Generator.py problem: Always mismatch for reverse strand

[zhenzuo2]

def _incorp_snp(seq, var, transId, pos, offset, isReverse=False):
    """
    Incorporates a snp into the given :class:`~epytope.Core.Transcript.Transcript` sequence (side effect!).

    :param list(char) seq: :class:`~epytope.Core.Transcript.Transcript` sequence as a list
    :param  var: The snp variant to incorporate
    :type var: :class:`~epytope.Core.Variant.Variant`
    :param str transId: The transcript ID of seq
    :param int pos: The position of the variant
    :param int offset: The offset which has to be added onto the :class:`~epytope.Core.Transcript.Transcript` position of
                       the :class:`~epytope.Core.Variant.Variant`
    :param bool isReverse: Defines whether current transcript is reverse oriented
    :return: The the modified offset
    :rtype: int
    """
    if VariationType.SNP != var.type:
        raise TypeError("%s is not a SNP"%str(var))
   
    ref = var.ref[::-1].translate(COMPLEMENT) if isReverse else var.ref
    obs = var.obs[::-1].translate(COMPLEMENT) if isReverse else var.obs

    #print transId, len(seq), var.get_transcript_position(transId)-1
    if seq[pos] != ref:
        warnings.warn("For %s bp does not match ref of assigned variant %s. Pos %i, var ref %s, seq ref %s " % (
        transId, str(var), pos, ref,
        seq[pos]))

    seq[pos] = obs

    return offset

This warnings always show up for reverse strand