Crate ciri_toolkit 

CIRI-toolkit: High-performance circular RNA identification.

This crate provides a high-performance Rust implementation of the CIRI3 algorithm for identifying circular RNA back-spliced junctions (BSJ) from SAM or BAM alignment files. It supports multi-threaded processing, deterministic read assignment, and parity-oriented optimization against the Java reference implementation.

Modules

annotation

Annotation module: GTF parsing and exon boundary mapping.

circ_catalog

External circRNA catalog parsing for multi-sample second-pass runs.

ciri_as

Post-Summary circRNA read reconstruction entry points.

cli

Command-line front ends for the two public binaries.

fasta

FASTA module: High-speed sequence loading with Needletail.

index_compare

Splice-signal lookup used by Scan1.

is_bsj_hg2

Validator module: Reproduces the core validation logic of Java CIRI3.

misd

Port of CIRI3 Misd.java.

runtime

Runtime diagnostics configuration shared by Scan1/Scan2/validator code.

sam_bam

Multi-format I/O module: SAM and BAM support.

scan1

Scan1: first-pass BSJ candidate discovery.

scan2

Scan2: second-pass rescue, candidate validation, and FSJ counting.

simulator

Standalone simulator for CIRI-toolkit full-length reconstruction fixtures.

summary

Summary module aligned to Java Summary.java logic.

tests

High-level integration-oriented tests for the public pipeline stages.

utils

Utility module: Common bioinformatics and string processing functions.