Module scan1 

Scan1: first-pass BSJ candidate discovery.

This module owns the initial read-group scan over SAM/BAM input and emits the Java-compatible BSJ intermediate file consumed by Scan2 and Summary. Performance work here is deliberately limited to ingestion, sharding, and temporary allocation control; the candidate semantics still follow Java CIRI3.

Structs

Scan1

First-pass BSJ detector.