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Release 1.22
2 parents 0f8bedc + a208ba2 commit 36f20e7

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‎.gitignore

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Original file line numberDiff line numberDiff line change
@@ -44,6 +44,7 @@ shlib-exports-*.txt
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/annot-tsv
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/bgzip
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/htsfile
47+
/ref_cache/ref-cache
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/tabix
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/test/*/FAIL*
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/test/bgzf_boundaries/*.tmp.*
@@ -56,6 +57,7 @@ shlib-exports-*.txt
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/test/pileup_mod
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/test/plugins-dlhts
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/test/sam
60+
/test/ref_cache/*.tmp.*
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/test/tabix/*.tmp.*
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/test/test-bcf-sr
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/test/test-bcf-translate

‎INSTALL

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Original file line numberDiff line numberDiff line change
@@ -285,6 +285,48 @@ sudo zypper install autoconf automake make gcc perl zlib-devel libbz2-devel xz-d
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Also install libdeflate-devel, available on OpenSUSE Leap 15.4 onwards
286286
or directly via git releases above.
287287

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FreeBSD
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-------
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As root:
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pkg install autoconf automake bash curl gmake libdeflate perl5
293+
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Build as a normal user. When building, compiler flags need to be set so that
295+
the packages installed above are found. It is also necessary to use "gmake":
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./configure CPPFLAGS='-I/usr/local/include' LDFLAGS='-L/usr/local/lib -Wl,-R/usr/local/lib'
298+
gmake && gmake check
299+
300+
NetBSD
301+
------
302+
303+
Make sure you have installed the "comp" file set to get a compiler, then
304+
get the following packages as root:
305+
306+
pkg_add autoconf automake bash curl gmake libdeflate perl
307+
308+
Build as a normal user. When building, compiler flags need to be set so that
309+
the packages installed above are found. It is also necessary to use "gmake":
310+
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./configure CPPFLAGS='-I/usr/pkg/include' LDFLAGS='-L/usr/pkg/lib -Wl,-R/usr/pkg/lib'
312+
gmake && gmake check
313+
314+
OpenBSD
315+
-------
316+
317+
Make sure you have installed the "comp" file set to get a compiler, then
318+
get the following packages as root:
319+
320+
pkg_add autoconf automake bash bzip2 curl gmake libdeflate xz
321+
322+
You should select the most recent versions of autoconf and automake if asked.
323+
324+
Build as a normal user. When building, compiler flags need to be set so that
325+
the packages installed above are found. It is also necessary to use "gmake":
326+
327+
./configure CPPFLAGS='-I/usr/local/include' LDFLAGS='-L/usr/local/lib -Wl,-R/usr/local/lib'
328+
gmake && gmake check
329+
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Windows MSYS2/MINGW64
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---------------------
290332

‎LICENSE

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Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@ according to the terms of the following MIT/Expat license.]
33

44
The MIT/Expat License
55

6-
Copyright (C) 2012-2024 Genome Research Ltd.
6+
Copyright (C) 2012-2025 Genome Research Ltd.
77

88
Permission is hereby granted, free of charge, to any person obtaining a copy
99
of this software and associated documentation files (the "Software"), to deal
@@ -29,7 +29,7 @@ according to the terms of the following Modified 3-Clause BSD license.]
2929

3030
The Modified-BSD License
3131

32-
Copyright (C) 2012-2024 Genome Research Ltd.
32+
Copyright (C) 2012-2025 Genome Research Ltd.
3333

3434
Redistribution and use in source and binary forms, with or without
3535
modification, are permitted provided that the following conditions are met:

‎Makefile

Lines changed: 93 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -158,8 +158,8 @@ LIBHTS_SOVERSION = 3
158158
# is not strictly necessary and should be removed the next time
159159
# LIBHTS_SOVERSION is bumped (see #1144 and
160160
# https://developer.apple.com/library/archive/documentation/DeveloperTools/Conceptual/DynamicLibraries/100-Articles/DynamicLibraryDesignGuidelines.html#//apple_ref/doc/uid/TP40002013-SW23)
161-
MACH_O_COMPATIBILITY_VERSION = 3.1.21
162-
MACH_O_CURRENT_VERSION = 3.1.21
161+
MACH_O_COMPATIBILITY_VERSION = 3.1.22
162+
MACH_O_CURRENT_VERSION = 3.1.22
163163

