Enum Commands 

pub enum Commands {
    PredictM6A(PredictM6AOptions),
    AddNucleosomes(AddNucleosomeOptions),
    Fire(FireOptions),
    Extract(ExtractOptions),
    Center(CenterOptions),
    Footprint(FootprintOptions),
    Qc(QcOpts),
    TrackDecorators(DecoratorOptions),
    Pileup(PileupOptions),
    ClearKinetics(ClearKineticsOptions),
    StripBasemods(StripBasemodsOptions),
    DddaToM6a(DddaToM6aOptions),
    FiberHmm(FiberHmmOptions),
    Validate(ValidateOptions),
    PgInject(PgInjectOptions),
    PgLift(PgLiftOptions),
    PgPansn(PgPansnOptions),
    Completions(CompletionOptions),
    Man {},
}

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/extracting/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/extracting/center.html for a description of the output.

Footprint(FootprintOptions)

Infer footprints from fiberseq data

Qc(QcOpts)

Collect QC metrics from a fiberseq bam file

TrackDecorators(DecoratorOptions)

Make decorated bed files for fiberseq data

Pileup(PileupOptions)

Make a pileup track of Fiber-seq features from a FIRE bam

ClearKinetics(ClearKineticsOptions)

Remove HiFi kinetics tags from the input bam file

StripBasemods(StripBasemodsOptions)

Strip out select base modifications

DddaToM6a(DddaToM6aOptions)

Convert a DddA BAM file to pseudo m6A BAM file

FiberHmm(FiberHmmOptions)

Apply FiberHMM to a bam file

Validate(ValidateOptions)

Validate a Fiber-seq BAM file for m6A, nucleosome, and optionally FIRE calls

PgInject(PgInjectOptions)

Create a mock BAM file from a reference FASTA with perfectly aligned sequences

PgLift(PgLiftOptions)

Lift annotations through a pangenome graph from source to target coordinates

PgPansn(PgPansnOptions)

Add or strip panSN-spec prefixes from BAM contig names

Completions(CompletionOptions)

Make command line completions

Man

Make a man page for fibertools-rs

Writes file for man to stdout.

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) -> Command

Append to Command so it can instantiate Self via FromArgMatches::from_arg_matches_mut

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

Append to Command so it can instantiate self via FromArgMatches::update_from_arg_matches_mut

fn has_subcommand(__clap_name: &str) -> bool

Test whether Self can parse a specific subcommand