# HG changeset patch
# User iuc
# Date 1609197568 0
# Node ID f1912d5575df56722b8febddcd604608ba0161c6
# Parent  326f9c294b092b15d9a3896c4f2bf8b0c9b6fe14
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 5bef07276e14b38cca31ef724d0b4d2f55809715"

diff -r 326f9c294b09 -r f1912d5575df macros.xml
--- a/macros.xml	Fri May 03 07:50:37 2019 -0400
+++ b/macros.xml	Mon Dec 28 23:19:28 2020 +0000
@@ -6,7 +6,7 @@
             <yield />
         </requirements>
     </xml>
-    <token name="@VERSION@">2.31.10</token>
+    <token name="@VERSION@">2.31.11</token>
 
     <xml name="citations">
         <citations>
diff -r 326f9c294b09 -r f1912d5575df test-data/Dfam_partial_test.h5
Binary file test-data/Dfam_partial_test.h5 has changed
diff -r 326f9c294b09 -r f1912d5575df test-data/annot_dfam.gff3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annot_dfam.gff3	Mon Dec 28 23:19:28 2020 +0000
@@ -0,0 +1,43 @@
+##gff-version 3
+HS08198	maker	gene	352	1848	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0;Name=maker-HS08198-exonerate_est2genome-gene-0.0
+HS08198	maker	mRNA	352	1848	2869	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1;Parent=maker-HS08198-exonerate_est2genome-gene-0.0;Name=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=70|1|1|1|0|0|7|0|192
+HS08198	maker	exon	352	397	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:9;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	421	582	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:10;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	812	894	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:11;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	1053	1123	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:12;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	1208	1315	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:13;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	1587	1688	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:14;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	1772	1848	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:15;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	five_prime_UTR	352	397	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	five_prime_UTR	421	444	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	445	582	.	+	0	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	812	894	.	+	0	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	1053	1123	.	+	1	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	1208	1315	.	+	2	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	1587	1688	.	+	2	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	1772	1848	.	+	2	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+###
+###
+HS04636	maker	gene	1813	6903	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0;Name=maker-HS04636-exonerate_est2genome-gene-0.0
+HS04636	maker	mRNA	1813	6903	8728	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;Parent=maker-HS04636-exonerate_est2genome-gene-0.0;Name=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=49|1|1|1|0|0|9|0|572
+HS04636	maker	exon	1813	1934	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:0;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	2055	2198	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:1;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	2852	2995	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:2;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	3426	3607	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:3;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	4340	4423	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:4;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	4543	4789	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:5;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	5072	5358	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:6;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	5860	6007	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:7;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	6494	6903	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:8;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	five_prime_UTR	1813	1861	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	1862	1934	.	+	0	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	2055	2198	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	2852	2995	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	3426	3607	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	4340	4423	.	+	0	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	4543	4789	.	+	0	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	5072	5358	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	5860	6007	.	+	0	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	6494	6903	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+###
+###
diff -r 326f9c294b09 -r f1912d5575df test-data/annot_dfam_up.gff3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annot_dfam_up.gff3	Mon Dec 28 23:19:28 2020 +0000
@@ -0,0 +1,43 @@
+##gff-version 3
+HS08198	maker	gene	352	1848	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0;Name=maker-HS08198-exonerate_est2genome-gene-0.0
+HS08198	maker	mRNA	352	1848	2869	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1;Parent=maker-HS08198-exonerate_est2genome-gene-0.0;Name=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=70|1|1|1|0|0|7|0|192
+HS08198	maker	exon	352	397	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:9;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	421	582	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:10;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	812	894	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:11;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	1053	1123	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:12;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	1208	1315	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:13;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	1587	1688	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:14;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	1772	1848	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:15;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	five_prime_UTR	352	397	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	five_prime_UTR	421	444	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	445	582	.	+	0	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	812	894	.	+	0	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	1053	1123	.	+	1	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	1208	1315	.	+	2	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	1587	1688	.	+	2	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	1772	1848	.	+	2	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+###
+###
+HS04636	maker	gene	1813	6903	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0;Name=maker-HS04636-exonerate_est2genome-gene-0.0
+HS04636	maker	mRNA	1813	6903	8728	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;Parent=maker-HS04636-exonerate_est2genome-gene-0.0;Name=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=49|1|1|1|0|0|9|0|572
+HS04636	maker	exon	1813	1934	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:0;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	2055	2198	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:1;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	2852	2995	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:2;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	3426	3607	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:3;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	4340	4423	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:4;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	4543	4789	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:5;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	5072	5358	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:6;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	5860	6007	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:7;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	6494	6903	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:8;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	five_prime_UTR	1813	1861	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	1862	1934	.	+	0	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	2055	2198	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	2852	2995	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	3426	3607	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	4340	4423	.	+	0	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	4543	4789	.	+	0	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	5072	5358	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	5860	6007	.	+	0	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	6494	6903	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+###
+###
diff -r 326f9c294b09 -r f1912d5575df test-data/annot_human.gff3
--- a/test-data/annot_human.gff3	Fri May 03 07:50:37 2019 -0400
+++ b/test-data/annot_human.gff3	Mon Dec 28 23:19:28 2020 +0000
@@ -1,44 +1,42 @@
 ##gff-version 3
-HS08198	maker	gene	352	1848	.	+	.	ID=maker-HS08198-augustus-gene-0.4;Name=maker-HS08198-augustus-gene-0.4
-HS08198	maker	mRNA	352	1848	.	+	.	ID=maker-HS08198-augustus-gene-0.4-mRNA-1;Parent=maker-HS08198-augustus-gene-0.4;Name=maker-HS08198-augustus-gene-0.4-mRNA-1;_AED=0.00;_eAED=0.00;_QI=70|1|1|1|0.83|0.85|7|0|192
-HS08198	maker	exon	352	397	.	+	.	ID=maker-HS08198-augustus-gene-0.4-mRNA-1:exon:10;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1
-HS08198	maker	exon	421	582	.	+	.	ID=maker-HS08198-augustus-gene-0.4-mRNA-1:exon:11;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1
-HS08198	maker	exon	812	894	.	+	.	ID=maker-HS08198-augustus-gene-0.4-mRNA-1:exon:12;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1
-HS08198	maker	exon	1053	1123	.	+	.	ID=maker-HS08198-augustus-gene-0.4-mRNA-1:exon:13;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1
-HS08198	maker	exon	1208	1315	.	+	.	ID=maker-HS08198-augustus-gene-0.4-mRNA-1:exon:14;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1
-HS08198	maker	exon	1587	1688	.	+	.	ID=maker-HS08198-augustus-gene-0.4-mRNA-1:exon:15;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1
-HS08198	maker	exon	1772	1848	.	+	.	ID=maker-HS08198-augustus-gene-0.4-mRNA-1:exon:16;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1
-HS08198	maker	five_prime_UTR	352	397	.	+	.	ID=maker-HS08198-augustus-gene-0.4-mRNA-1:five_prime_utr;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1
-HS08198	maker	five_prime_UTR	421	444	.	+	.	ID=maker-HS08198-augustus-gene-0.4-mRNA-1:five_prime_utr;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1
-HS08198	maker	CDS	445	582	.	+	0	ID=maker-HS08198-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1
-HS08198	maker	CDS	812	894	.	+	0	ID=maker-HS08198-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1
-HS08198	maker	CDS	1053	1123	.	+	1	ID=maker-HS08198-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1
-HS08198	maker	CDS	1208	1315	.	+	2	ID=maker-HS08198-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1
-HS08198	maker	CDS	1587	1688	.	+	2	ID=maker-HS08198-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1
-HS08198	maker	CDS	1772	1848	.	+	2	ID=maker-HS08198-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS08198-augustus-gene-0.4-mRNA-1
-###
+HS08198	maker	gene	352	1848	.	+	.	ID=maker-HS08198-augustus-gene-0.1;Name=maker-HS08198-augustus-gene-0.1
