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