060af3d26df40e600c7dd7bf50442396 *DESCRIPTION
a6914e3cf84cde3c27b17c70dd60a170 *NAMESPACE
119f30f11d44a539118fe655b6f300c8 *NEWS.md
3aac97f2fadcaceac4f892dee1b04b71 *R/bootstrap.R
334d15bf83d546eff2ffb9459b824225 *R/duckhts.R
7543cfd69ab8a5ecba55e38037922954 *README.md
bf4b0bb41c925b8aefd23c990af6d1b5 *cleanup
d15601d57efdd3739d4e978bd2fa09c4 *cleanup.win
b7c6bd8326dac38ed3b0cb3d4793b41e *configure
a795b3c69c2c156a212543b35f67413d *configure.win
35d81ef39659605bd13526a37bf22bdf *inst/COPYRIGHT
448ff943ea386284ceb34448393b724b *inst/WORDLIST
4ab60a2ef6d3e9f83c48245804105141 *inst/duckhts_extension/bam_reader.c
2646229609987b9015a3bb24d0a777fb *inst/duckhts_extension/bcf_reader.c
784a6171a1de06f6f33d7e6d55e3d0ff *inst/duckhts_extension/bcftools_filter.c
0f39ca9e9be49c4118b021f3ff2f2f1d *inst/duckhts_extension/bcftools_shim.c
35faf27ce7d75c456293148cebbf1e4f *inst/duckhts_extension/bgzip.c
d152fa3f7377157fa0178d5b8b02582e *inst/duckhts_extension/duckdb_capi/duckdb.h
aa58568cfb2de7fef9f6b3d2eb3f89f9 *inst/duckhts_extension/duckdb_capi/duckdb_extension.h
421df7e90620ba7c00ec0b905e13f1ca *inst/duckhts_extension/duckhts.c
5bfe87a78f0f6db00927e4416db9a4a5 *inst/duckhts_extension/hts_index_builder.c
f9b420c12575c99da4b1be095a87b901 *inst/duckhts_extension/hts_meta_reader.c
df8355cbd2744782bd6adf1cbfcc683a *inst/duckhts_extension/htslib/INSTALL
6821e26fadd0265beab686931edc9102 *inst/duckhts_extension/htslib/LICENSE
c791225c57d581aeb5bf2ecd5ce0dcc4 *inst/duckhts_extension/htslib/Makefile
7fe81f355bcd416954b16662c4f61980 *inst/duckhts_extension/htslib/NEWS
67a6a8c3e155b389bbe5ea3eb83f3cd5 *inst/duckhts_extension/htslib/README
06d0e1095be158487d8342ec8ad4c718 *inst/duckhts_extension/htslib/README.large_positions.md
9c9ef93c974700a840389d7e31420265 *inst/duckhts_extension/htslib/VERSION
fb4ef32fb1b9f73e0e26c2246ac54d2b *inst/duckhts_extension/htslib/annot-tsv.1
392d6f577dee0cb26f65c4e4060fe594 *inst/duckhts_extension/htslib/annot-tsv.c
93891a4df8b33cb94178cffa4cf33426 *inst/duckhts_extension/htslib/bcf_sr_sort.c
8984e5ea0386a0492e65770c85fddf5b *inst/duckhts_extension/htslib/bcf_sr_sort.h
5104aee52f30ff567bbc707dd2b10ddc *inst/duckhts_extension/htslib/bgzf.c
b7afcd22163c271abf5b7badbae5c435 *inst/duckhts_extension/htslib/bgzf_internal.h
0b792b103266b924ac3ea7c76e7153a9 *inst/duckhts_extension/htslib/bgzip.1
d3df3169f96163d8ab1180042070ebb5 *inst/duckhts_extension/htslib/bgzip.c
b5796965b73ef54e3a54fa2024dc5360 *inst/duckhts_extension/htslib/builddir_vars.mk.in
e8d73cefb6eef5a933e3552bcf1850fb *inst/duckhts_extension/htslib/config.guess
6176c68e6037df476e6c20a68a244874 *inst/duckhts_extension/htslib/config.h.in
77909896ab851ef81996f88e9d4b3357 *inst/duckhts_extension/htslib/config.mk.in
45c1d61d9e0b95c49e82a5fbf13a963f *inst/duckhts_extension/htslib/config.sub
d3f93fd9faa07874a85eddc9a637bbf5 *inst/duckhts_extension/htslib/configure
71e96d78e95ae8d6515a78df3ca4b4cd *inst/duckhts_extension/htslib/configure.ac
cb5a8b21e8f800c37f1bcb74e96dede6 *inst/duckhts_extension/htslib/cram/README
99062f826a4f0b604dc811c7d2c745fa *inst/duckhts_extension/htslib/cram/cram.h
286c298769deb5a6bc592230dc41d20e *inst/duckhts_extension/htslib/cram/cram_codecs.c
067484180840a3946929e69b5100e224 *inst/duckhts_extension/htslib/cram/cram_codecs.h
e2824a6bafa8020f765eb869e09d39ed *inst/duckhts_extension/htslib/cram/cram_decode.c
ba038afa7c06ffcb9c7f72f07ca20f6e *inst/duckhts_extension/htslib/cram/cram_decode.h
0ed7e74159b28489f2703ab02ef973f3 *inst/duckhts_extension/htslib/cram/cram_encode.c
8bdf95f27c4cedee5ce52a887fd67ce3 *inst/duckhts_extension/htslib/cram/cram_encode.h
d22de3d50eff8144a53107c111f2bf0e *inst/duckhts_extension/htslib/cram/cram_external.c
82775c36937b0e6031ac24271b95149a *inst/duckhts_extension/htslib/cram/cram_index.c
17e538b85cf182f911eb6f3caef6794d *inst/duckhts_extension/htslib/cram/cram_index.h