+HS08198	maker	mRNA	352	1848	.	+	.	ID=maker-HS08198-augustus-gene-0.1-mRNA-1;Parent=maker-HS08198-augustus-gene-0.1;Name=maker-HS08198-augustus-gene-0.1-mRNA-1;_AED=0.00;_eAED=0.00;_QI=70|1|1|1|0.83|0.85|7|0|192
+HS08198	maker	exon	352	397	.	+	.	ID=maker-HS08198-augustus-gene-0.1-mRNA-1:exon:10;Parent=maker-HS08198-augustus-gene-0.1-mRNA-1
+HS08198	maker	exon	421	582	.	+	.	ID=maker-HS08198-augustus-gene-0.1-mRNA-1:exon:11;Parent=maker-HS08198-augustus-gene-0.1-mRNA-1
+HS08198	maker	exon	812	894	.	+	.	ID=maker-HS08198-augustus-gene-0.1-mRNA-1:exon:12;Parent=maker-HS08198-augustus-gene-0.1-mRNA-1
+HS08198	maker	exon	1053	1123	.	+	.	ID=maker-HS08198-augustus-gene-0.1-mRNA-1:exon:13;Parent=maker-HS08198-augustus-gene-0.1-mRNA-1
+HS08198	maker	exon	1208	1315	.	+	.	ID=maker-HS08198-augustus-gene-0.1-mRNA-1:exon:14;Parent=maker-HS08198-augustus-gene-0.1-mRNA-1
+HS08198	maker	exon	1587	1688	.	+	.	ID=maker-HS08198-augustus-gene-0.1-mRNA-1:exon:15;Parent=maker-HS08198-augustus-gene-0.1-mRNA-1
+HS08198	maker	exon	1772	1848	.	+	.	ID=maker-HS08198-augustus-gene-0.1-mRNA-1:exon:16;Parent=maker-HS08198-augustus-gene-0.1-mRNA-1
+HS08198	maker	five_prime_UTR	352	397	.	+	.	ID=maker-HS08198-augustus-gene-0.1-mRNA-1:five_prime_utr;Parent=maker-HS08198-augustus-gene-0.1-mRNA-1
+HS08198	maker	five_prime_UTR	421	444	.	+	.	ID=maker-HS08198-augustus-gene-0.1-mRNA-1:five_prime_utr;Parent=maker-HS08198-augustus-gene-0.1-mRNA-1
+HS08198	maker	CDS	445	582	.	+	0	ID=maker-HS08198-augustus-gene-0.1-mRNA-1:cds;Parent=maker-HS08198-augustus-gene-0.1-mRNA-1
+HS08198	maker	CDS	812	894	.	+	0	ID=maker-HS08198-augustus-gene-0.1-mRNA-1:cds;Parent=maker-HS08198-augustus-gene-0.1-mRNA-1
+HS08198	maker	CDS	1053	1123	.	+	1	ID=maker-HS08198-augustus-gene-0.1-mRNA-1:cds;Parent=maker-HS08198-augustus-gene-0.1-mRNA-1
+HS08198	maker	CDS	1208	1315	.	+	2	ID=maker-HS08198-augustus-gene-0.1-mRNA-1:cds;Parent=maker-HS08198-augustus-gene-0.1-mRNA-1
+HS08198	maker	CDS	1587	1688	.	+	2	ID=maker-HS08198-augustus-gene-0.1-mRNA-1:cds;Parent=maker-HS08198-augustus-gene-0.1-mRNA-1
+HS08198	maker	CDS	1772	1848	.	+	2	ID=maker-HS08198-augustus-gene-0.1-mRNA-1:cds;Parent=maker-HS08198-augustus-gene-0.1-mRNA-1
 ###
-HS04636	maker	gene	966	6903	.	+	.	ID=maker-HS04636-augustus-gene-0.4;Name=maker-HS04636-augustus-gene-0.4
-HS04636	maker	mRNA	966	6903	.	+	.	ID=maker-HS04636-augustus-gene-0.4-mRNA-1;Parent=maker-HS04636-augustus-gene-0.4;Name=maker-HS04636-augustus-gene-0.4-mRNA-1;_AED=0.02;_eAED=0.02;_QI=0|0.88|0.8|0.9|1|1|10|0|604
-HS04636	maker	exon	966	1017	.	+	.	ID=maker-HS04636-augustus-gene-0.4-mRNA-1:exon:0;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1
-HS04636	maker	exon	1818	1934	.	+	.	ID=maker-HS04636-augustus-gene-0.4-mRNA-1:exon:1;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1
-HS04636	maker	exon	2055	2198	.	+	.	ID=maker-HS04636-augustus-gene-0.4-mRNA-1:exon:2;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1
-HS04636	maker	exon	2852	2995	.	+	.	ID=maker-HS04636-augustus-gene-0.4-mRNA-1:exon:3;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1
-HS04636	maker	exon	3426	3607	.	+	.	ID=maker-HS04636-augustus-gene-0.4-mRNA-1:exon:4;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1
-HS04636	maker	exon	4340	4423	.	+	.	ID=maker-HS04636-augustus-gene-0.4-mRNA-1:exon:5;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1
-HS04636	maker	exon	4543	4789	.	+	.	ID=maker-HS04636-augustus-gene-0.4-mRNA-1:exon:6;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1
-HS04636	maker	exon	5072	5358	.	+	.	ID=maker-HS04636-augustus-gene-0.4-mRNA-1:exon:7;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1
-HS04636	maker	exon	5860	6007	.	+	.	ID=maker-HS04636-augustus-gene-0.4-mRNA-1:exon:8;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1
-HS04636	maker	exon	6494	6903	.	+	.	ID=maker-HS04636-augustus-gene-0.4-mRNA-1:exon:9;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1
-HS04636	maker	CDS	966	1017	.	+	0	ID=maker-HS04636-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1
-HS04636	maker	CDS	1818	1934	.	+	2	ID=maker-HS04636-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1
-HS04636	maker	CDS	2055	2198	.	+	2	ID=maker-HS04636-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1
-HS04636	maker	CDS	2852	2995	.	+	2	ID=maker-HS04636-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1
-HS04636	maker	CDS	3426	3607	.	+	2	ID=maker-HS04636-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1
-HS04636	maker	CDS	4340	4423	.	+	0	ID=maker-HS04636-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1
-HS04636	maker	CDS	4543	4789	.	+	0	ID=maker-HS04636-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1
-HS04636	maker	CDS	5072	5358	.	+	2	ID=maker-HS04636-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1
-HS04636	maker	CDS	5860	6007	.	+	0	ID=maker-HS04636-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1
-HS04636	maker	CDS	6494	6903	.	+	2	ID=maker-HS04636-augustus-gene-0.4-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.4-mRNA-1
+HS04636	maker	gene	966	6903	.	+	.	ID=maker-HS04636-augustus-gene-0.3;Name=maker-HS04636-augustus-gene-0.3
+HS04636	maker	mRNA	966	6903	.	+	.	ID=maker-HS04636-augustus-gene-0.3-mRNA-1;Parent=maker-HS04636-augustus-gene-0.3;Name=maker-HS04636-augustus-gene-0.3-mRNA-1;_AED=0.02;_eAED=0.02;_QI=0|0.88|0.8|0.9|1|1|10|0|604
+HS04636	maker	exon	966	1017	.	+	.	ID=maker-HS04636-augustus-gene-0.3-mRNA-1:exon:0;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1
+HS04636	maker	exon	1818	1934	.	+	.	ID=maker-HS04636-augustus-gene-0.3-mRNA-1:exon:1;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1
+HS04636	maker	exon	2055	2198	.	+	.	ID=maker-HS04636-augustus-gene-0.3-mRNA-1:exon:2;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1
+HS04636	maker	exon	2852	2995	.	+	.	ID=maker-HS04636-augustus-gene-0.3-mRNA-1:exon:3;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1
+HS04636	maker	exon	3426	3607	.	+	.	ID=maker-HS04636-augustus-gene-0.3-mRNA-1:exon:4;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1
+HS04636	maker	exon	4340	4423	.	+	.	ID=maker-HS04636-augustus-gene-0.3-mRNA-1:exon:5;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1
+HS04636	maker	exon	4543	4789	.	+	.	ID=maker-HS04636-augustus-gene-0.3-mRNA-1:exon:6;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1
+HS04636	maker	exon	5072	5358	.	+	.	ID=maker-HS04636-augustus-gene-0.3-mRNA-1:exon:7;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1
+HS04636	maker	exon	5860	6007	.	+	.	ID=maker-HS04636-augustus-gene-0.3-mRNA-1:exon:8;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1
+HS04636	maker	exon	6494	6903	.	+	.	ID=maker-HS04636-augustus-gene-0.3-mRNA-1:exon:9;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1
+HS04636	maker	CDS	966	1017	.	+	0	ID=maker-HS04636-augustus-gene-0.3-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1
+HS04636	maker	CDS	1818	1934	.	+	2	ID=maker-HS04636-augustus-gene-0.3-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1
+HS04636	maker	CDS	2055	2198	.	+	2	ID=maker-HS04636-augustus-gene-0.3-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1
+HS04636	maker	CDS	2852	2995	.	+	2	ID=maker-HS04636-augustus-gene-0.3-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1
+HS04636	maker	CDS	3426	3607	.	+	2	ID=maker-HS04636-augustus-gene-0.3-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1
+HS04636	maker	CDS	4340	4423	.	+	0	ID=maker-HS04636-augustus-gene-0.3-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1
+HS04636	maker	CDS	4543	4789	.	+	0	ID=maker-HS04636-augustus-gene-0.3-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1
+HS04636	maker	CDS	5072	5358	.	+	2	ID=maker-HS04636-augustus-gene-0.3-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1
+HS04636	maker	CDS	5860	6007	.	+	0	ID=maker-HS04636-augustus-gene-0.3-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1
+HS04636	maker	CDS	6494	6903	.	+	2	ID=maker-HS04636-augustus-gene-0.3-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.3-mRNA-1
 ###
-###
diff -r 326f9c294b09 -r f1912d5575df test-data/annot_model.gff3
--- a/test-data/annot_model.gff3	Fri May 03 07:50:37 2019 -0400
+++ b/test-data/annot_model.gff3	Mon Dec 28 23:19:28 2020 +0000
@@ -1,41 +1,40 @@
 ##gff-version 3
-HS08198	maker	gene	352	1848	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0;Name=maker-HS08198-exonerate_est2genome-gene-0.0
-HS08198	maker	mRNA	352	1848	2869	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1;Parent=maker-HS08198-exonerate_est2genome-gene-0.0;Name=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=70|1|1|1|0|0|7|0|192
-HS08198	maker	exon	352	397	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:9;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
-HS08198	maker	exon	421	582	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:10;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
-HS08198	maker	exon	812	894	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:11;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
-HS08198	maker	exon	1053	1123	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:12;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
-HS08198	maker	exon	1208	1315	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:13;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
-HS08198	maker	exon	1587	1688	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:14;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
-HS08198	maker	exon	1772	1848	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:15;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
-HS08198	maker	five_prime_UTR	352	397	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
-HS08198	maker	five_prime_UTR	421	444	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
-HS08198	maker	CDS	445	582	.	+	0	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
-HS08198	maker	CDS	812	894	.	+	0	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
-HS08198	maker	CDS	1053	1123	.	+	1	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
-HS08198	maker	CDS	1208	1315	.	+	2	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
-HS08198	maker	CDS	1587	1688	.	+	2	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
-HS08198	maker	CDS	1772	1848	.	+	2	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	gene	99	1848	.	+	.	ID=maker-HS08198-snap-gene-0.3;Name=maker-HS08198-snap-gene-0.3
+HS08198	maker	mRNA	99	1848	.	+	.	ID=maker-HS08198-snap-gene-0.3-mRNA-1;Parent=maker-HS08198-snap-gene-0.3;Name=maker-HS08198-snap-gene-0.3-mRNA-1;_AED=0.07;_eAED=0.07;_QI=0|0.66|0.57|0.85|0.83|0.85|7|0|190
+HS08198	maker	exon	99	107	.	+	.	ID=maker-HS08198-snap-gene-0.3-mRNA-1:exon:9;Parent=maker-HS08198-snap-gene-0.3-mRNA-1
+HS08198	maker	exon	421	582	.	+	.	ID=maker-HS08198-snap-gene-0.3-mRNA-1:exon:10;Parent=maker-HS08198-snap-gene-0.3-mRNA-1
+HS08198	maker	exon	812	874	.	+	.	ID=maker-HS08198-snap-gene-0.3-mRNA-1:exon:11;Parent=maker-HS08198-snap-gene-0.3-mRNA-1
+HS08198	maker	exon	1072	1123	.	+	.	ID=maker-HS08198-snap-gene-0.3-mRNA-1:exon:12;Parent=maker-HS08198-snap-gene-0.3-mRNA-1
+HS08198	maker	exon	1208	1315	.	+	.	ID=maker-HS08198-snap-gene-0.3-mRNA-1:exon:13;Parent=maker-HS08198-snap-gene-0.3-mRNA-1
+HS08198	maker	exon	1587	1688	.	+	.	ID=maker-HS08198-snap-gene-0.3-mRNA-1:exon:14;Parent=maker-HS08198-snap-gene-0.3-mRNA-1
+HS08198	maker	exon	1772	1848	.	+	.	ID=maker-HS08198-snap-gene-0.3-mRNA-1:exon:15;Parent=maker-HS08198-snap-gene-0.3-mRNA-1
+HS08198	maker	CDS	99	107	.	+	0	ID=maker-HS08198-snap-gene-0.3-mRNA-1:cds;Parent=maker-HS08198-snap-gene-0.3-mRNA-1
+HS08198	maker	CDS	421	582	.	+	0	ID=maker-HS08198-snap-gene-0.3-mRNA-1:cds;Parent=maker-HS08198-snap-gene-0.3-mRNA-1
