ok positions

src/lib.rs

@@ -421,8 +421,6 @@ impl NeoContig {
         "POS", "MAPQ", "CIGAR", "RNEXT", "PNEXT", "TLEN", "SEQ", 
         "QUAL", "ALN"];
 
-        println!("BWA exec");
-        println!("  {}", format!("\">sequence_{}\n{}\"", self.name.to_string(), self.contig));
         let stdout = cmd!("echo", "-e", format!("\">sequence_{}\n{}\"", self.name.to_string(), self.contig))
         .pipe(cmd!("bwa", "mem", fasta_ref_path, "-"))
         .stdout_capture()
@@ -460,8 +458,6 @@ impl NeoContig {
                 }
             }
         });
-        println!("n bwa {:?}", alignments.len());
-        println!("Alignments {:?}", alignments);
         self.alignments = alignments;
     }
 
@@ -585,8 +581,6 @@ impl Fasta {
         Fasta { fa: IndexedFasta::from_file(path).expect("Error opening fa") }
     }
     fn get_sequence (&self, contig: &str, start: usize, end: usize) -> String { // end is included
-        // let start = start - 1;
-        
         let chr_index = self.fa.fai().tid(contig).expect("Cannot find chr in index");
         if (end as i64 - start as i64) < (0 as i64) {
             let fv = self.fa.view(chr_index, end, start + 1).expect("Cannot get .fa view");