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@@ -648,8 +648,22 @@ impl NeoContig {
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}
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res
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}
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+
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pub fn get_fasta(&self) -> String {
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- String::new()
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+ let res = String::new();
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+ let fa_lines = self.contig.chars()
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+ .collect::<Vec<char>>()
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+ .chunks(60)
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+ .map(|c| c.iter().collect::<String>())
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+ .collect::<Vec<String>>()
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+ .join("\n");
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+
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+ let mut name = String::new();
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+ for s in self.alignments {
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+ // contig:[pos-pos]
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+ name = format!("{}{}:{}-{}_", name, s.ref_name, s.ref_range.0, s.ref_range.0 - 1);
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+ }
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+ format!(">{}\n{}", name, fa_lines)
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}
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}
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pub struct Fasta {
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