# HG changeset patch
# User iuc
# Date 1675706807 0
# Node ID fc029a9b4d07fae7a1d33243a3fd7791023c35ae

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f

diff -r 000000000000 -r fc029a9b4d07 bbmerge.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bbmerge.xml	Mon Feb 06 18:06:47 2023 +0000
@@ -0,0 +1,255 @@
+<tool id="bbtools_bbmerge" name="BBTools: BBMerge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Merge overlapping mates of a read pair</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="edam_ontology"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+#import os
+#import re
+
+#if str($input_type_cond.input_type) in ['single', 'pair']:
+    #set read1 = $input_type_cond.read1
+    ## bbmerge uses the file extension to determine the input format.
+    #set ext = '.fastq'
+    #if $read1.ext.endswith('.gz'):
+        #set ext = $ext + '.gz'
+    #end if
+    #set read1_file = 'forward' + $ext
+    ln -s '${read1}' '${read1_file}' &&
+    #if str($input_type_cond.input_type) == 'pair':
+        #set read2 = $input_type_cond.read2
+        #set read2_file = 'reverse' + $ext
+        ln -s '${read2}' '${read2_file}' &&
+    #end if
+#else:
+    #set read1 = $input_type_cond.reads_collection['forward']
+    #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
+    ## bbmap uses the file extension to determine the input format.
+    #set ext = $read1_identifier + '.fastq'
+    #if $read1.ext.endswith('.gz'):
+        #set ext = $ext + '.gz'
+    #end if
+    #set read1_file = $read1_identifier + $ext
+    ln -s '${read1}' '${read1_file}' &&
+    #set read2 = $input_type_cond.reads_collection['reverse']
+    #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier))
+    #set read2_file = $read2_identifier + $ext
+    ln -s '${read2}' '${read2_file}' &&
+#end if
+
+bbmerge.sh
+#### Input parameters
+#if str($input_type_cond.input_type) == 'single':
+    in='${read1_file}'
+    interleaved=t
+#else:
+    in1='${read1_file}' in2='${read2_file}'
+    interleaved=f
+#end if
+
+#### Output options
+out=merged.fastq
+outu=unmerged.fastq
+ihist=ihist.tabular
+touppercase=t
+
+#### Quality and trimming parameters
+qtrim='$qt_options.qtrim'
+trimq='$qt_options.trimq'
+minlength='$qt_options.minlength_after_trim'
+usequality='$qt_options.usequality'
+
+#### Merging parameters
+usejni=f ## Do overlapping in C code, which is faster.
+ecco='$merge_options.ecco'
+trimnonoverlapping='$merge_options.trimnonoverlapping'
+mininsert='$merge_options.mininsert'
+minoverlap='$merge_options.minoverlap'
+minq='$merge_options.minq'
+maxq='$merge_options.maxq'
+entropy='$merge_options.entropy'
+efilter='$merge_options.efilter'
+pfilter='$merge_options.pfilter'
+kfilter='$merge_options.kfilter'
+usequality='$merge_options.usequality'
+
+#if $merge_options.adapters.selector == "with_adaptors":
+    adapter1='$merge_options.adapter1'
+    adapter2='$merge_options.adapter2'
+#end if
+
+#if $merge_options.merge_mode.selector == 'Ratio mode':
+    maxratio='$merge_options.merge_mode.maxratio'
+    ratiomargin='$merge_options.merge_mode.ratiomargin'
+    ratiooffset='$merge_options.merge_mode.ratiooffset'
+    maxmismatches='$merge_options.merge_mode.maxmismatches'
+    ratiominoverlapreduction=0
+    minsecondratio='$merge_options.merge_mode.minsecondratio'
+#else:
+    margin='$merge_options.merge_mode.margin'
+    mismatches='$merge_options.merge_mode.mismatches'
+    requireratiomatch='$merge_options.merge_mode.requireratiomatch'
+#end if
+
+$merge_options.strictness=t
+]]></command>
+    <inputs>
+        <expand macro="input_type_cond"/>
+        
+        <section name="qt_options" title="Quality and trimming options">
+            <param name="qtrim" type="select" label="Select option for quality trimming ends before mapping">
+                <option value="f" selected="true">No trimming</option>
+                <option value="l">Trim left</option>
+                <option value="r">Trim right</option>
+                <option value="lr">Trim both</option>
+            </param>
+            <param argument="trimq" type="integer" value="6" label="Trim regions with average quality below this value"/>
+            <param argument="minlength_after_trim" type="integer" value="60" label="Don't trim reads to be shorter than this value"/>
