# HG changeset patch
# User iuc
# Date 1619514782 0
# Node ID 0e79c31d2fee3b3962ac2a7179cc290148fed1cd
# Parent  6a17d0a4318aa635c200bc2245bca9f2d168a858
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"

diff -r 6a17d0a4318a -r 0e79c31d2fee macros.xml
--- a/macros.xml	Wed Jul 15 21:15:14 2020 +0000
+++ b/macros.xml	Tue Apr 27 09:13:02 2021 +0000
@@ -9,10 +9,9 @@
         </requirements>
     </xml>
 
-    <token name="@STACKS_VERSION@">2.53</token>
+    <token name="@STACKS_VERSION@">2.55</token>
     <token name="@WRAPPER_VERSION@">0</token>
-    <!-- fix to 18.01 since https://github.com/galaxyproject/galaxy/pull/7032 -->
-    <token name="@PROFILE@">18.01</token>
+    <token name="@PROFILE@">20.01</token>
 
     <xml name="citation">
         <citations>
@@ -67,6 +66,7 @@
         <option value="bsaHI">bsaHI</option>
         <option value="bspDI">bspDI</option>
         <option value="bstYI">bstYI</option>
+        <option value="btgI">btgI</option>
         <option value="cac8I">cac8I</option>
         <option value="claI">claI</option>
         <option value="csp6I">csp6I</option>
@@ -80,6 +80,7 @@
         <option value="hindIII">hindIII</option>
         <option value="hinP1I">hinP1I</option>
         <option value="hpaII">hpaII</option>
+        <option value="hpyCH4IV">hpyCH4IV</option>
         <option value="kpnI">kpnI</option>
         <option value="mluCI">mluCI</option>
         <option value="mseI">mseI</option>
@@ -88,10 +89,13 @@
         <option value="ncoI">ncoI</option>
         <option value="ndeI">ndeI</option>
         <option value="nheI">nheI</option>
+        <option value="ngoMIV">ngoMIV</option>
         <option value="nlaIII">nlaIII</option>
         <option value="notI">notI</option>
         <option value="nsiI">nsiI</option>
         <option value="nspI">nspI</option>
+        <option value="pacI">pacI</option>
+        <option value="pspXI">pspXI</option>
         <option value="pstI">pstI</option>
         <option value="rsaI">rsaI</option>
         <option value="sacI">sacI</option>
@@ -446,19 +450,19 @@
     <xml name="populations_output_full">
         <expand macro="populations_output_light"/>
 
-        <data format="txt" name="out_sql" label="${tool.name} @TOOLADD@ on ${on_string} Genotyping markers" from_work_dir="stacks_outputs/populations.sql.tsv">
+        <data format="txt" name="out_sql" label="${tool.name} on ${on_string} Genotyping markers" from_work_dir="stacks_outputs/populations.sql.tsv">
             <filter>genetic_map_options['map_type'] and genetic_map_options['map_format']</filter>
         </data>
 
         <!-- log_fst_comp populations.fst_summary.tsv populations.phistats_summary.tsv populations.phistats.tsv-->
         <data format="tabular" name="out_phistats" label="${tool.name} on ${on_string} Phi_st statistics" from_work_dir="stacks_outputs/populations.phistats.tsv">
-            <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter>
+            <filter>fstats_conditional['fstats']=='yes' or kernel_smoothing['options_kernel']['kernel'] in ['--k', '--smooth-fstats']</filter>
         </data>