f37aa8f449f968c15a5bc1048e2c0d27 *inst/duckhts_extension/htslib/cram/cram_io.c
41076460cd20be69beaa057ffb1e3810 *inst/duckhts_extension/htslib/cram/cram_io.h
0b2b7c32ca7040f0b104def891c17426 *inst/duckhts_extension/htslib/cram/cram_samtools.h
93e7d8ef7f1449d822b08ea40fe480a6 *inst/duckhts_extension/htslib/cram/cram_stats.c
951aef7d50ef880fe4ac2e1076b8df07 *inst/duckhts_extension/htslib/cram/cram_stats.h
829942f75b99a351afc3d107f0a3e90e *inst/duckhts_extension/htslib/cram/cram_structs.h
6eaf828206e64502054491af755ca346 *inst/duckhts_extension/htslib/cram/mFILE.c
e35f1f89f2ede5c5d475ac29a2d41c96 *inst/duckhts_extension/htslib/cram/mFILE.h
58b320fb959437220f9a9f62f0ef0bb9 *inst/duckhts_extension/htslib/cram/misc.h
fac31d90b24a2d14f6740b0e84fb519c *inst/duckhts_extension/htslib/cram/open_trace_file.c
5595dfafbeb8dd60580b37b615e4ad00 *inst/duckhts_extension/htslib/cram/open_trace_file.h
022071c2a8620a6d4b7535aba9d5ec60 *inst/duckhts_extension/htslib/cram/os.h
a9e19319f36b187e8600674dd5834100 *inst/duckhts_extension/htslib/cram/pooled_alloc.c
7a4726e77f89e6c1276c02d28699b490 *inst/duckhts_extension/htslib/cram/pooled_alloc.h
39466b96d7266add2413c1b193b28efb *inst/duckhts_extension/htslib/cram/string_alloc.c
6a1efd8ad6b21b9ff0fb7eccc074982c *inst/duckhts_extension/htslib/cram/string_alloc.h
4b8b0de755f832e704d02e0579a458a6 *inst/duckhts_extension/htslib/errmod.c
f3d9ad16d8ef733899632bb02c0045b2 *inst/duckhts_extension/htslib/faidx.5
e1ece9f9592a813be01dc9a86369a559 *inst/duckhts_extension/htslib/faidx.c
a006ef331e197adc0d8da63ee1286c10 *inst/duckhts_extension/htslib/fuzz_settings.h
b1a7cb119aa5f4b72b0ffbd06464c5eb *inst/duckhts_extension/htslib/header.c
8cbce47acd60fea0425af35aeefe147f *inst/duckhts_extension/htslib/header.h
ee836b7c7b310193a654237e71a01a2b *inst/duckhts_extension/htslib/hfile.c
07c2a1401ce59841450a222f508ce783 *inst/duckhts_extension/htslib/hfile_gcs.c
fa2dbfe8b01074920a007e742e16ffe6 *inst/duckhts_extension/htslib/hfile_internal.h
d3536af14a7835aba718415575058d65 *inst/duckhts_extension/htslib/hfile_libcurl.c
a1df6b47c7fdcf0bf2ff4685e3126d79 *inst/duckhts_extension/htslib/hfile_s3.c
7851a7a98c932ee770bb85c1545b66a1 *inst/duckhts_extension/htslib/hts.c
4b809626886f6ca3ddb46d8c98bc4fb8 *inst/duckhts_extension/htslib/hts_expr.c
0dc6785ff428b3c67906f50635ee84a3 *inst/duckhts_extension/htslib/hts_internal.h
271cdc2f751552ad5f4e0907a911889d *inst/duckhts_extension/htslib/hts_os.c
9f67b3b27b0d330d72616e376de69258 *inst/duckhts_extension/htslib/hts_probe_cc.sh
3bd0b8499f1d69ed4b6161b4702cf9ec *inst/duckhts_extension/htslib/hts_time_funcs.h
5715f77f3ea99872c9eb5c278fd87af1 *inst/duckhts_extension/htslib/htscodecs.mk
3e1094f4541b0a6f7cb8ba04a61c1768 *inst/duckhts_extension/htslib/htscodecs/BENCHMARKS.md
96776788ab6bf55c91df60a61da4d395 *inst/duckhts_extension/htslib/htscodecs/LICENSE.md
bcfb92bc838d0e099637f56ab3157530 *inst/duckhts_extension/htslib/htscodecs/MAINTAINERS.md
0ec08f0fe28503d41781923c01869758 *inst/duckhts_extension/htslib/htscodecs/NEWS.md
fd3a734f4f057225fd4da1d41950d38b *inst/duckhts_extension/htslib/htscodecs/htscodecs/arith_dynamic.c
3bebbf96ee7499fb67bd7e22dc2c02c7 *inst/duckhts_extension/htslib/htscodecs/htscodecs/arith_dynamic.h
64ddd57f0713ced05b1a85fed4a12da2 *inst/duckhts_extension/htslib/htscodecs/htscodecs/c_range_coder.h
8bd2345f88a7ef5bf3a250e44bd9f2a0 *inst/duckhts_extension/htslib/htscodecs/htscodecs/c_simple_model.h
d7cd6b82eb88d4a0a88ee221028c0339 *inst/duckhts_extension/htslib/htscodecs/htscodecs/fqzcomp_qual.c
a3e5911f443512aa790ae9266204f681 *inst/duckhts_extension/htslib/htscodecs/htscodecs/fqzcomp_qual.h
fcea74424bc7272d70c432e54b9a16c8 *inst/duckhts_extension/htslib/htscodecs/htscodecs/htscodecs.c
b82ec8df285ab9d543fa8c9500ebf306 *inst/duckhts_extension/htslib/htscodecs/htscodecs/htscodecs.h
b9acef1cd0aca8e5fa59f4d3da84c1c1 *inst/duckhts_extension/htslib/htscodecs/htscodecs/htscodecs_endian.h
