# HG changeset patch
# User iuc
# Date 1619516288 0
# Node ID 887cf585cafc7cfac5e2f827401193e9d39929b3
# Parent  b242deb589520bf47f092bb9308a84f932e66a81
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"

diff -r b242deb58952 -r 887cf585cafc macros.xml
--- a/macros.xml	Thu Jul 16 07:32:42 2020 -0400
+++ b/macros.xml	Tue Apr 27 09:38:08 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 b242deb58952 -r 887cf585cafc stacks_populations.xml
--- a/stacks_populations.xml	Thu Jul 16 07:32:42 2020 -0400
+++ b/stacks_populations.xml	Tue Apr 27 09:38:08 2021 +0000
@@ -129,6 +129,7 @@
 $populations_output.treemix
 $populations_output.no_hap_exports
 $populations_output.fasta_samples_raw
+$populations_output.gtf
 
 #if $genetic_map_options.map_type:
     --map-type $genetic_map_options.map_type
@@ -244,14 +245,15 @@
             <param argument="--treemix" truevalue="--treemix" falsevalue="" type="boolean" checked="false" label="Output SNPs in a format useable for the TreeMix program (Pickrell and Pritchard)."/>
             <param argument="--no-hap-exports" truevalue="--no-hap-exports" falsevalue="" type="boolean" checked="false" label="Omit haplotype outputs"/>
             <param argument="--fasta-samples-raw" truevalue="--fasta-samples-raw" falsevalue="" type="boolean" checked="false" label="Output all haplotypes observed in each sample, for each locus, in FASTA format"/>
+            <param argument="--gtf" truevalue="--gtf" falsevalue="" type="boolean" checked="false" label="output locus positions in a GTF annotation file"/>
         </section>
 
