# HG changeset patch
# User iuc
# Date 1508443160 14400
# Node ID 060ea7339911031c966e974fed91c3a622aca891

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e

diff -r 000000000000 -r 060ea7339911 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Oct 19 15:59:20 2017 -0400
@@ -0,0 +1,17 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">maker</requirement>
+            <yield />
+        </requirements>
+    </xml>
+    <token name="@VERSION@">2.31.9</token>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1002/0471250953.bi0411s48</citation>
+        </citations>
+    </xml>
+
+</macros>
diff -r 000000000000 -r 060ea7339911 map_ids.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/map_ids.xml	Thu Oct 19 15:59:20 2017 -0400
@@ -0,0 +1,39 @@
+<?xml version="1.0"?>
+<tool id="maker_map_ids" name="Map annotation ids" profile="16.04" version="@VERSION@">
+    <description>on a Maker annotation</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command><![CDATA[
+        cp '${maker_gff}' '${renamed}' &&
+        maker_map_ids --prefix '${prefix}' --justify ${justify} '${maker_gff}' > '${id_map}' &&
+        map_gff_ids '${id_map}' '${renamed}'
+    ]]></command>
+    <inputs>
+        <param name="maker_gff" type="data" format="gff" label="Maker annotation where to change ids"/>
+        <param name="prefix" type="text" label="Prefix for ids"/>
+        <param name="justify" type="integer" value="6" min="2" max="20" label="Justify numeric ids to this length"/>
+    </inputs>
+    <outputs>
+        <data format="gff" name="renamed" label="${tool.name} on ${on_string}: renamed GFF"/>
+        <data format="tabular" name="id_map" label="${tool.name} on ${on_string}: ID map"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="maker_gff" value="annot.gff3"/>
+            <param name="prefix" value="YES"/>
+            <param name="justify" value="6"/>
+            <output name="renamed" file="annot_mapped.gff3"/>
+            <output name="id_map" file="id_map.tsv"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on seusequent runs. MAKER's inputs are minimal and its ouputs can be directly loaded into a GMOD database. They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER should prove especially useful for emerging model organism projects with minimal bioinformatics expertise and computer resources.
+
+        This tool will automatically assign new ids to a Maker annotation respecting a specified pattern.
+
+        .. _Maker: http://www.yandell-lab.org/software/maker.html
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
diff -r 000000000000 -r 060ea7339911 test-data/annot.gff3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annot.gff3	Thu Oct 19 15:59:20 2017 -0400
@@ -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 000000000000 -r 060ea7339911 test-data/annot_human.gff3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annot_human.gff3	Thu Oct 19 15:59:20 2017 -0400
@@ -0,0 +1,44 @@
+##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
+###
+###
+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
+###
+###
diff -r 000000000000 -r 060ea7339911 test-data/annot_mapped.gff3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annot_mapped.gff3	Thu Oct 19 15:59:20 2017 -0400
@@ -0,0 +1,43 @@
+##gff-version 3
+HS08198	maker	gene	352	1848	.	+	.	ID=YES000002;Name=YES000002;Alias=maker-HS08198-exonerate_est2genome-gene-0.0;
+HS08198	maker	mRNA	352	1848	2869	+	.	ID=YES000002-RA;Parent=YES000002;Name=YES000002-RA;Alias=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_QI=70|1|1|1|0|0|7|0|192;_eAED=0.00;
+HS08198	maker	exon	352	397	.	+	.	ID=YES000002-RA:exon:9;Parent=YES000002-RA;
+HS08198	maker	exon	421	582	.	+	.	ID=YES000002-RA:exon:10;Parent=YES000002-RA;
+HS08198	maker	exon	812	894	.	+	.	ID=YES000002-RA:exon:11;Parent=YES000002-RA;
+HS08198	maker	exon	1053	1123	.	+	.	ID=YES000002-RA:exon:12;Parent=YES000002-RA;
+HS08198	maker	exon	1208	1315	.	+	.	ID=YES000002-RA:exon:13;Parent=YES000002-RA;
+HS08198	maker	exon	1587	1688	.	+	.	ID=YES000002-RA:exon:14;Parent=YES000002-RA;
+HS08198	maker	exon	1772	1848	.	+	.	ID=YES000002-RA:exon:15;Parent=YES000002-RA;
+HS08198	maker	five_prime_UTR	352	397	.	+	.	ID=YES000002-RA:five_prime_utr;Parent=YES000002-RA;
+HS08198	maker	five_prime_UTR	421	444	.	+	.	ID=YES000002-RA:five_prime_utr;Parent=YES000002-RA;
+HS08198	maker	CDS	445	582	.	+	0	ID=YES000002-RA:cds;Parent=YES000002-RA;
+HS08198	maker	CDS	812	894	.	+	0	ID=YES000002-RA:cds;Parent=YES000002-RA;
+HS08198	maker	CDS	1053	1123	.	+	1	ID=YES000002-RA:cds;Parent=YES000002-RA;
+HS08198	maker	CDS	1208	1315	.	+	2	ID=YES000002-RA:cds;Parent=YES000002-RA;
+HS08198	maker	CDS	1587	1688	.	+	2	ID=YES000002-RA:cds;Parent=YES000002-RA;
+HS08198	maker	CDS	1772	1848	.	+	2	ID=YES000002-RA:cds;Parent=YES000002-RA;
+###
+###
+HS04636	maker	gene	1813	6903	.	+	.	ID=YES000001;Name=YES000001;Alias=maker-HS04636-exonerate_est2genome-gene-0.0;
+HS04636	maker	mRNA	1813	6903	8728	+	.	ID=YES000001-RA;Parent=YES000001;Name=YES000001-RA;Alias=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_QI=49|1|1|1|0|0|9|0|572;_eAED=0.00;
+HS04636	maker	exon	1813	1934	.	+	.	ID=YES000001-RA:exon:0;Parent=YES000001-RA;
+HS04636	maker	exon	2055	2198	.	+	.	ID=YES000001-RA:exon:1;Parent=YES000001-RA;
+HS04636	maker	exon	2852	2995	.	+	.	ID=YES000001-RA:exon:2;Parent=YES000001-RA;
+HS04636	maker	exon	3426	3607	.	+	.	ID=YES000001-RA:exon:3;Parent=YES000001-RA;
+HS04636	maker	exon	4340	4423	.	+	.	ID=YES000001-RA:exon:4;Parent=YES000001-RA;
+HS04636	maker	exon	4543	4789	.	+	.	ID=YES000001-RA:exon:5;Parent=YES000001-RA;
+HS04636	maker	exon	5072	5358	.	+	.	ID=YES000001-RA:exon:6;Parent=YES000001-RA;
+HS04636	maker	exon	5860	6007	.	+	.	ID=YES000001-RA:exon:7;Parent=YES000001-RA;
+HS04636	maker	exon	6494	6903	.	+	.	ID=YES000001-RA:exon:8;Parent=YES000001-RA;
+HS04636	maker	five_prime_UTR	1813	1861	.	+	.	ID=YES000001-RA:five_prime_utr;Parent=YES000001-RA;
+HS04636	maker	CDS	1862	1934	.	+	0	ID=YES000001-RA:cds;Parent=YES000001-RA;
+HS04636	maker	CDS	2055	2198	.	+	2	ID=YES000001-RA:cds;Parent=YES000001-RA;
+HS04636	maker	CDS	2852	2995	.	+	2	ID=YES000001-RA:cds;Parent=YES000001-RA;
+HS04636	maker	CDS	3426	3607	.	+	2	ID=YES000001-RA:cds;Parent=YES000001-RA;
+HS04636	maker	CDS	4340	4423	.	+	0	ID=YES000001-RA:cds;Parent=YES000001-RA;
+HS04636	maker	CDS	4543	4789	.	+	0	ID=YES000001-RA:cds;Parent=YES000001-RA;
+HS04636	maker	CDS	5072	5358	.	+	2	ID=YES000001-RA:cds;Parent=YES000001-RA;
+HS04636	maker	CDS	5860	6007	.	+	0	ID=YES000001-RA:cds;Parent=YES000001-RA;
+HS04636	maker	CDS	6494	6903	.	+	2	ID=YES000001-RA:cds;Parent=YES000001-RA;
+###
+###
diff -r 000000000000 -r 060ea7339911 test-data/annot_model.gff3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annot_model.gff3	Thu Oct 19 15:59:20 2017 -0400
@@ -0,0 +1,41 @@
