Crate yara_mapper_sys 

Low-level FFI bindings to the YARA read mapper C++ shim.

This crate compiles a C++ shim layer that wraps YARA’s SeqAn2-based template code and exposes a C-compatible API for loading FM indices, ingesting reads, and retrieving alignment results as flat structs.

Structs

YaraAlignmentRecord

A single alignment record returned by the mapper.

YaraIndexerHandle

Opaque handle to a YARA Indexer instance. Allocated and owned by the C++ side; freed via yara_indexer_close.

YaraIndexerOptions

Indexer configuration passed to yara_indexer_build.

YaraMapperHandle

Opaque handle to a fully-configured YARA Mapper instance. Allocated and owned by the C++ side; freed via yara_mapper_close.

YaraMapperOptions

Mapper configuration passed to yara_mapper_open.

YaraReadBatch

A batch of paired-end reads to map.

Functions

yara_indexer_build^⚠

Build an FM index from a FASTA file. Returns null on error, with error_buf populated.

yara_indexer_close^⚠

Free the indexer handle and all associated memory.

yara_indexer_contig_count^⚠

Number of contigs in the built index.

yara_indexer_contig_length^⚠

Length of the contig at idx.

yara_indexer_contig_name^⚠

Name of the contig at idx. The returned pointer is valid for the lifetime of the handle.

yara_mapper_close^⚠

Free the mapper and all associated memory.

yara_mapper_contig_count^⚠

Number of reference contigs in the loaded index.

yara_mapper_contig_length^⚠

Length of the contig at idx.

yara_mapper_contig_name^⚠

Name of the contig at idx. The returned pointer is valid for the lifetime of the handle.

yara_mapper_free_record^⚠

Free a single record’s C++-owned memory (cigar, seq, qual, xa).

yara_mapper_free_records^⚠

Free a record batch’s C++-owned memory (cigar arrays, seq/qual strings, XA strings). Must be called after processing each batch.

yara_mapper_map_paired^⚠

Map a batch of paired-end reads. Returns the number of output records written to out, or -1 on error.

yara_mapper_open^⚠

Create a mapper and load the FM index. Returns null on error, with error_buf populated.