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MethylationMode

holodeck_lib::meth

Enum MethylationMode 

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pub enum MethylationMode {
    EmSeq,
    Taps,
}
Expand description

Methylation chemistry. Selects which class of cytosines is converted to thymine during chemistry simulation.

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EmSeq

Unmethylated cytosines convert to thymine; methylated cytosines are preserved. Matches classical bisulfite chemistry and enzymatic methyl-seq. Pass --methylation-mode bisulfite as an alias.

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Taps

Methylated cytosines convert to thymine (TET oxidation + pyridine borane); unmethylated cytosines are preserved. The inverse of bisulfite/em-seq: a C→T event at a CpG signals methylation.

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impl MethylationMode

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pub fn as_seed_str(self) -> &'static str

Canonical seed-string form of this mode. Used in crate::commands::simulate::Simulate::compute_seed so changes to the CLI alias system don’t accidentally shift seed determinism.

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impl Clone for MethylationMode

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fn clone(&self) -> MethylationMode

Returns a duplicate of the value. Read more
1.0.0 (const: unstable) · Source§

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source. Read more
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impl Copy for MethylationMode

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impl Debug for MethylationMode

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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 Eq for MethylationMode

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impl PartialEq for MethylationMode

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

Tests for self and other values to be equal, and is used by ==.
1.0.0 (const: unstable) · Source§

fn ne(&self, other: &Rhs) -> bool

Tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.
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impl StructuralPartialEq for MethylationMode

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impl ValueEnum for MethylationMode

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fn value_variants<'a>() -> &'a [Self]

All possible argument values, in display order.
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fn to_possible_value<'a>(&self) -> Option<PossibleValue>

The canonical argument value. Read more
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fn from_str(input: &str, ignore_case: bool) -> Result<Self, String>

Parse an argument into Self.

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

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fn type_id(&self) -> TypeId

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impl<T> Borrow<T> for T
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fn borrow(&self) -> &T

Immutably borrows from an owned value. Read more
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impl<T> BorrowMut<T> for T
where T: ?Sized,

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

Mutably borrows from an owned value. Read more
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impl<T> CloneToUninit for T
where T: Clone,

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unsafe fn clone_to_uninit(&self, dest: *mut u8)

🔬This is a nightly-only experimental API. (clone_to_uninit)
Performs copy-assignment from self to dest. Read more
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impl<T> Conv for T

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fn conv<T>(self) -> T
where Self: Into<T>,

Converts self into T using Into<T>. Read more
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impl<Q, K> Equivalent<K> for Q
where Q: Eq + ?Sized, K: Borrow<Q> + ?Sized,

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fn equivalent(&self, key: &K) -> bool

Checks if this value is equivalent to the given key. Read more
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impl<Q, K> Equivalent<K> for Q
where Q: Eq + ?Sized, K: Borrow<Q> + ?Sized,

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fn equivalent(&self, key: &K) -> bool

Compare self to key and return true if they are equal.
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impl<T> FmtForward for T

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fn fmt_binary(self) -> FmtBinary<Self>
where Self: Binary,

Causes self to use its Binary implementation when Debug-formatted.
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fn fmt_display(self) -> FmtDisplay<Self>
where Self: Display,

Causes self to use its Display implementation when Debug-formatted.
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fn fmt_lower_exp(self) -> FmtLowerExp<Self>
where Self: LowerExp,

Causes self to use its LowerExp implementation when Debug-formatted.
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fn fmt_lower_hex(self) -> FmtLowerHex<Self>
where Self: LowerHex,

Causes self to use its LowerHex implementation when Debug-formatted.
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fn fmt_octal(self) -> FmtOctal<Self>
where Self: Octal,

Causes self to use its Octal implementation when Debug-formatted.
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fn fmt_pointer(self) -> FmtPointer<Self>
where Self: Pointer,

Causes self to use its Pointer implementation when Debug-formatted.
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fn fmt_upper_exp(self) -> FmtUpperExp<Self>
where Self: UpperExp,

Causes self to use its UpperExp implementation when Debug-formatted.
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fn fmt_upper_hex(self) -> FmtUpperHex<Self>
where Self: UpperHex,

Causes self to use its UpperHex implementation when Debug-formatted.
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fn fmt_list(self) -> FmtList<Self>
where &'a Self: for<'a> IntoIterator,

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impl<T> From<T> for T

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fn from(t: T) -> T

Returns the argument unchanged.

