Struct NormalizeConfig 

pub struct NormalizeConfig {
    pub shuffle_direction: ShuffleDirection,
    pub cross_boundaries: bool,
    pub error_config: ErrorConfig,
    pub window_size: u64,
    pub prevent_overlap: bool,
}

Configuration for variant normalization

Fields

shuffle_direction: ShuffleDirection

Direction to shuffle variants (default: 3’)

cross_boundaries: bool

Whether to allow crossing exon-intron boundaries

error_config: ErrorConfig

Error handling configuration (controls reference validation behavior)

window_size: u64

Window size for reference sequence fetching

prevent_overlap: bool

Whether to prevent overlaps in compound variant normalization

When true, normalization will check if variants in an allele would overlap after shifting and constrain the normalization to prevent collisions.

Implementations

impl NormalizeConfig

pub fn new() -> Self

Create a new config with default values

pub fn strict() -> Self

Create a config with strict error handling (reject reference mismatches)

pub fn lenient() -> Self

Create a config with lenient error handling (warn on reference mismatches)

pub fn silent() -> Self

Create a config with silent error handling (ignore reference mismatches)

pub fn with_direction(self, direction: ShuffleDirection) -> Self

Set shuffle direction

pub fn allow_crossing_boundaries(self) -> Self

Allow crossing boundaries

pub fn with_error_mode(self, mode: ErrorMode) -> Self

Set error handling mode

pub fn with_error_override( self, error_type: ErrorType, action: ErrorOverride, ) -> Self

Set a specific error type override

pub fn skip_validation(self) -> Self

👎Deprecated since 0.2.0: Use with_error_mode(ErrorMode::Silent) instead

Disable reference validation (sets RefSeqMismatch to SilentCorrect)

pub fn with_overlap_prevention(self, prevent: bool) -> Self

Enable overlap prevention in compound variants

pub fn ref_mismatch_action(&self) -> ResolvedAction

Get the resolved action for reference sequence mismatch

pub fn should_reject_ref_mismatch(&self) -> bool

Returns true if reference mismatches should be rejected

pub fn should_warn_ref_mismatch(&self) -> bool

Returns true if reference mismatches should emit warnings

Trait Implementations

impl Clone for NormalizeConfig

fn clone(&self) -> NormalizeConfig

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for NormalizeConfig

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

Formats the value using the given formatter.

impl Default for NormalizeConfig

fn default() -> Self

Returns the “default value” for a type.

impl<'de> Deserialize<'de> for NormalizeConfig

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error>

where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl PartialEq for NormalizeConfig

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

Tests for self and other values to be equal, and is used by ==.

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

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

impl Serialize for NormalizeConfig

fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error>

where __S: Serializer,

Serialize this value into the given Serde serializer.

impl Eq for NormalizeConfig