+            <param argument="usequality" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Use quality scores when determining which read kmers to use as seeds?"/>
+        </section>
+        
+        <section name="merge_options" title="Merging parameters">
+            <param name="strictness" type="select" label="Select option for quality trimming ends before mapping">
+                <option value="xstrict">max strict</option>
+                <option value="ustrict">ultra strict</option>
+                <option value="vstrict">very strict</option>
+                <option value="strict">strict</option>
+                <option value="default" selected="true">default</option>
+                <option value="loose">loose</option>
+                <option value="vloose">very loose</option>
+                <option value="uloose">ultra loose</option>
+                <option value="xloose">max loose</option>
+                <option value="fast">fastest possible, less accurate</option>
+            </param>
+            <param argument="ecco" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Error-correct the overlapping part, but don't merge." help="If selected, the tool with find the overlaps as if merging reads, use this overlap information to correct sequencing errors on both strands. However, the strands from the mates will not be merged but provided as two separate reads after error correction."/>
+            <param argument="trimnonoverlapping" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Trim all non-overlapping portions, leaving only consensus sequence. By default, only sequence to the right of the overlap (adapter sequence) is trimmed."/>
+            <param argument="mininsert" type="integer" value="35" label="Minimum insert size to merge reads"/>
+            <param argument="minoverlap" type="integer" value="12" label="Minimum number of overlapping bases to allow merging"/>
+            
+            <param argument="minq" type="integer" value="9" label="Ignore bases with quality below this"/>
+            <param argument="maxq" type="integer" value="41" label="Cap output quality scores at this"/>
+            
+            <param argument="entropy" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Increase the minimum overlap requirement for low-complexity reads"/>
+            <param argument="efilter" type="integer" value="6" label="Ban overlaps with over this many times the expected number of errors." help="Lower is more strict, -1 disables."/>
+            <param argument="pfilter" type="float" value="0.00004" label="Probability filter to disallow improbable overlaps." help="Higher is stricter. 0 will disable the filter; 1 will allow only perfect overlaps."/>
+            <param argument="kfilter" type="integer" value="41" label="Ban overlaps that create kmers with count below this value" help="Requires good coverage, 0 disables."/>
+            <param argument="usequality" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Take quality factors into account" help="If disabled, quality values are completely ignored, both for overlap detection and filtering. May be useful for data with inaccurate quality values."/>
+            
+            <conditional name="adapters">
+                <param name="selector" type="select" label="Provide adapter sequences to improve accuracy?">
+                    <option value="wout_adapters" selected="true">No</option>
+                    <option value="with_adapters">Yes, use these adapter sequences</option>
+                </param>
+                <when value="wout_adapters"/>
+                <when value="with_adapters">
+                    <param argument="adapter1" type="text" value="" label="Left adapter sequence"/>
+                    <param argument="adapter2" type="text" value="" label="Right adapter sequence"/>
+                </when>
+            </conditional>
+
+            <conditional name="merge_mode">
+                <param name="selector" type="select" label="Evaluate overlaps via..." help="In the ratio mode, overlaps are decided based on the ratio of matching to mismatching bases. Flat mode scores overlaps based on the total number of mismatching bases only.">
+                    <option value="Ratio mode" selected="true">Ratio mode</option>
+                    <option value="Flat mode">Flat mode</option>
