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Release 1.16
2 parents 6811ac5 + fecbd67 commit 4e61c12

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‎.cirrus.yml‎

Lines changed: 34 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -72,7 +72,7 @@ gcc_task:
7272
USE_CONFIG: no
7373
- environment:
7474
USE_CONFIG: yes
75-
CFLAGS: -std=c99 -pedantic
75+
CFLAGS: -std=c99 -pedantic -Wformat=2
7676
USE_LIBDEFLATE: yes
7777

7878
<< : *LIBDEFLATE
@@ -84,8 +84,8 @@ gcc_task:
8484
ubuntu_task:
8585
name: ubuntu-clang
8686
container:
87-
#image: ubuntu:latest # use << : *LIBDEFLATE
88-
image: ubuntu:devel
87+
image: ubuntu:latest
88+
# image: ubuntu:devel
8989
cpu: 2
9090
memory: 1G
9191

@@ -121,7 +121,7 @@ ubuntu_task:
121121
rocky_task:
122122
name: rockylinux-gcc
123123
container:
124-
image: rockylinux:latest
124+
image: rockylinux:9
125125
cpu: 2
126126
memory: 1G
127127

@@ -133,9 +133,36 @@ rocky_task:
133133
# NB: we could consider building a docker image with these
134134
# preinstalled and specifying that instead, to speed up testing.
135135
install_script: |
136-
yum install -y autoconf automake make gcc perl-Data-Dumper zlib-devel \
137-
bzip2 bzip2-devel xz-devel curl-devel openssl-devel ncurses-devel \
138-
diffutils git
136+
yum install -y autoconf automake make gcc perl-Data-Dumper perl-FindBin \
137+
zlib-devel bzip2 bzip2-devel xz-devel curl-devel openssl-devel \
138+
ncurses-devel diffutils git
139+
140+
<< : *COMPILE
141+
<< : *TEST
142+
143+
# Arm Linux
144+
arm_ubuntu_task:
145+
name: ubuntu-arm
146+
arm_container:
147+
image: ubuntu:latest
148+
cpu: 2
149+
memory: 1G
150+
151+
environment:
152+
LC_ALL: C
153+
CIRRUS_CLONE_DEPTH: 1
154+
DO_UNTRACKED_FILE_CHECK: yes
155+
USE_CONFIG: yes
156+
CFLAGS: -g -Wall -O3 -std=c99 -pedantic
157+
158+
# NB: we could consider building a docker image with these
159+
# preinstalled and specifying that instead, to speed up testing.
160+
install_script: |
161+
apt-get update
162+
apt-get install -y --no-install-suggests --no-install-recommends \
163+
ca-certificates clang libc-dev make git autoconf automake \
164+
zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev \
165+
libdeflate-dev
139166
140167
<< : *COMPILE
141168
<< : *TEST

‎.gitignore‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -56,6 +56,7 @@ shlib-exports-*.txt
5656
/test/tabix/FAIL*
5757
/test/test-bcf-sr
5858
/test/test-bcf-translate
59+
/test/test-bcf_set_variant_type
5960
/test/test_bgzf
6061
/test/test_expr
6162
/test/test_index
@@ -67,6 +68,7 @@ shlib-exports-*.txt
6768
/test/test_realn
6869
/test/test-regidx
6970
/test/test_str2int
71+
/test/test_time_funcs
7072
/test/test-vcf-api
7173
/test/test-vcf-sweep
7274
/test/test_view

‎Makefile‎

Lines changed: 68 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -37,6 +37,7 @@ CPPFLAGS =
3737
#CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600
3838
CFLAGS = -g -Wall -O2 -fvisibility=hidden
3939
EXTRA_CFLAGS_PIC = -fpic
40+
TARGET_CFLAGS =
4041
LDFLAGS = -fvisibility=hidden
4142
LIBS = $(htslib_default_libs)
4243

@@ -85,6 +86,7 @@ BUILT_TEST_PROGRAMS = \
8586
test/test_realn \
8687
test/test-regidx \
8788
test/test_str2int \
89+
test/test_time_funcs \
8890
test/test_view \
8991
test/test_index \
9092
test/test-vcf-api \
@@ -93,7 +95,8 @@ BUILT_TEST_PROGRAMS = \
9395
test/fuzz/hts_open_fuzzer.o \
9496
test/test-bcf-translate \
9597
test/test-parse-reg \
96-
test/test_introspection
98+
test/test_introspection \
99+
test/test-bcf_set_variant_type
97100