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fn into(self) -> U

Calls U::from(self).

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

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impl<T> Pipe for T
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fn pipe<R>(self, func: impl FnOnce(Self) -> R) -> R
where Self: Sized,

Pipes by value. This is generally the method you want to use. Read more
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fn pipe_ref<'a, R>(&'a self, func: impl FnOnce(&'a Self) -> R) -> R
where R: 'a,

Borrows self and passes that borrow into the pipe function. Read more
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where R: 'a,

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where Self: BorrowMut<B>, B: 'a + ?Sized, R: 'a,

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where Self: AsRef<U>, U: 'a + ?Sized, R: 'a,

Borrows self, then passes self.as_ref() into the pipe function.
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where Self: AsMut<U>, U: 'a + ?Sized, R: 'a,

Mutably borrows self, then passes self.as_mut() into the pipe function.
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where Self: Deref<Target = T>, T: 'a + ?Sized, R: 'a,

Borrows self, then passes self.deref() into the pipe function.
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where Self: DerefMut<Target = T> + Deref, T: 'a + ?Sized, R: 'a,

Mutably borrows self, then passes self.deref_mut() into the pipe function.
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impl<T> Tap for T

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fn tap(self, func: impl FnOnce(&Self)) -> Self

Immutable access to a value. Read more
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fn tap_mut(self, func: impl FnOnce(&mut Self)) -> Self

Mutable access to a value. Read more
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fn tap_borrow<B>(self, func: impl FnOnce(&B)) -> Self
where Self: Borrow<B>, B: ?Sized,

Immutable access to the Borrow<B> of a value. Read more
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fn tap_borrow_mut<B>(self, func: impl FnOnce(&mut B)) -> Self
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Mutable access to the BorrowMut<B> of a value. Read more
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fn tap_ref<R>(self, func: impl FnOnce(&R)) -> Self
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fn tap_ref_mut<R>(self, func: impl FnOnce(&mut R)) -> Self
where Self: AsMut<R>, R: ?Sized,

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fn tap_deref<T>(self, func: impl FnOnce(&T)) -> Self
where Self: Deref<Target = T>, T: ?Sized,

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fn tap_deref_mut<T>(self, func: impl FnOnce(&mut T)) -> Self
where Self: DerefMut<Target = T> + Deref, T: ?Sized,

Mutable access to the Deref::Target of a value. Read more
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fn tap_dbg(self, func: impl FnOnce(&Self)) -> Self

Calls .tap() only in debug builds, and is erased in release builds.
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fn tap_mut_dbg(self, func: impl FnOnce(&mut Self)) -> Self

Calls .tap_mut() only in debug builds, and is erased in release builds.
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fn tap_borrow_dbg<B>(self, func: impl FnOnce(&B)) -> Self
where Self: Borrow<B>, B: ?Sized,

Calls .tap_borrow() only in debug builds, and is erased in release builds.
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fn tap_borrow_mut_dbg<B>(self, func: impl FnOnce(&mut B)) -> Self
where Self: BorrowMut<B>, B: ?Sized,

Calls .tap_borrow_mut() only in debug builds, and is erased in release builds.
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fn tap_ref_dbg<R>(self, func: impl FnOnce(&R)) -> Self
where Self: AsRef<R>, R: ?Sized,

Calls .tap_ref() only in debug builds, and is erased in release builds.
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fn tap_ref_mut_dbg<R>(self, func: impl FnOnce(&mut R)) -> Self
where Self: AsMut<R>, R: ?Sized,

Calls .tap_ref_mut() only in debug builds, and is erased in release builds.
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fn tap_deref_dbg<T>(self, func: impl FnOnce(&T)) -> Self
where Self: Deref<Target = T>, T: ?Sized,

Calls .tap_deref() only in debug builds, and is erased in release builds.
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fn tap_deref_mut_dbg<T>(self, func: impl FnOnce(&mut T)) -> Self
where Self: DerefMut<Target = T> + Deref, T: ?Sized,

Calls .tap_deref_mut() only in debug builds, and is erased in release builds.
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impl<T> ToOwned for T
where T: Clone,

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type Owned = T

The resulting type after obtaining ownership.
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type Error = Infallible

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Performs the conversion.
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fn vzip(self) -> V