bwa mem blocking -> mm2

src/io/bam.rs

@@ -181,108 +181,108 @@ pub fn create_bam_leave_two_out(input_path: &str) -> anyhow::Result<Vec<PathBuf>
     Ok(output_paths)
 }
 
-pub fn remap_bam(reference: &str, input_seq: &str, output_bam: &str) -> anyhow::Result<()> {
-    duct::cmd!("bwa", "index", reference).run()?;
-    let bwa = format!("bwa mem {reference} {input_seq}");
-    let samtools = "samtools sort /dev/stdin";
-    let pipe = format!("{bwa} | {samtools} > {output_bam}");
-    duct::cmd!("bash", "-c", pipe).run()?;
-    fs::remove_file(format!("{reference}.amb"))?;
-    fs::remove_file(format!("{reference}.ann"))?;
-    fs::remove_file(format!("{reference}.bwt"))?;
-    fs::remove_file(format!("{reference}.pac"))?;
-    fs::remove_file(format!("{reference}.sa"))?;
-
-    Ok(())
-}
 // pub fn remap_bam(reference: &str, input_seq: &str, output_bam: &str) -> anyhow::Result<()> {
-//     info!("Remaping {input_seq} to {reference} into {output_bam}");
-//     // Index the reference
-//     let index_output = Command::new("bwa")
-//         .args(["index", reference])
-//         .output()
-//         .context("Failed to run bwa index")?;
-//
-//     if !index_output.status.success() {
-//         anyhow::bail!(
-//             "bwa index failed: {}",
-//             String::from_utf8_lossy(&index_output.stderr)
-//         );
-//     }
-//
-//     // Prepare the bwa mem command
-//     let mut bwa_command = Command::new("bwa");
-//     bwa_command.args(["mem", reference, input_seq]);
-//     bwa_command.stdout(Stdio::piped());
-//     bwa_command.stderr(Stdio::piped());
-//
-//     let mut bwa_process = bwa_command
-//         .spawn()
-//         .context("Failed to spawn bwa mem command")?;
-//
-//     // Prepare the samtools sort command
-//     let mut samtools_command = Command::new("samtools");
-//     samtools_command.args(["sort", "/dev/stdin"]);
-//     samtools_command.stdin(Stdio::piped());
-//     samtools_command.stdout(Stdio::from(
-//         std::fs::File::create(output_bam).context("Failed to create output BAM file")?,
-//     ));
-//     samtools_command.stderr(Stdio::piped());
-//
-//     let mut samtools_process = samtools_command
-//         .spawn()
-//         .context("Failed to spawn samtools command")?;
-//
-//     // Connect bwa stdout to samtools stdin
-//     if let (Some(mut bwa_stdout), Some(mut samtools_stdin)) =
-//         (bwa_process.stdout.take(), samtools_process.stdin.take())
-//     {
-//         std::thread::spawn(move || std::io::copy(&mut bwa_stdout, &mut samtools_stdin));
-//     }
-//
-//     // Capture stderr from bwa
-//     let mut bwa_stderr = String::new();
-//     bwa_process
-//         .stderr
-//         .take()
-//         .unwrap()
-//         .read_to_string(&mut bwa_stderr)?;
-//
-//     // Wait for bwa to finish
-//     let bwa_status = bwa_process.wait().context("Failed to wait for bwa mem")?;
-//     if !bwa_status.success() {
-//         anyhow::bail!("bwa mem failed: {}", bwa_stderr);
-//     }
-//
-//     // Capture stderr from samtools
-//     let mut samtools_stderr = String::new();
-//     samtools_process
-//         .stderr
-//         .take()
-//         .unwrap()
-//         .read_to_string(&mut samtools_stderr)?;
-//
-//     // Wait for samtools to finish
-//     let samtools_status = samtools_process
-//         .wait()
-//         .context("Failed to wait for samtools")?;
-//     if !samtools_status.success() {
-//         anyhow::bail!("samtools sort failed: {}", samtools_stderr);
-//     }
-//
+//     duct::cmd!("bwa", "index", reference).run()?;
+//     let bwa = format!("bwa mem {reference} {input_seq}");
+//     let samtools = "samtools sort /dev/stdin";
+//     let pipe = format!("{bwa} | {samtools} > {output_bam}");
