--- a/test-data/mode_mp_output1.gff	Sat Jan 21 14:40:25 2017 -0500
+++ b/test-data/mode_mp_output1.gff	Mon Nov 06 23:19:50 2017 -0500
@@ -1,56 +1,56 @@
-chr1	cwpair	.	87182	87183	5699.0	.	.	cw_distance=51
-chr1	cwpair	.	123	124	4204.0	.	.	cw_distance=52
-chr1	cwpair	.	299	300	3296.0	.	.	cw_distance=68
-chr1	cwpair	.	229749	229750	3235.0	.	.	cw_distance=36
-chr1	cwpair	.	87138	87139	3164.0	.	.	cw_distance=60
-chr1	cwpair	.	197	198	3062.0	.	.	cw_distance=55
-chr1	cwpair	.	59	60	2881.0	.	.	cw_distance=2
-chr1	cwpair	.	92601	92602	2836.0	.	.	cw_distance=96
-chr1	cwpair	.	241	242	2689.0	.	.	cw_distance=60
-chr1	cwpair	.	265	266	2474.0	.	.	cw_distance=48
-chr1	cwpair	.	156	157	2177.0	.	.	cw_distance=59
-chr1	cwpair	.	70792	70793	2146.0	.	.	cw_distance=12
-chr1	cwpair	.	6218	6219	2125.0	.	.	cw_distance=91
-chr1	cwpair	.	87212	87213	2073.0	.	.	cw_distance=63
-chr1	cwpair	.	86982	86983	2013.0	.	.	cw_distance=37
-chr1	cwpair	.	229772	229773	1995.0	.	.	cw_distance=43
-chr1	cwpair	.	87070	87071	1903.0	.	.	cw_distance=82
-chr1	cwpair	.	155079	155080	1573.0	.	.	cw_distance=83
-chr1	cwpair	.	92421	92422	1388.0	.	.	cw_distance=0
-chr1	cwpair	.	185109	185110	1371.0	.	.	cw_distance=46
-chr1	cwpair	.	6454	6455	1249.0	.	.	cw_distance=63
-chr1	cwpair	.	25305	25306	1183.0	.	.	cw_distance=99
-chr1	cwpair	.	139230	139231	1179.0	.	.	cw_distance=15
-chr1	cwpair	.	87035	87036	972.0	.	.	cw_distance=47
-chr1	cwpair	.	55548	55549	956.0	.	.	cw_distance=86
-chr1	cwpair	.	350	351	885.0	.	.	cw_distance=66
-chr1	cwpair	.	72805	72806	869.0	.	.	cw_distance=29
-chr1	cwpair	.	22580	22581	863.0	.	.	cw_distance=-2
-chr1	cwpair	.	463	464	802.0	.	.	cw_distance=30
-chr1	cwpair	.	19213	19214	778.0	.	.	cw_distance=-25
-chr1	cwpair	.	113782	113783	716.0	.	.	cw_distance=-20
-chr1	cwpair	.	138876	138877	711.0	.	.	cw_distance=-4
-chr1	cwpair	.	72731	72732	710.0	.	.	cw_distance=100
-chr1	cwpair	.	389	390	707.0	.	.	cw_distance=62
-chr1	cwpair	.	95955	95956	689.0	.	.	cw_distance=51
-chr1	cwpair	.	134230	134231	659.0	.	.	cw_distance=100
-chr1	cwpair	.	170134	170135	657.0	.	.	cw_distance=10
-chr1	cwpair	.	228672	228673	626.0	.	.	cw_distance=58
-chr1	cwpair	.	65160	65161	618.0	.	.	cw_distance=-4
-chr1	cwpair	.	106047	106048	572.0	.	.	cw_distance=7
-chr1	cwpair	.	59228	59229	565.0	.	.	cw_distance=56
-chr1	cwpair	.	173276	173277	546.0	.	.	cw_distance=8
-chr1	cwpair	.	31670	31671	490.0	.	.	cw_distance=66
-chr1	cwpair	.	32483	32484	478.0	.	.	cw_distance=48
-chr1	cwpair	.	92657	92658	447.0	.	.	cw_distance=33
-chr1	cwpair	.	6714	6715	433.0	.	.	cw_distance=-4
-chr1	cwpair	.	136369	136370	365.0	.	.	cw_distance=-14
-chr1	cwpair	.	417	418	362.0	.	.	cw_distance=78
-chr1	cwpair	.	39237	39238	362.0	.	.	cw_distance=61
-chr1	cwpair	.	627	628	247.0	.	.	cw_distance=33
-chr1	cwpair	.	98551	98552	122.0	.	.	cw_distance=27
-chr1	cwpair	.	180331	180332	97.0	.	.	cw_distance=82
-chr1	cwpair	.	230151	230152	75.0	.	.	cw_distance=63
-chr1	cwpair	.	230166	230167	30.0	.	.	cw_distance=-13
-chr1	cwpair	.	96919	96920	12.0	.	.	cw_distance=3
-chr1	cwpair	.	230148	230149	10.0	.	.	cw_distance=-13
