(SHLIB_FLAVOUR).txt
+	-rm -rf htscodecs/tests/test.out
+
+# Only remove this in git checkouts
+DEL_HTSCODECS_VERSION := $(if $(wildcard htscodecs/.git),htscodecs/htscodecs/version.h)
+
+mostlyclean: testclean
+	-rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM config_vars.h version.h
+	-rm -f htscodecs/htscodecs/*.o htscodecs/htscodecs/*.pico $(DEL_HTSCODECS_VERSION)
+	-rm -f hts-object-files
+	-rm -f htscodecs/tests/*.o
+
+clean: mostlyclean clean-$(SHLIB_FLAVOUR)
+	-rm -f libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) $(BUILT_TEST_PROGRAMS) $(BUILT_THRASH_PROGRAMS)
+	-rm -f htscodecs/tests/rans4x8 htscodecs/tests/rans4x16pr htscodecs/tests/arith_dynamic htscodecs/tests/tokenise_name3 htscodecs/tests/fqzcomp_qual htscodecs/tests/varint
+
+distclean maintainer-clean: clean
+	-rm -f config.cache config.h config.log config.mk config.status
+	-rm -f TAGS *.pc.tmp *-uninstalled.pc htslib_static.mk htscodecs.mk
+	-rm -rf autom4te.cache
+
+clean-so:
+	-rm -f libhts.so libhts.so.*
+
+clean-cygdll:
+	-rm -f cyghts-*.dll libhts.dll.a
+
+clean-dll:
+	-rm -f hts-*.dll hts.dll.a
+
+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 $(PACKAGE_VERSION) as appropriate.
+# (The wildcards attempt to omit non-exported files (.git*, README.md,
+# etc) and other detritus that might be in the top-level directory.)
+distdir:
+	@if [ -z "$(distdir)" ]; then echo "Please supply a distdir=DIR argument."; false; fi
+	tar -c *.[ch15] [ILMNRchtv]*[ELSbcekmnth] | (cd $(distdir) && tar -x)
+	+cd $(distdir) && $(MAKE) distclean
+
+force:
+
+
+.PHONY: all check check-untracked clean distclean distdir force
+.PHONY: install install-pkgconfig installdirs lib-shared lib-static
+.PHONY: maintainer-check maintainer-clean mostlyclean plugins
+.PHONY: print-config print-version show-version tags
+.PHONY: test test-shlib-exports test_thrash testclean
+.PHONY: clean-so install-so
+.PHONY: clean-cygdll install-cygdll
+.PHONY: clean-dll install-dll
+.PHONY: clean-dylib install-dylib
+.PHONY: test_htscodecs_rans4x8 test_htscodecs_rans4x16 test_htscodecs_arith
+.PHONY: test_htscodecs_tok3 test_htscodecs_fqzcomp test_htscodecs_varint
\ No newline at end of file
diff --git a/recipes/recipes_emscripten/bioconductor-rhtslib/build.sh b/recipes/recipes_emscripten/bioconductor-rhtslib/build.sh
new file mode 100644
index 00000000000..6d3bda12799
--- /dev/null
+++ b/recipes/recipes_emscripten/bioconductor-rhtslib/build.sh
@@ -0,0 +1,36 @@
+# remove all shared zlib instances
+rm $PREFIX/lib/libz.so* || true
+
+
+
+echo "remove threading"
+
+find . \( -name "*.h" -o -name "*.c" \) -type f \
+    -exec sed -i.bak 's/#ifndef NO_THREADS/#ifdef ENABLE_THREADS/g' {} +
+
+echo "remove libcurl"
+
+sed -i.bak \
+    's/if test "\$enable_libcurl" != no; then/if false; then/' \
+    src/htslib-1.18/configure
+
+echo "remove libcurl even more"
+
+find . \( -name "*.h" -o -name "*.c" \) -type f \
+    -exec sed -i.bak 's/#ifdef HAVE_LIBCURL/#ifdef WE_NEVER_HAVE_LIBCURL/g' {} +
+
+cp $RECIPE_DIR/Makefile.Rhtslib src/htslib-1.18/Makefile.Rhtslib
+
+
+echo 'remove linkage to libcurl src/Makevars'
+#  PKG_LIBS+=-lcurl -lbz2 -llzma -lz
+# we replace -lcurl with an empty string to avoid linking against libcurl, which is not supported in Emscripten
+
+
+sed -i.bak 's/-lcurl//g' src/Makevars
+sed -i.bak 's/-lcurl//g' R/zzz.R
+
+
+
+
+$R CMD INSTALL $R_ARGS  .
\ No newline at end of file
diff --git a/recipes/recipes_emscripten/bioconductor-rhtslib/recipe.yaml b/recipes/recipes_emscripten/bioconductor-rhtslib/recipe.yaml
new file mode 100644
index 00000000000..8d1caba6d58
--- /dev/null
+++ b/recipes/recipes_emscripten/bioconductor-rhtslib/recipe.yaml
@@ -0,0 +1,55 @@
+context:
+  name : Rhtslib
+  version: 3.6.0
+  bioc: 3.22
+
+package:
+  name: bioconductor-${{ name | lower }}
+  version: ${{ version }}
+
+source:
+  url:
+    - https://bioconductor.org/packages/${{ bioc }}/bioc/src/contrib/${{ name }}_${{ version }}.tar.gz
+    - https://bioconductor.org/packages/${{ bioc }}/bioc/src/contrib/Archive/${{ name }}/${{ name }}_${{ version }}.tar.gz
+    - https://bioarchive.galaxyproject.org/${{ name }}_${{ version }}.tar.gz
+    - https://depot.galaxyproject.org/software/bioconductor-${{ name|lower }}/bioconductor-${{ name|lower }}_${{ version }}_src_all.tar.gz
+  sha256: 8b5fc0dfba39efb7371b5b0f930445047c7e06238d07c2293a50317612da6692
+
+build:
+  number: 0
+  skip: ${{ r_base != '4.6.0' }}
+
+
+requirements:
+  build:
+  - cross-r-base_${{ target_platform }} ==${{ r_base }}
+  - ${{ compiler('c') }}
+  host:
+  - r-base ==${{ r_base }}
+  - zlib
+  - bzip2
+  - liblzma
+
+
+tests:
+- package_contents:
+    lib:
+    - R/library/${{ name }}/libs/${{ name }}.so
+- script: run_r_test 
+  files:
+    recipe:
+    - test_import.R
+  requirements:
+    build:
+    - r-wasm-tester
+about:
+  repository: https://git.bioconductor.org/packages/Rhtslib
+  license: LGPL-2.0-or-later
+  license_file: LICENSE
+  summary: Provides memory efficient S4 classes for storing sequences "externally" (e.g. behind an R external pointer, or on disk).
+
+
+
+extra:
+  recipe-maintainers:
+  - DerThorsten
diff --git a/recipes/recipes_emscripten/bioconductor-rhtslib/test_import.R b/recipes/recipes_emscripten/bioconductor-rhtslib/test_import.R
new file mode 100644
index 00000000000..6520957a04a
--- /dev/null
+++ b/recipes/recipes_emscripten/bioconductor-rhtslib/test_import.R
@@ -0,0 +1,2 @@
+library(Rhtslib)
+