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@@ -476,36 +476,37 @@ pub fn create_bam(ref_path: &str, reads_path: &str, bam_path: &str) -> Result<()
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))
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.arg(ref_path)
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.arg(reads_path)
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- .stdout(Stdio::from(output_file))
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+ .stdout(Stdio::piped())
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+ // .stdout(Stdio::from(output_file))
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.spawn()
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.expect("Minimap2 failed to start");
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- mm2.wait().unwrap();
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-
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- // let view = Command::new("sambamba")
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- // .arg("view")
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- // .arg("-h")
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- // .arg("-S")
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- // .arg("-t")
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- // .arg("20")
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- // .arg("--format=bam")
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- // .arg("/dev/stdin")
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- // .stdin(Stdio::from(mm2.stdout.unwrap()))
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- // .stdout(Stdio::piped())
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- // .spawn()
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- // .expect("Sambamba view failed to start");
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- //
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- // let mut sort = Command::new("sambamba")
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- // .arg("sort")
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- // .arg("-t")
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- // .arg("20")
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- // .arg("/dev/stdin")
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- // .arg("-o")
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- // .arg(bam_path)
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- // .stdin(Stdio::from(view.stdout.unwrap()))
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- // .spawn()
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- // .expect("Sambamba sort failed to start");
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- //
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- // sort.wait().unwrap();
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+ // mm2.wait().unwrap();
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+
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+ let view = Command::new("sambamba")
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+ .arg("view")
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+ .arg("-h")
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+ .arg("-S")
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+ .arg("-t")
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+ .arg("20")
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+ .arg("--format=bam")
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+ .arg("/dev/stdin")
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+ .stdin(Stdio::from(mm2.stdout.unwrap()))
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+ .stdout(Stdio::piped())
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+ .spawn()
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+ .expect("Sambamba view failed to start");
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+
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+ let mut sort = Command::new("sambamba")
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+ .arg("sort")
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+ .arg("-t")
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+ .arg("20")
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+ .arg("/dev/stdin")
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+ .arg("-o")
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+ .arg(bam_path)
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+ .stdin(Stdio::from(view.stdout.unwrap()))
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+ .spawn()
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+ .expect("Sambamba sort failed to start");
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+
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+ sort.wait().unwrap();
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Ok(())
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}
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