Struct fibertools_rs::cli::PredictM6AOptions

pub struct PredictM6AOptions {

    pub bam: String,
    pub out: String,
    pub nucleosome_length: i64,
    pub combined_nucleosome_length: i64,
    pub min_distance_added: i64,
    pub distance_from_end: i64,
    pub allowed_m6a_skips: i64,
    pub keep: bool,
    pub min_ml_score: Option<u8>,
    pub all_calls: bool,
    pub xgb: bool,
    pub cnn: bool,
    pub semi: bool,
    pub full_float: bool,
    pub batch_size: usize,
}

Fields

bam: String

Bam HiFi file with kinetics

out: String

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

nucleosome_length: i64

Minium nucleosome length

combined_nucleosome_length: i64

Minium nucleosome length when combining over a single m6A

min_distance_added: i64

Minium distance needed to add to an already existing nuc by crossing an m6a

distance_from_end: i64

Minimum distance from the end of a fiber to call a nucleosome or MSP

allowed_m6a_skips: i64

Most m6A events we can skip over to get to the nucleosome length when using D-segment algorithm. 2 is often a good value, negative values disable D-segment for the simple caller.

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.

Trait Implementations

impl Args for PredictM6AOptions

fn group_id() -> Option<Id>

Report the [ArgGroup::id][crate::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 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.

impl PartialEq for PredictM6AOptions

fn eq(&self, other: &PredictM6AOptions) -> 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 Eq for PredictM6AOptions

impl StructuralPartialEq for PredictM6AOptions