918984f559ed4f4f47f9075de0dbf7de *inst/duckhts_extension/htslib/htscodecs/htscodecs/pack.c
f1ddaa4fec3541715aec5bc614f6b3e8 *inst/duckhts_extension/htslib/htscodecs/htscodecs/pack.h
df68c8c98266e391c4cb9496e2909a1f *inst/duckhts_extension/htslib/htscodecs/htscodecs/permute.h
381f84fc859100ca0cbcca474c06bd52 *inst/duckhts_extension/htslib/htscodecs/htscodecs/pooled_alloc.h
22c4fc39a735fc08dccf570d2f736ae3 *inst/duckhts_extension/htslib/htscodecs/htscodecs/rANS_byte.h
a47fa0cab341066c5fbbf6f299218755 *inst/duckhts_extension/htslib/htscodecs/htscodecs/rANS_static.c
4c6a3a1d2751bbc87fccc46cc4352807 *inst/duckhts_extension/htslib/htscodecs/htscodecs/rANS_static.h
71ab8a3552e4991f42b815cdf1099d30 *inst/duckhts_extension/htslib/htscodecs/htscodecs/rANS_static16_int.h
289a6fd88dbd3319436edcd600e448a7 *inst/duckhts_extension/htslib/htscodecs/htscodecs/rANS_static32x16pr.c
2ce42bd09401164653de93cffafe2fd5 *inst/duckhts_extension/htslib/htscodecs/htscodecs/rANS_static32x16pr.h
1122588bf14d1ae6bba961b93054ebd5 *inst/duckhts_extension/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c
1d70fa861b2b85f79fac90a6b9c33c4f *inst/duckhts_extension/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c
9bdbdad7ff4bf5fa1312398db37c7f07 *inst/duckhts_extension/htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c
b09ff468cd7fc5ff5d27dd25a6de5dd2 *inst/duckhts_extension/htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c
66c332e6abcbc2573bb542b5a2f6983a *inst/duckhts_extension/htslib/htscodecs/htscodecs/rANS_static4x16.h
bb7f3f8dfd094b77ddfebcacef96396a *inst/duckhts_extension/htslib/htscodecs/htscodecs/rANS_static4x16pr.c
c241b05fc9cff80ece4a68af6cb068ff *inst/duckhts_extension/htslib/htscodecs/htscodecs/rANS_word.h
57a8933f56b7163a135db846eee9e46c *inst/duckhts_extension/htslib/htscodecs/htscodecs/rle.c
096cae17d6ff1a8e9d45cf1f1b60d114 *inst/duckhts_extension/htslib/htscodecs/htscodecs/rle.h
19df981eac097fff01b3ba8cded80299 *inst/duckhts_extension/htslib/htscodecs/htscodecs/tokenise_name3.c
44c9835f7d7c96365e360b77e709ab3d *inst/duckhts_extension/htslib/htscodecs/htscodecs/tokenise_name3.h
754fa087faf7ccd9d7fddc8aa508e37e *inst/duckhts_extension/htslib/htscodecs/htscodecs/utils.c
6f2178782bbf944e03b7000579938877 *inst/duckhts_extension/htslib/htscodecs/htscodecs/utils.h
bc72d86f82839e0312444230129f3f5b *inst/duckhts_extension/htslib/htscodecs/htscodecs/varint.h
77b55b6b73fb30ed3524d9ab81933069 *inst/duckhts_extension/htslib/htscodecs/htscodecs/varint2.h
0cfbdf14fd59ef896f693052e46342ff *inst/duckhts_extension/htslib/htscodecs/htscodecs/version.h
4e498f70508061aa354616bce668ea9c *inst/duckhts_extension/htslib/htscodecs_bundled.mk
d42edb02d492dbfd97b73d1c2d38ddc9 *inst/duckhts_extension/htslib/htscodecs_external.mk
378ff85f78a544dfddb61a9b5ebd34e0 *inst/duckhts_extension/htslib/htsfile.1
be3af2fa2b7be7c7e9f01dbff5672416 *inst/duckhts_extension/htslib/htsfile.c
b2a61c77f5d47880c70f99c991c7b436 *inst/duckhts_extension/htslib/htslib-s3-plugin.7
7c2d5fa5bd7180893cb70a908acf821d *inst/duckhts_extension/htslib/htslib.map
375161f73d078c1ab6f839f75e7daafb *inst/duckhts_extension/htslib/htslib.mk
6258aeb1565a8e1afaa335072300d4ba *inst/duckhts_extension/htslib/htslib.pc.in
e88729157ab02f5f62fcfd7d68ee3f63 *inst/duckhts_extension/htslib/htslib/bgzf.h
171fc706b3a744b5e8c7d2d66b576fd5 *inst/duckhts_extension/htslib/htslib/cram.h
1acf7cd982576f6d65003656b721aef2 *inst/duckhts_extension/htslib/htslib/faidx.h
8e447fc96866891f134f2b0af0f76a67 *inst/duckhts_extension/htslib/htslib/hfile.h
937c09adaa9264eceae2493fbc4caf9d *inst/duckhts_extension/htslib/htslib/hts.h
f55c05b71048971b52ab310543fea318 *inst/duckhts_extension/htslib/htslib/hts_defs.h
3ace348d7e7ce5e203f3efd35285d3ee *inst/duckhts_extension/htslib/htslib/hts_endian.h
8a5f58a70ed340e3825294e799b841b6 *inst/duckhts_extension/htslib/htslib/hts_expr.h
