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FilterConfig

fgumi_lib::consensus_filter

Struct FilterConfig 

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pub struct FilterConfig {
    pub duplex_thresholds: Option<FilterThresholds>,
    pub ab_thresholds: Option<FilterThresholds>,
    pub ba_thresholds: Option<FilterThresholds>,
    pub single_strand_thresholds: Option<FilterThresholds>,
    pub min_base_quality: Option<u8>,
    pub min_mean_base_quality: Option<f64>,
    pub max_no_call_fraction: f64,
}
Expand description

Filtering configuration for consensus reads

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§duplex_thresholds: Option<FilterThresholds>

Thresholds for duplex consensus reads (if applicable)

§ab_thresholds: Option<FilterThresholds>

Thresholds for AB/top-strand consensus

§ba_thresholds: Option<FilterThresholds>

Thresholds for BA/bottom-strand consensus

§single_strand_thresholds: Option<FilterThresholds>

Thresholds for single-strand consensus

§min_base_quality: Option<u8>

Minimum base quality after masking (optional - None means no quality masking)

§min_mean_base_quality: Option<f64>

Minimum mean base quality after masking (optional)

§max_no_call_fraction: f64

Maximum fraction of no-calls (N bases) allowed (0.0-1.0)

Implementations§

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impl FilterConfig

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pub fn for_single_strand( thresholds: FilterThresholds, min_base_quality: Option<u8>, min_mean_base_quality: Option<f64>, max_no_call_fraction: f64, ) -> FilterConfig

Creates a filter configuration for single-strand (simplex) consensus reads.

This is the simplest configuration - one set of thresholds applied to all reads.

§Arguments
  • thresholds - Filter thresholds for single-strand consensus
  • min_base_quality - Minimum base quality after masking (None means no quality masking)
  • min_mean_base_quality - Optional minimum mean base quality
  • max_no_call_fraction - Maximum fraction of N bases allowed
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pub fn for_duplex( duplex: FilterThresholds, strand: FilterThresholds, min_base_quality: Option<u8>, min_mean_base_quality: Option<f64>, max_no_call_fraction: f64, ) -> FilterConfig

Creates a filter configuration for symmetric duplex consensus reads.

Uses the same thresholds for both AB and BA strands.

§Arguments
  • duplex - Filter thresholds for final duplex consensus
  • strand - Filter thresholds for both AB and BA strands (symmetric)
  • min_base_quality - Minimum base quality after masking (None means no quality masking)
  • min_mean_base_quality - Optional minimum mean base quality
  • max_no_call_fraction - Maximum fraction of N bases allowed
§Panics

Panics if thresholds violate ordering constraints (strand.min_reads <= duplex.min_reads, etc.)

Source

pub fn for_duplex_asymmetric( duplex: FilterThresholds, ab: FilterThresholds, ba: FilterThresholds, min_base_quality: Option<u8>, min_mean_base_quality: Option<f64>, max_no_call_fraction: f64, ) -> FilterConfig

Creates a filter configuration for asymmetric duplex consensus reads.

Uses different thresholds for AB (higher depth strand) and BA (lower depth strand).

§Arguments
  • duplex - Filter thresholds for final duplex consensus
  • ab - Filter thresholds for AB strand (typically higher depth)
  • ba - Filter thresholds for BA strand (typically lower depth)
  • min_base_quality - Minimum base quality after masking (None means no quality masking)
  • min_mean_base_quality - Optional minimum mean base quality
  • max_no_call_fraction - Maximum fraction of N bases allowed
§Panics

Panics if thresholds violate ordering constraints:

  • min_reads: BA <= AB <= duplex
  • error rates: AB <= BA (AB more stringent)
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pub fn duplex_thresholds( &self, ) -> Option<(&FilterThresholds, &FilterThresholds, &FilterThresholds)>

Returns duplex (CC), AB, and BA thresholds, or None if any are missing.

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pub fn effective_single_strand_thresholds(&self) -> Option<&FilterThresholds>

Returns the single-strand thresholds, falling back to duplex thresholds.

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pub fn new( min_reads: &[usize], max_read_error_rate: &[f64], max_base_error_rate: &[f64], min_base_quality: Option<u8>, min_mean_base_quality: Option<f64>, max_no_call_fraction: f64, ) -> FilterConfig

Creates a new filter configuration from parameter vectors

§Arguments
  • min_reads - 1-3 values for [duplex, AB, BA] or [single-strand]
  • max_read_error_rate - 1-3 values for [duplex, AB, BA] or [single-strand]
  • max_base_error_rate - 1-3 values for [duplex, AB, BA] or [single-strand]
  • min_base_quality - Minimum base quality after masking (None means no quality masking)
  • min_mean_base_quality - Optional minimum mean base quality
  • max_no_call_fraction - Maximum fraction of N bases allowed
§Panics

Panics if thresholds violate ordering constraints:

  • min_reads: BA <= AB <= duplex
  • error rates: AB <= BA (AB more stringent)

Trait Implementations§

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impl Clone for FilterConfig

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fn clone(&self) -> FilterConfig

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
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impl Debug for FilterConfig

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

Formats the value using the given formatter. Read more

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