Struct CodecConsensusOptions

Source

pub struct CodecConsensusOptions {Show 15 fields
    pub min_input_base_quality: u8,
    pub error_rate_pre_umi: u8,
    pub error_rate_post_umi: u8,
    pub min_reads_per_strand: usize,
    pub max_reads_per_strand: Option<usize>,
    pub min_duplex_length: usize,
    pub single_strand_qual: Option<u8>,
    pub outer_bases_qual: Option<u8>,
    pub outer_bases_length: usize,
    pub max_duplex_disagreements: usize,
    pub max_duplex_disagreement_rate: f64,
    pub cell_tag: Option<Tag>,
    pub produce_per_base_tags: bool,
    pub trim: bool,
    pub min_consensus_base_quality: u8,
}

Expand description

Options for CODEC consensus calling

Fields§

§min_input_base_quality: u8

Minimum base quality to include in consensus

§error_rate_pre_umi: u8

Pre-UMI error rate (Phred scale)

§error_rate_post_umi: u8

Post-UMI error rate (Phred scale)

§min_reads_per_strand: usize

Minimum number of read pairs required to form consensus per strand

§max_reads_per_strand: Option<usize>

Maximum number of read pairs to use per strand (downsample if exceeded)

§min_duplex_length: usize

Minimum duplex overlap length (in bases)

§single_strand_qual: Option<u8>

Reduce quality of single-strand regions to this value (if set)

§outer_bases_qual: Option<u8>

Reduce quality of outer bases to this value (if set)

§outer_bases_length: usize

Number of outer bases to reduce quality for

§max_duplex_disagreements: usize

Maximum number of duplex disagreements allowed

§max_duplex_disagreement_rate: f64

Maximum duplex disagreement rate allowed (0.0-1.0)

§cell_tag: Option<Tag>

Cell barcode tag (e.g., “CB”)

§produce_per_base_tags: bool

Whether to produce per-base tags (ad, ae, bd, be, etc.)

§trim: bool

Whether to quality-trim reads before consensus calling

§min_consensus_base_quality: u8

Minimum consensus base quality (output bases below this are masked to N)

Trait Implementations§

Source §

impl Clone for CodecConsensusOptions

Source §

fn clone(&self) -> CodecConsensusOptions

Returns a duplicate of the value. Read more

1.0.0 · Source§

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

Performs copy-assignment from source. Read more

Source §

impl Debug for CodecConsensusOptions

Source §

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

Formats the value using the given formatter. Read more

Source §

impl Default for CodecConsensusOptions

Source §

fn default() -> CodecConsensusOptions

Returns the “default value” for a type. Read more

Auto Trait Implementations§

§

impl UnwindSafe for CodecConsensusOptions

Blanket Implementations§

Source §

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

Source §

fn type_id(&self) -> TypeId

Gets the TypeId of self. Read more

Source §

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

Source §

fn borrow(&self) -> &T

Immutably borrows from an owned value. Read more

Source §

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

Source §

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

Mutably borrows from an owned value. Read more

Source §

impl<T> CloneToUninit for T
where T: Clone,

Source §

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

Source §

impl<T> From<T> for T

Source §

fn from(t: T) -> T

Returns the argument unchanged.

Source §

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

Source §

fn into(self) -> U

Calls U::from(self).

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

Source §

impl<T> IntoEither for T

Source §

fn into_either(self, into_left: bool) -> Either<Self, Self>

Converts self into a Left variant of Either<Self, Self> if into_left is true. Converts self into a Right variant of Either<Self, Self> otherwise. Read more

Source §

fn into_either_with<F>(self, into_left: F) -> Either<Self, Self>
where F: FnOnce(&Self) -> bool,

Converts self into a Left variant of Either<Self, Self> if into_left(&self) returns true. Converts self into a Right variant of Either<Self, Self> otherwise. Read more

Source §