8fb2df4647dee4d3e4fb3802c924da5f *inst/duckhts_extension/htslib/htslib/hts_log.h
3d406f82e08b95aa9a210b336f87cb7f *inst/duckhts_extension/htslib/htslib/hts_os.h
cf84c8ac0d1197a3bf11293ca2d19875 *inst/duckhts_extension/htslib/htslib/kbitset.h
905afa0bbfc0cae217b909aef543fa93 *inst/duckhts_extension/htslib/htslib/kfunc.h
be16e253e6c61dc112a833dc91c207f9 *inst/duckhts_extension/htslib/htslib/khash.h
163c505b6a47b236c04f9455ee4c493c *inst/duckhts_extension/htslib/htslib/khash_str2int.h
87c61d34e518ef252cb6e61da8a7ce05 *inst/duckhts_extension/htslib/htslib/klist.h
12a9d6f435e206d56eaec88ed5215b96 *inst/duckhts_extension/htslib/htslib/knetfile.h
06b42704ca4b4b17f448ef9d364b8783 *inst/duckhts_extension/htslib/htslib/kroundup.h
a138d9939ae49621509becabe3f58795 *inst/duckhts_extension/htslib/htslib/kseq.h
c2172de093bc9ba608764386d5f1ed68 *inst/duckhts_extension/htslib/htslib/ksort.h
d3554e8d96a2f30e34befb774f0c30ab *inst/duckhts_extension/htslib/htslib/kstring.h
a8d476786a1351aec6445026da0d1ac2 *inst/duckhts_extension/htslib/htslib/regidx.h
558e9c6f4371f4c0d125ead1396f94e2 *inst/duckhts_extension/htslib/htslib/sam.h
4ad0b65b23b03d2556ad8dd137bd8c11 *inst/duckhts_extension/htslib/htslib/synced_bcf_reader.h
e9cf83000919a022fa5d27872856e51e *inst/duckhts_extension/htslib/htslib/tbx.h
5d883251fe956346afb5db145274af76 *inst/duckhts_extension/htslib/htslib/thread_pool.h
9360b24b958300904dec45c022590c01 *inst/duckhts_extension/htslib/htslib/vcf.h
70eb4c499026fce028f561e6626fff0a *inst/duckhts_extension/htslib/htslib/vcf_sweep.h
8c149b90a7de95f0f7fbca92ca9ec218 *inst/duckhts_extension/htslib/htslib/vcfutils.h
3a8d2d3390337baf630fb24af72b3386 *inst/duckhts_extension/htslib/htslib_vars.mk
fb8f3dc0967408ebc323222c2d8c5751 *inst/duckhts_extension/htslib/kfunc.c
722795bed541d17da90719ca8943c183 *inst/duckhts_extension/htslib/kstring.c
248d825062a5ffd203201b7f47992dca *inst/duckhts_extension/htslib/m4/hts_check_compile_flags_needed.m4
5691e586e41ecb9442135ba7792dc8c9 *inst/duckhts_extension/htslib/m4/hts_hide_dynamic_syms.m4
6bb749e649e6905add5c8ab59957c33d *inst/duckhts_extension/htslib/m4/hts_prog_cc_warnings.m4
6456606f1e39c386878530c9c2853890 *inst/duckhts_extension/htslib/m4/pkg.m4
e8b45a3fbd028f136c504246f06d2700 *inst/duckhts_extension/htslib/md5.c
b6e15b1299ae473244c9bbd945558aa5 *inst/duckhts_extension/htslib/multipart.c
77adf0784cbf8d94d0c6dc39f043cd5a *inst/duckhts_extension/htslib/os/lzma_stub.h
711e7febb647564aec435289d0ddc52e *inst/duckhts_extension/htslib/os/rand.c
3f9a3f745564218937f519cd32b294a2 *inst/duckhts_extension/htslib/plugin.c
bff9af221731f95de8d64f77dffd17a2 *inst/duckhts_extension/htslib/probaln.c
3f955ca516498d1b89938d97c617764e *inst/duckhts_extension/htslib/realn.c
26d841c96c8a7ec3d4fcff07d69956bd *inst/duckhts_extension/htslib/ref_cache/cmsg_wrap.c
eb8aeb199544298512094af9eed2c8b6 *inst/duckhts_extension/htslib/ref_cache/cmsg_wrap.h
11bf41bf58fd30d886421478234167dd *inst/duckhts_extension/htslib/ref_cache/http_parser.c
40e00615a911464f69af55eedb67a875 *inst/duckhts_extension/htslib/ref_cache/http_parser.h
6dfdb38e3bd29d26a6070d7d66a41b25 *inst/duckhts_extension/htslib/ref_cache/listener.c
cda0255f64282c0c715a2fbc3264daad *inst/duckhts_extension/htslib/ref_cache/listener.h
a23a1b358c50e6f1bebc500df318a73d *inst/duckhts_extension/htslib/ref_cache/log_files.c
be56e5811f893ccb08a3ca4cdc07a0a3 *inst/duckhts_extension/htslib/ref_cache/log_files.h
a5e131c0d59f00bb4c982d6d2bd59481 *inst/duckhts_extension/htslib/ref_cache/main.c
3a4990a4abcf17b5cdb885d3481dd246 *inst/duckhts_extension/htslib/ref_cache/misc.c
57437cceaab6883b18284c6490bdbed0 *inst/duckhts_extension/htslib/ref_cache/misc.h
d2308d80e2b5450b55db5f98c4e21985 *inst/duckhts_extension/htslib/ref_cache/options.h
d798c6d993bb2b5728ae0323262296d9 *inst/duckhts_extension/htslib/ref_cache/ping.c
cf6f416dfe81c64aaf3036c9c9452ffe *inst/duckhts_extension/htslib/ref_cache/ping.h
