Struct fibertools_rs::cli::AddNucleosomeOptions

pub struct AddNucleosomeOptions {
    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 min_ml_score: u8,
}

Fields§

§bam: String

Bam HiFi file with m6A calls

§out: String

Output bam file with nucleosome calls

§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.

§min_ml_score: u8

Minium score in the ML tag to use in predicting nucleosomes

Implementations§

impl AddNucleosomeOptions

pub fn default_value() -> Self

Trait Implementations§

impl Args for AddNucleosomeOptions

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. Read more

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

Append to [Command] so it can update self. Read more

impl Debug for AddNucleosomeOptions

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

Formats the value using the given formatter. Read more

impl FromArgMatches for AddNucleosomeOptions

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

Instantiate Self from [ArgMatches], parsing the arguments as needed. Read more

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

Instantiate Self from [ArgMatches], parsing the arguments as needed. Read more

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.

Auto Trait Implementations§

impl RefUnwindSafe for AddNucleosomeOptions

impl Send for AddNucleosomeOptions

impl Sync for AddNucleosomeOptions

impl Unpin for AddNucleosomeOptions

impl UnwindSafe for AddNucleosomeOptions

Blanket Implementations§

impl<T> Any for T
where T: 'static + ?Sized,

fn type_id(&self) -> TypeId

Gets the TypeId of self. Read more

impl<T> Borrow<T> for T
where T: ?Sized,

fn borrow(&self) -> &T

Immutably borrows from an owned value. Read more

impl<T> BorrowMut<T> for T
where T: ?Sized,

fn borrow_mut(&mut self) -> &mut T

Mutably borrows from an owned value. Read more

impl<T> From<T> for T

fn from(t: T) -> T

Returns the argument unchanged.

impl<T, U> Into<U> for T
where U: From<T>,

fn into(self) -> U

Calls U::from(self).

That is, this conversion is whatever the implementation of From<T> for U chooses to do.

impl<T> Pointable for T

const ALIGN: usize = _

The alignment of pointer.

type Init = T

The type for initializers.

unsafe fn init(init: <T as Pointable>::Init) -> usize

Initializes a with the given initializer. Read more

unsafe fn deref<'a>(ptr: usize) -> &'a T

Dereferences the given pointer. Read more

unsafe fn deref_mut<'a>(ptr: usize) -> &'a mut T

Mutably dereferences the given pointer. Read more

unsafe fn drop(ptr: usize)

Drops the object pointed to by the given pointer. Read more

impl<T> Same for T

type Output = T

Should always be Self

impl<SS, SP> SupersetOf<SS> for SP
where SS: SubsetOf<SP>,

fn to_subset(&self) -> Option<SS>

The inverse inclusion map: attempts to construct self from the equivalent element of its superset. Read more

fn is_in_subset(&self) -> bool

Checks if self is actually part of its subset T (and can be converted to it).

fn to_subset_unchecked(&self) -> SS

Use with care! Same as self.to_subset but without any property checks. Always succeeds.

fn from_subset(element: &SS) -> SP

The inclusion map: converts self to the equivalent element of its superset.

impl<T, U> TryFrom<U> for T
where U: Into<T>,

type Error = Infallible

The type returned in the event of a conversion error.

fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>

Performs the conversion.

impl<T, U> TryInto<U> for T
where U: TryFrom<T>,

type Error = <U as TryFrom<T>>::Error

The type returned in the event of a conversion error.

fn try_into(self) -> Result<U, <U as TryFrom<T>>::Error>

Performs the conversion.

impl<V, T> VZip<V> for T
where V: MultiLane<T>,

fn vzip(self) -> V