+HS08198	maker	CDS	812	874	.	+	0	ID=maker-HS08198-snap-gene-0.3-mRNA-1:cds;Parent=maker-HS08198-snap-gene-0.3-mRNA-1
+HS08198	maker	CDS	1072	1123	.	+	0	ID=maker-HS08198-snap-gene-0.3-mRNA-1:cds;Parent=maker-HS08198-snap-gene-0.3-mRNA-1
+HS08198	maker	CDS	1208	1315	.	+	2	ID=maker-HS08198-snap-gene-0.3-mRNA-1:cds;Parent=maker-HS08198-snap-gene-0.3-mRNA-1
+HS08198	maker	CDS	1587	1688	.	+	2	ID=maker-HS08198-snap-gene-0.3-mRNA-1:cds;Parent=maker-HS08198-snap-gene-0.3-mRNA-1
+HS08198	maker	CDS	1772	1848	.	+	2	ID=maker-HS08198-snap-gene-0.3-mRNA-1:cds;Parent=maker-HS08198-snap-gene-0.3-mRNA-1
 ###
-HS04636	maker	gene	1813	6903	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0;Name=maker-HS04636-exonerate_est2genome-gene-0.0
-HS04636	maker	mRNA	1813	6903	8728	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;Parent=maker-HS04636-exonerate_est2genome-gene-0.0;Name=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=49|1|1|1|0|0|9|0|572
-HS04636	maker	exon	1813	1934	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:0;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	exon	2055	2198	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:1;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	exon	2852	2995	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:2;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	exon	3426	3607	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:3;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	exon	4340	4423	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:4;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	exon	4543	4789	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:5;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	exon	5072	5358	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:6;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	exon	5860	6007	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:7;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	exon	6494	6903	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:8;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	five_prime_UTR	1813	1861	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	CDS	1862	1934	.	+	0	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	CDS	2055	2198	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	CDS	2852	2995	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	CDS	3426	3607	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	CDS	4340	4423	.	+	0	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	CDS	4543	4789	.	+	0	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	CDS	5072	5358	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	CDS	5860	6007	.	+	0	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	CDS	6494	6903	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	gene	1813	6903	.	+	.	ID=maker-HS04636-augustus-gene-0.0;Name=maker-HS04636-augustus-gene-0.0
+HS04636	maker	mRNA	1813	6903	.	+	.	ID=maker-HS04636-augustus-gene-0.0-mRNA-1;Parent=maker-HS04636-augustus-gene-0.0;Name=maker-HS04636-augustus-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=49|1|1|1|1|1|9|0|572
+HS04636	maker	exon	1813	1934	.	+	.	ID=maker-HS04636-augustus-gene-0.0-mRNA-1:exon:0;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1
+HS04636	maker	exon	2055	2198	.	+	.	ID=maker-HS04636-augustus-gene-0.0-mRNA-1:exon:1;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1
+HS04636	maker	exon	2852	2995	.	+	.	ID=maker-HS04636-augustus-gene-0.0-mRNA-1:exon:2;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1
+HS04636	maker	exon	3426	3607	.	+	.	ID=maker-HS04636-augustus-gene-0.0-mRNA-1:exon:3;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1
+HS04636	maker	exon	4340	4423	.	+	.	ID=maker-HS04636-augustus-gene-0.0-mRNA-1:exon:4;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1
+HS04636	maker	exon	4543	4789	.	+	.	ID=maker-HS04636-augustus-gene-0.0-mRNA-1:exon:5;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1
+HS04636	maker	exon	5072	5358	.	+	.	ID=maker-HS04636-augustus-gene-0.0-mRNA-1:exon:6;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1
+HS04636	maker	exon	5860	6007	.	+	.	ID=maker-HS04636-augustus-gene-0.0-mRNA-1:exon:7;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1
+HS04636	maker	exon	6494	6903	.	+	.	ID=maker-HS04636-augustus-gene-0.0-mRNA-1:exon:8;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1
+HS04636	maker	five_prime_UTR	1813	1861	.	+	.	ID=maker-HS04636-augustus-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1
+HS04636	maker	CDS	1862	1934	.	+	0	ID=maker-HS04636-augustus-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1
+HS04636	maker	CDS	2055	2198	.	+	2	ID=maker-HS04636-augustus-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1
+HS04636	maker	CDS	2852	2995	.	+	2	ID=maker-HS04636-augustus-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1
+HS04636	maker	CDS	3426	3607	.	+	2	ID=maker-HS04636-augustus-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1
+HS04636	maker	CDS	4340	4423	.	+	0	ID=maker-HS04636-augustus-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1
+HS04636	maker	CDS	4543	4789	.	+	0	ID=maker-HS04636-augustus-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1
+HS04636	maker	CDS	5072	5358	.	+	2	ID=maker-HS04636-augustus-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1
+HS04636	maker	CDS	5860	6007	.	+	0	ID=maker-HS04636-augustus-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1
+HS04636	maker	CDS	6494	6903	.	+	2	ID=maker-HS04636-augustus-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-augustus-gene-0.0-mRNA-1
 ###
diff -r 326f9c294b09 -r f1912d5575df test-data/annot_repbase.gff3
--- a/test-data/annot_repbase.gff3	Fri May 03 07:50:37 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,43 +0,0 @@
-##gff-version 3
-HS08198	maker	gene	352	1848	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0;Name=maker-HS08198-exonerate_est2genome-gene-0.0
-HS08198	maker	mRNA	352	1848	2869	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1;Parent=maker-HS08198-exonerate_est2genome-gene-0.0;Name=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=70|1|1|1|0|0|7|0|192
-HS08198	maker	exon	352	397	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:9;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
-HS08198	maker	exon	421	582	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:10;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
-HS08198	maker	exon	812	894	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:11;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
-HS08198	maker	exon	1053	1123	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:12;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
-HS08198	maker	exon	1208	1315	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:13;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
-HS08198	maker	exon	1587	1688	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:14;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
-HS08198	maker	exon	1772	1848	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:15;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
-HS08198	maker	five_prime_UTR	352	397	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
-HS08198	maker	five_prime_UTR	421	444	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
-HS08198	maker	CDS	445	582	.	+	0	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
-HS08198	maker	CDS	812	894	.	+	0	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
-HS08198	maker	CDS	1053	1123	.	+	1	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
-HS08198	maker	CDS	1208	1315	.	+	2	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
-HS08198	maker	CDS	1587	1688	.	+	2	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
-HS08198	maker	CDS	1772	1848	.	+	2	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
-###
-###
-HS04636	maker	gene	1813	6903	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0;Name=maker-HS04636-exonerate_est2genome-gene-0.0
-HS04636	maker	mRNA	1813	6903	8728	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;Parent=maker-HS04636-exonerate_est2genome-gene-0.0;Name=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=49|1|1|1|0|0|9|0|572
-HS04636	maker	exon	1813	1934	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:0;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	exon	2055	2198	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:1;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	exon	2852	2995	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:2;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	exon	3426	3607	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:3;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	exon	4340	4423	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:4;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	exon	4543	4789	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:5;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	exon	5072	5358	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:6;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	exon	5860	6007	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:7;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	exon	6494	6903	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:8;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	five_prime_UTR	1813	1861	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	CDS	1862	1934	.	+	0	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	CDS	2055	2198	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	CDS	2852	2995	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	CDS	3426	3607	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	CDS	4340	4423	.	+	0	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	CDS	4543	4789	.	+	0	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	CDS	5072	5358	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	CDS	5860	6007	.	+	0	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-HS04636	maker	CDS	6494	6903	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
-###
-###
diff -r 326f9c294b09 -r f1912d5575df test-data/evidences_human.gff3
--- a/test-data/evidences_human.gff3	Fri May 03 07:50:37 2019 -0400
+++ b/test-data/evidences_human.gff3	Mon Dec 28 23:19:28 2020 +0000
@@ -1,99 +1,79 @@
 ##gff-version 3
 HS08198	.	contig	1	2344	.	.	.	ID=HS08198;Name=HS08198
-HS08198	augustus_masked	match	445	1848	1	+	.	ID=HS08198:hit:15:4.5.0.0;Name=augustus_masked-HS08198-abinit-gene-0.2-mRNA-1
-HS08198	augustus_masked	match_part	445	582	1	+	.	ID=HS08198:hsp:62:4.5.0.0;Parent=HS08198:hit:15:4.5.0.0;Target=augustus_masked-HS08198-abinit-gene-0.2-mRNA-1 1 138 +;Gap=M138
-HS08198	augustus_masked	match_part	812	894	1	+	.	ID=HS08198:hsp:63:4.5.0.0;Parent=HS08198:hit:15:4.5.0.0;Target=augustus_masked-HS08198-abinit-gene-0.2-mRNA-1 139 221 +;Gap=M83
-HS08198	augustus_masked	match_part	1053	1123	1	+	.	ID=HS08198:hsp:64:4.5.0.0;Parent=HS08198:hit:15:4.5.0.0;Target=augustus_masked-HS08198-abinit-gene-0.2-mRNA-1 222 292 +;Gap=M71
-HS08198	augustus_masked	match_part	1208	1315	1	+	.	ID=HS08198:hsp:65:4.5.0.0;Parent=HS08198:hit:15:4.5.0.0;Target=augustus_masked-HS08198-abinit-gene-0.2-mRNA-1 293 400 +;Gap=M108
-HS08198	augustus_masked	match_part	1587	1688	1	+	.	ID=HS08198:hsp:66:4.5.0.0;Parent=HS08198:hit:15:4.5.0.0;Target=augustus_masked-HS08198-abinit-gene-0.2-mRNA-1 401 502 +;Gap=M102
-HS08198	augustus_masked	match_part	1772	1848	1	+	.	ID=HS08198:hsp:67:4.5.0.0;Parent=HS08198:hit:15:4.5.0.0;Target=augustus_masked-HS08198-abinit-gene-0.2-mRNA-1 503 579 +;Gap=M77