+                </param>
+                <when value="Ratio mode">
+                    <param argument="maxratio" type="float" value="0.09" label="Max error rate; higher increases merge rate."/>
+                    <param argument="ratiomargin" type="float" value="5.5" label="Lower increases merge rate; min is 1."/>
+                    <param argument="ratiooffset" type="float" value="0.55" label="Lower increases merge rate; min is 0."/>
+                    <param argument="maxmismatches" type="integer" value="20" label="Maximum mismatches allowed in overlapping region."/>
+                    <param argument="minsecondratio" type="float" value="0.1" label="Cutoff for second-best overlap ratio."/>
+                </when>
+                <when value="Flat mode">
+                    <param argument="margin" type="integer" value="2" label="The best overlap must have at least 'margin' fewer mismatches than the second best."/>
+                    <param argument="mismatches" type="integer" value="3" label="Do not allow more than this many mismatches."/>
+                    <param argument="requireratiomatch" type="boolean" value="false" label="Require the answer from flat mode and ratio mode to agree, reducing false positives if both are enabled."/>
+                </when>
+            </conditional>
+        </section>
+    </inputs>
+    <outputs>
+        <data format="fastq" name="output_merged_reads" from_work_dir="merged.fastq" label="${tool.name} on ${on_string} (merged reads)"/>
+        <data format="fastq" name="output_unmerged_reads" from_work_dir="unmerged.fastq" label="${tool.name} on ${on_string} (unmerged reads)"/>
+        <data format="tabular" name="output_insertlen_hist" from_work_dir="ihist.tabular" label="${tool.name} on ${on_string} (insert size histogram)"/>
+    </outputs>
+    <tests>
+        <!-- Single interleaved file -->
+        <test expect_num_outputs="3">
+            <param name="input_type" value="single"/>
+            <param name="read1" value="bbmerge/input_interleaved.fastq"/>
+            <output name="output_unmerged_reads" ftype="fastq" value="bbmerge/unmerged.fastq"/>
+            <output name="output_merged_reads" ftype="fastq" value="bbmerge/merged.fastq"/>
+            <output name="output_insertlen_hist" ftype="tabular" value="bbmerge/insert_length_hist.tabular"/>
+        </test>
+        <!-- Paired mates in 2 separate files -->
+        <test expect_num_outputs="3">
+            <param name="input_type" value="pair"/>
+            <param name="read1" value="bbmerge/input_R1.fastq"/>
+            <param name="read2" value="bbmerge/input_R2.fastq"/>
+            <output name="output_unmerged_reads" ftype="fastq" value="bbmerge/unmerged.fastq"/>
+            <output name="output_merged_reads" ftype="fastq" value="bbmerge/merged.fastq"/>
+            <output name="output_insertlen_hist" ftype="tabular" value="bbmerge/insert_length_hist.tabular"/>
+        </test>
+        <!-- Paired mates provided via a paired collection -->
+        <test expect_num_outputs="3">
+            <param name="input_type" value="paired"/>
+            <param name="reads_collection">
+                <collection type="paired">
+                    <element name="forward" value="bbmerge/input_R1.fastq"/>
+                    <element name="reverse" value="bbmerge/input_R2.fastq"/>
+                </collection>
+            </param>
+            <output name="output_unmerged_reads" ftype="fastq" value="bbmerge/unmerged.fastq"/>
+            <output name="output_merged_reads" ftype="fastq" value="bbmerge/merged.fastq"/>
+            <output name="output_insertlen_hist" ftype="tabular" value="bbmerge/insert_length_hist.tabular"/>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+BBMerge merges two overlapping paired reads into a single read. A 2x100nt read pair, for instance can be merged into a single read of length 150nt if the last 50nt of the first read mate and the last 50nt of the second read map overlap. The accuracy of the base calling can also improve as a result of such a reconciliation between the read pairs. BBMerge is also capable of error-correcting the overlapping portion of reads without merging them, as well as merging nonoverlapping reads, if enough coverage is available. 
