Struct TemplateKey 

#[repr(C)]
pub struct TemplateKey {
    pub primary: u64,
    pub secondary: u64,
    pub tertiary: u64,
    pub name_hash_upper: u64,
}

Extended key for template-coordinate sorting.

Template-coordinate requires comparing multiple fields: tid1, tid2, pos1, pos2, neg1, neg2, library, MI, name, is_upper

We pack these into 4 u64 values for efficient comparison. The name_hash_upper field packs both name_hash and is_upper:

• Upper 63 bits: name hash (groups same names together)
• Lowest bit: is_upper (false=0, true=1)

This ensures reads from the same template stay together (same hash), with is_upper=false sorting before is_upper=true.

Fields

primary: u64

Packed: (tid1 << 48) | (tid2 << 32) | pos1 Comparison order matches samtools: tid1, tid2, pos1

secondary: u64

Packed: (pos2 << 32) | (!neg1 << 1) | !neg2 neg flags inverted so reverse (neg=true) sorts before forward (neg=false)

tertiary: u64

Packed: (library << 48) | (mi_value << 1) | mi_suffix

name_hash_upper: u64

Packed: (name_hash << 1) | is_upper This ensures same-name records group together, with is_upper as tie-breaker.

Implementations

impl TemplateKey

pub fn new( tid1: i32, pos1: i32, neg1: bool, tid2: i32, pos2: i32, neg2: bool, library: u32, mi: (u64, bool), name_hash: u64, is_upper: bool, ) -> Self

Create a new template key from extracted fields.

pub fn unmapped(name_hash: u64, is_read2: bool) -> Self

Create a key for completely unmapped records.

pub fn zeroed() -> Self

Create a zeroed key (used as dummy for memory operations).

impl TemplateKey

pub fn to_bytes(&self) -> [u8; 32]

Serialize to bytes for storage in keyed temp files.

pub fn from_bytes(buf: &[u8; 32]) -> Self

Deserialize from bytes read from keyed temp files.

impl TemplateKey

pub fn core_cmp(&self, other: &Self) -> Ordering

Compare only core fields (tid1, tid2, pos1, pos2, neg1, neg2, library, MI).

This ignores the name_hash tie-breaker, allowing verification to accept both fgumi and samtools sorted files (which differ only in tie-breaking).

Trait Implementations

impl Clone for TemplateKey

fn clone(&self) -> TemplateKey

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for TemplateKey

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

Formats the value using the given formatter.

impl Default for TemplateKey

fn default() -> Self

Returns the “default value” for a type.

impl Ord for TemplateKey

fn cmp(&self, other: &Self) -> Ordering

This method returns an Ordering between self and other.

fn max(self, other: Self) -> Self

where Self: Sized,

Compares and returns the maximum of two values.

fn min(self, other: Self) -> Self

where Self: Sized,

Compares and returns the minimum of two values.

fn clamp(self, min: Self, max: Self) -> Self

where Self: Sized,

Restrict a value to a certain interval.

impl PartialEq for TemplateKey

fn eq(&self, other: &TemplateKey) -> 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 PartialOrd for TemplateKey

fn partial_cmp(&self, other: &Self) -> Option<Ordering>

This method returns an ordering between self and other values if one exists.

fn lt(&self, other: &Rhs) -> bool

Tests less than (for self and other) and is used by the < operator.

fn le(&self, other: &Rhs) -> bool

Tests less than or equal to (for self and other) and is used by the <= operator.

fn gt(&self, other: &Rhs) -> bool

Tests greater than (for self and other) and is used by the > operator.

fn ge(&self, other: &Rhs) -> bool

Tests greater than or equal to (for self and other) and is used by the >= operator.

impl RawSortKey for TemplateKey

const SERIALIZED_SIZE: Option<usize>

Fixed byte size when serialized, or None for variable-length keys.

fn extract(_bam: &[u8], _ctx: &SortContext) -> Self

Extract a sort key from raw BAM record bytes.

fn write_to<W: Write>(&self, writer: &mut W) -> Result<()>

Serialize the key to a writer for temp file storage.

fn read_from<R: Read>(reader: &mut R) -> Result<Self>

Deserialize a key from a reader.

impl Zeroable for TemplateKey

fn zeroed() -> Self

Calls zeroed.

impl Copy for TemplateKey

impl Eq for TemplateKey

impl Pod for TemplateKey

impl StructuralPartialEq for TemplateKey