changes

src/lib.rs

@@ -459,8 +459,12 @@ pub fn write_fasta(fasta_path: &str, d: &Vec<(String, String)>) {
     }
 }
 
+// pub fn write_aln_sh()
+
 pub fn create_bam(ref_path: &str, reads_path: &str, bam_path: &str) -> Result<()> {
     let rg_id = uuid::Uuid::new_v4();
+    let output_file = File::create("test.sam").unwrap();
+
     let mut mm2 = Command::new("minimap2")
         .arg("-t")
         .arg("128")
@@ -472,12 +476,10 @@ pub fn create_bam(ref_path: &str, reads_path: &str, bam_path: &str) -> Result<()
         ))
         .arg(ref_path)
         .arg(reads_path)
-        .arg(" | sambamba view -h -S --format=bam /dev/stdin | sambamba sort /dev/stdin -o")
-        .arg(bam_path)
-        // .stdout(Stdio::piped())
+        .stdout(Stdio::from(output_file))
         .spawn()
         .expect("Minimap2 failed to start");
-    mm2.wait();
+    mm2.wait().unwrap();
 
     // let view = Command::new("sambamba")
     //     .arg("view")
@@ -502,7 +504,7 @@ pub fn create_bam(ref_path: &str, reads_path: &str, bam_path: &str) -> Result<()
     //     .stdin(Stdio::from(view.stdout.unwrap()))
     //     .spawn()
     //     .expect("Sambamba sort failed to start");
-
+    //
     // sort.wait().unwrap();
     Ok(())
 }