f02cbe6ba6359a3b827382a138ef8b57 *inst/duckhts_extension/htslib/ref_cache/poll_wrap.h
dc6bf8b68cea9a9f4405acb73beef691 *inst/duckhts_extension/htslib/ref_cache/poll_wrap_epoll.c
951ae3f4ed50fe4d4082de9ba501d2a0 *inst/duckhts_extension/htslib/ref_cache/poll_wrap_poll.c
0ac202016e207a503eaacf132356e687 *inst/duckhts_extension/htslib/ref_cache/ref-cache.1
440b8888b79b01e8f1418e5925fceb51 *inst/duckhts_extension/htslib/ref_cache/ref_files.c
0a262b1780c231077338cc75241eac95 *inst/duckhts_extension/htslib/ref_cache/ref_files.h
71b7e48afb044d697e2a6dff7a648230 *inst/duckhts_extension/htslib/ref_cache/request_handler.c
f75e7ec3328d96201a5db10ddd2b9f1d *inst/duckhts_extension/htslib/ref_cache/request_handler.h
c9b4aad6fa6c1a04f34af8b3bac66f92 *inst/duckhts_extension/htslib/ref_cache/sendfile_wrap.c
5af86178ff5c922c60f02d26dfd3cb63 *inst/duckhts_extension/htslib/ref_cache/sendfile_wrap.h
e4a30c918763aa45873bfb193cad3efc *inst/duckhts_extension/htslib/ref_cache/server.c
21a2b717b9d79de753463b204b718ba6 *inst/duckhts_extension/htslib/ref_cache/server.h
3eeb4c117e03abec493e4f8db46ebb1f *inst/duckhts_extension/htslib/ref_cache/transaction.c
cd06ecd9a4c0ce95393ad65ff97c7aa2 *inst/duckhts_extension/htslib/ref_cache/transaction.h
8460d60d577efa0a58408806d6efee48 *inst/duckhts_extension/htslib/ref_cache/types.h
70561e4d2b417c0e6a94231b1ce89c1a *inst/duckhts_extension/htslib/ref_cache/upstream.c
a9e2630f65d32b425384e0bae70b28dd *inst/duckhts_extension/htslib/ref_cache/upstream.h
b783d4eed71fd8964464b35d04d2b69c *inst/duckhts_extension/htslib/regidx.c
92a627b830a84b4698bbafaaae00fc1a *inst/duckhts_extension/htslib/region.c
dbbb70ea8ac7661080c2d1c835e8d8fb *inst/duckhts_extension/htslib/sam.5
025e8ec5e0c5bc85c26387c62287f0e1 *inst/duckhts_extension/htslib/sam.c
c9e7e133f95c9c3868bdca9b7a6fe197 *inst/duckhts_extension/htslib/sam_internal.h
e713ebde9511663a53f3659762af043a *inst/duckhts_extension/htslib/sam_mods.c
69e4c10eaaad5023640105bab74d7ba0 *inst/duckhts_extension/htslib/samples/DEMO.md
f43a3c66a1be1c12e3a7363b4907c863 *inst/duckhts_extension/htslib/samples/Makefile
98c5063e0272ae20581e8db7b2eebb79 *inst/duckhts_extension/htslib/samples/add_header.c
78898dc2cc9399015caeaa4d162c9f5b *inst/duckhts_extension/htslib/samples/cram.c
7c92844a52916ba1117c727a8e40ebb4 *inst/duckhts_extension/htslib/samples/dump_aux.c
25be92554330373549b693cc6b89d80c *inst/duckhts_extension/htslib/samples/flags_demo.c
a5816ca21ccf9d14e65c1936a30fd489 *inst/duckhts_extension/htslib/samples/flags_htsopt_field.c
cb54e72f945026b8b2438edbf42e6868 *inst/duckhts_extension/htslib/samples/index_fasta.c
bb7ee51ce714569049daa175168b63eb *inst/duckhts_extension/htslib/samples/index_multireg_read.c
f48cfccc3089cbaf3651e604e0723182 *inst/duckhts_extension/htslib/samples/index_reg_read.c
1167bf0e2db7c19f95a1785d44105b99 *inst/duckhts_extension/htslib/samples/index_write.c
9851c83ce337ccf3a3491c41da986e79 *inst/duckhts_extension/htslib/samples/mod_aux.c
1638140aaf3bf6f4c10c890ff79602ef *inst/duckhts_extension/htslib/samples/mod_aux_ba.c
1c150430c27a99c1ff07f635b943ec47 *inst/duckhts_extension/htslib/samples/mod_bam.c
fa71df98d3008771761b0154f99b539a *inst/duckhts_extension/htslib/samples/modstate.c
664a4bfc678928a170f2b62009135cfd *inst/duckhts_extension/htslib/samples/mpileup.c
0b8f5923f1abffb7b60c5fac432fe874 *inst/duckhts_extension/htslib/samples/pileup.c
0ea100148d2a2a84af6686eda29ad572 *inst/duckhts_extension/htslib/samples/pileup_mod.c
0c27a63edb281b42518c6324d20b6b79 *inst/duckhts_extension/htslib/samples/qtask_ordered.c
8bd8f8956e368dcbe0f21d85ea0893ef *inst/duckhts_extension/htslib/samples/qtask_unordered.c
020ee365658f4d9dca3443c975b6e144 *inst/duckhts_extension/htslib/samples/read_aux.c
e4011e35e78936b199153807930f4d13 *inst/duckhts_extension/htslib/samples/read_bam.c
5174a4e7adc048b4ba7ddc28d2bdb284 *inst/duckhts_extension/htslib/samples/read_fast.c