+//     duct::cmd!("bash", "-c", pipe).run()?;
 //     fs::remove_file(format!("{reference}.amb"))?;
 //     fs::remove_file(format!("{reference}.ann"))?;
 //     fs::remove_file(format!("{reference}.bwt"))?;
 //     fs::remove_file(format!("{reference}.pac"))?;
 //     fs::remove_file(format!("{reference}.sa"))?;
 //
-//     // Log the captured stderr
-//     // println!("bwa mem stderr: {}", bwa_stderr);
-//     // println!("samtools sort stderr: {}", samtools_stderr);
-//
 //     Ok(())
 // }
-//
+pub fn remap_bam(reference: &str, input_seq: &str, output_bam: &str) -> anyhow::Result<()> {
+    info!("Remaping {input_seq} to {reference} into {output_bam}");
+    // Index the reference
+    // let index_output = Command::new("bwa")
+    //     .args(["index", reference])
+    //     .output()
+    //     .context("Failed to run bwa index")?;
+    //
+    // if !index_output.status.success() {
+    //     anyhow::bail!(
+    //         "bwa index failed: {}",
+    //         String::from_utf8_lossy(&index_output.stderr)
+    //     );
+    // }
+
+    // Prepare the bwa mem command
+    let mut minimap2_command = Command::new("minimap2");
+    minimap2_command.args(["-a", reference, input_seq]);
+    minimap2_command.stdout(Stdio::piped());
+    minimap2_command.stderr(Stdio::piped());
+
+    let mut minimap2_process = minimap2_command
+        .spawn()
+        .context("Failed to spawn minimap2 command")?;
+
+    // Prepare the samtools sort command
+    let mut samtools_command = Command::new("samtools");
+    samtools_command.args(["sort", "/dev/stdin"]);
+    samtools_command.stdin(Stdio::piped());
+    samtools_command.stdout(Stdio::from(
+        std::fs::File::create(output_bam).context("Failed to create output BAM file")?,
+    ));
+    samtools_command.stderr(Stdio::piped());
+
+    let mut samtools_process = samtools_command
+        .spawn()
+        .context("Failed to spawn samtools command")?;
+
+    // Connect bwa stdout to samtools stdin
+    if let (Some(mut minimap2_stdout), Some(mut samtools_stdin)) =
+        (minimap2_process.stdout.take(), samtools_process.stdin.take())
+    {
+        std::thread::spawn(move || std::io::copy(&mut minimap2_stdout, &mut samtools_stdin));
+    }
+
+    // Capture stderr from bwa
+    let mut minimap2_stderr = String::new();
+    minimap2_process
+        .stderr
+        .take()
+        .unwrap()
+        .read_to_string(&mut minimap2_stderr)?;
+
+    // Wait for bwa to finish
+    let minimap2_status = minimap2_process.wait().context("Failed to wait for minimap2")?;
+    if !minimap2_status.success() {
+        anyhow::bail!("minimap2 failed: {}", minimap2_stderr);
+    }
+
+    // Capture stderr from samtools
+    let mut samtools_stderr = String::new();
+    samtools_process
+        .stderr
+        .take()
+        .unwrap()
+        .read_to_string(&mut samtools_stderr)?;
+
+    // Wait for samtools to finish
+    let samtools_status = samtools_process
+        .wait()
+        .context("Failed to wait for samtools")?;
+    if !samtools_status.success() {
+        anyhow::bail!("samtools sort failed: {}", samtools_stderr);
+    }
+
+    // fs::remove_file(format!("{reference}.amb"))?;
+    // fs::remove_file(format!("{reference}.ann"))?;
+    // fs::remove_file(format!("{reference}.bwt"))?;
+    // fs::remove_file(format!("{reference}.pac"))?;
+    // fs::remove_file(format!("{reference}.sa"))?;
+
+    // Log the captured stderr
+    // println!("bwa mem stderr: {}", bwa_stderr);
+    // println!("samtools sort stderr: {}", samtools_stderr);
+
+    Ok(())
+}
+
 pub fn run_modkit(bam_path: &str, contig_fa: &str, pileup_path: &str) -> anyhow::Result<()> {
     info!("Running Modkit pileup for {bam_path}");
     let mut cmd = Command::new("modkit")