chore: add basic ci

.github/workflows/ci.yaml

@@ -0,0 +1,25 @@
+# From https://github.com/actions-rust-lang/setup-rust-toolchain
+name: "Test Suite"
+on:
+  push:
+  pull_request:
+jobs:
+  test:
+    name: cargo test
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions-rust-lang/setup-rust-toolchain@v1
+      - run: cargo test --all-features
+  # Check formatting with rustfmt
+  formatting:
+    name: cargo fmt
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      # Ensure rustfmt is installed and setup problem matcher
+      - uses: actions-rust-lang/setup-rust-toolchain@v1
+        with:
+          components: rustfmt
+      - name: Rustfmt Check
+        uses: actions-rust-lang/rustfmt@v1

src/util/aux_counts.rs

@@ -6,15 +6,13 @@ use itertools::izip;
 pub struct CountInfo {
     pub unique_count: u32,
     pub total_count: u32,
-    pub expected_count: f64,
 }
 
 impl CountInfo {
     pub fn new() -> Self {
         Self {
             unique_count: 0,
             total_count: 0,
-            expected_count: 0.0,
         }
     }
 }

src/util/oarfish_types.rs

@@ -81,10 +81,6 @@ impl<T: sam::alignment::record::Record> From<&T> for AlnInfo {
 #[serde(rename_all = "PascalCase")]
 pub struct ShortReadRecord {
     pub name: String,
-    pub length: i32,
-    pub effective_length: f64,
-    #[serde(rename = "TPM")]
-    pub tpm: f64,
     pub num_reads: f64,
 }
 
@@ -93,9 +89,6 @@ impl ShortReadRecord {
     pub fn empty(name: &str) -> Self {
         Self {
             name: name.to_owned(),
-            length: 0,
-            effective_length: 0.0,
-            tpm: 0.0,
             num_reads: 0.0,
         }
     }