d2e666cbae04010b1f2a68b92d4b1fc7 *inst/duckhts_extension/htslib/samples/read_fast_index.c
7a1316a9835d557ab6056a2ae76916d0 *inst/duckhts_extension/htslib/samples/read_header.c
d5e45ffed298400b18cab523dbe72aa0 *inst/duckhts_extension/htslib/samples/read_refname.c
202750b60cb92eb07ed1c4dd4ad7db75 *inst/duckhts_extension/htslib/samples/rem_header.c
6e13aa4dd8e8270d6cea1cd81e412449 *inst/duckhts_extension/htslib/samples/sample.bed
573f6999a17bb23f0fce890ef4cc5eb8 *inst/duckhts_extension/htslib/samples/sample.ref.fa
15ef381612514ac9dc0118bca9bc9b8c *inst/duckhts_extension/htslib/samples/sample.ref.fq
f99522246f6b4e68b987d247f3d2bc83 *inst/duckhts_extension/htslib/samples/sample.sam
915c99bd6da7f682ada64726ce5a1139 *inst/duckhts_extension/htslib/samples/split.c
90899447d64853ca20d70654d0a5463a *inst/duckhts_extension/htslib/samples/split2.c
5920c379f42ebc33f26940362364850f *inst/duckhts_extension/htslib/samples/split_thread1.c
9ba514cef6b8cb0ca747def7aeed518f *inst/duckhts_extension/htslib/samples/split_thread2.c
5885d12f8a5a39d9c0c741620b0ee17d *inst/duckhts_extension/htslib/samples/update_header.c
6262950557bc21350a2d2caf091cc66c *inst/duckhts_extension/htslib/samples/write_fast.c
054378c5d14c420fb2dc0e401b20b1e4 *inst/duckhts_extension/htslib/simd.c
d10dd93e07098fb7414108aadaf3ef1d *inst/duckhts_extension/htslib/synced_bcf_reader.c
973339ceff8738ce7355739065386e4e *inst/duckhts_extension/htslib/tabix.1
6eb968cf0e3ea37c387503ebdddd88fb *inst/duckhts_extension/htslib/tabix.c
99c50a980fb9b0c94885c683cecd1d25 *inst/duckhts_extension/htslib/tbx.c
2b2511d513a82a0365dc066c1a1c3311 *inst/duckhts_extension/htslib/textutils.c
4995d2933bcd72486974af3e486d7292 *inst/duckhts_extension/htslib/textutils_internal.h
55847c7ec83ebd781a6d7eb5315747fa *inst/duckhts_extension/htslib/thread_pool.c
2e16113342c3d990e61cea8c67a1c0eb *inst/duckhts_extension/htslib/thread_pool_internal.h
556f60ca98d0facdff213bc9f9435d81 *inst/duckhts_extension/htslib/vcf.5
c1cfe0694c7788897c423e7e1cf5b63f *inst/duckhts_extension/htslib/vcf.c
a1765c57a7f7ec08dfba46d1d618cfc0 *inst/duckhts_extension/htslib/vcf_sweep.c
a30b5c5ad25005da2cd35bbec10290d1 *inst/duckhts_extension/htslib/vcfutils.c
1c8aaf6a30f8a54ee5fa9ba764a42183 *inst/duckhts_extension/htslib/version.sh
b6532b78f2d79879f430dba7fbc2023b *inst/duckhts_extension/include/bcftools_filter_config.h
96e6aa0e9c280ec4dedbc9df57def2db *inst/duckhts_extension/include/bcftools_shim.h
8ea41635f12b975aae720c43a4d446a8 *inst/duckhts_extension/include/filter.h
9321f5f3edef590d169028e82ae16170 *inst/duckhts_extension/include/quality_encoding.h
f7b2fa7224b7c83be60a41bbcd533329 *inst/duckhts_extension/include/seq_encoding.h
78d87cf03e3c3614e40e6f6feab2387f *inst/duckhts_extension/include/vcf_types.h
38ef80c843a343d1854cdc2b2af4942c *inst/duckhts_extension/include/vep_parser.h
3df1d2bc21e9f885d4423cc0534a5b70 *inst/duckhts_extension/interval_udf.c
c805192d16359a2881da6e6724d4fb2d *inst/duckhts_extension/kmer_udf.c
2863a6bcf9f05e9f3dd8a675b296d417 *inst/duckhts_extension/liftover_udf.c
584455a64d5adfa43ed76bff14a7de70 *inst/duckhts_extension/munge_udf.c
3c02d2b85267118afbbf60f65377e787 *inst/duckhts_extension/quality_encoding.c
71fa0c4e36f8ecff05f0319c2274fe65 *inst/duckhts_extension/quality_encoding_reader.c
756a039e51c33c7f8b5225e502880e9b *inst/duckhts_extension/score_udf.c
42edf50f2e3de0c47722be5c155d64fe *inst/duckhts_extension/seq_reader.c
62fbffd0c14acce5b2d0ef5e037d5427 *inst/duckhts_extension/tabix_reader.c
dd3d57768f422080d8e9822a1d164ddc *inst/duckhts_extension/vep_parser.c
654af0f0bb08471361e8e665165fcb85 *inst/extdata/aux_tags.sam.gz
cfdd101d3d08fc60f60f2aa63a7055d4 *inst/extdata/ce.fa
caf7cc4f77dcf116369d0b48ff83d5b4 *inst/extdata/ce.fa.fai
629a819966403880f878efe32d728104 *inst/extdata/colheaders.tsv
5058e161d7bb4ccae9c03e85ab2686c3 *inst/extdata/fixed_count_arrays.vcf
