Function alignment_short_cs 

pub fn alignment_short_cs(
    cigar: &str,
    seq: &str,
    chrom: &str,
    pos: i32,
    reference: &HashMap<String, String>,
) -> String

Builds a minimap2-compatible short-form cs payload for one mapper alignment.

This is used by Scan1/Scan2 sidecars to retain allele bases without spilling full read sequences. The payload intentionally stays in standard short-form cs syntax here; CIRI’s custom <...> back-splice op is added later when the post-Summary chain materializer joins selected blocks across a BSJ boundary.