164164
# Force version.h to be remade if $(PACKAGE_VERSION) has changed.
165165
version.h: $(if $(wildcard version.h),$(if $(findstring "$(PACKAGE_VERSION)",$(shell cat version.h)),,force))
@@ -196,6 +196,8 @@ config_vars.h:
196196
.c.pico:
197197
$(CC) $(CFLAGS) $(TARGET_CFLAGS) $(ALL_CPPFLAGS) $(EXTRA_CFLAGS_PIC) -c -o $@ $<
198198

199+
ref_cache/%.o: ref_cache/%.c
200+
$(CC) $(CFLAGS) $(REF_CACHE_EXTRA_C_FLAGS) $(TARGET_CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $<
199201

200202
LIBHTS_OBJS = \
201203
kfunc.o \
@@ -239,6 +241,24 @@ LIBHTS_OBJS = \
239241
$(HTSCODECS_OBJS) \
240242
$(NONCONFIGURE_OBJS)
241243

244+
REF_CACHE_OBJS = ref_cache/cmsg_wrap.o \
245+
ref_cache/http_parser.o \
246+
ref_cache/listener.o \
247+
ref_cache/log_files.o \
248+
ref_cache/main.o \
249+
ref_cache/misc.o \
250+
ref_cache/ping.o \
251+
ref_cache/poll_wrap_epoll.o \
252+
ref_cache/poll_wrap_poll.o \
253+
ref_cache/ref_files.o \
254+
ref_cache/request_handler.o \
255+
ref_cache/sendfile_wrap.o \
256+
ref_cache/server.o \
257+
ref_cache/transaction.o \
258+
ref_cache/upstream.o \
259+
cram/pooled_alloc.o \
260+
md5.o
261+
242262
# Without configure we wish to have a rich set of default figures,
243263
# but we still need conditional inclusion as we wish to still
244264
# support ./configure --disable-blah.
@@ -273,6 +293,9 @@ thread_pool_internal_h = thread_pool_internal.h $(htslib_thread_pool_h)
273293
# using the configure script or just comment the line out if you are not.
274294
-include config.mk
275295

296+
# Add optional built programs here
297+
all: $(REF_CACHE_PROGRAMS)
298+
276299
# Usually config.h is generated by running configure or config.status,
277300
# but if those aren't used create a default config.h here.
278301
config.h:
@@ -309,9 +332,17 @@ config.h:
309332
echo '#define HAVE_ATTRIBUTE_CONSTRUCTOR 1' >> $@
310333
echo '#endif' >> $@
311334
echo '#if (defined(__x86_64__) || defined(_M_X64))' >> $@
312-
echo '#define HAVE_ATTRIBUTE_TARGET 1' >> $@
335+
echo '#define HAVE_ATTRIBUTE_TARGET_SSSE3 1' >> $@
313336
echo '#define HAVE_BUILTIN_CPU_SUPPORT_SSSE3 1' >> $@
314337
echo '#endif' >> $@
338+
echo '#if defined __linux__' >> $@
339+
echo '#define HAVE_GETAUXVAL' >> $@
340+
echo '#elif defined __FreeBSD__' >> $@
341+
echo '#define HAVE_ELF_AUX_INFO' >> $@
342+
echo '#elif defined __OpenBSD__' >> $@
343+
echo '// Enable extra OpenBSD checks (see simd.c)' >> $@
344+
echo '#define HAVE_OPENBSD' >> $@
345+
echo '#endif' >> $@
315346

