From 923076149eb5a60a03c8ede101854083e1345ac0 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sat, 1 Nov 2025 21:23:58 +0000 Subject: [PATCH] chore(deps): Bump the noodles group with 4 updates Bumps the noodles group with 4 updates: [noodles-bgzf](https://github.com/zaeleus/noodles), [noodles-bam](https://github.com/zaeleus/noodles), [noodles-bed](https://github.com/zaeleus/noodles) and [noodles-fastq](https://github.com/zaeleus/noodles). Updates `noodles-bgzf` from 0.36.0 to 0.42.0 - [Commits](https://github.com/zaeleus/noodles/compare/noodles-bgzf-0.36.0...noodles-bgzf-0.42.0) Updates `noodles-bam` from 0.81.0 to 0.83.0 - [Commits](https://github.com/zaeleus/noodles/compare/noodles-bam-0.81.0...noodles-bam-0.83.0) Updates `noodles-bed` from 0.26.0 to 0.28.0 - [Commits](https://github.com/zaeleus/noodles/compare/noodles-bed-0.26.0...noodles-bed-0.28.0) Updates `noodles-fastq` from 0.19.0 to 0.21.0 - [Commits](https://github.com/zaeleus/noodles/compare/noodles-fastq-0.19.0...noodles-fastq-0.21.0) --- updated-dependencies: - dependency-name: noodles-bgzf dependency-version: 0.42.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: noodles - dependency-name: noodles-bam dependency-version: 0.83.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: noodles - dependency-name: noodles-bed dependency-version: 0.28.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: noodles - dependency-name: noodles-fastq dependency-version: 0.21.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: noodles ... Signed-off-by: dependabot[bot] --- Cargo.lock | 165 +++++++++++++++++-------- Cargo.toml | 2 +- datafusion/bio-format-bam/Cargo.toml | 2 +- datafusion/bio-format-bed/Cargo.toml | 2 +- datafusion/bio-format-fastq/Cargo.toml | 2 +- 5 files changed, 116 insertions(+), 57 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 8f9ddc7..70df2a1 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -904,8 +904,8 @@ dependencies = [ "futures", "futures-util", "log", - "noodles-bam 0.81.0", - "noodles-bgzf 0.36.0", + "noodles-bam 0.83.0", + "noodles-bgzf 0.42.0 (registry+https://github.com/rust-lang/crates.io-index)", "noodles-sam 0.77.0", "opendal", "tokio", @@ -929,7 +929,7 @@ dependencies = [ "log", "noodles 0.93.0", "noodles-bed", - "noodles-bgzf 0.36.0", + "noodles-bgzf 0.42.0 (registry+https://github.com/rust-lang/crates.io-index)", "opendal", "tokio", "tokio-util", @@ -946,7 +946,7 @@ dependencies = [ "futures", "log", "noodles 0.93.0", - "noodles-bgzf 0.36.0", + "noodles-bgzf 0.42.0 (registry+https://github.com/rust-lang/crates.io-index)", "opendal", "tempfile", "tokio", @@ -966,7 +966,7 @@ dependencies = [ "futures", "futures-util", "log", - "noodles-bgzf 0.36.0", + "noodles-bgzf 0.42.0 (registry+https://github.com/rust-lang/crates.io-index)", "noodles-cram 0.85.0", "noodles-fasta 0.55.0 (git+https://github.com/biodatageeks/noodles.git?rev=d6f205e9bb5369762236724fb54d24c5e1d9b79a)", "noodles-sam 0.78.0", @@ -989,7 +989,7 @@ dependencies = [ "futures-util", "log", "noodles 0.93.0", - "noodles-bgzf 0.36.0", + "noodles-bgzf 0.42.0 (registry+https://github.com/rust-lang/crates.io-index)", "noodles-fasta 0.55.0 (git+https://github.com/biodatageeks/noodles.git?rev=289ef32e7d43d142914fb3f02335044ae293871c)", "opendal", "tokio", @@ -1010,8 +1010,8 @@ dependencies = [ "futures-util", "log", "noodles 0.93.0", - "noodles-bgzf 0.36.0", - "noodles-fastq 0.19.0", + "noodles-bgzf 0.42.0 (registry+https://github.com/rust-lang/crates.io-index)", + "noodles-fastq 0.21.0", "opendal", "tokio", "tokio-util", @@ -1035,7 +1035,7 @@ dependencies = [ "futures-util", "log", "noodles 0.93.0", - "noodles-bgzf 0.36.0", + "noodles-bgzf 0.42.0 (registry+https://github.com/rust-lang/crates.io-index)", "noodles-gff 0.51.0", "opendal", "tokio", @@ -1058,7 +1058,7 @@ dependencies = [ "futures", "log", "noodles 0.100.0", - "noodles-bgzf 0.36.0", + "noodles-bgzf 0.42.0 (registry+https://github.com/rust-lang/crates.io-index)", "noodles-vcf 0.80.0", "opendal", "tempfile", @@ -2667,35 +2667,34 @@ dependencies = [ [[package]] name = "noodles-bam" -version = "0.81.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "05df875ba2b10c2fcc0b12700671682d28392af021339d5edcb918ea8b324811" +version = "0.82.0" +source = "git+https://github.com/biodatageeks/noodles.git?rev=d6f205e9bb5369762236724fb54d24c5e1d9b79a#d6f205e9bb5369762236724fb54d24c5e1d9b79a" dependencies = [ "bstr", - "byteorder", - "futures", "indexmap", "memchr", - "noodles-bgzf 0.41.0", - "noodles-core 0.17.0", - "noodles-csi 0.49.0", - "noodles-sam 0.77.0", - "pin-project-lite", - "tokio", + "noodles-bgzf 0.42.0 (git+https://github.com/biodatageeks/noodles.git?rev=d6f205e9bb5369762236724fb54d24c5e1d9b79a)", + "noodles-core 0.18.0 (git+https://github.com/biodatageeks/noodles.git?rev=d6f205e9bb5369762236724fb54d24c5e1d9b79a)", + "noodles-csi 0.50.0 (git+https://github.com/biodatageeks/noodles.git?rev=d6f205e9bb5369762236724fb54d24c5e1d9b79a)", + "noodles-sam 0.78.0", ] [[package]] name = "noodles-bam" -version = "0.82.0" -source = "git+https://github.com/biodatageeks/noodles.git?rev=d6f205e9bb5369762236724fb54d24c5e1d9b79a#d6f205e9bb5369762236724fb54d24c5e1d9b79a" +version = "0.83.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "7480c171f2d2e108f64e504b073dceccd886bf4a5af06d18e65497a4a48e6dd2" dependencies = [ "bstr", + "futures", "indexmap", "memchr", - "noodles-bgzf 0.42.0 (git+https://github.com/biodatageeks/noodles.git?rev=d6f205e9bb5369762236724fb54d24c5e1d9b79a)", - "noodles-core 0.18.0 (git+https://github.com/biodatageeks/noodles.git?rev=d6f205e9bb5369762236724fb54d24c5e1d9b79a)", - "noodles-csi 0.50.0 (git+https://github.com/biodatageeks/noodles.git?rev=d6f205e9bb5369762236724fb54d24c5e1d9b79a)", - "noodles-sam 0.78.0", + "noodles-bgzf 0.43.0", + "noodles-core 0.18.0 (registry+https://github.com/rust-lang/crates.io-index)", + "noodles-csi 0.51.0", + "noodles-sam 0.79.0", + "pin-project-lite", + "tokio", ] [[package]] @@ -2718,17 +2717,17 @@ dependencies = [ [[package]] name = "noodles-bed" -version = "0.26.0" +version = "0.28.