-HS08198	snap_masked	match	99	1848	233.121	+	.	ID=HS08198:hit:16:4.5.0.0;Name=snap_masked-HS08198-abinit-gene-0.1-mRNA-1
-HS08198	snap_masked	match_part	99	107	-2.800	+	.	ID=HS08198:hsp:68:4.5.0.0;Parent=HS08198:hit:16:4.5.0.0;Target=snap_masked-HS08198-abinit-gene-0.1-mRNA-1 1 9 +;Gap=M9
-HS08198	snap_masked	match_part	421	582	45.298	+	.	ID=HS08198:hsp:69:4.5.0.0;Parent=HS08198:hit:16:4.5.0.0;Target=snap_masked-HS08198-abinit-gene-0.1-mRNA-1 10 171 +;Gap=M162
-HS08198	snap_masked	match_part	812	874	24.711	+	.	ID=HS08198:hsp:70:4.5.0.0;Parent=HS08198:hit:16:4.5.0.0;Target=snap_masked-HS08198-abinit-gene-0.1-mRNA-1 172 234 +;Gap=M63
-HS08198	snap_masked	match_part	1024	1123	34.281	+	.	ID=HS08198:hsp:71:4.5.0.0;Parent=HS08198:hit:16:4.5.0.0;Target=snap_masked-HS08198-abinit-gene-0.1-mRNA-1 235 334 +;Gap=M100
-HS08198	snap_masked	match_part	1208	1315	53.852	+	.	ID=HS08198:hsp:72:4.5.0.0;Parent=HS08198:hit:16:4.5.0.0;Target=snap_masked-HS08198-abinit-gene-0.1-mRNA-1 335 442 +;Gap=M108
-HS08198	snap_masked	match_part	1587	1688	41.983	+	.	ID=HS08198:hsp:73:4.5.0.0;Parent=HS08198:hit:16:4.5.0.0;Target=snap_masked-HS08198-abinit-gene-0.1-mRNA-1 443 544 +;Gap=M102
-HS08198	snap_masked	match_part	1772	1848	35.796	+	.	ID=HS08198:hsp:74:4.5.0.0;Parent=HS08198:hit:16:4.5.0.0;Target=snap_masked-HS08198-abinit-gene-0.1-mRNA-1 545 621 +;Gap=M77
+HS08198	augustus	match	445	1848	1	+	.	ID=HS08198:hit:6:4.5.0.0;Name=augustus-HS08198-abinit-gene-0.2-mRNA-1
+HS08198	augustus	match_part	445	582	1	+	.	ID=HS08198:hsp:53:4.5.0.0;Parent=HS08198:hit:6:4.5.0.0;Target=augustus-HS08198-abinit-gene-0.2-mRNA-1 1 138 +;Gap=M138
+HS08198	augustus	match_part	812	894	1	+	.	ID=HS08198:hsp:54:4.5.0.0;Parent=HS08198:hit:6:4.5.0.0;Target=augustus-HS08198-abinit-gene-0.2-mRNA-1 139 221 +;Gap=M83
+HS08198	augustus	match_part	1053	1123	1	+	.	ID=HS08198:hsp:55:4.5.0.0;Parent=HS08198:hit:6:4.5.0.0;Target=augustus-HS08198-abinit-gene-0.2-mRNA-1 222 292 +;Gap=M71
+HS08198	augustus	match_part	1208	1315	1	+	.	ID=HS08198:hsp:56:4.5.0.0;Parent=HS08198:hit:6:4.5.0.0;Target=augustus-HS08198-abinit-gene-0.2-mRNA-1 293 400 +;Gap=M108
+HS08198	augustus	match_part	1587	1688	1	+	.	ID=HS08198:hsp:57:4.5.0.0;Parent=HS08198:hit:6:4.5.0.0;Target=augustus-HS08198-abinit-gene-0.2-mRNA-1 401 502 +;Gap=M102
+HS08198	augustus	match_part	1772	1848	1	+	.	ID=HS08198:hsp:58:4.5.0.0;Parent=HS08198:hit:6:4.5.0.0;Target=augustus-HS08198-abinit-gene-0.2-mRNA-1 503 579 +;Gap=M77
+HS08198	snap	match	99	1848	233.121	+	.	ID=HS08198:hit:7:4.5.0.0;Name=snap-HS08198-abinit-gene-0.4-mRNA-1
+HS08198	snap	match_part	99	107	-2.800	+	.	ID=HS08198:hsp:59:4.5.0.0;Parent=HS08198:hit:7:4.5.0.0;Target=snap-HS08198-abinit-gene-0.4-mRNA-1 1 9 +;Gap=M9
+HS08198	snap	match_part	421	582	45.298	+	.	ID=HS08198:hsp:60:4.5.0.0;Parent=HS08198:hit:7:4.5.0.0;Target=snap-HS08198-abinit-gene-0.4-mRNA-1 10 171 +;Gap=M162
+HS08198	snap	match_part	812	874	24.711	+	.	ID=HS08198:hsp:61:4.5.0.0;Parent=HS08198:hit:7:4.5.0.0;Target=snap-HS08198-abinit-gene-0.4-mRNA-1 172 234 +;Gap=M63
+HS08198	snap	match_part	1024	1123	34.281	+	.	ID=HS08198:hsp:62:4.5.0.0;Parent=HS08198:hit:7:4.5.0.0;Target=snap-HS08198-abinit-gene-0.4-mRNA-1 235 334 +;Gap=M100
+HS08198	snap	match_part	1208	1315	53.852	+	.	ID=HS08198:hsp:63:4.5.0.0;Parent=HS08198:hit:7:4.5.0.0;Target=snap-HS08198-abinit-gene-0.4-mRNA-1 335 442 +;Gap=M108
+HS08198	snap	match_part	1587	1688	41.983	+	.	ID=HS08198:hsp:64:4.5.0.0;Parent=HS08198:hit:7:4.5.0.0;Target=snap-HS08198-abinit-gene-0.4-mRNA-1 443 544 +;Gap=M102
+HS08198	snap	match_part	1772	1848	35.796	+	.	ID=HS08198:hsp:65:4.5.0.0;Parent=HS08198:hit:7:4.5.0.0;Target=snap-HS08198-abinit-gene-0.4-mRNA-1 545 621 +;Gap=M77
 ###
-HS08198	repeatmasker	match	578	651	13	+	.	ID=HS08198:hit:12:1.3.0.0;Name=species:%28AGAAGGT%29n|genus:Simple_repeat;Target=species:%28AGAAGGT%29n|genus:Simple_repeat 1 75 +
-HS08198	repeatmasker	match_part	578	651	13	+	.	ID=HS08198:hsp:47:1.3.0.0;Parent=HS08198:hit:12:1.3.0.0;Target=species:%2528AGAAGGT%2529n|genus:Simple_repeat 1 75 +
-###
-HS08198	blastn	expressed_sequence_match	444	1848	140	+	.	ID=HS08198:hit:13:3.2.0.0;Name=HS08198.g2
-HS08198	blastn	match_part	444	583	140	+	.	ID=HS08198:hsp:48:3.2.0.0;Parent=HS08198:hit:13:3.2.0.0;Target=HS08198.g2 79 218 +;Gap=M140
-HS08198	blastn	match_part	445	523	79	+	.	ID=HS08198:hsp:49:3.2.0.0;Parent=HS08198:hit:13:3.2.0.0;Target=HS08198.g2 1 79 +;Gap=M79
-HS08198	blastn	match_part	808	895	88	+	.	ID=HS08198:hsp:50:3.2.0.0;Parent=HS08198:hit:13:3.2.0.0;Target=HS08198.g2 214 301 +;Gap=M88
-HS08198	blastn	match_part	1053	1123	71	+	.	ID=HS08198:hsp:51:3.2.0.0;Parent=HS08198:hit:13:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71
-HS08198	blastn	match_part	1206	1315	110	+	.	ID=HS08198:hsp:52:3.2.0.0;Parent=HS08198:hit:13:3.2.0.0;Target=HS08198.g2 370 479 +;Gap=M110
-HS08198	blastn	match_part	1586	1689	104	+	.	ID=HS08198:hsp:53:3.2.0.0;Parent=HS08198:hit:13:3.2.0.0;Target=HS08198.g2 479 582 +;Gap=M104
-HS08198	blastn	match_part	1771	1848	78	+	.	ID=HS08198:hsp:54:3.2.0.0;Parent=HS08198:hit:13:3.2.0.0;Target=HS08198.g2 581 658 +;Gap=M78
-HS08198	est2genome	expressed_sequence_match	352	1848	2869	+	.	ID=HS08198:hit:14:3.2.0.0;Name=HS08198.g2
-HS08198	est2genome	match_part	352	397	2869	+	.	ID=HS08198:hsp:55:3.2.0.0;Parent=HS08198:hit:14:3.2.0.0;Target=HS08198.g2 3 52 +;Gap=M18 D1 M2 I4 M10 I1 M15
-HS08198	est2genome	match_part	421	582	2869	+	.	ID=HS08198:hsp:56:3.2.0.0;Parent=HS08198:hit:14:3.2.0.0;Target=HS08198.g2 53 217 +;Gap=M4 I2 M3 I3 M5 D1 M9 D1 M139
-HS08198	est2genome	match_part	812	894	2869	+	.	ID=HS08198:hsp:57:3.2.0.0;Parent=HS08198:hit:14:3.2.0.0;Target=HS08198.g2 218 300 +;Gap=M83
-HS08198	est2genome	match_part	1053	1123	2869	+	.	ID=HS08198:hsp:58:3.2.0.0;Parent=HS08198:hit:14:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71
-HS08198	est2genome	match_part	1208	1315	2869	+	.	ID=HS08198:hsp:59:3.2.0.0;Parent=HS08198:hit:14:3.2.0.0;Target=HS08198.g2 372 479 +;Gap=M108
-HS08198	est2genome	match_part	1587	1688	2869	+	.	ID=HS08198:hsp:60:3.2.0.0;Parent=HS08198:hit:14:3.2.0.0;Target=HS08198.g2 480 581 +;Gap=M102
-HS08198	est2genome	match_part	1772	1848	2869	+	.	ID=HS08198:hsp:61:3.2.0.0;Parent=HS08198:hit:14:3.2.0.0;Target=HS08198.g2 582 658 +;Gap=M77
+HS08198	blastn	expressed_sequence_match	444	1848	140	+	.	ID=HS08198:hit:4:3.2.0.0;Name=HS08198.g2
+HS08198	blastn	match_part	444	583	140	+	.	ID=HS08198:hsp:39:3.2.0.0;Parent=HS08198:hit:4:3.2.0.0;Target=HS08198.g2 79 218 +;Gap=M140
+HS08198	blastn	match_part	445	523	79	+	.	ID=HS08198:hsp:40:3.2.0.0;Parent=HS08198:hit:4:3.2.0.0;Target=HS08198.g2 1 79 +;Gap=M79
+HS08198	blastn	match_part	808	895	88	+	.	ID=HS08198:hsp:41:3.2.0.0;Parent=HS08198:hit:4:3.2.0.0;Target=HS08198.g2 214 301 +;Gap=M88
+HS08198	blastn	match_part	1053	1123	71	+	.	ID=HS08198:hsp:42:3.2.0.0;Parent=HS08198:hit:4:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71
+HS08198	blastn	match_part	1206	1315	110	+	.	ID=HS08198:hsp:43:3.2.0.0;Parent=HS08198:hit:4:3.2.0.0;Target=HS08198.g2 370 479 +;Gap=M110
+HS08198	blastn	match_part	1586	1689	104	+	.	ID=HS08198:hsp:44:3.2.0.0;Parent=HS08198:hit:4:3.2.0.0;Target=HS08198.g2 479 582 +;Gap=M104
+HS08198	blastn	match_part	1771	1848	78	+	.	ID=HS08198:hsp:45:3.2.0.0;Parent=HS08198:hit:4:3.2.0.0;Target=HS08198.g2 581 658 +;Gap=M78
+HS08198	est2genome	expressed_sequence_match	352	1848	2869	+	.	ID=HS08198:hit:5:3.2.0.0;Name=HS08198.g2
+HS08198	est2genome	match_part	352	397	2869	+	.	ID=HS08198:hsp:46:3.2.0.0;Parent=HS08198:hit:5:3.2.0.0;Target=HS08198.g2 3 52 +;Gap=M18 D1 M2 I4 M10 I1 M15
+HS08198	est2genome	match_part	421	582	2869	+	.	ID=HS08198:hsp:47:3.2.0.0;Parent=HS08198:hit:5:3.2.0.0;Target=HS08198.g2 53 217 +;Gap=M4 I2 M3 I3 M5 D1 M9 D1 M139
+HS08198	est2genome	match_part	812	894	2869	+	.	ID=HS08198:hsp:48:3.2.0.0;Parent=HS08198:hit:5:3.2.0.0;Target=HS08198.g2 218 300 +;Gap=M83
+HS08198	est2genome	match_part	1053	1123	2869	+	.	ID=HS08198:hsp:49:3.2.0.0;Parent=HS08198:hit:5:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71
+HS08198	est2genome	match_part	1208	1315	2869	+	.	ID=HS08198:hsp:50:3.2.0.0;Parent=HS08198:hit:5:3.2.0.0;Target=HS08198.g2 372 479 +;Gap=M108
+HS08198	est2genome	match_part	1587	1688	2869	+	.	ID=HS08198:hsp:51:3.2.0.0;Parent=HS08198:hit:5:3.2.0.0;Target=HS08198.g2 480 581 +;Gap=M102
+HS08198	est2genome	match_part	1772	1848	2869	+	.	ID=HS08198:hsp:52:3.2.0.0;Parent=HS08198:hit:5:3.2.0.0;Target=HS08198.g2 582 658 +;Gap=M77
 HS04636	.	contig	1	9453	.	.	.	ID=HS04636;Name=HS04636
-HS04636	augustus_masked	match	966	6903	1	+	.	ID=HS04636:hit:10:4.5.0.0;Name=augustus_masked-HS04636-abinit-gene-0.3-mRNA-1
-HS04636	augustus_masked	match_part	966	1017	1	+	.	ID=HS04636:hsp:27:4.5.0.0;Parent=HS04636:hit:10:4.5.0.0;Target=augustus_masked-HS04636-abinit-gene-0.3-mRNA-1 1 52 +;Gap=M52
-HS04636	augustus_masked	match_part	1818	1934	1	+	.	ID=HS04636:hsp:28:4.5.0.0;Parent=HS04636:hit:10:4.5.0.0;Target=augustus_masked-HS04636-abinit-gene-0.3-mRNA-1 53 169 +;Gap=M117
-HS04636	augustus_masked	match_part	2055	2198	1	+	.	ID=HS04636:hsp:29:4.5.0.0;Parent=HS04636:hit:10:4.5.0.0;Target=augustus_masked-HS04636-abinit-gene-0.3-mRNA-1 170 313 +;Gap=M144
-HS04636	augustus_masked	match_part	2852	2995	1	+	.	ID=HS04636:hsp:30:4.5.0.0;Parent=HS04636:hit:10:4.5.0.0;Target=augustus_masked-HS04636-abinit-gene-0.3-mRNA-1 314 457 +;Gap=M144
-HS04636	augustus_masked	match_part	3426	3607	1	+	.	ID=HS04636:hsp:31:4.5.0.0;Parent=HS04636:hit:10:4.5.0.0;Target=augustus_masked-HS04636-abinit-gene-0.3-mRNA-1 458 639 +;Gap=M182
-HS04636	augustus_masked	match_part	4340	4423	1	+	.	ID=HS04636:hsp:32:4.5.0.0;Parent=HS04636:hit:10:4.5.0.0;Target=augustus_masked-HS04636-abinit-gene-0.3-mRNA-1 640 723 +;Gap=M84
-HS04636	augustus_masked	match_part	4543	4789	1	+	.	ID=HS04636:hsp:33:4.5.0.0;Parent=HS04636:hit:10:4.5.0.0;Target=augustus_masked-HS04636-abinit-gene-0.3-mRNA-1 724 970 +;Gap=M247
-HS04636	augustus_masked	match_part	5072	5358	1	+	.	ID=HS04636:hsp:34:4.5.0.0;Parent=HS04636:hit:10:4.5.0.0;Target=augustus_masked-HS04636-abinit-gene-0.3-mRNA-1 971 1257 +;Gap=M287
-HS04636	augustus_masked	match_part	5860	6007	1	+	.	ID=HS04636:hsp:35:4.5.0.0;Parent=HS04636:hit:10:4.5.0.0;Target=augustus_masked-HS04636-abinit-gene-0.3-mRNA-1 1258 1405 +;Gap=M148
-HS04636	augustus_masked	match_part	6494	6903	1	+	.	ID=HS04636:hsp:36:4.5.0.0;Parent=HS04636:hit:10:4.5.0.0;Target=augustus_masked-HS04636-abinit-gene-0.3-mRNA-1 1406 1815 +;Gap=M410
-HS04636	snap_masked	match	1862	6903	761.916	+	.	ID=HS04636:hit:11:4.5.0.0;Name=snap_masked-HS04636-abinit-gene-0.1-mRNA-1
-HS04636	snap_masked	match_part	1862	1867	8.523	+	.	ID=HS04636:hsp:37:4.5.0.0;Parent=HS04636:hit:11:4.5.0.0;Target=snap_masked-HS04636-abinit-gene-0.1-mRNA-1 1 6 +;Gap=M6
-HS04636	snap_masked	match_part	1883	1934	20.348	+	.	ID=HS04636:hsp:38:4.5.0.0;Parent=HS04636:hit:11:4.5.0.0;Target=snap_masked-HS04636-abinit-gene-0.1-mRNA-1 7 58 +;Gap=M52
-HS04636	snap_masked	match_part	2055	2198	69.846	+	.	ID=HS04636:hsp:39:4.5.0.0;Parent=HS04636:hit:11:4.5.0.0;Target=snap_masked-HS04636-abinit-gene-0.1-mRNA-1 59 202 +;Gap=M144
-HS04636	snap_masked	match_part	2852	2995	67.055	+	.	ID=HS04636:hsp:40:4.5.0.0;Parent=HS04636:hit:11:4.5.0.0;Target=snap_masked-HS04636-abinit-gene-0.1-mRNA-1 203 346 +;Gap=M144
-HS04636	snap_masked	match_part	3426	3607	77.942	+	.	ID=HS04636:hsp:41:4.5.0.0;Parent=HS04636:hit:11:4.5.0.0;Target=snap_masked-HS04636-abinit-gene-0.1-mRNA-1 347 528 +;Gap=M182
-HS04636	snap_masked	match_part	4340	4423	47.588	+	.	ID=HS04636:hsp:42:4.5.0.0;Parent=HS04636:hit:11:4.5.0.0;Target=snap_masked-HS04636-abinit-gene-0.1-mRNA-1 529 612 +;Gap=M84
