Struct PairedAlignment 

pub struct PairedAlignment {

    pub chr1: u32,
    pub pos1: u64,
    pub strand1: bool,
    pub cigar1: String,
    pub score1: Score,
    pub edits1: u32,
    pub chr2: u32,
    pub pos2: u64,
    pub strand2: bool,
    pub cigar2: String,
    pub score2: Score,
    pub edits2: u32,
    pub insert_size: i32,
    pub alignment_type: PeAlignmentType,
    pub mapq: u8,
}

Result of a paired-end alignment

Fields

chr1: u32

Chromosome index for mate 1

pos1: u64

Position for mate 1 (0-based)

strand1: bool

Strand for mate 1 (true = forward)

cigar1: String

CIGAR for mate 1

score1: Score

Score for mate 1

edits1: u32

Number of edits for mate 1

chr2: u32

Chromosome index for mate 2

pos2: u64

Position for mate 2 (0-based)

strand2: bool

Strand for mate 2 (true = forward)

cigar2: String

CIGAR for mate 2

score2: Score

Score for mate 2

edits2: u32

Number of edits for mate 2

insert_size: i32

Insert size (TLEN in SAM)

alignment_type: PeAlignmentType

Alignment type

mapq: u8

Mapping quality

Implementations

impl PairedAlignment

pub fn new() -> Self

Create a new paired alignment

pub fn is_concordant(&self) -> bool

Check if this is a concordant alignment

pub fn sam_flag1(&self) -> u16

Calculate SAM flags for mate 1

pub fn sam_flag2(&self) -> u16

Calculate SAM flags for mate 2

Trait Implementations

impl Clone for PairedAlignment

fn clone(&self) -> PairedAlignment

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for PairedAlignment

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

Formats the value using the given formatter.

impl Default for PairedAlignment

fn default() -> PairedAlignment

Returns the “default value” for a type.