pub struct FireOptions {
Show 14 fields pub bam: String, pub out: String, pub extract: 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>, pub feats_to_text: bool,
}

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§bam: String

Bam HiFi file with m6A and MSP calls

§out: String

Output file (bam by default, table if –feats_to_text is used, and bed9 + if –extract is used)

§extract: bool

Output just FIRE elements in bed9 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

§fdr_table: Option<String>

Optional path to a FDR table

§feats_to_text: bool

Output FIREs features for training in a table format

Trait Implementations§

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impl Args for FireOptions

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fn group_id() -> Option<Id>

Report the ArgGroup::id for this set of arguments
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fn augment_args<'b>(__clap_app: Command) -> Command

Append to Command so it can instantiate Self. Read more
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fn augment_args_for_update<'b>(__clap_app: Command) -> Command

Append to Command so it can update self. Read more
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impl Debug for FireOptions

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

Formats the value using the given formatter. Read more
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impl FromArgMatches for FireOptions

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fn from_arg_matches(__clap_arg_matches: &ArgMatches) -> Result<Self, Error>

Instantiate Self from ArgMatches, parsing the arguments as needed. Read more
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fn from_arg_matches_mut( __clap_arg_matches: &mut ArgMatches ) -> Result<Self, Error>

Instantiate Self from ArgMatches, parsing the arguments as needed. Read more
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fn update_from_arg_matches( &mut self, __clap_arg_matches: &ArgMatches ) -> Result<(), Error>

Assign values from ArgMatches to self.
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fn update_from_arg_matches_mut( &mut self, __clap_arg_matches: &mut ArgMatches ) -> Result<(), Error>

Assign values from ArgMatches to self.
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impl PartialEq for FireOptions

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fn eq(&self, other: &FireOptions) -> bool

This method tests for self and other values to be equal, and is used by ==.
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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.
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impl Eq for FireOptions

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impl StructuralPartialEq for FireOptions

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const ALIGN: usize = _

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Dereferences the given pointer. Read more
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The inverse inclusion map: attempts to construct self from the equivalent element of its superset. Read more
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Checks if self is actually part of its subset T (and can be converted to it).
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fn to_subset_unchecked(&self) -> SS

Use with care! Same as self.to_subset but without any property checks. Always succeeds.
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The inclusion map: converts self to the equivalent element of its superset.
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