Struct YaraMapper 

pub struct YaraMapper { /* private fields */ }

Handle to a loaded YARA mapper with a pre-built FM index.

The mapper is configured at construction time and can be used to map multiple batches of reads. The FM index stays loaded in memory for the lifetime of this handle.

Thread safety

The underlying C++ mapper uses OpenMP internally but is not safe for concurrent map_paired calls. YaraMapper is Send but not Sync.

Implementations

impl YaraMapper

pub fn open<P: AsRef<Path>>( index_prefix: P, options: &MapperOptions, ) -> Result<Self, YaraError>

Open a pre-built YARA index and create a mapper.

index_prefix is the path prefix used when building the index (e.g., ref/hla.fasta if the index files are ref/hla.fasta.yara.*).

Errors

Returns YaraError::IndexOpen if the index files cannot be found or loaded, or if index_prefix contains non-UTF-8 characters or null bytes.

pub fn map_paired( &self, reads: &ReadBatch, ) -> Result<Vec<YaraRecord>, YaraError>

Map a batch of paired-end reads and return alignment records.

The returned records include primary and (depending on options) secondary alignments, plus unmapped entries for reads that could not be aligned.

Errors

Returns YaraError::Mapping if the underlying C++ mapper encounters an error during alignment.

pub fn contig_count(&self) -> usize

Number of reference contigs in the loaded index.

pub fn contig_names(&self) -> Vec<String>

Reference contig names (for SAM/BAM header construction).

pub fn contig_lengths(&self) -> Vec<usize>

Reference contig lengths.

Trait Implementations

impl Drop for YaraMapper

fn drop(&mut self)

Executes the destructor for this type.

impl Send for YaraMapper