# HG changeset patch
# User iuc
# Date 1630495744 0
# Node ID 7370bb65bad45c6fe338a035fde321d3f79a6b20
# Parent  eb784fa07f80df684f0ae26272db4a7ff1bdcaf8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"

diff -r eb784fa07f80 -r 7370bb65bad4 macros.xml
--- a/macros.xml	Tue Apr 27 09:31:18 2021 +0000
+++ b/macros.xml	Wed Sep 01 11:29:04 2021 +0000
@@ -10,8 +10,8 @@
     </xml>
 
     <token name="@STACKS_VERSION@">2.55</token>
-    <token name="@WRAPPER_VERSION@">0</token>
-    <token name="@PROFILE@">20.01</token>
+    <token name="@WRAPPER_VERSION@">1</token>
+    <token name="@PROFILE@">20.05</token>
 
     <xml name="citation">
         <citations>
@@ -424,11 +424,11 @@
             <filter>add_log_distribs</filter>
         </data>
         <collection name="gstacks_alns_out" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Read alignments">
-            <discover_datasets pattern="(?P&lt;name&gt;.*).alns.bam$" ext="bam" directory="stacks_outputs"/>
-            <filter>mode_cond['mode_select'] == 'denovo' and mode_cond['advanced_cond']['advanced_select'] == "yes" and mode_cond['advanced_cond']['write_alignments'] != "" and popmap!=None</filter>
+            <discover_datasets pattern="(?P&lt;name&gt;.*).alns.bam$" format="bam" directory="stacks_outputs"/>
+            <filter>mode_cond['mode_select'] == 'denovo' and mode_cond['advanced_cond']['advanced_select'] == "yes" and mode_cond['advanced_cond']['write_alignments'] and popmap!=None</filter>
         </collection>
         <data name="gstacks_aln_out" format="bam" label="${tool.name} @TOOLADD@ on ${on_string} Read alignment" from_work_dir="stacks_outputs/alignments.bam">
-            <filter>mode_cond['mode_select'] == 'denovo' and mode_cond['advanced_cond']['advanced_select'] == "yes" and mode_cond['advanced_cond']['write_alignments'] != "" and popmap==None</filter>
+            <filter>mode_cond['mode_select'] == 'denovo' and mode_cond['advanced_cond']['advanced_select'] == "yes" and mode_cond['advanced_cond']['write_alignments'] and popmap==None</filter>
         </data>
     </xml>
     <xml name="gstacks_outputs_macro" token_tooladd="">
diff -r eb784fa07f80 -r 7370bb65bad4 stacks_gstacks.xml
--- a/stacks_gstacks.xml	Tue Apr 27 09:31:18 2021 +0000
+++ b/stacks_gstacks.xml	Wed Sep 01 11:29:04 2021 +0000
@@ -4,7 +4,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="1.9">samtools</requirement>
+        <requirement type="package" version="1.13">samtools</requirement>
     </expand>
     <expand macro="version_cmd"/>
     <command detect_errors="aggressive"><![CDATA[
@@ -88,11 +88,11 @@
 ## exit codes and stderr output) this adds the samtools requirement
 ## for later versions where this is fixed the output bam files could just be moved
 ## to stacks_outputs if this is still necessary
-#if $mode_cond.mode_select == "denovo" and $mode_cond.advanced_cond.advanced_select == "yes" and $mode_cond.advanced_cond.write_alignments != ""
+#if $mode_cond.mode_select == "denovo" and $mode_cond.advanced_cond.advanced_select == "yes" and $mode_cond.advanced_cond.write_alignments
     #if $popmap:
-        && for b in stacks_outputs/*alns.bam; do (samtools view -b "\$b" || true) 2> /dev/null > tmp && mv tmp "\$b"; done
+        && for b in stacks_outputs/*alns.bam; do (samtools view --no-PG -b "\$b" || true) 2> /dev/null > tmp && mv tmp "\$b"; done
     #else
-        && (samtools view -b stacks_outputs/alignments.bam || true) 2> /dev/null > tmp && mv tmp stacks_outputs/alignments.bam
+        && (samtools view --no-PG -b stacks_outputs/alignments.bam || true) 2> /dev/null > tmp && mv tmp stacks_outputs/alignments.bam
     #end if
 #end if
 
@@ -117,17 +117,17 @@
                 <option value="refbased">Reference-based</option>
             </param>
