Merge branch 'master' of https://github.com/rust-bio/rust-htslib

Author: TomKellyGenetics

.cargo/config

@@ -0,0 +1,2 @@
+[target.x86_64-unknown-linux-musl]
+linker = "x86_64-linux-musl-gcc"

.github/workflows/rust.yml

@@ -0,0 +1,96 @@
+name: CI
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  Formatting:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: Install stable toolchain
+        uses: actions-rs/toolchain@v1
+        with:
+          toolchain: stable
+          override: true
+          components: rustfmt
+      
+      - name: Check format
+        run: cargo fmt -- --check
+     
+  Linting:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: Checkout submodules
+        uses: textbook/git-checkout-submodule-action@2.0.0
+
+      - name: Install stable toolchain
+        uses: actions-rs/toolchain@v1
+        with:
+          toolchain: stable
+          override: true
+          components: clippy
+
+      - name: Lint with clippy
+        uses: actions-rs/clippy-check@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+
+
+  Testing:
+    needs: Formatting
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: Checkout submodules
+        uses: textbook/git-checkout-submodule-action@2.0.0
+
+      - name: Install stable toolchain
+        uses: actions-rs/toolchain@v1
+        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
+
+      - name: Run cargo-tarpaulin
+        uses: actions-rs/tarpaulin@v0.1
+        with:
+          args: '--out Lcov -- --test-threads 1'
+
+      - name: Upload coverage
+        uses: coverallsapp/github-action@master
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          path-to-lcov: ./lcov.info
+
+      - name: Test musl build without default features
+        env:
+           CFLAGS: -I/usr/local/musl/include
+        uses: actions-rs/cargo@v1
+        with:
+          use-cross: true
+          command: build
+          args: --target x86_64-unknown-linux-musl --no-default-features
+
+      - name: Test musl build with all features
+        env:
+           CFLAGS: -I/usr/local/musl/include
+        uses: actions-rs/cargo@v1
+        with:
+          use-cross: true  
+          command: build
+          args: --target x86_64-unknown-linux-musl --all-features
+

.gitignore

@@ -1,4 +1,5 @@
 .vscode/
+.idea
 *~
 target
 Cargo.lock

.gitmodules

@@ -1,3 +1,3 @@
 [submodule "htslib"]
 	path = hts-sys/htslib
-	url = https://github.com/rust-bio/htslib.git
+	url = https://github.com/samtools/htslib.git

.travis.yml

@@ -2,24 +2,43 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
-## [0.27.0] - (TBD)
+## [0.30.0] - 2020-04-03
+### Changes
+- Removed `fn header_mut()` from `bam::Read` trait.
+- Fixed a major performance regression when reading bam files (issue #195).
+
+## [0.29.0] - 2020-03-26
+### Changes
+- Migrate buffer intervals to u64. 
+
+## [0.28.0] - 2020-03-26
+### Changes
+- Return u64 wherever htslib has migrated to using 64 bit.
+- Implement more bio-types (Interval, Locus, Strand).
+
+## [0.27.0] - 2020-03-17
+### Changes
+- Updated to Htslib 1.10.2.
 - bam::Record.set() will panic if seq.len() != qual.len(). Previously, mismatched length would cause
   uninitialized memory to be written into the BAM file.
 - use `serde_bytes` to serialize .data section of bam::Record when using serde - large speed improvement.
 - change build.rs to avoid re-running when htslib or wrapper.h haven't changed.
 - update some dependencies.
 - refactor native dependency into htslib-sys crate, for greater versioning flexibility
+- Record::from_sam require `&mut HeaderView`. Provide the appropriate accessor.
+- set() no longer invalidates tag data.
+- Various minor improvements.
 
 ## [0.26.1] - 2019-12-03
-## Changes
+### Changes
 - Various bug fixes in CIGAR string handling, INFO tag reading and FORMAT tag reading.
 
 ## [0.26.0] - 2019-09-27
-## Changes
+### Changes
 - Allow caching of CIGAR in bam::RecordBuffer.
 
 ## [0.25.0] - 2019-09-27
-## Changes
+### Changes
 - Migrated error handling to the snafu crate: https://docs.rs/snafu.
 - Cleaned up and simplified API (including breaking changes).
 - Allow writing SAM files from the bam::Writer.

CHANGELOG.md

@@ -1,6 +1,6 @@
 [package]
 name = "rust-htslib"
-version = "0.26.2-alpha.0"
+version = "0.30.1-alpha.0"
 authors = ["Christopher Schröder <christopher.schroeder@tu-dortmund.de>", "Johannes Köster <johannes.koester@tu-dortmund.de>"]
 description = "This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files."
 readme = "README.md"
@@ -17,7 +17,7 @@ tag-message = "Version {{version}} of Rust-HTSlib."
 
