Enum fibertools_rs::cli::Commands

pub enum Commands {
    PredictM6A(PredictM6AOptions),
    AddNucleosomes(AddNucleosomeOptions),
    Fire(FireOptions),
    Extract(ExtractOptions),
    Center(CenterOptions),
    Footprint(FootprintOptions),
    TrackDecorators(DecoratorOptions),
    ClearKinetics(ClearKineticsOptions),
    StripBasemods(StripBasemodsOptions),
    Completions(CompletionOptions),
    Man {},
}

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

Variants

PredictM6A(PredictM6AOptions)

Predict m6A positions using HiFi kinetics data and encode the results in the MM and ML bam tags. Also adds nucleosome (nl, ns) and MTase sensitive patches (al, as).

AddNucleosomes(AddNucleosomeOptions)

Add nucleosomes to a bam file with m6a predictions

Fire(FireOptions)

Add FIREs (Fiber-seq Inferred Regulatory Elements) to a bam file with m6a predictions

Extract(ExtractOptions)

Extract fiberseq data into plain text files.

See https://fiberseq.github.io/fibertools-rs/docs/extract.html for a description of the outputs.

Center(CenterOptions)

This command centers fiberseq data around given reference positions. This is useful for making aggregate m6A and CpG observations, as well as visualization of SVs.

See https://fiberseq.github.io/fibertools-rs/docs/center.html for a description of the output.

Footprint(FootprintOptions)

Infer footprints from fiberseq data

TrackDecorators(DecoratorOptions)

Make decorated bed files for fiberseq data

ClearKinetics(ClearKineticsOptions)

Remove HiFi kinetics tags from the input bam file

StripBasemods(StripBasemodsOptions)

Strip out select base modifications

Completions(CompletionOptions)

Make command line completions

Man

Make a man page for fibertools-rs

Writes file for man to stdout.

Trait Implementations

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) -> Command

Append to Command so it can instantiate Self.

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

Append to Command so it can update self.

fn has_subcommand(__clap_name: &str) -> bool

Test whether Self can parse a specific subcommand