             <when value="denovo">
-                <param argument="--ignore-pe-reads" name="ignore_pe_reads" type="boolean" checked="false" truevalue="--ignore-pe-reads" falsevalue="" label="Ignore paired-end reads" help="ignore paired-end reads even if present in the input"/>
+                <param argument="--ignore-pe-reads" type="boolean" checked="false" truevalue="--ignore-pe-reads" falsevalue="" label="Ignore paired-end reads" help="ignore paired-end reads even if present in the input"/>
                 <conditional name="advanced_cond">
                     <param name="advanced_select" type="select" label="Advanced options">
                         <option value="no">No</option>
                         <option value="yes">Yes</option>
                     </param>
                     <when value="yes">
-                        <param argument="--kmer-length" name="kmer_length" type="integer" value="31" min="2" max="31" label="K-mer length for the de Bruijn graph"/>
-                        <param argument="--max-debruijn-reads" name="max_debruijn_reads" type="integer" value="1000" min="1" label="Maximum number of reads to use in the de Bruijn graph"/>
-                        <param argument="--min-kmer-cov" name="min_kmer_cov" type="integer" value="2" label="Minimum coverage to consider a kmer"/>
-                        <param argument="--write-alignments" name="write_alignments" type="boolean" checked="false" truevalue="--write-alignments" falsevalue="" label="save read alignments" help="heavy BAM files"/>
+                        <param argument="--kmer-length" type="integer" value="31" min="2" max="31" label="K-mer length for the de Bruijn graph"/>
+                        <param argument="--max-debruijn-reads" type="integer" value="1000" min="1" label="Maximum number of reads to use in the de Bruijn graph"/>
+                        <param argument="--min-kmer-cov" type="integer" value="2" label="Minimum coverage to consider a kmer"/>
+                        <param argument="--write-alignments" type="boolean" checked="false" truevalue="--write-alignments" falsevalue="" label="save read alignments" help="heavy BAM files"/>
                     </when>
                     <when value="no"/>
                 </conditional>
@@ -140,8 +140,8 @@
                         <option value="--ignore-pe-reads" selected="true">ignore paired-end reads (--ignore-pe-reads)</option>
                     </param>
                     <when value="">
-                        <param argument="--rm-unpaired-reads" name="rm_unpaired_reads" type="boolean" checked="false" truevalue="--rm-unpaired-reads" falsevalue="" label="Discard unpaired reads"/>
-                        <param argument="--rm-pcr-duplicates" name="rm_pcr_duplicates" type="boolean" checked="false" truevalue="--rm-pcr-duplicates" falsevalue="" label="Remove read pairs of the same sample that have the same insert length" help="implies --rm-unpaired-reads"/>
+                        <param argument="--rm-unpaired-reads" type="boolean" checked="false" truevalue="--rm-unpaired-reads" falsevalue="" label="Discard unpaired reads"/>
+                        <param argument="--rm-pcr-duplicates" type="boolean" checked="false" truevalue="--rm-pcr-duplicates" falsevalue="" label="Remove read pairs of the same sample that have the same insert length" help="implies --rm-unpaired-reads"/>
                     </when>
                     <when value="--unpaired"/>
                     <when value="--ignore-pe-reads"/>
@@ -152,13 +152,13 @@
                         <option value="yes">Yes</option>
                     </param>
                     <when value="yes">
-                        <param argument="--min-mapq" name="min_mapq" type="integer" value="10" min="0" max="255" label="Minimum PHRED-scaled mapping quality to consider a read"/>