-HS04636	snap_masked	match_part	4543	4789	112.472	+	.	ID=HS04636:hsp:43:4.5.0.0;Parent=HS04636:hit:11:4.5.0.0;Target=snap_masked-HS04636-abinit-gene-0.1-mRNA-1 613 859 +;Gap=M247
-HS04636	snap_masked	match_part	5072	5358	122.974	+	.	ID=HS04636:hsp:44:4.5.0.0;Parent=HS04636:hit:11:4.5.0.0;Target=snap_masked-HS04636-abinit-gene-0.1-mRNA-1 860 1146 +;Gap=M287
-HS04636	snap_masked	match_part	5860	6007	72.046	+	.	ID=HS04636:hsp:45:4.5.0.0;Parent=HS04636:hit:11:4.5.0.0;Target=snap_masked-HS04636-abinit-gene-0.1-mRNA-1 1147 1294 +;Gap=M148
-HS04636	snap_masked	match_part	6494	6903	163.122	+	.	ID=HS04636:hsp:46:4.5.0.0;Parent=HS04636:hit:11:4.5.0.0;Target=snap_masked-HS04636-abinit-gene-0.1-mRNA-1 1295 1704 +;Gap=M410
+HS04636	snap	match	1862	6903	761.916	+	.	ID=HS04636:hit:2:4.5.0.0;Name=snap-HS04636-abinit-gene-0.0-mRNA-1
+HS04636	snap	match_part	1862	1867	8.523	+	.	ID=HS04636:hsp:19:4.5.0.0;Parent=HS04636:hit:2:4.5.0.0;Target=snap-HS04636-abinit-gene-0.0-mRNA-1 1 6 +;Gap=M6
+HS04636	snap	match_part	1883	1934	20.348	+	.	ID=HS04636:hsp:20:4.5.0.0;Parent=HS04636:hit:2:4.5.0.0;Target=snap-HS04636-abinit-gene-0.0-mRNA-1 7 58 +;Gap=M52
+HS04636	snap	match_part	2055	2198	69.846	+	.	ID=HS04636:hsp:21:4.5.0.0;Parent=HS04636:hit:2:4.5.0.0;Target=snap-HS04636-abinit-gene-0.0-mRNA-1 59 202 +;Gap=M144
+HS04636	snap	match_part	2852	2995	67.055	+	.	ID=HS04636:hsp:22:4.5.0.0;Parent=HS04636:hit:2:4.5.0.0;Target=snap-HS04636-abinit-gene-0.0-mRNA-1 203 346 +;Gap=M144
+HS04636	snap	match_part	3426	3607	77.942	+	.	ID=HS04636:hsp:23:4.5.0.0;Parent=HS04636:hit:2:4.5.0.0;Target=snap-HS04636-abinit-gene-0.0-mRNA-1 347 528 +;Gap=M182
+HS04636	snap	match_part	4340	4423	47.588	+	.	ID=HS04636:hsp:24:4.5.0.0;Parent=HS04636:hit:2:4.5.0.0;Target=snap-HS04636-abinit-gene-0.0-mRNA-1 529 612 +;Gap=M84
+HS04636	snap	match_part	4543	4789	112.472	+	.	ID=HS04636:hsp:25:4.5.0.0;Parent=HS04636:hit:2:4.5.0.0;Target=snap-HS04636-abinit-gene-0.0-mRNA-1 613 859 +;Gap=M247
+HS04636	snap	match_part	5072	5358	122.974	+	.	ID=HS04636:hsp:26:4.5.0.0;Parent=HS04636:hit:2:4.5.0.0;Target=snap-HS04636-abinit-gene-0.0-mRNA-1 860 1146 +;Gap=M287
+HS04636	snap	match_part	5860	6007	72.046	+	.	ID=HS04636:hsp:27:4.5.0.0;Parent=HS04636:hit:2:4.5.0.0;Target=snap-HS04636-abinit-gene-0.0-mRNA-1 1147 1294 +;Gap=M148
+HS04636	snap	match_part	6494	6903	163.122	+	.	ID=HS04636:hsp:28:4.5.0.0;Parent=HS04636:hit:2:4.5.0.0;Target=snap-HS04636-abinit-gene-0.0-mRNA-1 1295 1704 +;Gap=M410
+HS04636	augustus	match	966	6903	1	+	.	ID=HS04636:hit:3:4.5.0.0;Name=augustus-HS04636-abinit-gene-0.2-mRNA-1
+HS04636	augustus	match_part	966	1017	1	+	.	ID=HS04636:hsp:29:4.5.0.0;Parent=HS04636:hit:3:4.5.0.0;Target=augustus-HS04636-abinit-gene-0.2-mRNA-1 1 52 +;Gap=M52
+HS04636	augustus	match_part	1818	1934	1	+	.	ID=HS04636:hsp:30:4.5.0.0;Parent=HS04636:hit:3:4.5.0.0;Target=augustus-HS04636-abinit-gene-0.2-mRNA-1 53 169 +;Gap=M117
+HS04636	augustus	match_part	2055	2198	1	+	.	ID=HS04636:hsp:31:4.5.0.0;Parent=HS04636:hit:3:4.5.0.0;Target=augustus-HS04636-abinit-gene-0.2-mRNA-1 170 313 +;Gap=M144
+HS04636	augustus	match_part	2852	2995	1	+	.	ID=HS04636:hsp:32:4.5.0.0;Parent=HS04636:hit:3:4.5.0.0;Target=augustus-HS04636-abinit-gene-0.2-mRNA-1 314 457 +;Gap=M144
+HS04636	augustus	match_part	3426	3607	1	+	.	ID=HS04636:hsp:33:4.5.0.0;Parent=HS04636:hit:3:4.5.0.0;Target=augustus-HS04636-abinit-gene-0.2-mRNA-1 458 639 +;Gap=M182
+HS04636	augustus	match_part	4340	4423	1	+	.	ID=HS04636:hsp:34:4.5.0.0;Parent=HS04636:hit:3:4.5.0.0;Target=augustus-HS04636-abinit-gene-0.2-mRNA-1 640 723 +;Gap=M84
+HS04636	augustus	match_part	4543	4789	1	+	.	ID=HS04636:hsp:35:4.5.0.0;Parent=HS04636:hit:3:4.5.0.0;Target=augustus-HS04636-abinit-gene-0.2-mRNA-1 724 970 +;Gap=M247
+HS04636	augustus	match_part	5072	5358	1	+	.	ID=HS04636:hsp:36:4.5.0.0;Parent=HS04636:hit:3:4.5.0.0;Target=augustus-HS04636-abinit-gene-0.2-mRNA-1 971 1257 +;Gap=M287
+HS04636	augustus	match_part	5860	6007	1	+	.	ID=HS04636:hsp:37:4.5.0.0;Parent=HS04636:hit:3:4.5.0.0;Target=augustus-HS04636-abinit-gene-0.2-mRNA-1 1258 1405 +;Gap=M148
+HS04636	augustus	match_part	6494	6903	1	+	.	ID=HS04636:hsp:38:4.5.0.0;Parent=HS04636:hit:3:4.5.0.0;Target=augustus-HS04636-abinit-gene-0.2-mRNA-1 1406 1815 +;Gap=M410
 ###
-HS04636	repeatmasker	match	3852	3888	12	+	.	ID=HS04636:hit:0:1.3.0.0;Name=species:%28TTGTAAT%29n|genus:Simple_repeat;Target=species:%28TTGTAAT%29n|genus:Simple_repeat 1 37 +
-HS04636	repeatmasker	match_part	3852	3888	12	+	.	ID=HS04636:hsp:0:1.3.0.0;Parent=HS04636:hit:0:1.3.0.0;Target=species:%2528TTGTAAT%2529n|genus:Simple_repeat 1 37 +
-HS04636	repeatmasker	match	4518	4541	17	+	.	ID=HS04636:hit:1:1.3.0.0;Name=species:%28TTTA%29n|genus:Simple_repeat;Target=species:%28TTTA%29n|genus:Simple_repeat 1 24 +
-HS04636	repeatmasker	match_part	4518	4541	17	+	.	ID=HS04636:hsp:1:1.3.0.0;Parent=HS04636:hit:1:1.3.0.0;Target=species:%2528TTTA%2529n|genus:Simple_repeat 1 24 +
-HS04636	repeatmasker	match	939	980	13	+	.	ID=HS04636:hit:2:1.3.0.0;Name=species:%28CCGCG%29n|genus:Simple_repeat;Target=species:%28CCGCG%29n|genus:Simple_repeat 1 42 +
-HS04636	repeatmasker	match_part	939	980	13	+	.	ID=HS04636:hsp:2:1.3.0.0;Parent=HS04636:hit:2:1.3.0.0;Target=species:%2528CCGCG%2529n|genus:Simple_repeat 1 42 +
-HS04636	repeatmasker	match	3791	3839	22	+	.	ID=HS04636:hit:3:1.3.0.0;Name=species:%28AC%29n|genus:Simple_repeat;Target=species:%28AC%29n|genus:Simple_repeat 1 49 +
-HS04636	repeatmasker	match_part	3791	3839	22	+	.	ID=HS04636:hsp:3:1.3.0.0;Parent=HS04636:hit:3:1.3.0.0;Target=species:%2528AC%2529n|genus:Simple_repeat 1 49 +
-HS04636	repeatmasker	match	6028	6072	21	+	.	ID=HS04636:hit:4:1.3.0.0;Name=species:%28TTGT%29n|genus:Simple_repeat;Target=species:%28TTGT%29n|genus:Simple_repeat 1 46 +
-HS04636	repeatmasker	match_part	6028	6072	21	+	.	ID=HS04636:hsp:4:1.3.0.0;Parent=HS04636:hit:4:1.3.0.0;Target=species:%2528TTGT%2529n|genus:Simple_repeat 1 46 +
-HS04636	repeatmasker	match	6918	6977	17	+	.	ID=HS04636:hit:5:1.3.0.0;Name=species:%28TATT%29n|genus:Simple_repeat;Target=species:%28TATT%29n|genus:Simple_repeat 1 54 +
-HS04636	repeatmasker	match_part	6918	6977	17	+	.	ID=HS04636:hsp:5:1.3.0.0;Parent=HS04636:hit:5:1.3.0.0;Target=species:%2528TATT%2529n|genus:Simple_repeat 1 54 +
-HS04636	repeatmasker	match	3840	3847	17	+	.	ID=HS04636:hit:6:1.3.0.0;Name=species:%28ATAC%29n|genus:Simple_repeat;Target=species:%28ATAC%29n|genus:Simple_repeat 3 57 +
-HS04636	repeatmasker	match_part	3840	3847	17	+	.	ID=HS04636:hsp:6:1.3.0.0;Parent=HS04636:hit:6:1.3.0.0;Target=species:%2528ATAC%2529n|genus:Simple_repeat 3 57 +
-HS04636	repeatmasker	match	9419	9435	16	+	.	ID=HS04636:hit:7:1.3.0.0;Name=species:%28A%29n|genus:Simple_repeat;Target=species:%28A%29n|genus:Simple_repeat 1 17 +
-HS04636	repeatmasker	match_part	9419	9435	16	+	.	ID=HS04636:hsp:7:1.3.0.0;Parent=HS04636:hit:7:1.3.0.0;Target=species:%2528A%2529n|genus:Simple_repeat 1 17 +
-###
-HS04636	blastn	expressed_sequence_match	1815	6903	120	+	.	ID=HS04636:hit:8:3.2.0.0;Name=HS04636.g1
-HS04636	blastn	match_part	1815	1934	120	+	.	ID=HS04636:hsp:8:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 129 248 +;Gap=M120
-HS04636	blastn	match_part	1815	1845	31	+	.	ID=HS04636:hsp:9:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 50 80 +;Gap=M31
-HS04636	blastn	match_part	2055	2198	144	+	.	ID=HS04636:hsp:10:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144
-HS04636	blastn	match_part	2852	2997	146	+	.	ID=HS04636:hsp:11:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 393 538 +;Gap=M146
-HS04636	blastn	match_part	3424	3609	186	+	.	ID=HS04636:hsp:12:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 535 720 +;Gap=M186
-HS04636	blastn	match_part	4339	4423	85	+	.	ID=HS04636:hsp:13:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 718 802 +;Gap=M85
-HS04636	blastn	match_part	4541	4790	250	+	.	ID=HS04636:hsp:14:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 801 1050 +;Gap=M250
-HS04636	blastn	match_part	5068	5360	293	+	.	ID=HS04636:hsp:15:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 1046 1338 +;Gap=M293
-HS04636	blastn	match_part	5859	6008	150	+	.	ID=HS04636:hsp:16:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 1336 1485 +;Gap=M150
-HS04636	blastn	match_part	6490	6903	414	+	.	ID=HS04636:hsp:17:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 1481 1894 +;Gap=M414
-HS04636	est2genome	expressed_sequence_match	1813	6903	8728	+	.	ID=HS04636:hit:9:3.2.0.0;Name=HS04636.g1
-HS04636	est2genome	match_part	1813	1934	8728	+	.	ID=HS04636:hsp:18:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 127 248 +;Gap=M122
-HS04636	est2genome	match_part	2055	2198	8728	+	.	ID=HS04636:hsp:19:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144
-HS04636	est2genome	match_part	2852	2995	8728	+	.	ID=HS04636:hsp:20:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 393 536 +;Gap=M144
-HS04636	est2genome	match_part	3426	3607	8728	+	.	ID=HS04636:hsp:21:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 537 718 +;Gap=M182
-HS04636	est2genome	match_part	4340	4423	8728	+	.	ID=HS04636:hsp:22:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 719 802 +;Gap=M84
-HS04636	est2genome	match_part	4543	4789	8728	+	.	ID=HS04636:hsp:23:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 803 1049 +;Gap=M247
-HS04636	est2genome	match_part	5072	5358	8728	+	.	ID=HS04636:hsp:24:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 1050 1336 +;Gap=M287
-HS04636	est2genome	match_part	5860	6007	8728	+	.	ID=HS04636:hsp:25:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 1337 1484 +;Gap=M148
-HS04636	est2genome	match_part	6494	6903	8728	+	.	ID=HS04636:hsp:26:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 1485 1894 +;Gap=M410
+HS04636	blastn	expressed_sequence_match	1815	6903	120	+	.	ID=HS04636:hit:0:3.2.0.0;Name=HS04636.g1
+HS04636	blastn	match_part	1815	1934	120	+	.	ID=HS04636:hsp:0:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 129 248 +;Gap=M120
+HS04636	blastn	match_part	1815	1845	31	+	.	ID=HS04636:hsp:1:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 50 80 +;Gap=M31
+HS04636	blastn	match_part	2055	2198	144	+	.	ID=HS04636:hsp:2:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144
+HS04636	blastn	match_part	2852	2997	146	+	.	ID=HS04636:hsp:3:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 393 538 +;Gap=M146
+HS04636	blastn	match_part	3424	3609	186	+	.	ID=HS04636:hsp:4:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 535 720 +;Gap=M186
+HS04636	blastn	match_part	4339	4423	85	+	.	ID=HS04636:hsp:5:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 718 802 +;Gap=M85
+HS04636	blastn	match_part	4542	4790	249	+	.	ID=HS04636:hsp:6:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 802 1050 +;Gap=M249
+HS04636	blastn	match_part	5068	5360	293	+	.	ID=HS04636:hsp:7:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 1046 1338 +;Gap=M293
+HS04636	blastn	match_part	5859	6008	150	+	.	ID=HS04636:hsp:8:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 1336 1485 +;Gap=M150
+HS04636	blastn	match_part	6490	6903	414	+	.	ID=HS04636:hsp:9:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 1481 1894 +;Gap=M414
+HS04636	est2genome	expressed_sequence_match	1813	6903	8728	+	.	ID=HS04636:hit:1:3.2.0.0;Name=HS04636.g1
+HS04636	est2genome	match_part	1813	1934	8728	+	.	ID=HS04636:hsp:10:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 127 248 +;Gap=M122
+HS04636	est2genome	match_part	2055	2198	8728	+	.	ID=HS04636:hsp:11:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144
+HS04636	est2genome	match_part	2852	2995	8728	+	.	ID=HS04636:hsp:12:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 393 536 +;Gap=M144
