From f8672de2e23703fdbe324746410dbf9549dfc8ba Mon Sep 17 00:00:00 2001 From: Sebastian Schmidt Date: Wed, 25 Oct 2023 14:13:03 +0300 Subject: [PATCH] Update dependencies. --- Cargo.lock | 492 ++++++++++++++++++-------------------- Cargo.toml | 10 +- src/bin.rs | 30 +-- src/implementation/mod.rs | 8 +- 4 files changed, 256 insertions(+), 284 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 04209da..34a6109 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -4,9 +4,9 @@ version = 3 [[package]] name = "addr2line" -version = "0.19.0" +version = "0.21.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a76fd60b23679b7d19bd066031410fb7e458ccc5e958eb5c325888ce4baedc97" +checksum = "8a30b2e23b9e17a9f90641c7ab1549cd9b44f296d3ccbf309d2863cfe398a0cb" dependencies = [ "gimli", ] @@ -19,56 +19,56 @@ checksum = "f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe" [[package]] name = "ahash" -version = "0.8.3" +version = "0.8.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2c99f64d1e06488f620f932677e24bc6e2897582980441ae90a671415bd7ec2f" +checksum = "91429305e9f0a25f6205c5b8e0d2db09e0708a7a6df0f42212bb56c32c8ac97a" dependencies = [ "cfg-if", "once_cell", "version_check", + "zerocopy", ] [[package]] name = "aho-corasick" -version = "1.0.2" +version = "1.1.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "43f6cb1bf222025340178f382c426f13757b2960e89779dfcb319c32542a5a41" +checksum = "b2969dcb958b36655471fc61f7e416fa76033bdd4bfed0678d8fee1e2d07a1f0" dependencies = [ "memchr", ] [[package]] name = "allocator-api2" -version = "0.2.15" +version = "0.2.16" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "56fc6cf8dc8c4158eed8649f9b8b0ea1518eb62b544fe9490d66fa0b349eafe9" +checksum = "0942ffc6dcaadf03badf6e6a2d0228460359d5e34b57ccdc720b7382dfbd5ec5" [[package]] name = "anstream" -version = "0.3.2" +version = "0.6.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "0ca84f3628370c59db74ee214b3263d58f9aadd9b4fe7e711fd87dc452b7f163" +checksum = "2ab91ebe16eb252986481c5b62f6098f3b698a45e34b5b98200cf20dd2484a44" dependencies = [ "anstyle", "anstyle-parse", "anstyle-query", "anstyle-wincon", "colorchoice", - "is-terminal", "utf8parse", ] [[package]] name = "anstyle" -version = "1.0.0" +version = "1.0.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "41ed9a86bf92ae6580e0a31281f65a1b1d867c0cc68d5346e2ae128dddfa6a7d" +checksum = "7079075b41f533b8c61d2a4d073c4676e1f8b249ff94a393b0595db304e0dd87" [[package]] name = "anstyle-parse" -version = "0.2.0" +version = "0.2.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e765fd216e48e067936442276d1d57399e37bce53c264d6fefbe298080cb57ee" +checksum = "317b9a89c1868f5ea6ff1d9539a69f45dffc21ce321ac1fd1160dfa48c8e2140" dependencies = [ "utf8parse", ] @@ -84,9 +84,9 @@ dependencies = [ [[package]] name = "anstyle-wincon" -version = "1.0.1" +version = "3.0.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "180abfa45703aebe0093f79badacc01b8fd4ea2e35118747e5811127f926e188" +checksum = "f0699d10d2f4d628a98ee7b57b289abbc98ff3bad977cb3152709d4bf2330628" dependencies = [ "anstyle", "windows-sys", @@ -94,9 +94,9 @@ dependencies = [ [[package]] name = "anyhow" -version = "1.0.71" +version = "1.0.75" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "9c7d0618f0e0b7e8ff11427422b64564d5fb0be1940354bfe2e0529b18a9d9b8" +checksum = "a4668cab20f66d8d020e1fbc0ebe47217433c1b6c8f2040faf858554e394ace6" [[package]] name = "approx" @@ -121,24 +121,24 @@ checksum = "d468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa" [[package]] name = "backtrace" -version = "0.3.67" +version = "0.3.69" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "233d376d6d185f2a3093e58f283f60f880315b6c60075b01f36b3b85154564ca" +checksum = "2089b7e3f35b9dd2d0ed921ead4f6d318c27680d4a5bd167b3ee120edb105837" dependencies = [ "addr2line", "cc", "cfg-if", "libc", - "miniz_oxide 0.6.2", + "miniz_oxide", "object", "rustc-demangle", ] [[package]] name = "bigraph" -version = "3.0.0" +version = "5.0.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "fcee2058e309fb46c712c35377e4bea4db425530209dcbbafc44ead44b712dfe" +checksum = "acb6431ec45b2238d49e578ae6d71498dc5f9b6c007e0e0574f70fb60b09b912" dependencies = [ "bitvector", "traitgraph", @@ -147,9 +147,9 @@ dependencies = [ [[package]] name = "bio" -version = "1.3.0" +version = "1.4.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b55f42d2f1632ae6453f58124d75f3f7e32ba2a265188a920ae57a3f3cf08cbe" +checksum = "ea643e25059ce02b94e8f6eb4e902d160baa6d0beb91834ed971dd5a880c02ba" dependencies = [ "anyhow", "approx", @@ -159,6 +159,7 @@ dependencies = [ "bytecount", "csv", "custom_derive", + "editdistancek", "enum-map", "fxhash", "getset", @@ -186,9 +187,9 @@ dependencies = [ [[package]] name = "bio-types" -version = "1.0.0" +version = "1.0.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c915bf6c578d40e1e497f8c571a4514bc89c3195cec2abb8be6dd5500405c752" +checksum = "9d45749b87f21808051025e9bf714d14ff4627f9d8ca967eade6946ea769aa4a" dependencies = [ "derive-new", "lazy_static", @@ -212,12 +213,6 @@ version = "0.6.3" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "349f9b6a179ed607305526ca489b34ad0a41aed5f7980fa90eb03160b69598fb" -[[package]] -name = "bitflags" -version = "1.3.2" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a" - [[package]] name = "bitvec" version = "1.0.1" @@ -248,27 +243,30 @@ dependencies = [ [[package]] name = "bytecount" -version = "0.6.3" +version = "0.6.7" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2c676a478f63e9fa2dd5368a42f28bba0d6c560b775f38583c8bbaa7fcd67c9c" +checksum = "e1e5f035d16fc623ae5f74981db80a439803888314e3a555fd6f04acd51a3205" [[package]] name = "bytemuck" -version = "1.13.1" +version = "1.14.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "17febce684fd15d89027105661fec94afb475cb995fbc59d2865198446ba2eea" +checksum = "374d28ec25809ee0e23827c2ab573d729e293f281dfe393500e7ad618baa61c6" [[package]] name = "byteorder" -version = "1.4.3" +version = "1.5.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "14c189c53d098945499cdfa7ecc63567cf3886b3332b312a5b4585d8d3a6a610" +checksum = "1fd0f2584146f6f2ef48085050886acf353beff7305ebd1ae69500e27c67f64b" [[package]] name = "cc" -version = "1.0.79" +version = "1.0.83" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "50d30906286121d95be3d479533b458f87493b30a4b5f79a607db8f5d11aa91f" +checksum = "f1174fb0b6ec23863f8b971027804a42614e347eafb0a95bf0b12cdae21fc4d0" +dependencies = [ + "libc", +] [[package]] name = "cfg-if" @@ -278,46 +276,43 @@ checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd" [[package]] name = "clap" -version = "4.3.4" +version = "4.4.7" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "80672091db20273a15cf9fdd4e47ed43b5091ec9841bf4c6145c9dfbbcae09ed" +checksum = "ac495e00dcec98c83465d5ad66c5c4fabd652fd6686e7c6269b117e729a6f17b" dependencies = [ "clap_builder", "clap_derive", - "once_cell", ] [[package]] name = "clap_builder" -version = "4.3.4" +version = "4.4.7" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c1458a1df40e1e2afebb7ab60ce55c1fa8f431146205aa5f4887e0b111c27636" +checksum = "c77ed9a32a62e6ca27175d00d29d05ca32e396ea1eb5fb01d8256b669cec7663" dependencies = [ "anstream", "anstyle", - "bitflags", "clap_lex", - "once_cell", "strsim", ] [[package]] name = "clap_derive" -version = "4.3.2" +version = "4.4.7" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b8cd2b2a819ad6eec39e8f1d6b53001af1e5469f8c177579cdaeb313115b825f" +checksum = "cf9804afaaf59a91e75b022a30fb7229a7901f60c755489cc61c9b423b836442" dependencies = [ "heck", "proc-macro2", "quote", - "syn 2.0.18", + "syn 2.0.38", ] [[package]] name = "clap_lex" -version = "0.5.0" +version = "0.6.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2da6da31387c7e4ef160ffab6d5e7f00c42626fe39aea70a7b0f1773f7dd6c1b" +checksum = "702fc72eb24e5a1e48ce58027a675bc24edd52096d5397d4aea7c6dd9eca0bd1" [[package]] name = "colorchoice" @@ -327,14 +322,15 @@ checksum = "acbf1af155f9b9ef647e42cdc158db4b64a1b61f743629225fde6f3e0be2a7c7" [[package]] name = "compact-genome" -version = "1.3.1" +version = "2.1.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e1db9ae4fa1eaca78521c34cd0900972b260e36e3afb4d9cbf87ed0ef576a55d" +checksum = "7b9bf5dfd6642561b3d70b4c9657ea8c0c2a5f072fb94e4bce7b230e929bd7e2" dependencies = [ "bitvec", "itertools", "lazy_static", "ref-cast", + "thiserror", "traitsequence", ] @@ -416,9 +412,9 @@ dependencies = [ [[package]] name = "csv" -version = "1.2.2" +version = "1.3.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "626ae34994d3d8d668f4269922248239db4ae42d538b14c398b74a52208e8086" +checksum = "ac574ff4d437a7b5ad237ef331c17ccca63c46479e5b5453eb8e10bb99a759fe" dependencies = [ "csv-core", "itoa", @@ -428,9 +424,9 @@ dependencies = [ [[package]] name = "csv-core" -version = "0.1.10" +version = "0.1.11" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2b2466559f260f48ad25fe6317b3c8dac77b5bdb5763ac7d9d6103530663bc90" +checksum = "5efa2b3d7902f4b634a20cae3c9c4e6209dc4779feb6863329607560143efa70" dependencies = [ "memchr", ] @@ -441,6 +437,15 @@ version = "0.1.7" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "ef8ae57c4978a2acd8b869ce6b9ca1dfe817bff704c220209fdef2c0b75a01b9" +[[package]] +name = "deranged" +version = "0.3.9" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "0f32d04922c60427da6f9fef14d042d9edddef64cb9d4ce0d64d0685fbeb1fd3" +dependencies = [ + "powerfmt", +] + [[package]] name = "derive-new" version = "0.5.9" @@ -458,11 +463,17 @@ version = "0.4.2" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "4ccbbca7d6a247007ca2535c616d4bb4a5fcad176ef0218671f96b88c52c3d34" +[[package]] +name = "editdistancek" +version = "1.0.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "3e02df23d5b1c6f9e69fa603b890378123b93073df998a21e6e33b9db0a32613" + [[package]] name = "either" -version = "1.8.1" +version = "1.9.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7fcaabb2fef8c910e7f4c7ce9f67a1283a1715879a7c230ca9d6d1ae31f16d91" +checksum = "a26ae43d7bcc3b814de94796a5e736d4029efb0ee900c12e2d54c993ad1a1e07" [[package]] name = "enum-map" @@ -485,25 +496,10 @@ dependencies = [ ] [[package]] -name = "errno" -version = "0.3.1" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4bcfec3a70f97c962c307b2d2c56e358cf1d00b558d74262b5f929ee8cc7e73a" -dependencies = [ - "errno-dragonfly", - "libc", - "windows-sys", -] - -[[package]] -name = "errno-dragonfly" -version = "0.1.2" +name = "equivalent" +version = "1.0.