Migrate BAM I/O from rust-htslib to noodles (#115)

* Migrate BAM I/O from rust-htslib to noodles (#113)

Replace rust-htslib with a pure-Rust noodles backend behind a
compatibility shim at src/rna/bam/. The shim preserves the existing
Reader/IndexedReader/Record API used across dupRadar, RSeQC, preseq,
Qualimap, and samtools-compatible outputs.

Key changes:
- Add noodles-backed BAM/SAM/CRAM readers with indexed fetch support
- Preserve samtools-identical CHK checksums via packed sequence bytes
- Update build docs: no cmake/htslib system deps required
- All integration and unit tests pass in release mode

Co-authored-by: Phil Ewels <phil.ewels@seqera.io>

* Update docs, Dockerfile, and CI for noodles migration

Replace rust-htslib build prerequisites with noodles (pure Rust) across
the website docs, Dockerfile, GitHub Actions workflows, and CHANGELOG.

Co-authored-by: Phil Ewels <phil.ewels@seqera.io>

* Fix CI: rustfmt and bump MSRV to 1.89 for noodles

- Remove extra blank line in main.rs (cargo fmt --check)
- Bump rust-version to 1.89 (required by noodles 0.111)
- Update MSRV CI job to match

Co-authored-by: Phil Ewels <phil.ewels@seqera.io>

---------

Co-authored-by: Cursor Agent <cursoragent@cursor.com>

Author: ewels

.cargo/audit.toml

@@ -2,8 +2,4 @@
 # https://github.com/rustsec/rustsec/tree/main/cargo-audit
 
 [advisories]
-# custom_derive v0.1.7 — unmaintained crate pulled in transitively by
-# rust-htslib v1.0.0.  There is no newer rust-htslib release that drops it,
-# and this is an "unmaintained" notice, not a vulnerability.
-# Re-evaluate when rust-htslib releases a version without custom_derive.
-ignore = ["RUSTSEC-2025-0058"]
+ignore = []

.github/workflows/ci.yml

@@ -10,6 +10,7 @@ permissions:
 
 env:
   CARGO_TERM_COLOR: always
+  CXX: g++
 
 jobs:
   test:
@@ -36,12 +37,11 @@ jobs:
         if: runner.os == 'Linux'
         run: |
           sudo apt-get update
-          sudo apt-get install -y cmake zlib1g-dev libbz2-dev liblzma-dev \
-            libcurl4-openssl-dev libssl-dev libfontconfig1-dev pkg-config clang
+          sudo apt-get install -y g++ libfontconfig1-dev pkg-config
 
       - name: Install macOS build deps
         if: runner.os == 'macOS'
-        run: brew install bzip2 xz
+        run: brew install fontconfig
 
       - uses: Swatinem/rust-cache@c19371144df3bb44fab255c43d04cbc2ab54d1c4 # ratchet:Swatinem/rust-cache@v2.9.1
 
@@ -87,8 +87,7 @@ jobs:
       - name: Install Linux build deps
         run: |
           sudo apt-get update
-          sudo apt-get install -y cmake zlib1g-dev libbz2-dev liblzma-dev \
-            libcurl4-openssl-dev libssl-dev libfontconfig1-dev pkg-config clang
+          sudo apt-get install -y g++ libfontconfig1-dev pkg-config
 
       - uses: Swatinem/rust-cache@c19371144df3bb44fab255c43d04cbc2ab54d1c4 # ratchet:Swatinem/rust-cache@v2.9.1
 
@@ -103,13 +102,12 @@ jobs:
       - name: Install Rust MSRV toolchain
         uses: dtolnay/rust-toolchain@631a55b12751854ce901bb631d5902ceb48146f7 # ratchet:dtolnay/rust-toolchain@master
         with:
-          toolchain: "1.87"
+          toolchain: "1.89"
 
       - name: Install Linux build deps
         run: |
           sudo apt-get update
-          sudo apt-get install -y cmake zlib1g-dev libbz2-dev liblzma-dev \
-            libcurl4-openssl-dev libssl-dev libfontconfig1-dev pkg-config clang
+          sudo apt-get install -y g++ libfontconfig1-dev pkg-config
 
