Changes gff output to always use + strand coordinates in the Target attribute (i.e. coords in the input sequence).
This is vaguely defined in the gff3 specification, but seems like more sensible thing to do, because neither the main coordinates in the gff file are inverted when the strand is -.
This also matches the behavior of gmap, which is handy when using output of those two mappers interchangeably.
Also contains a little fix escaping the == intron marks according to gff3 spec.