+##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 000000000000 -r 060ea7339911 test-data/annot_norm.gff3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annot_norm.gff3	Thu Oct 19 15:59:20 2017 -0400
@@ -0,0 +1,41 @@
+##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 000000000000 -r 060ea7339911 test-data/annot_proc.gff3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annot_proc.gff3	Thu Oct 19 15:59:20 2017 -0400
@@ -0,0 +1,3 @@
+##gff-version 3
+###
+###
diff -r 000000000000 -r 060ea7339911 test-data/annot_reuse.gff3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annot_reuse.gff3	Thu Oct 19 15:59:20 2017 -0400
@@ -0,0 +1,43 @@
+##gff-version 3
+HS08198	maker	gene	352	1848	.	+	.	ID=maker-HS08198-est2genome-gene-0.0;Name=maker-HS08198-est2genome-gene-0.0;score=2869
+HS08198	maker	mRNA	352	1848	2869	+	.	ID=maker-HS08198-est2genome-gene-0.0-mRNA-1;Parent=maker-HS08198-est2genome-gene-0.0;Name=maker-HS08198-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-est2genome-gene-0.0-mRNA-1:exon:9;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	421	582	.	+	.	ID=maker-HS08198-est2genome-gene-0.0-mRNA-1:exon:10;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	812	894	.	+	.	ID=maker-HS08198-est2genome-gene-0.0-mRNA-1:exon:11;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	1053	1123	.	+	.	ID=maker-HS08198-est2genome-gene-0.0-mRNA-1:exon:12;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	1208	1315	.	+	.	ID=maker-HS08198-est2genome-gene-0.0-mRNA-1:exon:13;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	1587	1688	.	+	.	ID=maker-HS08198-est2genome-gene-0.0-mRNA-1:exon:14;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	1772	1848	.	+	.	ID=maker-HS08198-est2genome-gene-0.0-mRNA-1:exon:15;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1
+HS08198	maker	five_prime_UTR	352	397	.	+	.	ID=maker-HS08198-est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1
+HS08198	maker	five_prime_UTR	421	444	.	+	.	ID=maker-HS08198-est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	445	582	.	+	0	ID=maker-HS08198-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	812	894	.	+	0	ID=maker-HS08198-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	1053	1123	.	+	1	ID=maker-HS08198-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	1208	1315	.	+	2	ID=maker-HS08198-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	1587	1688	.	+	2	ID=maker-HS08198-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	1772	1848	.	+	2	ID=maker-HS08198-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1
+###
+###
+HS04636	maker	gene	1813	6903	.	+	.	ID=maker-HS04636-est2genome-gene-0.0;Name=maker-HS04636-est2genome-gene-0.0;score=8728
+HS04636	maker	mRNA	1813	6903	8728	+	.	ID=maker-HS04636-est2genome-gene-0.0-mRNA-1;Parent=maker-HS04636-est2genome-gene-0.0;Name=maker-HS04636-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-est2genome-gene-0.0-mRNA-1:exon:0;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	2055	2198	.	+	.	ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:exon:1;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	2852	2995	.	+	.	ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:exon:2;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	3426	3607	.	+	.	ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:exon:3;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	4340	4423	.	+	.	ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:exon:4;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	4543	4789	.	+	.	ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:exon:5;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	5072	5358	.	+	.	ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:exon:6;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	5860	6007	.	+	.	ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:exon:7;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	6494	6903	.	+	.	ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:exon:8;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1
+HS04636	maker	five_prime_UTR	1813	1861	.	+	.	ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	1862	1934	.	+	0	ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	2055	2198	.	+	2	ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	2852	2995	.	+	2	ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	3426	3607	.	+	2	ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	4340	4423	.	+	0	ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	4543	4789	.	+	0	ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	5072	5358	.	+	2	ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	5860	6007	.	+	0	ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	6494	6903	.	+	2	ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1
+###
+###
diff -r 000000000000 -r 060ea7339911 test-data/est.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/est.fasta	Thu Oct 19 15:59:20 2017 -0400
@@ -0,0 +1,35 @@
+>HS04636.g1
+atgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtca
+tgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtcaa
+aaccgaggtgtatgtatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggagaaaactg
+ctcaacaccggaatttttgacaagaataaaattatttctgaaacccactccaaacacagtgcactacatacttacccact
+tcaagggattttggaacgttgtgaataacattcccttccttcgaaatgcaattatgagttatgtcttgacatccagatca
+catttgattgacagtccaccaacttacaatgctgactatggctacaaaagctgggaagccttctctaacctctcctatta
+tactagagcccttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtaaaaagcagcttcctgattcaa
+atgagattgtggaaaaattgcttctaagaagaaagttcatccctgatccccagggctcaaacatgatgtttgcattcttt
+gcccagcacttcacgcatcagtttttcaagacagatcataagcgagggccagctttcaccaacgggctgggccatggggt
+ggacttaaatcatatttacggtgaaactctggctagacagcgtaaactgcgccttttcaaggatggaaaaatgaaatatc
+agataattgatggagagatgtatcctcccacagtcaaagatactcaggcagagatgatctaccctcctcaagtccctgag
+catctacggtttgctgtggggcaggaggtctttggtctggtgcctggtctgatgatgtatgccacaatctggctgcggga
+acacaacagagtatgcgatgtgcttaaacaggagcatcctgaatggggtgatgagcagttgttccagacaagcaggctaa
+tactgataggagagactattaagattgtgattgaagattatgtgcaacacttgagtggctatcacttcaaactgaaattt
+gacccagaactacttttcaacaaacaattccagtaccaaaatcgtattgctgctgaatttaacaccctctatcactggca
+tccccttctgcctgacacctttcaaattcatgaccagaaatacaactatcaacagtttatctacaacaactctatattgc
+tggaacatggaattacccagtttgttgaatcattcaccaggcaaattgctggcagggttgctggtggtaggaatgttcca
+cccgcagtacagaaagtatcacaggcttccattgaccagagcaggcagatgaaataccagtcttttaatgagtaccgcaa
+acgctttatgctgaagccctatgaatcatttgaagaacttacaggagaaaaggaaatgtctgcagagttggaagcactct
+atggtgacatcgatgctgtggagctgtatcctgcccttctggtagaaaagcctcggccagatgccatctttggtgaaacc
+atggtagaagttggagcaccattctccttgaaaggacttatgggtaatgttatatgttctcctgcctactggaagccaag
+cacttttggtggagaagtgggttttcaaatcatcaacactgcctcaattcagtctctcatctgcaataacgtgaagggct
+gtccctttacttcattcagtgttccagatccagagctcattaaaacagtcaccatcaatgcaagttcttcccgctccgga
+ctagatgatatcaatcccacagtactactaaaagaacgttcgactgaactgtag
+>HS08198.g2
+atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccaca
+tgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccacgc
+cggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgaggc
+caccacactgcatgtggctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcagg
+tgcgccagctctatggagacacaggggtcctcggccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcacgtg
+gttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcgggcggggcagctgtcagtgaagctctacgc
+ccgctcgctccctgtgagcgactcggtcctgagtgggtttgagcagcgggtccaggaggcccacctgactgaggaccaga
+tcttctacttccccaagtacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggggca
+agcatggcggcgtggtga
diff -r 000000000000 -r 060ea7339911 test-data/evidences.gff3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/evidences.gff3	Thu Oct 19 15:59:20 2017 -0400
@@ -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	9419	9435	16	+	.	ID=HS04636:hit:0:1.3.0.0;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:0:1.3.0.0;Parent=HS04636:hit:0:1.3.0.0;Target=species:%2528A%2529n|genus:Simple_repeat 1 17 +
+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	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	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	4518	4541	17	+	.	ID=HS04636:hit:5:1.3.0.0;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:5:1.3.0.0;Parent=HS04636:hit:5:1.3.0.0;Target=species:%2528TTTA%2529n|genus:Simple_repeat 1 24 +
+HS04636	repeatmasker	match	3852	3888	12	+	.	ID=HS04636:hit:6:1.3.0.0;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:6:1.3.0.0;Parent=HS04636:hit:6:1.3.0.0;Target=species:%2528TTGTAAT%2529n|genus:Simple_repeat 1 37 +
+HS04636	repeatmasker	match	3840	3847	17	+	.	ID=HS04636:hit:7:1.3.0.0;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:7:1.3.0.0;Parent=HS04636:hit:7:1.3.0.0;Target=species:%2528ATAC%2529n|genus:Simple_repeat 3 57 +
+###
+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 000000000000 -r 060ea7339911 test-data/evidences_human.gff3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/evidences_human.gff3	Thu Oct 19 15:59:20 2017 -0400
@@ -0,0 +1,99 @@
+##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	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
+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	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
diff -r 000000000000 -r 060ea7339911 test-data/evidences_model.gff3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/evidences_model.gff3	Thu Oct 19 15:59:20 2017 -0400
@@ -0,0 +1,42 @@
+##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
+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
diff -r 000000000000 -r 060ea7339911 test-data/evidences_norm.gff3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/evidences_norm.gff3	Thu Oct 19 15:59:20 2017 -0400
@@ -0,0 +1,42 @@
+##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
+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
diff -r 000000000000 -r 060ea7339911 test-data/evidences_proc.gff3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/evidences_proc.gff3	Thu Oct 19 15:59:20 2017 -0400
@@ -0,0 +1,5 @@
+##gff-version 3
+HS08198	.	contig	1	2344	.	.	.	ID=HS08198;Name=HS08198
+###
+HS04636	.	contig	1	9453	.	.	.	ID=HS04636;Name=HS04636
+###
diff -r 000000000000 -r 060ea7339911 test-data/evidences_reuse.gff3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/evidences_reuse.gff3	Thu Oct 19 15:59:20 2017 -0400
@@ -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:11:3.12.0.0;Name=HS08198.g2;score=140
+HS08198	blastn	match_part	444	583	140	+	.	ID=HS08198:hsp:28:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 79 218 +;Gap=M140
+HS08198	blastn	match_part	445	523	79	+	.	ID=HS08198:hsp:29:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 1 79 +;Gap=M79
+HS08198	blastn	match_part	808	895	88	+	.	ID=HS08198:hsp:30:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 214 301 +;Gap=M88
+HS08198	blastn	match_part	1053	1123	71	+	.	ID=HS08198:hsp:31:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 301 371 +;Gap=M71
+HS08198	blastn	match_part	1206	1315	110	+	.	ID=HS08198:hsp:32:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 370 479 +;Gap=M110
+HS08198	blastn	match_part	1586	1689	104	+	.	ID=HS08198:hsp:33:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 479 582 +;Gap=M104
+HS08198	blastn	match_part	1771	1848	78	+	.	ID=HS08198:hsp:34:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 581 658 +;Gap=M78
+HS08198	est2genome	expressed_sequence_match	352	1848	2869	+	.	ID=HS08198:hit:12:3.12.0.0;Name=HS08198.g2;score=2869
+HS08198	est2genome	match_part	352	397	2869	+	.	ID=HS08198:hsp:35:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 3 52 +;Gap=M46
+HS08198	est2genome	match_part	421	582	2869	+	.	ID=HS08198:hsp:36:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 53 217 +;Gap=M162
+HS08198	est2genome	match_part	812	894	2869	+	.	ID=HS08198:hsp:37:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 218 300 +;Gap=M83
+HS08198	est2genome	match_part	1053	1123	2869	+	.	ID=HS08198:hsp:38:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 301 371 +;Gap=M71
+HS08198	est2genome	match_part	1208	1315	2869	+	.	ID=HS08198:hsp:39:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 372 479 +;Gap=M108
+HS08198	est2genome	match_part	1587	1688	2869	+	.	ID=HS08198:hsp:40:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 480 581 +;Gap=M102
+HS08198	est2genome	match_part	1772	1848	2869	+	.	ID=HS08198:hsp:41:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 582 658 +;Gap=M77
+HS04636	.	contig	1	9453	.	.	.	ID=HS04636;Name=HS04636
+###
+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	6028	6072	21	+	.	ID=HS04636:hit:1:1.3.0.0;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:1:1.3.0.0;Parent=HS04636:hit:1:1.3.0.0;Target=species:%2528TTGT%2529n|genus:Simple_repeat 1 46 +
+HS04636	repeatmasker	match	3840	3847	17	+	.	ID=HS04636:hit:2:1.3.0.0;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:2:1.3.0.0;Parent=HS04636:hit:2:1.3.0.0;Target=species:%2528ATAC%2529n|genus:Simple_repeat 3 57 +
+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	9419	9435	16	+	.	ID=HS04636:hit:4:1.3.0.0;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:4:1.3.0.0;Parent=HS04636:hit:4:1.3.0.0;Target=species:%2528A%2529n|genus:Simple_repeat 1 17 +
+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	6918	6977	17	+	.	ID=HS04636:hit:6:1.3.0.0;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:6:1.3.0.0;Parent=HS04636:hit:6:1.3.0.0;Target=species:%2528TATT%2529n|genus:Simple_repeat 1 54 +
+HS04636	repeatmasker	match	4518	4541	17	+	.	ID=HS04636:hit:7:1.3.0.0;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:7:1.3.0.0;Parent=HS04636:hit:7:1.3.0.0;Target=species:%2528TTTA%2529n|genus:Simple_repeat 1 24 +
+###
+HS04636	blastn	expressed_sequence_match	1815	6903	120	+	.	ID=HS04636:hit:8:3.12.0.0;Name=HS04636.g1;score=120