316347
# And similarly for htslib.pc.tmp ("pkg-config template"). No dependency
317348
# on htslib.pc.in listed, as if that file is newer the usual way to regenerate
@@ -493,13 +524,13 @@ cram/cram_decode.o cram/cram_decode.pico: cram/cram_decode.c config.h $(cram_h)
493524
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)
494525
cram/cram_external.o cram/cram_external.pico: cram/cram_external.c config.h $(htscodecs_rANS_static4x16_h) $(htslib_hfile_h) $(cram_h)
495526
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)
496-
cram/cram_io.o cram/cram_io.pico: cram/cram_io.c config.h os/lzma_stub.h $(fuzz_settings_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)
527+
cram/cram_io.o cram/cram_io.pico: cram/cram_io.c config.h os/lzma_stub.h $(fuzz_settings_h) $(cram_h) $(cram_os_h) $(htslib_hts_h) $(hts_internal_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)
497528
cram/cram_stats.o cram/cram_stats.pico: cram/cram_stats.c config.h $(cram_h) $(cram_os_h)
498529
cram/mFILE.o cram/mFILE.pico: cram/mFILE.c config.h $(htslib_hts_log_h) $(cram_os_h) cram/mFILE.h
499530
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)
500531
cram/pooled_alloc.o cram/pooled_alloc.pico: cram/pooled_alloc.c config.h cram/pooled_alloc.h $(cram_misc_h)
501532
cram/string_alloc.o cram/string_alloc.pico: cram/string_alloc.c config.h cram/string_alloc.h
502-
thread_pool.o thread_pool.pico: thread_pool.c config.h $(thread_pool_internal_h) $(htslib_hts_log_h)
533+
thread_pool.o thread_pool.pico: thread_pool.c config.h $(thread_pool_internal_h) $(htslib_hts_log_h) $(hts_internal_h)
503534

504535
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)
505536
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)
@@ -533,11 +564,46 @@ htsfile: htsfile.o libhts.a
533564
tabix: tabix.o libhts.a
534565
$(CC) $(LDFLAGS) -o $@ tabix.o libhts.a $(LIBS) -lpthread
535566

567+
ref_cache/ref-cache: $(REF_CACHE_OBJS)
568+
$(CC) $(LDFLAGS) $(REF_CACHE_EXTRA_LD_FLAGS) -o $@ $(REF_CACHE_OBJS) -lcurl
569+
536570
annot-tsv.o: annot-tsv.c config.h $(htslib_hts_h) $(htslib_hts_defs_h) $(htslib_khash_str2int_h) $(htslib_kstring_h) $(htslib_kseq_h) $(htslib_bgzf_h) $(htslib_regidx_h) $(textutils_internal_h)
537571
bgzip.o: bgzip.c config.h $(htslib_bgzf_h) $(htslib_hts_h) $(htslib_hfile_h)
538572
htsfile.o: htsfile.c config.h $(htslib_hfile_h) $(htslib_hts_h) $(htslib_sam_h) $(htslib_vcf_h)
539573
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) $(htslib_thread_pool_h)
540574

