Enum varlociraptor::cli::PreprocessKind

pub enum PreprocessKind {
    Variants {
        reference: PathBuf,
        candidates: Option<PathBuf>,
        bam: PathBuf,
        alignment_properties: Option<PathBuf>,
        output: Option<PathBuf>,
        spurious_ins_rate: f64,
        spurious_del_rate: f64,
        spurious_insext_rate: f64,
        spurious_delext_rate: f64,
        protocol_strandedness: ProtocolStrandedness,
        omit_snvs: bool,
        omit_indels: bool,
        max_indel_len: u32,
        indel_window: u32,
        max_depth: usize,
    },
}

Variants

Variants

Fields of Variants

reference: PathBufcandidates: Option<PathBuf>bam: PathBufalignment_properties: Option<PathBuf>output: Option<PathBuf>spurious_ins_rate: f64spurious_del_rate: f64spurious_insext_rate: f64spurious_delext_rate: f64protocol_strandedness: ProtocolStrandednessomit_snvs: boolomit_indels: boolmax_indel_len: u32indel_window: u32max_depth: usize

Trait Implementations

impl Clone for PreprocessKind

fn clone(&self) -> PreprocessKind

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for PreprocessKind

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

Formats the value using the given formatter.

impl<'de> Deserialize<'de> for PreprocessKind

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

Deserialize this value from the given Serde deserializer.

impl Serialize for PreprocessKind

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 PreprocessKind

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

Returns the corresponding clap::App.

fn from_clap(matches: &ArgMatches) -> Self

Creates the struct from clap::ArgMatches. It cannot fail with a parameter generated by clap by construction.

fn from_args() -> Self

Gets the struct from the command line arguments. Print the error message and quit the program in case of failure.

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

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

impl StructOptInternal for PreprocessKind

fn augment_clap<'a, 'b>(app: App<'a, 'b>) -> App<'a, 'b>

fn from_subcommand<'a, 'b>(
    sub: (&'b str, Option<&'b ArgMatches<'a>>)
) -> Option<Self>

fn is_subcommand() -> bool