m

src/lib.rs

@@ -400,7 +400,7 @@ impl NeoContig {
         "POS", "MAPQ", "CIGAR", "RNEXT", "PNEXT", "TLEN", "SEQ", 
         "QUAL", "ALN"];
 
-        let stdout = cmd!("echo", "-e", format!("\"{}\"", self.contig))
+        let stdout = cmd!("echo", "-e", format!("\">sequence\n{}\"", self.contig))
         .pipe(cmd!("bwa", "mem", fasta_ref_path, "-"))
         .stdout_capture()
         .stderr_capture()
@@ -410,7 +410,7 @@ impl NeoContig {
         stdout.split("\n").for_each(|line|{
             println!("{:?}", line);
             if line.len() > 9 {
-                if &line[0..9] == "sequence_" {
+                if &line[0..9] == "sequence" {
                     
                     let mut qname: Option<String> = None;
                     let mut flag: Option<i32> = None;