98101
BUILT_THRASH_PROGRAMS = \
99102
test/thrash_threads1 \
@@ -114,10 +117,16 @@ ALL_CPPFLAGS = -I. $(CPPFLAGS)
114117
htscodecs.mk:
115118
echo '# Default htscodecs.mk generated by Makefile' > $@
116119
echo 'include $$(HTSPREFIX)htscodecs_bundled.mk' >> $@
120+
$(srcdir)/hts_probe_cc.sh '$(CC)' '$(CFLAGS) $(CPPFLAGS)' '$(LDFLAGS)' >> $@
117121

118122
srcdir = .
119123
srcprefix =
120124
HTSPREFIX =
125+
126+
HTS_CFLAGS_AVX2 =
127+
HTS_CFLAGS_AVX512 =
128+
HTS_CFLAGS_SSE4 =
129+
121130
include htslib_vars.mk
122131
include htscodecs.mk
123132

@@ -131,8 +140,8 @@ LIBHTS_SOVERSION = 3
131140
# is not strictly necessary and should be removed the next time
132141
# LIBHTS_SOVERSION is bumped (see #1144 and
133142
# https://developer.apple.com/library/archive/documentation/DeveloperTools/Conceptual/DynamicLibraries/100-Articles/DynamicLibraryDesignGuidelines.html#//apple_ref/doc/uid/TP40002013-SW23)
134-
MACH_O_COMPATIBILITY_VERSION = 3.1.15
135-
MACH_O_CURRENT_VERSION = 3.1.15
143+
MACH_O_COMPATIBILITY_VERSION = 3.1.16
144+
MACH_O_CURRENT_VERSION = 3.1.16
136145

137146
# $(NUMERIC_VERSION) is for items that must have a numeric X.Y.Z string
138147
# even if this is a dirty or untagged Git working tree.
@@ -161,10 +170,10 @@ config_vars.h:
161170
.SUFFIXES: .bundle .c .cygdll .dll .o .pico .so
162171

163172
.c.o:
164-
$(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $<
173+
$(CC) $(CFLAGS) $(TARGET_CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $<
165174

166175
.c.pico:
167-
$(CC) $(CFLAGS) $(ALL_CPPFLAGS) $(EXTRA_CFLAGS_PIC) -c -o $@ $<
176+
$(CC) $(CFLAGS) $(TARGET_CFLAGS) $(ALL_CPPFLAGS) $(EXTRA_CFLAGS_PIC) -c -o $@ $<
168177

169178

170179
LIBHTS_OBJS = \
@@ -226,6 +235,7 @@ bcf_sr_sort_h = bcf_sr_sort.h $(htslib_synced_bcf_reader_h) $(htslib_kbitset_h)
226235
header_h = header.h cram/string_alloc.h cram/pooled_alloc.h $(htslib_khash_h) $(htslib_kstring_h) $(htslib_sam_h)
227236
hfile_internal_h = hfile_internal.h $(htslib_hts_defs_h) $(htslib_hfile_h) $(textutils_internal_h)
228237
hts_internal_h = hts_internal.h $(htslib_hts_h) $(textutils_internal_h)
238+
hts_time_funcs_h = hts_time_funcs.h
229239
sam_internal_h = sam_internal.h $(htslib_sam_h)
230240
textutils_internal_h = textutils_internal.h $(htslib_kstring_h)
231241
thread_pool_internal_h = thread_pool_internal.h $(htslib_thread_pool_h)
@@ -253,6 +263,20 @@ config.h:
253263
echo '#endif' >> $@
254264
echo '#define HAVE_DRAND48 1' >> $@
255265
echo '#define HAVE_LIBCURL 1' >> $@
266+
if [ "x$(HTS_CFLAGS_SSE4)" != "x" ] ; then \
267+
echo '#define HAVE_POPCNT 1' >> $@ ; \
268+
echo '#define HAVE_SSE4_1 1' >> $@ ; \
269+
echo '#define HAVE_SSSE3 1' >> $@ ; \
270+
echo '#if defined(HTS_ALLOW_UNALIGNED) && HTS_ALLOW_UNALIGNED == 0' >> $@ ; \
271+
echo '#define UBSAN 1' >> $@ ; \
272+
echo '#endif' >> $@ ; \
273+
fi
274+
if [ "x$(HTS_CFLAGS_AVX2)" != "x" ] ; then \
275+
echo '#define HAVE_AVX2 1' >> $@ ; \
276+
fi
277+
if [ "x$(HTS_CFLAGS_AVX512)" != "x" ] ; then \
278+
echo '#define HAVE_AVX512 1' >> $@ ; \
279+
fi
256280

