diff --git a/Cargo.lock b/Cargo.lock index bdfd5da..5bcf011 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -96,7 +96,7 @@ dependencies = [ "rand_xoshiro", "rayon", "serde", - "thiserror", + "thiserror 1.0.65", ] [[package]] @@ -111,7 +111,7 @@ dependencies = [ "num-integer", "num-traits", "rand", - "thiserror", + "thiserror 1.0.65", ] [[package]] @@ -154,6 +154,26 @@ dependencies = [ "serde", ] +[[package]] +name = "bindgen" +version = "0.69.5" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "271383c67ccabffb7381723dea0672a673f292304fcb45c01cc648c7a8d58088" +dependencies = [ + "bitflags", + "cexpr", + "clang-sys", + "itertools 0.11.0", + "lazy_static", + "lazycell", + "proc-macro2", + "quote", + "regex", + "rustc-hash", + "shlex", + "syn 2.0.90", +] + [[package]] name = "bio" version = "1.6.0" @@ -188,7 +208,7 @@ dependencies = [ "statrs 0.16.1", "strum", "strum_macros 0.25.3", - "thiserror", + "thiserror 1.0.65", "triple_accel", "vec_map", ] @@ -203,7 +223,7 @@ dependencies = [ "lazy_static", "regex", "strum_macros 0.26.4", - "thiserror", + "thiserror 1.0.65", ] [[package]] @@ -277,12 +297,32 @@ dependencies = [ "shlex", ] +[[package]] +name = "cexpr" +version = "0.6.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "6fac387a98bb7c37292057cffc56d62ecb629900026402633ae9160df93a8766" +dependencies = [ + "nom", +] + [[package]] name = "cfg-if" version = "1.0.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd" +[[package]] +name = "clang-sys" +version = "1.8.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "0b023947811758c97c59bf9d1c188fd619ad4718dcaa767947df1cadb14f39f4" +dependencies = [ + "glob", + "libc", + "libloading", +] + [[package]] name = "clap" version = "4.5.20" @@ -314,7 +354,7 @@ dependencies = [ "heck 0.5.0", "proc-macro2", "quote", - "syn 2.0.85", + "syn 2.0.90", ] [[package]] @@ -395,9 +435,9 @@ dependencies = [ [[package]] name = "curl-sys" -version = "0.4.77+curl-8.10.1" +version = "0.4.78+curl-8.11.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f469e8a5991f277a208224f6c7ad72ecb5f986e36d09ae1f2c1bb9259478a480" +checksum = "8eec768341c5c7789611ae51cf6c459099f22e64a5d5d0ce4892434e33821eaf" dependencies = [ "cc", "libc", @@ -425,24 +465,24 @@ dependencies = [ [[package]] name = "derive-new" -version = "0.5.9" +version = "0.6.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "3418329ca0ad70234b9735dc4ceed10af4df60eff9c8e7b06cb5e520d92c3535" +checksum = "d150dea618e920167e5973d70ae6ece4385b7164e0d799fe7c122dd0a5d912ad" dependencies = [ "proc-macro2", "quote", - "syn 1.0.109", + "syn 2.0.90", ] [[package]] name = "derive-new" -version = "0.6.0" +version = "0.7.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "d150dea618e920167e5973d70ae6ece4385b7164e0d799fe7c122dd0a5d912ad" +checksum = "2cdc8d50f426189eef89dac62fabfa0abb27d5cc008f25bf4156a0203325becc" dependencies = [ "proc-macro2", "quote", - "syn 2.0.85", + "syn 2.0.90", ] [[package]] @@ -495,7 +535,7 @@ checksum = "f282cfdfe92516eb26c2af8589c274c7c17681f5ecc03c18255fe741c6aa64eb" dependencies = [ "proc-macro2", "quote", - "syn 2.0.85", + "syn 2.0.90", ] [[package]] @@ -598,10 +638,11 @@ checksum = "fbf6a919d6cf397374f7dfeeea91d974c7c0a7221d0d0f4f20d859d329e53fcc" [[package]] name = "hts-sys" -version = "2.1.4" +version = "2.2.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e9f348d14cb4e50444e39fcd6b00302fe2ed2bc88094142f6278391d349a386d" +checksum = "e38d7f1c121cd22aa214cb4dadd4277dc5447391eac518b899b29ba6356fbbb2" dependencies = [ + "bindgen", "bzip2-sys", "cc", "curl-sys", @@ -722,12 +763,28 @@ version = "1.5.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "bbd2bcb4c963f2ddae06a2efc7e9f3591312473c50c6685e1f298068316e66fe" +[[package]] +name = "lazycell" +version = "1.3.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "830d08ce1d1d941e6b30645f1a0eb5643013d835ce3779a5fc208261dbe10f55" + [[package]] name = "libc" version = "0.2.161" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "8e9489c2807c139ffd9c1794f4af0ebe86a828db53ecdc7fea2111d0fed085d1" +[[package]] +name = "libloading" +version = "0.8.6" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "fc2f4eb4bc735547cfed7c0a4922cbd04a4655978c09b54f1f7b228750664c34" +dependencies = [ + "cfg-if", + "windows-targets", +] + [[package]] name = "libm" version = "0.2.8" @@ -796,6 +853,12 @@ version = "2.7.4" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "78ca9ab1a0babb1e7d5695e3530886289c18cf2f87ec19a575a0abdce112e3a3" +[[package]] +name = "minimal-lexical" +version = "0.2.