Merge branch 'master' into ar/header-remove-unwrap

rust-bio · Nov 12, 2024 · 74d9201 · 74d9201
2 parents bc5c9f8 + 4b3cbcb
commit 74d9201
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Showing 23 changed files with 817 additions and 209 deletions.
diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
@@ -52,10 +52,10 @@ jobs:
         with:
           submodules: recursive
 
-      - name: Install stable toolchain
+      - name: Install nightly toolchain
         uses: actions-rs/[email protected]
         with:
-          toolchain: stable
+          toolchain: nightly
           override: true
 
       - name: Install system dependencies
@@ -67,8 +67,9 @@ jobs:
       - 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 --out Lcov -- --test-threads 1"
+          args: "--all-features --run-types Tests,Doctests --out Lcov -- --test-threads 1"
 
       - name: Upload coverage
         uses: coverallsapp/github-action@v1
@@ -84,9 +85,6 @@ jobs:
         target:
           - no-default-features
           - all-features
-          - musl-release-no-default-features
-          - musl-release-all-features
-          - musl-all-features
         include:
           - target: no-default-features
             args: --no-default-features
@@ -95,18 +93,6 @@ jobs:
             args: --all-features
             toolchain_target: x86_64-unknown-linux-musl
             use_cross: false
-          - target: musl-release-no-default-features
-            args: --release --target x86_64-unknown-linux-musl --no-default-features
-            toolchain_target: x86_64-unknown-linux-musl
-            use_cross: true
-          - target: musl-release-all-features
-            args: --release --target x86_64-unknown-linux-musl --all-features --verbose
-            toolchain_target: x86_64-unknown-linux-musl
-            use_cross: true
-          - target: musl-all-features
-            args: --target x86_64-unknown-linux-musl --all-features --verbose
-            toolchain_target: x86_64-unknown-linux-musl
-            use_cross: true
 
     steps:
       - name: Checkout repository
@@ -139,29 +125,28 @@ jobs:
     strategy:
       matrix:
         target:
-          - intel-catalina
-          - intel-bigsur
-          - m1-bigsur
+          - intel-monterey
+          - intel-ventura
+          - silicon-sonoma
         include:
-          - target: intel-catalina
-            os: macOS-10.15
+          - target: intel-monterey
+            os: macOS-12.0
             toolchain_target: x86_64-apple-darwin
             toolchain: stable
-            aux_args: ""
-            default: false
-          - target: intel-bigsur
-            os: macOS-11.0
+            aux_args: --target x86_64-apple-darwin
+            default: true
+          - target: intel-ventura
+            os: macOS-13.0
             toolchain_target: x86_64-apple-darwin
             toolchain: stable
+            aux_args: --target x86_64-apple-darwin
+            default: true
+          - target: silicon-sonoma
+            os: macOS-14.0
+            toolchain_target: aarch64-apple-darwin
+            toolchain: stable
             aux_args: ""
             default: false
-          # TODO enable again and try to find out why this fails
-          # - target: m1-bigsur
-          #   os: macOS-11.0
-          #   toolchain_target: aarch64-apple-darwin
-          #   toolchain: nightly
-          #   aux_args: --target aarch64-apple-darwin
-          #   default: true
 
     steps:
       - name: Checkout repository
@@ -172,19 +157,14 @@ jobs:
       - name: Install stable toolchain
         uses: actions-rs/[email protected]
         with:
-          toolchain: stable
+          toolchain: ${{ matrix.toolchain }}
+          target: ${{ matrix.toolchain_target }}
           override: true
+          default: ${{ matrix.default }}
 
       - name: Install htslib dependencies
         run: brew install bzip2 zlib xz curl-openssl
 
