no chrM

src/assembler/mod.rs

@@ -149,6 +149,7 @@ pub fn assemble_whole(
         .filter(|path| {
             path.file_name()
                 .and_then(|name| name.to_str())
+                .filter(|name| !name.contains("chrM"))
                 .map(|name| name.matches('_').count() == 1)
                 .unwrap_or(false)
         })

src/io/bam.rs

@@ -181,34 +181,8 @@ 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 minimap2_command = Command::new("minimap2");