Bump rust version and transitive deps. (#65)

* Bump rust version to 1.59.0.

Also run clippy --fix.

* Update transitive dependencies.

* explicit dep on libz-sys to fix OSX segfault issue.

Co-authored-by: Luiz Irber <83029587+luiz10x@users.noreply.github.com>

.github/workflows/release.yaml

@@ -65,7 +65,7 @@ jobs:
       - name: Install Rust
         uses: actions-rs/toolchain@v1
         with:
-          toolchain: 1.58.1
+          toolchain: 1.59.0
           default: true
       - name: Make release build
         run: |

.github/workflows/test.yaml

@@ -17,7 +17,7 @@ jobs:
       - name: Install Rust
         uses: actions-rs/toolchain@v1
         with:
-          toolchain: 1.58.1
+          toolchain: 1.59.0
           components: rustfmt
           default: true
       - name: Checkout bamtofastq master
@@ -36,7 +36,7 @@ jobs:
       - name: Install Rust
         uses: actions-rs/toolchain@v1
         with:
-          toolchain: 1.58.1
+          toolchain: 1.59.0
           components: rustfmt, clippy
           default: true
       - name: Checkout bamtofastq master

Cargo.toml

@@ -20,6 +20,7 @@ curl = ["rust-htslib/curl"]
 docopt = "*"
 rust-htslib = { version = "0.38", default-features = false }
 flate2 = { version = "1.0", features = ["zlib"], default-features = false }
+libz-sys = "1.1.5"
 shardio = "0.8.2"
 bincode = "1"
 itertools = ">=0.8.0"

src/locus.rs

@@ -21,7 +21,7 @@ impl fmt::Display for Locus {
 
 fn remove_commas(s: &str) -> String {
     let ss = s.to_string();
-    ss.replace(",", "")
+    ss.replace(',', "")
 }
 
 impl FromStr for Locus {

src/main.rs

@@ -214,8 +214,8 @@ impl FormatBamRecords {
                 rg_spec: rgs,
                 r1_spec: spec.remove("R1").unwrap(),
                 r2_spec: spec.remove("R2").unwrap(),
-                i1_spec: spec.remove("I1").unwrap_or_else(Vec::new),
-                i2_spec: spec.remove("I2").unwrap_or_else(Vec::new),
+                i1_spec: spec.remove("I1").unwrap_or_default(),
+                i2_spec: spec.remove("I2").unwrap_or_default(),
                 rename: seq_names,
                 order: [1, 3, 2, 4],
             })
@@ -668,7 +668,7 @@ impl FastqManager {
         for (_, &(ref _samp, lane)) in formatter.rg_spec.iter() {
             let samp = _samp.clone();
             let path = sample_def_paths.entry(samp).or_insert_with(|| {
-                let suffix = _samp.replace(":", "_");
+                let suffix = _samp.replace(':', "_");
 
                 //create_dir(&samp_path).expect("couldn't create output directory");
                 out_path.join(suffix)