Enum fibertools_rs::cli::Commands

pub enum Commands {
    Extract {
        bam: String,
        reference: bool,
        simplify: bool,
        quality: bool,
        min_ml_score: u8,
        m6a: Option<String>,
        cpg: Option<String>,
        msp: Option<String>,
        nuc: Option<String>,
        all: Option<String>,
        full_float: bool,
    },
    Center {
        bam: String,
        bed: String,
        min_ml_score: u8,
        wide: bool,
    },
    PredictM6A {
        bam: String,
        out: String,
        keep: bool,
        cnn: bool,
        full_float: bool,
    },
}

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.

simplify: bool

simplify output by remove fiber sequence

quality: bool

include per base quality scores in “fiber_qual”

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 .

full_float: bool

Add the full floating point predictions of the ML model

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 a 4th strand column is included.

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.

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

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

cnn: bool

use CNN model for prediction instead of XGB.

full_float: bool

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

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

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