Merge branch 'master' into #407-trailing-omitted-format

.github/workflows/rust.yml

@@ -85,9 +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
@@ -96,18 +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

CHANGELOG.md

@@ -2,6 +2,30 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## [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)
 
 

Cargo.toml

@@ -9,13 +9,14 @@ license = "MIT"
 name = "rust-htslib"
 readme = "README.md"
 repository = "https://github.com/rust-bio/rust-htslib.git"
-version = "0.44.1"
+version = "0.46.0"
 
 [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"

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`:

src/bam/buffer.rs

@@ -57,16 +57,16 @@ 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())
     }
 

src/bam/record.rs

@@ -4,6 +4,7 @@
 // except according to those terms.
 
 use std::convert::TryFrom;
+use std::convert::TryInto;
 use std::ffi;
 use std::fmt;
 use std::marker::PhantomData;
@@ -2216,7 +2217,7 @@ impl fmt::Display for CigarStringView {
 pub struct BaseModificationMetadata {
     pub strand: i32,
     pub implicit: i32,
-    pub canonical: i8,
+    pub canonical: u8,
 }
 
 /// struct containing the internal state required to access
@@ -2314,7 +2315,8 @@ impl BaseModificationState<'_> {
         unsafe {
             let mut strand: i32 = 0;
             let mut implicit: i32 = 0;
-            let mut canonical: i8 = 0;
+            // This may be i8 or u8 in hts_sys.
+            let mut canonical: c_char = 0;
 
             let ret = hts_sys::bam_mods_query_type(
                 self.state,
@@ -2329,7 +2331,7 @@ impl BaseModificationState<'_> {
                 return Ok(BaseModificationMetadata {
                     strand,
                     implicit,
-                    canonical,
+                    canonical: canonical.try_into().unwrap(),
                 });
             }
         }