+HS04636	est2genome	match_part	3426	3607	8728	+	.	ID=HS04636:hsp:13:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 537 718 +;Gap=M182
+HS04636	est2genome	match_part	4340	4423	8728	+	.	ID=HS04636:hsp:14:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 719 802 +;Gap=M84
+HS04636	est2genome	match_part	4543	4789	8728	+	.	ID=HS04636:hsp:15:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 803 1049 +;Gap=M247
+HS04636	est2genome	match_part	5072	5358	8728	+	.	ID=HS04636:hsp:16:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 1050 1336 +;Gap=M287
+HS04636	est2genome	match_part	5860	6007	8728	+	.	ID=HS04636:hsp:17:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 1337 1484 +;Gap=M148
+HS04636	est2genome	match_part	6494	6903	8728	+	.	ID=HS04636:hsp:18:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 1485 1894 +;Gap=M410
diff -r 326f9c294b09 -r f1912d5575df test-data/evidences_model.gff3
--- a/test-data/evidences_model.gff3	Fri May 03 07:50:37 2019 -0400
+++ b/test-data/evidences_model.gff3	Mon Dec 28 23:19:28 2020 +0000
@@ -1,23 +1,51 @@
 ##gff-version 3
 HS08198	.	contig	1	2344	.	.	.	ID=HS08198;Name=HS08198
+HS08198	snap	match	99	1848	233.121	+	.	ID=HS08198:hit:6:4.5.0.0;Name=snap-HS08198-abinit-gene-0.0-mRNA-1
+HS08198	snap	match_part	99	107	-2.800	+	.	ID=HS08198:hsp:51:4.5.0.0;Parent=HS08198:hit:6:4.5.0.0;Target=snap-HS08198-abinit-gene-0.0-mRNA-1 1 9 +;Gap=M9
+HS08198	snap	match_part	421	582	45.298	+	.	ID=HS08198:hsp:52:4.5.0.0;Parent=HS08198:hit:6:4.5.0.0;Target=snap-HS08198-abinit-gene-0.0-mRNA-1 10 171 +;Gap=M162
+HS08198	snap	match_part	812	874	24.711	+	.	ID=HS08198:hsp:53:4.5.0.0;Parent=HS08198:hit:6:4.5.0.0;Target=snap-HS08198-abinit-gene-0.0-mRNA-1 172 234 +;Gap=M63
+HS08198	snap	match_part	1024	1123	34.281	+	.	ID=HS08198:hsp:54:4.5.0.0;Parent=HS08198:hit:6:4.5.0.0;Target=snap-HS08198-abinit-gene-0.0-mRNA-1 235 334 +;Gap=M100
+HS08198	snap	match_part	1208	1315	53.852	+	.	ID=HS08198:hsp:55:4.5.0.0;Parent=HS08198:hit:6:4.5.0.0;Target=snap-HS08198-abinit-gene-0.0-mRNA-1 335 442 +;Gap=M108
+HS08198	snap	match_part	1587	1688	41.983	+	.	ID=HS08198:hsp:56:4.5.0.0;Parent=HS08198:hit:6:4.5.0.0;Target=snap-HS08198-abinit-gene-0.0-mRNA-1 443 544 +;Gap=M102
+HS08198	snap	match_part	1772	1848	35.796	+	.	ID=HS08198:hsp:57:4.5.0.0;Parent=HS08198:hit:6:4.5.0.0;Target=snap-HS08198-abinit-gene-0.0-mRNA-1 545 621 +;Gap=M77
 ###
-HS08198	blastn	expressed_sequence_match	444	1848	140	+	.	ID=HS08198:hit:2:3.2.0.0;Name=HS08198.g2
-HS08198	blastn	match_part	444	583	140	+	.	ID=HS08198:hsp:19:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 79 218 +;Gap=M140
-HS08198	blastn	match_part	445	523	79	+	.	ID=HS08198:hsp:20:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 1 79 +;Gap=M79
-HS08198	blastn	match_part	808	895	88	+	.	ID=HS08198:hsp:21:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 214 301 +;Gap=M88
-HS08198	blastn	match_part	1053	1123	71	+	.	ID=HS08198:hsp:22:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71
-HS08198	blastn	match_part	1206	1315	110	+	.	ID=HS08198:hsp:23:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 370 479 +;Gap=M110
-HS08198	blastn	match_part	1586	1689	104	+	.	ID=HS08198:hsp:24:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 479 582 +;Gap=M104
-HS08198	blastn	match_part	1771	1848	78	+	.	ID=HS08198:hsp:25:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 581 658 +;Gap=M78
-HS08198	est2genome	expressed_sequence_match	352	1848	2869	+	.	ID=HS08198:hit:3:3.2.0.0;Name=HS08198.g2
-HS08198	est2genome	match_part	352	397	2869	+	.	ID=HS08198:hsp:26:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 3 52 +;Gap=M18 D1 M2 I4 M10 I1 M15
-HS08198	est2genome	match_part	421	582	2869	+	.	ID=HS08198:hsp:27:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 53 217 +;Gap=M4 I2 M3 I3 M5 D1 M9 D1 M139
-HS08198	est2genome	match_part	812	894	2869	+	.	ID=HS08198:hsp:28:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 218 300 +;Gap=M83
-HS08198	est2genome	match_part	1053	1123	2869	+	.	ID=HS08198:hsp:29:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71
-HS08198	est2genome	match_part	1208	1315	2869	+	.	ID=HS08198:hsp:30:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 372 479 +;Gap=M108
-HS08198	est2genome	match_part	1587	1688	2869	+	.	ID=HS08198:hsp:31:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 480 581 +;Gap=M102
-HS08198	est2genome	match_part	1772	1848	2869	+	.	ID=HS08198:hsp:32:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 582 658 +;Gap=M77
+HS08198	blastn	expressed_sequence_match	444	1848	140	+	.	ID=HS08198:hit:4:3.2.0.0;Name=HS08198.g2
+HS08198	blastn	match_part	444	583	140	+	.	ID=HS08198:hsp:37:3.2.0.0;Parent=HS08198:hit:4:3.2.0.0;Target=HS08198.g2 79 218 +;Gap=M140
+HS08198	blastn	match_part	445	523	79	+	.	ID=HS08198:hsp:38:3.2.0.0;Parent=HS08198:hit:4:3.2.0.0;Target=HS08198.g2 1 79 +;Gap=M79
+HS08198	blastn	match_part	808	895	88	+	.	ID=HS08198:hsp:39:3.2.0.0;Parent=HS08198:hit:4:3.2.0.0;Target=HS08198.g2 214 301 +;Gap=M88
+HS08198	blastn	match_part	1053	1123	71	+	.	ID=HS08198:hsp:40:3.2.0.0;Parent=HS08198:hit:4:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71
+HS08198	blastn	match_part	1206	1315	110	+	.	ID=HS08198:hsp:41:3.2.0.0;Parent=HS08198:hit:4:3.2.0.0;Target=HS08198.g2 370 479 +;Gap=M110
+HS08198	blastn	match_part	1586	1689	104	+	.	ID=HS08198:hsp:42:3.2.0.0;Parent=HS08198:hit:4:3.2.0.0;Target=HS08198.g2 479 582 +;Gap=M104
+HS08198	blastn	match_part	1771	1848	78	+	.	ID=HS08198:hsp:43:3.2.0.0;Parent=HS08198:hit:4:3.2.0.0;Target=HS08198.g2 581 658 +;Gap=M78
+HS08198	est2genome	expressed_sequence_match	352	1848	2869	+	.	ID=HS08198:hit:5:3.2.0.0;Name=HS08198.g2
+HS08198	est2genome	match_part	352	397	2869	+	.	ID=HS08198:hsp:44:3.2.0.0;Parent=HS08198:hit:5:3.2.0.0;Target=HS08198.g2 3 52 +;Gap=M18 D1 M2 I4 M10 I1 M15
+HS08198	est2genome	match_part	421	582	2869	+	.	ID=HS08198:hsp:45:3.2.0.0;Parent=HS08198:hit:5:3.2.0.0;Target=HS08198.g2 53 217 +;Gap=M4 I2 M3 I3 M5 D1 M9 D1 M139
+HS08198	est2genome	match_part	812	894	2869	+	.	ID=HS08198:hsp:46:3.2.0.0;Parent=HS08198:hit:5:3.2.0.0;Target=HS08198.g2 218 300 +;Gap=M83
+HS08198	est2genome	match_part	1053	1123	2869	+	.	ID=HS08198:hsp:47:3.2.0.0;Parent=HS08198:hit:5:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71
+HS08198	est2genome	match_part	1208	1315	2869	+	.	ID=HS08198:hsp:48:3.2.0.0;Parent=HS08198:hit:5:3.2.0.0;Target=HS08198.g2 372 479 +;Gap=M108
+HS08198	est2genome	match_part	1587	1688	2869	+	.	ID=HS08198:hsp:49:3.2.0.0;Parent=HS08198:hit:5:3.2.0.0;Target=HS08198.g2 480 581 +;Gap=M102
+HS08198	est2genome	match_part	1772	1848	2869	+	.	ID=HS08198:hsp:50:3.2.0.0;Parent=HS08198:hit:5:3.2.0.0;Target=HS08198.g2 582 658 +;Gap=M77
 HS04636	.	contig	1	9453	.	.	.	ID=HS04636;Name=HS04636
+HS04636	snap	match	1862	6903	761.916	+	.	ID=HS04636:hit:2:4.5.0.0;Name=snap-HS04636-abinit-gene-0.2-mRNA-1
+HS04636	snap	match_part	1862	1867	8.523	+	.	ID=HS04636:hsp:19:4.5.0.0;Parent=HS04636:hit:2:4.5.0.0;Target=snap-HS04636-abinit-gene-0.2-mRNA-1 1 6 +;Gap=M6
+HS04636	snap	match_part	1883	1934	20.348	+	.	ID=HS04636:hsp:20:4.5.0.0;Parent=HS04636:hit:2:4.5.0.0;Target=snap-HS04636-abinit-gene-0.2-mRNA-1 7 58 +;Gap=M52
+HS04636	snap	match_part	2055	2198	69.846	+	.	ID=HS04636:hsp:21:4.5.0.0;Parent=HS04636:hit:2:4.5.0.0;Target=snap-HS04636-abinit-gene-0.2-mRNA-1 59 202 +;Gap=M144
+HS04636	snap	match_part	2852	2995	67.055	+	.	ID=HS04636:hsp:22:4.5.0.0;Parent=HS04636:hit:2:4.5.0.0;Target=snap-HS04636-abinit-gene-0.2-mRNA-1 203 346 +;Gap=M144
+HS04636	snap	match_part	3426	3607	77.942	+	.	ID=HS04636:hsp:23:4.5.0.0;Parent=HS04636:hit:2:4.5.0.0;Target=snap-HS04636-abinit-gene-0.2-mRNA-1 347 528 +;Gap=M182
+HS04636	snap	match_part	4340	4423	47.588	+	.	ID=HS04636:hsp:24:4.5.0.0;Parent=HS04636:hit:2:4.5.0.0;Target=snap-HS04636-abinit-gene-0.2-mRNA-1 529 612 +;Gap=M84
+HS04636	snap	match_part	4543	4789	112.472	+	.	ID=HS04636:hsp:25:4.5.0.0;Parent=HS04636:hit:2:4.5.0.0;Target=snap-HS04636-abinit-gene-0.2-mRNA-1 613 859 +;Gap=M247
+HS04636	snap	match_part	5072	5358	122.974	+	.	ID=HS04636:hsp:26:4.5.0.0;Parent=HS04636:hit:2:4.5.0.0;Target=snap-HS04636-abinit-gene-0.2-mRNA-1 860 1146 +;Gap=M287
+HS04636	snap	match_part	5860	6007	72.046	+	.	ID=HS04636:hsp:27:4.5.0.0;Parent=HS04636:hit:2:4.5.0.0;Target=snap-HS04636-abinit-gene-0.2-mRNA-1 1147 1294 +;Gap=M148
+HS04636	snap	match_part	6494	6903	163.122	+	.	ID=HS04636:hsp:28:4.5.0.0;Parent=HS04636:hit:2:4.5.0.0;Target=snap-HS04636-abinit-gene-0.2-mRNA-1 1295 1704 +;Gap=M410
+HS04636	augustus	match	966	6903	0.1	+	.	ID=HS04636:hit:3:4.5.0.0;Name=augustus-HS04636-abinit-gene-0.3-mRNA-1
+HS04636	augustus	match_part	966	1017	0.1	+	.	ID=HS04636:hsp:29:4.5.0.0;Parent=HS04636:hit:3:4.5.0.0;Target=augustus-HS04636-abinit-gene-0.3-mRNA-1 1 52 +;Gap=M52
+HS04636	augustus	match_part	2852	2995	0.1	+	.	ID=HS04636:hsp:30:4.5.0.0;Parent=HS04636:hit:3:4.5.0.0;Target=augustus-HS04636-abinit-gene-0.3-mRNA-1 53 196 +;Gap=M144
+HS04636	augustus	match_part	3426	3607	0.1	+	.	ID=HS04636:hsp:31:4.5.0.0;Parent=HS04636:hit:3:4.5.0.0;Target=augustus-HS04636-abinit-gene-0.3-mRNA-1 197 378 +;Gap=M182
+HS04636	augustus	match_part	4340	4423	0.1	+	.	ID=HS04636:hsp:32:4.5.0.0;Parent=HS04636:hit:3:4.5.0.0;Target=augustus-HS04636-abinit-gene-0.3-mRNA-1 379 462 +;Gap=M84
+HS04636	augustus	match_part	4543	4789	0.1	+	.	ID=HS04636:hsp:33:4.5.0.0;Parent=HS04636:hit:3:4.5.0.0;Target=augustus-HS04636-abinit-gene-0.3-mRNA-1 463 709 +;Gap=M247
+HS04636	augustus	match_part	5072	5358	0.1	+	.	ID=HS04636:hsp:34:4.5.0.0;Parent=HS04636:hit:3:4.5.0.0;Target=augustus-HS04636-abinit-gene-0.3-mRNA-1 710 996 +;Gap=M287
+HS04636	augustus	match_part	5860	6007	0.1	+	.	ID=HS04636:hsp:35:4.5.0.0;Parent=HS04636:hit:3:4.5.0.0;Target=augustus-HS04636-abinit-gene-0.3-mRNA-1 997 1144 +;Gap=M148
+HS04636	augustus	match_part	6494	6903	0.1	+	.	ID=HS04636:hsp:36:4.5.0.0;Parent=HS04636:hit:3:4.5.0.0;Target=augustus-HS04636-abinit-gene-0.3-mRNA-1 1145 1554 +;Gap=M410
 ###
 HS04636	blastn	expressed_sequence_match	1815	6903	120	+	.	ID=HS04636:hit:0:3.2.0.0;Name=HS04636.g1
 HS04636	blastn	match_part	1815	1934	120	+	.	ID=HS04636:hsp:0:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 129 248 +;Gap=M120
@@ -26,7 +54,7 @@
 HS04636	blastn	match_part	2852	2997	146	+	.	ID=HS04636:hsp:3:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 393 538 +;Gap=M146
 HS04636	blastn	match_part	3424	3609	186	+	.	ID=HS04636:hsp:4:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 535 720 +;Gap=M186
 HS04636	blastn	match_part	4339	4423	85	+	.	ID=HS04636:hsp:5:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 718 802 +;Gap=M85
-HS04636	blastn	match_part	4541	4790	250	+	.	ID=HS04636:hsp:6:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 801 1050 +;Gap=M250
+HS04636	blastn	match_part	4542	4790	249	+	.	ID=HS04636:hsp:6:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 802 1050 +;Gap=M249
 HS04636	blastn	match_part	5068	5360	293	+	.	ID=HS04636:hsp:7:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 1046 1338 +;Gap=M293
 HS04636	blastn	match_part	5859	6008	150	+	.	ID=HS04636:hsp:8:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 1336 1485 +;Gap=M150
 HS04636	blastn	match_part	6490	6903	414	+	.	ID=HS04636:hsp:9:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 1481 1894 +;Gap=M414
diff -r 326f9c294b09 -r f1912d5575df test-data/evidences_norm.gff3
--- a/test-data/evidences_norm.gff3	Fri May 03 07:50:37 2019 -0400
+++ b/test-data/evidences_norm.gff3	Mon Dec 28 23:19:28 2020 +0000
@@ -1,42 +1,66 @@
 ##gff-version 3
 HS08198	.	contig	1	2344	.	.	.	ID=HS08198;Name=HS08198
