Struct PeConstraints 

pub struct PeConstraints {
    pub min_insert: u32,
    pub max_insert: u32,
    pub policy: PePolicy,
    pub allow_overlap: bool,
    pub allow_dovetail: bool,
    pub allow_contain: bool,
}

Paired-end constraints

Defines the constraints for valid paired-end alignments.

Fields

min_insert: u32

Minimum fragment/insert size (outer distance between mates)

max_insert: u32

Maximum fragment/insert size

policy: PePolicy

Orientation policy

allow_overlap: bool

Whether to allow overlapping mates

allow_dovetail: bool

Whether to allow dovetailing (one mate extends past the other)

allow_contain: bool

Whether to allow one mate containing the other

Implementations

impl PeConstraints

pub fn new(min_insert: u32, max_insert: u32, policy: PePolicy) -> Self

Create new paired-end constraints

pub fn is_concordant( &self, pos1: u64, len1: u32, strand1: bool, chr1: u32, pos2: u64, len2: u32, strand2: bool, chr2: u32, ) -> Option<i32>

Check if a pair of alignments is concordant (properly paired)

Arguments

• pos1 - Position of mate 1 (0-based)
• len1 - Length of mate 1
• strand1 - Strand of mate 1 (true = forward, false = reverse)
• chr1 - Chromosome of mate 1
• pos2 - Position of mate 2 (0-based)
• len2 - Length of mate 2
• strand2 - Strand of mate 2
• chr2 - Chromosome of mate 2

Returns

Some(insert_size) if concordant, None if discordant

pub fn mate_search_range( &self, anchor_pos: u64, anchor_len: u32, anchor_is_r1: bool, anchor_strand: bool, ) -> (u64, u64, bool)

Calculate the expected position range for the opposite mate

Given an anchor alignment, calculate where the opposite mate should align based on insert size constraints.

Arguments

• anchor_pos - Position of the anchor mate (0-based)
• anchor_len - Length of the anchor mate
• anchor_is_r1 - True if anchor is read 1, false if read 2
• anchor_strand - True if anchor is forward strand

Returns

(start_pos, end_pos, expected_strand) for the opposite mate search

Trait Implementations

impl Clone for PeConstraints

fn clone(&self) -> PeConstraints

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for PeConstraints

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

Formats the value using the given formatter.

impl Default for PeConstraints

fn default() -> Self

Returns the “default value” for a type.

impl Copy for PeConstraints