257281
# And similarly for htslib.pc.tmp ("pkg-config template"). No dependency
258282
# on htslib.pc.in listed, as if that file is newer the usual way to regenerate
@@ -293,6 +317,9 @@ endif
293317

294318
BUILT_PLUGINS = $(PLUGIN_OBJS:.o=$(PLUGIN_EXT))
295319

320+
ifneq "$(BUILT_PLUGINS)" ""
321+
plugins: lib-shared
322+
endif
296323
plugins: $(BUILT_PLUGINS)
297324

298325

@@ -302,6 +329,10 @@ libhts.a: $(LIBHTS_OBJS)
302329
-$(RANLIB) $@
303330

304331
print-config:
332+
@echo HTS_CFLAGS_AVX2 = $(HTS_CFLAGS_AVX2)
333+
@echo HTS_CFLAGS_AVX512 = $(HTS_CFLAGS_AVX512)
334+
@echo HTS_CFLAGS_SSE4 = $(HTS_CFLAGS_SSE4)
335+
@echo HTS_HAVE_NEON = $(HTS_HAVE_NEON)
305336
@echo LDFLAGS = $(LDFLAGS)
306337
@echo LIBHTS_OBJS = $(LIBHTS_OBJS)
307338
@echo LIBS = $(LIBS)
@@ -399,9 +430,9 @@ hfile.o hfile.pico: hfile.c config.h $(htslib_hfile_h) $(hfile_internal_h) $(hts
399430
hfile_gcs.o hfile_gcs.pico: hfile_gcs.c config.h $(htslib_hts_h) $(htslib_kstring_h) $(hfile_internal_h)
400431
hfile_libcurl.o hfile_libcurl.pico: hfile_libcurl.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h) $(htslib_khash_h)
401432
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)
402-
hfile_s3.o hfile_s3.pico: hfile_s3.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h)
433+
hfile_s3.o hfile_s3.pico: hfile_s3.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h) $(hts_time_funcs_h)
403434
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)
404-
hts_expr.o hts_expr.pico: hts_expr.c config.h $(htslib_hts_expr_h) $(textutils_internal_h)
435+
hts_expr.o hts_expr.pico: hts_expr.c config.h $(htslib_hts_expr_h) $(htslib_hts_log_h) $(textutils_internal_h)
405436
hts_os.o hts_os.pico: hts_os.c config.h $(htslib_hts_defs_h) os/rand.c
406437
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)
407438
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)
@@ -423,7 +454,7 @@ textutils.o textutils.pico: textutils.c config.h $(htslib_hfile_h) $(htslib_kstr
423454

424455
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)
425456
cram/cram_decode.o cram/cram_decode.pico: cram/cram_decode.c config.h $(cram_h) $(cram_os_h) $(htslib_hts_h)
426-
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)
457+
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)
427458
cram/cram_external.o cram/cram_external.pico: cram/cram_external.c config.h $(htslib_hfile_h) $(cram_h)
428459
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)
429460
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)
@@ -435,14 +466,24 @@ cram/string_alloc.o cram/string_alloc.pico: cram/string_alloc.c config.h cram/st
435466
thread_pool.o thread_pool.pico: thread_pool.c config.h $(thread_pool_internal_h) $(htslib_hts_log_h)
436467

437468
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)
438-
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_c_simple_model_h)
469+
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)
439470
htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.pico: htscodecs/htscodecs/htscodecs.c $(htscodecs_htscodecs_h) $(htscodecs_version_h)
440471
htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.pico: htscodecs/htscodecs/pack.c config.h $(htscodecs_pack_h)
441-
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_varint_h) $(htscodecs_pack_h) $(htscodecs_rle_h) $(htscodecs_utils_h)
472+
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)
473+
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)
474+
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)
475+
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)
476+
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)
477+
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)
442478
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)
443479
htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.pico: htscodecs/htscodecs/rle.c config.h $(htscodecs_varint_h) $(htscodecs_rle_h)
444-
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)
480+
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)
481+
htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.pico: htscodecs/htscodecs/utils.c config.h $(htscodecs_utils_h)
445482

483+
# Extra CFLAGS for specific files
484+
htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.pico: TARGET_CFLAGS = $(HTS_CFLAGS_AVX2)
485+
htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.pico: TARGET_CFLAGS = $(HTS_CFLAGS_AVX512)
486+
htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.pico: TARGET_CFLAGS = $(HTS_CFLAGS_SSE4)
446487

