Merge branch 'master' into master

Author: rLannes

.github/dependabot.yml

@@ -4,3 +4,9 @@ updates:
     directory: "/"
     schedule:
       interval: "weekly"
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+  

.github/workflows/conventional-prs.yml

@@ -11,6 +11,6 @@ jobs:
   title-format:
     runs-on: ubuntu-latest
     steps:
-      - uses: amannn/action-semantic-pull-request@v3.4.0
+      - uses: amannn/action-semantic-pull-request@v5.5.3
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/release-please.yml

@@ -10,38 +10,34 @@ jobs:
     if: github.repository_owner == 'rust-bio'
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           submodules: recursive
 
-      - uses: GoogleCloudPlatform/release-please-action@v3
+      - uses: GoogleCloudPlatform/release-please-action@v4
         id: release_main
         with:
           release-type: rust
           package-name: rust-htslib
           bump-minor-pre-major: true
 
       - name: Install stable toolchain
-        uses: actions-rs/toolchain@v1
+        uses: dtolnay/rust-toolchain@stable
         if: ${{ steps.release_main.outputs.release_created }}
         with:
           toolchain: stable
-          override: true
 
       - name: Install system dependencies
         if: ${{ steps.release_main.outputs.release_created }}
         run: |
           sudo apt-get install --yes zlib1g-dev libbz2-dev musl musl-dev musl-tools clang libc6-dev
 
-      - uses: Swatinem/rust-cache@v1.3.0
+      - uses: Swatinem/rust-cache@v2
         if: ${{ steps.release_main.outputs.release_created }}
 
       - name: Publish rust-htslib
         if: ${{ steps.release_main.outputs.release_created }}
-        uses: actions-rs/cargo@v1
-        with:
-          command: publish
-          args: --token ${{ secrets.CRATES_IO_TOKEN }}
+        run: cargo publish --token ${{ secrets.CRATES_IO_TOKEN }}
 
       # - uses: katyo/publish-crates@v1
       #   if: ${{ steps.release_main.outputs.release_created || steps.release_sys.outputs.release_created }}

.github/workflows/rust.yml

@@ -8,116 +8,113 @@ on:
 
 jobs:
   Formatting:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       - name: Install stable toolchain
-        uses: actions-rs/toolchain@v1.0.6
+        uses: dtolnay/rust-toolchain@stable
         with:
           toolchain: stable
-          override: true
           components: rustfmt
 
       - name: Check format
         run: cargo fmt -- --check
 
   Linting:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           submodules: recursive
 
       - name: Install stable toolchain
-        uses: actions-rs/toolchain@v1.0.6
+        uses: dtolnay/rust-toolchain@stable
         with:
           toolchain: stable
-          override: true
           components: clippy
 
       - name: Lint with clippy
-        uses: actions-rs/clippy-check@v1
-        with:
-          token: ${{ secrets.GITHUB_TOKEN }}
+        run: RUSTFLAGS="-Dwarnings" cargo clippy --all-features --all-targets -- -Dclippy::all -Dunused_imports
 
   Testing:
     needs: Formatting
-    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        os: [ubuntu-22.04, ubuntu-22.04-arm]
+    runs-on: ${{ matrix.os }}
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           submodules: recursive
 
       - name: Install nightly toolchain
-        uses: actions-rs/toolchain@v1.0.6
+        uses: dtolnay/rust-toolchain@stable
         with:
           toolchain: nightly
-          override: true
 
       - name: Install system dependencies
         run: |
           sudo apt-get install --yes zlib1g-dev libbz2-dev musl musl-dev musl-tools clang libc6-dev
 
-      - uses: Swatinem/rust-cache@v1.3.0
+      - uses: Swatinem/rust-cache@v2
 
       - name: Run cargo-tarpaulin
-        uses: actions-rs/[email protected]
-        with:
-          # TODO: update to latest tarpaulin once artefact download is fixed: https://github.com/actions-rs/tarpaulin/pull/23
-          version: "0.22.0"
-          args: "--all-features --run-types Tests,Doctests --out Lcov -- --test-threads 1"
+        run: |
+          set -x
+          cargo install cargo-tarpaulin
+          cargo tarpaulin --all-features --tests --doc --out Lcov -- --test-threads 1
 
       - name: Upload coverage
-        uses: coverallsapp/github-action@v1
+        uses: coverallsapp/github-action@v2
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           path-to-lcov: ./lcov.info
 
   Testing-Features:
     needs: Formatting
-    runs-on: ubuntu-latest
     strategy:
       matrix:
+        os: [ubuntu-22.04, ubuntu-22.04-arm]
         target:
           - no-default-features
           - all-features
         include:
           - target: no-default-features
             args: --no-default-features
-            use_cross: false
           - target: all-features
+            os: ubuntu-22.04
             args: --all-features
             toolchain_target: x86_64-unknown-linux-musl
-            use_cross: false
+          - target: all-features
+            os: ubuntu-22.04-arm
+            args: --all-features
+            toolchain_target: aarch64-unknown-linux-musl
+    runs-on: ${{ matrix.os }}
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           submodules: recursive
 
       - name: Install stable toolchain
-        uses: actions-rs/toolchain@v1.0.6
+        uses: dtolnay/rust-toolchain@stable
         with:
           toolchain: stable
-          override: true
 
       - name: Install system dependencies
         run: |
           sudo apt-get install --yes zlib1g-dev libbz2-dev musl musl-dev musl-tools clang libc6-dev
 
