Bump Rust to 1.58.1 in CI and clippy cleanups (#55)

* update Rust to 1.58.1
* clippy cleanup
* Rename BGW and use slices instead of Vec
* Make Rust installation closer to 10x repos
* reorganize parse_spec to use iterator adapters with collect
* use next_tuple for header parsing

Co-authored-by: Adam Azarchs <adam.azarchs@10xgenomics.com>

.github/workflows/release.yaml

@@ -54,6 +54,11 @@ jobs:
     steps:
       - name: Checkout git repository
         uses: actions/checkout@master
+      - name: Install Rust
+        uses: actions-rs/toolchain@v1
+        with:
+          toolchain: 1.58.1
+          default: true
       - name: Make release build
         run: |
           cargo build --release

.github/workflows/test.yaml

@@ -14,10 +14,12 @@ jobs:
     # This job runs on MacOS Catalina
     runs-on: macos-latest
     steps:
-      - name: rust version
-        run: rustup default 1.44.0
-      - name: add rustfmt 
-        run: rustup component add rustfmt
+      - name: Install Rust
+        uses: actions-rs/toolchain@v1
+        with:
+          toolchain: 1.58.1
+          components: rustfmt
+          default: true
       - name: Checkout bamtofastq master
         uses: actions/checkout@master
       - name: Check Rust formatting
@@ -31,10 +33,12 @@ jobs:
     # This job runs on Linux
     runs-on: ubuntu-latest
     steps:
-      - name: rust version
-        run: rustup default 1.55.0
-      - name: add rustfmt
-        run: rustup component add rustfmt clippy
+      - name: Install Rust
+        uses: actions-rs/toolchain@v1
+        with:
+          toolchain: 1.58.1
+          components: rustfmt, clippy
+          default: true
       - name: Checkout bamtofastq master
         uses: actions/checkout@master
       - name: Check Rust formatting

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "bamtofastq"
-version = "1.4.0"
+version = "1.4.1"
 authors = ["Patrick Marks <patrick@10xgenomics.com>"]
 license = "MIT"
 repository = "https://github.com/10XGenomics/bamtofastq.git"

src/bx_index.rs

@@ -64,7 +64,7 @@ impl BxIndex {
 pub fn get_records_for_bx<R: Read>(
     index: &BxIndex,
     reader: &mut R,
-    bx: &String,
+    bx: &str,
 ) -> Result<Vec<Record>, Error> {
     let start = index.get_voffset(bx);
     reader.seek(start as i64)?;
@@ -78,9 +78,9 @@ pub fn get_records_for_bx<R: Read>(
             _ => "".to_string(),
         };
 
-        if &bx_read == bx {
+        if bx_read == bx {
             recs.push(rec);
-        } else if &bx_read < bx {
+        } else if bx_read.as_str() < bx {
             continue;
         } else {
             break;
@@ -150,9 +150,8 @@ impl<R: Read> Iterator for BxListIter<R> {
                 self.cur_vec.reverse();
             }
 
-            match self.cur_vec.pop() {
-                Some(v) => return Some(Ok(v)),
-                None => (),
+            if let Some(v) = self.cur_vec.pop() {
+                return Some(Ok(v));
             }
         }