Enum fibertools_rs::cli::Commands

pub enum Commands {
    Extract {
        bam: String,
        reference: bool,
        m6a: Option<String>,
        cpg: Option<String>,
        msp: Option<String>,
        nuc: Option<String>,
    },
}

This structure contains all the subcommands for fiberseq-rs and their help descriptions.

Variants

Extract

Fields

bam: String

fiberseq bam file

reference: bool

report in reference sequence coordinates.

m6a: Option<String>

Output path for m6a bed12.

cpg: Option<String>

Output path for CpG (primrose) bed12.

msp: Option<String>

Output path for methylation sensitive patch (msp) bed12.

nuc: Option<String>

Output path for nucleosome bed12.

Extract fiberseq data into plain text files.

Trait Implementations

impl Debug for Commands

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

Formats the value using the given formatter.

impl FromArgMatches for Commands

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<'b>(
    &mut self,
    __clap_arg_matches: &mut ArgMatches
) -> Result<(), Error>

Assign values from ArgMatches to self.

impl Subcommand for Commands

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

Append to Command so it can instantiate Self.

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

Append to Command so it can update self.

fn has_subcommand(__clap_name: &str) -> bool

Test whether Self can parse a specific subcommand