Add option to force mapAD to overwrite existing output files

src/distributed/dispatcher.rs

@@ -55,6 +55,7 @@ pub struct Dispatcher<'a, 'b> {
     reads_path: &'b Path,
     reference_path: &'b Path,
     out_file_path: &'b Path,
+    force_overwrite: bool,
     alignment_parameters: &'a AlignmentParameters,
     connections: HashMap<Token, Connection>,
     accept_connections: bool,
@@ -68,6 +69,7 @@ impl<'a, 'b> Dispatcher<'a, 'b> {
         reads_path: &'b str,
         reference_path: &'b str,
         out_file_path: &'b str,
+        force_overwrite: bool,
         alignment_parameters: &'a AlignmentParameters,
     ) -> Result<Self> {
         let reads_path = Path::new(reads_path);
@@ -83,6 +85,7 @@ impl<'a, 'b> Dispatcher<'a, 'b> {
             reads_path,
             reference_path: Path::new(reference_path),
             out_file_path,
+            force_overwrite,
             alignment_parameters,
             connections: HashMap::new(),
             accept_connections: true,
@@ -122,7 +125,10 @@ impl<'a, 'b> Dispatcher<'a, 'b> {
             OpenOptions::new()
                 .read(false)
                 .write(true)
-                .create_new(true)
+                // If .create_new(true) is set, .create() and .truncate() are ignored
+                .create_new(!self.force_overwrite)
+                .create(true)
+                .truncate(true)
                 .open(self.out_file_path)?,
         );
 

src/main.rs

@@ -249,6 +249,12 @@ fn define_cli() -> ArgMatches {
                         .help("Abort alignment when stack size limit is reached instead of trying to recover.")
                         .action(ArgAction::SetTrue)
                 )
+                .arg(
+                    Arg::new("force_overwrite")
+                        .long("force_overwrite")
+                        .help(format!("Force {CRATE_NAME} to overwrite the output BAM file."))
+                        .action(ArgAction::SetTrue)
+                )
         )
         .subcommand(
             Command::new("worker")
@@ -315,6 +321,7 @@ fn start_mapper(map_matches: &ArgMatches, _seed: u64) {
     let out_file_path = map_matches
         .get_one::<String>("output")
         .expect("Presence is ensured by CLI definition");
+    let force_overwrite = map_matches.get_flag("force_overwrite");
 
     let num_threads = *map_matches
         .get_one("num_threads")
@@ -335,6 +342,7 @@ fn start_mapper(map_matches: &ArgMatches, _seed: u64) {
             reads_path,
             reference_path,
             out_file_path,
+            force_overwrite,
             &alignment_parameters,
         )
         .and_then(|mut dispatcher| dispatcher.run(port))
@@ -343,6 +351,7 @@ fn start_mapper(map_matches: &ArgMatches, _seed: u64) {
             reads_path,
             reference_path,
             out_file_path,
+            force_overwrite,
             &alignment_parameters,
         )
     } {

src/map/mapping.rs

@@ -54,6 +54,7 @@ pub fn run(
     reads_path: &str,
     reference_path: &str,
     out_file_path: &str,
+    force_overwrite: bool,
     alignment_parameters: &AlignmentParameters,
 ) -> Result<()> {
     let reads_path = Path::new(reads_path);
@@ -87,7 +88,10 @@ pub fn run(
         OpenOptions::new()
             .read(false)
             .write(true)
-            .create_new(true)
+            // If .create_new(true) is set, .create() and .truncate() are ignored
+            .create_new(!force_overwrite)
+            .create(true)
+            .truncate(true)
             .open(out_file_path)?,
     );
 

tests/integration_tests.rs

@@ -172,6 +172,7 @@ fn integration_1_local() {
         env.input_bam_path.to_str().unwrap(),
         env.test_genome_path.to_str().unwrap(),
         output_bam_path_local.to_str().unwrap(),
+        false,
         &env.alignment_parameters,
     )
     .unwrap();
@@ -196,6 +197,7 @@ fn integration_1_distributed() {
                 env.input_bam_path.to_str().unwrap(),
                 env.test_genome_path.to_str().unwrap(),
                 output_bam_path_distr_clone.to_str().unwrap(),
+                false,
                 &env.alignment_parameters,
             )
             .unwrap();