Struct bigtools::utils::cli::bigwigaverageoverbed::BigWigAverageOverBedArgs

pub struct BigWigAverageOverBedArgs {
    pub bigwig: String,
    pub bedin: String,
    pub output: String,
    pub namecol: Option<String>,
    pub chrom: Option<String>,
    pub start: Option<u32>,
    pub end: Option<u32>,
    pub nthreads: usize,
}

Fields

bigwig: String

The input bigwig file

bedin: String

The input bed file

output: String

The output bed file

namecol: Option<String>

Supports three types of options: interval, none, or a column number (one indexed). If interval, the name column in the output will be the interval in the form of chrom:start-end. If none, then all columns will be included in the output file. Otherwise, the one-indexed column will be used as the name. By default, column 4 is used as a name column.

chrom: Option<String>

If set, restrict output to given chromosome

start: Option<u32>

If set, restrict output to regions greater than or equal to it

end: Option<u32>

If set, restrict output to regions less than it

nthreads: usize

Set the number of threads to use. This tool will nearly always benefit from more cores. Note: for parts of the runtime, the actual usage may be nthreads+1

Trait Implementations

impl Args for BigWigAverageOverBedArgs

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.

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

Append to Command so it can update self.

impl Clone for BigWigAverageOverBedArgs

fn clone(&self) -> BigWigAverageOverBedArgs

Returns a copy of the value.

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

Performs copy-assignment from source.

impl CommandFactory for BigWigAverageOverBedArgs

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 BigWigAverageOverBedArgs

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

Formats the value using the given formatter.

impl FromArgMatches for BigWigAverageOverBedArgs

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 BigWigAverageOverBedArgs

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.

impl PartialEq for BigWigAverageOverBedArgs

fn eq(&self, other: &BigWigAverageOverBedArgs) -> bool

This method tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

This method tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl StructuralPartialEq for BigWigAverageOverBedArgs