Function ms1_to_ms2_map 

pub fn ms1_to_ms2_map(
    ms1_len: usize,
    ms2_to_best_ms1: &[Option<usize>],
) -> Vec<Vec<usize>>

Build an MS1 → Vec map from a winner list (ms2→best ms1). Returns a Vec<Vec> with length ms1.len(), where each entry lists MS2 indices.