Expand description
Command-line interface for ref-solver.
This module implements the CLI using clap. Available commands:
- identify: Identify the reference genome from a BAM/SAM/CRAM file
- compare: Compare two headers or a header against a known reference
- catalog: List, show, or export references from the catalog
- serve: Start the interactive web interface
§Usage
# Identify reference from a BAM file
ref-solver identify sample.bam
# Pipe from samtools
samtools view -H sample.bam | ref-solver identify -
# JSON output for scripting
ref-solver identify sample.bam --format json
# Compare against a known reference
ref-solver compare sample.bam hg38_ucsc --reference
# Start web UI
ref-solver serve --port 8080 --open