+HS04636	blastn	match_part	1815	1934	120	+	.	ID=HS04636:hsp:8:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 129 248 +;Gap=M120
+HS04636	blastn	match_part	1815	1845	31	+	.	ID=HS04636:hsp:9:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 50 80 +;Gap=M31
+HS04636	blastn	match_part	2055	2198	144	+	.	ID=HS04636:hsp:10:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 249 392 +;Gap=M144
+HS04636	blastn	match_part	2852	2997	146	+	.	ID=HS04636:hsp:11:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 393 538 +;Gap=M146
+HS04636	blastn	match_part	3424	3609	186	+	.	ID=HS04636:hsp:12:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 535 720 +;Gap=M186
+HS04636	blastn	match_part	4339	4423	85	+	.	ID=HS04636:hsp:13:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 718 802 +;Gap=M85
+HS04636	blastn	match_part	4541	4790	250	+	.	ID=HS04636:hsp:14:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 801 1050 +;Gap=M250
+HS04636	blastn	match_part	5068	5360	293	+	.	ID=HS04636:hsp:15:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 1046 1338 +;Gap=M293
+HS04636	blastn	match_part	5859	6008	150	+	.	ID=HS04636:hsp:16:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 1336 1485 +;Gap=M150
+HS04636	blastn	match_part	6490	6903	414	+	.	ID=HS04636:hsp:17:3.12.0.0;Parent=HS04636:hit:8:3.12.0.0;Target=HS04636.g1 1481 1894 +;Gap=M414
+HS04636	est2genome	expressed_sequence_match	1813	6903	8728	+	.	ID=HS04636:hit:9:3.12.0.0;Name=HS04636.g1;score=8728
+HS04636	est2genome	match_part	1813	1934	8728	+	.	ID=HS04636:hsp:18:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 127 248 +;Gap=M122
+HS04636	est2genome	match_part	2055	2198	8728	+	.	ID=HS04636:hsp:19:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 249 392 +;Gap=M144
+HS04636	est2genome	match_part	2852	2995	8728	+	.	ID=HS04636:hsp:20:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 393 536 +;Gap=M144
+HS04636	est2genome	match_part	3426	3607	8728	+	.	ID=HS04636:hsp:21:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 537 718 +;Gap=M182
+HS04636	est2genome	match_part	4340	4423	8728	+	.	ID=HS04636:hsp:22:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 719 802 +;Gap=M84
+HS04636	est2genome	match_part	4543	4789	8728	+	.	ID=HS04636:hsp:23:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 803 1049 +;Gap=M247
+HS04636	est2genome	match_part	5072	5358	8728	+	.	ID=HS04636:hsp:24:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 1050 1336 +;Gap=M287
+HS04636	est2genome	match_part	5860	6007	8728	+	.	ID=HS04636:hsp:25:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 1337 1484 +;Gap=M148
+HS04636	est2genome	match_part	6494	6903	8728	+	.	ID=HS04636:hsp:26:3.12.0.0;Parent=HS04636:hit:9:3.12.0.0;Target=HS04636.g1 1485 1894 +;Gap=M410
diff -r 000000000000 -r 060ea7339911 test-data/genome.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome.fasta	Thu Oct 19 15:59:20 2017 -0400
@@ -0,0 +1,200 @@
+>HS04636
+gagctcacattaactatttacagggtaactgcttaggaccagtattatgaggagaattta
+cctttcccgcctctctttccaagaaacaaggagggggtgaaggtacggagaacagtattt
+cttctgttgaaagcaacttagctacaaagataaattacagctatgtacactgaaggtagc
+tatttcattccacaaaataagagttttttaaaaagctatgtatgtatgtgctgcatatag
+agcagatatacagcctattaagcgtcgtcactaaaacataaaacatgtcagcctttctta
+accttactcgccccagtctgtcccgacgtgacttcctcgaccctctaaagacgtacagac
+cagacacggcggcggcggcgggagaggggattccctgcgcccccggacctcagggccgct
+cagattcctggagaggaagccaagtgtccttctgccctcccccggtatcccatccaaggc
+gatcagtccagaactggctctcggaagcgctcgggcaaagactgcgaagaagaaaagaca
+tctggcggaaacctgtgcgcctggggcggtggaactcggggaggagagggagggatcaga
+caggagagtggggactaccccctctgctcccaaattggggcagcttcctgggtttccgat
+tttctcatttccgtgggtaaaaaaccctgcccccaccgggcttacgcaatttttttaagg
+ggagaggagggaaaaaatttgtgggggggtacgaaaaggcggaaagaaacagtcattcac
+atgggcttggttttcagtcttataaaaaggaaggttctctcggttagcgaccaattgtca
+tacgacttgcagtgagcgtcaggagcacgtccaggaactcctcagcagcgcctccttcag
+ctccacagccagacgccctcagacagcaaagcctacccccgcgccgcgccctgcccgccg
+ctcggatgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacaggtg
+agtacctggcgccgcgcaccggggactccggttccacgcacccgggcagagtttccgctc
+tgacctcctgggtctatcccagtactccgacttctctccgaatagagaagctacgtgact
+tgggaaagagcttggaccgctagagtccgaaagaactccgtggatattccagctttccca
+caagcactgatcattatgagccagttacttaaccgatctgagacactctcacctcctaaa
+tagggatagatgatactaatttgcaggttgtcattatgataagacaggatctgatcaata
+tatgtgaattgtttatatttggaacctttttattgagtggaagaagttgttttaaatatt
+ctagtcagttctttcctgctcccaggaaagcccggattatgttttaagataagcaaaatg
+tcttaaaagtaagctgttttactttgaatttttccctaaatgttgattagtgtactagat
+ccattttaatttggaaagtgaagtgctacttatttgaacttcttaaaaatgctaatttta
+acatctaaagagttaactaagaaaagcttagtaacatgatgtaccaagttgaatatgctg
+ttatccttatttagaatagaaaattggtatttctacgttttatccattctaaggcaggtt
+aaaaaattgtatttccatgactacctatatatttcttgaatttattattgtaaagttgat
+tcatagtcaaacaattaaatgtttaaattaagattaagacactagagaatgatttatttg
+ctgtcctttaattgcagcaaatccttgctgttcccacccatgtcaaaaccgaggtgtatg
+tatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggaga
+aaactgctcaacacgtaagtttgtcctttggttgcctcattaggagtggggctggataca
+gttatcattgtatagatttgtgtcttataatgagtcccattaatttctccctccctttct
+tcgtcttcttgcagcggaatttttgacaagaataaaattatttctgaaacccactccaaa
+cacagtgcactacatacttacccacttcaagggattttggaacgttgtgaataacattcc
+cttccttcgaaatgcaattatgagttatgtcttgacatgtaagtacaagtgtctttctaa
+ggtttttagccttctcaaagaaaaatatgctttataatactgtaagcctaatctaaaaac
+atatttccaagcttatcaaaaagactttaagatagcttttaagtttgccttccatcttaa
+tcgccaaaaatattgacatttagtcccatccagtttatacagtctgctcacaactctgta
+tacctcttctaacctttactgtttggtcagtttgtggaggtagcatggtccagctgttta
+ttgaatgcccatgggccacagaattgttctgaacatgtagcacccattaaaataaatttg
+gatttggatcagcaagaaaataactttccatgattctaaagtgggtgccatactcagcca
+ttcctttcataggcctcttggatagtgagcagatggctacctgaaaaatcaatattgcca
+gattataatgtgcagagtatatgtattttattaaagatgtatttcaagtggccattagac
+tataaagtgtagttgtttaaaaatagattttttttattttggagttacattcaacctcag
+gtgccactttccacattttacaataaaaataatggttgatttacttaacaaatgagaata
+aataaaacatttttttctttgaaaatttcagccagatcacatttgattgacagtccacca
+acttacaatgctgactatggctacaaaagctgggaagccttctctaacctctcctattat
+actagagcccttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtgag
+taagaagaatccattagagatgtattaactataagacgggctgcattgctgccaaaaaaa
+aaaattgaccttagactaccatttatttattaacaaaagcagtttttacttttagcatgg
+ttatctatgggtattttttaaagtatgagtctatataaactattatgtaaaagcaaatga
+gcgtcttggtataatgtcttaatattttcaaattatttctttagaaatgaaataattcta
+attaaaatagataaaatcattcagtaagaagttgttccaccatatcttagaactgttgtt
+tatattatgatcctattcacaattgtaattctcatataaatgaagaattcttggtagatt
+gacagtcaccatctcctttcttgaatacatagatggattcttaccttagctttctcattt
+ttcaggtaaaaagcagcttcctgattcaaatgagattgtggaaaaattgcttctaagaag
+aaagttcatccctgatccccagggctcaaacatgatgtttgcattctttgcccagcactt
+cacgcatcagtttttcaagacagatcataagcgagggccagctttcaccaacgggctggg
+ccatggggtaagatagagttaatatcttagagttagtaaaattataccaaatcatagtca
+agggctaacattaaaggagatatacagatagatagatccaaataacttatccactttttt
+taaaaagaagtcttatctataaaaaccttaaaggaattttccatttacttcactggtcta
+gtaaaattatacacacacacagacatgcacacacatatataaacattcacacacatacat
