From 8685c7eea89311400b19a39876914e0d93a8e297 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 2 Feb 2026 10:58:40 +0000 Subject: [PATCH] Bump bio from 2.3.0 to 3.0.0 Bumps [bio](https://github.com/rust-bio/rust-bio) from 2.3.0 to 3.0.0. - [Release notes](https://github.com/rust-bio/rust-bio/releases) - [Changelog](https://github.com/rust-bio/rust-bio/blob/master/CHANGELOG.md) - [Commits](https://github.com/rust-bio/rust-bio/compare/v2.3.0...v3.0.0) --- updated-dependencies: - dependency-name: bio dependency-version: 3.0.0 dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- Cargo.lock | 141 +++++++++++++++++++++++++++++++++++++++++------------ Cargo.toml | 2 +- 2 files changed, 112 insertions(+), 31 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 558cf95..5ab6ba5 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -90,9 +90,9 @@ checksum = "c08606f8c3cbf4ce6ec8e28fb0014a2c086708fe954eaa885384a6165172e7e8" [[package]] name = "bio" -version = "2.3.0" +version = "3.0.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "add46f280e82963d4abb6f2c78f491a1f45be23ba27516856a1efbf194107bb7" +checksum = "2169c40f17068bcf0563e5060ed6ccab694f68068133055f6e96bcdf987b3f32" dependencies = [ "anyhow", "approx", @@ -102,12 +102,13 @@ dependencies = [ "bytecount", "csv", "custom_derive", + "derefable", "editdistancek", "enum-map", "fxhash", + "getset", "itertools", "itertools-num", - "lazy_static", "multimap", "ndarray", "newtype_derive", @@ -260,9 +261,9 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "2a0b5487afeab2deb2ff4e03a807ad1a03ac532ff5a2cee5d86884440c7f7671" dependencies = [ "heck", - "proc-macro2", - "quote", - "syn", + "proc-macro2 1.0.103", + "quote 1.0.41", + "syn 2.0.108", ] [[package]] @@ -356,15 +357,26 @@ version = "0.1.7" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "ef8ae57c4978a2acd8b869ce6b9ca1dfe817bff704c220209fdef2c0b75a01b9" +[[package]] +name = "derefable" +version = "0.1.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "e519abf1289075763071c981958e89948b079fc54962617a0e6413d9ce44cbe7" +dependencies = [ + "proc-macro2 0.4.30", + "quote 0.6.13", + "syn 0.15.44", +] + [[package]] name = "derive-new" version = "0.6.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "d150dea618e920167e5973d70ae6ece4385b7164e0d799fe7c122dd0a5d912ad" dependencies = [ - "proc-macro2", - "quote", - "syn", + "proc-macro2 1.0.103", + "quote 1.0.41", + "syn 2.0.108", ] [[package]] @@ -394,9 +406,9 @@ version = "0.17.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "f282cfdfe92516eb26c2af8589c274c7c17681f5ecc03c18255fe741c6aa64eb" dependencies = [ - "proc-macro2", - "quote", - "syn", + "proc-macro2 1.0.103", + "quote 1.0.41", + "syn 2.0.108", ] [[package]] @@ -460,6 +472,18 @@ dependencies = [ "wasi", ] +[[package]] +name = "getset" +version = "0.1.6" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "9cf0fc11e47561d47397154977bc219f4cf809b2974facc3ccb3b89e2436f912" +dependencies = [ + "proc-macro-error2", + "proc-macro2 1.0.103", + "quote 1.0.41", + "syn 2.0.108", +] + [[package]] name = "hashbrown" version = "0.15.5" @@ -800,6 +824,37 @@ dependencies = [ "zerocopy", ] +[[package]] +name = "proc-macro-error-attr2" +version = "2.0.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "96de42df36bb9bba5542fe9f1a054b8cc87e172759a1868aa05c1f3acc89dfc5" +dependencies = [ + "proc-macro2 1.0.103", + "quote 1.0.41", +] + +[[package]] +name = "proc-macro-error2" +version = "2.0.