优化代码结构

kr2r/src/args.rs

@@ -125,6 +125,14 @@ pub struct ClassifyArgs {
     #[clap(long = "output-dir", value_parser)]
     pub kraken_output_dir: Option<PathBuf>,
 
+    /// 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<String>,

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,

kr2r/src/bin/squid.rs

@@ -95,6 +95,8 @@ impl From<ClassifyArgs> 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,
         }
     }
 }