-                        <param argument="--max-clipped" name="max_clipped" type="float" value="0.2" min="0.0" max="1.1" label="Maximum soft-clipping level" help="in fraction of read length"/>
-                        <param argument="--max-insert-len" name="max_insert_len" type="integer" value="1000" min="0" label="Maximum allowed sequencing insert length"/>
+                        <param argument="--min-mapq" type="integer" value="10" min="0" max="255" label="Minimum PHRED-scaled mapping quality to consider a read"/>
+                        <param argument="--max-clipped" type="float" value="0.2" min="0.0" max="1.1" label="Maximum soft-clipping level" help="in fraction of read length"/>
+                        <param argument="--max-insert-len" type="integer" value="1000" min="0" label="Maximum allowed sequencing insert length"/>
                         <param argument="--details" type="boolean" checked="false" truevalue="--details" falsevalue="" label="Write a heaview output"/>
                         <param name="phasing_cooccurrences_thr_min" type="integer" value="1" min="0" label="Edge coverage min" help="(--phasing-cooccurrences-thr-range)"/>
                         <param name="phasing_cooccurrences_thr_max" type="integer" value="2" min="0" label="Edge coverage max" help="range of edge coverage thresholds to iterate over when building the graph of allele cooccurrences for SNP phasing (--phasing-cooccurrences-thr-range)"/>
-                        <param argument="--phasing-dont-prune-hets" name="phasing_dont_prune_hets" type="boolean" checked="false" truevalue="--phasing-dont-prune-hets" falsevalue="" label="Don't try to ignore dubious heterozygote genotypes during phasing"/>
+                        <param argument="--phasing-dont-prune-hets" type="boolean" checked="false" truevalue="--phasing-dont-prune-hets" falsevalue="" label="Don't try to ignore dubious heterozygote genotypes during phasing"/>
                     </when>
                     <when value="no"/>
                 </conditional>
@@ -203,7 +203,7 @@
             <output name="distribs" ftype="txt" file="gstacks/gstacks.log.distribs" compare="sim_size" delta="10"/>
             <output_collection name="gstacks_out" type="list" count="2">
                 <element name="catalog.calls.vcf" file="gstacks/catalog.calls.vcf" ftype="vcf" lines_diff="4"/>
-                <element name="catalog.fa.gz" file="gstacks/catalog.fa.gz" ftype="fasta.gz" compare="diff"/>
+                <element name="catalog.fa.gz" file="gstacks/catalog.fa.gz" ftype="fasta.gz" decompress="true" compare="diff"/>
             </output_collection>
         </test>
         <!-- denovomode, w popmap, write alignments -->
@@ -214,7 +214,7 @@
                 <param name="mode_select" value="denovo"/>
                 <conditional name="advanced_cond">
                     <param name="advanced_select" value="yes"/>
-                    <param name="write_alignments" value="--write-alignments"/>
+                    <param name="write_alignments" value="true"/>
                 </conditional>
             </conditional>
             <param name="add_log" value="yes"/>
diff -r eb784fa07f80 -r 7370bb65bad4 test-data/cstacks/catalog.alleles.tsv
--- a/test-data/cstacks/catalog.alleles.tsv	Tue Apr 27 09:31:18 2021 +0000
+++ b/test-data/cstacks/catalog.alleles.tsv	Wed Sep 01 11:29:04 2021 +0000
@@ -1,4 +1,4 @@
-# cstacks version 2.52; catalog generated on 2020-03-16 15:39:40
+# cstacks version 2.55; catalog generated on 2021-08-24 13:29:01
 0	1	AC	0	0
 0	1	CA	0	0
-# cstacks completed on 2020-03-16 15:39:40
+# cstacks completed on 2021-08-24 13:29:01
diff -r eb784fa07f80 -r 7370bb65bad4 test-data/cstacks/catalog.snps.tsv
