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Expand file tree Collapse file tree Original file line number Diff line number Diff line change 1- //! This module handles the `classify` subcommand.
2- //!
3- //! It performs lineage typing by identifying known genetic markers within assembled
4- //! genome sequences. The process involves:
5- //! 1. Reading a list of variants (SNPs, MNVs, Indels) and their corresponding lineages.
6- //! 2. Dynamically generating a unique diagnostic k-mer for each variant's alternate allele.
7- //! 3. Scanning input genomes (from a list of FASTA files or a single multifasta)
8- //! for the presence of these diagnostic marker k-mers in parallel.
9- //! 4. Reporting all found markers for each genome and its annotations.
10- //! 5. Generating a summary file that lists the most likely lineage(s) for each genome.
11-
121use bio:: io:: fasta;
132use bio:: io:: gff:: { GffType , Reader } ;
143use bio_types:: strand:: Strand as BioStrand ; // Renamed to avoid conflict
@@ -658,6 +647,3 @@ pub fn run(args: Args) -> Result<(), Box<dyn Error>> {
658647
659648 Ok ( ( ) )
660649}
661- info ! ( "✅ Process completed." ) ;
662- Ok ( ( ) )
663- }
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