Enum jam_rs::cli::Commands

pub enum Commands {
    Sketch {
        input: Vec<PathBuf>,
        output: Option<PathBuf>,
        kmer_size: u8,
        fscale: Option<u64>,
        kscale: Option<u64>,
        nmin: Option<u64>,
        nmax: Option<u64>,
        format: OutputFormats,
        algorithm: HashAlgorithms,
        singleton: bool,
    },
    Merge {
        inputs: Vec<PathBuf>,
        output: PathBuf,
    },
    Dist {
        input: PathBuf,
        database: Vec<PathBuf>,
        output: Option<PathBuf>,
        cutoff: f64,
        stats: bool,
        gc_lower: Option<u8>,
        gc_upper: Option<u8>,
    },
}

Variants

Sketch

Fields

input: Vec<PathBuf>

Input file(s), one directory or one file with list of files to be hashed

output: Option<PathBuf>

Output file

kmer_size: u8

kmer size, all sketches must have the same size to be compared

fscale: Option<u64>

Scale the hash space to a minimum fraction of the maximum hash value (FracMinHash)

kscale: Option<u64>

Scale the hash space to a minimum fraction of all k-mers (SizeMinHash)

nmin: Option<u64>

Minimum number of k-mers (per record) to be hashed, bottom cut-off

nmax: Option<u64>

Maximum number of k-mers (per record) to be hashed, top cut-off

format: OutputFormats

Change to other output formats

algorithm: HashAlgorithms

Change the hashing algorithm

singleton: bool

Create a separate sketch for each sequence record

Sketch one or more files and write the result to an output file (or stdout)

Merge

Fields

inputs: Vec<PathBuf>

One or more input sketches

output: PathBuf

Output file

Merge multiple input sketches into a single sketch

Dist

Fields

input: PathBuf

Input sketch or raw file

database: Vec<PathBuf>

Database sketch(es)

output: Option<PathBuf>

Output to file instead of stdout

cutoff: f64

Cut-off value for similarity

stats: bool

Use the Stats params for restricting results

gc_lower: Option<u8>

Use GC stats with an upper bound of x% (gc_lower and gc_upper must be set)

gc_upper: Option<u8>

Use GC stats with an lower bound of y% (gc_lower and gc_upper must be set)

Estimate containment of a (small) sketch against a subset of one or more sketches as database. Requires all sketches to have the same kmer size

Trait Implementations

impl Clone for Commands

fn clone(&self) -> Commands

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for Commands

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

Formats the value using the given formatter.

impl FromArgMatches for Commands

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 Commands

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

Append to [Command] so it can instantiate Self.

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

Append to [Command] so it can update self.

fn has_subcommand(__clap_name: &str) -> bool

Test whether Self can parse a specific subcommand