--- a/test-data/cstacks/catalog.snps.tsv	Tue Apr 27 09:31:18 2021 +0000
+++ b/test-data/cstacks/catalog.snps.tsv	Wed Sep 01 11:29:04 2021 +0000
@@ -1,4 +1,4 @@
-# cstacks version 2.52; catalog generated on 2020-03-16 15:39:40
+# cstacks version 2.55; catalog generated on 2021-08-24 13:29:01
 0	1	33	E	0	A	C	-	-
 0	1	88	E	0	A	C	-	-
-# cstacks completed on 2020-03-16 15:39:40
+# cstacks completed on 2021-08-24 13:29:01
diff -r eb784fa07f80 -r 7370bb65bad4 test-data/cstacks/catalog.tags.tsv
--- a/test-data/cstacks/catalog.tags.tsv	Tue Apr 27 09:31:18 2021 +0000
+++ b/test-data/cstacks/catalog.tags.tsv	Wed Sep 01 11:29:04 2021 +0000
@@ -1,5 +1,5 @@
-# cstacks version 2.52; catalog generated on 2020-03-16 15:39:40
+# cstacks version 2.55; catalog generated on 2021-08-24 13:29:01
 0	1	consensus	0	1_1,2_1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC	0	0	0
 0	2	consensus	0	1_2,2_2	AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT	0	0	0
 0	3	consensus	0	1_3,2_3	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA	0	0	0
-# cstacks completed on 2020-03-16 15:39:40
+# cstacks completed on 2021-08-24 13:29:01
diff -r eb784fa07f80 -r 7370bb65bad4 test-data/denovo_map/denovo_map.log
--- a/test-data/denovo_map/denovo_map.log	Tue Apr 27 09:31:18 2021 +0000
+++ b/test-data/denovo_map/denovo_map.log	Wed Sep 01 11:29:04 2021 +0000
@@ -1,5 +1,5 @@
-denovo_map.pl version 2.52 started at 2020-03-16 15:39:40
-/home/berntm/miniconda3/envs/__stacks@2.52/bin/denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired
+denovo_map.pl version 2.55 started at 2021-08-24 13:29:01
+/home/berntm/miniconda3/envs/mulled-v1-4cbe4390dde1292aa8dbfc7f3537b788791787f5ad55cd86edeadacb1e3df63a/bin/denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired
 
 ustacks
 ==========
@@ -305,4 +305,4 @@
 Populations is done.
 denovo_map.pl is done.
 
-denovo_map.pl completed at 2020-03-16 15:39:40
+denovo_map.pl completed at 2021-08-24 13:29:01
diff -r eb784fa07f80 -r 7370bb65bad4 test-data/gentest.sh
--- a/test-data/gentest.sh	Tue Apr 27 09:31:18 2021 +0000
+++ b/test-data/gentest.sh	Wed Sep 01 11:29:04 2021 +0000
@@ -1,9 +1,6 @@
 #!/usr/bin/env bash
-eval "$(conda shell.bash hook)"
-conda activate __stacks@2.52
-
-
-
+#eval "$(conda shell.bash hook)"
+#conda activate __stacks@2.52
 
 mkdir stacks_outputs
 denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired  && 
diff -r eb784fa07f80 -r 7370bb65bad4 test-data/gstacks/PopA_01.alns.bam
Binary file test-data/gstacks/PopA_01.alns.bam has changed
diff -r eb784fa07f80 -r 7370bb65bad4 test-data/gstacks/PopA_02.alns.bam
Binary file test-data/gstacks/PopA_02.alns.bam has changed
diff -r eb784fa07f80 -r 7370bb65bad4 test-data/gstacks/alignments.bam
Binary file test-data/gstacks/alignments.bam has changed
diff -r eb784fa07f80 -r 7370bb65bad4 test-data/gstacks/catalog.calls.vcf
--- a/test-data/gstacks/catalog.calls.vcf	Tue Apr 27 09:31:18 2021 +0000
+++ b/test-data/gstacks/catalog.calls.vcf	Wed Sep 01 11:29:04 2021 +0000
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.2
-##fileDate=20200316
-##source="Stacks v2.52"
+##fileDate=20210824
+##source="Stacks v2.55"
 ##INFO=<ID=AD,Number=R,Type=Integer,Description="Total Depth for Each Allele">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
diff -r eb784fa07f80 -r 7370bb65bad4 test-data/gstacks/gstacks.log
--- a/test-data/gstacks/gstacks.log	Tue Apr 27 09:31:18 2021 +0000
+++ b/test-data/gstacks/gstacks.log	Wed Sep 01 11:29:04 2021 +0000
@@ -1,4 +1,4 @@
-gstacks v2.52, executed 2020-03-16 15:39:40 (zlib-1.2.11)
+gstacks v2.55, executed 2021-08-24 13:29:01 (zlib-1.2.11)
 gstacks -P stacks_outputs -M denovo_map/popmap_cstacks.tsv
 Locus/sample distributions will be written to 'stacks_outputs/gstacks.log.distribs'.
