Disambiguate Strand column in alignment table file

[pbordron]

Is your feature request related to a problem? Please describe.

When an alignment is produced, we can obtain an alignment table such as the one from rat_vs_mouse:

Query	Target	Strand	Q-len	Q-start	Q-stop	T-len	T-start	T-stop
1	7	+	282763074	1562214	278905080	145441459	3149354	145340809
10	11	+	112626471	871555	112549653	122082543	20782251	121881087
11	16	+	90463843	3408	90410991	98207768	14701487	97986567
12	5	+	52716770	444771	52711413	151834684	7179396	151733900
13	1	+	114033958	72114	114033923	195471971	3755552	195221714
14	5	+	115493446	61596	107942287	151834684	5781530	150707500
15	14	+	111246239	4272	111246073	124902244	3803626	124767944
16	8	+	90668790	15971169	90660996	129401213	4708816	84672738
17	13	+	90843779	78145	90843273	120421639	3521785	94048446
18	18	+	88201929	779907	87645915	90702639	7926082	90597557
19	8	+	62275575	396	62188497	129401213	19589839	129186170
2	3	+	266435125	398472	266430715	160039680	3388228	159939029
20	10	+	56205956	695269	56155841	130694993	7283877	110730930
3	2	+	177699992	57447	177456239	182113224	11867910	181878389
4	6	+	184226339	3121023	184226265	149736546	3298672	149586006
5	4	+	173707219	594811	173681704	156508116	3424260	156255887
6	12	+	147991367	123953	147977513	120129022	3246248	120028303
7	15	+	145729302	8028201	145712591	104043685	12574823	103941715
8	9	+	133307652	399915	133291248	124595110	3273802	124411199
9	1	+	122095297	639036	121396551	195471971	4996331	183206415
X	X	+	159970021	472338	159969676	171031299	3320330	169984084
Y	Y	+	3310458	149940	1405717	91744698	721336	2793886
KL568162.1	1	+	10937627	354299	10655860	195471971	4992111	162673012
KL568139.1	5	+	9752924	686641	9735034	151834684	108796043	125864912
KL568161.1	5	+	7627431	975484	6915410	151834684	108796043	125864912
KL568148.1	5	+	6483517	2473416	5461819	151834684	108796043	125864912
KL568157.1	5	+	5447879	536476	5440996	151834684	125771973	125864912
KL568160.1	5	+	4317250	69406	672501	151834684	108796043	125864912
KL568151.1	5	+	3931032	1809013	3208994	151834684	125798887	125864912
KL568149.1	5	+	3292674	4831	1927913	151834684	109084506	125864912
KL568141.1	1	+	2733323	512630	2673387	195471971	4992429	162673012

Some associations have positive slope, some others have negative slope, but Strand column is alway +.
The "sort" button will change orientation of some contigs to "diagonalize" the dotplot. It is what Strand column encodes for. Right clicking on intersection between contig and chromosome and then clicking on "Reverse Query" will also change the Strand sign

Query	Target	Strand	Q-len	Q-start	Q-stop	T-len	T-start	T-stop
9	1	+	122095297	639036	121396551	195471971	4996331	183206415
KL568162.1	1	+	10937627	354299	10655860	195471971	4992111	162673012
KL568141.1	1	+	2733323	512630	2673387	195471971	4992429	162673012
13	1	+	114033958	72114	114033923	195471971	3755552	195221714
20	10	+	56205956	695269	56155841	130694993	7283877	110730930
10	11	+	112626471	871555	112549653	122082543	20782251	121881087
6	12	+	147991367	123953	147977513	120129022	3246248	120028303
17	13	+	90843779	78145	90843273	120421639	3521785	94048446
15	14	+	111246239	4272	111246073	124902244	3803626	124767944
7	15	+	145729302	8028201	145712591	104043685	12574823	103941715
11	16	+	90463843	3408	90410991	98207768	14701487	97986567
18	18	+	88201929	779907	87645915	90702639	7926082	90597557
3	2	+	177699992	57447	177456239	182113224	11867910	181878389
2	3	+	266435125	398472	266430715	160039680	3388228	159939029
5	4	+	173707219	594811	173681704	156508116	3424260	156255887
14	5	+	115493446	61596	107942287	151834684	5781530	150707500
KL568160.1	5	+	4317250	69406	672501	151834684	108796043	125864912
KL568148.1	5	+	6483517	2473416	5461819	151834684	108796043	125864912
KL568161.1	5	+	7627431	975484	6915410	151834684	108796043	125864912
KL568139.1	5	+	9752924	686641	9735034	151834684	108796043	125864912
KL568149.1	5	+	3292674	4831	1927913	151834684	109084506	125864912
KL568157.1	5	+	5447879	536476	5440996	151834684	125771973	125864912
KL568151.1	5	+	3931032	1809013	3208994	151834684	125798887	125864912
12	5	-	52716770	5357	52271999	151834684	7179396	151733900
4	6	+	184226339	3121023	184226265	149736546	3298672	149586006
1	7	+	282763074	1562214	278905080	145441459	3149354	145340809
16	8	+	90668790	15971169	90660996	129401213	4708816	84672738
19	8	+	62275575	396	62188497	129401213	19589839	129186170
8	9	+	133307652	399915	133291248	124595110	3273802	124411199
X	X	+	159970021	472338	159969676	171031299	3320330	169984084
Y	Y	+	3310458	149940	1405717	91744698	721336	2793886

Some users think that Strand column describes the slope between contig on query and chromosome on target at any time.
It is true when the contigs are "sorted" automatically and/or manually, but not before.

Describe the solution you'd like

• Document this behavior in D-Genies help and format description.
  How to produce an association table:

  1. click on 'sort',
  2. adjust by hand by right clicking on segments with negative slope and choose 'reverse query',
  3. 'export -> association table'

• Maybe disable the 'export -> association table' button until the sorting is done.

• Maybe change column name to something more explicit