+
+-----
+
+**A Martian PE sequencing result is expected to be processed as follows:**
+
+input_R1.fastq::
+
+    @read_header_1/1
+    AAAAATTTTTAAAAACCCCCGGGGG
+    +
+    FFFFFFFFFFFFFFFEFFFFFF,FF
+    @read_header_2/1
+    AAAATTTTAAAACCCCCGGGGG
+    +
+    FFFFFFFFFFFFFFFEFFFFFF
+
+
+input_R2.fastq::
+
+    @read_header_1/2
+    TTAATTAATTCCCCCGGGGG
+    +
+    FFFFFFFFFFFFFFFFFFFF
+    @read_header_2/2
+    TTTAAATTTAAACCCCCGGGGG
+    +
+    FFFFFFFFFFFFFFFFFFFFEF
+
+
+output.fastq::
+
+    @read_header_1
+    AAAAATTTTTAAAAACCCCCGGGGGAATTAATTAA
+    +
+    FFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFF
+    @read_header_2
+    AAAATTTTAAAACCCCCGGGGGTTTAAATTTAAA
+    +
+    FFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFF
+    </help>
+    <expand macro="citations"/>
+</tool>
+
diff -r 000000000000 -r fc029a9b4d07 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon Feb 06 18:06:47 2023 +0000
@@ -0,0 +1,107 @@
+<macros>
+    <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="@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">
+        <expand macro="dbKeyActions">
+            <option type="from_data_table" name="fasta_indexes" column="1" offset="0">
+                <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+                <filter type="param_value" ref="ref_source_cond.reference" column="1"/>
+            </option>
+        </expand>
+    </macro>
+    <macro name="dbKeyActions">
+        <actions>
+            <conditional name="ref_source_cond.ref_source">
+                <when value="cached">
+                    <action type="metadata" name="dbkey">
+                        <yield/>
+                    </action>
+                </when>
+                <when value="history">
+                    <action type="metadata" name="dbkey">
+                        <option type="from_param" name="ref_source_cond.reference" param_attribute="dbkey"/>
+                    </action>
+                </when>
+            </conditional>
+        </actions>
+    </macro>
+    <macro name="input_type_cond">
+        <conditional name="input_type_cond">
+            <param name="input_type" type="select" label="Choose the category of the files to be analyzed">
+                <option value="single" selected="true">Single dataset</option>
+                <option value="pair">Dataset pair</option>
+                <option value="paired">List of dataset pairs</option>
+            </param>
+            <when value="single">
+                <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Fastq file"/>
+            </when>
+            <when value="pair">
