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Release 1.16
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@daviesrob
daviesrob committed Aug 18, 2022
2 parents 6811ac5 + fecbd67 commit 4e61c12
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Showing 73 changed files with 3,263 additions and 478 deletions.
41 changes: 34 additions & 7 deletions .cirrus.yml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,7 @@ gcc_task:
USE_CONFIG: no
- environment:
USE_CONFIG: yes
CFLAGS: -std=c99 -pedantic
CFLAGS: -std=c99 -pedantic -Wformat=2
USE_LIBDEFLATE: yes

<< : *LIBDEFLATE
Expand All @@ -84,8 +84,8 @@ gcc_task:
ubuntu_task:
name: ubuntu-clang
container:
#image: ubuntu:latest # use << : *LIBDEFLATE
image: ubuntu:devel
image: ubuntu:latest
# image: ubuntu:devel
cpu: 2
memory: 1G

Expand Down Expand Up @@ -121,7 +121,7 @@ ubuntu_task:
rocky_task:
name: rockylinux-gcc
container:
image: rockylinux:latest
image: rockylinux:9
cpu: 2
memory: 1G

Expand All @@ -133,9 +133,36 @@ rocky_task:
# NB: we could consider building a docker image with these
# preinstalled and specifying that instead, to speed up testing.
install_script: |
yum install -y autoconf automake make gcc perl-Data-Dumper zlib-devel \
bzip2 bzip2-devel xz-devel curl-devel openssl-devel ncurses-devel \
diffutils git
yum install -y autoconf automake make gcc perl-Data-Dumper perl-FindBin \
zlib-devel bzip2 bzip2-devel xz-devel curl-devel openssl-devel \
ncurses-devel diffutils git
<< : *COMPILE
<< : *TEST

# Arm Linux
arm_ubuntu_task:
name: ubuntu-arm
arm_container:
image: ubuntu:latest
cpu: 2
memory: 1G

environment:
LC_ALL: C
CIRRUS_CLONE_DEPTH: 1
DO_UNTRACKED_FILE_CHECK: yes
USE_CONFIG: yes
CFLAGS: -g -Wall -O3 -std=c99 -pedantic

# NB: we could consider building a docker image with these
# preinstalled and specifying that instead, to speed up testing.
install_script: |
apt-get update
apt-get install -y --no-install-suggests --no-install-recommends \
ca-certificates clang libc-dev make git autoconf automake \
zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev \
libdeflate-dev
<< : *COMPILE
<< : *TEST
Expand Down
2 changes: 2 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -56,6 +56,7 @@ shlib-exports-*.txt
/test/tabix/FAIL*
/test/test-bcf-sr
/test/test-bcf-translate
/test/test-bcf_set_variant_type
/test/test_bgzf
/test/test_expr
/test/test_index
Expand All @@ -67,6 +68,7 @@ shlib-exports-*.txt
/test/test_realn
/test/test-regidx
/test/test_str2int
/test/test_time_funcs
/test/test-vcf-api
/test/test-vcf-sweep
/test/test_view
Expand Down
82 changes: 68 additions & 14 deletions Makefile
View file
Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,7 @@ CPPFLAGS =
#CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600
CFLAGS = -g -Wall -O2 -fvisibility=hidden
EXTRA_CFLAGS_PIC = -fpic
TARGET_CFLAGS =
LDFLAGS = -fvisibility=hidden
LIBS = $(htslib_default_libs)

Expand Down Expand Up @@ -85,6 +86,7 @@ BUILT_TEST_PROGRAMS = \
test/test_realn \
test/test-regidx \
test/test_str2int \
test/test_time_funcs \
test/test_view \
test/test_index \
test/test-vcf-api \
Expand All @@ -93,7 +95,8 @@ BUILT_TEST_PROGRAMS = \
test/fuzz/hts_open_fuzzer.o \
test/test-bcf-translate \
test/test-parse-reg \
test/test_introspection
test/test_introspection \
test/test-bcf_set_variant_type