+atgtacaggtattgttatttgtaatttgacccttgtattttttagtttaaaatgttagta
+ctgcaaaatgttatgtcctcaaaaacacattgtaccatgattatgccgctttcaatattg
+taaagtgaggtttttgccgcattattattttttggatttcaatagcatagcttcaagtta
+ttcgtaagaattttttataaataatacatttttatacttttttataattaccatatcatc
+atagtgaagtatataatatatatgatataagctcaatatagtatattaattccgttaaac
+acaaagacatatcagtttgtagctttggtggataaacaaattaatttagcaattcatggc
+tatgaaaaatgtatattttatttaaaaattttaaagaaagctaaatgatcaaattattta
+atgatgaattatatgatagacactttatataagaaaaacttcaacagcaacaaattaaaa
+ttttttcatcattttctaggtggacttaaatcatatttacggtgaaactctggctagaca
+gcgtaaactgcgccttttcaaggatggaaaaatgaaatatcaggtatgcttcctttgact
+attaagacttagttattaccgcttatacccatattttaaaatccctaaaaatgtgttcct
+taactttttaactgatgtttatttatttatttatttttttagataattgatggagagatg
+tatcctcccacagtcaaagatactcaggcagagatgatctaccctcctcaagtccctgag
+catctacggtttgctgtggggcaggaggtctttggtctggtgcctggtctgatgatgtat
+gccacaatctggctgcgggaacacaacagagtatgcgatgtgcttaaacaggagcatcct
+gaatggggtgatgagcagttgttccagacaagcaggctaatactgataggtaaacaagaa
+aatgatttatataaaaccctcttccccagggaaaattagtgtgctatctttgttatgttt
+tgagtaaatgacaagatgtggtaaatgaaaactcacacattctatatacattaaatatgt
+aagcatgactgataaaatagctatcttttgatactgacaaggaagaaaacagaaatgaag
+gaatagcaaattttaaaaattgcattccagttgcttgaaagcttgtgatcagatgcaata
+aatgtttttattatttattttgtgcaaataggagagactattaagattgtgattgaagat
+tatgtgcaacacttgagtggctatcacttcaaactgaaatttgacccagaactacttttc
+aacaaacaattccagtaccaaaatcgtattgctgctgaatttaacaccctctatcactgg
+catccccttctgcctgacacctttcaaattcatgaccagaaatacaactatcaacagttt
+atctacaacaactctatattgctggaacatggaattacccagtttgttgaatcattcacc
+aggcaaattgctggcagggtaagcattattattgaaaaccaaaacaaaagactagtcagt
+aactttagaatttctgccacggaaattatttttcttaaacttactaaaagagtagttagt
+tatattgctagtaaaattattttattgatataagaagcctaactttgtttgaaaagtcta
+aacttttagtctagtctacagttgtcagacaaatagcaaattgtacccctaccttaaaaa
+tattttcaaaaagtatctataatcttataggaataaatattttaggcttgaatactagtg
+ttatttttgaaatgtaaaaaggcaaattagttctaggctggtgtcccattgaattttaag
+cagagctcctgttgaaatgtaggtaagcatctttccagcaaataaaaattgtctccgctg
+ggagtttcagttttacctgatttgtacctaaggcaagctgaatacaaacagtaaatatgc
+ctaaaattcttgttttacaactaattttactttccacaggttgctggtggtaggaatgtt
+ccacccgcagtacagaaagtatcacaggcttccattgaccagagcaggcagatgaaatac
+cagtcttttaatgagtaccgcaaacgctttatgctgaagccctatgaatcatttgaagaa
+cttacaggtaagaaacagtttctaaacttcttcgttttttgtttgtttgtttgtttttgt
+tgtttttggttttcttttcgagatggagccgccctctgtcacccaggctggagtgcagtg
+gcgccatctcggctcactgcaacctccgcctcctgggttcaagcaattctcctgcctcaa
+cttcctgagtagctgggactacaggctcacgtcgcacgcatggataattttttgtatttt
+cagtatagacggggtttcaccgtgttagccaggctggtctcaaactcctgacctagtgat
+ccgccggcttcggcctcccgaagtgctgggattacaggcgtgagccaccgcgcctggccc
+ctaaacttcttaaaagaatcaggggtcaaatggaaacagagaagttggcagcaaattgag
+caaaagaatcaaactgttttttattttgtgaagtttgacattggttgtatctctgtcttc
+atcgccttcacaggagaaaaggaaatgtctgcagagttggaagcactctatggtgacatc
+gatgctgtggagctgtatcctgcccttctggtagaaaagcctcggccagatgccatcttt
+ggtgaaaccatggtagaagttggagcaccattctccttgaaaggacttatgggtaatgtt
+atatgttctcctgcctactggaagccaagcacttttggtggagaagtgggttttcaaatc
+atcaacactgcctcaattcagtctctcatctgcaataacgtgaagggctgtccctttact
+tcattcagtgttccagatccagagctcattaaaacagtcaccatcaatgcaagttcttcc
+cgctccggactagatgatatcaatcccacagtactactaaaagaacgttcgactgaactg
+tagaagtctaatgatcatatttatttatttatatgaaccatgtctattaatttaattatt
+taataatatttatattaaactccttatgttacttaacatcttctgtaacagaagtcagta
+ctcctgttgcggagaaaggagtcatacttgtgaagacttttatgtcactactctaaagat
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+tttaacttatgtaaaagataagtctggaaataaatgtctgtttatttttgtactatttaa
+aaaaaaaaaaaaaaatcgatgtcgactcgagtc
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+tgtgacagcagagtagactctgtcctgggacttggtggtgctacccttggcctcccacag
+tcctgccaccctgctgccgccaccatgctgccccctgggactgcgaccctcttgactctg
+ctcctggcagctggctcgctgggccagaagcctcagaggccacgccggcccgcatccccc
+atcagcaccatccagcccaaggccaattttgatgcgcagcaggtagaagttggggggggt
+agagggaggcaggtagaagttgtgggaggggtagagggagacaggtagaagttgttgcgg
+gggagagggaagcaggtgaagttgtggggggtgtagagggaagcaggtgaggggccctcc
+cacagtgccctcgagttctcccatggtctgcccccagtttgcagggacctggctccttgt
+ggctgtgggctccgcttgccgtttcctgcaggagcagggccaccgggccgaggccaccac
+actgcatgtggctccccagggcacagccatggctgtcagtaccttccgaaagctgtgagt
+cccagagcagccctgcaccctaaccccaaccctcctctcagcccccggacttcagccctg
+ctctggcccctgaccccaccccggctgtggcctggactaggattcctggttggggtctcc
+cagcctgtggtgcctcctccccgcccccccagggatgggatctgctggcaggtgcgccag
+ctctatggagacacaggggtcctcggccgcttcctgcttcaaggtgaggcaggggctgca
+ggtcatgtgggtgggggatgacgcagccactgtggctctctgacatggctactgtggctc
+tgcccagcccgaggcgcccgaggggctgtgcacgtggttgtcgctgagaccgactaccag
+agtttcgctgtcctgtacctggagcgggcggggcagctgtcagtgaagctctacggtatg
+tgggggccagcctctgtgaccaggcaggcgctcaagctctgcacactcactgggccaccc
+cgaggggctgggtgagccatggggacacacttcctttctcccatcctgatcctcctgcta
+agcaggggcccagggagtagtgacagacaggcctggtgtgggagcagggaggagggcccc
+gaggggcaggggacacacagaccccgttcccagagccctccacgccgcctggtgccagga
+ccccaggaaccctgtctgccctgcagcccgctcgctccctgtgagcgactcggtcctgag
+tgggtttgagcagcgggtccaggaggcccacctgactgaggaccagatcttctacttccc
+caagtacggtgagtgtccccagcaggtccccagctcagccacccccactctctggctgat
+gtccagcctgacccctgccttggcgccccaggcttctgcgaggctgcagaccagttccac
+gtcctggacggtgagtgcacagcgggggcaagcatggcggcgtggtgaggggggccactc
+gcaccggctgagtctcgtctctgctgcagaagtgaggaggtgaggccggcacacagctcc
+agtgctgagaagtcagtgccccgagagacgaccccaccagtggggtgcccgctgcctgtc
+ctccgtgaaaccagcctcagatcagggccctgccacccagggcaggggatcttctgccgg
+ctgccccagaggacagtgggtggagtggtacctacttattaaatgtctcagacccctctc
+tgactcttctgtccactctggaccggcgccagtaccaccaaggccctctctgcccccacc
+ccgcctctttaaaagcccggcgctccctgttggctggagtccacgcagggtcactgggcc
+gatttcggctcttgggatttgggaggggagatcctctctggcatatgccatcttgtgccc
+tgctggacctgggggcgtccacgtcactccaaggctgctcttgcctgggccatgcctgca
+gccc
diff -r 000000000000 -r 060ea7339911 test-data/id_map.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/id_map.tsv	Thu Oct 19 15:59:20 2017 -0400
@@ -0,0 +1,4 @@
+maker-HS04636-exonerate_est2genome-gene-0.0	YES000001
+maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1	YES000001-RA
+maker-HS08198-exonerate_est2genome-gene-0.0	YES000002
+maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1	YES000002-RA
diff -r 000000000000 -r 060ea7339911 test-data/local.tar.gz
Binary file test-data/local.tar.gz has changed
diff -r 000000000000 -r 060ea7339911 test-data/snap.hmm
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/snap.hmm	Thu Oct 19 15:59:20 2017 -0400
@@ -0,0 +1,1612 @@
+zoeHMM snap_training 6 8 6 7
+
+<STATES>
+
+Einit	0	0	3	-1	explicit
+Esngl	0	0	150	-1	explicit
+Eterm	0	0	3	-1	explicit
+Exon	0	0	6	-1	explicit
+Inter	0.9	0.9	0	0	geometric
+Intron	0.1	0.1	0	0	geometric
+
+<STATE_TRANSITIONS>
+
+Einit	Intron	1
+Esngl	Inter	1
+Eterm	Inter	1
+Exon	Intron	1
+Inter	Einit	1.000000
+Inter	Esngl	0.000000
+Intron	Eterm	0.153846
+Intron	Exon	0.846154
+
+<PHASE_PREFERENCES>
+
+0.500000
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+
+<STATE_DURATIONS>
+
+Einit 2
+	DEFINED 0 249
+		-2.459 -2.611 -2.781 -2.974 -3.196 
+		-3.459 -3.781 -4.196 -4.781 -5.781 
+		. . . . . 