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "68354c5c6bd36d73ff3feceb05efa59b6acb7626617f4962be322a825e61f79a" + [[package]] name = "multimap" version = "0.9.1" @@ -860,7 +923,7 @@ checksum = "254a5372af8fc138e36684761d3c0cdb758a4410e938babcff1c860ce14ddbfc" dependencies = [ "proc-macro2", "quote", - "syn 2.0.85", + "syn 2.0.90", ] [[package]] @@ -921,6 +984,16 @@ dependencies = [ "num-traits", ] +[[package]] +name = "nom" +version = "7.1.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "d273983c5a657a70a3e8f2a01329822f3b8c8172b73826411a55751e404a0a4a" +dependencies = [ + "memchr", + "minimal-lexical", +] + [[package]] name = "num-complex" version = "0.4.6" @@ -1047,9 +1120,9 @@ dependencies = [ [[package]] name = "proc-macro2" -version = "1.0.89" +version = "1.0.92" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f139b0662de085916d1fb67d2b4169d1addddda1919e696f3252b740b629986e" +checksum = "37d3544b3f2748c54e147655edb5025752e2303145b5aefb3c3ea2c78b973bb0" dependencies = [ "unicode-ident", ] @@ -1153,7 +1226,7 @@ checksum = "ba009ff324d1fc1b900bd1fdb31564febe58a8ccc8a6fdbb93b543d33b13ca43" dependencies = [ "getrandom", "libredox", - "thiserror", + "thiserror 1.0.65", ] [[package]] @@ -1187,14 +1260,14 @@ checksum = "2b15c43186be67a4fd63bee50d0303afffcef381492ebe2c5d87f324e1b8815c" [[package]] name = "rust-htslib" -version = "0.46.0" +version = "0.49.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "aec6f9ca4601beb4ae75ff8c99144dd15de5a873f6adf058da299962c760968e" +checksum = "115ae57b89deb942275566eca8c31da053d8df0d8bda12e50c4c4aa994877068" dependencies = [ "bio-types", "byteorder", "custom_derive", - "derive-new 0.5.9", + "derive-new 0.7.0", "hts-sys", "ieee754", "lazy_static", @@ -1203,10 +1276,16 @@ dependencies = [ "linear-map", "newtype_derive", "regex", - "thiserror", + "thiserror 2.0.3", "url", ] +[[package]] +name = "rustc-hash" +version = "1.1.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "08d43f7aa6b08d49f382cde6a7982047c3426db949b1424bc4b7ec9ae12c6ce2" + [[package]] name = "rustc_version" version = "0.1.7" @@ -1292,7 +1371,7 @@ checksum = "7e85ad2009c50b58e87caa8cd6dac16bdf511bbfb7af6c33df902396aa480fa5" dependencies = [ "proc-macro2", "quote", - "syn 2.0.85", + "syn 2.0.90", ] [[package]] @@ -1439,7 +1518,7 @@ dependencies = [ "proc-macro2", "quote", "rustversion", - "syn 2.0.85", + "syn 2.0.90", ] [[package]] @@ -1452,7 +1531,7 @@ dependencies = [ "proc-macro2", "quote", "rustversion", - "syn 2.0.85", + "syn 2.0.90", ] [[package]] @@ -1468,9 +1547,9 @@ dependencies = [ [[package]] name = "syn" -version = "2.0.85" +version = "2.0.90" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "5023162dfcd14ef8f32034d8bcd4cc5ddc61ef7a247c024a33e24e1f24d21b56" +checksum = "919d3b74a5dd0ccd15aeb8f93e7006bd9e14c295087c9896a110f490752bcf31" dependencies = [ "proc-macro2", "quote", @@ -1500,7 +1579,16 @@ version = "1.0.65" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "5d11abd9594d9b38965ef50805c5e469ca9cc6f197f883f717e0269a3057b3d5" dependencies = [ - "thiserror-impl", + "thiserror-impl 1.0.65", +] + +[[package]] +name = "thiserror" +version = "2.0.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "c006c85c7651b3cf2ada4584faa36773bd07bac24acfb39f3c431b36d7e667aa" +dependencies = [ + "thiserror-impl 2.0.3", ] [[package]] @@ -1511,7 +1599,18 @@ checksum = "ae71770322cbd277e69d762a16c444af02aa0575ac0d174f0b9562d3b37f8602" dependencies = [ "proc-macro2", "quote", - "syn 2.0.85", + "syn 2.0.90", +] + +[[package]] +name = "thiserror-impl" +version = "2.0.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "f077553d607adc1caf65430528a576c757a71ed73944b66ebb58ef2bbd243568" +dependencies = [ + "proc-macro2", + "quote", + "syn 2.0.90", ] [[package]] @@ -1773,5 +1872,5 @@ checksum = "fa4f8080344d4671fb4e831a13ad1e68092748387dfc4f55e356242fae12ce3e" dependencies = [ "proc-macro2", "quote", - "syn 2.0.85", + "syn 2.0.90", ] diff --git a/Cargo.toml b/Cargo.toml index 028978c..cdc42b6 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -28,7 +28,7 @@ ndarray-ndimage = "0.4.0" rand = { version = "0.8.5", features = ["small_rng"] } rand_xoshiro = "0.6.0" rayon = "1.8.1" -rust-htslib = "0.46.0" +rust-htslib = "0.49.0" serde = "1.0.197" serde_json = "1.0.114" slog = "2.7.0"