-      #- uses: actions-rs/[email protected]
-      #  with:
-      #    toolchain: ${{ matrix.toolchain }}
-      #    target: ${{ matrix.toolchain_target }}
-      #    #override: true
-      #    default: ${{ matrix.default }}
-
       - name: Test
         uses: actions-rs/[email protected]
         with:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,67 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## [0.47.0](https://github.com/rust-bio/rust-htslib/compare/v0.46.0...v0.47.0) (2024-05-22)
+
+
+### Features
+
+* Add fasta::build function + FaidxBuildError ([#418](https://github.com/rust-bio/rust-htslib/issues/418)) ([7c575ef](https://github.com/rust-bio/rust-htslib/commit/7c575ef549908745f34d9371986551f3d70ed444))
+* Add rust_htslib::bcf::index::build ([#408](https://github.com/rust-bio/rust-htslib/issues/408)) ([79d70cd](https://github.com/rust-bio/rust-htslib/commit/79d70cd6683f1a019e9052baa495dada709db432))
+* derive PartialEq and Eq for bam:: and bcf::Format ([#428](https://github.com/rust-bio/rust-htslib/issues/428)) ([528e543](https://github.com/rust-bio/rust-htslib/commit/528e54367367487a28bbc2566bd37de995f8ed1d))
+
+
+### Bug Fixes
+
+* bam::Record:new should return a valid record ([#361](https://github.com/rust-bio/rust-htslib/issues/361)) ([87f2011](https://github.com/rust-bio/rust-htslib/commit/87f20116c4337eda17a416ebafb8976abc188d87))
+* build for macOS ([#431](https://github.com/rust-bio/rust-htslib/issues/431)) ([d869fdd](https://github.com/rust-bio/rust-htslib/commit/d869fdda03900cafae0f4f60b033121dcd57b723))
+* in bam record buffer, change the start of the window to the first added item in last iteration ([#430](https://github.com/rust-bio/rust-htslib/issues/430)) ([56ee2bd](https://github.com/rust-bio/rust-htslib/commit/56ee2bd562788dad0dc8516d0e3db90ffa916320))
+* Panic on trailing omitted FORMAT records ([#417](https://github.com/rust-bio/rust-htslib/issues/417)) ([9f575ee](https://github.com/rust-bio/rust-htslib/commit/9f575ee40e15737731bc8234812c0cf36c1157f4))
+
+## [0.46.0](https://github.com/rust-bio/rust-htslib/compare/v0.45.0...v0.46.0) (2024-02-22)
+
+
+### Features
+
+* making several RecordBuffer methods public ([6757f52](https://github.com/rust-bio/rust-htslib/commit/6757f5219955fd4edba4f61e62978ce1e001068e))
+
+
+### Bug Fixes
+
+* fix building libz-sys ([#420](https://github.com/rust-bio/rust-htslib/issues/420)) ([01c8849](https://github.com/rust-bio/rust-htslib/commit/01c884945686e7a6756406b579fde28657f70b36))
+
+## [0.45.0](https://github.com/rust-bio/rust-htslib/compare/v0.44.1...v0.45.0) (2024-02-07)
+
+
+### Features
+
+* adding function to get sequence length to faidx mod ([#410](https://github.com/rust-bio/rust-htslib/issues/410)) ([ae79eba](https://github.com/rust-bio/rust-htslib/commit/ae79eba82ef6929105bdbe08246a8e973660899e))
+
+
+### Bug Fixes
+
+* Loosen acceptable types to support current linux build on aarch64 ([#415](https://github.com/rust-bio/rust-htslib/issues/415)) ([1d78d12](https://github.com/rust-bio/rust-htslib/commit/1d78d1251a052461605d28cd8cf832ccad93ef73))
+
+## [0.44.1](https://github.com/rust-bio/rust-htslib/compare/v0.44.0...v0.44.1) (2023-06-21)
+
+
+### Bug Fixes
+
+* use correct return value in bcf_get_format and bcf_get_info_values ([#398](https://github.com/rust-bio/rust-htslib/issues/398)) ([f9a1981](https://github.com/rust-bio/rust-htslib/commit/f9a1981fa84eef39e35f868ddfc773ea265b94b3))
+
+## [0.44.0](https://github.com/rust-bio/rust-htslib/compare/v0.43.1...v0.44.0) (2023-06-20)
+
+
+### Features
+
+* implement Clone for bcf::Record ([#394](https://github.com/rust-bio/rust-htslib/issues/394)) ([e89538d](https://github.com/rust-bio/rust-htslib/commit/e89538d5a9971c6508ac38d92ac468f3d70241aa))
+* implement htslib basemod api ([#385](https://github.com/rust-bio/rust-htslib/issues/385)) ([8beee14](https://github.com/rust-bio/rust-htslib/commit/8beee145a116f7ae936f1b6e36d876116dca18f1))
+
+
+### Bug Fixes
+
+* include doctests in test coverage calculations ([#397](https://github.com/rust-bio/rust-htslib/issues/397)) ([8ed0837](https://github.com/rust-bio/rust-htslib/commit/8ed083783fa1dce09535564a090d37f687fc832f))
+
 ## [0.43.1](https://github.com/rust-bio/rust-htslib/compare/v0.43.0...v0.43.1) (2023-05-16)
 
 

diff --git a/Cargo.toml b/Cargo.toml
@@ -9,18 +9,19 @@ license = "MIT"
 name = "rust-htslib"
 readme = "README.md"
 repository = "https://github.com/rust-bio/rust-htslib.git"
-version = "0.43.1"
+version = "0.47.0"
 
 [package.metadata.release]
 pre-release-commit-message = "release version {{version}}"
 tag-message = "Version {{version}} of Rust-HTSlib."
 