         <data format="tabular" name="out_phistats_sum" label="${tool.name} on ${on_string} Summary of Phi_st statistics" from_work_dir="stacks_outputs/populations.phistats_summary.tsv">
-            <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter>
+            <filter>fstats_conditional['fstats']=='yes' or kernel_smoothing['options_kernel']['kernel'] in ['--k', '--smooth-fstats']</filter>
         </data>
         <data format="tabular" name="out_fststats_sum" label="${tool.name} on ${on_string} Summary of Fst statistics" from_work_dir="stacks_outputs/populations.fst_summary.tsv">
-            <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter>
+            <filter>fstats_conditional['fstats']=='yes' or kernel_smoothing['options_kernel']['kernel'] in ['--k', '--smooth-fstats']</filter>
         </data>
 
         <!-- fasta_loci populations.loci.fa
@@ -531,23 +535,28 @@
         <data format="tabular" name="out_treemix" label="${tool.name} on ${on_string} Treemix format" from_work_dir="stacks_outputs/populations.treemix">
             <filter>populations_output['treemix']</filter>
         </data>
+
+        <!-- gtf populations.treemix -->
+        <data format="gtf" name="out_gtf" label="${tool.name} on ${on_string} gtf" from_work_dir="stacks_outputs/populations.gtf">
+            <filter>populations_output['gtf']</filter>
+        </data>
     </xml>
 
     <!-- fastq output for kmer/clone-filter -->
-    <xml name="fastq_output_filter">
-        <data name="clean" format_source="fqinputs" label="${tool.name} on ${on_string}">
+    <xml name="fastq_output_filter" token_format="">
+        <data name="clean" format="@FORMAT@" label="${tool.name} on ${on_string}">
             <filter>input_type['input_type_select'] == 'single'</filter>
             <yield/>
         </data>
-        <collection name="clean_pair" type="paired" format_source="fqinputs" label="${tool.name} on ${on_string}">
+        <collection name="clean_pair" type="paired" format="@FORMAT@" label="${tool.name} on ${on_string}">
             <filter>input_type['input_type_select'] == 'paired'</filter>
             <yield/>
         </collection>
-        <data name="discarded" format_source="fqinputs" label="${tool.name} on ${on_string}: discarded reads">
+        <data name="discarded" format="@FORMAT@" label="${tool.name} on ${on_string}: discarded reads">
             <filter>capture and input_type['input_type_select'] == 'single'</filter>
             <yield/>
         </data>
-        <collection name="discarded_pair" format_source="fqinputs" type="paired" label="${tool.name} on ${on_string}: discarded reads">
+        <collection name="discarded_pair" format="@FORMAT@" type="paired" label="${tool.name} on ${on_string}: discarded reads">
             <filter>capture and input_type['input_type_select'] == 'paired'</filter>
             <yield/>
         </collection>
diff -r 6a17d0a4318a -r 0e79c31d2fee stacks_clonefilter.xml
--- a/stacks_clonefilter.xml	Wed Jul 15 21:15:14 2020 +0000
+++ b/stacks_clonefilter.xml	Tue Apr 27 09:13:02 2021 +0000
@@ -65,7 +65,7 @@
     </inputs>
     <outputs>
         <expand macro="out_log"/>
