Enum varlociraptor::cli::EstimateKind

pub enum EstimateKind {
    AlignmentProperties {
        reference: PathBuf,
        bam: PathBuf,
        num_records: Option<usize>,
        epsilon_gap: f64,
    },
    Contamination {
        sample: PathBuf,
        contaminant: PathBuf,
        prior_estimate: Option<f64>,
        prior_considered_cells: Option<u32>,
        output: Option<PathBuf>,
        output_plot: Option<PathBuf>,
    },
    MutationalBurden {
        events: Vec<String>,
        sample: Vec<String>,
        coding_genome_size: f64,
        mode: PlotMode,
        cutoff: f64,
    },
}

Variants

AlignmentProperties

Fields

reference: PathBuf

bam: PathBuf

num_records: Option<usize>

epsilon_gap: f64

Contamination

Fields

sample: PathBuf

contaminant: PathBuf

prior_estimate: Option<f64>

prior_considered_cells: Option<u32>

output: Option<PathBuf>

output_plot: Option<PathBuf>

MutationalBurden

Fields

events: Vec<String>

sample: Vec<String>

coding_genome_size: f64

mode: PlotMode

cutoff: f64

Trait Implementations

impl Clone for EstimateKind

fn clone(&self) -> EstimateKind

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for EstimateKind

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

Formats the value using the given formatter.

impl<'de> Deserialize<'de> for EstimateKind

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error>where
    __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl Serialize for EstimateKind

fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error>where
    __S: Serializer,

Serialize this value into the given Serde serializer.

impl StructOpt for EstimateKind

fn clap<'a, 'b>() -> App<'a, 'b>

Returns clap::App corresponding to the struct.

fn from_clap(matches: &ArgMatches<'_>) -> Self

Builds the struct from clap::ArgMatches. It’s guaranteed to succeed if matches originates from an App generated by StructOpt::clap called on the same type, otherwise it must panic.

fn from_args() -> Selfwhere
    Self: Sized,

Builds the struct from the command line arguments (std::env::args_os). Calls clap::Error::exit on failure, printing the error message and aborting the program.

fn from_args_safe() -> Result<Self, Error>where
    Self: Sized,

Builds the struct from the command line arguments (std::env::args_os). Unlike StructOpt::from_args, returns clap::Error on failure instead of aborting the program, so calling .exit is up to you.

fn from_iter<I>(iter: I) -> Selfwhere
    Self: Sized,
    I: IntoIterator,
    <I as IntoIterator>::Item: Into<OsString> + Clone,

Gets the struct from any iterator such as a Vec of your making. Print the error message and quit the program in case of failure.

fn from_iter_safe<I>(iter: I) -> Result<Self, Error>where
    Self: Sized,
    I: IntoIterator,
    <I as IntoIterator>::Item: Into<OsString> + Clone,

Gets the struct from any iterator such as a Vec of your making.