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "11ec05c52be0a07b08061f7dd003e7d7092e0472bc731b4af7bb1ef876109802" +dependencies = [ + "proc-macro-error-attr2", + "proc-macro2 1.0.103", + "quote 1.0.41", + "syn 2.0.108", +] + +[[package]] +name = "proc-macro2" +version = "0.4.30" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "cf3d2011ab5c909338f7887f4fc896d35932e29146c12c8d01da6b22a80ba759" +dependencies = [ + "unicode-xid", +] + [[package]] name = "proc-macro2" version = "1.0.103" @@ -809,13 +864,22 @@ dependencies = [ "unicode-ident", ] +[[package]] +name = "quote" +version = "0.6.13" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "6ce23b6b870e8f94f81fb0a363d65d86675884b34a09043c81e5562f11c1f8e1" +dependencies = [ + "proc-macro2 0.4.30", +] + [[package]] name = "quote" version = "1.0.41" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "ce25767e7b499d1b604768e7cde645d14cc8584231ea6b295e9c9eb22c02e1d1" dependencies = [ - "proc-macro2", + "proc-macro2 1.0.103", ] [[package]] @@ -974,9 +1038,9 @@ version = "1.0.228" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "d540f220d3187173da220f885ab66608367b6574e925011a9353e4badda91d79" dependencies = [ - "proc-macro2", - "quote", - "syn", + "proc-macro2 1.0.103", + "quote 1.0.41", + "syn 2.0.108", ] [[package]] @@ -1035,10 +1099,21 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "4c6bee85a5a24955dc440386795aa378cd9cf82acd5f764469152d2270e581be" dependencies = [ "heck", - "proc-macro2", - "quote", + "proc-macro2 1.0.103", + "quote 1.0.41", "rustversion", - "syn", + "syn 2.0.108", +] + +[[package]] +name = "syn" +version = "0.15.44" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "9ca4b3b69a77cbe1ffc9e198781b7acb0c7365a883670e8f1c1bc66fba79a5c5" +dependencies = [ + "proc-macro2 0.4.30", + "quote 0.6.13", + "unicode-xid", ] [[package]] @@ -1047,8 +1122,8 @@ version = "2.0.108" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "da58917d35242480a05c2897064da0a80589a2a0476c9a3f2fdc83b53502e917" dependencies = [ - "proc-macro2", - "quote", + "proc-macro2 1.0.103", + "quote 1.0.41", "unicode-ident", ] @@ -1076,9 +1151,9 @@ version = "1.0.69" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "4fee6c4efc90059e10f81e6d42c60a18f76588c3d74cb83a0b242a2b6c7504c1" dependencies = [ - "proc-macro2", - "quote", - "syn", + "proc-macro2 1.0.103", + "quote 1.0.41", + "syn 2.0.108", ] [[package]] @@ -1087,9 +1162,9 @@ version = "2.0.17" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "3ff15c8ecd7de3849db632e14d18d2571fa09dfc5ed93479bc4485c7a517c913" dependencies = [ - "proc-macro2", - "quote", - "syn", + "proc-macro2 1.0.103", + "quote 1.0.41", + "syn 2.0.108", ] [[package]] @@ -1110,6 +1185,12 @@ version = "1.0.22" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "9312f7c4f6ff9069b165498234ce8be658059c6728633667c526e27dc2cf1df5" +[[package]] +name = "unicode-xid" +version = "0.1.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "fc72304796d0818e357ead4e000d19c9c174ab23dc11093ac919054d20a6a7fc" + [[package]] name = "utf8parse" version = "0.2.2" @@ -1251,7 +1332,7 @@ version = "0.8.27" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "88d2b8d9c68ad2b9e4340d7832716a4d21a22a1154777ad56ea55c51a9cf3831" dependencies = [ - "proc-macro2", - "quote", - "syn", + "proc-macro2 1.0.103", + "quote 1.0.41", + "syn 2.0.108", ] diff --git a/Cargo.toml b/Cargo.toml index 177f821..c9179bb 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -9,7 +9,7 @@ description = "A tool to filter fastq files" # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html [dependencies] -bio = "2.2.0" +bio = "3.0.0" clap = { version = "4.5.37", features = ["derive"] } crossbeam-channel = "0.5" rayon = "1.7.0"