-        <expand macro="fastq_output_filter"/>
+        <expand macro="fastq_output_filter" format="fastqsanger.gz"/>
     </outputs>
     <tests>
         <!-- single end, defaults-->
@@ -76,8 +76,12 @@
             </conditional>
             <param name="oligo_len_1" value="6"/>
             <param name="add_log" value="yes"/>
+            <assert_command>
+                <has_text text="--oligo_len_1 6"/>
+                <not_has_text text="-D"/>
+            </assert_command>
             <output name="output_log" ftype="txt" file="clonefilter/clonefilter.log" lines_diff="8"/>
-            <output name="clean" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/>
+            <output name="clean" compare="diff"  ftype="fastqsanger.gz" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/>
         </test>
         <!-- single end, alt BCencoding, capture-->
         <test expect_num_outputs="3">
@@ -86,14 +90,15 @@
                 <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz"/>
                 <param name="barcode_encoding" value="--index_null"/>
             </conditional>
-            <param name="capture" value="-D"/>
+            <param name="capture" value="true"/>
             <param name="oligo_len_1" value="6"/>
             <assert_command>
+                <has_text text="--oligo_len_1 6"/>
                 <has_text text="-D"/>
             </assert_command>
             <output name="output_log" ftype="txt"><assert_contents><has_text text="5 pairs of reads input."/></assert_contents></output>
-            <output name="clean"     compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Removed1_0001.1.1.fq.single-alt.gz"/>
-            <output name="discarded" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Discarded1_0001.1.1.fq.single.gz"/>
+            <output name="clean" compare="diff" ftype="fastqsanger.gz" file="clonefilter/Removed1_0001.1.1.fq.single-alt.gz"/>
+            <output name="discarded" compare="diff" ftype="fastqsanger.gz" file="clonefilter/Discarded1_0001.1.1.fq.single.gz"/>
         </test>
         <!-- paired end, defaults-->
         <test expect_num_outputs="4">
@@ -107,11 +112,13 @@
                 </param>
             </conditional>
             <param name="oligo_len_1" value="6"/>
+            <assert_command>
+                <has_text text="--oligo_len_1 6"/>
+                <not_has_text text="--oligo_len_2"/>
+                <not_has_text text="-D"/>
+            </assert_command>
             <output name="output_log" ftype="txt"><assert_contents><has_text text="4 pairs of reads input."/></assert_contents></output>
-            <output_collection name="clean_pair" type="paired">
-                <element name="forward" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
-                <element name="reverse" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Removed2_0001.2.2.fq.gz"/>
-            </output_collection>
+            <output_collection name="clean_pair" type="paired" count="2"/>
         </test>
         <!-- paired end, non defaults -->
         <test expect_num_outputs="7">
@@ -125,20 +132,18 @@
                 </param>
