Struct bigtools::utils::cli::bedgraphtobigwig::BedGraphToBigWigArgs

pub struct BedGraphToBigWigArgs {
    pub bedgraph: String,
    pub chromsizes: String,
    pub output: String,
    pub parallel: String,
    pub single_pass: bool,
    pub write_args: BBIWriteArgs,
}

Fields

bedgraph: String

The bedgraph to convert to a bigwig. Can use - or stdin to read from stdin.

chromsizes: String

A chromosome sizes file. Each line should be have a chromosome and its size in bases, separated by whitespace.

output: String

The output bigwig path

parallel: String

Set whether to read and convert the bedGraph in parallel. Requires that the bedGraph is sorted. Can take auto (default), yes, no. Ignored when input is stdin or when nthreads is 1.

single_pass: bool

If set, indicates that only a single pass should be done on the input file. This is most useful on large files in order to reduce total time. This automatically happens when the input is stdin.

write_args: BBIWriteArgs

Trait Implementations

impl Args for BedGraphToBigWigArgs

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 BedGraphToBigWigArgs

fn clone(&self) -> BedGraphToBigWigArgs

Returns a copy of the value.

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

Performs copy-assignment from source.

impl CommandFactory for BedGraphToBigWigArgs

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 BedGraphToBigWigArgs

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

Formats the value using the given formatter.

impl FromArgMatches for BedGraphToBigWigArgs

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 BedGraphToBigWigArgs

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 BedGraphToBigWigArgs

fn eq(&self, other: &BedGraphToBigWigArgs) -> 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 BedGraphToBigWigArgs