95f1de7557e5fea2299311bdc7063243 *inst/extdata/format_string_list.vcf
fc431af724da7ba15c848a82520b5f1b *inst/extdata/formatcols.vcf.gz
aed70d556c515d25b3542059e98e35d3 *inst/extdata/formatcols.vcf.gz.csi
930e9a3645bbeb5a7bb724d58b7bb7a7 *inst/extdata/gff_file.gff.gz
d89c706364e3c19b452810815aeda860 *inst/extdata/gff_file.gff.gz.tbi
f4d195da2debbf499e46e46fc11e7973 *inst/extdata/header_tabix.tsv.gz
3a0494761cad4363b78fd1b3e021152a *inst/extdata/header_tabix.tsv.gz.tbi
248db259c9d231f96708e25f82980179 *inst/extdata/interleaved.fq
dd5c64690a6ee0e2f0cfe499a284fd12 *inst/extdata/legacy_phred64.fq
4e6d64cf882019fd136c2148b03f7af7 *inst/extdata/mapping_number_families.vcf
d0293c3261f7c60b5ab6d8a38a336b6a *inst/extdata/meta_tabix.tsv.gz
71674b4842d4fd13d7434a34e3232c4a *inst/extdata/meta_tabix.tsv.gz.tbi
91888d15b994fb97a347be3c82e9b759 *inst/extdata/parallel_empty_contigs.bam
44017cd693fd7cce40eda0a55b5f1f73 *inst/extdata/parallel_empty_contigs.bam.bai
0b75b300c53f2120d5d37b50b16916d1 *inst/extdata/parallel_empty_contigs.vcf
8583a37cb25fe73d7dc8925652804942 *inst/extdata/parallel_empty_contigs.vcf.gz
9f978fe03cf1a2d047683b8c2e578eae *inst/extdata/parallel_empty_contigs.vcf.gz.tbi
c0f38afc0194d9d791d875ea7fbe2a9b *inst/extdata/r1.fq
8ee7dbe0739320d25ab8e9f0eef0251e *inst/extdata/r2.fq
1c23eaabeb31d8cbafe19d6e5b3a5999 *inst/extdata/range.bam
228b8278fbcb305773a6839df44b640e *inst/extdata/range.bam.bai
f3802d15f9b780fef5427c356353bd85 *inst/extdata/range.cram
f0b65f254ccdd75b45aef37b309df9eb *inst/extdata/range.cram.crai
2d298fb75099fbf0c1eda326536df856 *inst/extdata/rg.sam
8e15c570193a84507694dfcf97dc646f *inst/extdata/rg.sam.gz
e65167395c5cc08c6ff33ffd117b21d8 *inst/extdata/rg.sam.gz.tbi
78898ca1eea44c297de5a3c01f32ff4c *inst/extdata/score_as.vcf
c8a2bd96ad5cc9b275c3ed87b857bdc8 *inst/extdata/score_chrprefix.vcf
39ae6b2ecb550198d388abd07fb73357 *inst/extdata/score_columns.tsv
3ee4ad6c3fb16d4295d1378e89613320 *inst/extdata/score_dosage.vcf
7cf975cd8f26cb7668605e1be5cde707 *inst/extdata/score_gwas_summary.vcf
be6251a547a6b160a72380bc7184ce12 *inst/extdata/score_input.vcf
dac50b48718024ca8d69cfd534c0cd05 *inst/extdata/score_missing_ds.vcf
3b1c62e5ae55355127232e3bfb008cc9 *inst/extdata/score_missing_gt.vcf
635b20ef4ba9f7e8793a26323b3728e2 *inst/extdata/score_regions.txt
068b09ec35c095e32a8daf427cf369da *inst/extdata/score_summary.tsv
ef43823e034efc34593da380402320ed *inst/extdata/score_summary_bolt.tsv
10ad07297e795b1092e98c675d16add4 *inst/extdata/score_summary_custom.tsv
25905a91e8b2b9129286723d60da00ac *inst/extdata/score_summary_log10p.tsv
085916aa927ae3ae9b00ba996c9d270c *inst/extdata/score_summary_metal.tsv
6f30fe59735a6345a7d2a681bf621940 *inst/extdata/score_summary_mismatch.tsv
02d23332c15b9c8386582646d9171b23 *inst/extdata/score_summary_na.tsv
20e8be59ff072c63f3f6646e1a22ae3f *inst/extdata/score_summary_no_snp.tsv
9dc48f00305fd0d2c6ebb40c3b87bbd3 *inst/extdata/score_summary_or.tsv
4a6e64fa93747906a0ebfb961940b7fa *inst/extdata/score_summary_pgs.tsv
9caeea2bc59d930c414ce56a15989f1c *inst/extdata/score_summary_plink2.tsv
7dc09de79fd79788bfc50e78c4b89ae7 *inst/extdata/score_summary_regenie.tsv
7d214dc101a720083085887bc0a09c7e *inst/extdata/score_summary_rsid.tsv
59da68d1a0c56d22974f49b80aa4e011 *inst/extdata/score_summary_saige.tsv
529a2cc8f01bb62f0f9c76d7b83129ea *inst/extdata/score_summary_smallp.tsv
3155909df0e451ade23fffdb5dd85970 *inst/extdata/score_summary_ssf.tsv
635b20ef4ba9f7e8793a26323b3728e2 *inst/extdata/score_targets.txt
922d22189a603ebb2311645d54c5f090 *inst/extdata/spec_standard_corrections.vcf
66d32def38168136f0d5a0a524892baf *inst/extdata/targets.bed
027212190bc3777423c0a20fa81b83c6 *inst/extdata/test_vep.vcf
b61a5de8f859b6449471c1bcab1808ff *inst/extdata/test_vep_snpeff.vcf
f4942b236e66a028bc8bca7843be4ac6 *inst/extdata/test_vep_types.vcf
dac6b73f431e51a58577cd7b251471bc *inst/extdata/vcf_file.bcf
