Enum fibertools_rs::cli::Commands

pub enum Commands {
    Extract {
        bam: String,
        reference: bool,
        min_ml_score: u8,
        m6a: Option<String>,
        cpg: Option<String>,
        msp: Option<String>,
        nuc: Option<String>,
        all: Option<String>,
        quality: bool,
        full_float: bool,
        simplify: bool,
    },
    Center {
        bam: String,
        bed: String,
        min_ml_score: u8,
        dist: Option<i64>,
        wide: bool,
    },
    PredictM6A {
        bam: String,
        out: String,
        keep: bool,
        min_ml_score: Option<u8>,
        all_calls: bool,
        xgb: bool,
        cnn: bool,
        semi: bool,
        full_float: bool,
        batch_size: usize,
    },
    ClearKinetics {
        bam: String,
        out: String,
    },
    Completions {
        shell: Shell,
    },
    Man {},
}

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

min_ml_score: u8

Minium score in the ML tag to include in the output

m6a: Option<String>

Output path for m6a bed12

cpg: Option<String>

Output path for 5mC (CpG, primrose) bed12

msp: Option<String>

Output path for methylation sensitive patch (msp) bed12

nuc: Option<String>

Output path for nucleosome bed12

all: Option<String>

Output path for a tabular format including “all” fiberseq information in the bam

quality: bool

Include per base quality scores in “fiber_qual”

full_float: bool

Add the full floating point predictions of the ML model

simplify: bool

Simplify output by remove fiber sequence

Extract fiberseq data into plain text files

Center

Fields

bam: String

Fiberseq bam file, must be aligned and have an index

bed: String

Bed file on which to center fiberseq reads. Data is adjusted to the start position of the bed file and corrected for strand if the strand is indicated in the 6th column of the bed file. The 4th column will also be checked for the strand but only after the 6th is.

If you include strand information in the 4th column it will orient data accordingly and use the end position of bed record instead of the start if on the minus strand. This means that profiles of motifs in both the forward and minus orientation will align to the same central position.

min_ml_score: u8

Minium score in the ML tag to include in the output

dist: Option<i64>

Set a maximum distance from the start of the motif to keep a feature

wide: bool

Provide data in wide format, one row per read

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

PredictM6A

Fields

bam: String

Bam HiFi file with kinetics

out: String

Output bam file with m6A calls in new/extended MM and ML bam tags

keep: bool

Keep hifi kinetics data

min_ml_score: Option<u8>

Set a minimum ML score to keep on instead of using the model specific minimum ML score.

all_calls: bool

Keep all m6A calls regardless of how low the ML value is

xgb: bool

Use the XGBoost model for prediction

cnn: bool

Use the CNN model for prediction

semi: bool

Use the semi-supervised CNN model for prediction [default: true]

full_float: bool

Add a bam tag (mp) with the full floating point predictions of the ML model

For debugging only.

batch_size: usize

Number of reads to include in batch prediction

Increasing improves GPU performance at the cost of memory.

Predict m6A positions using HiFi kinetics data and encode the results in the MM and ML bam tags

ClearKinetics

Fields

bam: String

Bam HiFi file with kinetics

out: String

Output bam file without hifi kinetics

Remove HiFi kinetics tags from the input bam file

Completions

Fields

shell: Shell

If provided, outputs the completion file for given shell

Make command line completions

Man

Fields

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 PartialEq<Commands> for Commands

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

impl Eq for Commands

impl StructuralEq for Commands

impl StructuralPartialEq for Commands