Update to htslib 1.10.2 (without musl)

.cargo/config

@@ -0,0 +1,12 @@
+[target.x86_64-apple-darwin]
+rustflags = [
+  "-C", "link-arg=-undefined",
+  "-C", "link-arg=dynamic_lookup",
+]
+
+[target.x86_64-unknown-linux-musl]
+rustflags = [
+  "-C", "link-arg=-undefined",
+  "-C", "link-arg=dynamic_lookup",
+]
+linker = "x86_64-linux-musl-gcc"

.github/workflows/rust.yml

@@ -39,10 +39,6 @@ jobs:
           override: true
           components: clippy
 
-      - name: Install system dependencies
-        run: |
-            sudo apt-get install --yes zlib1g-dev libbz2-dev musl musl-dev musl-tools
-
       - name: Lint with clippy
         uses: actions-rs/clippy-check@v1
         with:
@@ -67,7 +63,7 @@ jobs:
 
       - name: Install system dependencies
         run: |
-            sudo apt-get install --yes zlib1g-dev libbz2-dev musl musl-dev musl-tools
+            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
@@ -79,3 +75,17 @@ jobs:
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           path-to-lcov: ./lcov.info
+
+#      - name: Test musl build without default features
+#        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
+#        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

Cargo.toml

@@ -33,9 +33,11 @@ snafu = ">= 0.5.0, <= 0.6.0"
 hts-sys = { version = "^1.9", 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"]
 
 [dev-dependencies]

Cross.toml

@@ -0,0 +1,4 @@
+[target.x86_64-unknown-linux-musl]
+image = "brainstorm/rust_musl_docker:stable-latest-libcurl"
+[target.x86_64-unknown-linux-gnu]
+image = "brainstorm/cross-x86_64-unknown-linux-gnu:libcurl-openssl"

README.md

@@ -19,7 +19,18 @@ If you only want to use the library, there is no need to clone the repository. G
 
 ## Requirements
 
-To compile this crate you need the development headers of zlib, bzip2 and xz.
+To compile this crate you need 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
+```
+
+On OSX, this will take a significant amount of time due to musl cross compiling toolchain:
+
+```shell
+$ brew install FiloSottile/musl-cross/musl-cross
+$ brew install bzip2 zlib xz curl-openssl
+```
 
 ## Usage
 

docker/Dockerfile.gnu

@@ -0,0 +1,8 @@
+FROM rustembedded/cross:x86_64-unknown-linux-gnu
+
+ENV LIBCLANG_PATH /usr/lib/x86_64-linux-gnu
+ENV LLVM_CONFIG_PATH /usr/bin
+RUN apt-get update && \
+    apt-get install -y libcurl4-openssl-dev zlib1g-dev libbz2-dev liblzma-dev clang-8 && \
+    ln -sf /usr/bin/llvm-config-8 /usr/bin/llvm-config && \
+    ln -sf /usr/lib/x86_64-linux-gnu/libclang-8.so.1 /usr/lib/x86_64-linux-gnu/libclang.so.1

docker/Dockerfile.musl

@@ -0,0 +1,7 @@
+FROM rustembedded/cross:x86_64-unknown-linux-musl
+
+ENV PKG_CONFIG_ALLOW_CROSS 1
+ENV OPENSSL_LIB_DIR /usr/lib/x86_64-linux-gnu
+ENV OPENSSL_INCLUDE_DIR /usr/include/openssl
+RUN apt-get update && \
+    apt-get install -y libssl-dev libcurl4-openssl-dev zlib1g-dev libbz2-dev liblzma-dev musl musl-dev musl-tools linux-libc-dev linux-headers-4.15.0-20-generic

docker/README.md

@@ -0,0 +1,17 @@
+# cross rustembedded containers
+
+Allows to compile (rust-)htslib in a variety of environments and architectures via [rustembedded cross](https://github.com/rust-embedded/cross).
+
+## Quickstart
+
+```shell
+$ cd docker
+$ docker build -t brainstorm/cross-x86_64-unknown-linux-musl:libcurl-openssl . -f Dockerfile.musl
+$ docker build -t brainstorm/cross-x86_64-unknown-linux-gnu:libcurl-openssl . -f Dockerfile.gnu
+```
+
+Then to build and test rust-htslib with the above containers, proceed as you would with `cargo`, using `cross` instead, i.e:
+
+```shell
+$ cross build --target x86_64-unknown-linux-musl 
+```

hts-sys/Cargo.toml

@@ -8,7 +8,7 @@ description = "This library provides HTSlib bindings."
 readme = "README.md"
 keywords = ["htslib", "bam", "bioinformatics", "pileup", "sequencing"]
 license = "MIT"
-repository = "https://github.com/rust-bio/rust-htslib.git"
+repository = "https://github.com/samtools/htslib.git"
 documentation = "https://docs.rs/rust-htslib"
 edition = "2018"
 
