Function base_at_ref_pos 

pub fn base_at_ref_pos(
    gapped_query: &[u8],
    gapped_ref: &[u8],
    ref_start: usize,
    ref_pos: usize,
) -> Option<u8>

Return the query base at a given reference position, or None if the position is outside the aligned region or the query has a deletion ('-') there.