+                <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Forward reads fastq file"/>
+                <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Reverse reads fastq file"/>
+            </when>
+            <when value="paired">
+                <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of fastqsanger paired read files"/>
+            </when>
+        </conditional>
+    </macro>
+    <macro name="reference_source_cond">
+        <conditional name="ref_source_cond">
+            <param name="ref_source" type="select" label="Select reference genome source; a cached reference or one from the history">
+                <option value="cached" selected="True">Use a cached reference</option>
+                <option value="history">Use a reference from the history</option>
+            </param>
+            <when value="cached">
+                <param name="reference" type="select" label="Using reference genome">
+                    <options from_data_table="fasta_indexes">
+                        <filter type="sort_by" column="2"/>
+                        <validator type="no_options" message="A built-in reference genome is not available"/>
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param name="reference" type="data" format="fasta" label="Using reference genome"/>
+            </when>
+        </conditional>
+    </macro>
+    <macro name="ktrim_cond">
+        <conditional name="ktrim_cond">
+            <param name="ktrim_select"  type="select" label="Trim reads to remove bases matching reference kmers?">
+                <option value="no" selected="true">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no"/>
+            <when value="yes">
+                <param argument="ktrim"  type="select" label="Select trimming position">
+                    <option value="r">Trim to the right</option>
+                    <option value="l">Trim to the left</option>
+                </param>
+                <param argument="minlength" type="integer" value="10" label="Minimum read length" help="Trimmed reads shorter than this will be discarded, pairs will be discarded if both are shorter."/>
+             </when>
+        </conditional>
+    </macro>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">
+                https://doi.org/10.1371/journal.pone.0185056
+            </citation>
+        </citations>
+    </xml>
+</macros>
+
diff -r 000000000000 -r fc029a9b4d07 test-data/13-1941-6_S4_L001_R1_600000.fastq.gz
Binary file test-data/13-1941-6_S4_L001_R1_600000.fastq.gz has changed
diff -r 000000000000 -r fc029a9b4d07 test-data/13-1941-6_S4_L001_R2_600000.fastq.gz
