changes

src/lib.rs

@@ -541,10 +541,9 @@ pub fn create_bam(ref_path: &str, reads_path: &str, bam_path: &str) -> Result<()
         .arg(ref_path)
         .arg(reads_path)
         .stdout(Stdio::piped())
-        // .stdout(Stdio::from(output_file))
+        .stderr(Stdio::piped())
         .spawn()
         .expect("Minimap2 failed to start");
-    // mm2.wait().unwrap();
 
     let view = Command::new("sambamba")
         .arg("view")
@@ -556,6 +555,7 @@ pub fn create_bam(ref_path: &str, reads_path: &str, bam_path: &str) -> Result<()
         .arg("/dev/stdin")
         .stdin(Stdio::from(mm2.stdout.unwrap()))
         .stdout(Stdio::piped())
+        .stderr(Stdio::piped())
         .spawn()
         .expect("Sambamba view failed to start");
 
@@ -566,6 +566,7 @@ pub fn create_bam(ref_path: &str, reads_path: &str, bam_path: &str) -> Result<()
         .arg("/dev/stdin")
         .arg("-o")
         .arg(bam_path)
+        .stderr(Stdio::piped())
         .stdin(Stdio::from(view.stdout.unwrap()))
         .spawn()
         .expect("Sambamba sort failed to start");