Module misd 

Port of CIRI3 Misd.java.

This module parses CIGAR strings using an efficient manual state machine instead of regex to determine the alignment type (SM, MS, SMS) and mapped length. The structure is intentionally close to the Java logic because Scan1 and Scan2 both use the returned shape to decide candidate ordering and rescue behavior.

Functions

misd

Parses a CIGAR string and returns CIRI-style classification metadata.