diff --git a/Cargo.lock b/Cargo.lock index 278129e..3e9ec57 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -16,10 +16,10 @@ checksum = "e89da841a80418a9b391ebaea17f5c112ffaaa96f621d2c285b5174da76b9011" dependencies = [ "cfg-if", "const-random", - "getrandom", + "getrandom 0.2.15", "once_cell", "version_check", - "zerocopy", + "zerocopy 0.7.35", ] [[package]] @@ -317,13 +317,34 @@ version = "0.22.1" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "72b3254f16251a8381aa12e40e3c4d2f0199f8c6508fbecb9d91f575e0fbb8c6" +[[package]] +name = "base64-simd" +version = "0.8.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "339abbe78e73178762e23bea9dfd08e697eb3f3301cd4be981c0f78ba5859195" +dependencies = [ + "outref", + "vsimd", +] + [[package]] name = "bincode" -version = "1.3.3" +version = "2.0.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b1f45e9417d87227c7a56d22e471c6206462cba514c7590c09aff4cf6d1ddcad" +checksum = "36eaf5d7b090263e8150820482d5d93cd964a81e4019913c972f4edcc6edb740" dependencies = [ + "bincode_derive", "serde", + "unty", +] + +[[package]] +name = "bincode_derive" +version = "2.0.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "bf95709a440f45e986983918d0e8a1f30a9b1df04918fc828670606804ac3c09" +dependencies = [ + "virtue", ] [[package]] @@ -376,6 +397,20 @@ name = "bytemuck" version = "1.21.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "ef657dfab802224e671f5818e9a4935f9b1957ed18e58292690cc39e7a4092a3" +dependencies = [ + "bytemuck_derive", +] + +[[package]] +name = "bytemuck_derive" +version = "1.9.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "7ecc273b49b3205b83d648f0690daa588925572cc5063745bfe547fe7ec8e1a1" +dependencies = [ + "proc-macro2", + "quote", + "syn 2.0.96", +] [[package]] name = "byteorder" @@ -414,7 +449,9 @@ checksum = "1a7964611d71df112cb1730f2ee67324fcf4d0fc6606acbbe9bfe06df124637c" dependencies = [ "android-tzdata", "iana-time-zone", + "js-sys", "num-traits", + "wasm-bindgen", "windows-link", ] @@ -492,7 +529,7 @@ version = "0.1.16" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "f9d839f2a20b0aee515dc581a6172f2321f96cab76c1a38a4c584a194955390e" dependencies = [ - "getrandom", + "getrandom 0.2.15", "once_cell", "tiny-keccak", ] @@ -596,6 +633,12 @@ version = "1.0.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "34aa73646ffb006b8f5147f3dc182bd4bcb190227ce861fc4a4844bf8e3cb2c0" +[[package]] +name = "equivalent" +version = "1.0.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "877a4ace8713b0bcf2a4e7eec82529c029f1d0619886d18145fea96c3ffe5c0f" + [[package]] name = "fallible-iterator" version = "0.3.0" @@ -634,6 +677,15 @@ version = "1.0.7" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "3f9eec918d3f24069decb9af1554cad7c880e2da24a9afd88aca000531ab82c1" +[[package]] +name = "font-types" +version = "0.8.4" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "1fa6a5e5a77b5f3f7f9e32879f484aa5b3632ddfbe568a16266c904a6f32cdaf" +dependencies = [ + "bytemuck", +] + [[package]] name = "gethostname" version = "0.2.3" @@ -652,7 +704,19 @@ checksum = "c4567c8db10ae91089c99af84c68c38da3ec2f087c3f82960bcdbf3656b6f4d7" dependencies = [ "cfg-if", "libc", - "wasi", + "wasi 0.11.0+wasi-snapshot-preview1", +] + +[[package]] +name = "getrandom" +version = "0.3.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "73fea8450eea4bac3940448fb7ae50d91f034f941199fcd9d909a5a07aa455f0" +dependencies = [ + "cfg-if", + "libc", + "r-efi", + "wasi 0.14.2+wasi-0.2.4", ] [[package]] @@ -725,6 +789,23 @@ dependencies = [ "cc", ] +[[package]] +name = "identity-hash" +version = "0.1.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "dfdd7caa900436d8f13b2346fe10257e0c05c1f1f9e351f4f5d57c03bd5f45da" + +[[package]] +name = "indexmap" +version = "2.9.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "cea70ddb795996207ad57735b50c5982d8844f38ba9ee5f1aedcfb708a2aa11e" +dependencies = [ + "equivalent", + "hashbrown 0.15.2", + "serde", +] + [[package]] name = "indicatif" version = "0.17.11" @@ -753,9 +834,9 @@ checksum = "7943c866cc5cd64cbc25b2e01621d07fa8eb2a1a23160ee81ce38704e97b8ecf" [[package]] name = "itertools" -version = "0.12.1" +version = "0.14.