 
diff -r eb784fa07f80 -r 7370bb65bad4 test-data/gstacks/gstacks.log.distribs
--- a/test-data/gstacks/gstacks.log.distribs	Tue Apr 27 09:31:18 2021 +0000
+++ b/test-data/gstacks/gstacks.log.distribs	Wed Sep 01 11:29:04 2021 +0000
@@ -19,25 +19,25 @@
 Num. threads: 1
 Parallel time: 0.0
 Average thread time spent:
-     0.0  reading (3.0%)
-     0.0  processing (95.7%)
-             0.0 pre-alignments block (74.4%)
-             0.0  reformatting fw-reads (0.2%)
-             0.0  assembling (27.3%)
-             0.0  initializing alignments (8.7%)
-             0.0  aligning (36.6%)
+     0.0  reading (2.8%)
+     0.0  processing (95.9%)
+             0.0 pre-alignments block (76.1%)
+             0.0  reformatting fw-reads (0.1%)
+             0.0  assembling (17.5%)
+             0.0  initializing alignments (4.0%)
+             0.0  aligning (52.9%)
              0.0  merging read pairs (1.6%)
-             0.0 post-alignments block (19.8%)
+             0.0 post-alignments block (18.7%)
              0.0  filtering reads (0.0%)
-             0.0  counting nucleotides (3.2%)
-             0.0  genotyping (1.5%)
-             0.0  haplotyping (0.9%)
+             0.0  counting nucleotides (2.8%)
+             0.0  genotyping (1.2%)
+             0.0  haplotyping (1.0%)
              0.0  computing consensus (0.1%)
              0.0  building_fa (0.1%)
-             0.0  building_vcf (14.0%)
+             0.0  building_vcf (13.4%)
      0.0  writing_fa (0.0%)
      0.0  writing_vcf (0.9%)
-     0.0  clocking (0.1%)
-Total time spent writing vcf: 0.0 (0.8%)
+     0.0  clocking (0.2%)
+Total time spent writing vcf: 0.0 (0.9%)
 VCFwrite block size: mean=1.0(n=3); max=1
 END clockings
diff -r eb784fa07f80 -r 7370bb65bad4 test-data/populations/populations.log
--- a/test-data/populations/populations.log	Tue Apr 27 09:31:18 2021 +0000
+++ b/test-data/populations/populations.log	Wed Sep 01 11:29:04 2021 +0000
@@ -1,4 +1,4 @@
-populations v2.52, executed 2020-03-16 15:39:40 (zlib-1.2.11)
+populations v2.55, executed 2021-08-24 13:29:01 (zlib-1.2.11)
 populations -P stacks_outputs -M denovo_map/popmap_cstacks.tsv
 Locus/sample distributions will be written to 'stacks_outputs/populations.log.distribs'.