447488
bgzip: bgzip.o libhts.a
448489
$(CC) $(LDFLAGS) -o $@ bgzip.o libhts.a $(LIBS) -lpthread
@@ -525,16 +566,21 @@ SRC = $(srcprefix)
525566
#
526567
# If using MSYS, avoid poor shell expansion via:
527568
# MSYS2_ARG_CONV_EXCL="*" make check
528-
check test: $(BUILT_PROGRAMS) $(BUILT_TEST_PROGRAMS) $(BUILT_PLUGINS) $(HTSCODECS_TEST_TARGETS)
569+
check test: all $(HTSCODECS_TEST_TARGETS)
529570
test/hts_endian
530571
test/test_expr
531572
test/test_kfunc
532573
test/test_kstring
533574
test/test_str2int
575+
test/test_time_funcs
534576
test/fieldarith test/fieldarith.sam
535577
test/hfile
536-
HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.$(SHLIB_FLAVOUR)
537-
HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -l ./libhts.$(SHLIB_FLAVOUR)
578+
if test "x$(BUILT_PLUGINS)" != "x"; then \
579+
HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.$(SHLIB_FLAVOUR); \
580+
fi
581+
if test "x$(BUILT_PLUGINS)" != "x"; then \
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HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -l ./libhts.$(SHLIB_FLAVOUR); \
583+
fi
538584
test/test_bgzf test/bgziptest.txt
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test/test-parse-reg -t test/colons.bam
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cd test/sam_filter && ./filter.sh filter.tst
@@ -597,6 +643,9 @@ test/test-parse-reg: test/test-parse-reg.o libhts.a
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test/test_str2int: test/test_str2int.o libhts.a
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$(CC) $(LDFLAGS) -o $@ test/test_str2int.o libhts.a $(LIBS) -lpthread
599645

646+
test/test_time_funcs: test/test_time_funcs.o
647+
$(CC) $(LDFLAGS) -o $@ test/test_time_funcs.o
648+
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test/test_view: test/test_view.o libhts.a
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$(CC) $(LDFLAGS) -o $@ test/test_view.o libhts.a $(LIBS) -lpthread
602651

@@ -618,6 +667,9 @@ test/test-bcf-translate: test/test-bcf-translate.o libhts.a
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test/test_introspection: test/test_introspection.o libhts.a
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$(CC) $(LDFLAGS) -o $@ test/test_introspection.o libhts.a $(LIBS) -lpthread
620669

670+
test/test-bcf_set_variant_type: test/test-bcf_set_variant_type.o libhts.a
671+
$(CC) $(LDFLAGS) -o $@ test/test-bcf_set_variant_type.o libhts.a $(LIBS) -lpthread
672+
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# Extra tests for bundled htscodecs
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test_htscodecs_rans4x8: htscodecs/tests/rans4x8
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cd htscodecs/tests && srcdir=. && export srcdir && ./rans4x8.test
@@ -685,13 +737,15 @@ test/test-parse-reg.o: test/test-parse-reg.c config.h $(htslib_hts_h) $(htslib_s
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test/test_realn.o: test/test_realn.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h)
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test/test-regidx.o: test/test-regidx.c config.h $(htslib_kstring_h) $(htslib_regidx_h) $(htslib_hts_defs_h) $(textutils_internal_h)
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test/test_str2int.o: test/test_str2int.c config.h $(textutils_internal_h)
740+
test/test_time_funcs.o: test/test_time_funcs.c config.h $(hts_time_funcs_h)
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test/test_view.o: test/test_view.c config.h $(cram_h) $(htslib_sam_h) $(htslib_vcf_h) $(htslib_hts_log_h)
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test/test_index.o: test/test_index.c config.h $(htslib_sam_h) $(htslib_vcf_h)
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test/test-vcf-api.o: test/test-vcf-api.c config.h $(htslib_hts_h) $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_kseq_h)
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test/test-vcf-sweep.o: test/test-vcf-sweep.c config.h $(htslib_vcf_sweep_h)
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test/test-bcf-sr.o: test/test-bcf-sr.c config.h $(htslib_synced_bcf_reader_h)
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test/test-bcf-translate.o: test/test-bcf-translate.c config.h $(htslib_vcf_h)
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test/test_introspection.o: test/test_introspection.c config.h $(htslib_hts_h) $(htslib_hfile_h)
748+
test/test-bcf_set_variant_type.o: test/test-bcf_set_variant_type.c config.h $(htslib_hts_h) vcf.c
695749

696750

697751
test/thrash_threads1: test/thrash_threads1.o libhts.a

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