Struct FireOptions 

pub struct FireOptions {

    pub input: InputBam,
    pub out: String,
    pub ont: bool,
    pub human: bool,
    pub yeast: bool,
    pub extract: bool,
    pub all: bool,
    pub feats_to_text: bool,
    pub skip_no_m6a: bool,
    pub min_msp: usize,
    pub min_ave_msp_size: i64,
    pub width_bin: i64,
    pub bin_num: i64,
    pub best_window_size: i64,
    pub use_5mc: bool,
    pub min_msp_length_for_positive_fire_call: i64,
    pub model: Option<String>,
    pub fdr_table: Option<String>,
}

Fields

input: InputBam

out: String

Output file (BAM by default, table of MSP features if --feats-to-text is used, and bed9 + if `–extract`` is used)

ont: bool

Use a ONT heuristic adjustment for FIRE calling. This adjusts the observed number of m6A counts by adding pseudo counts to account for the single stranded nature of ONT data.

human: bool

Use a human model for FIRE calling

yeast: bool

Use a yeast model for FIRE calling

extract: bool

Output just FIRE elements in bed9 format

all: bool

When extracting bed9 format include all MSPs and nucleosomes

feats_to_text: bool

Output FIREs features for training in a table format

skip_no_m6a: bool

Don’t write reads with no m6A calls to the output bam

min_msp: usize

Skip reads without at least N MSP calls

min_ave_msp_size: i64

Skip reads without an average MSP size greater than N

width_bin: i64

Width of bin for feature collection

bin_num: i64

Number of bins to collect

best_window_size: i64

Calculate stats for the highest X bp window within each MSP Should be a fair amount higher than the expected linker length.

use_5mc: bool

Use 5mC data in FIREs

min_msp_length_for_positive_fire_call: i64

Minium length of msp to call a FIRE

model: Option<String>

Optional path to a model json file. If not provided ft will use the default model (recommended).

fdr_table: Option<String>

Optional path to a FDR table

Trait Implementations

impl Args for FireOptions

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 via FromArgMatches::from_arg_matches_mut

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

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

impl Debug for FireOptions

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

Formats the value using the given formatter.

impl Default for FireOptions

fn default() -> Self

Returns the “default value” for a type.

impl FromArgMatches for FireOptions

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.