 [dependencies]
 libc = "0.2"
-itertools = "0.8"
+itertools = "0.9.0"
 newtype_derive = "0.1"
 custom_derive = "0.1"
 url = "2.1"
@@ -28,15 +28,18 @@ regex = "1.3"
 linear-map = "1.2"
 serde_base = { version = "^1", optional = true, package = "serde" }
 serde_bytes = { version = "0.11", optional = true }
-bio-types = ">=0.5.1"
-snafu = ">= 0.5.0, <= 0.6.0"
-hts-sys = { version = "^1.9", path = "hts-sys", default-features = false }
+bio-types = ">=0.6"
+snafu = "0.6.8"
+hts-sys = { version = "^1.10", path = "hts-sys", default-features = false }
 
 [features]
-default = ["bzip2", "lzma"]
+default = ["bzip2", "lzma", "curl"]
 bzip2 = ["hts-sys/bzip2"]
 lzma = ["hts-sys/lzma"]
+curl = ["hts-sys/curl"]
+#openssl = ["hts-sys/openssl"]
 serde = ["serde_base", "serde_bytes"]
+static = []
 
 [dev-dependencies]
 tempdir = "0.3"

Cargo.toml

@@ -0,0 +1,12 @@
+[build.env]
+passthrough = [
+    "RUST_DEBUG",
+    "RUST_BACKTRACE",
+    "CFLAGS"
+]
+
+
+[target.x86_64-unknown-linux-musl]
+image = "brainstorm/cross-x86_64-unknown-linux-musl:latest"
+[target.x86_64-unknown-linux-gnu]
+image = "brainstorm/cross-x86_64-unknown-linux-gnu:libcurl-openssl"

Cross.toml

@@ -2,24 +2,49 @@
 [![Crates.io](https://img.shields.io/crates/v/rust-htslib.svg)](https://crates.io/crates/rust-htslib)
 [![Crates.io](https://img.shields.io/crates/l/rust-htslib.svg)](https://crates.io/crates/rust-htslib)
 [![docs.rs](https://docs.rs/rust-htslib/badge.svg)](https://docs.rs/rust-htslib)
-[![Travis](https://img.shields.io/travis/rust-bio/rust-htslib.svg)](https://travis-ci.org/rust-bio/rust-htslib)
+![GitHub Workflow Status](https://img.shields.io/github/workflow/status/rust-bio/rust-htslib/CI/master?label=tests)
 
 # HTSlib bindings for Rust
 
 This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files.
 
 To clone this repository, issue
 
-```
-git clone --recursive https://github.com/rust-bio/rust-htslib.git
+```shell
+$ git clone --recursive https://github.com/rust-bio/rust-htslib.git
 ```
 
 ensuring that the HTSlib submodule is fetched, too.
 If you only want to use the library, there is no need to clone the repository. Go on to the **Usage** section in this case.
 
 ## Requirements
 
-To compile this crate you need the development headers of zlib, bzip2 and xz.
+To compile this crate you need docker and cross:
+
+```shell
+$ cargo install cross
+$ cross build 				              # will build with GNU toolchain
+```
+
+If you want to run rust-htslib code on AWS lambda, you'll need to statically compile it with MUSL as follows:
+
+```shell
+$ export CFLAGS="-I/usr/local/musl/include"
+$ 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
+```
+
+On OSX:
+
+```shell
+$ brew install FiloSottile/musl-cross/musl-cross
+$ brew install bzip2 zlib xz curl-openssl
+```
 
 ## Usage
 
@@ -46,6 +71,10 @@ rust-htslib = { version = "*", features = ["serde"] }
 
 For more information, please see the [docs](https://docs.rs/rust-htslib).
 
+# Alternatives
+
+There's [noodles](https://github.com/zaeleus/noodles) by [Michael Macias](https://github.com/zaeleus) which implements a large part of htslib's C functionality in pure Rust (still experimental though).
+
 # Authors
 
 * [Johannes Köster](https://github.com/johanneskoester)

README.md

@@ -0,0 +1,9 @@
+FROM rustembedded/cross:x86_64-unknown-linux-gnu
+
+#ENV LIBCLANG_PATH /usr/lib/x86_64-linux-musl
+ENV LIBCLANG_PATH /usr/lib/llvm-10/lib
+ENV LLVM_CONFIG_PATH /usr/bin
+RUN apt-get update
+RUN apt-get install -y wget gnupg lsb-release software-properties-common apt-transport-https ca-certificates # Otherwise LLVM bump below fails
+RUN bash -c "$(wget -O - https://apt.llvm.org/llvm.sh)"
+RUN apt-get install -y libssl-dev libcurl4-openssl-dev zlib1g-dev libbz2-dev liblzma-dev # htslib deps