Binary file test-data/13-1941-6_S4_L001_R2_600000.fastq.gz has changed
diff -r 000000000000 -r fc029a9b4d07 test-data/NC_002945v4.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NC_002945v4.fasta	Mon Feb 06 18:06:47 2023 +0000
@@ -0,0 +1,101 @@
+>NC_002945.4 Mycobacterium bovis AF2122/97 genome assembly, chromosome: Mycobacterium_bovis_AF2122/97
+TTGACCGATGACCCCGGTTCAGGCTTCACCACAGTGTGGAACGCGGTCGTCTCCGAACTTAACGGCGACC
+CTAAGGTTGACGACGGACCCAGCAGTGATGCTAATCTCAGCGCTCCGCTGACCCCTCAGCAAAGGGCTTG
+GCTCAATCTCGTCCAGCCATTGACCATCGTCGAGGGGTTTGCTCTGTTATCCGTGCCGAGCAGCTTTGTC
+CAAAACGAAATCGAGCGCCATCTGCGGGCCCCGATTACCGACGCTCTCAGCCGCCGACTCGGACATCAGA
+TCCAACTCGGGGTCCGCATCGCTCCGCCGGCGACCGACGAAGCCGACGACACTACCGTGCCGCCTTCCGA
+AAATCCTGCTACCACATCGCCAGACACCACAACCGACAACGACGAGATTGATGACAGCGCTGCGGCACGG
+GGCGATAACCAGCACAGTTGGCCAAGTTACTTCACCGAGCGCCCGCGCAATACCGATTCCGCTACCGCTG
+GCGTAACCAGCCTTAACCGTCGCTACACCTTTGATACGTTCGTTATCGGCGCCTCCAACCGGTTCGCGCA
+CGCCGCCGCCTTGGCGATCGCAGAAGCACCCGCCCGCGCTTACAACCCCCTGTTCATCTGGGGCGAGTCC
+GGTCTCGGCAAGACACACCTGCTACACGCGGCAGGCAACTATGCCCAACGGTTGTTCCCGGGAATGCGGG
+TCAAATATGTCTCCACCGAGGAATTCACCAACGACTTCATTAACTCGCTCCGCGATGACCGCAAGGTCGC
+ATTCAAACGCAGCTACCGCGACGTAGACGTGCTGTTGGTCGACGACATCCAATTCATTGAAGGCAAAGAG
+GGTATTCAAGAGGAGTTCTTCCACACCTTCAACACCTTGCACAATGCCAACAAGCAAATCGTCATCTCAT
+CTGACCGCCCACCCAAGCAGCTCGCCACCCTCGAGGACCGGCTGAGAACCCGCTTTGAGTGGGGGCTGAT
+CACTGACGTACAACCACCCGAGCTGGAGACCCGCATCGCCATCTTGCGCAAGAAAGCACAGATGGAACGG
+CTCGCGATCCCCGACGATGTCCTCGAACTCATCGCCAGCAGTATCGAACGCAATATCCGTGAACTCGAGG
+GCGCGCTGATCCGGGTCACCGCGTTCGCCTCATTGAACAAAACACCAATCGACAAAGCGCTGGCCGAGAT
+TGTGCTTCGCGATCTGATCGCCGACGCCAACACCATGCAAATCAGCGCGGCGACGATCATGGCTGCCACC
+GCCGAATACTTCGACACTACCGTCGAAGAGCTTCGCGGGCCCGGCAAGACCCGAGCACTGGCCCAGTCAC
+GACAGATTGCGATGTACCTGTGTCGTGAGCTCACCGATCTTTCGTTGCCCAAAATCGGCCAAGCGTTCGG
+CCGTGATCACACAACCGTCATGTACGCCCAACGCAAGATCCTGTCCGAGATGGCCGAGCGCCGTGAGGTC
+TTTGATCACGTCAAAGAACTCACCACTCGCATCCGTCAGCGCTCCAAGCGCTAGCACGGCGTGTTCTTCC
+GACAACGTTCTTAAAAAAACTTCTCTCTCCCAGGTCACACCAGTCACAGAGATTGGCTGTGAGTGTCGCT
+GTGCACAAACCGCGCACAGACTCATACAGTCCCGGCGGTTCCGTTCACAACCCACGCCTCATCCCCACCG
+ACCCAACACACACCCCACAGTCATCGCCACCGTCATCCACAACTCCGACCGACGTCGACCTGCACCAAGA
+CCAGACTGTCCCCAAACTGCACACCCTCTAATACTGTTACCGAGATTTCTTCGTCGTTTGTTCTTGGAAA
+GACAGCGCTGGGGATCGTTCGCTGGATACCACCCGCATAACTGGCTCGTCGCGGTGGGTCAGAGGTCAAT
+GATGAACTTTCAAGTTGACGTGAGAAGCTCTACGGTTGTTGTTCGACTGCTGTTGCGGCCGTCGTGGCGG
+GTCACGCGTCATGGGCGTTCGTCGTTGGCAGTCCCCACGCTAGCGGGGCGCTAGCCACGGGATCGAACTC
+ATCGTGAGGTGAAAGGGCGCAATGGACGCGGCTACGACAAGAGTTGGCCTCACCGACTTGACGTTTCGTT
+TGCTACGAGAGTCTTTCGCCGATGCGGTGTCGTGGGTGGCTAAAAATCTGCCAGCCAGGCCCGCGGTGCC
+GGTGCTCTCCGGCGTGTTGTTGACCGGCTCGGACAACGGTCTGACGATTTCCGGATTCGACTACGAGGTT
+TCCGCCGAGGCCCAGGTTGGCGCTGAAATTGTTTCTCCTGGAAGCGTTTTAGTTTCTGGCCGATTGTTGT
