From e96d8278acffd24230bbf845d594a103fc341c7c Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 24 Apr 2026 22:26:32 +0000 Subject: [PATCH 1/2] Bump noodles from 0.80.0 to 0.109.0 Bumps [noodles](https://github.com/zaeleus/noodles) from 0.80.0 to 0.109.0. - [Commits](https://github.com/zaeleus/noodles/compare/noodles-0.80.0...noodles-0.109.0) --- updated-dependencies: - dependency-name: noodles dependency-version: 0.109.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- Cargo.lock | 86 ++++++++++++++++++++++++++---------------------------- Cargo.toml | 2 +- 2 files changed, 42 insertions(+), 46 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 888dffb..1513a1f 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -105,9 +105,12 @@ checksum = "c08606f8c3cbf4ce6ec8e28fb0014a2c086708fe954eaa885384a6165172e7e8" [[package]] name = "bit-vec" -version = "0.8.0" +version = "0.9.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "5e764a1d40d510daf35e07be9eb06e75770908c27d411ee6c92109c9840eaaf7" +checksum = "b71798fca2c1fe1086445a7258a4bc81e6e49dcd24c8d0dd9a1e57395b603f51" +dependencies = [ + "serde", +] [[package]] name = "bitflags" @@ -353,6 +356,7 @@ checksum = "843fba2746e448b37e26a819579957415c8cef339bf08564fe8b7ddbd959573c" dependencies = [ "crc32fast", "miniz_oxide", + "zlib-rs", ] [[package]] @@ -481,9 +485,9 @@ dependencies = [ [[package]] name = "lexical-core" -version = "0.8.5" +version = "1.0.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2cde5de06e8d4c2faabc400238f9ae1c74d5412d03a7bd067645ccbc47070e46" +checksum = "7d8d125a277f807e55a77304455eb7b1cb52f2b18c143b60e766c120bd64a594" dependencies = [ "lexical-parse-float", "lexical-parse-integer", @@ -494,53 +498,46 @@ dependencies = [ [[package]] name = "lexical-parse-float" -version = "0.8.5" +version = "1.0.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "683b3a5ebd0130b8fb52ba0bdc718cc56815b6a097e28ae5a6997d0ad17dc05f" +checksum = "52a9f232fbd6f550bc0137dcb5f99ab674071ac2d690ac69704593cb4abbea56" dependencies = [ "lexical-parse-integer", "lexical-util", - "static_assertions", ] [[package]] name = "lexical-parse-integer" -version = "0.8.6" +version = "1.0.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "6d0994485ed0c312f6d965766754ea177d07f9c00c9b82a5ee62ed5b47945ee9" +checksum = "9a7a039f8fb9c19c996cd7b2fcce303c1b2874fe1aca544edc85c4a5f8489b34" dependencies = [ "lexical-util", - "static_assertions", ] [[package]] name = "lexical-util" -version = "0.8.5" +version = "1.0.7" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "5255b9ff16ff898710eb9eb63cb39248ea8a5bb036bea8085b1a767ff6c4e3fc" -dependencies = [ - "static_assertions", -] +checksum = "2604dd126bb14f13fb5d1bd6a66155079cb9fa655b37f875b3a742c705dbed17" [[package]] name = "lexical-write-float" -version = "0.8.5" +version = "1.0.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "accabaa1c4581f05a3923d1b4cfd124c329352288b7b9da09e766b0668116862" +checksum = "50c438c87c013188d415fbabbb1dceb44249ab81664efbd31b14ae55dabb6361" dependencies = [ "lexical-util", "lexical-write-integer", - "static_assertions", ] [[package]] name = "lexical-write-integer" -version = "0.8.5" +version = "1.0.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e1b6f3d1f4422866b68192d62f77bc5c700bee84f3069f2469d7bc8c77852446" +checksum = "409851a618475d2d5796377cad353802345cba92c867d9fbcde9cf4eac4e14df" dependencies = [ "lexical-util", - "static_assertions", ] [[package]] @@ -597,9 +594,9 @@ dependencies = [ [[package]] name = "noodles" -version = "0.80.0" +version = "0.109.