 ###
-HS08198	blastn	expressed_sequence_match	444	1848	140	+	.	ID=HS08198:hit:2:3.2.0.0;Name=HS08198.g2
-HS08198	blastn	match_part	444	583	140	+	.	ID=HS08198:hsp:19:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 79 218 +;Gap=M140
-HS08198	blastn	match_part	445	523	79	+	.	ID=HS08198:hsp:20:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 1 79 +;Gap=M79
-HS08198	blastn	match_part	808	895	88	+	.	ID=HS08198:hsp:21:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 214 301 +;Gap=M88
-HS08198	blastn	match_part	1053	1123	71	+	.	ID=HS08198:hsp:22:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71
-HS08198	blastn	match_part	1206	1315	110	+	.	ID=HS08198:hsp:23:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 370 479 +;Gap=M110
-HS08198	blastn	match_part	1586	1689	104	+	.	ID=HS08198:hsp:24:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 479 582 +;Gap=M104
-HS08198	blastn	match_part	1771	1848	78	+	.	ID=HS08198:hsp:25:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 581 658 +;Gap=M78
-HS08198	est2genome	expressed_sequence_match	352	1848	2869	+	.	ID=HS08198:hit:3:3.2.0.0;Name=HS08198.g2
-HS08198	est2genome	match_part	352	397	2869	+	.	ID=HS08198:hsp:26:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 3 52 +;Gap=M18 D1 M2 I4 M10 I1 M15
-HS08198	est2genome	match_part	421	582	2869	+	.	ID=HS08198:hsp:27:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 53 217 +;Gap=M4 I2 M3 I3 M5 D1 M9 D1 M139
-HS08198	est2genome	match_part	812	894	2869	+	.	ID=HS08198:hsp:28:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 218 300 +;Gap=M83
-HS08198	est2genome	match_part	1053	1123	2869	+	.	ID=HS08198:hsp:29:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71
-HS08198	est2genome	match_part	1208	1315	2869	+	.	ID=HS08198:hsp:30:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 372 479 +;Gap=M108
-HS08198	est2genome	match_part	1587	1688	2869	+	.	ID=HS08198:hsp:31:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 480 581 +;Gap=M102
-HS08198	est2genome	match_part	1772	1848	2869	+	.	ID=HS08198:hsp:32:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 582 658 +;Gap=M77
+HS08198	repeatmasker	match	578	651	13	+	.	ID=HS08198:hit:12:1.3.0.0;Name=species:%28AGAAGGT%29n|genus:Simple_repeat;Target=species:%28AGAAGGT%29n|genus:Simple_repeat 1 75 +
+HS08198	repeatmasker	match_part	578	651	13	+	.	ID=HS08198:hsp:29:1.3.0.0;Parent=HS08198:hit:12:1.3.0.0;Target=species:%2528AGAAGGT%2529n|genus:Simple_repeat 1 75 +
+###
+HS08198	blastn	expressed_sequence_match	444	1848	140	+	.	ID=HS08198:hit:13:3.2.0.0;Name=HS08198.g2
+HS08198	blastn	match_part	444	583	140	+	.	ID=HS08198:hsp:30:3.2.0.0;Parent=HS08198:hit:13:3.2.0.0;Target=HS08198.g2 79 218 +;Gap=M140
+HS08198	blastn	match_part	445	523	79	+	.	ID=HS08198:hsp:31:3.2.0.0;Parent=HS08198:hit:13:3.2.0.0;Target=HS08198.g2 1 79 +;Gap=M79
+HS08198	blastn	match_part	808	895	88	+	.	ID=HS08198:hsp:32:3.2.0.0;Parent=HS08198:hit:13:3.2.0.0;Target=HS08198.g2 214 301 +;Gap=M88
+HS08198	blastn	match_part	1053	1123	71	+	.	ID=HS08198:hsp:33:3.2.0.0;Parent=HS08198:hit:13:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71
+HS08198	blastn	match_part	1206	1315	110	+	.	ID=HS08198:hsp:34:3.2.0.0;Parent=HS08198:hit:13:3.2.0.0;Target=HS08198.g2 370 479 +;Gap=M110
+HS08198	blastn	match_part	1586	1689	104	+	.	ID=HS08198:hsp:35:3.2.0.0;Parent=HS08198:hit:13:3.2.0.0;Target=HS08198.g2 479 582 +;Gap=M104
+HS08198	blastn	match_part	1771	1848	78	+	.	ID=HS08198:hsp:36:3.2.0.0;Parent=HS08198:hit:13:3.2.0.0;Target=HS08198.g2 581 658 +;Gap=M78
+HS08198	est2genome	expressed_sequence_match	352	1848	2869	+	.	ID=HS08198:hit:14:3.2.0.0;Name=HS08198.g2
+HS08198	est2genome	match_part	352	397	2869	+	.	ID=HS08198:hsp:37:3.2.0.0;Parent=HS08198:hit:14:3.2.0.0;Target=HS08198.g2 3 52 +;Gap=M18 D1 M2 I4 M10 I1 M15
+HS08198	est2genome	match_part	421	582	2869	+	.	ID=HS08198:hsp:38:3.2.0.0;Parent=HS08198:hit:14:3.2.0.0;Target=HS08198.g2 53 217 +;Gap=M4 I2 M3 I3 M5 D1 M9 D1 M139
+HS08198	est2genome	match_part	812	894	2869	+	.	ID=HS08198:hsp:39:3.2.0.0;Parent=HS08198:hit:14:3.2.0.0;Target=HS08198.g2 218 300 +;Gap=M83
+HS08198	est2genome	match_part	1053	1123	2869	+	.	ID=HS08198:hsp:40:3.2.0.0;Parent=HS08198:hit:14:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71
+HS08198	est2genome	match_part	1208	1315	2869	+	.	ID=HS08198:hsp:41:3.2.0.0;Parent=HS08198:hit:14:3.2.0.0;Target=HS08198.g2 372 479 +;Gap=M108
+HS08198	est2genome	match_part	1587	1688	2869	+	.	ID=HS08198:hsp:42:3.2.0.0;Parent=HS08198:hit:14:3.2.0.0;Target=HS08198.g2 480 581 +;Gap=M102
+HS08198	est2genome	match_part	1772	1848	2869	+	.	ID=HS08198:hsp:43:3.2.0.0;Parent=HS08198:hit:14:3.2.0.0;Target=HS08198.g2 582 658 +;Gap=M77
 HS04636	.	contig	1	9453	.	.	.	ID=HS04636;Name=HS04636
 ###
-HS04636	blastn	expressed_sequence_match	1815	6903	120	+	.	ID=HS04636:hit:0:3.2.0.0;Name=HS04636.g1
-HS04636	blastn	match_part	1815	1934	120	+	.	ID=HS04636:hsp:0:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 129 248 +;Gap=M120
-HS04636	blastn	match_part	1815	1845	31	+	.	ID=HS04636:hsp:1:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 50 80 +;Gap=M31
-HS04636	blastn	match_part	2055	2198	144	+	.	ID=HS04636:hsp:2:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144
-HS04636	blastn	match_part	2852	2997	146	+	.	ID=HS04636:hsp:3:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 393 538 +;Gap=M146
-HS04636	blastn	match_part	3424	3609	186	+	.	ID=HS04636:hsp:4:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 535 720 +;Gap=M186
-HS04636	blastn	match_part	4339	4423	85	+	.	ID=HS04636:hsp:5:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 718 802 +;Gap=M85
-HS04636	blastn	match_part	4541	4790	250	+	.	ID=HS04636:hsp:6:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 801 1050 +;Gap=M250
-HS04636	blastn	match_part	5068	5360	293	+	.	ID=HS04636:hsp:7:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 1046 1338 +;Gap=M293
-HS04636	blastn	match_part	5859	6008	150	+	.	ID=HS04636:hsp:8:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 1336 1485 +;Gap=M150
-HS04636	blastn	match_part	6490	6903	414	+	.	ID=HS04636:hsp:9:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 1481 1894 +;Gap=M414
-HS04636	est2genome	expressed_sequence_match	1813	6903	8728	+	.	ID=HS04636:hit:1:3.2.0.0;Name=HS04636.g1
-HS04636	est2genome	match_part	1813	1934	8728	+	.	ID=HS04636:hsp:10:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 127 248 +;Gap=M122
-HS04636	est2genome	match_part	2055	2198	8728	+	.	ID=HS04636:hsp:11:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144
-HS04636	est2genome	match_part	2852	2995	8728	+	.	ID=HS04636:hsp:12:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 393 536 +;Gap=M144
-HS04636	est2genome	match_part	3426	3607	8728	+	.	ID=HS04636:hsp:13:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 537 718 +;Gap=M182
-HS04636	est2genome	match_part	4340	4423	8728	+	.	ID=HS04636:hsp:14:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 719 802 +;Gap=M84
-HS04636	est2genome	match_part	4543	4789	8728	+	.	ID=HS04636:hsp:15:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 803 1049 +;Gap=M247
-HS04636	est2genome	match_part	5072	5358	8728	+	.	ID=HS04636:hsp:16:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 1050 1336 +;Gap=M287
-HS04636	est2genome	match_part	5860	6007	8728	+	.	ID=HS04636:hsp:17:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 1337 1484 +;Gap=M148
-HS04636	est2genome	match_part	6494	6903	8728	+	.	ID=HS04636:hsp:18:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 1485 1894 +;Gap=M410
+HS04636	repeatmasker	match	3840	3847	17	+	.	ID=HS04636:hit:0:1.3.0.0;Name=species:%28ATAC%29n|genus:Simple_repeat;Target=species:%28ATAC%29n|genus:Simple_repeat 3 57 +
+HS04636	repeatmasker	match_part	3840	3847	17	+	.	ID=HS04636:hsp:0:1.3.0.0;Parent=HS04636:hit:0:1.3.0.0;Target=species:%2528ATAC%2529n|genus:Simple_repeat 3 57 +
+HS04636	repeatmasker	match	9419	9435	16	+	.	ID=HS04636:hit:1:1.3.0.0;Name=species:%28A%29n|genus:Simple_repeat;Target=species:%28A%29n|genus:Simple_repeat 1 17 +
+HS04636	repeatmasker	match_part	9419	9435	16	+	.	ID=HS04636:hsp:1:1.3.0.0;Parent=HS04636:hit:1:1.3.0.0;Target=species:%2528A%2529n|genus:Simple_repeat 1 17 +
+HS04636	repeatmasker	match	3852	3888	12	+	.	ID=HS04636:hit:2:1.3.0.0;Name=species:%28TTGTAAT%29n|genus:Simple_repeat;Target=species:%28TTGTAAT%29n|genus:Simple_repeat 1 37 +
+HS04636	repeatmasker	match_part	3852	3888	12	+	.	ID=HS04636:hsp:2:1.3.0.0;Parent=HS04636:hit:2:1.3.0.0;Target=species:%2528TTGTAAT%2529n|genus:Simple_repeat 1 37 +
+HS04636	repeatmasker	match	6918	6977	17	+	.	ID=HS04636:hit:3:1.3.0.0;Name=species:%28TATT%29n|genus:Simple_repeat;Target=species:%28TATT%29n|genus:Simple_repeat 1 54 +
+HS04636	repeatmasker	match_part	6918	6977	17	+	.	ID=HS04636:hsp:3:1.3.0.0;Parent=HS04636:hit:3:1.3.0.0;Target=species:%2528TATT%2529n|genus:Simple_repeat 1 54 +
+HS04636	repeatmasker	match	3791	3839	22	+	.	ID=HS04636:hit:4:1.3.0.0;Name=species:%28AC%29n|genus:Simple_repeat;Target=species:%28AC%29n|genus:Simple_repeat 1 49 +
+HS04636	repeatmasker	match_part	3791	3839	22	+	.	ID=HS04636:hsp:4:1.3.0.0;Parent=HS04636:hit:4:1.3.0.0;Target=species:%2528AC%2529n|genus:Simple_repeat 1 49 +
+HS04636	repeatmasker	match	939	980	13	+	.	ID=HS04636:hit:5:1.3.0.0;Name=species:%28CCGCG%29n|genus:Simple_repeat;Target=species:%28CCGCG%29n|genus:Simple_repeat 1 42 +
+HS04636	repeatmasker	match_part	939	980	13	+	.	ID=HS04636:hsp:5:1.3.0.0;Parent=HS04636:hit:5:1.3.0.0;Target=species:%2528CCGCG%2529n|genus:Simple_repeat 1 42 +
+HS04636	repeatmasker	match	4518	4541	17	+	.	ID=HS04636:hit:6:1.3.0.0;Name=species:%28TTTA%29n|genus:Simple_repeat;Target=species:%28TTTA%29n|genus:Simple_repeat 1 24 +
+HS04636	repeatmasker	match_part	4518	4541	17	+	.	ID=HS04636:hsp:6:1.3.0.0;Parent=HS04636:hit:6:1.3.0.0;Target=species:%2528TTTA%2529n|genus:Simple_repeat 1 24 +
+HS04636	repeatmasker	match	1124	1335	391	+	.	ID=HS04636:hit:7:1.3.0.0;Name=species:MIRb|genus:SINE%2FMIR;Target=species:MIRb|genus:SINE%2FMIR 2 217 +
+HS04636	repeatmasker	match_part	1124	1335	391	+	.	ID=HS04636:hsp:7:1.3.0.0;Parent=HS04636:hit:7:1.3.0.0;Target=species:MIRb|genus:SINE%252FMIR 2 217 +
+HS04636	repeatmasker	match	6050	6359	2256	+	.	ID=HS04636:hit:8:1.3.0.0;Name=species:AluSc8|genus:SINE%2FAlu;Target=species:AluSc8|genus:SINE%2FAlu 1 311 +
+HS04636	repeatmasker	match_part	6050	6359	2256	+	.	ID=HS04636:hsp:8:1.3.0.0;Parent=HS04636:hit:8:1.3.0.0;Target=species:AluSc8|genus:SINE%252FAlu 1 311 +
+HS04636	repeatmasker	match	8994	9045	191	+	.	ID=HS04636:hit:9:1.3.0.0;Name=species:L2a|genus:LINE%2FL2;Target=species:L2a|genus:LINE%2FL2 3374 3425 +
+HS04636	repeatmasker	match_part	8994	9045	191	+	.	ID=HS04636:hsp:9:1.3.0.0;Parent=HS04636:hit:9:1.3.0.0;Target=species:L2a|genus:LINE%252FL2 3374 3425 +
+###
+HS04636	blastn	expressed_sequence_match	1815	6903	120	+	.	ID=HS04636:hit:10:3.2.0.0;Name=HS04636.g1
+HS04636	blastn	match_part	1815	1934	120	+	.	ID=HS04636:hsp:10:3.2.0.0;Parent=HS04636:hit:10:3.2.0.0;Target=HS04636.g1 129 248 +;Gap=M120
+HS04636	blastn	match_part	1815	1845	31	+	.	ID=HS04636:hsp:11:3.2.0.0;Parent=HS04636:hit:10:3.2.0.0;Target=HS04636.g1 50 80 +;Gap=M31
+HS04636	blastn	match_part	2055	2198	144	+	.	ID=HS04636:hsp:12:3.2.0.0;Parent=HS04636:hit:10:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144
+HS04636	blastn	match_part	2852	2997	146	+	.	ID=HS04636:hsp:13:3.2.0.0;Parent=HS04636:hit:10:3.2.0.0;Target=HS04636.g1 393 538 +;Gap=M146
+HS04636	blastn	match_part	3424	3609	186	+	.	ID=HS04636:hsp:14:3.2.0.0;Parent=HS04636:hit:10:3.2.0.0;Target=HS04636.g1 535 720 +;Gap=M186
+HS04636	blastn	match_part	4339	4423	85	+	.	ID=HS04636:hsp:15:3.2.0.0;Parent=HS04636:hit:10:3.2.0.0;Target=HS04636.g1 718 802 +;Gap=M85
