Struct CodecConsensusCaller 

pub struct CodecConsensusCaller { /* private fields */ }

CODEC consensus caller

Calls consensus from CODEC sequencing data where R1 and R2 from a single read-pair sequence opposite strands of the same molecule.

Implementations

impl CodecConsensusCaller

pub fn new( read_name_prefix: String, read_group_id: String, options: CodecConsensusOptions, ) -> CodecConsensusCaller

Creates a new CODEC consensus caller

Arguments

• read_name_prefix - Prefix for consensus read names
• read_group_id - Read group ID for consensus reads
• options - CODEC consensus calling options

pub fn new_with_rejects_tracking( read_name_prefix: String, read_group_id: String, options: CodecConsensusOptions, track_rejects: bool, ) -> CodecConsensusCaller

Creates a new CODEC consensus caller with optional rejected-reads tracking.

When track_rejects is true, raw BAM bytes of rejected reads are stored and can be retrieved via [rejected_reads] / [take_rejected_reads].

pub fn statistics(&self) -> &CodecConsensusStats

Returns the statistics for this caller

pub fn clear(&mut self)

Clears all per-group state to prepare for reuse

This resets statistics while preserving the caller’s configuration and reusable components (consensus builder, RNG, etc.).

pub fn rejected_reads(&self) -> &[Vec<u8>]

Returns a reference to the rejected reads (raw BAM bytes).

pub fn clear_rejected_reads(&mut self)

Clears the stored rejected reads.

pub fn take_rejected_reads(&mut self) -> Vec<Vec<u8>>

Takes ownership of the stored rejected reads, leaving an empty vec.

impl CodecConsensusCaller

Bridge methods for encoding RecordBuf to raw bytes. Used by tests (both unit and integration) to call the raw-byte pipeline.

pub fn consensus_reads_from_sam_records( &mut self, recs: Vec<RecordBuf>, ) -> Result<ConsensusOutput, Error>

Encode RecordBufs to raw bytes and delegate to consensus_reads.

Errors

Returns an error if consensus calling fails on the provided records.

Trait Implementations

impl ConsensusCaller for CodecConsensusCaller

Implementation of the ConsensusCaller trait for CODEC consensus calling.

This allows CodecConsensusCaller to be used polymorphically with other consensus callers (e.g., VanillaUmiConsensusCaller, DuplexConsensusCaller).

fn consensus_reads( &mut self, records: Vec<Vec<u8>>, ) -> Result<ConsensusOutput, Error>

Takes a group of raw-byte BAM records with the same UMI and generates consensus reads.

fn total_reads(&self) -> usize

Returns the total number of input reads examined by the consensus caller

fn total_filtered(&self) -> usize

Returns the total number of reads filtered/rejected for any reason

fn consensus_reads_constructed(&self) -> usize

Returns the number of consensus reads constructed by this caller

fn statistics(&self) -> ConsensusCallingStats

Returns statistics about the consensus calling process

fn log_statistics(&self)

Logs statistics about consensus calling to the logger