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "15ea7a4ffa2e3684ce476156d199e388b465d860d702b739f3e39257ded7d174" +checksum = "4876a9caa25647b9ddc09883263b61fd6500ec7a4394f31daa5428026d5eb415" dependencies = [ "noodles-bam", "noodles-bgzf", @@ -609,14 +606,13 @@ dependencies = [ [[package]] name = "noodles-bam" -version = "0.67.0" +version = "0.88.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "53bc69bd00891e3e1c5faffe4f55d00c94d9e53d4bdbe63ec8c7e2b881f3bc85" +checksum = "ff57687677d53f36c3574d2350a4668825ff2fa762b6d086f779d3eeaa96b0aa" dependencies = [ "bstr", - "byteorder", - "bytes", "indexmap", + "memchr", "noodles-bgzf", "noodles-core", "noodles-csi", @@ -625,11 +621,10 @@ dependencies = [ [[package]] name = "noodles-bgzf" -version = "0.33.0" +version = "0.46.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "3b50aaa8f0a3c8a0b738b641a6d1a78d9fd30a899ab2d398779ee3c4eb80f1c1" +checksum = "37290f565045fd2775b549e62dffca7e1afadc70d8d5a3a2ef19609eb3d8193b" dependencies = [ - "byteorder", "bytes", "crossbeam-channel", "flate2", @@ -637,21 +632,21 @@ dependencies = [ [[package]] name = "noodles-core" -version = "0.15.0" +version = "0.19.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c5a8c6b020d1205abef2b0fab4463a6c5ecc3c8f4d561ca8b0d1a42323376200" +checksum = "53e1e8a419dbba0e4000b0e60830b124138c7f2277ad556463506f1a81d32d17" dependencies = [ "bstr", ] [[package]] name = "noodles-csi" -version = "0.38.0" +version = "0.55.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a69e79dbc09bd0cb86d29469ed29066e9a163bce6640527b343bdea458144618" +checksum = "c9c846d8128bd80b18d891b13cb9e0bc1d364429d6ab3ec3c83939f3d32ba105" dependencies = [ "bit-vec", - "byteorder", + "bstr", "indexmap", "noodles-bgzf", "noodles-core", @@ -659,9 +654,9 @@ dependencies = [ [[package]] name = "noodles-fastq" -version = "0.14.0" +version = "0.22.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c596792c857f37e6a85e2cf1e68578f5b70f867cad028bf95c1e2b5d7c9c84eb" +checksum = "56a2d83379751760aec332a2b6a2060852e2d393bfc1d3ef481c97b0e88372f8" dependencies = [ "bstr", "memchr", @@ -669,9 +664,9 @@ dependencies = [ [[package]] name = "noodles-sam" -version = "0.64.0" +version = "0.84.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "72da678e9332b32a916f8c5d5a7c4324da11891bc7148077744566981acaf00c" +checksum = "baa5367d794dd6b766b7e9fe7ae93accfc9288f590ac61a881c29b7b307dbad2" dependencies = [ "bitflags", "bstr", @@ -944,6 +939,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "9a8e94ea7f378bd32cbbd37198a4a91436180c5bb472411e48b5ec2e2124ae9e" dependencies = [ "serde_core", + "serde_derive", ] [[package]] @@ -984,12 +980,6 @@ version = "1.15.1" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "67b1b7a3b5fe4f1376887184045fcf45c69e92af734b7aaddc05fb777b6fbd03" -[[package]] -name = "static_assertions" -version = "1.1.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a2eb9349b6444b326872e140eb1cf5e7c522154d69e7a0ffb0fb81c06b37543f" - [[package]] name = "strsim" version = "0.11.1" @@ -1220,3 +1210,9 @@ dependencies = [ "quote", "syn", ] + +[[package]] +name = "zlib-rs" +version = "0.6.