Update readme.md

Author: Paururo

readme.md

@@ -61,14 +61,15 @@ cargo build --release
 # 1. Train a Random Forest model
 pathotypr train --input training_genomes.fasta --output my_species.model.gz
 
-# 2. Predict the class of a new genome
-pathotypr predict --input new_genome.fasta --model my_species.model.gz --output prediction.tsv
+# 2. Predict the class of a new genome (with debug logging)
+pathotypr predict --input new_genome.fasta --model my_species.model.gz --output prediction.tsv -v
 
 # 3. Genotype variants in an assembled genome
-pathotypr classify --markers variants.tsv --reference ref.fasta --genome-fasta my_genome.fasta --output classified_variants.tsv
+pathotypr classify --markers variants.tsv --reference ref.fasta --input my_genome.fasta --output-prefix classified_variants
 
 # 4. Genotype variants directly from raw reads
 pathotypr split-fastq --markers variants.tsv --reference ref.fasta -i sample_R1.fq.gz -i sample_R2.fq.gz --paired --output-prefix sample_genotyping
+
 ```
 
 ## Documentation
@@ -85,6 +86,7 @@ Builds and trains a Random Forest model from a multifasta file where headers are
 | --kmer-size | -k | The size of the k-mers to generate from sequences. | 6 |
 | --test-split | -s | Proportion of the data to use for the test set. | 0.2 (20%) |
 | --threads | -t | Number of CPU threads to use. | All available |
+| --verbose | -v | Set the verbosity level. Use -v for debug, -vv for trace. | Off |
 
 _The tool will warn you if it detects a strong class imbalance in your training data._
 
@@ -106,6 +108,7 @@ Classifies new genomes using a model file generated by `train`.
 | --model | -m | Path to the unified model file created by the train command. | Required |
 | --output | -o | Path for the output file where predictions will be written in TSV format. | Required |
 | --threads | -t | Number of CPU threads to use. | All available |
+| --verbose | -v | Set the verbosity level. Use -v for debug, -vv for trace. | Off |
 
 **Usage**:
 ```bash
@@ -155,6 +158,7 @@ Both commands use the same flexible TSV format for defining variants:
 | --gff | | Optional GFF file for annotation when using --input. | Optional |
 | --kmer-size | -k | The size of the diagnostic k-mers to use. | 21 |
 | --threads | -t | Number of CPU threads to use. | All available |
+| --verbose | -v | Set the verbosity level. Use -v for debug, -vv for trace. | Off |
 
 **Usage**:
 ```bash
@@ -207,6 +211,7 @@ Perform ultra-fast, alignment-free genotyping of SNPs, MNVs, and both small and
 | --min-depth | | Minimum read depth required to call a variant. | 10 |
 | --min-alt-percent| | Minimum frequency of the alternate allele to call a variant (%). | 95 |
 | --threads | -t | Number of CPU threads to use. | All available |
+| --verbose | -v | Set the verbosity level. Use -v for debug, -vv for trace. | Off |
 
 **Usage**:
 ```bash
@@ -223,11 +228,13 @@ pathotypr split-fastq \
 ```
 pathotypr/
 ├── src/
-│   ├── main.rs                 # CLI handling
-│   ├── train.rs                # Model training logic
-│   ├── predict.rs              # Model prediction logic
-│   ├── classify.rs             # Variant detection in assemblies
-│   ├── classify_split_fastq.rs # Variant detection in reads
+│   ├── main.rs                 # CLI handling and dispatch
+│   ├── errors.rs               # Custom error types
+│   ├── common.rs               # Shared code (model bundle, kmerize)
+│   ├── train.rs                # `train` subcommand logic
+│   ├── predict.rs              # `predict` subcommand logic
+│   ├── classify.rs             # `classify` subcommand logic
+│   ├── classify_split_fastq.rs # `split-fastq` subcommand logic
 │   └── split_kmer.rs           # Core dynamic k-mer engine
 └── Cargo.toml