575+
# ref_cache dependencies
576+
ref_cache_cmsg_wrap_h = ref_cache/cmsg_wrap.h
577+
ref_cache_http_parser_h = ref_cache/http_parser.h $(htslib_hts_defs_h) $(ref_cache_types_h)
578+
ref_cache_listener_h = ref_cache/listener.h $(ref_cache_types_h)
579+
ref_cache_log_files_h = ref_cache/log_files.h $(htslib_hts_defs_h) $(ref_types_h)
580+
ref_cache_misc_h = ref_cache/misc.h $(htslib_hts_defs_h)
581+
ref_cache_options_h = ref_cache/options.h $(ref_cache_types_h)
582+
ref_cache_ping_h = ref_cache/ping.h
583+
ref_cache_poll_wrap_h = ref_cache/poll_wrap.h $(ref_cache_types_h)
584+
ref_cache_ref_files_h = ref_cache/ref_files.h $(htslib_hts_defs_h) $(ref_cache_types_h)
585+
ref_cache_request_handler_h = ref_cache/request_handler.h $(htslib_hts_defs_h) $(ref_cache_types_h)
586+
ref_cache_sendfile_wrap_h = ref_cache/sendfile_wrap.h
587+
ref_cache_server_h = ref_cache/server.h $(htslib_hts_defs_h) $(ref_cache_types_h)
588+
ref_cache_transaction_h = ref_cache/transaction.h $(htslib_hts_defs_h) $(ref_cache_types_h)
589+
ref_cache_types_h = ref_cache/types.h
590+
ref_cache_upstream_h = ref_cache/upstream.h $(ref_cache_types_h)
591+
592+
ref_cache/cmsg_wrap.o: ref_cache/cmsg_wrap.c config.h $(ref_cache_cmsg_wrap_h)
593+
ref_cache/http_parser.o: ref_cache/http_parser.c config.h $(ref_cache_http_parser_h) $(ref_cache_misc_h) $(ref_cache_options_h) $(ref_cache_request_handler_h) $(ref_cache_server_h) cram/pooled_alloc.h
594+
ref_cache/listener.o: ref_cache/listener.c config.h $(ref_cache_listener_h) $(ref_cache_misc_h) $(ref_cache_options_h) $(ref_cache_poll_wrap_h)
595+
ref_cache/log_files.o: ref_cache/log_files.c config.h $(ref_cache_log_files_h) $(ref_cache_options_h)
596+
ref_cache/main.o: ref_cache/main.c config.h $(ref_cache_listener_h) $(ref_cache_log_files_h) $(ref_cache_misc_h) $(ref_cache_options_h) $(ref_cache_ping_h) $(ref_cache_poll_wrap_h) $(ref_cache_server_h) $(ref_cache_upstream_h)
597+
ref_cache/ping.o: ref_cache/ping.c config.h $(ref_cache_ping_h) $(ref_cache_misc_h) $(ref_cache_options_h)
598+
ref_cache/poll_wrap_epoll.o: ref_cache/poll_wrap_epoll.c config.h $(ref_cache_poll_wrap_h) cram/pooled_alloc.h
599+
ref_cache/poll_wrap_poll.o: ref_cache/poll_wrap_poll.c config.h $(ref_cache_poll_wrap_h) cram/pooled_alloc.h
600+
ref_cache/ref_files.o: ref_cache/ref_files.c config.h $(ref_cache_ref_files_h) $(ref_cache_misc_h) $(ref_cache_options_h) $(ref_cache_upstream_h)
601+
ref_cache/request_handler.o: ref_cache/request_handler.c config.h $(ref_cache_request_handler_h) $(ref_cache_http_parser_h) $(ref_cache_misc_h) $(ref_cache_options_h) $(ref_cache_ref_files_h) $(ref_cache_transaction_h) $(ref_cache_upstream_h)
602+
ref_cache/sendfile_wrap.o: ref_cache/sendfile_wrap.c config.h $(ref_cache_sendfile_wrap_h)
603+
ref_cache/server.o: ref_cache/server.c config.h $(ref_cache_server_h) $(ref_cache_http_parser_h) $(ref_cache_listener_h) $(ref_cache_misc_h) $(ref_cache_options_h) $(ref_cache_poll_wrap_h) $(ref_cache_ref_files_h) $(ref_cache_request_handler_h) $(ref_cache_transaction_h) $(ref_cache_upstream_h) cram/pooled_alloc.h
604+
ref_cache/transaction.o: ref_cache/transaction.c config.h $(ref_cache_transaction_h) $(ref_cache_http_parser_h) $(ref_cache_options_h) $(ref_cache_poll_wrap_h) $(ref_cache_ref_files_h) $(ref_cache_sendfile_wrap_h) $(ref_cache_server_h) cram/pooled_alloc.h
605+
ref_cache/upstream.o: ref_cache/upstream.c config.h $(ref_cache_upstream_h) $(ref_cache_cmsg_wrap_h) $(ref_cache_misc_h) $(ref_cache_options_h) $(ref_cache_poll_wrap_h) $(htslib_hts_defs_h)
606+
541607
# Runes to check that the htscodecs submodule is present
542608
ifdef HTSCODECS_SOURCES
543609
htscodecs/htscodecs/%.c: | htscodecs/htscodecs
@@ -568,7 +634,7 @@ htscodecs/htscodecs:
568634
@false
569635