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ba291022dbbd398a455acf126c1e341954079855bc60dfdda641363bd6922569" +checksum = "2b192c782037fadd9cfa75548310488aabdbf3d2da73885b31bd0abd03351285" dependencies = [ "either", ] @@ -912,6 +993,16 @@ dependencies = [ "regex-automata 0.1.10", ] +[[package]] +name = "matrixmultiply" +version = "0.3.9" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "9380b911e3e96d10c1f415da0876389aaf1b56759054eeb0de7df940c456ba1a" +dependencies = [ + "autocfg", + "rawpointer", +] + [[package]] name = "memchr" version = "2.7.4" @@ -936,6 +1027,50 @@ dependencies = [ "adler2", ] +[[package]] +name = "mzdata" +version = "0.52.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "2c697aaf28d7028f10a4812acf50a01cf75251ebe6088bb6ba4991bfab0b6780" +dependencies = [ + "base64-simd", + "bitflags 2.8.0", + "bytemuck", + "chrono", + "flate2", + "identity-hash", + "indexmap", + "log", + "mzpeaks", + "num-traits", + "regex", + "thiserror 2.0.12", +] + +[[package]] +name = "mzpeaks" +version = "1.0.8" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "61c80f7e47ba5ae9c9f94085156573fd9cf7d7e601633f14d68754bb2cebafce" +dependencies = [ + "num-traits", +] + +[[package]] +name = "ndarray" +version = "0.16.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "882ed72dce9365842bf196bdeedf5055305f11fc8c03dee7bb0194a6cad34841" +dependencies = [ + "matrixmultiply", + "num-complex", + "num-integer", + "num-traits", + "portable-atomic", + "portable-atomic-util", + "rawpointer", +] + [[package]] name = "nohash-hasher" version = "0.2.0" @@ -974,6 +1109,7 @@ checksum = "a5e44f723f1133c9deac646763579fdb3ac745e418f2a7af9cd0c431da1f20b9" dependencies = [ "num-integer", "num-traits", + "serde", ] [[package]] @@ -983,6 +1119,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "73f88a1307638156682bada9d7604135552957b7818057dcef22705b4d509495" dependencies = [ "num-traits", + "serde", ] [[package]] @@ -1020,6 +1157,7 @@ dependencies = [ "num-bigint", "num-integer", "num-traits", + "serde", ] [[package]] @@ -1055,15 +1193,21 @@ dependencies = [ [[package]] name = "ordered-float" -version = "4.6.0" +version = "5.0.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7bb71e1b3fa6ca1c61f383464aaf2bb0e2f8e772a1f01d486832464de363b951" +checksum = "e2c1f9f56e534ac6a9b8a4600bdf0f530fb393b5f393e7b4d03489c3cf0c3f01" dependencies = [ "num-traits", - "rand", + "rand 0.8.5", "serde", ] +[[package]] +name = "outref" +version = "0.5.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "1a80800c0488c3a21695ea981a54918fbb37abf04f4d0720c453632255e2ff0e" + [[package]] name = "overload" version = "0.1.1" @@ -1183,6 +1327,15 @@ version = "1.10.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "280dc24453071f1b63954171985a0b0d30058d287960968b9b2aca264c8d4ee6" +[[package]] +name = "portable-atomic-util" +version = "0.2.4" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "d8a2f0d8d040d7848a709caf78912debcc3f33ee4b3cac47d73d1e1069e83507" +dependencies = [ + "portable-atomic", +] + [[package]] name = "powerfmt" version = "0.2.0" @@ -1195,7 +1348,7 @@ version = "0.2.20" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "77957b295656769bb8ad2b6a6b09d897d94f05c41b069aede1fcdaa675eaea04" dependencies = [ - "zerocopy", + "zerocopy 0.7.35", ] [[package]] @@ -1248,6 +1401,12 @@ dependencies = [ "proc-macro2", ] +[[package]] +name = "r-efi" +version = "5.2.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "74765f6d916ee2faa39bc8e68e4f3ed8949b48cccdac59983d287a7cb71ce9c5" + [[package]] name = "rand" version = "0.8.5" @@ -1255,11 +1414,22 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "34af8d1a0e25924bc5b7c43c079c942339d8f0a8b57c39049bef581b46327404" dependencies = [ "libc", - "rand_chacha", - "rand_core", + "rand_chacha 0.3.1", + "rand_core 0.6.4", "serde", ] +[[package]] +name = "rand" +version = "0.9.