 populations parameters selected:
diff -r eb784fa07f80 -r 7370bb65bad4 test-data/sstacks/PopA_01.matches.tsv
--- a/test-data/sstacks/PopA_01.matches.tsv	Tue Apr 27 09:31:18 2021 +0000
+++ b/test-data/sstacks/PopA_01.matches.tsv	Wed Sep 01 11:29:04 2021 +0000
@@ -1,6 +1,6 @@
-# sstacks version 2.52; generated on 2020-03-16 15:39:40
+# sstacks version 2.55; generated on 2021-08-24 13:29:01
 1	1	1	AC	9	94M
 1	1	1	CA	9	94M
 2	1	2	consensus	28	94M
 3	1	3	consensus	20	94M
-# sstacks completed on 2020-03-16 15:39:40
+# sstacks completed on 2021-08-24 13:29:01
diff -r eb784fa07f80 -r 7370bb65bad4 test-data/sstacks/PopA_02.matches.tsv
--- a/test-data/sstacks/PopA_02.matches.tsv	Tue Apr 27 09:31:18 2021 +0000
+++ b/test-data/sstacks/PopA_02.matches.tsv	Wed Sep 01 11:29:04 2021 +0000
@@ -1,6 +1,6 @@
-# sstacks version 2.52; generated on 2020-03-16 15:39:40
+# sstacks version 2.55; generated on 2021-08-24 13:29:01
 1	2	1	AC	6	94M
 1	2	1	CA	6	94M
 2	2	2	consensus	28	94M
 3	2	3	consensus	20	94M
-# sstacks completed on 2020-03-16 15:39:40
+# sstacks completed on 2021-08-24 13:29:01
diff -r eb784fa07f80 -r 7370bb65bad4 test-data/tsv2bam/tsv2bam.log
--- a/test-data/tsv2bam/tsv2bam.log	Tue Apr 27 09:31:18 2021 +0000
+++ b/test-data/tsv2bam/tsv2bam.log	Wed Sep 01 11:29:04 2021 +0000
@@ -1,4 +1,4 @@
-tsv2bam v2.52, executed 2020-03-16 15:39:40 (zlib-1.2.11)
+tsv2bam v2.55, executed 2021-08-24 13:29:01 (zlib-1.2.11)
 tsv2bam -P stacks_outputs -M denovo_map/popmap_cstacks.tsv -R demultiplexed/
 Configuration for this run:
   Stacks directory: 'stacks_outputs/'
diff -r eb784fa07f80 -r 7370bb65bad4 test-data/ustacks/PopA_01.alleles.tsv
--- a/test-data/ustacks/PopA_01.alleles.tsv	Tue Apr 27 09:31:18 2021 +0000
+++ b/test-data/ustacks/PopA_01.alleles.tsv	Wed Sep 01 11:29:04 2021 +0000
@@ -1,4 +1,4 @@
-# ustacks version 2.52; generated on 2020-03-16 15:39:40
+# ustacks version 2.55; generated on 2021-08-24 13:29:01
 1	1	AC	50.00	9
 1	1	CA	50.00	9
-# ustacks completed on 2020-03-16 15:39:40
+# ustacks completed on 2021-08-24 13:29:01
diff -r eb784fa07f80 -r 7370bb65bad4 test-data/ustacks/PopA_01.snps.tsv
--- a/test-data/ustacks/PopA_01.snps.tsv	Tue Apr 27 09:31:18 2021 +0000
+++ b/test-data/ustacks/PopA_01.snps.tsv	Wed Sep 01 11:29:04 2021 +0000
@@ -1,4 +1,4 @@
-# ustacks version 2.52; generated on 2020-03-16 15:39:40
+# ustacks version 2.55; generated on 2021-08-24 13:29:01
 1	1	0	O	24.95	A	-		
 1	1	1	O	24.95	A	-		
 1	1	2	O	24.95	T	-		
@@ -281,4 +281,4 @@
 1	3	91	O	27.73	A	-		
 1	3	92	O	27.73	G	-		
 1	3	93	O	27.73	A	-		
-# ustacks completed on 2020-03-16 15:39:40
+# ustacks completed on 2021-08-24 13:29:01
diff -r eb784fa07f80 -r 7370bb65bad4 test-data/ustacks/PopA_01.tags.tsv
--- a/test-data/ustacks/PopA_01.tags.tsv	Tue Apr 27 09:31:18 2021 +0000
+++ b/test-data/ustacks/PopA_01.tags.tsv	Wed Sep 01 11:29:04 2021 +0000
@@ -1,4 +1,4 @@
-# ustacks version 2.52; generated on 2020-03-16 15:39:40