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "aa68f1b12764fab894d2755d2518754e71b4fd80ecfb822714a1206c2aab39bf" -dependencies = [ - "cc", - "libc", -] +checksum = "5443807d6dff69373d433ab9ef5378ad8df50ca6298caf15de6e52e24aaf54d5" [[package]] name = "error-chain" @@ -529,12 +525,12 @@ checksum = "0ce7134b9999ecaf8bcd65542e436736ef32ddca1b3e06094cb6ec5755203b80" [[package]] name = "flate2" -version = "1.0.26" +version = "1.0.28" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "3b9429470923de8e8cbd4d2dc513535400b4b3fef0319fb5c4e1f520a7bef743" +checksum = "46303f565772937ffe1d394a4fac6f411c6013172fadde9dcdb1e147a086940e" dependencies = [ "crc32fast", - "miniz_oxide 0.7.1", + "miniz_oxide", ] [[package]] @@ -554,9 +550,9 @@ dependencies = [ [[package]] name = "genome-graph" -version = "6.0.0" +version = "8.0.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "278775bab4575622649800057b39fabb2ce0db885ba3af625c2885ea4e4c7581" +checksum = "de5c5b44a78e779835b77017dfa878343643f626ec9ccee967520eceae6115e7" dependencies = [ "anyhow", "bigraph", @@ -595,21 +591,15 @@ dependencies = [ [[package]] name = "gimli" -version = "0.27.3" +version = "0.28.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b6c80984affa11d98d1b88b66ac8853f143217b399d3c74116778ff8fdb4ed2e" +checksum = "6fb8d784f27acf97159b40fc4db5ecd8aa23b9ad5ef69cdd136d3bc80665f0c0" [[package]] name = "hashbrown" -version = "0.12.3" +version = "0.14.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8a9ee70c43aaf417c914396645a0fa852624801b24ebb7ae78fe8272889ac888" - -[[package]] -name = "hashbrown" -version = "0.14.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2c6201b9ff9fd90a5a3bac2e56a830d0caa509576f0e503818ee82c181b3437a" +checksum = "f93e7192158dbcda357bdec5fb5788eebf8bbac027f3f33e719d29135ae84156" dependencies = [ "ahash", "allocator-api2", @@ -621,50 +611,21 @@ version = "0.4.1" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8" -[[package]] -name = "hermit-abi" -version = "0.3.1" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "fed44880c466736ef9a5c5b5facefb5ed0785676d0c02d612db14e54f0d84286" - [[package]] name = "indexmap" -version = "1.9.3" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "bd070e393353796e801d209ad339e89596eb4c8d430d18ede6a1cced8fafbd99" -dependencies = [ - "autocfg", - "hashbrown 0.12.3", -] - -[[package]] -name = "io-lifetimes" -version = "1.0.11" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "eae7b9aee968036d54dce06cebaefd919e4472e753296daccd6d344e3e2df0c2" -dependencies = [ - "hermit-abi", - "libc", - "windows-sys", -] - -[[package]] -name = "is-terminal" -version = "0.4.7" +version = "2.0.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "adcf93614601c8129ddf72e2d5633df827ba6551541c6d8c59520a371475be1f" +checksum = "8adf3ddd720272c6ea8bf59463c04e0f93d0bbf7c5439b691bca2987e0270897" dependencies = [ - "hermit-abi", - "io-lifetimes", - "rustix", - "windows-sys", + "equivalent", + "hashbrown", ] [[package]] name = "itertools" -version = "0.10.5" +version = "0.11.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b0fd2260e829bddf4cb6ea802289de2f86d6a7a690192fbe91b3f46e0f2c8473" +checksum = "b1c173a5686ce8bfa551b3563d0c2170bf24ca44da99c7ca4bfdab5418c3fe57" dependencies = [ "either", ] @@ -680,9 +641,9 @@ dependencies = [ [[package]] name = "itoa" -version = "1.0.6" +version = "1.0.9" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "453ad9f582a441959e5f0d088b02ce04cfe8d51a8eaf077f12ac6d3e94164ca6" +checksum = "af150ab688ff2122fcef229be89cb50dd66af9e01a4ff320cc137eecc9bacc38" [[package]] name = "lazy_static" @@ -692,27 +653,21 @@ checksum = "e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646" [[package]] name = "libc" -version = "0.2.146" +version = "0.2.149" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f92be4933c13fd498862a9e02a3055f8a8d9c039ce33db97306fd5a6caa7f29b" +checksum = "a08173bc88b7955d1b3145aa561539096c421ac8debde8cbc3612ec635fee29b" [[package]] name = "libm" -version = "0.2.7" +version = "0.2.8" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f7012b1bbb0719e1097c47611d3898568c546d597c2e74d66f6087edd5233ff4" - -[[package]] -name = "linux-raw-sys" -version = "0.3.8" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ef53942eb7bf7ff43a617b3e2c1c4a5ecf5944a7c1bc12d7ee39bbb15e5c1519" +checksum = "4ec2a862134d2a7d32d7983ddcdd1c4923530833c9f2ea1a44fc5fa473989058" [[package]] name = "log" -version = "0.4.19" +version = "0.4.20" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b06a4cde4c0f271a446782e3eff8de789548ce57dbc8eca9292c27f4a42004b4" +checksum = "b5e6163cb8c49088c2c36f57875e58ccd8c87c7427f7fbd50ea6710b2f3f2e8f" [[package]] name = "matchtigs" @@ -724,7 +679,7 @@ dependencies = [ "disjoint-sets", "flate2", "genome-graph", - "hashbrown 0.14.0", + "hashbrown", "itertools", "log", "memory-stats", @@ -735,9 +690,9 @@ dependencies = [ [[package]] name = "matrixmultiply" -version = "0.3.7" +version = "0.3.8" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "090126dc04f95dc0d1c1c91f61bdd474b3930ca064c1edc8a849da2c6cbe1e77" +checksum = "7574c1cf36da4798ab73da5b215bbf444f50718207754cb522201d78d1cd0ff2" dependencies = [ "autocfg", "rawpointer", @@ -745,9 +700,9 @@ dependencies = [ [[package]] name = "memchr" -version = "2.5.0" +version = "2.6.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2dffe52ecf27772e601905b7522cb4ef790d2cc203488bbd0e2fe85fcb74566d" +checksum = "f665ee40bc4a3c5590afb1e9677db74a508659dfd71e126420da8274909a0167" [[package]] name = "memoffset" @@ -768,15 +723,6 @@ dependencies = [ "winapi", ] -[[package]] -name = "miniz_oxide" -version = "0.6.2" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b275950c28b37e794e8c55d88aeb5e139d0ce23fdbbeda68f8d7174abdf9e8fa" -dependencies = [ - "adler", -] - [[package]] name = "miniz_oxide" version = "0.7.1" @@ -848,9 +794,9 @@ dependencies = [ [[package]] name = "num-complex" -version = "0.4.3" +version = "0.4.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "02e0d21255c828d6f128a1e41534206671e8c3ea0c62f32291e808dc82cff17d" +checksum = "1ba157ca0885411de85d6ca030ba7e2a83a28636056c7c699b07c8b6f7383214" dependencies = [ "num-traits", ] @@ -878,9 +824,9 @@ dependencies = [ [[package]] name = "num-traits" -version = "0.2.15" +version = "0.2.17" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "578ede34cf02f8924ab9447f50c28075b4d3e5b269972345e7e0372b38c6cdcd" +checksum = "39e3200413f237f41ab11ad6d161bc7239c84dcb631773ccd7de3dfe4b5c267c" dependencies = [ "autocfg", "libm", @@ -897,9 +843,9 @@ dependencies = [ [[package]] name = "object" -version = "0.30.4" +version = "0.32.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = 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= [ "unicode-ident", ] [[package]] name = "quote" -version = "1.0.28" +version = "1.0.33" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "1b9ab9c7eadfd8df19006f1cf1a4aed13540ed5cbc047010ece5826e10825488" +checksum = "5267fca4496028628a95160fc423a33e8b2e6af8a5302579e322e4b520293cae" dependencies = [ "proc-macro2", ] @@ -1043,29 +995,41 @@ checksum = "60a357793950651c4ed0f3f52338f53b2f809f32d83a07f72909fa13e4c6c1e3" [[package]] name = "ref-cast" -version = "1.0.16" +version = "1.0.20" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f43faa91b1c8b36841ee70e97188a869d37ae21759da6846d4be66de5bf7b12c" +checksum = "acde58d073e9c79da00f2b5b84eed919c8326832648a5b109b3fce1bb1175280" dependencies = [ "ref-cast-impl", ] [[package]] name = "ref-cast-impl" -version = "1.0.16" +version = "1.0.20" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8d2275aab483050ab2a7364c1a46604865ee7d6906684e08db0f090acf74f9e7" 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"time-core", "time-macros", @@ -1295,26 +1247,26 @@ dependencies = [ [[package]] name = "time-core" -version = "0.1.1" +version = "0.1.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7300fbefb4dadc1af235a9cef3737cea692a9d97e1b9cbcd4ebdae6f8868e6fb" +checksum = "ef927ca75afb808a4d64dd374f00a2adf8d0fcff8e7b184af886c3c87ec4a3f3" [[package]] name = "time-macros" -version = "0.2.9" +version = "0.2.15" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "372950940a5f07bf38dbe211d7283c9e6d7327df53794992d293e534c733d09b" +checksum = "4ad70d68dba9e1f8aceda7aa6711965dfec1cac869f311a51bd08b3a2ccbce20" dependencies = [ "time-core", ] [[package]] name = "traitgraph" -version = "3.1.0" +version = "5.0.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "1ecbd1001637cb1bac78513e81023901f83c5291ac206667752f72c205525086" +checksum = "a66933f4a960dc78d44acff16f192c2483de79da8af184c51e5ee128205a78f4" dependencies = [ - "bitvector", + "bitvec", "num-traits", "petgraph", "traitsequence", @@ -1322,20 +1274,20 @@ dependencies = [ [[package]] name = "traitgraph-algo" -version = "6.1.0" +version = "8.1.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c4d16d8f25edb80778bff6387d616f392cd3493059a2811d3cc9001d13c17260" +checksum = "7b20270073caa8de64c3f37449b256ab8ada29787f73882f4d44f3fd4d7037d3" dependencies = [ - "hashbrown 0.14.0", + "hashbrown", "rand", "traitgraph", ] [[package]] name = "traitsequence" -version = "1.1.0" +version = "2.0.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e43e9c5a3771f5149c0290c829e87524803a89e466c5d170d0b14face79b299d" +checksum = "c4cd2caadbd36e66fb9aea075afd8c4e693773b276e9842928fb2c8a8d29d889" [[package]] name = "triple_accel" @@ -1345,15 +1297,15 @@ checksum = "22048bc95dfb2ffd05b1ff9a756290a009224b60b2f0e7525faeee7603851e63" [[package]] name = "typenum" -version = "1.16.0" +version = "1.17.0" source = 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checksum = "ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6" [[package]] name = "winapi-util" -version = "0.1.5" +version = "0.1.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "70ec6ce85bb158151cae5e5c87f95a8e97d2c0c4b001223f33a334e3ce5de178" +checksum = "f29e6f9198ba0d26b4c9f07dbe6f9ed633e1f3d5b8b414090084349e46a52596" dependencies = [ "winapi", ] @@ -1434,9 +1386,9 @@ dependencies = [ [[package]] name = "windows-targets" -version = "0.48.0" +version = "0.48.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7b1eb6f0cd7c80c79759c929114ef071b87354ce476d9d94271031c0497adfd5" +checksum = "9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c" dependencies = [ "windows_aarch64_gnullvm", "windows_aarch64_msvc", @@ -1449,45 +1401,45 @@ dependencies = [ [[package]] name = "windows_aarch64_gnullvm" -version = "0.48.0" +version = "0.48.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "91ae572e1b79dba883e0d315474df7305d12f569b400fcf90581b06062f7e1bc" +checksum = "2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8" [[package]] name = "windows_aarch64_msvc" -version = "0.48.0" +version = "0.48.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b2ef27e0d7bdfcfc7b868b317c1d32c641a6fe4629c171b8928c7b08d98d7cf3" +checksum = "dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc" [[package]] name = "windows_i686_gnu" -version = "0.48.0" +version = "0.48.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "622a1962a7db830d6fd0a69683c80a18fda201879f0f447f065a3b7467daa241" +checksum = "a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e" [[package]] name = "windows_i686_msvc" -version = "0.48.0" +version = "0.48.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4542c6e364ce21bf45d69fdd2a8e455fa38d316158cfd43b3ac1c5b1b19f8e00" +checksum = 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"wyz" @@ -1497,3 +1449,23 @@ checksum = "05f360fc0b24296329c78fda852a1e9ae82de9cf7b27dae4b7f62f118f77b9ed" dependencies = [ "tap", ] + +[[package]] +name = "zerocopy" +version = "0.7.14" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "69c48d63854f77746c68a5fbb4aa17f3997ece1cb301689a257af8cb80610d21" +dependencies = [ + "zerocopy-derive", +] + +[[package]] +name = "zerocopy-derive" +version = "0.7.14" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "c258c1040279e4f88763a113de72ce32dde2d50e2a94573f15dd534cea36a16d" +dependencies = [ + "proc-macro2", + "quote", + "syn 2.0.38", +] diff --git a/Cargo.toml b/Cargo.toml index cdb4d32..a9f443a 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -29,12 +29,12 @@ lto = true debug = true [dependencies] -genome-graph = {version = "6.0.0", features = ["traitgraph-algo"]} -traitgraph-algo = {version = "6.0.0", features = ["hashbrown_dijkstra_node_weight_array"]} -log = "0.4.14" +genome-graph = {version = "8.0.0", features = ["traitgraph-algo"]} +traitgraph-algo = {version = "8.1.0", features = ["hashbrown_dijkstra_node_weight_array"]} +log = "0.4.20" simplelog = "0.12.0" -clap = {version = "4.0.17", features = ["derive", "cargo"]} -itertools = "0.10.3" +clap = {version = "4.4.7", features = ["derive", "cargo"]} +itertools = "0.11.0" atomic-counter = "1.0.1" disjoint-sets = "0.4.2" permutation = "0.4.0" diff --git a/src/bin.rs b/src/bin.rs index 17ec369..3cefae4 100644 --- a/src/bin.rs +++ b/src/bin.rs @@ -18,8 +18,8 @@ use flate2::write::GzEncoder; use flate2::Compression; use genome_graph::bigraph::interface::BidirectedData; use genome_graph::bigraph::traitgraph::index::GraphIndex; -use genome_graph::bigraph::traitgraph::interface::ImmutableGraphContainer; use genome_graph::bigraph::traitgraph::interface::StaticGraph; +use genome_graph::bigraph::traitgraph::interface::{DynamicGraph, ImmutableGraphContainer}; use genome_graph::bigraph::traitgraph::traitsequence::interface::Sequence; use genome_graph::bigraph::traitgraph::walks::EdgeWalk; use genome_graph::compact_genome::implementation::{DefaultGenome, DefaultSequenceStore}; @@ -266,8 +266,8 @@ impl> } fn