             </conditional>
             <param name="oligo_len_1" value="6"/>
-            <param name="capture" value="-D"/>
-            <param name="retain_oligo" value="--retain_oligo"/>
+            <param name="oligo_len_2" value="6"/>
+            <param name="capture" value="true"/>
+            <param name="retain_oligo" value="true"/>
             <assert_command>
+                <has_text text="--oligo_len_1 6"/>
+                <has_text text="--oligo_len_2 6"/>
+                <has_text text="-D"/>
                 <has_text text="--retain_oligo"/>
             </assert_command>
             <output name="output_log" ftype="txt"><assert_contents><has_text text="4 pairs of reads input."/></assert_contents></output>
-            <output_collection name="clean_pair" type="paired">
-                <element name="forward" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
-                <element name="reverse" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Removed2_0001.2.2.fq.gz"/>
-            </output_collection>
-            <output_collection name="discarded_pair" type="paired">
-                <element name="forward" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
-                <element name="reverse" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Removed2_0001.2.2.fq.gz"/>
-            </output_collection>
+            <output_collection name="clean_pair" type="paired" count="2"/>
+            <output_collection name="discarded_pair" type="paired" count="2"/>
         </test>
     </tests>
     <help>
diff -r 6a17d0a4318a -r 0e79c31d2fee test-data/kmerfilter/Discarded1_0001.1.1.fq
diff -r 6a17d0a4318a -r 0e79c31d2fee test-data/kmerfilter/Discarded2_0001.2.2.fq
diff -r 6a17d0a4318a -r 0e79c31d2fee test-data/kmerfilter/Removed1_0001.1.1.fq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kmerfilter/Removed1_0001.1.1.fq	Tue Apr 27 09:13:02 2021 +0000
@@ -0,0 +1,16 @@
+@K00392:16:HJ2G2BBXX:7:1102:10825:462401 1:N:0:ATCACG
+GGACATTGGCTGCAGTACTCTGACCCTGGCCACCTCAACCTGTCTCTCTCGCACCGGAAACCTCCGATCCGCAGAAACATGAGCAACCCTACAGTTGACACACACAACAGTTTTCGACCGAAACTACACATTCCTCTGTCCCATTTCCTC
++
+--A-FF-F-<A<-FAF7AAF--F--FF-A<-JJFJFFFF-<<-7--<FFF--77<7-77-<---7-7<-7-AA--<<-7<----<-A-FJFF-7A-F--7FF-<7A-A-<7F7---7-7-77-<7<<A--<J7--<-)-7)-7---7F<-
+@K00392:16:HJ2G2BBXX:7:1102:10825:46240 1:N:0:ATCACG
+GGACATTGGCTGCAGTACTCTGACCCTGGCCACCTCAACCTGTCTCTCTCGCACCGGAAACCTCCGATCCGCAGAAACATGAGCAACCCTACAGTTGACACACACAACAGTTTTCGACCGAAACTACACATTCCTCTGTCCCATTTCCTC
++
+--A-FF-F-<A<-FAF7AAF--F--FF-A<-JJFJFFFF-<<-7--<FFF--77<7-77-<---7-7<-7-AA--<<-7<----<-A-FJFF-7A-F--7FF-<7A-A-<7F7---7-7-77-<7<<A--<J7--<-)-7)-7---7F<-
+@K00392:16:HJ2G2BBXX:8:1201:4929:9367 1:N:0:ATCACG
+GGATTGAGGATGCAGCAACGTTCTAACATCTAGTGGAAAGCCTTCCCAGAAGAGTGGAGGCTGTTATAGCAGCAAAGGGGGGACCAACTCCATATTATTGCCCATGACTTTTGAATGAGATGTTTGACGAGCAGGGGTCGACATACTTTT
++
+AAAFFJJJJJJJFJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFAJAJFFJFJJFJFJ7FJAJJJAFFJJJJJJAJAFFFFA<JJJAJJFAFJA7<AFAFFA7F7F<-77<F<--7-7-))---)AFF-<A-7FA
+@K00392:16:HJ2G2BBXX:7:1104:19268:28727 1:N:0:ATCACG
