cli: Change quantify output option to be optional

If not set, output is written to stdout.

src/cli.rs

@@ -80,9 +80,11 @@ pub struct Quantify {
     #[arg(long, value_parser = parse_mapping_quality, default_value = "10")]
     pub min_mapping_quality: MappingQuality,
 
-    /// Output destination for feature counts.
+    /// Output destination.
+    ///
+    /// If not set, output is written to stdout.
     #[arg(short = 'o', long)]
-    pub output: PathBuf,
+    pub output: Option<PathBuf>,
 
     /// Input annotations file (GFF3).
     #[arg(short = 'a', long)]

src/commands/quantify.rs

@@ -1,4 +1,9 @@
-use std::{fs::File, io::BufWriter, num::NonZeroUsize, path::Path};
+use std::{
+    fs::File,
+    io::{self, BufWriter, Write},
+    num::NonZeroUsize,
+    path::Path,
+};
 
 use anyhow::Context as AnyhowContext;
 use noodles::{bam, bgzf};
@@ -20,7 +25,7 @@ pub fn quantify<P, Q, R>(
     filter: Filter,
     strand_specification_option: StrandSpecificationOption,
     worker_count: NonZeroUsize,
-    results_dst: R,
+    dst: Option<R>,
 ) -> anyhow::Result<()>
 where
     P: AsRef<Path>,
@@ -97,9 +102,15 @@ where
         )?,
     };
 
-    let writer = File::create(results_dst.as_ref())
-        .map(BufWriter::new)
-        .with_context(|| format!("Could not open {}", results_dst.as_ref().display()))?;
+    let writer: Box<dyn Write> = if let Some(dst) = dst {
+        File::create(dst.as_ref())
+            .map(BufWriter::new)
+            .map(Box::new)
+            .with_context(|| format!("Could not open {}", dst.as_ref().display()))?
+    } else {
+        let stdout = io::stdout().lock();
+        Box::new(BufWriter::new(stdout))
+    };
 
     info!("writing counts");
 

src/main.rs

@@ -18,8 +18,6 @@ fn quantify(options: cli::Quantify) -> anyhow::Result<()> {
     let bam_src = options.src;
     let annotations_src = options.annotations;
 
-    let results_dst = options.output;
-
     let threads = match options.threads {
         Some(n) => n,
         None => thread::available_parallelism()?,
@@ -44,7 +42,7 @@ fn quantify(options: cli::Quantify) -> anyhow::Result<()> {
         filter,
         strand_specification_option,
         threads,
-        results_dst,
+        options.output,
     )
 }
 

tests/quantify_single_end_forward_test.rs

@@ -24,7 +24,7 @@ fn test_quantify_with_single_end_forward_sample() -> anyhow::Result<()> {
         filter,
         strand_specification_option,
         worker_count,
-        &results_dst,
+        Some(&results_dst),
     )?;
 
     let actual = fs::read_to_string(results_dst)?;