Expand description
Scan2: second-pass rescue, candidate validation, and FSJ counting.
This stage consumes the Java-compatible BSJ output from Scan1, rebuilds the de-duplicated candidate indexes expected by Java CIRI3, and then revisits the input alignments to rescue additional support while counting FSJ evidence.
Structsยง
- Candidate
Breakpoint - Scan2
- Core logic for the second scan pass.
- Scan2
Segment Artifacts - Temporary sidecar paths produced while Scan2 feeds the segments stage.