Expand description
Standalone simulator for CIRI-toolkit full-length reconstruction fixtures.
The simulator is intentionally separate from the user-facing ciri
pipeline. It reads FASTA/GTF directly, samples circular isoforms and linear
background reads, writes paired FASTQ, emits a linear-only annotation GTF, and
records two truth tables: one row per circRNA and one row per read pair. The
output contract follows docs/06-simulation-truth-design.md and is designed
for CIRI-AS-style internal-structure/full-length isoform validation rather
than for reproducing the historical Perl simulator files.
Structs§
- Simulate
Args - Command-line options for the standalone simulator.
- Simulation
Summary - User-facing summary returned by one simulator run.
Functions§
- run
- Loads annotation/reference data, simulates reads, and writes all formal outputs.