570636
# Build the htscodecs/htscodecs/version.h file if necessary
571-
htscodecs/htscodecs/version.h: force
637+
htscodecs/htscodecs/version.h: force | htscodecs/htscodecs
572638
@if test -e $(srcdir)/htscodecs/.git && test -e $(srcdir)/htscodecs/configure.ac ; then \
573639
vers=`cd $(srcdir)/htscodecs && git describe --always --dirty --match 'v[0-9]\.[0-9]*'` && \
574640
case "$$vers" in \
@@ -635,7 +701,12 @@ check test: all $(HTSCODECS_TEST_TARGETS)
635701
cd test/base_mods && ./base-mods.sh base-mods.tst
636702
REF_PATH=: test/sam test/ce.fa test/faidx/faidx.fa test/faidx/fastqs.fq
637703
test/test-regidx
638-
cd test && REF_PATH=: ./test.pl $${TEST_OPTS:-}
704+
cd test && \
705+
if test "x$(BUILT_PLUGINS)" != "x"; then \
706+
REF_PATH=: HTS_PATH=.. ./with-shlib.sh ./test.pl $(REF_CACHE_TEST_OPTS) $${TEST_OPTS:-} ; \
707+
else \
708+
REF_PATH=: ./test.pl $(REF_CACHE_TEST_OPTS) $${TEST_OPTS:-} ; \
709+
fi
639710

640711
test/hts_endian: test/hts_endian.o
641712
$(CC) $(LDFLAGS) -o $@ test/hts_endian.o $(LIBS)
@@ -803,7 +874,7 @@ test/test_faidx.o: test/test_faidx.c config.h $(htslib_faidx_h)
803874
test/test_index.o: test/test_index.c config.h $(htslib_sam_h) $(htslib_vcf_h)
804875
test/test-vcf-api.o: test/test-vcf-api.c config.h $(htslib_hts_h) $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_kseq_h)
805876
test/test-vcf-sweep.o: test/test-vcf-sweep.c config.h $(htslib_vcf_sweep_h)
806-
test/test-bcf-sr.o: test/test-bcf-sr.c config.h $(htslib_synced_bcf_reader_h) $(htslib_hts_h) $(htslib_vcf_h)
877+
test/test-bcf-sr.o: test/test-bcf-sr.c config.h $(htslib_hts_defs_h) $(htslib_synced_bcf_reader_h) $(htslib_hts_h) $(htslib_vcf_h)
807878
test/test-bcf-translate.o: test/test-bcf-translate.c config.h $(htslib_vcf_h)
808879
test/test_introspection.o: test/test_introspection.c config.h $(htslib_hts_h) $(htslib_hfile_h)
809880
test/test-bcf_set_variant_type.o: test/test-bcf_set_variant_type.c config.h $(htslib_hts_h) vcf.c
@@ -881,19 +952,21 @@ $(srcprefix)htslib.map: libhts.so
881952
printf '\n%s {\n' "HTSLIB_$$curr_vers" >> $@.new.tmp && \
882953
cat $@.tmp >> $@.new.tmp && \
883954
printf '} %s;\n' "$$last_vers" >> $@.new.tmp && \
884-
rm -f $@.tmp && \
885-
mv $@.new.tmp $@ ; \
886-
fi ; \
955+
rm -f $@.tmp && \
956+
mv $@.new.tmp $@ ; \
887957
else \
888958
rm -f $@.tmp ; \
889959
fi
890960

891-
install: libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) installdirs install-$(SHLIB_FLAVOUR) install-pkgconfig
892-
$(INSTALL_PROGRAM) $(BUILT_PROGRAMS) $(DESTDIR)$(bindir)
961+
install: libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) $(REF_CACHE_PROGRAMS) installdirs install-$(SHLIB_FLAVOUR) install-pkgconfig
962+
$(INSTALL_PROGRAM) $(BUILT_PROGRAMS) $(REF_CACHE_PROGRAMS) $(DESTDIR)$(bindir)
893963
if test -n "$(BUILT_PLUGINS)"; then $(INSTALL_PROGRAM) $(BUILT_PLUGINS) $(DESTDIR)$(plugindir); fi
894964
$(INSTALL_DATA) $(SRC)htslib/*.h $(DESTDIR)$(includedir)/htslib
895965
$(INSTALL_DATA) libhts.a $(DESTDIR)$(libdir)/libhts.a
896966
$(INSTALL_MAN) $(SRC)annot-tsv.1 $(SRC)bgzip.1 $(SRC)htsfile.1 $(SRC)tabix.1 $(DESTDIR)$(man1dir)
967+
if test "x$(REF_CACHE_PROGRAMS)" != "x" ; then \
968+
$(INSTALL_MAN) $(SRC)ref_cache/ref-cache.1 $(DESTDIR)$(man1dir) ; \
969+
fi
897970
$(INSTALL_MAN) $(SRC)faidx.5 $(SRC)sam.5 $(SRC)vcf.5 $(DESTDIR)$(man5dir)
898971
$(INSTALL_MAN) $(SRC)htslib-s3-plugin.7 $(DESTDIR)$(man7dir)
899972