+ATGCCGCGGCCCTTGCAGAGCAAGGGGAACCACTACTTCAACTCAAGGTCTCAAAGCGAGTGACGTAACTGATTGAAACGCTATTAGCGCGCACCACCGCTAACTAGCTATCCATTTCACATCCGTTACATATGTATGTATGTACACACA
++
+AAFFFJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJFJJJFJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJFAFJJJJJJJJ
diff -r 6a17d0a4318a -r 0e79c31d2fee test-data/kmerfilter/Removed1_0001.1.1.fq.single
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kmerfilter/Removed1_0001.1.1.fq.single	Tue Apr 27 09:13:02 2021 +0000
@@ -0,0 +1,20 @@
+@K00392:16:HJ2G2BBXX:7:1102:10825:462401 1:N:0:ATCACG
+GGACATTGGCTGCAGTACTCTGACCCTGGCCACCTCAACCTGTCTCTCTCGCACCGGAAACCTCCGATCCGCAGAAACATGAGCAACCCTACAGTTGACACACACAACAGTTTTCGACCGAAACTACACATTCCTCTGTCCCATTTCCTC
++
+--A-FF-F-<A<-FAF7AAF--F--FF-A<-JJFJFFFF-<<-7--<FFF--77<7-77-<---7-7<-7-AA--<<-7<----<-A-FJFF-7A-F--7FF-<7A-A-<7F7---7-7-77-<7<<A--<J7--<-)-7)-7---7F<-
+@K00392:16:HJ2G2BBXX:7:1102:10825:46240 1:N:0:ATCACG
+GGACATTGGCTGCAGTACTCTGACCCTGGCCACCTCAACCTGTCTCTCTCGCACCGGAAACCTCCGATCCGCAGAAACATGAGCAACCCTACAGTTGACACACACAACAGTTTTCGACCGAAACTACACATTCCTCTGTCCCATTTCCTC
++
+--A-FF-F-<A<-FAF7AAF--F--FF-A<-JJFJFFFF-<<-7--<FFF--77<7-77-<---7-7<-7-AA--<<-7<----<-A-FJFF-7A-F--7FF-<7A-A-<7F7---7-7-77-<7<<A--<J7--<-)-7)-7---7F<-
+@K00392:16:HJ2G2BBXX:8:1201:4929:9367 1:N:0:ATCACG
+GGATTGAGGATGCAGCAACGTTCTAACATCTAGTGGAAAGCCTTCCCAGAAGAGTGGAGGCTGTTATAGCAGCAAAGGGGGGACCAACTCCATATTATTGCCCATGACTTTTGAATGAGATGTTTGACGAGCAGGGGTCGACATACTTTT
++
+AAAFFJJJJJJJFJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFAJAJFFJFJJFJFJ7FJAJJJAFFJJJJJJAJAFFFFA<JJJAJJFAFJA7<AFAFFA7F7F<-77<F<--7-7-))---)AFF-<A-7FA
+@K00392:16:HJ2G2BBXX:7:1104:19268:28727 1:N:0:ATCACG
+ATGCCGCGGCCCTTGCAGAGCAAGGGGAACCACTACTTCAACTCAAGGTCTCAAAGCGAGTGACGTAACTGATTGAAACGCTATTAGCGCGCACCACCGCTAACTAGCTATCCATTTCACATCCGTTACATATGTATGTATGTACACACA
++
+AAFFFJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJFJJJFJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJFAFJJJJJJJJ
+@K00392:16:HJ2G2BBXX:8:2125:3011:15574 1:N:0:ATCACG
+TCAGAAGAAAAACCCACAAAATAGAACCGGAGTCCTATTCCATTATTCCTAGCTGCGGTATTCAGGCGACCGGGCCTGCTTTGAACACTCTAATTTTTTCAAAGTAAACGCTTCGGACCCCGCGGGCCACTCAGTTAAGAGCATCGAGGG
++
+AAFFFJJJJJJJJFJFJFJFJJJJFJJJJJ<J-7FJFAJJJJJJJJAJJFJAJJJJJJJJFJJFAAFAJJJJJFJJJJJFAJJJJJFFJJ<J-FFAJJJF-J<7-7<<A<---AF<7JJJJ-A)77-7--)F-7----<--7A7A<--7-
diff -r 6a17d0a4318a -r 0e79c31d2fee test-data/kmerfilter/Removed1_0001.1.1.fq.single.gz
--- a/test-data/kmerfilter/Removed1_0001.1.1.fq.single.gz	Wed Jul 15 21:15:14 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-@K00392:16:HJ2G2BBXX:7:1102:10825:462401 1:N:0:ATCACG
-GGACATTGGCTGCAGTACTCTGACCCTGGCCACCTCAACCTGTCTCTCTCGCACCGGAAACCTCCGATCCGCAGAAACATGAGCAACCCTACAGTTGACACACACAACAGTTTTCGACCGAAACTACACATTCCTCTGTCCCATTTCCTC
-+
---A-FF-F-<A<-FAF7AAF--F--FF-A<-JJFJFFFF-<<-7--<FFF--77<7-77-<---7-7<-7-AA--<<-7<----<-A-FJFF-7A-F--7FF-<7A-A-<7F7---7-7-77-<7<<A--<J7--<-)-7)-7---7F<-
-@K00392:16:HJ2G2BBXX:7:1102:10825:46240 1:N:0:ATCACG
-GGACATTGGCTGCAGTACTCTGACCCTGGCCACCTCAACCTGTCTCTCTCGCACCGGAAACCTCCGATCCGCAGAAACATGAGCAACCCTACAGTTGACACACACAACAGTTTTCGACCGAAACTACACATTCCTCTGTCCCATTTCCTC
-+
---A-FF-F-<A<-FAF7AAF--F--FF-A<-JJFJFFFF-<<-7--<FFF--77<7-77-<---7-7<-7-AA--<<-7<----<-A-FJFF-7A-F--7FF-<7A-A-<7F7---7-7-77-<7<<A--<J7--<-)-7)-7---7F<-