       - uses: Swatinem/rust-cache@c19371144df3bb44fab255c43d04cbc2ab54d1c4 # ratchet:Swatinem/rust-cache@v2.9.1
 

.github/workflows/release.yml

@@ -12,6 +12,7 @@ permissions:
 
 env:
   CARGO_TERM_COLOR: always
+  CXX: g++
   IMAGE_NAME: ${{ github.repository }}
 
 jobs:
@@ -130,13 +131,12 @@ jobs:
         if: runner.os == 'Linux'
         run: |
           sudo apt-get update
-          sudo apt-get install -y cmake zlib1g-dev libbz2-dev liblzma-dev \
-            libcurl4-openssl-dev libssl-dev libfontconfig1-dev pkg-config clang
+          sudo apt-get install -y g++ libfontconfig1-dev pkg-config
 
       # macOS build dependencies
       - name: Install macOS build deps
         if: runner.os == 'macOS'
-        run: brew install bzip2 xz
+        run: brew install fontconfig
 
       - name: Build
         run: >

AGENTS.md

@@ -244,7 +244,7 @@ To prepare a release:
 | Crate                  | Purpose                               |
 | ---------------------- | ------------------------------------- |
 | `clap` v4              | CLI argument parsing (derive)         |
-| `rust-htslib`          | BAM file I/O (statically linked)      |
+| `noodles`              | BAM/SAM/CRAM file I/O (pure Rust)     |
 | `plotters`             | Chart generation (PNG + SVG)          |
 | `serde`                | YAML config deserialization           |
 | `anyhow`               | Error handling                        |
@@ -282,7 +282,7 @@ forwarded to `count_reads()` as the `skip_dup_check: bool` parameter).
 - Test data is generated by `tests/create_test_data.R` — do not modify `tests/expected/` by hand.
 - Float output formatting must match R's behavior (15 significant digits, "NA" for NaN, trailing-zero trimming).
 - The pipeline processes BAM files which can be very large — performance matters.
-- System dependencies needed for building: cmake, zlib, bz2, lzma, curl, ssl, clang (for `rust-htslib`).
+- System dependencies needed for building: a C++ compiler (for the preseq RNG FFI shim), libfontconfig (for plot rendering). noodles handles BAM/SAM/CRAM I/O in pure Rust with no htslib/cmake dependency.
 - Benchmark results are produced by the [RustQC-benchmarks](https://github.com/seqeralabs/RustQC-benchmarks)
   Nextflow pipeline. When benchmarks are re-run, verify that all results referenced in the docs
   and the top-level `README.md` are updated to reflect the new numbers.

CHANGELOG.md

@@ -1,5 +1,13 @@
 # RustQC Changelog
 
+## [Unreleased]
+
+### Other changes
+
+- Migrate BAM/SAM/CRAM I/O from rust-htslib to pure-Rust [noodles](https://crates.io/crates/noodles) (#113)
+- Simplify build requirements: no cmake or htslib system libraries needed
+- Bump MSRV to Rust 1.89 (required by noodles 0.111)
+
 ## [Version 0.2.1](https://github.com/seqeralabs/RustQC/releases/tag/v0.2.1) - 2026-04-09
 
 ### Bug fixes

CONTRIBUTING.md

@@ -6,24 +6,18 @@ Thanks for your interest in contributing to RustQC! This document covers how to
 
 ### Prerequisites
 
-You need a working Rust toolchain (stable) and the following system libraries for building `rust-htslib`:
-
-- cmake, clang
-- zlib, libbz2, liblzma
-- libcurl, libssl
-- libfontconfig (for plot rendering)
+You need a working Rust toolchain (stable), a C++ compiler (for the preseq RNG FFI shim), and libfontconfig (for plot rendering). BAM/SAM/CRAM I/O is handled by the pure-Rust [noodles](https://crates.io/crates/noodles) crate — no htslib or cmake required.
 
 On Ubuntu/Debian:
 
 ```bash
-sudo apt-get install cmake clang zlib1g-dev libbz2-dev liblzma-dev \
-  libcurl4-openssl-dev libssl-dev libfontconfig1-dev
+sudo apt-get install g++ libfontconfig1-dev
 ```
 
 On macOS (with Homebrew):
 
 ```bash
-brew install cmake xz
+brew install fontconfig
 ```
 
 ### Building