Enum BiasCommands 

pub enum BiasCommands {
    Create {
        positive: Vec<PathBuf>,
        negative: Vec<PathBuf>,
        output: PathBuf,
        kmer_size: u8,
        fscale: u64,
        cms_width: usize,
        cms_depth: usize,
        alpha: f32,
        fold_enrichment: Option<f32>,
        threads: Option<usize>,
    },
    Stats {
        input: PathBuf,
        output: Option<PathBuf>,
    },
}

Variants

Create

Create a bias table from positive (target) and negative (background) FASTA files. Target signal is always subtracted from background before computing bias weights.

Fields

positive: Vec<PathBuf>

Positive (target) FASTA file(s) - sequences to enrich for

negative: Vec<PathBuf>

Negative (background) FASTA file(s) - sequences to deplete. Target signal is subtracted from background automatically.

output: PathBuf

Output bias table file (.bias)

kmer_size: u8

K-mer size (must match sketch k-mer size)

fscale: u64

FracMinHash scale (must match sketch fscale)

cms_width: usize

Count-Min Sketch width (columns, power of 2 recommended)

cms_depth: usize

Count-Min Sketch depth (number of hash functions)

alpha: f32

Smoothing parameter for log-ratio computation

fold_enrichment: Option<f32>

Target fold enrichment. If not set, maximizes automatically. A warning is shown if the requested value exceeds the maximum achievable by the data.

threads: Option<usize>

Number of threads to use for bias sketching

Stats

Display statistics for a bias table (.bias file)

Fields

input: PathBuf

Input bias table file (.bias)

output: Option<PathBuf>

Output JSON report to file instead of stderr

Trait Implementations

impl Clone for BiasCommands

fn clone(&self) -> BiasCommands

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for BiasCommands

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl FromArgMatches for BiasCommands

fn from_arg_matches(__clap_arg_matches: &ArgMatches) -> Result<Self, Error>

Instantiate Self from ArgMatches, parsing the arguments as needed.

fn from_arg_matches_mut( __clap_arg_matches: &mut ArgMatches, ) -> Result<Self, Error>

Instantiate Self from ArgMatches, parsing the arguments as needed.

fn update_from_arg_matches( &mut self, __clap_arg_matches: &ArgMatches, ) -> Result<(), Error>

Assign values from ArgMatches to self.

fn update_from_arg_matches_mut<'b>( &mut self, __clap_arg_matches: &mut ArgMatches, ) -> Result<(), Error>

Assign values from ArgMatches to self.

impl Subcommand for BiasCommands

fn augment_subcommands<'b>(__clap_app: Command) -> Command

Append to Command so it can instantiate Self via FromArgMatches::from_arg_matches_mut

fn augment_subcommands_for_update<'b>(__clap_app: Command) -> Command

Append to Command so it can instantiate self via FromArgMatches::update_from_arg_matches_mut

fn has_subcommand(__clap_name: &str) -> bool

Test whether Self can parse a specific subcommand