WIP

.github/workflows/comparison.yml

@@ -0,0 +1,27 @@
+name: Compare
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  crossmap:
+    runs-on: ubuntu-latest 
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/cache@v4
+        with:
+          path: chainfiles
+          key: ${{ runner.os }}-chainfiles
+      - name: Update Rust
+        run: rustup update stable && rustup default stable
+      - name: Install CrossMap
+        run: pip install CrossMap
+      - uses: Swatinem/rust-cache@v2
+        with:
+          workspaces: .
+      - run: |
+        mkdir -p chainfiles
+        cargo run --release --features=binaries -- -d chainfiles hg19ToHg38 -v

src/bin/kitchen_sink.rs

@@ -142,18 +142,18 @@ impl std::fmt::Display for LiftoverResult {
 // CrossMap execution
 ////////////////////////////////////////////////////////////////////////////////////////
 
-/// A struct for working with `crossmap`.
+/// A struct for working with `CrossMap`.
 struct CrossMap;
 
 impl CrossMap {
-    /// Ensures the `crossmap` is installed.
+    /// Ensures the `CrossMap` is installed.
     fn ensure_installed() -> Result<()> {
-        Command::new("crossmap")
+        Command::new("CrossMap")
             .arg("--version")
             .stdout(Stdio::piped())
             .stderr(Stdio::piped())
             .status()
-            .context("retrieving `crossmap`'s version")
+            .context("retrieving `CrossMap`'s version")
             .map(|_| ())
     }
 
@@ -181,7 +181,7 @@ impl CrossMap {
             let stderr = String::from_utf8_lossy(&output.stderr);
             for line in stderr.lines() {
                 if !line.contains("[INFO]") {
-                    panic!("`crossmap` returned something on stderr: {stderr}");
+                    panic!("`CrossMap` returned something on stderr: {stderr}");
                 }
             }
         }
@@ -193,7 +193,7 @@ impl CrossMap {
             let parts = line.split("\t").collect::<Vec<_>>();
             assert!(
                 parts.len() > 3,
-                "should always have at least four parts of a `crossmap` result line; found \
+                "should always have at least four parts of a `CrossMap` result line; found \
                  `{line}`"
             );
 
@@ -221,7 +221,7 @@ impl CrossMap {
 
                     LiftoverResult::Mapped(to)
                 }
-                _ => unreachable!("cannot parse `crossmap` result: `{line}`"),
+                _ => unreachable!("cannot parse `CrossMap` result: `{line}`"),
             };
 
             results.insert(from, to);
@@ -333,7 +333,7 @@ impl WorkDirectory {
         self.0.join("reference")
     }
 
-    /// The input positions bed file to `crossmap`.
+    /// The input positions bed file to `CrossMap`.
     fn input_bed_file(&self) -> PathBuf {
         self.0.join("input.bed")
     }
@@ -389,10 +389,10 @@ impl Deref for WorkDirectory {
 }
 
 ////////////////////////////////////////////////////////////////////////////////////////
-// Comparsion between `chainfile` and `crossmap`
+// Comparsion between `chainfile` and`CrossMap`
 ////////////////////////////////////////////////////////////////////////////////////////
 
-/// A comparison of liftover results between `chainfile` and `crossmap`.
+/// A comparison of liftover results between `chainfile` and `CrossMap`.
 #[derive(Clone, Debug)]
 struct Comparison {
     /// The original position.
@@ -401,7 +401,7 @@ struct Comparison {
     /// The lifted position from `chainfile`.
     chainfile: LiftoverResult,
 
-    /// The lifted position from `crossmap`.
+    /// The lifted position from `CrossMap`.
     crossmap: LiftoverResult,
 }
 
@@ -475,8 +475,8 @@ fn throw(args: &Args) -> Result<()> {
 
     info!("working directory: {}", work_dir.display());
 
-    info!("crossmap: ensuring `crossmap` is installed");
-    CrossMap::ensure_installed().context("ensuring `crossmap` is installed")?;
+    info!("crossmap: ensuring `CrossMap` is installed");
+    CrossMap::ensure_installed().context("ensuring `CrossMap` is installed")?;
 
     let chain_file_path = work_dir
         .download_chain_file(&args.chain)
@@ -510,7 +510,7 @@ fn throw(args: &Args) -> Result<()> {
 
     info!("crossmap: running liftover");
     for (from, crossmap_result) in CrossMap::run_bed(&chain_file_path, &work_dir.input_bed_file())
-        .context("getting the `crossmap` mappings")?
+        .context("getting the `CrossMap` mappings")?
     {
         let start =
             Coordinate::<Interbase>::new(from.contig.as_str(), Strand::Positive, from.start);
@@ -570,7 +570,7 @@ fn throw(args: &Args) -> Result<()> {
     let matched_percent = (n_matches as f64 * 100.0) / total_comparisons as f64;
 
     println!(
-        "`chainfile` and `crossmap` matched in {matched_percent:.2}% of cases (n = {})",
+        "`chainfile` and `CrossMap` matched in {matched_percent:.2}% of cases (n = {})",
         total_comparisons
     );