Struct fibertools_rs::cli::PredictM6AOptions

pub struct PredictM6AOptions {
    pub input: InputBam,
    pub out: String,
    pub nuc: NucleosomeParameters,
    pub keep: bool,
    pub force_min_ml_score: Option<u8>,
    pub all_calls: bool,
    pub batch_size: usize,
    pub fake: bool,
}

Fields

input: InputBam

out: String

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

nuc: NucleosomeParameters

keep: bool

Keep hifi kinetics data

force_min_ml_score: Option<u8>

Force a different minimum ML score

all_calls: bool

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

batch_size: usize

Number of reads to include in batch prediction

Increasing improves GPU performance at the cost of memory.

fake: bool

Skip the actual prediction step to allow for testing the speed of other parts of the code

Trait Implementations

impl Args for PredictM6AOptions

fn group_id() -> Option<Id>

Report the ArgGroup::id for this set of arguments

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

Append to Command so it can instantiate Self.

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

Append to Command so it can update self.

impl Debug for PredictM6AOptions

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

Formats the value using the given formatter.

impl Default for PredictM6AOptions

fn default() -> Self

Returns the “default value” for a type.

impl FromArgMatches for PredictM6AOptions

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

Assign values from ArgMatches to self.