763f4e15adcd1d7a8f77910929e8ec7c *inst/extdata/vcf_file.bcf.csi
adb33a28d20f915355e168210e4065ea *inst/extdata/vcfpp_manifest.tsv
2f71bba87fec89bd6dcdb789d630dd90 *inst/function_catalog/functions.md
8312abb6f5ba0be775884dd48383c171 *inst/function_catalog/functions.tsv
b45cf913ccc32f69c0f2ab0765598504 *inst/function_catalog/functions.yaml
f1aae85b70eaaf1e2f3224a70da6d130 *inst/patches/duckdb_capi_strict_prototypes.patch
9637bd62ab5c89800c97e80e16dc9fa8 *inst/tinytest/test_bam_file_offset.R
2e7081709f8d8c22a6f9303f3dd2f838 *inst/tinytest/test_basic.R
bddf98220a34843a2af06faad92b3cc6 *inst/tinytest/test_bcf.R
24da8d7260821e88ca7a2baaa408f7c3 *inst/tinytest/test_cigar_utils.R
84accf7479e6923b70a9ef7c83aa3465 *inst/tinytest/test_indexes_bgzip.R
fa93c5e14ba63bd18bd96d996cb004c3 *inst/tinytest/test_integration.R
6f5e6ffc6ac3a902da521168e0c55087 *inst/tinytest/test_intervals.R
2a4f892c11b4b29ca3d53dfd2293c02f *inst/tinytest/test_liftover.R
0af50e4fa86f781c71dbe351fa97a01b *inst/tinytest/test_liftover_stress.R
9ea8663f699d47a451d369df96b0bb2f *inst/tinytest/test_munge.R
96916b69f940c4306a8c3d05e7a15aab *inst/tinytest/test_munge_threading.R
852fe88d2c674e3c6486bff5b84372a3 *inst/tinytest/test_parallel_empty_contigs.R
5d04a80edd6233b4c8669673197c0759 *inst/tinytest/test_quality_encoding.R
8ebca5e1a42bae7401aee437b4dd85c1 *inst/tinytest/test_score.R
37f352fc4e421994e12e95940b18b4be *inst/tinytest/test_seq_ops.R
9fac14a50c095ed909ecfbdbe071473b *inst/tinytest/test_type_mappings.R
138386c7d2c509812d6d0e6d91c465f2 *man/Rduckhts.Rd
065c4b741940684b86e251e86ce3e27c *man/detect_complex_types.Rd
06d65047d0511df044c75beacf2cb5bf *man/duckdb_type_mappings.Rd
af8dd95781664b6bc873e8e15ef7cbd5 *man/duckhts_append_metadata.Rd
8a77a5b9eeb51888c89595ebd3579116 *man/duckhts_bootstrap.Rd
4bb663b40daac2fe8b9a50be6c7e5bb5 *man/duckhts_build.Rd
80ab4b97cfe5807ccf0c1c301bffb42e *man/duckhts_detect_platform.Rd
4882947c2914dd44a0e5700f8f175bc9 *man/duckhts_load.Rd
80f3e1eec7d3ccd82f283667693e38f6 *man/extract_array_element.Rd
bb0ce02e05ae1199eff3b1f7388ec68a *man/extract_map_data.Rd
f450ddcf2d25d52abae1bef5877b0c7b *man/normalize_tabix_types.Rd
a10125554a142e4d8f198e3ad24a9c37 *man/rduckhts_bam.Rd
1e09c44b9e1f111d0980e0e73ff62351 *man/rduckhts_bam_index.Rd
9f7b0ec4335a21b9a8fadf8a8cdd667c *man/rduckhts_bcf.Rd
eb14599a804d4a700524bc5d49ff937c *man/rduckhts_bcf_index.Rd
a75c861dd3122c3cfa702be9d748037c *man/rduckhts_bed.Rd
14cd2f5d4c8c12f9cf2ece0f9be86e72 *man/rduckhts_bgunzip.Rd
3ff606836c2d509839d9030b61f380c2 *man/rduckhts_bgzip.Rd
9fc18ffee46e71b3654eb0c0efb0030e *man/rduckhts_detect_quality_encoding.Rd
da02eb478aa8a8b0168b262333ff7cd0 *man/rduckhts_fasta.Rd
13122b4ea7111563d2975944cc83bcb3 *man/rduckhts_fasta_index.Rd
494c0fe665dda4521aab751af7b94e33 *man/rduckhts_fasta_nuc.Rd
27b3f92969d952cc3652680fc28f823e *man/rduckhts_fastq.Rd
fa061d0da557ec9179792b9265bc25a1 *man/rduckhts_functions.Rd
8c71a427a4f6a749170489f4d8cd6677 *man/rduckhts_gff.Rd
35f5232b996a6f430d905ef39b8f133b *man/rduckhts_gtf.Rd
602008943eaceb011055b75fc4b5bdc4 *man/rduckhts_hts_header.Rd
0c1120170d947b204f719d486d718fcd *man/rduckhts_hts_index.Rd
519d9f3cc0deb539eb37902d374b6084 *man/rduckhts_hts_index_raw.Rd
e6c09c0fc3e456364854e27d0c1372e5 *man/rduckhts_hts_index_spans.Rd
3759c1e44d41d9c66bc30c206762d07e *man/rduckhts_liftover.Rd
3f853780c30e856efc841f9b37157fa0 *man/rduckhts_load.Rd
f6f0adc3dd8b2e0b21ef86f348e5629e *man/rduckhts_munge.Rd
c9ecb6f5ca18d04c7f6383a0a1809af7 *man/rduckhts_score.Rd
e7ca9871045e620c29d322cfc1c5a2a0 *man/rduckhts_tabix.Rd
e568c7f3700aa44b3b17926fcd5034ac *man/rduckhts_tabix_index.Rd
be0d53e4166c0ab7bbcbe81bdbe28092 *man/setup_hts_env.Rd
1f62058d63e11dc901404cff2cbcf300 *tests/tinytest.R
f02dfeb340e8ab518b55270472535113 *tools/append_extension_metadata.R
9a91b3f75e444f5b1f90e77d670d213c *tools/bootstrap.R
