优化代码结构

README.md

@@ -519,7 +519,7 @@ classify [OPTIONS] --index-filename <INDEX_FILENAME> --taxonomy-filename <TAXONO
 * -t, --taxonomy-filename <TAXONOMY_FILENAME>: Path to the Kraken 2 taxonomy file. This file contains taxonomic information used for classification.
 * -o, --options-filename <OPTIONS_FILENAME>: Path to the Kraken 2 options file. This file includes additional configuration options for Kraken 2.
 * -T, --confidence-threshold <CONFIDENCE_THRESHOLD>: Sets the confidence score threshold for classification. Sequences with a confidence score below this threshold will not be * classified. The default value is 0.0.
-* -p, --num-threads <NUM_THREADS>: Specifies the number of threads to use for processing. Increasing the number of threads can speed up the classification process. The default is 1.
+* -p, --num-threads <NUM_THREADS>: Specifies the number of threads to use for processing. Increasing the number of threads can speed up the classification process. The default is 10.
 * -g, --minimum-hit-groups <MINIMUM_HIT_GROUPS>: The minimum number of hit groups required for a classification call. The default is 2.
 * -P, --paired-end-processing: Enables processing of paired-end reads. This option should be used if your input files contain paired-end sequence data.
 * -S, --single-file-pairs: Indicates that pairs with mates are located in the same file. This option is relevant for paired-end processing.

kr2r/src/args.rs

@@ -91,7 +91,7 @@ pub struct ClassifyArgs {
     )]
     pub minimum_quality_score: i32,
 
-    /// The number of threads to use, default is 1.
+    /// The number of threads to use, default is 10.
     #[clap(short = 'p', long = "num-threads", value_parser, default_value_t = 10)]
     pub num_threads: i32,
 

kr2r/src/bin/classify.rs

@@ -49,8 +49,8 @@ struct Args {
     // /// Enable quick mode for faster processing.
     // #[clap(short = 'q', long = "quick-mode", action)]
     // quick_mode: bool,
-    /// The number of threads to use, default is 1.
-    #[clap(short = 'p', long = "num-threads", value_parser, default_value_t = 1)]
+    /// The number of threads to use, default is 10.
+    #[clap(short = 'p', long = "num-threads", value_parser, default_value_t = 10)]
     num_threads: i32,
 
     /// The minimum number of hit groups needed for a call.

kr2r/src/bin/splitr.rs

@@ -52,7 +52,7 @@ pub struct Args {
     )]
     pub minimum_quality_score: i32,
 
-    /// The number of threads to use, default is 1.
+    /// The number of threads to use, default is 10.
     #[clap(short = 'p', long = "num-threads", value_parser, default_value_t = 10)]
     pub num_threads: i32,