+HS04636	blastn	match_part	4541	4790	250	+	.	ID=HS04636:hsp:16:3.2.0.0;Parent=HS04636:hit:10:3.2.0.0;Target=HS04636.g1 801 1050 +;Gap=M250
+HS04636	blastn	match_part	5068	5360	293	+	.	ID=HS04636:hsp:17:3.2.0.0;Parent=HS04636:hit:10:3.2.0.0;Target=HS04636.g1 1046 1338 +;Gap=M293
+HS04636	blastn	match_part	5859	5999	141	+	.	ID=HS04636:hsp:18:3.2.0.0;Parent=HS04636:hit:10:3.2.0.0;Target=HS04636.g1 1336 1476 +;Gap=M141
+HS04636	blastn	match_part	6490	6903	414	+	.	ID=HS04636:hsp:19:3.2.0.0;Parent=HS04636:hit:10:3.2.0.0;Target=HS04636.g1 1481 1894 +;Gap=M414
+HS04636	est2genome	expressed_sequence_match	1813	6903	8728	+	.	ID=HS04636:hit:11:3.2.0.0;Name=HS04636.g1
+HS04636	est2genome	match_part	1813	1934	8728	+	.	ID=HS04636:hsp:20:3.2.0.0;Parent=HS04636:hit:11:3.2.0.0;Target=HS04636.g1 127 248 +;Gap=M122
+HS04636	est2genome	match_part	2055	2198	8728	+	.	ID=HS04636:hsp:21:3.2.0.0;Parent=HS04636:hit:11:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144
+HS04636	est2genome	match_part	2852	2995	8728	+	.	ID=HS04636:hsp:22:3.2.0.0;Parent=HS04636:hit:11:3.2.0.0;Target=HS04636.g1 393 536 +;Gap=M144
+HS04636	est2genome	match_part	3426	3607	8728	+	.	ID=HS04636:hsp:23:3.2.0.0;Parent=HS04636:hit:11:3.2.0.0;Target=HS04636.g1 537 718 +;Gap=M182
+HS04636	est2genome	match_part	4340	4423	8728	+	.	ID=HS04636:hsp:24:3.2.0.0;Parent=HS04636:hit:11:3.2.0.0;Target=HS04636.g1 719 802 +;Gap=M84
+HS04636	est2genome	match_part	4543	4789	8728	+	.	ID=HS04636:hsp:25:3.2.0.0;Parent=HS04636:hit:11:3.2.0.0;Target=HS04636.g1 803 1049 +;Gap=M247
+HS04636	est2genome	match_part	5072	5358	8728	+	.	ID=HS04636:hsp:26:3.2.0.0;Parent=HS04636:hit:11:3.2.0.0;Target=HS04636.g1 1050 1336 +;Gap=M287
+HS04636	est2genome	match_part	5860	6007	8728	+	.	ID=HS04636:hsp:27:3.2.0.0;Parent=HS04636:hit:11:3.2.0.0;Target=HS04636.g1 1337 1484 +;Gap=M148
+HS04636	est2genome	match_part	6494	6903	8728	+	.	ID=HS04636:hsp:28:3.2.0.0;Parent=HS04636:hit:11:3.2.0.0;Target=HS04636.g1 1485 1894 +;Gap=M410
diff -r 326f9c294b09 -r f1912d5575df test-data/evidences_norm_dfam_up.gff3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/evidences_norm_dfam_up.gff3	Mon Dec 28 23:19:28 2020 +0000
@@ -0,0 +1,62 @@
+##gff-version 3
+HS08198	.	contig	1	2344	.	.	.	ID=HS08198;Name=HS08198
+###
+HS08198	repeatmasker	match	578	651	13	+	.	ID=HS08198:hit:10:1.3.0.0;Name=species:%28AGAAGGT%29n|genus:Simple_repeat;Target=species:%28AGAAGGT%29n|genus:Simple_repeat 1 75 +
+HS08198	repeatmasker	match_part	578	651	13	+	.	ID=HS08198:hsp:27:1.3.0.0;Parent=HS08198:hit:10:1.3.0.0;Target=species:%2528AGAAGGT%2529n|genus:Simple_repeat 1 75 +
+###
+HS08198	blastn	expressed_sequence_match	444	1848	140	+	.	ID=HS08198:hit:11:3.2.0.0;Name=HS08198.g2
+HS08198	blastn	match_part	444	583	140	+	.	ID=HS08198:hsp:28:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 79 218 +;Gap=M140
+HS08198	blastn	match_part	445	523	79	+	.	ID=HS08198:hsp:29:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 1 79 +;Gap=M79
+HS08198	blastn	match_part	808	895	88	+	.	ID=HS08198:hsp:30:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 214 301 +;Gap=M88
+HS08198	blastn	match_part	1053	1123	71	+	.	ID=HS08198:hsp:31:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71
+HS08198	blastn	match_part	1206	1315	110	+	.	ID=HS08198:hsp:32:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 370 479 +;Gap=M110
+HS08198	blastn	match_part	1586	1689	104	+	.	ID=HS08198:hsp:33:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 479 582 +;Gap=M104
+HS08198	blastn	match_part	1771	1848	78	+	.	ID=HS08198:hsp:34:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 581 658 +;Gap=M78
+HS08198	est2genome	expressed_sequence_match	352	1848	2869	+	.	ID=HS08198:hit:12:3.2.0.0;Name=HS08198.g2
+HS08198	est2genome	match_part	352	397	2869	+	.	ID=HS08198:hsp:35:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 3 52 +;Gap=M18 D1 M2 I4 M10 I1 M15
+HS08198	est2genome	match_part	421	582	2869	+	.	ID=HS08198:hsp:36:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 53 217 +;Gap=M4 I2 M3 I3 M5 D1 M9 D1 M139
+HS08198	est2genome	match_part	812	894	2869	+	.	ID=HS08198:hsp:37:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 218 300 +;Gap=M83
+HS08198	est2genome	match_part	1053	1123	2869	+	.	ID=HS08198:hsp:38:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71
+HS08198	est2genome	match_part	1208	1315	2869	+	.	ID=HS08198:hsp:39:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 372 479 +;Gap=M108
+HS08198	est2genome	match_part	1587	1688	2869	+	.	ID=HS08198:hsp:40:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 480 581 +;Gap=M102
+HS08198	est2genome	match_part	1772	1848	2869	+	.	ID=HS08198:hsp:41:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 582 658 +;Gap=M77
+HS04636	.	contig	1	9453	.	.	.	ID=HS04636;Name=HS04636
+###
+HS04636	repeatmasker	match	6918	6977	17	+	.	ID=HS04636:hit:0:1.3.0.0;Name=species:%28TATT%29n|genus:Simple_repeat;Target=species:%28TATT%29n|genus:Simple_repeat 1 54 +
+HS04636	repeatmasker	match_part	6918	6977	17	+	.	ID=HS04636:hsp:0:1.3.0.0;Parent=HS04636:hit:0:1.3.0.0;Target=species:%2528TATT%2529n|genus:Simple_repeat 1 54 +
+HS04636	repeatmasker	match	939	980	13	+	.	ID=HS04636:hit:1:1.3.0.0;Name=species:%28CCGCG%29n|genus:Simple_repeat;Target=species:%28CCGCG%29n|genus:Simple_repeat 1 42 +
+HS04636	repeatmasker	match_part	939	980	13	+	.	ID=HS04636:hsp:1:1.3.0.0;Parent=HS04636:hit:1:1.3.0.0;Target=species:%2528CCGCG%2529n|genus:Simple_repeat 1 42 +
+HS04636	repeatmasker	match	3791	3839	22	+	.	ID=HS04636:hit:2:1.3.0.0;Name=species:%28AC%29n|genus:Simple_repeat;Target=species:%28AC%29n|genus:Simple_repeat 1 49 +
+HS04636	repeatmasker	match_part	3791	3839	22	+	.	ID=HS04636:hsp:2:1.3.0.0;Parent=HS04636:hit:2:1.3.0.0;Target=species:%2528AC%2529n|genus:Simple_repeat 1 49 +
+HS04636	repeatmasker	match	4518	4541	17	+	.	ID=HS04636:hit:3:1.3.0.0;Name=species:%28TTTA%29n|genus:Simple_repeat;Target=species:%28TTTA%29n|genus:Simple_repeat 1 24 +
+HS04636	repeatmasker	match_part	4518	4541	17	+	.	ID=HS04636:hsp:3:1.3.0.0;Parent=HS04636:hit:3:1.3.0.0;Target=species:%2528TTTA%2529n|genus:Simple_repeat 1 24 +
+HS04636	repeatmasker	match	3840	3847	17	+	.	ID=HS04636:hit:4:1.3.0.0;Name=species:%28ATAC%29n|genus:Simple_repeat;Target=species:%28ATAC%29n|genus:Simple_repeat 3 57 +
+HS04636	repeatmasker	match_part	3840	3847	17	+	.	ID=HS04636:hsp:4:1.3.0.0;Parent=HS04636:hit:4:1.3.0.0;Target=species:%2528ATAC%2529n|genus:Simple_repeat 3 57 +
+HS04636	repeatmasker	match	3852	3888	12	+	.	ID=HS04636:hit:5:1.3.0.0;Name=species:%28TTGTAAT%29n|genus:Simple_repeat;Target=species:%28TTGTAAT%29n|genus:Simple_repeat 1 37 +
+HS04636	repeatmasker	match_part	3852	3888	12	+	.	ID=HS04636:hsp:5:1.3.0.0;Parent=HS04636:hit:5:1.3.0.0;Target=species:%2528TTGTAAT%2529n|genus:Simple_repeat 1 37 +
+HS04636	repeatmasker	match	6028	6072	21	+	.	ID=HS04636:hit:6:1.3.0.0;Name=species:%28TTGT%29n|genus:Simple_repeat;Target=species:%28TTGT%29n|genus:Simple_repeat 1 46 +
+HS04636	repeatmasker	match_part	6028	6072	21	+	.	ID=HS04636:hsp:6:1.3.0.0;Parent=HS04636:hit:6:1.3.0.0;Target=species:%2528TTGT%2529n|genus:Simple_repeat 1 46 +
+HS04636	repeatmasker	match	9419	9435	16	+	.	ID=HS04636:hit:7:1.3.0.0;Name=species:%28A%29n|genus:Simple_repeat;Target=species:%28A%29n|genus:Simple_repeat 1 17 +
+HS04636	repeatmasker	match_part	9419	9435	16	+	.	ID=HS04636:hsp:7:1.3.0.0;Parent=HS04636:hit:7:1.3.0.0;Target=species:%2528A%2529n|genus:Simple_repeat 1 17 +
+###
+HS04636	blastn	expressed_sequence_match	1815	6903	120	+	.	ID=HS04636:hit:8:3.2.0.0;Name=HS04636.g1
+HS04636	blastn	match_part	1815	1934	120	+	.	ID=HS04636:hsp:8:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 129 248 +;Gap=M120
+HS04636	blastn	match_part	1815	1845	31	+	.	ID=HS04636:hsp:9:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 50 80 +;Gap=M31
+HS04636	blastn	match_part	2055	2198	144	+	.	ID=HS04636:hsp:10:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144
+HS04636	blastn	match_part	2852	2997	146	+	.	ID=HS04636:hsp:11:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 393 538 +;Gap=M146
+HS04636	blastn	match_part	3424	3609	186	+	.	ID=HS04636:hsp:12:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 535 720 +;Gap=M186
+HS04636	blastn	match_part	4339	4423	85	+	.	ID=HS04636:hsp:13:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 718 802 +;Gap=M85
+HS04636	blastn	match_part	4541	4790	250	+	.	ID=HS04636:hsp:14:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 801 1050 +;Gap=M250
+HS04636	blastn	match_part	5068	5360	293	+	.	ID=HS04636:hsp:15:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 1046 1338 +;Gap=M293
+HS04636	blastn	match_part	5859	6008	150	+	.	ID=HS04636:hsp:16:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 1336 1485 +;Gap=M150
+HS04636	blastn	match_part	6490	6903	414	+	.	ID=HS04636:hsp:17:3.2.0.0;Parent=HS04636:hit:8:3.2.0.0;Target=HS04636.g1 1481 1894 +;Gap=M414
+HS04636	est2genome	expressed_sequence_match	1813	6903	8728	+	.	ID=HS04636:hit:9:3.2.0.0;Name=HS04636.g1
+HS04636	est2genome	match_part	1813	1934	8728	+	.	ID=HS04636:hsp:18:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 127 248 +;Gap=M122
+HS04636	est2genome	match_part	2055	2198	8728	+	.	ID=HS04636:hsp:19:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144
+HS04636	est2genome	match_part	2852	2995	8728	+	.	ID=HS04636:hsp:20:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 393 536 +;Gap=M144
+HS04636	est2genome	match_part	3426	3607	8728	+	.	ID=HS04636:hsp:21:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 537 718 +;Gap=M182
+HS04636	est2genome	match_part	4340	4423	8728	+	.	ID=HS04636:hsp:22:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 719 802 +;Gap=M84
+HS04636	est2genome	match_part	4543	4789	8728	+	.	ID=HS04636:hsp:23:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 803 1049 +;Gap=M247
+HS04636	est2genome	match_part	5072	5358	8728	+	.	ID=HS04636:hsp:24:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 1050 1336 +;Gap=M287
+HS04636	est2genome	match_part	5860	6007	8728	+	.	ID=HS04636:hsp:25:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 1337 1484 +;Gap=M148
+HS04636	est2genome	match_part	6494	6903	8728	+	.	ID=HS04636:hsp:26:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 1485 1894 +;Gap=M410
diff -r 326f9c294b09 -r f1912d5575df test-data/evidences_reuse.gff3
--- a/test-data/evidences_reuse.gff3	Fri May 03 07:50:37 2019 -0400
+++ b/test-data/evidences_reuse.gff3	Mon Dec 28 23:19:28 2020 +0000
@@ -26,7 +26,7 @@
 HS04636	blastn	match_part	2852	2997	146	+	.	ID=HS04636:hsp:3:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 393 538 +;Gap=M146
 HS04636	blastn	match_part	3424	3609	186	+	.	ID=HS04636:hsp:4:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 535 720 +;Gap=M186
 HS04636	blastn	match_part	4339	4423	85	+	.	ID=HS04636:hsp:5:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 718 802 +;Gap=M85
-HS04636	blastn	match_part	4541	4790	250	+	.	ID=HS04636:hsp:6:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 801 1050 +;Gap=M250
+HS04636	blastn	match_part	4542	4790	249	+	.	ID=HS04636:hsp:6:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 802 1050 +;Gap=M249
 HS04636	blastn	match_part	5068	5360	293	+	.	ID=HS04636:hsp:7:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 1046 1338 +;Gap=M293
 HS04636	blastn	match_part	5859	6008	150	+	.	ID=HS04636:hsp:8:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 1336 1485 +;Gap=M150
 HS04636	blastn	match_part	6490	6903	414	+	.	ID=HS04636:hsp:9:3.12.0.0;Parent=HS04636:hit:0:3.12.0.0;Target=HS04636.g1 1481 1894 +;Gap=M414