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "3779b94aeb87e8bd4e834cee3650289ee9e0d5677f976ecdb6d219e5f4f6cd94" +dependencies = [ + "rand_chacha 0.9.0", + "rand_core 0.9.3", + "zerocopy 0.8.24", +] + [[package]] name = "rand_chacha" version = "0.3.1" @@ -1267,7 +1437,17 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "e6c10a63a0fa32252be49d21e7709d4d4baf8d231c2dbce1eaa8141b9b127d88" dependencies = [ "ppv-lite86", - "rand_core", + "rand_core 0.6.4", +] + +[[package]] +name = "rand_chacha" +version = "0.9.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "d3022b5f1df60f26e1ffddd6c66e8aa15de382ae63b3a0c1bfc0e4d3e3f325cb" +dependencies = [ + "ppv-lite86", + "rand_core 0.9.3", ] [[package]] @@ -1276,16 +1456,31 @@ version = "0.6.4" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "ec0be4795e2f6a28069bec0b5ff3e2ac9bafc99e6a9a7dc3547996c5c816922c" dependencies = [ - "getrandom", + "getrandom 0.2.15", "serde", ] +[[package]] +name = "rand_core" +version = "0.9.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "99d9a13982dcf210057a8a78572b2217b667c3beacbf3a0d8b454f6f82837d38" +dependencies = [ + "getrandom 0.3.2", +] + [[package]] name = "random" version = "0.13.2" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "474c42c904f04dfe2a595a02f71e1a0e5e92ffb5761cc9a4c02140b93b8dd504" +[[package]] +name = "rawpointer" +version = "0.2.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "60a357793950651c4ed0f3f52338f53b2f809f32d83a07f72909fa13e4c6c1e3" + [[package]] name = "rayon" version = "1.10.0" @@ -1306,6 +1501,16 @@ dependencies = [ "crossbeam-utils", ] +[[package]] +name = "read-fonts" +version = "0.25.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "f6f9e8a4f503e5c8750e4cd3b32a4e090035c46374b305a15c70bad833dca05f" +dependencies = [ + "bytemuck", + "font-types", +] + [[package]] name = "regex" version = "1.11.1" @@ -1381,20 +1586,26 @@ checksum = "f7c45b9784283f1b2e7fb61b42047c2fd678ef0960d4f6f1eba131594cc369d4" [[package]] name = "rustyms" -version = "0.8.3" +version = "0.10.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4831e9fe077e1d905b993838753820e0d70f81a20bf86f8837374c0823523353" +checksum = "2c4c4248bb25b2e7911154def35d8129e248c109ecd1ddf85f2ad3000a8ee823" dependencies = [ "bincode", "flate2", "itertools", - "ordered-float 4.6.0", + "mzdata", + "ndarray", + "ordered-float 5.0.0", "probability", + "rand 0.9.0", "rayon", "regex", "serde", "similar", + "swash", + "thin-vec", "uom", + "zeno", ] [[package]] @@ -1470,9 +1681,19 @@ checksum = "e3a9fe34e3e7a50316060351f37187a3f546bce95496156754b601a5fa71b76e" [[package]] name = "similar" -version = "2.6.0" +version = "2.7.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "bbbb5d9659141646ae647b42fe094daf6c6192d1620870b449d9557f748b2daa" + +[[package]] +name = "skrifa" +version = "0.26.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "1de1d4f81173b03af4c0cbed3c898f6bff5b870e4a7f5d6f4057d62a7a4b686e" +checksum = "8cc1aa86c26dbb1b63875a7180aa0819709b33348eb5b1491e4321fae388179d" +dependencies = [ + "bytemuck", + "read-fonts", +] [[package]] name = "smallvec" @@ -1507,6 +1728,17 @@ version = "0.11.1" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "7da8b5736845d9f2fcb837ea5d9e2628564b3b043a70948a3f0b778838c5fb4f" +[[package]] +name = "swash" +version = "0.2.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "fae9a562c7b46107d9c78cd78b75bbe1e991c16734c0aee8ff0ee711fb8b620a" +dependencies = [ + "skrifa", + "yazi", + "zeno", +] + [[package]] name = "syn" version = "1.0.109" @@ -1552,13 +1784,31 @@ dependencies = [ "syn 1.0.109", ] +[[package]] +name = "thin-vec" +version = "0.2.14" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "144f754d318415ac792f9d69fc87abbbfc043ce2ef041c60f16ad828f638717d" +dependencies = [ + "serde", +] + [[package]] name = "thiserror" version = "1.0.69" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "b6aaf5339b578ea85b50e080feb250a3e8ae8cfcdff9a461c9ec2904bc923f52" dependencies = [ - "thiserror-impl", + "thiserror-impl 1.0.69", +] + +[[package]] +name = "thiserror" +version = "2.0.12" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "567b8a2dae586314f7be2a752ec7474332959c6460e02bde30d702a66d488708" +dependencies = [ + "thiserror-impl 