# HG changeset patch
# User iuc
# Date 1675706679 0
# Node ID 008b8c6f6b26777503bce9fb27f5f3b4166e4dca
# Parent  0247076a9567ad84e039a87872f81add0d0598bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f

diff -r 0247076a9567 -r 008b8c6f6b26 bbduk.xml
--- a/bbduk.xml	Thu Feb 03 21:11:56 2022 +0000
+++ b/bbduk.xml	Mon Feb 06 18:04:39 2023 +0000
@@ -1,8 +1,9 @@
-<tool id="bbtools_bbduk" name="BBTools: BBduk" version="@WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+<tool id="bbtools_bbduk" name="BBTools: BBduk" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>decontamination using kmers</description>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="edam_ontology"/>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 #import os
diff -r 0247076a9567 -r 008b8c6f6b26 macros.xml
--- a/macros.xml	Thu Feb 03 21:11:56 2022 +0000
+++ b/macros.xml	Mon Feb 06 18:04:39 2023 +0000
@@ -1,10 +1,21 @@
 <macros>
-    <token name="@WRAPPER_VERSION@">1.0.0</token>
-    <token name="@VERSION_SUFFIX@">3</token>
-    <token name="@PROFILE@">20.09</token>
+    <token name="@TOOL_VERSION@">39.01</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">22.01</token>
+    <xml name="edam_ontology">
+        <edam_topics>
+            <edam_topic>topic_0622</edam_topic> <!-- Genomics -->
+            <edam_topic>topic_0091</edam_topic> <!-- Bioinformatics -->
+        </edam_topics>
+        <edam_operations>
+            <edam_operation>operation_0496</edam_operation> <!-- Global alignment -->
+            <edam_operation>operation_0491</edam_operation> <!-- Pairwise sequence alignment -->
+        </edam_operations>
+    </xml>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="38.93">bbmap</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">bbmap</requirement>
+            <requirement type="package" version="1.16.1">samtools</requirement> <!-- automatic solving installs 1.6 in some cases, instead -->
         </requirements>
     </xml>
     <macro name="dbKeyActionsBBMap">
diff -r 0247076a9567 -r 008b8c6f6b26 test-data/SRX7529235_SRR10859038_1.fastq.gz
Binary file test-data/SRX7529235_SRR10859038_1.fastq.gz has changed
diff -r 0247076a9567 -r 008b8c6f6b26 test-data/SRX7529235_SRR10859038_2.fastq.gz
Binary file test-data/SRX7529235_SRR10859038_2.fastq.gz has changed
diff -r 0247076a9567 -r 008b8c6f6b26 test-data/bbmerge/input_R1.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bbmerge/input_R1.fastq	Mon Feb 06 18:04:39 2023 +0000
@@ -0,0 +1,40 @@
+@A00604:500:HKMVNDSX3:2:1101:8196:1000 1:N:0:ATCGTCTC+NTAACCGA
+NATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGTGGAATCGCAGCCGAACCTGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:20419:1000 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF,,,F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:20853:1000 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGGCCGCGGACATCTCGGTGGGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFF:FF,FFFFFFFFFFFFFFFFF:FFFFFF:FF:FFFFF
+@A00604:500:HKMVNDSX3:2:1101:20943:1000 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGTAAGTCATGGAGATTGTGTCTATATAAAAAGTGGTAGTGAAATCTGCATTATAAGATGACACTATCTCAAAGTGTATATCAATGAAGAGGATTGGTCATCCAGAAGTAGCACTGGAA
++
+FFFFFFFFFFFFFFFFFFFF:FFFFFF:FFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:29460:1000 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGTCGATTCGGCCGCAGACGGGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FF,FFFFFFFFFFFFF:FFFFFFFFFF:FFFFFF:FFFFFFFF:FFFFFFFFF,FFFFFFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:12979:1016 1:N:0:ATCGTCTC+NTAACCGA
+ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACTGCGCACTGCAGGTGCCATCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:17517:1016 1:N:0:ATCGTCTC+NTAACCGA
+ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGATGAAACTATGGGACCCTCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF,FF:FFFFFFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:25310:1016 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCAAAGCCCCGGTAGGGCCGGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFF:FFFFFF:FFFFFFF:FFFF:F:FF:FFFFF::FFFFFFFF::FFF:FFF:FFFFFFFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:7346:1031 1:N:0:ATCGTCTC+GTAACCGA
+ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGGACTCGCCCACCTATGTCCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFFFFF:FF
+@A00604:500:HKMVNDSX3:2:1101:8919:1031 1:N:0:ATCGTCTC+GTAACCGA
+GATCTCATTCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCTCACCGGTTCTGCAGTAAGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAA
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:F
diff -r 0247076a9567 -r 008b8c6f6b26 test-data/bbmerge/input_R2.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bbmerge/input_R2.fastq	Mon Feb 06 18:04:39 2023 +0000
@@ -0,0 +1,40 @@
+@A00604:500:HKMVNDSX3:2:1101:8196:1000 2:N:0:ATCGTCTC+NTAACCGA
+ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACAGGTTCGGCTGCGATTCCACGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF
