From 442c195f5c846c56f0a5f2c1903840bbfc584a1d Mon Sep 17 00:00:00 2001 From: Marko Malenic Date: Tue, 2 Jan 2024 12:32:06 +1100 Subject: [PATCH] build(deps): update noodles to 0.60, new clippy warnings --- Cargo.lock | 1002 ++++++++++++++---------- htsget-actix/src/lib.rs | 3 +- htsget-config/Cargo.toml | 2 +- htsget-lambda/Cargo.toml | 2 +- htsget-lambda/src/lib.rs | 2 +- htsget-search/Cargo.toml | 2 +- htsget-search/src/htsget/bam_search.rs | 17 +- htsget-search/src/htsget/bcf_search.rs | 9 +- htsget-search/src/htsget/search.rs | 31 +- htsget-search/src/htsget/vcf_search.rs | 12 +- htsget-test/Cargo.toml | 2 +- 11 files changed, 629 insertions(+), 455 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 945f4df9..afa9683c 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -21,9 +21,9 @@ dependencies = [ [[package]] name = "actix-cors" -version = "0.6.4" +version = "0.6.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b340e9cfa5b08690aae90fb61beb44e9b06f44fe3d0f93781aaa58cfba86245e" +checksum = "0346d8c1f762b41b458ed3145eea914966bb9ad20b9be0d6d463b20d45586370" dependencies = [ "actix-utils", "actix-web", @@ -36,9 +36,9 @@ dependencies = [ [[package]] name = "actix-http" -version = "3.4.0" +version = "3.5.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a92ef85799cba03f76e4f7c10f533e66d87c9a7e7055f3391f09000ad8351bc9" +checksum = "129d4c88e98860e1758c5de288d1632b07970a16d59bdf7b8d66053d582bb71f" dependencies = [ "actix-codec", "actix-rt", @@ -46,8 +46,8 @@ dependencies = [ "actix-tls", "actix-utils", "ahash", - "base64", - "bitflags 2.4.0", + "base64 0.21.5", + "bitflags 2.4.1", "brotli", "bytes", "bytestring", @@ -81,14 +81,14 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "e01ed3140b2f8d422c68afa1ed2e85d996ea619c988ac834d255db32138655cb" dependencies = [ "quote", - "syn 2.0.37", + "syn 2.0.45", ] [[package]] name = "actix-router" -version = "0.5.1" +version = "0.5.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "d66ff4d247d2b160861fa2866457e85706833527840e4133f8f49aa423a38799" +checksum = "d22475596539443685426b6bdadb926ad0ecaefdfc5fb05e5e3441f15463c511" dependencies = [ "bytestring", "http", @@ -119,7 +119,7 @@ dependencies = [ "futures-core", "futures-util", "mio", - "socket2 0.5.4", + "socket2", "tokio", "tracing", ] @@ -168,9 +168,9 @@ dependencies = [ [[package]] name = "actix-web" -version = "4.4.0" +version = "4.4.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "0e4a5b5e29603ca8c94a77c65cf874718ceb60292c5a5c3e5f4ace041af462b9" +checksum = "e43428f3bf11dee6d166b00ec2df4e3aa8cc1606aaa0b7433c146852e2f4e03b" dependencies = [ "actix-codec", "actix-http", @@ -202,7 +202,7 @@ dependencies = [ "serde_json", "serde_urlencoded", "smallvec", - "socket2 0.5.4", + "socket2", "time", "url", ] @@ -216,7 +216,7 @@ dependencies = [ "actix-router", "proc-macro2", "quote", - "syn 2.0.37", + "syn 2.0.45", ] [[package]] @@ -236,21 +236,22 @@ checksum = "f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe" [[package]] name = "ahash" -version = "0.8.3" +version = "0.8.7" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2c99f64d1e06488f620f932677e24bc6e2897582980441ae90a671415bd7ec2f" +checksum = "77c3a9648d43b9cd48db467b3f87fdd6e146bcc88ab0180006cef2179fe11d01" dependencies = [ "cfg-if", "getrandom", "once_cell", "version_check", + "zerocopy", ] [[package]] name = "aho-corasick" -version = "1.1.1" +version = "1.1.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ea5d730647d4fadd988536d06fecce94b7b4f2a7efdae548f1cf4b63205518ab" +checksum = "b2969dcb958b36655471fc61f7e416fa76033bdd4bfed0678d8fee1e2d07a1f0" dependencies = [ "memchr", ] @@ -293,9 +294,9 @@ checksum = "4b46cbb362ab8752921c97e041f5e366ee6297bd428a31275b9fcf1e380f7299" [[package]] name = "anstream" -version = "0.6.4" +version = "0.6.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2ab91ebe16eb252986481c5b62f6098f3b698a45e34b5b98200cf20dd2484a44" +checksum = "d664a92ecae85fd0a7392615844904654d1d5f5514837f471ddef4a057aba1b6" dependencies = [ "anstyle", "anstyle-parse", @@ -313,30 +314,30 @@ checksum = "7079075b41f533b8c61d2a4d073c4676e1f8b249ff94a393b0595db304e0dd87" [[package]] name = "anstyle-parse" -version = "0.2.2" +version = "0.2.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "317b9a89c1868f5ea6ff1d9539a69f45dffc21ce321ac1fd1160dfa48c8e2140" +checksum = "c75ac65da39e5fe5ab759307499ddad880d724eed2f6ce5b5e8a26f4f387928c" dependencies = [ "utf8parse", ] [[package]] name = "anstyle-query" -version = "1.0.0" +version = "1.0.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "5ca11d4be1bab0c8bc8734a9aa7bf4ee8316d462a08c6ac5052f888fef5b494b" +checksum = "e28923312444cdd728e4738b3f9c9cac739500909bb3d3c94b43551b16517648" dependencies = [ - "windows-sys", + "windows-sys 0.52.0", ] [[package]] name = "anstyle-wincon" -version = "3.0.1" +version = "3.0.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f0699d10d2f4d628a98ee7b57b289abbc98ff3bad977cb3152709d4bf2330628" +checksum = "1cd54b81ec8d6180e24654d0b371ad22fc3dd083b6ff8ba325b72e00c87660a7" dependencies = [ "anstyle", - "windows-sys", + "windows-sys 0.52.0", ] [[package]] @@ -358,9 +359,9 @@ dependencies = [ [[package]] name = "async-compression" -version = "0.4.3" +version = "0.4.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "bb42b2197bf15ccb092b62c74515dbd8b86d0effd934795f6687c93b6e679a2c" +checksum = "bc2d0cfb2a7388d34f590e76686704c494ed7aaceed62ee1ba35cbf363abc2a5" dependencies = [ "flate2", "futures-core", @@ -388,18 +389,18 @@ checksum = "16e62a023e7c117e27523144c5d2459f4397fcc3cab0085af8e2224f643a0193" dependencies = [ "proc-macro2", "quote", - "syn 2.0.37", + "syn 2.0.45", ] [[package]] name = "async-trait" -version = "0.1.73" +version = "0.1.76" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "bc00ceb34980c03614e35a3a4e218276a0a824e911d07651cd0d858a51e8c0f0" +checksum = "531b97fb4cd3dfdce92c35dedbfdc1f0b9d8091c8ca943d6dae340ef5012d514" dependencies = [ "proc-macro2", "quote", - "syn 2.0.37", + "syn 2.0.45", ] [[package]] @@ -413,9 +414,12 @@ dependencies = [ [[package]] name = "atomic" -version = "0.5.3" +version = "0.6.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c59bdb34bc650a32731b31bd8f0829cc15d24a708ee31559e0bb34f2bc320cba" +checksum = "8d818003e740b63afc82337e3160717f4f63078720a810b7b903e70a5d1d2994" +dependencies = [ + "bytemuck", +] [[package]] name = "autocfg" @@ -445,7 +449,7 @@ dependencies = [ "hex", "http", "hyper", - "ring", + "ring 0.16.20", "time", "tokio", "tower", @@ -840,11 +844,11 @@ dependencies = [ [[package]] name = "aws_lambda_events" -version = "0.10.0" +version = "0.12.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "65991dbc3bfb586939ba1527eefdc99bc21157b6ec891f180fb1e16e2dddc7a9" +checksum = "03611508dd1e514e311caec235b581c99a4cb66fa1771bd502819eed69894f12" dependencies = [ - "base64", + "base64 0.21.5", "bytes", "http", "http-body", @@ -920,9 +924,15 @@ dependencies = [ [[package]] name = "base64" -version = "0.21.4" +version = "0.20.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "9ba43ea6f343b788c8764558649e08df62f86c6ef251fdaeb1ffd010a9ae50a2" +checksum = "0ea22880d78093b0cbe17c89f64a7d457941e65759157ec6cb31a31d652b05e5" + +[[package]] +name = "base64" +version = "0.21.5" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "35636a1494ede3b646cc98f74f8e62c773a38a659ebc777a2cf26b9b74171df9" [[package]] name = "base64-simd" @@ -948,9 +958,9 @@ checksum = "bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a" [[package]] name = "bitflags" -version = "2.4.0" +version = "2.4.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b4682ae6287fcf752ecaabbfcc7b6f9b72aa33933dc23a554d853aea8eea8635" +checksum = "327762f6e5a765692301e5bb513e0d9fef63be86bbc14528052b1cd3e6f03e07" [[package]] name = "block-buffer" @@ -974,9 +984,9 @@ dependencies = [ [[package]] name = "brotli-decompressor" -version = "2.5.0" +version = "2.5.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "da74e2b81409b1b743f8f0c62cc6254afefb8b8e50bbfe3735550f7aeefa3448" +checksum = "4e2e4afe60d7dd600fdd3de8d0f08c2b7ec039712e3b6137ff98b7004e82de4f" dependencies = [ "alloc-no-stdlib", "alloc-stdlib", @@ -988,11 +998,17 @@ version = "3.14.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "7f30e7476521f6f8af1a1c4c0b8cc94f0bee37d91763d0ca2665f299b6cd8aec" +[[package]] +name = "bytemuck" +version = "1.14.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +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 = "bytes" @@ -1005,9 +1021,9 @@ dependencies = [ [[package]] name = "bytes-utils" -version = "0.1.3" +version = "0.1.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e47d3a8076e283f3acd27400535992edb3ba4b5bb72f8891ad8fbe7932a7d4b9" +checksum = "7dafe3a8757b027e2be6e4e5601ed563c55989fcf1546e933c66c8eb3a058d35" dependencies = [ "bytes", "either", @@ -1015,9 +1031,9 @@ dependencies = [ [[package]] name = "bytestring" -version = "1.3.0" +version = "1.3.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "238e4886760d98c4f899360c834fa93e62cf7f721ac3c2da375cbdf4b8679aae" +checksum = "74d80203ea6b29df88012294f62733de21cfeab47f17b41af3a38bc30a03ee72" dependencies = [ "bytes", ] @@ -1075,7 +1091,7 @@ dependencies = [ "iana-time-zone", "num-traits", "serde", - "windows-targets", + "windows-targets 0.48.5", ] [[package]] @@ -1107,9 +1123,9 @@ dependencies = [ [[package]] name = "clap" -version = "4.4.6" +version = "4.4.12" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "d04704f56c2cde07f43e8e2c154b43f216dc5c92fc98ada720177362f953b956" +checksum = "dcfab8ba68f3668e89f6ff60f5b205cea56aa7b769451a59f34b8682f51c056d" dependencies = [ "clap_builder", "clap_derive", @@ -1117,9 +1133,9 @@ dependencies = [ [[package]] name = "clap_builder" -version = "4.4.6" +version = "4.4.12" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "0e231faeaca65ebd1ea3c737966bf858971cd38c3849107aa3ea7de90a804e45" +checksum = "fb7fb5e4e979aec3be7791562fcba452f94ad85e954da024396433e0e25a79e9" dependencies = [ "anstream", "anstyle", @@ -1129,21 +1145,21 @@ dependencies = [ [[package]] name = "clap_derive" -version = "4.4.2" +version = "4.4.7" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "0862016ff20d69b84ef8247369fabf5c008a7417002411897d40ee1f4532b873" +checksum = "cf9804afaaf59a91e75b022a30fb7229a7901f60c755489cc61c9b423b836442" dependencies = [ "heck", "proc-macro2", "quote", - "syn 2.0.37", + "syn 2.0.45", ] [[package]] name = "clap_lex" -version = "0.5.1" +version = "0.6.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "cd7cc57abe963c6d3b9d8be5b06ba7c8957a930305ca90304f24ef040aa6f961" +checksum = "702fc72eb24e5a1e48ce58027a675bc24edd52096d5397d4aea7c6dd9eca0bd1" [[package]] name = "colorchoice" @@ -1170,9 +1186,9 @@ dependencies = [ [[package]] name = "core-foundation" -version = "0.9.3" +version = "0.9.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "194a7a9e6de53fa55116934067c844d9d749312f75c6f6d0980e8c252f8c2146" +checksum = "91e195e091a93c46f7102ec7818a2aa394e1e1771c3ab4825963fa03e45afb8f" dependencies = [ "core-foundation-sys", "libc", @@ -1180,15 +1196,15 @@ dependencies = [ [[package]] name = "core-foundation-sys" -version = "0.8.4" +version = "0.8.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e496a50fda8aacccc86d7529e2c1e0892dbd0f898a6b5645b5561b89c3210efa" +checksum = "06ea2b9bc92be3c2baa9334a323ebca2d6f074ff852cd1d7b11064035cd3868f" [[package]] name = "cpufeatures" -version = "0.2.9" +version = "0.2.11" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a17b76ff3a4162b0b27f354a0c87015ddad39d35f9c0c36607a3bdd175dde1f1" +checksum = "ce420fe07aecd3e67c5f910618fe65e94158f6dcc0adf44e00d69ce2bdfe0fd0" dependencies = [ "libc", ] @@ -1251,9 +1267,9 @@ dependencies = [ [[package]] name = "crossbeam-channel" -version = "0.5.8" +version = "0.5.10" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a33c2bf77f2df06183c3aa30d1e96c0695a313d4f9c453cc3762a6db39f99200" +checksum = "82a9b73a36529d9c47029b9fb3a6f0ea3cc916a261195352ba19e770fc1748b2" dependencies = [ "cfg-if", "crossbeam-utils", @@ -1261,9 +1277,9 @@ dependencies = [ [[package]] name = "crossbeam-deque" -version = "0.8.3" +version = "0.8.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ce6fd6f855243022dcecf8702fef0c297d4338e226845fe067f6341ad9fa0cef" +checksum = "fca89a0e215bab21874660c67903c5f143333cab1da83d041c7ded6053774751" dependencies = [ "cfg-if", "crossbeam-epoch", @@ -1272,22 +1288,20 @@ dependencies = [ [[package]] name = "crossbeam-epoch" -version = "0.9.15" +version = "0.9.17" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ae211234986c545741a7dc064309f67ee1e5ad243d0e48335adc0484d960bcc7" +checksum = "0e3681d554572a651dda4186cd47240627c3d0114d45a95f6ad27f2f22e7548d" dependencies = [ "autocfg", "cfg-if", "crossbeam-utils", - "memoffset", - "scopeguard", ] [[package]] name = "crossbeam-utils" -version = "0.8.16" +version = "0.8.18" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "5a22b2d63d4d1dc0b7f1b6b2747dd0088008a9be28b6ddf0b1e7d335e3037294" +checksum = "c3a430a770ebd84726f584a90ee7f020d28db52c6d02138900f22341f866d39c" dependencies = [ "cfg-if", ] @@ -1323,7 +1337,7 @@ dependencies = [ "proc-macro2", "quote", "strsim", - "syn 2.0.37", + "syn 2.0.45", ] [[package]] @@ -1334,21 +1348,22 @@ checksum = "836a9bbc7ad63342d6d6e7b815ccab164bc77a2d95d84bc3117a8c0d5c98e2d5" dependencies = [ "darling_core", "quote", - "syn 2.0.37", + "syn 2.0.45", ] [[package]] name = "data-url" -version = "0.3.0" +version = "0.3.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "41b319d1b62ffbd002e057f36bebd1f42b9f97927c9577461d855f3513c4289f" +checksum = "5c297a1c74b71ae29df00c3e22dd9534821d60eb9af5a0192823fa2acea70c2a" [[package]] name = "deranged" -version = "0.3.8" +version = "0.3.11" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f2696e8a945f658fd14dc3b87242e6b80cd0f36ff04ea560fa39082368847946" +checksum = "b42b6fa04a440b495c8b04d0e71b707c585f83cb9cb28cf8cd0d976c315e31b4" dependencies = [ + "powerfmt", "serde", ] @@ -1405,23 +1420,12 @@ checksum = "5443807d6dff69373d433ab9ef5378ad8df50ca6298caf15de6e52e24aaf54d5" [[package]] name = "errno" -version = "0.3.4" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "add4f07d43996f76ef320709726a556a9d4f965d9410d8d0271132d2f8293480" -dependencies = [ - "errno-dragonfly", - "libc", - "windows-sys", -] - -[[package]] -name = "errno-dragonfly" -version = "0.1.2" +version = "0.3.8" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "aa68f1b12764fab894d2755d2518754e71b4fd80ecfb822714a1206c2aab39bf" +checksum = "a258e46cdc063eb8519c00b9fc845fc47bcfca4130e2f08e88665ceda8474245" dependencies = [ - "cc", "libc", + "windows-sys 0.52.0", ] [[package]] @@ -1444,25 +1448,25 @@ checksum = "25cbce373ec4653f1a01a31e8a5e5ec0c622dc27ff9c4e6606eefef5cbbed4a5" [[package]] name = "figment" -version = "0.10.10" +version = "0.10.13" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4547e226f4c9ab860571e070a9034192b3175580ecea38da34fcdb53a018c9a5" +checksum = "7629b8c7bcd214a072c2c88b263b5bb3ceb54c34365d8c41c1665461aeae0993" dependencies = [ "atomic", "parking_lot", "pear", "serde", "tempfile", - "toml", + "toml 0.8.8", "uncased", "version_check", ] [[package]] name = "flate2" -version = "1.0.27" +version = "1.0.28" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c6c98ee8095e9d1dcbf2fcc6d95acccb90d1c81db1e44725c6a984b1dbdfb010" +checksum = "46303f565772937ffe1d394a4fac6f411c6013172fadde9dcdb1e147a086940e" dependencies = [ "crc32fast", "miniz_oxide", @@ -1476,18 +1480,18 @@ checksum = "3f9eec918d3f24069decb9af1554cad7c880e2da24a9afd88aca000531ab82c1" [[package]] name = "form_urlencoded" -version = "1.2.0" +version = "1.2.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a62bc1cf6f830c2ec14a513a9fb124d0a213a629668a4186f329db21fe045652" +checksum = "e13624c2627564efccf4934284bdd98cbaa14e79b0b5a141218e507b3a823456" dependencies = [ "percent-encoding", ] [[package]] name = "futures" -version = "0.3.28" +version = "0.3.30" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "23342abe12aba583913b2e62f22225ff9c950774065e4bfb61a19cd9770fec40" +checksum = "645c6916888f6cb6350d2550b80fb63e734897a8498abe35cfb732b6487804b0" dependencies = [ "futures-channel", "futures-core", @@ -1500,9 +1504,9 @@ dependencies = [ [[package]] name = "futures-channel" -version = "0.3.28" +version = "0.3.30" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "955518d47e09b25bbebc7a18df10b81f0c766eaf4c4f1cccef2fca5f2a4fb5f2" +checksum = "eac8f7d7865dcb88bd4373ab671c8cf4508703796caa2b1985a9ca867b3fcb78" dependencies = [ "futures-core", "futures-sink", @@ -1510,15 +1514,15 @@ dependencies = [ [[package]] name = "futures-core" -version = "0.3.28" +version = "0.3.30" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4bca583b7e26f571124fe5b7561d49cb2868d79116cfa0eefce955557c6fee8c" +checksum = "dfc6580bb841c5a68e9ef15c77ccc837b40a7504914d52e47b8b0e9bbda25a1d" [[package]] name = "futures-executor" -version = "0.3.28" +version = "0.3.30" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ccecee823288125bd88b4d7f565c9e58e41858e47ab72e8ea2d64e93624386e0" +checksum = "a576fc72ae164fca6b9db127eaa9a9dda0d61316034f33a0a0d4eda41f02b01d" dependencies = [ "futures-core", "futures-task", @@ -1527,38 +1531,38 @@ 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-1595,15 +1599,15 @@ dependencies = [ [[package]] name = "gimli" -version = "0.28.0" +version = "0.28.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "6fb8d784f27acf97159b40fc4db5ecd8aa23b9ad5ef69cdd136d3bc80665f0c0" +checksum = "4271d37baee1b8c7e4b708028c57d816cf9d2434acb33a549475f78c181f6253" [[package]] name = "h2" -version = "0.3.21" +version = "0.3.22" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "91fc23aa11be92976ef4729127f1a74adf36d8436f7816b185d18df956790833" +checksum = "4d6250322ef6e60f93f9a2162799302cd6f68f79f6e5d85c8c16f14d1d958178" dependencies = [ "bytes", "fnv", @@ -1611,7 +1615,7 @@ dependencies = [ "futures-sink", "futures-util", "http", - "indexmap 1.9.3", + "indexmap 2.1.0", "slab", "tokio", "tokio-util", @@ -1632,9 +1636,9 @@ checksum = "8a9ee70c43aaf417c914396645a0fa852624801b24ebb7ae78fe8272889ac888" [[package]] name = "hashbrown" -version = "0.14.1" +version = "0.14.3" source = 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dependencies = [ "bytes", "fnv", @@ -1838,9 +1842,9 @@ dependencies = [ [[package]] name = "http-body" -version = "0.4.5" +version = "0.4.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "d5f38f16d184e36f2408a55281cd658ecbd3ca05cce6d6510a176eca393e26d1" +checksum = "7ceab25649e9960c0311ea418d17bee82c0dcec1bd053b5f9a66e265a693bed2" dependencies = [ "bytes", "http", @@ -1877,9 +1881,9 @@ checksum = "df3b46402a9d5adb4c86a0cf463f42e19994e3ee891101b1841f30a545cb49a9" [[package]] name = "hyper" -version = "0.14.27" +version = "0.14.28" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ffb1cfd654a8219eaef89881fdb3bb3b1cdc5fa75ded05d6933b2b382e395468" +checksum = "bf96e135eb83a2a8ddf766e426a841d8ddd7449d5f00d34ea02b41d2f19eef80" dependencies = [ "bytes", "futures-channel", @@ -1892,7 +1896,7 @@ dependencies = [ "httpdate", "itoa", "pin-project-lite", - "socket2 0.4.9", + "socket2", "tokio", "tower-service", "tracing", @@ -1901,9 +1905,9 @@ dependencies = [ [[package]] name = "hyper-rustls" -version = "0.24.1" +version = "0.24.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8d78e1e73ec14cf7375674f74d7dde185c8206fd9dea6fb6295e8a98098aaa97" +checksum = "ec3efd23720e2049821a693cbc7e65ea87c72f1c58ff2f9522ff332b1491e590" dependencies = [ "futures-util", "http", @@ -1917,16 +1921,16 @@ dependencies = [ [[package]] name = "iana-time-zone" -version = "0.1.57" +version = "0.1.59" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2fad5b825842d2b38bd206f3e81d6957625fd7f0a361e345c30e01a0ae2dd613" +checksum = "b6a67363e2aa4443928ce15e57ebae94fd8949958fd1223c4cfc0cd473ad7539" dependencies = [ "android_system_properties", "core-foundation-sys", "iana-time-zone-haiku", "js-sys", "wasm-bindgen", - "windows", + "windows-core", ] [[package]] @@ -1946,9 +1950,9 @@ checksum = "b9e0384b61958566e926dc50660321d12159025e767c18e043daf26b70104c39" [[package]] name = "idna" -version = "0.4.0" +version = "0.5.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7d20d6b07bfbc108882d88ed8e37d39636dcc260e15e30c45e6ba089610b917c" +checksum = "634d9b1461af396cad843f47fdba5597a4f9e6ddd4bfb6ff5d85028c25cb12f6" dependencies = [ "unicode-bidi", "unicode-normalization", @@ -1973,12 +1977,12 @@ dependencies = [ [[package]] name = "indexmap" -version = "2.0.2" +version = "2.1.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8adf3ddd720272c6ea8bf59463c04e0f93d0bbf7c5439b691bca2987e0270897" +checksum = "d530e1a18b1cb4c484e6e34556a0d948706958449fca0cab753d649f2bce3d1f" dependencies = [ "equivalent", - "hashbrown 0.14.1", + "hashbrown 0.14.3", "serde", ] @@ -1990,19 +1994,19 @@ checksum = "c8fae54786f62fb2918dcfae3d568594e50eb9b5c25bf04371af6fe7516452fb" [[package]] name = "ipnet" -version = "2.8.0" +version = "2.9.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = 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dependencies = [ "serde", "serde_json", "serde_urlencoded", + "tokio-stream", "url", ] [[package]] name = "lambda_runtime" -version = "0.8.2" +version = "0.8.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8300e2e10ab2a49016584d9f248736a9da5ea819648df4c9d6c82fa2231fb510" +checksum = "deca8f65d7ce9a8bfddebb49d7d91b22e788a59ca0c5190f26794ab80ed7a702" dependencies = [ "async-stream", + "base64 0.20.0", "bytes", "futures", "http", + "http-body", "http-serde", "hyper", "lambda_runtime_api_client", @@ -2173,21 +2180,21 @@ dependencies = [ [[package]] name = "libc" -version = "0.2.148" +version = "0.2.151" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "9cdc71e17332e86d2e1d38c1f99edcb6288ee11b815fb1a4b049eaa2114d369b" +checksum = "302d7ab3130588088d277783b1e2d2e10c9e9e4a16dd9050e6ec93fb3e7048f4" [[package]] name = "linux-raw-sys" -version = "0.4.8" +version = "0.4.12" source = 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-2419,13 +2424,13 @@ dependencies = [ [[package]] name = "noodles-csi" -version = "0.24.0" +version = "0.29.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "1b2bb780250c88bc9ea69b56c1aa9df75decc6b79035f3f5ab10c0cd84d24fc6" +checksum = "9abd5616c374ad3da6677603dc1637ef518388537ec4a0263b8e4471ee5b0801" dependencies = [ "bit-vec", "byteorder", - "indexmap 2.0.2", + "indexmap 2.1.0", "noodles-bgzf", "noodles-core", "tokio", @@ -2433,9 +2438,9 @@ dependencies = [ [[package]] name = "noodles-fasta" -version = "0.29.0" +version = "0.31.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "1012431f881aad1912f9650a8d33e7f7493c6202bc2e889949ec1bc26a55f26d" +checksum = "cc8985866ee2464904d71f26661797ed610afcdb926523afc1b8a88f34d512c0" dependencies = [ "bytes", "memchr", @@ -2446,9 +2451,9 @@ dependencies = [ [[package]] name = "noodles-fastq" -version = "0.8.0" +version = "0.10.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e1763486d2d1a1e39a86676a47aa05728c75f73f0f883415e36439711ead2641" +checksum = "03559005dc319f23454e0ae6804f72d27da2d4293c2dcc01ff7b0d8c5d59ab9f" dependencies = [ "futures", "memchr", @@ -2457,13 +2462,13 @@ dependencies = [ [[package]] name = "noodles-sam" -version = "0.41.0" +version = "0.49.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "25168f31309cb35103ea5216e30beb1dfbff5f173889c0a056b8f3d7c32e5105" +checksum = "2b94966806ac7aec118d41eea7080bfbd0e8b843ba64f46522c57f0f55cfb1f0" dependencies = [ - "bitflags 2.4.0", + "bitflags 2.4.1", "futures", - "indexmap 2.0.2", + "indexmap 2.1.0", "lexical-core", "memchr", "noodles-bgzf", @@ -2474,12 +2479,13 @@ dependencies = [ [[package]] name = "noodles-tabix" -version = "0.29.0" +version = "0.35.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "056e394ddb4c64bcc9806551a69833294062159600aa8ecf7167a922512bda4f" +checksum = "edd762c360b3d611d0457bc7db5f30741f3b658f27e8541538171d058f3d2379" dependencies = [ "bit-vec", "byteorder", + "indexmap 2.1.0", "noodles-bgzf", "noodles-core", "noodles-csi", @@ -2488,12 +2494,12 @@ dependencies = [ [[package]] name = "noodles-vcf" -version = "0.38.0" +version = "0.48.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e9306e749f9d094f4cf0cb6275d106a8a5da90f97700bcc4e0e86480a074d25d" +checksum = "0a7799c5e60ff2a3234a778e9bd4dbed470d8ccd5e934fd75028a951f1f11099" dependencies = [ "futures", - "indexmap 2.0.2", + "indexmap 2.1.0", "memchr", "noodles-bgzf", "noodles-core", @@ -2534,9 +2540,9 @@ dependencies = [ [[package]] name = "num-traits" -version = "0.2.16" +version = "0.2.17" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f30b0abd723be7e2ffca1272140fac1a2f084c77ec3e123c192b66af1ee9e6c2" +checksum = "39e3200413f237f41ab11ad6d161bc7239c84dcb631773ccd7de3dfe4b5c267c" dependencies = [ "autocfg", ] @@ -2559,18 +2565,18 @@ checksum = "cf70ee2d9b1737d1836c20d9f8f96ec3901b2bf92128439db13237ddce9173a5" [[package]] name = "object" -version = "0.32.1" +version = "0.32.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "9cf5f9dd3933bd50a9e1f149ec995f39ae2c496d31fd772c1fd45ebc27e902b0" +checksum = "a6a622008b6e321afc04970976f62ee297fdbaa6f95318ca343e3eebb9648441" dependencies = [ "memchr", ] [[package]] name = "once_cell" -version = "1.18.0" +version = "1.19.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "dd8b5dd2ae5ed71462c540258bedcb51965123ad7e7ccf4b9a8cafaa4a63576d" +checksum = "3fdb12b2476b595f9358c5161aa467c2438859caa136dec86c26fdd2efe17b92" [[package]] name = "oorandom" @@ -2608,15 +2614,15 @@ dependencies = [ [[package]] name = "parking_lot_core" -version = "0.9.8" +version = "0.9.9" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "93f00c865fe7cabf650081affecd3871070f26767e7b2070a3ffae14c654b447" +checksum = "4c42a9226546d68acdd9c0a280d17ce19bfe27a46bf68784e4066115788d008e" dependencies = [ "cfg-if", "libc", "redox_syscall", "smallvec", - "windows-targets", + "windows-targets 0.48.5", ] [[package]] @@ -2645,9 +2651,9 @@ dependencies = [ [[package]] name = "pear" -version = "0.2.7" +version = "0.2.8" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "61a386cd715229d399604b50d1361683fe687066f42d56f54be995bc6868f71c" +checksum = "4ccca0f6c17acc81df8e242ed473ec144cbf5c98037e69aa6d144780aad103c8" dependencies = [ "inlinable_string", "pear_codegen", @@ -2656,31 +2662,31 @@ dependencies = [ [[package]] name = "pear_codegen" -version = "0.2.7" +version = "0.2.8" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "da9f0f13dac8069c139e8300a6510e3f4143ecf5259c60b116a9b271b4ca0d54" +checksum = "2e22670e8eb757cff11d6c199ca7b987f352f0346e0be4dd23869ec72cb53c77" dependencies = [ "proc-macro2", "proc-macro2-diagnostics", "quote", - "syn 2.0.37", + "syn 2.0.45", ] [[package]] name = "pem" -version = "3.0.2" +version = "3.0.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "3163d2912b7c3b52d651a055f2c7eec9ba5cd22d26ef75b8dd3a59980b185923" +checksum = "1b8fcc794035347fb64beda2d3b462595dd2753e3f268d89c5aae77e8cf2c310" dependencies = [ - "base64", + "base64 0.21.5", "serde", ] [[package]] name = "percent-encoding" -version = "2.3.0" +version = "2.3.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "9b2a4787296e9989611394c33f193f676704af1686e70b8f8033ab5ba9a35a94" +checksum = "e3148f5046208a5d56bcfc03053e3ca6334e51da8dfb19b6cdc8b306fae3283e" [[package]] name = "pin-project" @@ -2699,7 +2705,7 @@ checksum = "4359fd9c9171ec6e8c62926d6faaf553a8dc3f64e1507e76da7911b4f6a04405" dependencies = [ "proc-macro2", "quote", - "syn 2.0.37", + "syn 2.0.45", ] [[package]] @@ -2716,9 +2722,9 @@ checksum = "8b870d8c151b6f2fb93e84a13146138f05d02ed11c7e7c54f8826aaaf7c9f184" [[package]] name = "pkg-config" -version = "0.3.27" +version = "0.3.28" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "26072860ba924cbfa98ea39c8c19b4dd6a4a25423dbdf219c1eca91aa0cf6964" +checksum = "69d3587f8a9e599cc7ec2c00e331f71c4e69a5f9a4b8a6efd5b07466b9736f9a" [[package]] name = "plotters" @@ -2748,6 +2754,12 @@ dependencies = [ "plotters-backend", ] +[[package]] +name = "powerfmt" +version = "0.2.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "439ee305def115ba05938db6eb1644ff94165c5ab5e9420d1c1bcedbba909391" + [[package]] name = "ppv-lite86" version = "0.2.17" @@ -2790,9 +2802,9 @@ dependencies = [ [[package]] name = "proc-macro2" -version = "1.0.67" +version = "1.0.73" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "3d433d9f1a3e8c1263d9456598b16fec66f4acc9a74dacffd35c7bb09b3a1328" +checksum = "2dd5e8a1f1029c43224ad5898e50140c2aebb1705f19e67c918ebf5b9e797fe1" dependencies = [ "unicode-ident", ] @@ -2805,16 +2817,16 @@ checksum = "af066a9c399a26e020ada66a034357a868728e72cd426f3adcd35f80d88d88c8" dependencies = [ "proc-macro2", "quote", - "syn 2.0.37", + "syn 2.0.45", "version_check", "yansi 1.0.0-rc.1", ] [[package]] name = "query_map" -version = "0.6.0" +version = "0.7.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4465aacac3bebc9484cf7a56dc8b2d7feacb657da6002a9198b4f7af4247a204" +checksum = "5eab6b8b1074ef3359a863758dae650c7c0c6027927a085b7af911c8e0bf3a15" dependencies = [ "form_urlencoded", "serde", @@ -2833,9 +2845,9 @@ dependencies = [ [[package]] name = "quote" -version = "1.0.33" +version = "1.0.34" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "5267fca4496028628a95160fc423a33e8b2e6af8a5302579e322e4b520293cae" +checksum = "22a37c9326af5ed140c86a46655b5278de879853be5573c01df185b6f49a580a" dependencies = [ "proc-macro2", ] @@ -2897,30 +2909,30 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "52c4f3084aa3bc7dfbba4eff4fab2a54db4324965d8872ab933565e6fbd83bc6" dependencies = [ "pem", - "ring", + "ring 0.16.20", "time", "yasna", ] [[package]] name = "redox_syscall" -version = "0.3.5" +version = "0.4.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "567664f262709473930a4bf9e51bf2ebf3348f2e748ccc50dea20646858f8f29" +checksum = "4722d768eff46b75989dd134e5c353f0d6296e5aaa3132e776cbdb56be7731aa" dependencies = [ "bitflags 1.3.2", ] [[package]] name = "regex" -version = "1.9.6" +version = "1.10.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ebee201405406dbf528b8b672104ae6d6d63e6d118cb10e4d51abbc7b58044ff" +checksum = "380b951a9c5e80ddfd6136919eef32310721aa4aacd4889a8d39124b026ab343" dependencies = [ "aho-corasick", "memchr", - "regex-automata 0.3.9", - "regex-syntax 0.7.5", + "regex-automata 0.4.3", + "regex-syntax 0.8.2", ] [[package]] @@ -2934,13 +2946,13 @@ dependencies = [ [[package]] name = "regex-automata" -version = "0.3.9" +version = "0.4.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "59b23e92ee4318893fa3fe3e6fb365258efbfe6ac6ab30f090cdcbb7aa37efa9" +checksum = "5f804c7828047e88b2d32e2d7fe5a105da8ee3264f01902f796c8e067dc2483f" dependencies = [ "aho-corasick", "memchr", - "regex-syntax 0.7.5", + "regex-syntax 0.8.2", ] [[package]] @@ -2951,17 +2963,17 @@ checksum = "f162c6dd7b008981e4d40210aca20b4bd0f9b60ca9271061b07f78537722f2e1" [[package]] name = "regex-syntax" -version = "0.7.5" +version = "0.8.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "dbb5fb1acd8a1a18b3dd5be62d25485eb770e05afb408a9627d14d451bae12da" +checksum = "c08c74e62047bb2de4ff487b251e4a92e24f48745648451635cec7d591162d9f" [[package]] name = "reqwest" -version = "0.11.20" +version = "0.11.23" source = 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dependencies = [ [[package]] name = "rustix" -version = "0.38.20" +version = "0.38.28" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "67ce50cb2e16c2903e30d1cbccfd8387a74b9d4c938b6a4c5ec6cc7556f7a8a0" +checksum = "72e572a5e8ca657d7366229cdde4bd14c4eb5499a9573d4d366fe1b599daa316" dependencies = [ - "bitflags 2.4.0", + "bitflags 2.4.1", "errno", "libc", "linux-raw-sys", - "windows-sys", + "windows-sys 0.52.0", ] [[package]] name = "rustls" -version = "0.21.7" +version = "0.21.10" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "cd8d6c9f025a446bc4d18ad9632e69aec8f287aa84499ee335599fabd20c3fd8" +checksum = "f9d5a6813c0759e4609cd494e8e725babae6a2ca7b62a5536a13daaec6fcb7ba" dependencies = [ "log", - "ring", + "ring 0.17.7", "rustls-webpki", "sct", ] @@ -3072,21 +3099,21 @@ dependencies = [ [[package]] name = "rustls-pemfile" -version = "1.0.3" +version = "1.0.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2d3987094b1d07b653b7dfdc3f70ce9a1da9c51ac18c1b06b662e4f9a0e9f4b2" +checksum = "1c74cae0a4cf6ccbbf5f359f08efdf8ee7e1dc532573bf0db71968cb56b1448c" dependencies = [ - "base64", + "base64 0.21.5", ] [[package]] name = "rustls-webpki" -version = "0.101.6" +version = "0.101.7" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "3c7d5dece342910d9ba34d259310cae3e0154b873b35408b787b59bce53d34fe" +checksum = "8b6275d1ee7a1cd780b64aca7726599a1dbc893b1e64144529e55c3c2f745765" dependencies = [ - "ring", - "untrusted", + "ring 0.17.7", + "untrusted 0.9.0", ] [[package]] @@ -3097,9 +3124,9 @@ checksum = "7ffc183a10b4478d04cbbbfc96d0873219d962dd5accaff2ffbd4ceb7df837f4" [[package]] name = "ryu" -version = "1.0.15" +version = "1.0.16" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "1ad4cc8da4ef723ed60bced201181d83791ad433213d8c24efffda1eec85d741" +checksum = "f98d2aa92eebf49b69786be48e4477826b256916e84a57ff2a4f21923b48eb4c" [[package]] name = "s3s" @@ -3207,11 +3234,11 @@ dependencies = [ [[package]] name = "schannel" -version = "0.1.22" +version = "0.1.23" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "0c3733bf4cf7ea0880754e19cb5a462007c4a8c1914bff372ccc95b464f1df88" +checksum = "fbc91545643bcf3a0bbb6569265615222618bdf33ce4ffbbd13c4bbd4c093534" dependencies = [ - "windows-sys", + "windows-sys 0.52.0", ] [[package]] @@ -3222,12 +3249,12 @@ checksum = "94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49" [[package]] name = "sct" -version = "0.7.0" +version = "0.7.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "d53dcdb7c9f8158937a7981b48accfd39a43af418591a5d008c7b22b5e1b7ca4" +checksum = "da046153aa2352493d6cb7da4b6e5c0c057d8a1d0a9aa8560baffdd945acd414" dependencies = [ - "ring", - "untrusted", + "ring 0.17.7", + "untrusted 0.9.0", ] [[package]] @@ -3255,37 +3282,37 @@ dependencies = [ [[package]] name = "semver" -version = 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checksum = "2047c6ded9c721764247e62cd3b03c09ffc529b2ba5b10ec482ae507a4a70160" +[[package]] +name = "system-configuration" +version = "0.5.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "ba3a3adc5c275d719af8cb4272ea1c4a6d668a777f37e115f6d11ddbc1c8e0e7" +dependencies = [ + "bitflags 1.3.2", + "core-foundation", + "system-configuration-sys", +] + +[[package]] +name = "system-configuration-sys" +version = "0.5.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "a75fb188eb626b924683e3b95e3a48e63551fcfb51949de2f06a9d91dbee93c9" +dependencies = [ + "core-foundation-sys", + "libc", +] + [[package]] name = "tempfile" -version = "3.8.0" +version = "3.9.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "cb94d2f3cc536af71caac6b6fcebf65860b347e7ce0cc9ebe8f70d3e521054ef" +checksum = "01ce4141aa927a6d1bd34a041795abd0db1cccba5d5f24b009f694bdf3a1f3fa" dependencies = [ "cfg-if", "fastrand", "redox_syscall", "rustix", - "windows-sys", + "windows-sys 0.52.0", ] [[package]] name = "thiserror" -version = "1.0.49" +version = "1.0.53" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "1177e8c6d7ede7afde3585fd2513e611227efd6481bd78d2e82ba1ce16557ed4" +checksum = "b2cd5904763bad08ad5513ddbb12cf2ae273ca53fa9f68e843e236ec6dfccc09" dependencies = [ "thiserror-impl", ] [[package]] name = "thiserror-impl" -version = "1.0.49" +version = "1.0.53" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "10712f02019e9288794769fba95cd6847df9874d49d871d062172f9dd41bc4cc" +checksum = "3dcf4a824cce0aeacd6f38ae6f24234c8e80d68632338ebaa1443b5df9e29e19" dependencies = [ "proc-macro2", "quote", - "syn 2.0.37", + "syn 2.0.45", ] [[package]] @@ -3539,12 +3583,13 @@ dependencies = [ [[package]] name = "time" -version = "0.3.29" +version = "0.3.31" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = 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"c89b4efa943be685f629b149f53829423f8f5531ea21249408e8e2f8671ec104" dependencies = [ "backtrace", "bytes", @@ -3604,20 +3649,20 @@ dependencies = [ "parking_lot", "pin-project-lite", "signal-hook-registry", - "socket2 0.5.4", + "socket2", "tokio-macros", - "windows-sys", + "windows-sys 0.48.0", ] [[package]] name = "tokio-macros" -version = "2.1.0" +version = "2.2.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "630bdcf245f78637c13ec01ffae6187cca34625e8c63150d424b59e55af2675e" +checksum = "5b8a1e28f2deaa14e508979454cb3a223b10b938b45af148bc0986de36f1923b" dependencies = [ "proc-macro2", "quote", - "syn 2.0.37", + "syn 2.0.45", ] [[package]] @@ -3643,9 +3688,9 @@ dependencies = [ [[package]] name = "tokio-util" -version = "0.7.9" +version = "0.7.10" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "1d68074620f57a0b21594d9735eb2e98ab38b17f80d3fcb189fca266771ca60d" +checksum = 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"log", "once_cell", "proc-macro2", "quote", - "syn 2.0.37", + "syn 2.0.45", "wasm-bindgen-shared", ] [[package]] name = "wasm-bindgen-futures" -version = "0.4.37" +version = "0.4.39" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c02dbc21516f9f1f04f187958890d7e6026df8d16540b7ad9492bc34a67cea03" +checksum = "ac36a15a220124ac510204aec1c3e5db8a22ab06fd6706d881dc6149f8ed9a12" dependencies = [ "cfg-if", "js-sys", @@ -4021,9 +4097,9 @@ dependencies = [ [[package]] name = "wasm-bindgen-macro" -version = "0.2.87" +version = "0.2.89" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "dee495e55982a3bd48105a7b947fd2a9b4a8ae3010041b9e0faab3f9cd028f1d" +checksum = "0162dbf37223cd2afce98f3d0785506dcb8d266223983e4b5b525859e6e182b2" dependencies = [ "quote", "wasm-bindgen-macro-support", @@ -4031,28 +4107,28 @@ dependencies = [ [[package]] name = "wasm-bindgen-macro-support" -version = "0.2.87" +version = "0.2.89" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "54681b18a46765f095758388f2d0cf16eb8d4169b639ab575a8f5693af210c7b" +checksum = "f0eb82fcb7930ae6219a7ecfd55b217f5f0893484b7a13022ebb2b2bf20b5283" dependencies = [ "proc-macro2", "quote", - "syn 2.0.37", + "syn 2.0.45", "wasm-bindgen-backend", "wasm-bindgen-shared", ] [[package]] name = "wasm-bindgen-shared" -version = "0.2.87" +version = "0.2.89" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ca6ad05a4870b2bf5fe995117d3728437bd27d7cd5f06f13c17443ef369775a1" +checksum = "7ab9b36309365056cd639da3134bf87fa8f3d86008abf99e612384a6eecd459f" [[package]] name = "web-sys" -version = "0.3.64" +version = "0.3.66" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "9b85cbef8c220a6abc02aefd892dfc0fc23afb1c6a426316ec33253a3877249b" +checksum = "50c24a44ec86bb68fbecd1b3efed7e85ea5621b39b35ef2766b66cd984f8010f" dependencies = [ "js-sys", "wasm-bindgen", @@ -4060,9 +4136,9 @@ dependencies = [ [[package]] name = "webpki-roots" -version = "0.25.2" +version = "0.25.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "14247bb57be4f377dfb94c72830b8ce8fc6beac03cf4bf7b9732eadd414123fc" +checksum = "1778a42e8b3b90bff8d0f5032bf22250792889a5cdc752aa0020c84abe3aaf10" [[package]] name = "winapi" @@ -4096,12 +4172,12 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f" [[package]] -name = "windows" -version = "0.48.0" +name = "windows-core" +version = "0.52.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e686886bc078bc1b0b600cac0147aadb815089b6e4da64016cbd754b6342700f" +checksum = "33ab640c8d7e35bf8ba19b884ba838ceb4fba93a4e8c65a9059d08afcfc683d9" dependencies = [ - "windows-targets", + "windows-targets 0.52.0", ] [[package]] @@ -4110,7 +4186,16 @@ version = "0.48.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "677d2418bec65e3338edb076e806bc1ec15693c5d0104683f2efe857f61056a9" dependencies = [ - "windows-targets", + "windows-targets 0.48.5", +] + +[[package]] +name = "windows-sys" +version = "0.52.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d" +dependencies = [ + "windows-targets 0.52.0", ] [[package]] @@ -4119,13 +4204,28 @@ version = "0.48.5" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c" dependencies = [ - "windows_aarch64_gnullvm", - "windows_aarch64_msvc", - "windows_i686_gnu", - "windows_i686_msvc", - "windows_x86_64_gnu", - "windows_x86_64_gnullvm", - "windows_x86_64_msvc", + "windows_aarch64_gnullvm 0.48.5", + "windows_aarch64_msvc 0.48.5", + "windows_i686_gnu 0.48.5", + "windows_i686_msvc 0.48.5", + "windows_x86_64_gnu 0.48.5", + "windows_x86_64_gnullvm 0.48.5", + "windows_x86_64_msvc 0.48.5", +] + +[[package]] +name = "windows-targets" +version = "0.52.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "8a18201040b24831fbb9e4eb208f8892e1f50a37feb53cc7ff887feb8f50e7cd" +dependencies = [ + "windows_aarch64_gnullvm 0.52.0", + "windows_aarch64_msvc 0.52.0", + "windows_i686_gnu 0.52.0", + "windows_i686_msvc 0.52.0", + "windows_x86_64_gnu 0.52.0", + "windows_x86_64_gnullvm 0.52.0", + "windows_x86_64_msvc 0.52.0", ] [[package]] @@ -4134,47 +4234,89 @@ version = "0.48.5" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8" +[[package]] +name = "windows_aarch64_gnullvm" +version = "0.52.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "cb7764e35d4db8a7921e09562a0304bf2f93e0a51bfccee0bd0bb0b666b015ea" + [[package]] name = "windows_aarch64_msvc" version = 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"windows_i686_msvc" +version = "0.52.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "ffe5e8e31046ce6230cc7215707b816e339ff4d4d67c65dffa206fd0f7aa7b9a" + [[package]] name = "windows_x86_64_gnu" version = "0.48.5" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e" +[[package]] +name = "windows_x86_64_gnu" +version = "0.52.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "3d6fa32db2bc4a2f5abeacf2b69f7992cd09dca97498da74a151a3132c26befd" + [[package]] name = "windows_x86_64_gnullvm" version = "0.48.5" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc" +[[package]] +name = "windows_x86_64_gnullvm" +version = "0.52.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "1a657e1e9d3f514745a572a6846d3c7aa7dbe1658c056ed9c3344c4109a6949e" + [[package]] name = "windows_x86_64_msvc" version = "0.48.5" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538" +[[package]] +name = "windows_x86_64_msvc" +version = "0.52.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "dff9641d1cd4be8d1a070daf9e3773c5f67e78b4d9d42263020c057706765c04" + [[package]] name = "winnow" -version = "0.5.15" +version = "0.5.31" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7c2e3184b9c4e92ad5167ca73039d0c42476302ab603e2fec4487511f38ccefc" +checksum = "97a4882e6b134d6c28953a387571f1acdd3496830d5e36c5e3a1075580ea641c" dependencies = [ "memchr", ] @@ -4186,7 +4328,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "524e57b2c537c0f9b1e69f1965311ec12182b4122e45035b1508cd24d2adadb1" dependencies = [ "cfg-if", - "windows-sys", + "windows-sys 0.48.0", ] [[package]] @@ -4225,38 +4367,56 @@ dependencies = [ "time", ] +[[package]] +name = "zerocopy" +version = "0.7.32" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "74d4d3961e53fa4c9a25a8637fc2bfaf2595b3d3ae34875568a5cf64787716be" +dependencies = [ + "zerocopy-derive", +] + +[[package]] +name = "zerocopy-derive" +version = "0.7.32" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "9ce1b18ccd8e73a9321186f97e46f9f04b778851177567b1975109d26a08d2a6" +dependencies = [ + "proc-macro2", + "quote", + "syn 2.0.45", +] + [[package]] name = "zeroize" -version = "1.6.0" +version = "1.7.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2a0956f1ba7c7909bfb66c2e9e4124ab6f6482560f6628b5aaeba39207c9aad9" +checksum = "525b4ec142c6b68a2d10f01f7bbf6755599ca3f81ea53b8431b7dd348f5fdb2d" [[package]] name = "zstd" -version = "0.12.4" +version = "0.13.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "1a27595e173641171fc74a1232b7b1c7a7cb6e18222c11e9dfb9888fa424c53c" +checksum = "bffb3309596d527cfcba7dfc6ed6052f1d39dfbd7c867aa2e865e4a449c10110" dependencies = [ "zstd-safe", ] [[package]] name = "zstd-safe" -version = "6.0.6" +version = "7.0.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ee98ffd0b48ee95e6c5168188e44a54550b1564d9d530ee21d5f0eaed1069581" +checksum = "43747c7422e2924c11144d5229878b98180ef8b06cca4ab5af37afc8a8d8ea3e" dependencies = [ - "libc", "zstd-sys", ] [[package]] name = "zstd-sys" -version = "2.0.8+zstd.1.5.5" +version = "2.0.9+zstd.1.5.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "5556e6ee25d32df2586c098bbfa278803692a20d0ab9565e049480d52707ec8c" +checksum = "9e16efa8a874a0481a574084d34cc26fdb3b99627480f785888deb6386506656" dependencies = [ "cc", - "libc", "pkg-config", ] diff --git a/htsget-actix/src/lib.rs b/htsget-actix/src/lib.rs index 3e84edf5..5408cd36 100644 --- a/htsget-actix/src/lib.rs +++ b/htsget-actix/src/lib.rs @@ -201,8 +201,7 @@ mod tests { #[async_trait(?Send)] impl TestServer> for ActixTestServer { async fn get_expected_path(&self) -> String { - let mut bind_data_server = - BindDataServer::try_from(self.get_config().data_server().clone()).unwrap(); + let mut bind_data_server = BindDataServer::from(self.get_config().data_server().clone()); let server = bind_data_server.bind_data_server().await.unwrap(); let addr = server.local_addr(); diff --git a/htsget-config/Cargo.toml b/htsget-config/Cargo.toml index b8803d42..d8e6eb89 100644 --- a/htsget-config/Cargo.toml +++ b/htsget-config/Cargo.toml @@ -18,7 +18,7 @@ default = [] [dependencies] thiserror = "1.0" async-trait = "0.1" -noodles = { version = "0.50", features = ["core"] } +noodles = { version = "0.60", features = ["core"] } serde = { version = "1.0", features = ["derive"] } serde_with = "3.0" serde_regex = "1.1" diff --git a/htsget-lambda/Cargo.toml b/htsget-lambda/Cargo.toml index 41b249ab..e5b13059 100644 --- a/htsget-lambda/Cargo.toml +++ b/htsget-lambda/Cargo.toml @@ -34,5 +34,5 @@ bytes = "1.4" [dev-dependencies] async-trait = "0.1" -query_map = { version = "0.6", features = ["url-query"] } +query_map = { version = "0.7", features = ["url-query"] } tempfile = "3.6" diff --git a/htsget-lambda/src/lib.rs b/htsget-lambda/src/lib.rs index e6c5ae0b..a4c141ba 100644 --- a/htsget-lambda/src/lib.rs +++ b/htsget-lambda/src/lib.rs @@ -708,7 +708,7 @@ mod tests { } async fn spawn_server(config: &Config) -> String { - let mut bind_data_server = BindDataServer::try_from(config.data_server().clone()).unwrap(); + let mut bind_data_server = BindDataServer::from(config.data_server().clone()); let server = bind_data_server.bind_data_server().await.unwrap(); let addr = server.local_addr(); diff --git a/htsget-search/Cargo.toml b/htsget-search/Cargo.toml index 4e62e303..ef479878 100644 --- a/htsget-search/Cargo.toml +++ b/htsget-search/Cargo.toml @@ -47,7 +47,7 @@ futures-util = "0.3" async-trait = "0.1" # Noodles -noodles = { version = "0.50", features = ["async", "core", "bgzf", "bam", "bcf", "cram", "csi", "sam", "tabix", "vcf"] } +noodles = { version = "0.60", features = ["async", "core", "bgzf", "bam", "bcf", "cram", "csi", "sam", "tabix", "vcf"] } # Amazon S3 bytes = { version = "1.4", optional = true } diff --git a/htsget-search/src/htsget/bam_search.rs b/htsget-search/src/htsget/bam_search.rs index 610cd47f..6eafaabc 100644 --- a/htsget-search/src/htsget/bam_search.rs +++ b/htsget-search/src/htsget/bam_search.rs @@ -7,10 +7,12 @@ use std::sync::Arc; use async_trait::async_trait; use noodles::bam; use noodles::bam::bai; +use noodles::bam::bai::Index; use noodles::bgzf; use noodles::bgzf::VirtualPosition; -use noodles::csi::index::ReferenceSequence; -use noodles::csi::Index; +use noodles::csi::binning_index::index::reference_sequence::index::LinearIndex; +use noodles::csi::binning_index::index::ReferenceSequence; +use noodles::csi::BinningIndex; use noodles::sam::header::record::value::map::read_group::platform::ParseError; use noodles::sam::header::record::value::map::read_group::Platform; use noodles::sam::Header; @@ -35,7 +37,8 @@ pub struct BamSearch { } #[async_trait] -impl BgzfSearch, Header> for BamSearch +impl BgzfSearch, Header> + for BamSearch where S: Storage + Send + Sync + 'static, ReaderType: AsyncRead + Unpin + Send + Sync, @@ -47,7 +50,7 @@ where index: &Index, ) -> Result> { trace!("getting byte ranges for unmapped reads"); - let last_interval = index.first_record_in_last_linear_bin_start_position(); + let last_interval = index.last_first_record_start_position(); let start = match last_interval { Some(start) => start, None => { @@ -78,7 +81,8 @@ where } #[async_trait] -impl Search, Header> +impl + Search, Index, AsyncReader, Header> for BamSearch where S: Storage + Send + Sync + 'static, @@ -121,7 +125,6 @@ where async fn read_index_inner(inner: T) -> io::Result { let mut reader = bai::AsyncReader::new(BufReader::new(inner)); - reader.read_header().await?; reader.read_index().await } @@ -150,7 +153,7 @@ where #[async_trait] impl - SearchReads, Header> + SearchReads, Index, AsyncReader, Header> for BamSearch where S: Storage + Send + Sync + 'static, diff --git a/htsget-search/src/htsget/bcf_search.rs b/htsget-search/src/htsget/bcf_search.rs index 6b62433e..fa5717aa 100644 --- a/htsget-search/src/htsget/bcf_search.rs +++ b/htsget-search/src/htsget/bcf_search.rs @@ -7,7 +7,8 @@ use async_trait::async_trait; use futures_util::stream::FuturesOrdered; use noodles::bcf; use noodles::bgzf::VirtualPosition; -use noodles::csi::index::ReferenceSequence; +use noodles::csi::binning_index::index::reference_sequence::index::BinnedIndex; +use noodles::csi::binning_index::index::ReferenceSequence; use noodles::csi::Index; use noodles::vcf::Header; use noodles::{bgzf, csi}; @@ -28,7 +29,8 @@ pub struct BcfSearch { } #[async_trait] -impl BgzfSearch, Header> for BcfSearch +impl BgzfSearch, Header> + for BcfSearch where S: Storage + Send + Sync + 'static, ReaderType: AsyncRead + Unpin + Send + Sync, @@ -43,7 +45,8 @@ where } #[async_trait] -impl Search, Header> +impl + Search, Index, AsyncReader, Header> for BcfSearch where S: Storage + Send + Sync + 'static, diff --git a/htsget-search/src/htsget/search.rs b/htsget-search/src/htsget/search.rs index b3d9beba..88fc56d9 100644 --- a/htsget-search/src/htsget/search.rs +++ b/htsget-search/src/htsget/search.rs @@ -12,9 +12,11 @@ use async_trait::async_trait; use futures::StreamExt; use futures_util::stream::FuturesOrdered; use noodles::bgzf::{gzi, VirtualPosition}; -use noodles::csi::index::reference_sequence::bin::Chunk; -use noodles::csi::index::ReferenceSequence; -use noodles::csi::Index; +use noodles::csi::binning_index::index::reference_sequence::bin::Chunk; +use noodles::csi::binning_index::index::Index; +use noodles::csi::binning_index::index::{reference_sequence, ReferenceSequence}; +use noodles::csi::binning_index::ReferenceSequence as ReferenceSequenceExt; +use noodles::csi::BinningIndex; use tokio::io; use tokio::io::{AsyncRead, BufReader}; use tokio::select; @@ -373,22 +375,24 @@ where /// BAM, BCF, and VCF. /// /// [S] is the storage type. +/// [I] the index type used for the `ReferenceSequence`. /// [ReaderType] is the inner type used for [Reader]. /// [ReferenceSequence] is the reference sequence type of the format's index. /// [Index] is the format's index type. /// [Reader] is the format's reader type. /// [Header] is the format's header type. #[async_trait] -pub trait BgzfSearch: - Search +pub trait BgzfSearch: + Search, Index, Reader, Header> where S: Storage + Send + Sync + 'static, + I: reference_sequence::Index + Send + Sync, ReaderType: AsyncRead + Unpin + Send + Sync, Reader: Send + Sync, Header: Send + Sync, { #[instrument(level = "trace", skip_all)] - fn index_positions(index: &Index) -> BTreeSet { + fn index_positions(index: &Index) -> BTreeSet { trace!("getting possible index positions"); let mut positions = BTreeSet::new(); @@ -425,7 +429,7 @@ where &self, query: &Query, ref_seq_id: usize, - index: &Index, + index: &Index, ) -> Result> { let chunks: Result> = trace_span!("querying chunks").in_scope(|| { trace!(id = ?query.id(), ref_seq_id = ?ref_seq_id, "querying chunks"); @@ -538,7 +542,7 @@ where async fn get_byte_ranges_for_unmapped( &self, _query: &Query, - _index: &Index, + _index: &Index, ) -> Result> { Ok(Vec::new()) } @@ -551,14 +555,15 @@ where } #[async_trait] -impl - SearchAll for T +impl + SearchAll, Index, Reader, Header> for T where S: Storage + Send + Sync + 'static, + I: reference_sequence::Index + Send + Sync, ReaderType: AsyncRead + Unpin + Send + Sync, Reader: Send + Sync, Header: Send + Sync, - T: BgzfSearch + Send + Sync, + T: BgzfSearch + Send + Sync, { #[instrument(level = "debug", skip(self), ret)] async fn get_byte_ranges_for_all(&self, query: &Query) -> Result> { @@ -568,7 +573,7 @@ where } #[instrument(level = "trace", skip_all, ret)] - async fn get_header_end_offset(&self, index: &Index) -> Result { + async fn get_header_end_offset(&self, index: &Index) -> Result { let first_index_position = Self::index_positions(index) .into_iter() @@ -587,7 +592,7 @@ where async fn get_byte_ranges_for_header( &self, - index: &Index, + index: &Index, header: &Header, reader: &mut Reader, query: &Query, diff --git a/htsget-search/src/htsget/vcf_search.rs b/htsget-search/src/htsget/vcf_search.rs index 80aad9fe..0573273e 100644 --- a/htsget-search/src/htsget/vcf_search.rs +++ b/htsget-search/src/htsget/vcf_search.rs @@ -7,9 +7,11 @@ use async_trait::async_trait; use futures_util::stream::FuturesOrdered; use noodles::bgzf; use noodles::bgzf::VirtualPosition; -use noodles::csi::index::ReferenceSequence; -use noodles::csi::Index; +use noodles::csi::binning_index::index::reference_sequence::index::LinearIndex; +use noodles::csi::binning_index::index::ReferenceSequence; +use noodles::csi::BinningIndex; use noodles::tabix; +use noodles::tabix::Index; use noodles::vcf; use noodles::vcf::Header; use tokio::io; @@ -30,7 +32,8 @@ pub struct VcfSearch { } #[async_trait] -impl BgzfSearch, Header> for VcfSearch +impl BgzfSearch, Header> + for VcfSearch where S: Storage + Send + Sync + 'static, ReaderType: AsyncRead + Unpin + Send + Sync, @@ -48,7 +51,8 @@ where } #[async_trait] -impl Search, Header> +impl + Search, Index, AsyncReader, Header> for VcfSearch where S: Storage + Send + Sync + 'static, diff --git a/htsget-test/Cargo.toml b/htsget-test/Cargo.toml index ed3037a0..60c5ca1a 100644 --- a/htsget-test/Cargo.toml +++ b/htsget-test/Cargo.toml @@ -47,7 +47,7 @@ default = [] # Server tests dependencies htsget-config = { version = "0.8.0", path = "../htsget-config", default-features = false, optional = true } -noodles = { version = "0.50", optional = true, features = ["async", "bgzf", "vcf"] } +noodles = { version = "0.60", optional = true, features = ["async", "bgzf", "vcf"] } reqwest = { version = "0.11", default-features = false, features = ["json", "rustls-tls"], optional = true } tokio = { version = "1", features = ["rt-multi-thread"], optional = true }