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "3b1628807aa4c3068c91c84592389b38304825dcbe0f9b0bb0f9382c94f11fc7" +checksum = "42f763310372b00c358bb7450111595bc9c50a0abc39d673f65b0904c9790633" dependencies = [ "bstr", "lexical-core", "memchr", - "noodles-bgzf 0.41.0", - "noodles-core 0.17.0", - "noodles-csi 0.49.0", - "noodles-tabix 0.55.0", + "noodles-bgzf 0.43.0", + "noodles-core 0.18.0 (registry+https://github.com/rust-lang/crates.io-index)", + "noodles-csi 0.51.0", + "noodles-tabix 0.57.0", ] [[package]] @@ -2742,7 +2741,6 @@ dependencies = [ "crossbeam-channel", "flate2", "futures", - "libdeflater", "pin-project-lite", "tokio", "tokio-util", @@ -2758,10 +2756,18 @@ dependencies = [ "bytes", "crossbeam-channel", "flate2", - "futures", - "pin-project-lite", - "tokio", - "tokio-util", +] + +[[package]] +name = "noodles-bgzf" +version = "0.42.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "7c1c3e3f19c4afd0c540104e596a9312074de9d0c01bedd5370ffba62ba3b439" +dependencies = [ + "bytes", + "crossbeam-channel", + "flate2", + "libdeflater", ] [[package]] @@ -2798,6 +2804,21 @@ dependencies = [ "flate2", ] +[[package]] +name = "noodles-bgzf" +version = "0.43.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "a29d42d77c0d9cac346e94e788a1f5627b5721f211edcd268b3ef93a50723208" +dependencies = [ + "bytes", + "crossbeam-channel", + "flate2", + "futures", + "pin-project-lite", + "tokio", + "tokio-util", +] + [[package]] name = "noodles-core" version = "0.16.0" @@ -2816,6 +2837,15 @@ dependencies = [ "bstr", ] +[[package]] +name = "noodles-core" +version = "0.18.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "8ebfc6396fb51059c98a35bb81b96422ac41ea1bc60b6c8e9c6b2550212e9493" +dependencies = [ + "bstr", +] + [[package]] name = "noodles-core" version = "0.18.0" @@ -2939,6 +2969,19 @@ dependencies = [ "noodles-core 0.18.0 (git+https://github.com/biodatageeks/noodles.git?rev=d6f205e9bb5369762236724fb54d24c5e1d9b79a)", ] +[[package]] +name = "noodles-csi" +version = "0.51.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "03338575b1537f6fa1006bb6138fafea98b73dd3dd687b96727076531de924cc" +dependencies = [ + "bit-vec", + "bstr", + "indexmap", + "noodles-bgzf 0.43.0", + "noodles-core 0.18.0 (registry+https://github.com/rust-lang/crates.io-index)", +] + [[package]] name = "noodles-fasta" version = "0.49.0" @@ -2995,9 +3038,9 @@ dependencies = [ [[package]] name = "noodles-fastq" -version = "0.19.0" +version = "0.21.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "509abf632d0aca5181eb137e4662bd2bdce9f82d75a46689b4d926df00074223" +checksum = "db9a66608bdbe2a2e1ece0b963a9c3bcbf922ca5600c3b6ba6cb96cf6f8d6458" dependencies = [ "bstr", "futures", @@ -3089,30 +3132,33 @@ dependencies = [ ] [[package]] -name = "noodles-tabix" -version = "0.50.0" +name = "noodles-sam" +version = "0.79.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e46ee069d57770840554e3d8bd02e7415b3a2d972cdea7525bea02472032c234" +checksum = "61c64ab4f1c784a44cef043f2c630b0e08fffc7757d5ccb2a0a698369041b987" dependencies = [ - "byteorder", + "bitflags", + "bstr", "indexmap", - "noodles-bgzf 0.36.0", - "noodles-core 0.16.0", - "noodles-csi 0.44.0", - "tokio", + "lexical-core", + "memchr", + "noodles-bgzf 0.43.0", + "noodles-core 0.18.0 (registry+https://github.com/rust-lang/crates.io-index)", + "noodles-csi 0.51.0", ] [[package]] name = "noodles-tabix" -version = "0.55.0" +version = "0.50.