+		. . . . . 
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+		. . . . . 
+		. . . . . 
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+		. . . . . 
+		. . . . . 
+		. . . . . 
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+		. . . . . 
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+		. . . . . 
+		. . . . . 
+		. . . . . 
+	GEOMETRIC 250 -1
+		3
+
+Esngl 1
+	GEOMETRIC 0 -1
+		1000
+
+Eterm 2
+	DEFINED 0 249
+		-14.718 -14.718 -14.718 -14.718 -14.718 
+		-14.718 -14.718 -14.718 -14.718 -14.718 
+		-14.718 -14.718 -14.718 -14.718 -14.718 
+		-14.718 -14.718 -14.718 -14.718 -14.718 
+		-14.718 -14.718 -14.718 -14.718 -14.718 
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+		-14.718 -14.718 -14.718 -14.718 -14.718 
+		-14.718 -10.052 -9.080 -8.505 -8.095 
+		-7.776 -7.515 -7.294 -7.102 -6.933 
+		-6.782 -6.782 -6.782 -6.782 -6.782 
+		-6.782 -6.782 -6.782 -6.782 -6.782 
+		-6.782 -6.782 -6.782 -6.782 -6.782 
+		-6.782 -6.782 -6.782 -6.782 -6.782 
+		-6.782 -6.782 -6.782 -6.782 -6.782 
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+		-6.782 -6.933 -7.102 -7.294 -7.515 
+		-7.776 -8.095 -8.505 -9.080 -10.052 
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+	GEOMETRIC 250 -1
+		668
+
+Exon 2
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+		-6.846 -6.775 -6.708 -6.644 -6.583 
+		-6.524 -6.553 -6.583 -6.613 -6.644 
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+		-7.260 -7.260 -7.260 -7.260 -7.260 
+		-7.260 -7.360 -7.466 -7.582 -7.707 
+		-7.844 -7.996 -8.165 -8.357 -8.579 
+		-8.841 -8.841 -8.841 -8.841 -8.841 
+		-8.841 -8.841 -8.841 -8.841 -8.841 
+		-8.841 -8.841 -8.841 -8.841 -8.841 
+		-8.841 -8.841 -8.841 -8.841 -8.841 
+		-8.841 -8.841 -8.841 -8.841 -8.841 
+		-8.841 -8.841 -8.841 -8.841 -8.841 
+		-8.841 -8.993 -9.162 -9.353 -9.574 
+		-9.835 -10.154 -10.565 -11.140 -12.111 
+		-16.777 -16.777 -16.777 -16.777 -16.777 
+		-16.777 -16.777 -16.777 -16.777 -16.777 
+		-16.777 -12.111 -11.140 -10.565 -10.154 
+		-9.835 -9.574 -9.353 -9.162 -8.993 
+		-8.841 -8.841 -8.841 -8.841 -8.841 
+		-8.841 -8.841 -8.841 -8.841 -8.841 
+		-8.841 -8.841 -8.841 -8.841 -8.841 
+		-8.841 -8.841 -8.841 -8.841 -8.841 
+		-8.841 -8.841 -8.841 -8.841 -8.841 
+		-8.841 -8.841 -8.841 -8.841 -8.841 
+	GEOMETRIC 250 -1
+		241
+
+Inter 1
+	GEOMETRIC 0 -1
+		500
+
+Intron 1
+	GEOMETRIC 0 -1
+		388
+
+<SEQUENCE_MODELS>
+
+Acceptor SDT 2 1 4 2 0.000
+	AG WMM 30 26 4 0 0.000
+		0.234	-2.087	-0.503	0.913	
+		-0.503	-0.087	0.234	0.234	
+		-0.087	-0.087	-1.087	0.720	
+		-2.087	0.497	-0.503	0.720	
+		0.497	-0.503	-0.503	0.234	
+		0.234	0.234	-1.087	0.234	
+		-0.087	-0.087	-0.087	0.234	
+		-0.503	0.234	-0.503	0.497	
+		-0.503	0.497	-1.087	0.497	
+		-0.087	-1.087	-1.087	1.082	
+		-0.503	0.497	-1.087	0.497	
+		-1.087	0.497	-2.087	0.913	
+		-1.087	-0.503	-1.087	1.234	
+		-1.087	-0.087	-0.503	0.913	
+		-1.087	0.497	-1.087	0.720	
+		-1.087	-0.087	-0.503	0.913	
+		-1.087	-0.087	-0.087	0.720	
+		-0.503	0.497	0.234	-0.503	
+		-0.087	-0.503	-0.503	0.720	
+		-1.087	0.497	-1.087	0.720	
+		-1.087	0.497	-1.087	0.720	
+		-1.087	0.497	-1.087	0.720	
+		-1.087	0.497	-2.087	0.913	
+		-0.087	0.234	-0.087	-0.087	
+		-2.087	1.372	-2.087	-0.087	
+		1.720	-2.087	-2.087	-2.087	
+		-2.087	-2.087	1.720	-2.087	
+		-1.087	0.234	1.082	-2.087	
+		-0.087	0.234	-0.503	0.234	
+		0.234	-0.503	0.497	-0.503	
+	NN TRM 0 0 0 0 0.000
+
+Coding CDS 3 2 4 3 0.000
+	frame0 LUT 5 4 4 0 0.000
+		-0.322	-0.322	0.678	-0.322	
+		0.193	0.193	-0.807	0.193	
+		-0.322	0.678	-0.322	-0.322	
+		-1.170	-0.170	0.415	0.415	
+		-0.322	0.263	0.263	-0.322	
+		-0.322	0.678	-0.322	-0.322	
+		-0.585	0.415	-0.585	0.415	
+		-0.170	-1.170	0.830	-0.170	
+		0.585	-1.000	-1.000	0.585	
+		0.415	0.415	-0.585	-0.585	
+		0.678	-0.322	-0.322	-0.322	
+		0.000	0.000	0.000	0.000	
+		-0.807	0.778	-0.807	0.193	
+		1.000	-0.585	-0.585	-0.585	
+		-0.322	-0.322	0.678	-0.322	
+		-0.322	-0.322	-0.322	0.678	
+		0.126	0.862	-1.459	-0.459	
+		0.415	0.415	-1.170	-0.170	
+		0.415	-0.585	-0.585	0.415	
+		0.000	0.000	0.000	0.000	
+		-0.585	-1.585	1.415	-1.585	
+		0.415	-0.585	-0.585	0.415	
+		-0.585	0.415	0.415	-0.585	
+		-0.807	0.193	0.778	-0.807	
+		0.000	0.000	0.000	0.000	
+		0.000	0.000	0.000	0.000	
+		-0.807	-0.807	0.193	0.778	
+		-1.000	0.000	0.585	0.000	
+		-1.000	0.585	-1.000	0.585	
+		-0.585	-0.585	0.415	0.415	
+		-0.807	0.193	0.778	-0.807	
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+		1.193	-0.807	-0.807	-0.807	
+		-0.585	0.415	0.415	-0.585	
+		1.000	-0.585	-0.585	-0.585	
+		0.778	-0.807	-0.807	0.193	
+		0.415	-0.585	0.415	-0.585	
+		0.000	0.000	0.000	0.000	
+		-0.322	0.678	-0.322	-0.322	
+		-0.322	0.678	-0.322	-0.322	
+		0.000	0.000	0.000	0.000	
+		-0.322	0.678	-0.322	-0.322	
+		0.678	-0.322	-0.322	-0.322	
+		0.000	0.000	0.000	0.000	
