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Update classify.rs
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src/classify.rs

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//! This module handles the `classify` subcommand.
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//!
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//! It performs lineage typing by identifying known genetic markers within assembled
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//! genome sequences. The process involves:
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//! 1. Reading a list of variants (SNPs, MNVs, Indels) and their corresponding lineages.
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//! 2. Dynamically generating a unique diagnostic k-mer for each variant's alternate allele.
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//! 3. Scanning input genomes (from a list of FASTA files or a single multifasta)
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//! for the presence of these diagnostic marker k-mers in parallel.
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//! 4. Reporting all found markers for each genome and its annotations.
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//! 5. Generating a summary file that lists the most likely lineage(s) for each genome.
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use bio::io::fasta;
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use bio::io::gff::{GffType, Reader};
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use bio_types::strand::Strand as BioStrand; // Renamed to avoid conflict
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Ok(())
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}
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info!("✅ Process completed.");
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Ok(())
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}

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