Struct PrimaryAlignmentInfo 

pub struct PrimaryAlignmentInfo {
    pub tid1: i32,
    pub pos1: i32,
    pub neg1: bool,
    pub tid2: i32,
    pub pos2: i32,
    pub neg2: bool,
}

Primary alignment info for secondary/supplementary reads.

Stores the template-coordinate sort key from the primary alignments, enabling secondary/supplementary reads to sort adjacent to their primaries.

Binary Format

Stored as a B:i (int32 array) BAM tag with 6 elements: [tid1, pos1, neg1, tid2, pos2, neg2] where neg1/neg2 are 0 for forward, 1 for reverse strand.

This format is faster to parse than a string representation and ensures supplementary reads get the exact same sort key as their primary reads.

Fields

tid1: i32

Reference ID of the earlier mate (lower position).

pos1: i32

Unclipped 5’ position of the earlier mate.

neg1: bool

True if earlier mate is on reverse strand.

tid2: i32

Reference ID of the later mate.

pos2: i32

Unclipped 5’ position of the later mate.

neg2: bool

True if later mate is on reverse strand.

Implementations

impl PrimaryAlignmentInfo

pub const fn new( tid1: i32, pos1: i32, neg1: bool, tid2: i32, pos2: i32, neg2: bool, ) -> Self

Creates a new PrimaryAlignmentInfo.

pub fn to_tag_value(&self) -> Value

Serializes to a BAM tag value (B:i array with 6 elements).

pub fn from_tag_value(value: &Value) -> Option<Self>

Deserializes from a BAM tag value (B:i array with 6 int32 elements).

Optimized with a fast path for Int32 arrays (the expected format) that avoids heap allocation by directly indexing the array.

pub fn from_record(record: &RecordBuf) -> Option<Self>

Extracts from a BAM record’s PA tag.

Trait Implementations

impl Clone for PrimaryAlignmentInfo

fn clone(&self) -> PrimaryAlignmentInfo

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for PrimaryAlignmentInfo

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

Formats the value using the given formatter.

impl PartialEq for PrimaryAlignmentInfo

fn eq(&self, other: &PrimaryAlignmentInfo) -> 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 Copy for PrimaryAlignmentInfo

impl Eq for PrimaryAlignmentInfo

impl StructuralPartialEq for PrimaryAlignmentInfo