Struct fibertools_rs::cli::FireOptions
source · 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,
}
Fields§
§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§
source§impl Args for FireOptions
impl Args for FireOptions
source§fn augment_args<'b>(__clap_app: Command) -> Command
fn augment_args<'b>(__clap_app: Command) -> Command
source§impl Debug for FireOptions
impl Debug for FireOptions
source§impl FromArgMatches for FireOptions
impl FromArgMatches for FireOptions
source§fn from_arg_matches(__clap_arg_matches: &ArgMatches) -> Result<Self, Error>
fn from_arg_matches(__clap_arg_matches: &ArgMatches) -> Result<Self, Error>
source§fn from_arg_matches_mut(
__clap_arg_matches: &mut ArgMatches
) -> Result<Self, Error>
fn from_arg_matches_mut( __clap_arg_matches: &mut ArgMatches ) -> Result<Self, Error>
source§fn update_from_arg_matches(
&mut self,
__clap_arg_matches: &ArgMatches
) -> Result<(), Error>
fn update_from_arg_matches( &mut self, __clap_arg_matches: &ArgMatches ) -> Result<(), Error>
Assign values from
ArgMatches
to self
.source§fn update_from_arg_matches_mut(
&mut self,
__clap_arg_matches: &mut ArgMatches
) -> Result<(), Error>
fn update_from_arg_matches_mut( &mut self, __clap_arg_matches: &mut ArgMatches ) -> Result<(), Error>
Assign values from
ArgMatches
to self
.source§impl PartialEq for FireOptions
impl PartialEq for FireOptions
source§fn eq(&self, other: &FireOptions) -> bool
fn eq(&self, other: &FireOptions) -> bool
This method tests for
self
and other
values to be equal, and is used
by ==
.impl Eq for FireOptions
impl StructuralPartialEq for FireOptions
Auto Trait Implementations§
impl Freeze for FireOptions
impl RefUnwindSafe for FireOptions
impl Send for FireOptions
impl Sync for FireOptions
impl Unpin for FireOptions
impl UnwindSafe for FireOptions
Blanket Implementations§
source§impl<T> BorrowMut<T> for Twhere
T: ?Sized,
impl<T> BorrowMut<T> for Twhere
T: ?Sized,
source§fn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Mutably borrows from an owned value. Read more
source§impl<Q, K> Equivalent<K> for Q
impl<Q, K> Equivalent<K> for Q
source§impl<Q, K> Equivalent<K> for Q
impl<Q, K> Equivalent<K> for Q
source§fn equivalent(&self, key: &K) -> bool
fn equivalent(&self, key: &K) -> bool
Compare self to
key
and return true
if they are equal.source§impl<T> Pointable for T
impl<T> Pointable for T
source§impl<SS, SP> SupersetOf<SS> for SPwhere
SS: SubsetOf<SP>,
impl<SS, SP> SupersetOf<SS> for SPwhere
SS: SubsetOf<SP>,
source§fn to_subset(&self) -> Option<SS>
fn to_subset(&self) -> Option<SS>
The inverse inclusion map: attempts to construct
self
from the equivalent element of its
superset. Read moresource§fn is_in_subset(&self) -> bool
fn is_in_subset(&self) -> bool
Checks if
self
is actually part of its subset T
(and can be converted to it).source§fn to_subset_unchecked(&self) -> SS
fn to_subset_unchecked(&self) -> SS
Use with care! Same as
self.to_subset
but without any property checks. Always succeeds.source§fn from_subset(element: &SS) -> SP
fn from_subset(element: &SS) -> SP
The inclusion map: converts
self
to the equivalent element of its superset.