Struct SketchParams

pub struct SketchParams {
    pub alg: SketchAlg,
    pub rc: bool,
    pub k: usize,
    pub s: usize,
    pub b: usize,
    pub filter_empty: bool,
}

Fields

alg: SketchAlg

Sketch algorithm to use. Defaults to bucket because of its much faster comparisons.

rc: bool

When set, use forward instead of canonical k-mer hashes.

k: usize

k-mer size.

s: usize

Bottom-s sketch, or number of buckets.

b: usize

For bucket-sketch, store only the lower b bits.

filter_empty: bool

For bucket-sketch, store a bitmask of empty buckets, to increase accuracy on small genomes.

Implementations

impl SketchParams

pub fn build(&self) -> Sketcher

pub fn default(k: usize) -> Self

Default sketcher that very fast at comparisons, but 20% slower at sketching. Use for >= 50000 seqs, and safe default when input sequences are > 500’000 characters.

When sequences are < 100’000 characters, inaccuracies may occur due to empty buckets.

pub fn default_fast_sketching(k: usize) -> Self

Default sketcher that is fast at sketching, but somewhat slower at comparisons. Use for <= 5000 seqs, or when input sequences are < 100’000 characters.

Trait Implementations

impl Args for SketchParams

fn group_id() -> Option<Id>

Report the ArgGroup::id for this set of arguments

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

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

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

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

impl Clone for SketchParams

fn clone(&self) -> SketchParams

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for SketchParams

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

Formats the value using the given formatter.

impl FromArgMatches for SketchParams

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

Assign values from ArgMatches to self.

impl Copy for SketchParams