Invalid dovetail overlaps orientation in GFA2 Edges

[dlobba]

The recognition of dovetail overlaps in GFA2 edges has been done has follow, considering the positions
of the two sequences (beg1, end1, beg2 and end2 respectively) the edge represents a dovetail overlap
if: beg1=0 or end1=x$ and beg2=0 or end2=y$. If this is true then extremes taken into account
are computed as the one described in GFA1, if segment1 is + then from_segment_end is R otherwise
is L. If segment2 is + then to_segment_end is L otherwise R.

This is not correct in GFA2 since a dovetail overlap could be, erroneously, such this one:
E l12 1+ 2+ 0 3 0 3 *
So this situations must be solved in a different way then the one used by GFA1.

[dlobba]

I have analyzed this situation more carefully.
E l12 1+ 2+ 0 3 0 3 *
It's not a dovetail overlap situation, but it's a partial (general) overlap correctly described
by a generic edge line. The GFA1 specification couldn't describe this situation.

So, I've read again the specification and I have changed the assumption for a dovetail overlap
in GFA2 edges.
The statement:" For example a GFA edge which encodes what is called a dovetail overlap (because two ends overlap) is a GFA2 edge where either beg1 = 0 or end1 = x$ and either beg2 = 0 or end2 = y$."

Is incorrect to me, since could lead to the situation described in this issue post.

The interpretation I have used is:
"An Edge encodes a dovetail overlap if beg1 = 0 and end2 = y$ (so the end of the second segment
overlaps with the begin of the first one) or end1 = x$ and beg2 = 0 (this is the normal Link case)."
So, after this preamble, I have to check which of the two segments is the "from_segment" (regarding the
dovetail overlap) and apply the sign rules as Link describes.

The code for this is the following (after checking that the edge is a dovetail overlap):

    def _set_segments_end_link(self):
        if self.from_orn == "+":
            self._from_segment_end = "R"
        else:
            self._from_segment_end = "L"
        if self.to_orn == "+":
            self._to_segment_end = "L"
        else:
            self._to_segment_end = "R"

    def _set_segments_end_edge(self):
        beg1, end1 = self.from_positions
        beg2, end2 = self.to_positions

        # the dovetail is from the end of from_node to
        # the beginning of to_node, just like a GFA1 Link
        if beg2 == "0":
            self._set_segments_end_link()
        else: # dovetail between end of to_node and begin of from_node
            if self.from_orn == "+":
                self._from_segment_end = "L"
            else:
                self._from_segment_end = "R"
            if self.to_orn == "+":
                self._to_segment_end = "R"
            else:
                self._to_segment_end = "L"