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "3be3d40e40a133f9c916ee3f9f4fa2d9d63435b5fbe1bfc6d9dae0aa0ada1513" diff --git a/Cargo.toml b/Cargo.toml index acd50a0..4eae7db 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -43,7 +43,7 @@ log = "0.4" env_logger = "0.11" memmap2 = "0.9" byteorder = "1" -noodles = { version = "0.80", features = ["fastq", "sam", "bam", "bgzf"] } +noodles = { version = "0.109", features = ["fastq", "sam", "bam", "bgzf"] } bstr = "1" flate2 = "1" rayon = "1" From 5067593f1a529671e1677ad0fcb69d9549028f07 Mon Sep 17 00:00:00 2001 From: "Philipp A." Date: Sat, 16 May 2026 13:46:31 +0200 Subject: [PATCH 2/2] fix API changes --- src/io/bam.rs | 15 +++++++-------- src/io/fastq.rs | 4 ++-- 2 files changed, 9 insertions(+), 10 deletions(-) diff --git a/src/io/bam.rs b/src/io/bam.rs index b77ab16..23b28be 100644 --- a/src/io/bam.rs +++ b/src/io/bam.rs @@ -4,10 +4,9 @@ use crate::genome::Genome; use crate::params::Parameters; use crate::quant::transcriptome::TranscriptomeIndex; use byteorder::{LittleEndian, WriteBytesExt}; -use noodles::bam; -use noodles::sam; use noodles::sam::alignment::io::Write as SamWrite; use noodles::sam::alignment::record_buf::RecordBuf; +use noodles::{bam, bgzf, sam}; use std::ffi::CString; use std::fs::File; use std::io::{BufWriter, Write}; @@ -36,8 +35,8 @@ impl BufferedBamRecords { /// Convert STAR's `--outBAMcompression` integer (-1..9) to a noodles level. /// /// STAR mapping: -1 or 0 = uncompressed, 1-9 = deflate levels, default 1. -fn bgzf_compression(level: i32) -> noodles::bgzf::writer::CompressionLevel { - use noodles::bgzf::writer::CompressionLevel; +fn bgzf_compression(level: i32) -> bgzf::io::writer::CompressionLevel { + use bgzf::io::writer::CompressionLevel; match level { n if n <= 0 => CompressionLevel::NONE, n if n >= 9 => CompressionLevel::BEST, @@ -46,8 +45,8 @@ fn bgzf_compression(level: i32) -> noodles::bgzf::writer::CompressionLevel { } /// Create a BGZF writer with the given STAR compression level. -fn make_bgzf_writer(inner: W, compression: i32) -> noodles::bgzf::Writer { - noodles::bgzf::writer::Builder::default() +fn make_bgzf_writer(inner: W, compression: i32) -> bgzf::io::Writer { + bgzf::io::writer::Builder::default() .set_compression_level(bgzf_compression(compression)) .build_from_writer(inner) } @@ -58,7 +57,7 @@ fn make_bgzf_writer(inner: W, compression: i32) -> noodles::b /// without buffering or sorting. The output is BGZF-compressed but unsorted. /// Users can sort the output with `samtools sort` if needed. pub struct BamWriter { - writer: bam::io::Writer>>, + writer: bam::io::Writer>>, header: sam::Header, } @@ -372,7 +371,7 @@ fn render_sam_text_lenient(header: &sam::Header, sort_order: Option<&str>) -> Ve /// Streaming unsorted BAM writer that writes to stdout. pub struct BamStdoutWriter { - writer: bam::io::Writer>>, + writer: bam::io::Writer>>, header: sam::Header, } diff --git a/src/io/fastq.rs b/src/io/fastq.rs index 2edc7f7..5a36320 100644 --- a/src/io/fastq.rs +++ b/src/io/fastq.rs @@ -70,7 +70,7 @@ pub struct PairedRead { /// FASTQ reader that handles decompression and base encoding pub struct FastqReader { - inner: fastq::Reader>, + inner: fastq::io::Reader>, } impl FastqReader { @@ -102,7 +102,7 @@ impl FastqReader { } }; - let fastq_reader = fastq::Reader::new(reader); + let fastq_reader = fastq::io::Reader::new(reader); Ok(Self { inner: fastq_reader,