Enum MoleculeId 

pub enum MoleculeId {
    None,
    Single(u64),
    PairedA(u64),
    PairedB(u64),
}

Molecule identifier for UMI grouping.

Represents the assigned molecule ID during UMI-based grouping. The ID is stored as an integer during processing for efficiency, and only converted to a string when writing the final BAM output.

Variants

None

Not yet assigned (default state)

Single(u64)

Non-paired strategy: simple integer ID (e.g., “42”)

PairedA(u64)

Paired strategy, top strand (e.g., “42/A”)

PairedB(u64)

Paired strategy, bottom strand (e.g., “42/B”)

Implementations

impl MoleculeId

pub fn id(&self) -> Option<u64>

Get the base molecule ID value, if assigned.

pub fn is_assigned(&self) -> bool

Check if a molecule ID has been assigned.

pub fn to_string_with_offset(&self, base: u64) -> String

Convert to string representation with a base offset applied.

Used when serializing to BAM output, where local IDs (0, 1, 2, …) need to be converted to global IDs by adding the base offset.

pub fn write_with_offset<'a>(&self, base: u64, buf: &'a mut String) -> &'a [u8]

Write string representation into a reusable buffer, returning the bytes.

Avoids per-call String allocation by reusing the caller’s buffer.

pub fn to_vec_index(&self) -> Option<usize>

Convert to a Vec index for grouping templates by molecule ID.

Returns None for unassigned MoleculeIds. For assigned IDs:

• Single(id): returns id (indices: 0, 1, 2, …)
• PairedA(id): returns id * 2 (indices: 0, 2, 4, …)
• PairedB(id): returns id * 2 + 1 (indices: 1, 3, 5, …)

This preserves the sort order (A before B for same base id) and allows efficient Vec-based grouping instead of HashMap.

pub fn is_paired(&self) -> bool

Check if this is a paired molecule ID (PairedA or PairedB).

pub fn base_id_string(&self) -> String

Get the base ID without suffix for grouping purposes.

For paired MoleculeIds, this returns the base ID (without /A or /B). Used when grouping templates that share the same molecule but different strands.

Trait Implementations

impl Clone for MoleculeId

fn clone(&self) -> MoleculeId

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for MoleculeId

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

Formats the value using the given formatter.

impl Default for MoleculeId

fn default() -> MoleculeId

Returns the “default value” for a type.

impl Display for MoleculeId

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

Formats the value using the given formatter.

impl Hash for MoleculeId

fn hash<__H>(&self, state: &mut __H)

where __H: Hasher,

Feeds this value into the given Hasher.

fn hash_slice<H>(data: &[Self], state: &mut H)

where H: Hasher, Self: Sized,

Feeds a slice of this type into the given Hasher.

impl PartialEq for MoleculeId

fn eq(&self, other: &MoleculeId) -> 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 MoleculeId

impl Eq for MoleculeId

impl StructuralPartialEq for MoleculeId