 [dependencies]
+libz-sys = ">=1.1.15"
 bio-types = ">=0.9"
 byteorder = "1.3"
 custom_derive = "0.1"
 derive-new = "0.5"
-hts-sys = {version = "2.0.3", default-features = false}
+hts-sys = {version = "2.1.4", default-features = false, features = ["bindgen"]}
 ieee754 = "0.2"
 lazy_static = "1.4"
 libc = "0.2"

diff --git a/Cross.toml b/Cross.toml
diff --git a/README.md b/README.md
@@ -22,36 +22,6 @@ If you only want to use the library, there is no need to clone the repository. G
 
 rust-htslib comes with pre-built bindings to htslib for Mac and Linux. You will need a C toolchain compatible with the `cc` crate. The build script for this crate will automatically build a link htslib.
 
-
-### MUSL build
-To compile this for MUSL crate you need docker and cross:
-
-```shell
-$ cargo install cross
-$ cross build 				              # will build with GNU GCC or LLVM toolchains
-```
-
-If you want to run rust-htslib code on AWS lambda, [you'll need to statically compile it with MUSL](https://github.com/awslabs/aws-lambda-rust-runtime/issues/17#issuecomment-577490373) as follows:
-
-```shell
-$ cross build --target x86_64-unknown-linux-musl      # will build with MUSL toolchain
-```
-
-Alternatively, you can also install it locally by installing the development headers of zlib, bzip2 and xz. For instance, in Debian systems one needs the following dependencies:
-
-```shell
-$ sudo apt-get install zlib1g-dev libbz2-dev liblzma-dev clang pkg-config
-```
-
-We provide Dockerfile bases that provide these dependencies. Refer to the [docker](https://github.com/rust-bio/rust-htslib/tree/master/docker) directory in this repository for the latest instructions, including LLVM installation.
-
-On OSX:
-
-```shell
-$ brew install FiloSottile/musl-cross/musl-cross
-$ brew install bzip2 zlib xz curl-openssl
-```
-
 ## Usage
 
 Add this to your `Cargo.toml`:

diff --git a/docker/Dockerfile.gnu b/docker/Dockerfile.gnu
diff --git a/docker/Dockerfile.musl b/docker/Dockerfile.musl
diff --git a/docker/README.md b/docker/README.md
diff --git a/docker/config-musl-cross-make.mak b/docker/config-musl-cross-make.mak
diff --git a/src/bam/buffer.rs b/src/bam/buffer.rs
@@ -11,7 +11,6 @@ use std::str;
 use crate::bam;
 use crate::bam::Read;
 use crate::errors::{Error, Result};
-
 /// A buffer for BAM records. This allows access regions in a sorted BAM file while iterating
 /// over it in a single pass.
 /// The buffer is implemented as a ringbuffer, such that extension or movement to the right has
@@ -25,6 +24,7 @@ pub struct RecordBuffer {
     cache_cigar: bool,
     min_refetch_distance: u64,
     buffer_record: Rc<bam::Record>,
+    start_pos: Option<u64>,
 }
 
 unsafe impl Sync for RecordBuffer {}
@@ -45,6 +45,7 @@ impl RecordBuffer {
             cache_cigar,
             min_refetch_distance: 1,
             buffer_record: Rc::new(bam::Record::new()),
+            start_pos: Some(0),
         }
     }
 
@@ -57,16 +58,16 @@ impl RecordBuffer {
     }
 
     /// Return start position of buffer
-    fn start(&self) -> Option<u64> {
+    pub fn start(&self) -> Option<u64> {
         self.inner.front().map(|rec| rec.pos() as u64)
     }
 
     /// Return end position of buffer.
-    fn end(&self) -> Option<u64> {
+    pub fn end(&self) -> Option<u64> {
         self.inner.back().map(|rec| rec.pos() as u64)
     }
 
-    fn tid(&self) -> Option<i32> {
+    pub fn tid(&self) -> Option<i32> {
         self.inner.back().map(|rec| rec.tid())
     }
 
@@ -89,7 +90,7 @@ impl RecordBuffer {
             if self.inner.is_empty()
                 || window_start.saturating_sub(self.end().unwrap()) >= self.min_refetch_distance
                 || self.tid().unwrap() != tid as i32
-                || self.start().unwrap() > window_start
+                || self.start().unwrap() > self.start_pos.unwrap()
             {
                 let end = self.reader.header.target_len(tid).unwrap();
                 self.reader.fetch((tid, window_start, end))?;
@@ -145,6 +146,7 @@ impl RecordBuffer {
                     added += 1;
                 }
             }
+            self.start_pos = Some(self.start().unwrap_or(window_start));
 
             Ok((added, deleted))
         } else {

diff --git a/src/bam/ext.rs b/src/bam/ext.rs
@@ -434,6 +434,9 @@ impl BamRecordExtensions for bam::Record {
     fn reference_start(&self) -> i64 {
         self.pos()
     }
+
+    /// Calculate the rightmost base position of an alignment on the reference genome.
+    /// Returns the coordinate of the first base after the alignment (0-based).
     fn reference_end(&self) -> i64 {
         unsafe { htslib::bam_endpos(self.inner_ptr()) }
     }