         <!-- Kernel-smoothing algorithm -->
         <section name="kernel_smoothing" title="Kernel smoothing" expanded="false">
             <conditional name="options_kernel">
-                <param name="kernel" type="select" label="Enable kernel-smoothed calculations" >
+                <param name="kernel" type="select" label="Enable kernel-smoothed calculations" help="The options -k and --smooth-fstats implicitly enable --fstats. Note that, in order to set non-default values for --fst-correction or --p-value-cutoff the option --fstats still needs to be enabled in the tool form." >
                     <option value="">No</option>
-                    <option value="-k">For Pi, Fis, Fst, Fst', and Phi_st (-k)</option>
+                    <option value="-k">For Pi, Fis, Fst, Fst', and Phi_st (-k/--smooth)</option>
                     <option value="--smooth-fstats">For Fst, Fst', and Phi_st (--smooth-fstats)</option>
                     <option value="--smooth-popstats">For Pi and Fis (--smooth-popstats)</option>
                 </param>
@@ -348,7 +350,7 @@
             <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output>
         </test>
         <!-- test w gstacks output as input and + all outputs -->
-        <test expect_num_outputs="26">
+        <test expect_num_outputs="27">
             <param name="options_usage|input_type" value="stacks"/>
             <param name="options_usage|input_aln">
                 <collection type="list">
@@ -372,6 +374,7 @@
             <param name="populations_output|structure" value="yes"/>
             <param name="populations_output|radpainter" value="yes"/>
             <param name="populations_output|treemix" value="yes"/>
+            <param name="populations_output|gtf" value="yes"/>
             <assert_command>
                 <has_text text="--log-fst-comp"/>
             </assert_command>
@@ -402,6 +405,7 @@
             <output ftype="tabular" name="out_structure" value="populations/populations.structure" compare="sim_size" delta="50"/><!-- " -->
             <output ftype="tabular" name="out_radpainter" value="populations/populations.haps.radpainter" compare="sim_size" delta="50"/><!-- " -->
             <output ftype="tabular" name="out_treemix" value="populations/populations.treemix" compare="sim_size" delta="50"/><!-- " -->
+            <output ftype="gtf" name="out_gtf" value="populations/populations.gtf" lines_diff="2"/><!-- " -->
         </test>
         <!-- test w vcf input and default options, just checking if finished -->
         <test expect_num_outputs="6">
@@ -526,7 +530,7 @@
             <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output>
         </test>
         <!-- test w gstacks output as input and non default fstats/kernel/bootstrap -->
-        <test expect_num_outputs="6">
+        <test expect_num_outputs="9">
             <param name="options_usage|input_type" value="stacks"/>
             <param name="options_usage|input_aln">
                 <collection type="list">
@@ -564,8 +568,54 @@
             <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output>
             <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output>
             <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output>
+            <output ftype="tabular" name="out_phistats" value="populations/populations.phistats.tsv"/>
+            <output ftype="tabular" name="out_phistats_sum" value="populations/populations.phistats_summary.tsv"/>
+            <output ftype="tabular" name="out_fststats_sum" value="populations/populations.fst_summary.tsv"/>
         </test>
-         <!-- test w gstacks output as input and default options -->
+        <!-- same as previous test but without fstats parameter in order to check if the filter 
+             for out_phistats* and out_fststats_sum works (also instead of -k \-\-smooth-fstats
+             is used) -->
+        <test expect_num_outputs="9">
+            <param name="options_usage|input_type" value="stacks"/>
+            <param name="options_usage|input_aln">
+                <collection type="list">
+                    <element name="catalog.calls.vcf" ftype="vcf" value="refmap/catalog.calls.vcf"/>
+                    <element name="catalog.fa.gz" ftype="fasta.gz" value="refmap/catalog.fa.gz"/>
+               </collection>
+            </param>
+            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
+            <conditional name="fstats_conditional">
+                <param name="fstats" value="no"/>
+            </conditional>
+            <conditional name="options_kernel">
+                <param name="kernel" value="--smooth-fstats"/>
+                <param name="sigma" value="150001"/>
+            </conditional>
+            <conditional name="bootstrap_resampling_mode">
+                <param name="bootstrap" value="--bootstrap"/>
+            </conditional>
+            <param name="bootstrap_reps" value="23"/>
+            <param name="add_log" value="yes"/>
+            <assert_command>
+                <not_has_text text="--fstats"/>
+                <not_has_text text="--fst-correction"/>
+                <not_has_text text="--p-value-cutoff 0.01"/>
+                <has_text text="--smooth-fstats "/>
+                <has_text text="--sigma 150001"/>
+                <has_text text="--bootstrap"/>
+                <has_text text="--bootstrap-reps 23"/>
+            </assert_command>
+            <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output>
+            <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text=""/></assert_contents></output>
+            <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text=""/></assert_contents></output>
+            <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text=""/></assert_contents></output>
+            <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output>
+            <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output>
+            <output ftype="tabular" name="out_phistats" value="populations/populations.phistats.tsv"/>
+            <output ftype="tabular" name="out_phistats_sum" value="populations/populations.phistats_summary.tsv"/>
+            <output ftype="tabular" name="out_fststats_sum" value="populations/populations.fst_summary.tsv"/>
+        </test>
+        <!-- test w gstacks output as input and default options -->
         <test expect_num_outputs="6">
             <param name="options_usage|input_type" value="stacks"/>
             <param name="options_usage|input_aln">
diff -r b242deb58952 -r 887cf585cafc test-data/kmerfilter/Discarded1_0001.1.1.fq
diff -r b242deb58952 -r 887cf585cafc test-data/kmerfilter/Discarded2_0001.2.2.fq
diff -r b242deb58952 -r 887cf585cafc 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 09:38:08 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 b242deb58952 -r 887cf585cafc 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 09:38:08 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 b242deb58952 -r 887cf585cafc test-data/kmerfilter/Removed1_0001.1.1.fq.single.gz
--- a/test-data/kmerfilter/Removed1_0001.1.1.fq.single.gz	Thu Jul 16 07:32:42 2020 -0400
+++ /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 b242deb58952 -r 887cf585cafc 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 09:38:08 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 b242deb58952 -r 887cf585cafc test-data/populations/populations.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/populations/populations.gtf	Tue Apr 27 09:38:08 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"