Enum MateResolutionStrategy

pub enum MateResolutionStrategy {
    BaseQualMapQualFirstInPair,
    BaseQualMapQualIUPAC,
    BaseQualMapQualN,
    MapQualBaseQualFirstInPair,
    MapQualBaseQualIUPAC,
    MapQualBaseQualN,
    IUPAC,
    N,
    Original,
}

Strategies for resolving which mate to use when overlapping mates disagree on a base call.

All strategies first check user-based read filters. If one mate fails filters, the other is chosen. If both fail, the first mate is chosen by default.

For reads that are deletions / ref skips or lack a base call, all strategies fall back to the Original strategy (MAPQ → first in pair).

Variants

BaseQualMapQualFirstInPair

Base quality → MAPQ → first in pair

Priority order:

1. Higher base quality score wins
2. If base qualities are equal, higher MAPQ wins
3. If both are equal, first mate in pair wins

BaseQualMapQualIUPAC

Base quality → MAPQ → IUPAC ambiguity code

Priority order:

1. Higher base quality score wins
2. If base qualities are equal, higher MAPQ wins
3. If both are equal, return IUPAC ambiguity code (e.g., A+G→R)

BaseQualMapQualN

Base quality → MAPQ → N

Priority order:

1. Higher base quality score wins
2. If base qualities are equal, higher MAPQ wins
3. If both are equal, return N (unknown base), if ambiguous

MapQualBaseQualFirstInPair

MAPQ → base quality → first in pair

Priority order:

1. Higher MAPQ wins
2. If MAPQ is equal, higher base quality wins
3. If both are equal, first mate in pair wins

MapQualBaseQualIUPAC

MAPQ → base quality → IUPAC ambiguity code

Priority order:

1. Higher MAPQ wins
2. If MAPQ is equal, higher base quality wins
3. If both are equal, return IUPAC ambiguity code (e.g., A+G→R)

MapQualBaseQualN

MAPQ → base quality → N

Priority order:

1. Higher MAPQ wins
2. If MAPQ is equal, higher base quality wins
3. If both are equal, return N (unknown base), if ambiguous

IUPAC

Always return IUPAC ambiguity code for different bases

Returns the appropriate IUPAC code for the base combination:

• Same bases: return the base (A+A→A)
• Different bases: return IUPAC code (A+G→R, C+T→Y, etc.)

N

Always return N for different bases

Returns N for different bases, but identical bases return themselves:

• Same bases: return the base (A+A→A)
• Different bases: return N

Original

Original strategy: MAPQ → first in pair

Priority order:

1. Higher MAPQ wins
2. If MAPQ is equal, first mate in pair wins
3. If neither is marked as first in pair, choose first mate by default

Trait Implementations

impl Clone for MateResolutionStrategy

fn clone(&self) -> MateResolutionStrategy

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for MateResolutionStrategy

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

Formats the value using the given formatter.

impl FromStr for MateResolutionStrategy

type Err = ParseError

The associated error which can be returned from parsing.

fn from_str(s: &str) -> Result<MateResolutionStrategy, <Self as FromStr>::Err>

Parses a string s to return a value of this type.

impl TryFrom<&str> for MateResolutionStrategy

type Error = ParseError

The type returned in the event of a conversion error.

fn try_from( s: &str, ) -> Result<MateResolutionStrategy, <Self as TryFrom<&str>>::Error>

Performs the conversion.

impl Copy for MateResolutionStrategy