BUILT_THRASH_PROGRAMS = \
test/thrash_threads1 \
Expand All @@ -114,10 +117,16 @@ ALL_CPPFLAGS = -I. $(CPPFLAGS)
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 =

HTS_CFLAGS_AVX2 =
HTS_CFLAGS_AVX512 =
HTS_CFLAGS_SSE4 =

include htslib_vars.mk
include htscodecs.mk

Expand All @@ -131,8 +140,8 @@ LIBHTS_SOVERSION = 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 = 3.1.15
MACH_O_CURRENT_VERSION = 3.1.15
MACH_O_COMPATIBILITY_VERSION = 3.1.16
MACH_O_CURRENT_VERSION = 3.1.16

# $(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.
Expand Down Expand Up @@ -161,10 +170,10 @@ config_vars.h:
.SUFFIXES: .bundle .c .cygdll .dll .o .pico .so

.c.o:
$(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $<
$(CC) $(CFLAGS) $(TARGET_CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $<

.c.pico:
$(CC) $(CFLAGS) $(ALL_CPPFLAGS) $(EXTRA_CFLAGS_PIC) -c -o $@ $<
$(CC) $(CFLAGS) $(TARGET_CFLAGS) $(ALL_CPPFLAGS) $(EXTRA_CFLAGS_PIC) -c -o $@ $<


LIBHTS_OBJS = \
Expand Down Expand Up @@ -226,6 +235,7 @@ 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)
Expand Down Expand Up @@ -253,6 +263,20 @@ config.h:
echo '#endif' >> $@
echo '#define HAVE_DRAND48 1' >> $@
echo '#define HAVE_LIBCURL 1' >> $@
if [ "x$(HTS_CFLAGS_SSE4)" != "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_CFLAGS_AVX2)" != "x" ] ; then \
echo '#define HAVE_AVX2 1' >> $@ ; \
fi
if [ "x$(HTS_CFLAGS_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
Expand Down Expand Up @@ -293,6 +317,9 @@ endif

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

ifneq "$(BUILT_PLUGINS)" ""
plugins: lib-shared
endif
plugins: $(BUILT_PLUGINS)


Expand All @@ -302,6 +329,10 @@ libhts.a: $(LIBHTS_OBJS)
-$(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)
Expand Down Expand Up @@ -399,9 +430,9 @@ hfile.o hfile.pico: hfile.c config.h $(htslib_hfile_h) $(hfile_internal_h) $(hts
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)
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) $(textutils_internal_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)
Expand All @@ -423,7 +454,7 @@ textutils.o textutils.pico: textutils.c config.h $(htslib_hfile_h) $(htslib_kstr

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)
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 $(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)
Expand All @@ -435,14 +466,24 @@ cram/string_alloc.o cram/string_alloc.pico: cram/string_alloc.c config.h cram/st
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_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_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)
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/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
Expand Down Expand Up @@ -525,16 +566,21 @@ SRC = $(srcprefix)
#
# If using MSYS, avoid poor shell expansion via:
# MSYS2_ARG_CONV_EXCL="*" make check
check test: $(BUILT_PROGRAMS) $(BUILT_TEST_PROGRAMS) $(BUILT_PLUGINS) $(HTSCODECS_TEST_TARGETS)
check test: all $(HTSCODECS_TEST_TARGETS)
test/hts_endian
test/test_expr
test/test_kfunc
test/test_kstring
test/test_str2int
test/test_time_funcs
test/fieldarith test/fieldarith.sam
test/hfile
HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.$(SHLIB_FLAVOUR)
HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -l ./libhts.$(SHLIB_FLAVOUR)
if test "x$(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/sam_filter && ./filter.sh filter.tst
Expand Down Expand Up @@ -597,6 +643,9 @@ test/test-parse-reg: test/test-parse-reg.o libhts.a
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

Expand All @@ -618,6 +667,9 @@ test/test-bcf-translate: test/test-bcf-translate.o libhts.a
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
Expand Down Expand Up @@ -685,13 +737,15 @@ test/test-parse-reg.o: test/test-parse-reg.c config.h $(htslib_hts_h) $(htslib_s
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_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)
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
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