+		0.000	0.000	0.000	0.000	
+		-0.322	-0.322	-0.322	0.678	
+		0.778	0.193	-0.807	-0.807	
+		0.541	-0.459	-0.459	0.126	
+		-0.322	0.678	-0.322	-0.322	
+		0.263	0.263	-0.322	-0.322	
+		-0.322	0.678	-0.322	-0.322	
+		-0.585	-0.585	-0.585	1.000	
+		0.415	-0.585	0.415	-0.585	
+		-0.322	-0.322	-0.322	0.678	
+		0.415	-0.170	-1.170	0.415	
+		0.778	-0.807	-0.807	0.193	
+		0.585	0.000	0.000	-1.000	
+		-0.807	-0.807	0.193	0.778	
+
+Donor SDT 2 0 4 2 0.000
+	GT WMM 9 3 4 0 0.000
+		0.497	0.497	-0.503	-1.087	
+		1.082	-0.087	-0.503	-2.087	
+		-2.087	-1.087	1.372	-0.503	
+		-2.087	-2.087	1.720	-2.087	
+		-2.087	-2.087	-2.087	1.720	
+		1.234	-2.087	0.234	-2.087	
+		1.372	-2.087	-1.087	-0.503	
+		-0.503	-2.087	1.497	-2.087	
+		-0.087	-0.087	-1.087	0.720	
+	NN TRM 0 0 0 0 0.000
+
+Inter LUT 5 4 4 0 0.000
+	-0.415	-0.415	-0.193	0.700	
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+	-0.624	-0.209	0.250	0.376	
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+	-0.415	0.322	-2.000	0.807	
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+	0.300	0.300	-0.115	-0.700	
+	-0.202	-0.524	0.284	0.284	
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+	0.337	0.074	-1.248	0.337	
+	-0.322	-1.907	-0.322	1.093	
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+	-0.170	-1.170	-1.170	1.152	
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+	-0.222	0.778	-0.807	-0.222	
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+	-0.222	-0.222	0.193	0.193	
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+	0.585	0.000	-1.000	0.000	
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+	-2.170	0.830	-0.585	0.415	
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+	-0.222	0.193	-0.807	0.515	
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+	-0.222	0.193	-1.807	0.778	
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+	-0.392	-0.807	-0.807	1.067	
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+	-0.322	-0.322	0.678	-0.322	
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+	-1.907	-0.907	1.093	0.093	
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+	-0.585	0.415	0.415	-0.585	
+	-0.524	-0.524	1.177	-1.524	
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+	-0.040	-0.888	-0.624	0.878	
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+	-0.248	0.559	-1.248	0.337	
+	0.646	-0.524	0.061	-0.524	
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+
+Intron LUT 5 4 4 0 0.000
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+	-0.379	-1.115	0.107	0.759	
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+	-0.123	-0.931	-1.123	1.069	
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+	-0.222	1.000	-0.222	-1.807	
+	-1.170	0.415	-0.170	0.415	
+	-1.807	-0.222	0.515	0.515	
+	-0.663	0.074	0.337	0.074	
+	0.263	1.000	-2.322	-0.737	
+	-1.459	-0.044	0.278	0.541	
+	-0.138	-0.874	-0.874	1.000	
+	-2.248	-0.663	0.337	0.922	
+	-0.115	-0.115	-0.700	0.621	
+	-0.248	-1.248	0.922	-0.248	
+	0.322	-0.193	-0.415	0.170	
+	1.126	-0.459	-0.459	-1.459	
+	0.074	0.337	-0.663	0.074	
+	-0.585	0.415	0.415	-0.585	
+	-0.379	-0.115	-0.115	0.469	
+	-1.858	-0.858	0.949	0.312	
+	0.553	-0.100	-0.100	-0.585	
+	0.541	-0.459	0.126	-0.459	
+	-0.202	0.476	0.284	-0.939	
+	0.193	-0.807	0.778	-0.807	
+	-0.907	0.678	-0.907	0.415	
+	0.193	0.778	-0.807	-0.807	
+	-1.000	-1.000	0.000	1.000	
+	1.193	-0.807	-0.807	-0.807	
+	-0.322	0.816	-1.644	0.163	
+	0.193	0.193	0.193	-0.807	
+	0.126	-0.459	-0.459	0.541	
+	-0.322	-0.322	0.678	-0.322	
+	0.000	0.000	0.000	0.000	
+	0.000	-1.000	0.585	0.000	
+	0.000	0.000	0.000	0.000	
+	-1.000	0.000	0.000	0.585	
+	-0.322	0.093	-0.322	0.415	
+	-0.322	0.678	-0.322	-0.322	
+	-1.170	-0.170	-0.170	0.830	
+	0.415	0.415	-0.585	-0.585	
+	-1.000	0.000	-1.000	1.000	
+	-0.807	0.193	0.778	-0.807	
+	0.415	-0.585	0.415	-0.585	
+	1.000	-0.585	-0.585	-0.585	
+	-0.807	-0.807	0.193	0.778	
+	0.415	-0.585	-0.585	0.415	
+	0.000	0.000	-1.000	0.585	
+	0.798	-0.202	-0.524	-0.524	
+	0.263	0.678	-1.322	-0.322	
+	-1.585	-1.585	0.000	1.222	
+	0.720	-0.503	-0.503	-0.087	
+	0.348	0.126	-0.138	-0.459	
+	-1.644	0.526	-0.644	0.678	
+	0.415	-0.585	0.415	-0.585	
+	-2.248	-0.248	1.074	-0.248	
+	-0.170	0.415	-1.170	0.415	
+	0.710	0.541	-2.459	-0.459	
+	-0.524	-0.202	0.284	0.284	
+	-0.807	-0.392	0.608	0.193	
+	0.526	-1.059	-0.059	0.163	
+	0.284	0.061	-0.524	0.061	
+	-0.087	-0.503	0.234	0.234	
+	-0.322	0.456	-0.322	0.041	
+	1.000	-1.115	-1.115	0.107	
+	0.193	0.193	-0.807	0.193	
+	-0.392	-0.392	-1.392	1.067	
+	0.415	-0.392	-1.392	0.608	
+	-0.248	-0.248	0.074	0.337	
+	-0.700	0.885	-1.700	0.300	
+	-0.807	0.193	0.778	-0.807	
+	1.000	-1.807	-0.807	0.193	
+	0.126	-0.459	-0.459	0.541	
+	0.515	0.515	-0.807	-0.807	
+	-1.170	-0.585	1.152	-0.585	
+	0.415	-0.392	-0.392	0.193	
+	0.074	-0.663	0.559	-0.248	
+	0.541	0.862	-1.459	-1.459	