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "461b6173ee2ec38d7ddbce206c31c83d8c7b61d6a5db2b2c4ff2ac74653ac751" +checksum = "e46ee069d57770840554e3d8bd02e7415b3a2d972cdea7525bea02472032c234" dependencies = [ "byteorder", "indexmap", - "noodles-bgzf 0.41.0", - "noodles-core 0.17.0", - "noodles-csi 0.49.0", + "noodles-bgzf 0.36.0", + "noodles-core 0.16.0", + "noodles-csi 0.44.0", + "tokio", ] [[package]] @@ -3128,6 +3174,19 @@ dependencies = [ "tokio", ] +[[package]] +name = "noodles-tabix" +version = "0.57.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "caff826ea6e432861b726ae3be1100e72d07a238c7615c12ddc257ff3c23f555" +dependencies = [ + "bstr", + "indexmap", + "noodles-bgzf 0.43.0", + "noodles-core 0.18.0 (registry+https://github.com/rust-lang/crates.io-index)", + "noodles-csi 0.51.0", +] + [[package]] name = "noodles-vcf" version = "0.74.0" diff --git a/Cargo.toml b/Cargo.toml index ed59a76..0b6f2f1 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -22,7 +22,7 @@ async-trait = "0.1.85" opendal = { version = "0.53.3", features = ["services-gcs", "services-s3","layers-blocking", "services-azblob", "services-http"] } noodles = { version = "0.93.0", features = ["bam", "vcf", "bgzf", "cram", "async"]} -noodles-bgzf = { version = "0.36.0",features = ["libdeflate"] } +noodles-bgzf = { version = "0.42.0",features = ["libdeflate"] } noodles-cram = { git = "https://github.com/biodatageeks/noodles.git",rev = "d6f205e9bb5369762236724fb54d24c5e1d9b79a", features = ["async"] } noodles-sam = { git = "https://github.com/biodatageeks/noodles.git",rev = "d6f205e9bb5369762236724fb54d24c5e1d9b79a" } noodles-fasta = { git = "https://github.com/biodatageeks/noodles.git",rev = "d6f205e9bb5369762236724fb54d24c5e1d9b79a", features = ["async"] } diff --git a/datafusion/bio-format-bam/Cargo.toml b/datafusion/bio-format-bam/Cargo.toml index 3d34309..1ab57f2 100644 --- a/datafusion/bio-format-bam/Cargo.toml +++ b/datafusion/bio-format-bam/Cargo.toml @@ -19,7 +19,7 @@ bytes.workspace = true datafusion-bio-format-core = {path = "../bio-format-core"} futures.workspace = true futures-util.workspace = true -noodles-bam = {version = "0.81.0" , features = ["async"]} +noodles-bam = {version = "0.83.0" , features = ["async"]} noodles-sam = "0.77.0" async-stream = "0.3.6" log = "0.4.27" diff --git a/datafusion/bio-format-bed/Cargo.toml b/datafusion/bio-format-bed/Cargo.toml index 8cb87a1..bae8cbf 100644 --- a/datafusion/bio-format-bed/Cargo.toml +++ b/datafusion/bio-format-bed/Cargo.toml @@ -25,7 +25,7 @@ futures = "0.3.31" log = "0.4.27" async-stream = "0.3.6" env_logger = "0.11.8" -noodles-bed = "0.26.0" +noodles-bed = "0.28.0" futures-util = "0.3.31" [[example]] diff --git a/datafusion/bio-format-fastq/Cargo.toml b/datafusion/bio-format-fastq/Cargo.toml index 260b805..5020032 100644 --- a/datafusion/bio-format-fastq/Cargo.toml +++ b/datafusion/bio-format-fastq/Cargo.toml @@ -18,7 +18,7 @@ tokio-util.workspace = true tokio.workspace = true bytes.workspace = true datafusion-bio-format-core = {path = "../bio-format-core"} -noodles-fastq = {version = "0.19.0", features = ["async"]} +noodles-fastq = {version = "0.21.0", features = ["async"]} futures.workspace = true futures-util.workspace = true async-compression.workspace = true