sequence_owned< - ResultSequence: for<'a> OwnedGenomeSequence<'a, AlphabetType, ResultSubsequence>, - ResultSubsequence: for<'a> GenomeSequence<'a, AlphabetType, ResultSubsequence> + ?Sized, + ResultSequence: OwnedGenomeSequence, + ResultSubsequence: GenomeSequence + ?Sized, >( &self, source_sequence_store: &GenomeSequenceStore, @@ -358,12 +358,12 @@ pub type CliGraph = pub fn compute_edge_weights< NodeData, SequenceHandle: HandleWithLength, - Graph: StaticGraph>, + Graph: DynamicGraph>, >( graph: &mut Graph, k: usize, ) { - for edge_index in graph.edge_indices() { + for edge_index in graph.edge_indices_copied() { let edge_data = graph.edge_data_mut(edge_index); let weight = edge_data.sequence_handle.len() + 1 - k; debug_assert_ne!( @@ -423,8 +423,8 @@ pub fn write_walks_fasta_to_file< GenomeSequenceStore: SequenceStore, GraphEdgeData: MatchtigEdgeData + SequenceData, Graph: StaticGraph, - Walk: 'ws + for<'w> EdgeWalk<'w, Graph, SubWalk>, - SubWalk: for<'w> EdgeWalk<'w, Graph, SubWalk> + ?Sized, + Walk: 'ws + EdgeWalk, + SubWalk: EdgeWalk + ?Sized, WalkSource: IntoIterator, OutPath: AsRef, DebugOutPath: AsRef, @@ -469,8 +469,8 @@ pub fn write_walks_fasta< GenomeSequenceStore: SequenceStore, GraphEdgeData: MatchtigEdgeData + SequenceData, Graph: StaticGraph, - Walk: 'ws + for<'w> EdgeWalk<'w, Graph, SubWalk>, - SubWalk: for<'w> EdgeWalk<'w, Graph, SubWalk> + ?Sized, + Walk: 'ws + EdgeWalk, + SubWalk: EdgeWalk + ?Sized, WalkSource: IntoIterator, Writer: Write, DebugWriter: Write, @@ -614,8 +614,8 @@ pub fn write_walks_gfa_to_file< GenomeSequenceStore: SequenceStore, GraphEdgeData: MatchtigEdgeData + SequenceData, Graph: StaticGraph, - Walk: 'ws + for<'w> EdgeWalk<'w, Graph, SubWalk>, - SubWalk: for<'w> EdgeWalk<'w, Graph, SubWalk> + ?Sized, + Walk: 'ws + EdgeWalk, + SubWalk: EdgeWalk + ?Sized, WalkSource: IntoIterator, OutPath: AsRef, DebugOutPath: AsRef, @@ -670,8 +670,8 @@ pub fn write_walks_gfa< GenomeSequenceStore: SequenceStore, GraphEdgeData: MatchtigEdgeData + SequenceData, Graph: StaticGraph, - Walk: 'ws + for<'w> EdgeWalk<'w, Graph, SubWalk>, - SubWalk: for<'w> EdgeWalk<'w, Graph, SubWalk> + ?Sized, + Walk: 'ws + EdgeWalk, + SubWalk: EdgeWalk + ?Sized, WalkSource: IntoIterator, Writer: Write, DebugWriter: Write, @@ -819,8 +819,8 @@ pub fn write_walks_gfa< fn debug_print_walks< 'ws, Graph: ImmutableGraphContainer, - Walk: 'ws + for<'w> EdgeWalk<'w, Graph, Subwalk>, - Subwalk: for<'w> EdgeWalk<'w, Graph, Subwalk> + ?Sized, + Walk: 'ws + EdgeWalk, + Subwalk: EdgeWalk + ?Sized, WalkSource: 'ws + IntoIterator, >( _graph: &Graph, diff --git a/src/implementation/mod.rs b/src/implementation/mod.rs index f7cfb7f..d6ba2dd 100644 --- a/src/implementation/mod.rs +++ b/src/implementation/mod.rs @@ -654,8 +654,8 @@ pub fn write_duplication_bitvector_to_file< SequenceHandle, EdgeData: MatchtigEdgeData, Graph: ImmutableGraphContainer, - Walk: 'ws + for<'w> EdgeWalk<'w, Graph, Subwalk>, - Subwalk: for<'w> EdgeWalk<'w, Graph, Subwalk> + ?Sized, + Walk: 'ws + EdgeWalk, + Subwalk: EdgeWalk + ?Sized, WalkSource: 'ws + IntoIterator, >( graph: &Graph, @@ -673,8 +673,8 @@ pub fn write_duplication_bitvector< SequenceHandle, EdgeData: MatchtigEdgeData, Graph: ImmutableGraphContainer, - Walk: 'ws + for<'w> EdgeWalk<'w, Graph, Subwalk>, - Subwalk: for<'w> EdgeWalk<'w, Graph, Subwalk> + ?Sized, + Walk: 'ws + EdgeWalk, + Subwalk: EdgeWalk + ?Sized, WalkSource: 'ws + IntoIterator, >( graph: &Graph,