2.0.12", ] [[package]] @@ -1572,6 +1822,17 @@ dependencies = [ "syn 2.0.96", ] +[[package]] +name = "thiserror-impl" +version = "2.0.12" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "7f7cf42b4507d8ea322120659672cf1b9dbb93f8f2d4ecfd6e51350ff5b17a1d" +dependencies = [ + "proc-macro2", + "quote", + "syn 2.0.96", +] + [[package]] name = "thread_local" version = "1.1.8" @@ -1631,8 +1892,8 @@ dependencies = [ "clap", "indicatif", "nohash-hasher", - "rand", - "rand_chacha", + "rand 0.8.5", + "rand_chacha 0.3.1", "rayon", "serde", "serde_json", @@ -1658,7 +1919,7 @@ dependencies = [ "rusqlite", "serde", "serde_json", - "thiserror", + "thiserror 1.0.69", "zstd", ] @@ -1857,12 +2118,20 @@ version = "0.2.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "1fc81956842c57dac11422a97c3b8195a1ff727f06e85c84ed2e8aa277c9a0fd" +[[package]] +name = "unty" +version = "0.0.4" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "6d49784317cd0d1ee7ec5c716dd598ec5b4483ea832a2dced265471cc0f690ae" + [[package]] name = "uom" -version = "0.35.0" +version = "0.36.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8362194c7a9845a7a7f3562173d6e1da3f24f7132018cb78fe77a5b4474187b2" +checksum = "ffd36e5350a65d112584053ee91843955826bf9e56ec0d1351214e01f6d7cd9c" dependencies = [ + "num-bigint", + "num-complex", "num-rational", "num-traits", "serde", @@ -1893,12 +2162,33 @@ version = "0.9.5" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "0b928f33d975fc6ad9f86c8f283853ad26bdd5b10b7f1542aa2fa15e2289105a" +[[package]] +name = "virtue" +version = "0.0.18" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "051eb1abcf10076295e815102942cc58f9d5e3b4560e46e53c21e8ff6f3af7b1" + +[[package]] +name = "vsimd" +version = "0.8.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "5c3082ca00d5a5ef149bb8b555a72ae84c9c59f7250f013ac822ac2e49b19c64" + [[package]] name = "wasi" version = "0.11.0+wasi-snapshot-preview1" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423" +[[package]] +name = "wasi" +version = "0.14.2+wasi-0.2.4" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "9683f9a5a998d873c0d21fcbe3c083009670149a8fab228644b8bd36b2c48cb3" +dependencies = [ + "wit-bindgen-rt", +] + [[package]] name = "wasm-bindgen" version = "0.2.100" @@ -2077,6 +2367,27 @@ version = "0.52.6" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec" +[[package]] +name = "wit-bindgen-rt" +version = "0.39.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "6f42320e61fe2cfd34354ecb597f86f413484a798ba44a8ca1165c58d42da6c1" +dependencies = [ + "bitflags 2.8.0", +] + +[[package]] +name = "yazi" +version = "0.2.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "e01738255b5a16e78bbb83e7fbba0a1e7dd506905cfc53f4622d89015a03fbb5" + +[[package]] +name = "zeno" +version = "0.3.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "cc0de2315dc13d00e5df3cd6b8d2124a6eaec6a2d4b6a1c5f37b7efad17fcc17" + [[package]] name = "zerocopy" version = "0.7.35" @@ -2084,7 +2395,16 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "1b9b4fd18abc82b8136838da5d50bae7bdea537c574d8dc1a34ed098d6c166f0" dependencies = [ "byteorder", - "zerocopy-derive", + "zerocopy-derive 0.7.35", +] + +[[package]] +name = "zerocopy" +version = "0.8.24" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "2586fea28e186957ef732a5f8b3be2da217d65c5969d4b1e17f973ebbe876879" +dependencies = [ + "zerocopy-derive 0.8.24", ] [[package]] @@ -2098,6 +2418,17 @@ dependencies = [ "syn 2.0.96", ] +[[package]] +name = "zerocopy-derive" +version = "0.8.24" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "a996a8f63c5c4448cd959ac1bab0aaa3306ccfd060472f85943ee0750f0169be" +dependencies = [ + "proc-macro2", + "quote", + "syn 2.0.96", +] + [[package]] name = "zstd" version = "0.13.2" diff --git a/rust/timsseek/Cargo.toml b/rust/timsseek/Cargo.toml index b02493c..9a16938 100644 --- a/rust/timsseek/Cargo.toml +++ b/rust/timsseek/Cargo.toml @@ -5,7 +5,7 @@ edition = "2021" license = "Apache-2.0" [dependencies] -rustyms = "0.8.3" +rustyms = "0.10.0" timsquery = { path = "../timsquery" } regex = "1.10.6" csv = "1.3.0"