+	-0.322	-0.907	0.093	0.678	
+	-0.170	-0.170	-1.170	0.830	
+	1.000	-0.737	-0.737	-0.322	
+	0.415	0.415	-0.170	-1.170	
+	-0.585	-0.585	1.115	-1.000	
+	-0.807	-0.807	0.515	0.515	
+	-0.874	0.541	-0.138	0.126	
+	-0.392	0.608	-2.392	0.608	
+	-1.322	1.000	-0.322	-0.322	
+	-0.585	0.415	0.222	-0.263	
+	0.000	0.000	0.000	0.000	
+	-1.000	1.000	-1.000	0.000	
+	-0.322	-0.322	0.678	-0.322	
+	-0.585	0.415	0.415	-0.585	
+	0.300	-0.115	-0.700	0.300	
+	0.720	-0.087	-2.087	0.234	
+	-0.807	-0.392	0.778	-0.070	
+	-0.585	-0.170	0.152	0.415	
+	0.193	-0.807	0.193	0.193	
+	0.126	0.126	-1.459	0.541	
+	-0.248	-0.663	0.337	0.337	
+	0.415	-0.907	-0.907	0.678	
+	0.126	-1.459	1.126	-1.459	
+	0.234	0.497	-2.087	0.234	
+	-1.000	1.000	-1.000	0.000	
+	-0.379	0.107	0.759	-1.115	
+	-0.392	-0.070	0.778	-0.807	
+	-1.087	0.720	-2.087	0.720	
+	-0.632	0.046	0.368	0.046	
+	0.497	-0.503	0.234	-0.503	
+	0.348	-2.459	0.541	0.126	
+	0.300	-0.115	-1.700	0.621	
+	0.559	0.074	-0.663	-0.248	
+	-0.807	-0.807	0.515	0.515	
+	0.652	-1.807	0.778	-1.222	
+	0.263	0.678	-1.322	-0.322	
+	0.752	0.074	-1.248	-0.248	
+	0.585	-1.000	-0.585	0.415	
+	0.000	0.000	0.415	-0.585	
+	-0.222	1.000	-1.807	-0.222	
+	-0.322	0.678	-0.322	-0.322	
+	0.126	-0.459	-0.459	0.541	
+	-0.322	-0.737	1.000	-0.737	
+	0.193	0.778	-1.807	-0.222	
+	-0.939	0.284	0.798	-0.939	
+	-0.322	0.415	-0.322	0.093	
+	-0.737	-1.322	0.000	1.000	
+	-0.459	0.541	-1.459	0.541	
+	-0.807	-0.392	-0.392	0.930	
+	-0.402	-0.888	0.376	0.491	
+	0.925	-0.561	-0.713	-0.298	
+	0.000	-0.415	-2.000	1.000	
+	0.759	0.300	-1.115	-0.700	
+	-0.170	-0.755	-0.170	0.705	
+	-0.070	-1.392	0.608	0.193	
+	0.234	-0.503	-1.087	0.720	
+	-0.585	-0.585	1.000	-0.585	
+	-0.503	-1.087	0.497	0.497	
+	0.052	-0.433	0.052	0.245	
+	0.752	-0.663	-2.248	0.559	
+	0.415	0.415	-1.585	0.000	
+	-0.115	-0.115	0.107	0.107	
+	0.663	-0.415	-1.263	0.322	
+	0.234	-1.087	-2.087	1.082	
+	0.193	-0.070	-1.392	0.608	
+	-0.143	-2.143	-0.558	1.130	
+	0.678	-0.644	-0.059	-0.322	
+	0.585	0.000	-1.000	0.000	
+	-0.737	0.263	-0.322	0.485	
+	0.152	-0.170	-0.585	0.415	
+	-0.737	0.263	0.263	0.000	
+	0.930	-0.070	-1.392	-0.392	
+	-1.170	1.152	-1.170	-0.170	
+	-1.644	-0.322	0.678	0.356	
+	-0.585	-0.585	1.000	-0.585	
+	0.193	0.778	-0.807	-0.807	
+	-0.585	1.000	-0.585	-0.585	
+	0.193	0.193	-0.807	0.193	
+	0.608	-1.392	-0.070	0.193	
+	0.263	0.678	-1.322	-0.322	
+	-0.585	0.637	-0.585	0.152	
+	0.415	-0.237	-0.237	-0.044	
+	0.759	-1.700	-0.115	0.107	
+	0.678	0.485	-1.322	-0.737	
+	-1.322	0.263	-0.322	0.678	
+	0.126	0.126	-0.459	0.126	
+	0.000	-0.322	0.678	-0.737	
+	0.222	0.000	-0.585	0.222	
+	-0.322	-0.322	0.678	-0.322	
+	0.193	-0.222	-0.222	0.193	
+	-1.170	-1.170	0.152	1.000	
+	-1.248	0.074	-0.663	0.922	
+	-0.059	-0.644	0.526	-0.059	
+	-0.524	0.061	0.061	0.284	
+	0.263	-0.585	-0.322	0.415	
+	-0.503	0.497	-2.087	0.720	
+	-0.379	-0.700	1.107	-1.115	
+	-0.193	-1.000	-0.678	1.000	
+	1.037	-0.700	-0.963	-0.285	
+	0.152	0.152	-2.170	0.637	
+	0.245	-0.170	-1.170	0.567	
+	0.255	-1.248	-1.248	0.974	
+	0.515	-0.222	0.000	-0.485	
+	0.798	-0.939	-1.524	0.476	
+	-0.170	-1.170	-0.170	0.830	
+	0.126	-0.044	-1.459	0.656	
+	0.816	0.163	-1.059	-0.644	
+	0.000	0.585	-1.000	0.000	
+	0.263	-0.737	-0.737	0.678	
+	0.227	-1.358	-0.188	0.642	
+	-0.026	-0.663	-0.373	0.691	
+	0.491	-0.209	-2.209	0.598	
+	-0.115	-1.285	-0.115	0.802	
+	0.258	-1.015	-0.899	0.826	
+
+Start SDT 3 0 4 2 0.000
+	ATG WMM 15 9 4 0 0.000
+		-0.585	-0.585	1.000	-0.585	
+		-0.585	0.415	0.415	-0.585	
+		-0.585	0.415	-0.585	0.415	
+		-0.585	-0.585	1.000	-0.585	
+		-0.585	0.415	-0.585	0.415	
+		0.415	0.415	-0.585	-0.585	
+		0.415	-0.585	-0.585	0.415	
+		-0.585	0.415	0.415	-0.585	
+		-0.585	0.415	-0.585	0.415	
+		1.000	-0.585	-0.585	-0.585	
+		-0.585	-0.585	-0.585	1.000	
+		-0.585	-0.585	1.000	-0.585	
+		0.415	0.415	-0.585	-0.585	
+		-0.585	-0.585	0.415	0.415	
+		-0.585	-0.585	0.415	0.415	
+	NNN TRM 0 0 0 0 0.000
+
+Stop SDT 3 0 4 4 0.000
+	TAA WMM 9 6 4 0 0.000
+		0.000	0.000	0.000	0.000	
+		0.000	0.000	0.000	0.000	
+		0.000	0.000	0.000	0.000	
+		0.000	0.000	0.000	0.000	
+		0.000	0.000	0.000	0.000	
+		0.000	0.000	0.000	0.000	
+		0.000	0.000	0.000	0.000	
+		0.000	0.000	0.000	0.000	
+		0.000	0.000	0.000	0.000	
+	TAG WMM 9 6 4 0 0.000
+		-0.322	-0.322	0.678	-0.322	
+		0.678	-0.322	-0.322	-0.322	
+		0.678	-0.322	-0.322	-0.322	
+		-0.322	0.678	-0.322	-0.322	
+		-0.322	-0.322	-0.322	0.678	
+		-0.322	-0.322	0.678	-0.322	
+		-0.322	-0.322	-0.322	0.678	
+		0.678	-0.322	-0.322	-0.322	
+		-0.322	-0.322	0.678	-0.322	
+	TGA WMM 9 6 4 0 0.000
+		-0.322	-0.322	0.678	-0.322	
+		-0.322	0.678	-0.322	-0.322	
+		-0.322	-0.322	0.678	-0.322	
+		-0.322	-0.322	-0.322	0.678	
+		-0.322	-0.322	0.678	-0.322	
+		-0.322	-0.322	0.678	-0.322	
+		-0.322	-0.322	-0.322	0.678	
+		-0.322	-0.322	0.678	-0.322	
+		0.678	-0.322	-0.322	-0.322	
+	NNN TRM 0 0 0 0 0.000
+