diff --git a/kr2r/src/args.rs b/kr2r/src/args.rs index e47b195..b694d1e 100644 --- a/kr2r/src/args.rs +++ b/kr2r/src/args.rs @@ -125,6 +125,14 @@ pub struct ClassifyArgs { #[clap(long = "output-dir", value_parser)] pub kraken_output_dir: Option, + /// In comb. w/ -R, provide minimizer information in report + #[clap(short = 'K', long, value_parser, default_value_t = false)] + pub report_kmer_data: bool, + + /// In comb. w/ -R, report taxa w/ 0 count + #[clap(short = 'z', long, value_parser, default_value_t = false)] + pub report_zero_counts: bool, + /// A list of input file paths (FASTA/FASTQ) to be processed by the classify program. // #[clap(short = 'F', long = "files")] pub input_files: Vec, diff --git a/kr2r/src/bin/resolve.rs b/kr2r/src/bin/resolve.rs index 4cfd990..cd7c941 100644 --- a/kr2r/src/bin/resolve.rs +++ b/kr2r/src/bin/resolve.rs @@ -100,6 +100,14 @@ pub struct Args { )] pub confidence_threshold: f64, + /// In comb. w/ -R, provide minimizer information in report + #[clap(short = 'K', long, value_parser, default_value_t = false)] + pub report_kmer_data: bool, + + /// In comb. w/ -R, report taxa w/ 0 count + #[clap(short = 'z', long, value_parser, default_value_t = false)] + pub report_zero_counts: bool, + /// The minimum number of hit groups needed for a call. #[clap( short = 'g', @@ -243,8 +251,8 @@ pub fn run(args: Args) -> Result<()> { let filename = output.join("output.krepot2"); report_kraken_style( filename, - false, - false, + args.report_zero_counts, + args.report_kmer_data, &taxo, &total_taxon_counts, total_seqs as u64, diff --git a/kr2r/src/bin/squid.rs b/kr2r/src/bin/squid.rs index 3eefeec..169df30 100644 --- a/kr2r/src/bin/squid.rs +++ b/kr2r/src/bin/squid.rs @@ -95,6 +95,8 @@ impl From for resolve::Args { confidence_threshold: item.confidence_threshold, minimum_hit_groups: item.minimum_hit_groups, kraken_output_dir: item.kraken_output_dir, + report_kmer_data: item.report_kmer_data, + report_zero_counts: item.report_zero_counts, } } }