+chr1	cwpair	.	87162	87163	5531.0	.	.	cw_distance=11.0
+chr1	cwpair	.	229759	229760	4531.0	.	.	cw_distance=16.0
+chr1	cwpair	.	123	124	4204.0	.	.	cw_distance=52.0
+chr1	cwpair	.	277	278	4138.0	.	.	cw_distance=24.0
+chr1	cwpair	.	218	219	4022.0	.	.	cw_distance=14.0
+chr1	cwpair	.	87194	87195	3643.0	.	.	cw_distance=27.0
+chr1	cwpair	.	59	60	2881.0	.	.	cw_distance=2.0
+chr1	cwpair	.	256	257	2424.0	.	.	cw_distance=30.0
+chr1	cwpair	.	92645	92646	2397.0	.	.	cw_distance=8.0
+chr1	cwpair	.	87109	87110	2259.0	.	.	cw_distance=3.0
+chr1	cwpair	.	156	157	2177.0	.	.	cw_distance=59.0
+chr1	cwpair	.	70792	70793	2146.0	.	.	cw_distance=12.0
+chr1	cwpair	.	6218	6219	2125.0	.	.	cw_distance=91.0
+chr1	cwpair	.	86982	86983	2013.0	.	.	cw_distance=37.0
+chr1	cwpair	.	155079	155080	1573.0	.	.	cw_distance=83.0
+chr1	cwpair	.	92421	92422	1388.0	.	.	cw_distance=0.0
+chr1	cwpair	.	185109	185110	1371.0	.	.	cw_distance=46.0
+chr1	cwpair	.	6454	6455	1249.0	.	.	cw_distance=63.0
+chr1	cwpair	.	87044	87045	1191.0	.	.	cw_distance=30.0
+chr1	cwpair	.	25305	25306	1183.0	.	.	cw_distance=99.0
+chr1	cwpair	.	139230	139231	1179.0	.	.	cw_distance=15.0
+chr1	cwpair	.	325	326	1171.0	.	.	cw_distance=16.0
+chr1	cwpair	.	55548	55549	956.0	.	.	cw_distance=86.0
+chr1	cwpair	.	370	371	899.0	.	.	cw_distance=25.0
+chr1	cwpair	.	72805	72806	869.0	.	.	cw_distance=29.0
+chr1	cwpair	.	22580	22581	863.0	.	.	cw_distance=-2.0
+chr1	cwpair	.	92567	92568	789.0	.	.	cw_distance=28.0
+chr1	cwpair	.	19213	19214	778.0	.	.	cw_distance=-25.0
+chr1	cwpair	.	113782	113783	716.0	.	.	cw_distance=-20.0
+chr1	cwpair	.	138876	138877	711.0	.	.	cw_distance=-4.0
+chr1	cwpair	.	72731	72732	710.0	.	.	cw_distance=100.0
+chr1	cwpair	.	229762	229763	699.0	.	.	cw_distance=63.0
+chr1	cwpair	.	95955	95956	689.0	.	.	cw_distance=51.0
+chr1	cwpair	.	134230	134231	659.0	.	.	cw_distance=100.0
+chr1	cwpair	.	170134	170135	657.0	.	.	cw_distance=10.0
+chr1	cwpair	.	228672	228673	626.0	.	.	cw_distance=58.0
+chr1	cwpair	.	65160	65161	618.0	.	.	cw_distance=-4.0
+chr1	cwpair	.	106047	106048	572.0	.	.	cw_distance=7.0
+chr1	cwpair	.	477	478	566.0	.	.	cw_distance=1.0
+chr1	cwpair	.	59228	59229	565.0	.	.	cw_distance=56.0
+chr1	cwpair	.	173276	173277	546.0	.	.	cw_distance=8.0
+chr1	cwpair	.	452	453	504.0	.	.	cw_distance=8.0
+chr1	cwpair	.	31670	31671	490.0	.	.	cw_distance=66.0
+chr1	cwpair	.	32483	32484	478.0	.	.	cw_distance=48.0
+chr1	cwpair	.	6714	6715	433.0	.	.	cw_distance=-4.0
+chr1	cwpair	.	136369	136370	365.0	.	.	cw_distance=-14.0
+chr1	cwpair	.	39237	39238	362.0	.	.	cw_distance=61.0
+chr1	cwpair	.	388	389	359.0	.	.	cw_distance=20.0
+chr1	cwpair	.	627	628	247.0	.	.	cw_distance=33.0
+chr1	cwpair	.	98551	98552	122.0	.	.	cw_distance=27.0
+chr1	cwpair	.	180286	180287	63.0	.	.	cw_distance=-8.0
+chr1	cwpair	.	230178	230179	56.0	.	.	cw_distance=10.0
+chr1	cwpair	.	230131	230132	44.0	.	.	cw_distance=22.0
+chr1	cwpair	.	230157	230158	15.0	.	.	cw_distance=5.0
+chr1	cwpair	.	96919	96920	12.0	.	.	cw_distance=3.0
+chr1	cwpair	.	197535	197536	5.0	.	.	cw_distance=73.0