-      - uses: Swatinem/rust-cache@v1.3.0
+      - uses: Swatinem/rust-cache@v2
 
       - name: Test
-        uses: actions-rs/cargo@v1
-        with:
-          command: test
-          args: ${{ matrix.args }}
-          use-cross: ${{ matrix.use_cross }}
+        run: |
+          cargo test ${{ matrix.args }}
 
   Testing-MacOS:
     needs: Formatting
@@ -150,27 +147,23 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           submodules: recursive
 
       - name: Install stable toolchain
-        uses: actions-rs/toolchain@v1.0.6
+        uses: dtolnay/rust-toolchain@stable
         with:
           toolchain: ${{ matrix.toolchain }}
-          target: ${{ matrix.toolchain_target }}
+          targets: ${{ matrix.toolchain_target }}
           override: true
-          default: ${{ matrix.default }}
 
       - name: Install htslib dependencies
         run: brew install bzip2 zlib xz curl-openssl
 
       - name: Test
-        uses: actions-rs/[email protected]
-        with:
-          use-cross: false # cross is not supported on GHA OSX runner, see: https://github.community/t/why-is-docker-not-installed-on-macos/17017
-          command: test
-          args: --release --all-features --verbose ${{ matrix.aux_args }}
+        run: |
+          cargo test --release --all-features --verbose ${{ matrix.aux_args }}
 #  Testing-OSX-MUSL-BigSur:
 #   needs: Formatting
 #   runs-on: macOS-11.0

CHANGELOG.md

@@ -2,6 +2,31 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## [0.50.0](https://github.com/rust-bio/rust-htslib/compare/v0.49.0...v0.50.0) (2025-07-09)
+
+
+### Features
+
+* Add bam::Record::set_cigar ([#477](https://github.com/rust-bio/rust-htslib/issues/477)) ([f1bb470](https://github.com/rust-bio/rust-htslib/commit/f1bb470d836e3cd8affae000f0fc14308f156c88))
+* Allow for non-diploid genotypes ([#476](https://github.com/rust-bio/rust-htslib/issues/476)) ([1c22ac5](https://github.com/rust-bio/rust-htslib/commit/1c22ac598edaa9fc1be354b857dc8f8f5c892984))
+
+
+### Bug Fixes
+
+* clippy and fmt after merging PR [#466](https://github.com/rust-bio/rust-htslib/issues/466) and [#467](https://github.com/rust-bio/rust-htslib/issues/467) ([141e01c](https://github.com/rust-bio/rust-htslib/commit/141e01c74aa3d087f4c2e7fe380d06b1e272865b))
+
+## [0.49.0](https://github.com/rust-bio/rust-htslib/compare/v0.48.0...v0.49.0) (2024-12-02)
+
+
+### Features
+
+* move empty_record to header ([#453](https://github.com/rust-bio/rust-htslib/issues/453)) ([797965c](https://github.com/rust-bio/rust-htslib/commit/797965c5ab815112b1a2a1bcdb32716c1bc1f92a))
+
+
+### Bug Fixes
+
+* memory leak in faidx when fetching sequences ([#455](https://github.com/rust-bio/rust-htslib/issues/455)) ([d9fe03a](https://github.com/rust-bio/rust-htslib/commit/d9fe03acfb81278a09a7e6091b9e1c38dd7b6cb4))
+
 ## [0.48.0](https://github.com/rust-bio/rust-htslib/compare/v0.47.1...v0.48.0) (2024-11-12)
 
 

Cargo.toml

@@ -9,7 +9,7 @@ license = "MIT"
 name = "rust-htslib"
 readme = "README.md"
 repository = "https://github.com/rust-bio/rust-htslib.git"
-version = "0.48.0"
+version = "0.50.0"
 
 [package.metadata.release]
 pre-release-commit-message = "release version {{version}}"
@@ -21,7 +21,7 @@ bio-types = ">=0.9"
 byteorder = "1.3"
 custom_derive = "0.1"
 derive-new = "0.7"
-hts-sys = {version = "2.1.4", default-features = false, features = ["bindgen"]}
+hts-sys = {version = "2.2.0", default-features = false, features = ["bindgen"]}
 ieee754 = "0.2"
 lazy_static = "1.4"
 libc = "0.2"
@@ -30,8 +30,8 @@ newtype_derive = "0.1"
 regex = "1.3"
 serde = {version = "^1", optional = true, features = ["derive"]}
 serde_bytes = {version = "0.11", optional = true}
-thiserror = "2"
-url = "2.1"
+thiserror = {version = "^2" }
+url = "2.5"
 
 [features]
 bindgen = ["hts-sys/bindgen"]

src/bam/buffer.rs

@@ -182,7 +182,7 @@ mod tests {
 
     #[test]
     fn test_buffer() {
-        let reader = bam::IndexedReader::from_path(&"test/test.bam").unwrap();
+        let reader = bam::IndexedReader::from_path("test/test.bam").unwrap();
         let mut buffer = RecordBuffer::new(reader, false);
 
         buffer.fetch(b"CHROMOSOME_I", 1, 5).unwrap();

src/bam/ext.rs

@@ -1,4 +1,4 @@
-//// Copyright 2019 Johannes Köster and Florian Finkernagel.
+// Copyright 2019 Johannes Köster and Florian Finkernagel.
 // Licensed under the MIT license (http://opensource.org/licenses/MIT)
 // This file may not be copied, modified, or distributed
 // except according to those terms.

src/bam/header.rs

@@ -165,7 +165,7 @@ mod tests {
     fn test_push_tag() {
         let mut record = HeaderRecord::new(b"HD");
         record.push_tag(b"X1", 0);
-        record.push_tag(b"X2", &0);
+        record.push_tag(b"X2", 0);
 
         let x = "x".to_string();
         record.push_tag(b"X3", x.as_str());