+# ustacks version 2.55; generated on 2021-08-24 13:29:01
 1	1	consensus			AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC	0	0	0
 1	1	model			OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOEOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOEOOOOO			
 1	1	primary	0	lane1_fakedata7_0 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC			
@@ -71,4 +71,4 @@
 1	3	primary	0	lane1_fakedata2_19 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
 1	3	secondary		lane1_fakedata2_5 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTAAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
 1	3	secondary		lane1_fakedata2_17 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCCAGA			
-# ustacks completed on 2020-03-16 15:39:40
+# ustacks completed on 2021-08-24 13:29:01
diff -r eb784fa07f80 -r 7370bb65bad4 test-data/ustacks/PopA_02.alleles.tsv
--- a/test-data/ustacks/PopA_02.alleles.tsv	Tue Apr 27 09:31:18 2021 +0000
+++ b/test-data/ustacks/PopA_02.alleles.tsv	Wed Sep 01 11:29:04 2021 +0000
@@ -1,4 +1,4 @@
-# ustacks version 2.52; generated on 2020-03-16 15:39:40
+# ustacks version 2.55; generated on 2021-08-24 13:29:01
 2	1	AC	50.00	6
 2	1	CA	50.00	6
-# ustacks completed on 2020-03-16 15:39:40
+# ustacks completed on 2021-08-24 13:29:01
diff -r eb784fa07f80 -r 7370bb65bad4 test-data/ustacks/PopA_02.snps.tsv
--- a/test-data/ustacks/PopA_02.snps.tsv	Tue Apr 27 09:31:18 2021 +0000
+++ b/test-data/ustacks/PopA_02.snps.tsv	Wed Sep 01 11:29:04 2021 +0000
@@ -1,4 +1,4 @@
-# ustacks version 2.52; generated on 2020-03-16 15:39:40
+# ustacks version 2.55; generated on 2021-08-24 13:29:01
 2	1	0	O	16.64	A	-		
 2	1	1	O	16.64	A	-		
 2	1	2	O	16.64	T	-		
@@ -281,4 +281,4 @@
 2	3	91	O	27.73	A	-		
 2	3	92	O	27.73	G	-		
 2	3	93	O	27.73	A	-		
-# ustacks completed on 2020-03-16 15:39:40
+# ustacks completed on 2021-08-24 13:29:01
diff -r eb784fa07f80 -r 7370bb65bad4 test-data/ustacks/PopA_02.tags.tsv
--- a/test-data/ustacks/PopA_02.tags.tsv	Tue Apr 27 09:31:18 2021 +0000
+++ b/test-data/ustacks/PopA_02.tags.tsv	Wed Sep 01 11:29:04 2021 +0000
@@ -1,4 +1,4 @@
-# ustacks version 2.52; generated on 2020-03-16 15:39:40
+# ustacks version 2.55; generated on 2021-08-24 13:29:01
 2	1	consensus			AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC	0	0	0
 2	1	model			OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOEOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOEOOOOO			
 2	1	primary	0	lane1_fakedata7_7 1:N:0:/1	AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC			
@@ -65,4 +65,4 @@
 2	3	primary	0	lane1_fakedata2_18 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
 2	3	primary	0	lane1_fakedata2_19 1:N:0:/1	AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
 2	3	secondary		lane1_fakedata2_1 1:N:0:/1	AATTCTCTACACCACTGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA			
-# ustacks completed on 2020-03-16 15:39:40
+# ustacks completed on 2021-08-24 13:29:01