+@A00604:500:HKMVNDSX3:2:1101:20419:1000 2:N:0:ATCGTCTC+NTAACCGA
+ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:20853:1000 2:N:0:ATCGTCTC+NTAACCGA
+ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACCCACCGAGATGTCCGCGGCCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF,FFFFFFFFFFFFFFFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:20943:1000 2:N:0:ATCGTCTC+NTAACCGA
+ACTCGGTGCCACTTTTTCAACCAAGAGGGGCTAAAAATTTTCAAAGGTTACCTATATGATCAGATAAGTTCTGTTGGAAAGAAAATCAATTGATATGACATTGTCAGTCAACTGACATGGATTTTCTCATGACCTAACATGATATATTAAC
++
+FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:29460:1000 2:N:0:ATCGTCTC+NTAACCGA
+ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACCCGTCTGCGGCCGAATCGACGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFF:FFFFFFFFFFFFFFF:F:FFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:12979:1016 2:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGATGGCACCTGCAGTGCGCAGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:17517:1016 2:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGAGGGTCCCATAGTTTCATCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:25310:1016 2:N:0:ATCGTCTC+NTAACCGA
+ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACCGGCCCTACCGGGGCTTTGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:7346:1031 2:N:0:ATCGTCTC+GTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGGACATAGGTGGGCGAGTCCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFF:FFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFF:FFF
+@A00604:500:HKMVNDSX3:2:1101:8919:1031 2:N:0:ATCGTCTC+GTAACCGA
+ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACTTACTGCAGAACCGGTGAGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FFFFF
diff -r 0247076a9567 -r 008b8c6f6b26 test-data/bbmerge/input_interleaved.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bbmerge/input_interleaved.fastq	Mon Feb 06 18:04:39 2023 +0000
@@ -0,0 +1,80 @@
+@A00604:500:HKMVNDSX3:2:1101:8196:1000 1:N:0:ATCGTCTC+NTAACCGA
+NATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGTGGAATCGCAGCCGAACCTGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:8196:1000 2:N:0:ATCGTCTC+NTAACCGA
+ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACAGGTTCGGCTGCGATTCCACGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF
+@A00604:500:HKMVNDSX3:2:1101:20419:1000 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF,,,F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:20419:1000 2:N:0:ATCGTCTC+NTAACCGA
+ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:20853:1000 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGGCCGCGGACATCTCGGTGGGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFF:FF,FFFFFFFFFFFFFFFFF:FFFFFF:FF:FFFFF
+@A00604:500:HKMVNDSX3:2:1101:20853:1000 2:N:0:ATCGTCTC+NTAACCGA
+ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACCCACCGAGATGTCCGCGGCCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF,FFFFFFFFFFFFFFFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:20943:1000 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGTAAGTCATGGAGATTGTGTCTATATAAAAAGTGGTAGTGAAATCTGCATTATAAGATGACACTATCTCAAAGTGTATATCAATGAAGAGGATTGGTCATCCAGAAGTAGCACTGGAA
++
+FFFFFFFFFFFFFFFFFFFF:FFFFFF:FFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:20943:1000 2:N:0:ATCGTCTC+NTAACCGA
+ACTCGGTGCCACTTTTTCAACCAAGAGGGGCTAAAAATTTTCAAAGGTTACCTATATGATCAGATAAGTTCTGTTGGAAAGAAAATCAATTGATATGACATTGTCAGTCAACTGACATGGATTTTCTCATGACCTAACATGATATATTAAC
++
+FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:29460:1000 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGTCGATTCGGCCGCAGACGGGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FF,FFFFFFFFFFFFF:FFFFFFFFFF:FFFFFF:FFFFFFFF:FFFFFFFFF,FFFFFFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:29460:1000 2:N:0:ATCGTCTC+NTAACCGA
+ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACCCGTCTGCGGCCGAATCGACGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFF:FFFFFFFFFFFFFFF:F:FFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:12979:1016 1:N:0:ATCGTCTC+NTAACCGA
+ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACTGCGCACTGCAGGTGCCATCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:12979:1016 2:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGATGGCACCTGCAGTGCGCAGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:17517:1016 1:N:0:ATCGTCTC+NTAACCGA
+ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGATGAAACTATGGGACCCTCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF,FF:FFFFFFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:17517:1016 2:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGAGGGTCCCATAGTTTCATCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:25310:1016 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCAAAGCCCCGGTAGGGCCGGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFF:FFFFFF:FFFFFFF:FFFF:F:FF:FFFFF::FFFFFFFF::FFF:FFF:FFFFFFFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:25310:1016 2:N:0:ATCGTCTC+NTAACCGA
+ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACCGGCCCTACCGGGGCTTTGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:7346:1031 1:N:0:ATCGTCTC+GTAACCGA
+ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGGACTCGCCCACCTATGTCCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFFFFF:FF
+@A00604:500:HKMVNDSX3:2:1101:7346:1031 2:N:0:ATCGTCTC+GTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGGACATAGGTGGGCGAGTCCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFF:FFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFF:FFF
+@A00604:500:HKMVNDSX3:2:1101:8919:1031 1:N:0:ATCGTCTC+GTAACCGA
+GATCTCATTCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCTCACCGGTTCTGCAGTAAGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAA
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:F
+@A00604:500:HKMVNDSX3:2:1101:8919:1031 2:N:0:ATCGTCTC+GTAACCGA
+ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACTTACTGCAGAACCGGTGAGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT
++
+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FFFFF
diff -r 0247076a9567 -r 008b8c6f6b26 test-data/bbmerge/insert_length_hist.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bbmerge/insert_length_hist.tabular	Mon Feb 06 18:04:39 2023 +0000
@@ -0,0 +1,8 @@
+#Mean	165.889
+#Median	166
+#Mode	166
+#STDev	0.314
+#PercentOfPairs	90.000
+#InsertSize	Count
+165	1
+166	8
diff -r 0247076a9567 -r 008b8c6f6b26 test-data/bbmerge/merged.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bbmerge/merged.fastq	Mon Feb 06 18:04:39 2023 +0000
@@ -0,0 +1,36 @@
+@A00604:500:HKMVNDSX3:2:1101:8196:1000 1:N:0:ATCGTCTC+NTAACCGA
+NATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGTGGAATCGCAGCCGAACCTGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGT
++
+!FFFFFFFFFFFFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFFFFFFFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:20419:1000 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGT
++
+FFFFFFFFFFFFFFFJJJJJJJJJJJJJJJJJJJJHHHJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFFFFFFFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:20853:1000 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGGCCGCGGACATCTCGGTGGGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGT
++
+FFFFFFFFFFFFFFFJJJJJJJJJJJJJJJJJJJJJHJJJJJHJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFFFFFFFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:29460:1000 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGTCGATTCGGCCGCAGACGGGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGT
++
+FFFFFFFFFFFFFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHJJJJJJJJJJJJFFFFFFFFFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:12979:1016 1:N:0:ATCGTCTC+NTAACCGA
+ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACTGCGCACTGCAGGTGCCATCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC
++
+FFFFFFFFFFFFFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFFFFFFFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:17517:1016 1:N:0:ATCGTCTC+NTAACCGA
+ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGATGAAACTATGGGACCCTCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC
++
+FFFFFFFFFFFFFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJH<JJJJJJJJJJJJJJJFFFFFFFFFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:25310:1016 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCAAAGCCCCGGTAGGGCCGGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGT
++
+FFFFFFFFFFFFFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFFFFFFFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:7346:1031 1:N:0:ATCGTCTC+GTAACCGA
+ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGGACTCGCCCACCTATGTCCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC
++
+FFFFFFFFFFFFFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHJJJJJJJHJJJJJJJHJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFFFFFFFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:8919:1031 1:N:0:ATCGTCTC+GTAACCGA
+GATCTCATTCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCTCACCGGTTCTGCAGTAAGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGT
++
+FFFFFFFFFFFFFFJJJJJHJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFFFFFFFFFFFF
diff -r 0247076a9567 -r 008b8c6f6b26 test-data/bbmerge/unmerged.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bbmerge/unmerged.fastq	Mon Feb 06 18:04:39 2023 +0000
@@ -0,0 +1,8 @@
+@A00604:500:HKMVNDSX3:2:1101:20943:1000 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGTAAGTCATGGAGATTGTGTCTATATAAAAAGTGGTAGTGAAATCTGCATTATAAGATGACACTATCTCAAAGTGTATATCAATGAAGAGGATTGGTCATCCAGAAGTAGCACTGGAA
++
+FFFFFFFFFFFFFFFFFFFF:FFFFFF:FFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@A00604:500:HKMVNDSX3:2:1101:20943:1000 2:N:0:ATCGTCTC+NTAACCGA
+ACTCGGTGCCACTTTTTCAACCAAGAGGGGCTAAAAATTTTCAAAGGTTACCTATATGATCAGATAAGTTCTGTTGGAAAGAAAATCAATTGATATGACATTGTCAGTCAACTGACATGGATTTTCTCATGACCTAACATGATATATTAAC
++
+FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFFFFFFFF