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@@ -16,6 +16,11 @@ use crate::{
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}; // ton module existant
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const CONTIG_SEPARATOR: u8 = 0;
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+const BASE_A: u8 = 1;
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+const BASE_C: u8 = 2;
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+const BASE_G: u8 = 3;
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+const BASE_T: u8 = 4;
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+const BASE_N: u8 = 5;
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#[derive(Debug, Clone, PartialEq, Eq)]
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pub struct GenomicPos {
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@@ -114,6 +119,17 @@ impl GenomeIndex {
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"contig {} contains reserved separator byte",
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entry.name
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);
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+ let seq: Vec<u8> = seq
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+ .into_iter()
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+ .map(|base| match base {
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+ b'A' => BASE_A,
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+ b'C' => BASE_C,
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+ b'G' => BASE_G,
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+ b'T' => BASE_T,
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+ b'N' => BASE_N,
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+ _ => BASE_N,
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+ })
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+ .collect();
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anyhow::ensure!(
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genome.len() + seq.len() <= u32::MAX as usize,
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"concatenated genome exceeds u32::MAX bases"
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