Struct Mutate 

pub struct Mutate {
    pub reference: ReferenceOptions,
    pub bed: BedOptions,
    pub seed: SeedOptions,
    pub output: PathBuf,
    pub snp_rate: f64,
    pub indel_rate: f64,
    pub mnp_rate: f64,
    pub indel_length_param: f64,
    pub het_hom_ratio: f64,
    pub ploidy: u8,
    pub ploidy_override: Vec<String>,
}

Generate a VCF of random mutations from a reference genome.

Produces a standard VCF with proper GT fields that can be fed directly to holodeck simulate. Supports independent control of SNP, indel, and MNP rates, with configurable ploidy including per-contig and per-region overrides for handling sex chromosomes and pseudo-autosomal regions.

Fields

reference: ReferenceOptions

bed: BedOptions

seed: SeedOptions

output: PathBuf

Output VCF file path.

snp_rate: f64

Rate of SNP mutations per base.

indel_rate: f64

Rate of indel mutations per base.

mnp_rate: f64

Rate of MNP (multi-nucleotide polymorphism) mutations per base.

indel_length_param: f64

Parameter for the geometric distribution of indel lengths. Larger values produce shorter indels on average.

het_hom_ratio: f64

Ratio of heterozygous to homozygous variants. A value of 2.0 means twice as many het as hom variants.

ploidy: u8

Default ploidy for all contigs.

ploidy_override: Vec<String>

Per-contig or per-region ploidy override. Format: CONTIG=PLOIDY or CONTIG:START-END=PLOIDY (1-based coordinates). Later values override earlier ones for the same positions (last-writer-wins).

Example: --ploidy-override chrX=1 --ploidy-override chrX:10001-2781479=2

Trait Implementations

impl Args for Mutate

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 Command for Mutate

fn execute(&self) -> Result<()>

Execute the command.

impl CommandFactory for Mutate

fn command<'b>() -> Command

Build a Command that can instantiate Self.

fn command_for_update<'b>() -> Command

Build a Command that can update self.

impl Debug for Mutate

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

Formats the value using the given formatter.

impl FromArgMatches for Mutate

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 Parser for Mutate

fn parse() -> Self

Parse from std::env::args_os(), exit on error.

fn try_parse() -> Result<Self, Error>

Parse from std::env::args_os(), return Err on error.

fn parse_from<I, T>(itr: I) -> Self

where I: IntoIterator<Item = T>, T: Into<OsString> + Clone,

Parse from iterator, exit on error.

fn try_parse_from<I, T>(itr: I) -> Result<Self, Error>

where I: IntoIterator<Item = T>, T: Into<OsString> + Clone,

Parse from iterator, return Err on error.

fn update_from<I, T>(&mut self, itr: I)

where I: IntoIterator<Item = T>, T: Into<OsString> + Clone,

Update from iterator, exit on error.

fn try_update_from<I, T>(&mut self, itr: I) -> Result<(), Error>

where I: IntoIterator<Item = T>, T: Into<OsString> + Clone,

Update from iterator, return Err on error.