sam/examples: Add async query example

noodles-sam/Cargo.toml

@@ -36,6 +36,10 @@ features = ["async"]
 name = "sam_count_async"
 required-features = ["async"]
 
+[[example]]
+name = "sam_query_async"
+required-features = ["async"]
+
 [[example]]
 name = "sam_read_header_async"
 required-features = ["async"]

noodles-sam/examples/sam_query_async.rs

@@ -0,0 +1,46 @@
+//! Queries a bgzipped SAM file with a given region.
+//!
+//! The input bgzipped SAM file must have an associated coordinate-sorted index (CSI) in the same
+//! directory.
+//!
+//! The result matches the output of `samtools view <src> <region>`.
+
+use std::{env, path::PathBuf};
+
+use futures::TryStreamExt;
+use noodles_bgzf as bgzf;
+use noodles_csi as csi;
+use noodles_sam as sam;
+use tokio::{
+    fs::File,
+    io::{self, AsyncWriteExt},
+};
+
+#[tokio::main]
+async fn main() -> Result<(), Box<dyn std::error::Error>> {
+    let mut args = env::args().skip(1);
+
+    let src = args.next().map(PathBuf::from).expect("missing src");
+    let raw_region = args.next().expect("missing region");
+
+    let mut reader = File::open(&src)
+        .await
+        .map(bgzf::AsyncReader::new)
+        .map(sam::r#async::io::Reader::new)?;
+
+    let header = reader.read_header().await?;
+
+    let index = csi::r#async::read(src.with_extension("sam.csi")).await?;
+    let region = raw_region.parse()?;
+    let mut query = reader.query(&header, &index, &region)?;
+
+    let mut writer = sam::r#async::io::Writer::new(io::stdout());
+
+    while let Some(record) = query.try_next().await? {
+        writer.write_alignment_record(&header, &record).await?;
+    }
+
+    writer.get_mut().shutdown().await?;
+
+    Ok(())
+}