@@ -932,12 +1005,12 @@ install-pkgconfig: htslib.pc.tmp installdirs
9321005
# A pkg-config file (suitable for copying to $PKG_CONFIG_PATH) that provides
9331006
# flags for building against the uninstalled library in this build directory.
9341007
htslib-uninstalled.pc: htslib.pc.tmp
935-
sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > $@
1008+
sed -e "s#@-includedir@#`pwd`#g;s#@-libdir@#`pwd`#g" htslib.pc.tmp > $@
9361009

9371010

9381011
testclean:
9391012
-rm -f test/*.tmp test/*.tmp.* test/faidx/*.tmp* \
940-
test/longrefs/*.tmp.* test/tabix/*.tmp.* \
1013+
test/longrefs/*.tmp.* test/ref_cache/*.tmp.* test/tabix/*.tmp.* \
9411014
test/bgzf_boundaries/*.tmp.* test/*/FAIL* \
9421015
header-exports.txt shlib-exports-$(SHLIB_FLAVOUR).txt
9431016
-rm -rf htscodecs/tests/test.out
@@ -950,9 +1023,10 @@ mostlyclean: testclean
9501023
-rm -f htscodecs/htscodecs/*.o htscodecs/htscodecs/*.pico $(DEL_HTSCODECS_VERSION)
9511024
-rm -f hts-object-files
9521025
-rm -f htscodecs/tests/*.o
1026+
-rm -f ref_cache/*.o
9531027

9541028
clean: mostlyclean clean-$(SHLIB_FLAVOUR)
955-
-rm -f libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) $(BUILT_TEST_PROGRAMS) $(BUILT_THRASH_PROGRAMS)
1029+
-rm -f libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) $(BUILT_TEST_PROGRAMS) $(BUILT_THRASH_PROGRAMS) $(REF_CACHE_PROGRAMS)
9561030
-rm -f htscodecs/tests/rans4x8 htscodecs/tests/rans4x16pr htscodecs/tests/arith_dynamic htscodecs/tests/tokenise_name3 htscodecs/tests/fqzcomp_qual htscodecs/tests/varint
9571031

9581032
distclean maintainer-clean: clean
@@ -981,11 +1055,11 @@ tags TAGS:
9811055
# code with your program, this hook enables Automake-style "make dist"
9821056
# for this subdirectory. If you do bundle an htslib snapshot, please
9831057
# add identifying information to $(PACKAGE_VERSION) as appropriate.
984-
# (The wildcards attempt to omit non-exported files (.git*, README.md,
1058+
# (The wildcards attempt to omit non-exported files (.git, .gitignore,
9851059
# etc) and other detritus that might be in the top-level directory.)
986-
distdir:
1060+
distdir: htscodecs/htscodecs/version.h
9871061
@if [ -z "$(distdir)" ]; then echo "Please supply a distdir=DIR argument."; false; fi
988-
tar -c *.[ch15] [ILMNRchtv]*[ELSbcekmnth] | (cd $(distdir) && tar -x)
1062+
tar -c *.[ch157] [I-R]*[ELSde] [cmors]*[bcemns4] [bhtv]*[bhknpt] htscodecs/*.md htscodecs/[ht]*/*[chp-t0-9] | (cd $(distdir) && tar -x)
9891063
+cd $(distdir) && $(MAKE) distclean
9901064

9911065
force:

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