@@ -21,14 +21,18 @@ libc = "0.2"
 libz-sys = "1.0"
 bzip2-sys = { version = "0.1", optional = true }
 lzma-sys = { version = "0.1", optional = true }
+curl-sys = { version = "0.4.26", optional = true }
+openssl-sys = { version = "0.9.54", optional = true }
 
 [features]
-default = ["bzip2", "lzma"]
+default = ["bzip2", "lzma", "curl"]
 bzip2 = ["bzip2-sys"]
 lzma = ["lzma-sys"]
+openssl = ["openssl-sys"]
+curl = ["curl-sys"]
 
 [build-dependencies]
 fs-utils = "1.1"
-bindgen = { version = "0.52.0", default-features = false, features = ["runtime"] }
+bindgen = { version = "0.53.1", default-features = false, features = ["runtime"] }
 cc = "1.0"
 glob = "0.3.0"

hts-sys/build.rs

@@ -13,9 +13,9 @@ use std::fs;
 use std::path::PathBuf;
 use std::process::Command;
 
-fn sed_htslib_makefile(out: &PathBuf, patterns: &Vec<&str>, feature: &str) {
+fn sed_htslib_makefile(out: &PathBuf, patterns: &[&str], feature: &str) {
     for pattern in patterns {
-        if Command::new("sed")
+        if !Command::new("sed")
             .current_dir(out.join("htslib"))
             .arg("-i")
             .arg("-e")
@@ -24,7 +24,6 @@ fn sed_htslib_makefile(out: &PathBuf, patterns: &Vec<&str>, feature: &str) {
             .status()
             .unwrap()
             .success()
-            != true
         {
             panic!("failed to strip {} support", feature);
         }
@@ -63,10 +62,18 @@ fn main() {
         cfg.include(inc);
     }
 
+    let use_curl = env::var("CARGO_FEATURE_CURL").is_ok();
+    if !use_curl {
+        let curl_patterns = vec!["s/ -lcurl//", "/#define HAVE_LIBCURL/d"];
+        sed_htslib_makefile(&out, &curl_patterns, "curl");
+    } else if let Ok(inc) = env::var("DEP_CURL_INCLUDE").map(PathBuf::from) {
+        cfg.include(inc);
+    }
+
     let tool = cfg.get_compiler();
     let (cc_path, cflags_env) = (tool.path(), tool.cflags_env());
     let cc_cflags = cflags_env.to_string_lossy().replace("-O0", "");
-    if Command::new("make")
+    if !Command::new("make")
         .current_dir(out.join("htslib"))
         .arg(format!("CC={}", cc_path.display()))
         .arg(format!("CFLAGS={}", cc_cflags))
@@ -75,7 +82,6 @@ fn main() {
         .status()
         .unwrap()
         .success()
-        != true
     {
         panic!("failed to build htslib");
     }

hts-sys/src/lib.rs

@@ -11,6 +11,8 @@ extern crate libz_sys;
 extern crate bzip2_sys;
 #[cfg(feature = "lzma")]
 extern crate lzma_sys;
+#[cfg(feature = "curl")]
+extern crate curl_sys;
 
 // include on-the-fly generated bindings
 include!(concat!(env!("OUT_DIR"), "/bindings.rs"));

src/bam/buffer.rs

@@ -86,7 +86,7 @@ impl RecordBuffer {
                 let to_remove = self
                     .inner
                     .iter()
-                    .take_while(|rec| rec.pos() < window_start as i32)
+                    .take_while(|rec| rec.pos() < window_start as i64)
                     .count();
                 for _ in 0..to_remove {
                     self.inner.pop_front();
@@ -111,7 +111,7 @@ impl RecordBuffer {
                     record.cache_cigar();
                 }
 
-                if pos >= end as i32 {
+                if pos >= end as i64 {
                     self.overflow = Some(record);
                     break;
                 } else {