def is_paired(aln):
    """
    Input:
        pysam.AlignedSegment

    "properly" paired (correct reference and orientation)
    
    NB: This is used instead of the properly_paired flag as rare superamplicons
    fall outside the expected insert size distribution and are not marked as such. 
    
    NB: It does not check if the orientation is FR as RF orientations are discarded due
    to no biological sequence.

    Returns:
        Boolean
    
    """
    return aln.is_paired and aln.is_reverse != aln.mate_is_reverse