rsomics-common

rsomics-common is the narrow Layer-A contract shared by current rsomics products:

• consistent machine-output and worker-count CLI controls;
• typed error categories and contextual propagation;
• stable process exit codes;
• versioned JSON success and error envelopes;
• static product identity;
• output/input alias rejection across equivalent paths and links;
• transactional single-file and paired-file output;
• runners that map ordinary results and structured validation reports to plain or JSON output.

The public CLI surface contains OutputArgs for --json and ThreadArgs for --threads. OutputArgs is exercised by rsomics-seq, rsomics-fastq-preprocess, and rsomics-bed. ThreadArgs has concrete consumers in rsomics-fastq-preprocess and rsomics-fastq-qc; it standardizes selection while each product continues to own its parallel runtime and work partitioning. write_atomic is the named-file commit contract exercised by rsomics-bed and rsomics-vcf; it preserves existing permissions and never replaces the destination when the producing operation fails. write_output adds the shared product boundary: an omitted path or - streams to standard output, while a named path uses that transactional commit contract. rsomics-bed and rsomics-call are its concrete consumers. write_atomic_pair stages two named outputs and restores the first if the second cannot commit. rsomics-liftover and rsomics-count provide the two consumer contracts; format-specific naming and serialization remain in those products. reject_output_alias is the fail-loud preflight shared by rsomics-seq and rsomics-bed; it recognizes exact and normalized paths, hard links, and symbolic links without hiding filesystem errors. run_validation preserves a failed validator's report in the JSON error envelope while returning the shared invalid-input exit code. Its concrete consumers are rsomics-vcf validate and the planned rsomics-bam validate contract.

Thread pools, work scheduling, RNG policy, logging verbosity, format I/O, and fixture discovery are deliberately not part of this crate.

use clap::Parser;
use rsomics_common::{OutputArgs, Result, ThreadArgs, ToolMeta, run};

#[derive(Parser)]
struct Cli {
    #[command(flatten)]
    output: OutputArgs,
    #[command(flatten)]
    threads: ThreadArgs,
}

fn execute() -> Result<()> {
    Ok(())
}

fn main() -> std::process::ExitCode {
    let cli = rsomics_help::parse::<Cli>();
    run(
        &cli.output,
        ToolMeta {
            name: env!("CARGO_PKG_NAME"),
            version: env!("CARGO_PKG_VERSION"),
        },
        execute,
    )
}

License: MIT OR Apache-2.0.