-@K00392:16:HJ2G2BBXX:8:1201:4929:9367 1:N:0:ATCACG
-GGATTGAGGATGCAGCAACGTTCTAACATCTAGTGGAAAGCCTTCCCAGAAGAGTGGAGGCTGTTATAGCAGCAAAGGGGGGACCAACTCCATATTATTGCCCATGACTTTTGAATGAGATGTTTGACGAGCAGGGGTCGACATACTTTT
-+
-AAAFFJJJJJJJFJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFAJAJFFJFJJFJFJ7FJAJJJAFFJJJJJJAJAFFFFA<JJJAJJFAFJA7<AFAFFA7F7F<-77<F<--7-7-))---)AFF-<A-7FA
-@K00392:16:HJ2G2BBXX:7:1104:19268:28727 1:N:0:ATCACG
-ATGCCGCGGCCCTTGCAGAGCAAGGGGAACCACTACTTCAACTCAAGGTCTCAAAGCGAGTGACGTAACTGATTGAAACGCTATTAGCGCGCACCACCGCTAACTAGCTATCCATTTCACATCCGTTACATATGTATGTATGTACACACA
-+
-AAFFFJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJFJJJFJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJFAFJJJJJJJJ
-@K00392:16:HJ2G2BBXX:8:2125:3011:15574 1:N:0:ATCACG
-TCAGAAGAAAAACCCACAAAATAGAACCGGAGTCCTATTCCATTATTCCTAGCTGCGGTATTCAGGCGACCGGGCCTGCTTTGAACACTCTAATTTTTTCAAAGTAAACGCTTCGGACCCCGCGGGCCACTCAGTTAAGAGCATCGAGGG
-+
-AAFFFJJJJJJJJFJFJFJFJJJJFJJJJJ<J-7FJFAJJJJJJJJAJJFJAJJJJJJJJFJJFAAFAJJJJJFJJJJJFAJJJJJFFJJ<J-FFAJJJF-J<7-7<<A<---AF<7JJJJ-A)77-7--)F-7----<--7A7A<--7-
diff -r 6a17d0a4318a -r 0e79c31d2fee test-data/kmerfilter/Removed2_0001.2.2.fq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kmerfilter/Removed2_0001.2.2.fq	Tue Apr 27 09:13:02 2021 +0000
@@ -0,0 +1,16 @@
+@K00392:16:HJ2G2BBXX:7:1102:10825:462401 2:N:0:ATCACG
+GGACATTGGCTGATGTGTTATAGGTGTCTACGTTTATGGGCATGTCGCAGCAGTGTGTAGGAGGGAGATTCCAAGATGTGTGAAGTGTGTAGGAGGACATGGGACAGAGGAATGTGTAGTTTCGGTAGAAAACGGTTGTGTGTGTGAACT
++
+AAFAF7FJ77FA--<AF-<FJF<FFA7AJJJ77-<AJ<A-FJJ-<7A7FF-7FA<-AAAA7F7J<<JJFAAAAAF--7<--<--A7F-A--7F-<---7-FFF<-<F-AFF<--FJJFA<A-77F--7-A----7-7)7<7FFAJ7----
+@K00392:16:HJ2G2BBXX:7:1102:10825:46240 2:N:0:ATCACG
+GGACATTGGCTGATGTGTTATAGGTGTCTACGTTTATGGGCATGTCGCAGCAGTGTGTAGGAGGGAGATTCCAAGATGTGTGAAGTGTGTAGGAGGACATGGGACAGAGGAATGTGTAGTTTCGGTAGAAAACGGTTGTGTGTGTGAACT
++
+AAFAF7FJ77FA--<AF-<FJF<FFA7AJJJ77-<AJ<A-FJJ-<7A7FF-7FA<-AAAA7F7J<<JJFAAAAAF--7<--<--A7F-A--7F-<---7-FFF<-<F-AFF<--FJJFA<A-77F--7-A----7-7)7<7FFAJ7----
+@K00392:16:HJ2G2BBXX:8:1201:4929:9367 2:N:0:ATCACG
+GTAATGGAAACATGTGCAACCTGTCAAAATACACCAAAAGTATGTGGACACCTGCTCGTCAAACATCTCATTCAAAAGTCATGGGCAATAATATGGAGTTGGTCCCCCCTTTGCTGCTATAACAGCCTCCACTCTTCTGGGAAGGCTTTC
++
+AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJFJJFJJJJJJJJJJJJJJJJJ7JJJFJA<JFJFJJJJ<JJJJJJFJJJJJJJJJJAFJF-AJJFJJFJJJFJJJJ7AAAAFFAFJJAJJJJJJJFFJJF
+@K00392:16:HJ2G2BBXX:7:1104:19268:28727 2:N:0:ATCACG
+GGACACTGACTGCAGCCAGAGTTTGTCCACCCTCTCGGTCATCGAGGAGTTCTTGGCCAAGAGGCCCATACCGGCGGGCAGTGCCAGAGAGGGCCACAACCAAAACTGGCTCCGCAACCACAACTACTACAGTATGTTTTATTTGTGCTT
++
+AAAFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJFJFJJJJJJJJJJJJJFJJJFJJJJJAJFJJJJAJJJJ----<F<JFJJFJFJFF
diff -r 6a17d0a4318a -r 0e79c31d2fee test-data/populations/populations.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/populations/populations.gtf	Tue Apr 27 09:13:02 2021 +0000
@@ -0,0 +1,4 @@
+# Stacks v2.55; GTF export; March 16, 2021
+un	Stacks	locus	1	204	.	+	.	locus_id "1"; sample_cnt "2"
+un	Stacks	locus	205	409	.	+	.	locus_id "2"; sample_cnt "2"
+un	Stacks	locus	410	613	.	+	.	locus_id "3"; sample_cnt "2"