+CCGATATTACCCGGGCGTTGCCTAACAAGCCCGTAGGCGTTCATGTCGAAGGTAACCGGGTCGCATTGAC
+CTGCGGTAACGCCAGGTTTTCGCTACCGACGATGCCAGTCGAGGATTATCCGACGCTGCCGACGCTGCCG
+GAAGAGACCGGATTGTTGCCTGCGGAATTATTCGCCGAGGCAATCAGTCAGGTCGCTATCGCCGCCGGCC
+GGGACGACACGCTGCCTATGTTGACCGGCATCCGGGTCGAAATCCTCGGTGAGACGGTGGTTTTGGCCGC
+TACCGACAGGTTTCGCCTGGCTGTTCGAGAACTGAAGTGGTCGGCGTCGTCGCCAGATATCGAAGCGGCT
+GTGCTGGTCCCGGCCAAGACGCTGGCCGAGGCCGCCAAAGCGGGCATCGGCGGCTCTGACGTTCGTTTGT
+CGTTGGGTACTGGGCCGGGGGTGGGCAAGGATGGCCTGCTCGGTATCAGTGGGAACGGCAAGCGCAGCAC
+CACGCGACTTCTTGATGCCGAGTTCCCGAAGTTTCGGCAGTTGCTACCAACCGAACACACCGCGGTGGCC
+ACCATGGACGTGGCCGAGTTGATCGAAGCGATCAAGCTGGTTGCGTTGGTAGCTGATCGGGGCGCGCAGG
+TGCGCATGGAGTTCGCTGATGGCAGCGTGCGGCTTTCTGCGGGTGCCGATGATGTTGGACGAGCCGAGGA
+AGATCTTGTTGTTGACTATGCCGGTGAACCATTGACGATTGCGTTTAACCCAACCTATCTAACGGACGGT
+TTGAGTTCGTTGCGCTCGGAGCGAGTGTCTTTCGGGTTTACGACTGCGGGTAAGCCTGCCTTGCTACGTC
+CGGTGTCCGGGGACGATCGCCCTGTGGCGGGTCTGAATGGCAACGGTCCGTTCCCGGCGGTGTCGACGGA
+CTATGTCTATCTGTTGATGCCGGTTCGGTTGCCGGGCTGAGCACTTGGCGCCCGGGTAGGTGTACGTCCG
+TCATTTGGGGCTGCGTGACTTCCGGTCCTGGGCATGTGTAGATCTGGAATTGCATCCAGGGCGGACGGTT
+TTTGTTGGGCCTAACGGTTATGGTAAGACGAATCTTATTGAGGCACTGTGGTATTCGACGACGTTAGGTT
+CGCACCGCGTTAGCGCCGATTTGCCGTTGATCCGGGTAGGTACCGATCGTGCGGTGATCTCCACGATCGT
+GGTGAACGACGGTAGAGAATGTGCCGTCGACCTCGAGATCGCCACGGGGCGAGTCAACAAAGCGCGATTG
+AATCGATCATCGGTCCGAAGTACACGTGATGTGGTCGGAGTGCTTCGAGCTGTGTTGTTTGCCCCTGAGG
+ATCTGGGGTTGGTTCGTGGGGATCCCGCTGACCGGCGGCGCTATCTGGATGATCTGGCGATCGTGCGTAG
+GCCTGCGATCGCTGCGGTACGAGCCGAATATGAGAGGGTGGTGCGCCAGCGGACGGCGTTATTGAAGTCC
+GTACCTGGAGCACGGTATCGGGGTGACCGGGGTGTGTTTGACACTCTTGAGGTATGGGACAGTCGTTTGG
+CGGAGCACGGGGCTGAACTGGTGGCCGCCCGCATCGATTTGGTCAACCAGTTGGCACCGGAAGTGAAGAA
+GGCATACCAGCTGTTGGCGCCGGAATCGCGATCGGCGTCTATCGGTTATCGGGCCAGCATGGATGTAACC
+GGTCCCAGCGAGCAGTCAGATACCGATCGGCAATTGTTAGCAGCTCGGCTGTTGGCGGCGCTGGCGGCCC
+GTCGGGATGCCGAACTCGAGCGTGGGGTTTGTCTAGTTGGTCCGCACCGTGACGACCTAATACTGCGACT
+AGGCGATCAACCCGCGAAAGGATTTGCTAGCCATGGGGAGGCGTGGTCGTTGGCGGTGGCACTGCGGTTG
+GCGGCCTATCAACTGTTACGCGTTGATGGTGGTGAGCCGGTGTTGTTGCTCGACGACGTGTTCGCCGAAC
+TGGATGTCATGCGCCGTCGAGCGTTGGCGACGGCGGCCGAGTCCGCCGAACAGGTGTTGGTGACTGCCGC
+GGTGCTCGAGGATATTCCCGCCGGCTGGGACGCCAGGCGGGTGCACATCGATGTGCGTGCCGATGACACC
+GGATCGATGTCGGTGGTTCTGCCATGACGGGTTCTGTTGACCGGCCCGACCAGAATCGCGGTGAGCGATT
+AATGAAGTCACCAGGGTTGGATTTGGTCAGGCGCACCCTGGACGAAGCTCGTGCTGCTGCCCGCGCGCGC
+GGACAAGACGCCGGTCGAGGGCGGGTCGCTTCCGTTGCGTCGGGTCGGGTGGCCGGACGGCGACGAAGCT
+GGTCGGGTCCGGGGCCCGACATTCGTGATCCACAACCGCTGGGTAAGGCCGCTCGTGAGCTGGCAAAGAA
+ACGCGGCTGGTCGGTGCGGGTCGCCGAGGGTATGGTGCTCGGCCAGTGGTCTGCGGTGGTCGGCCACCAG
+ATCGCCGAACATGCACGCCCGACTGCGCTAAACGACGGGGTGTTGAGCGTGATTGCGGAGTCGACGGCGT
+GGGCGACGCAGTTGAGGATCATGCAGGCCCAGCTTCTGGCCAAGATCGCCGCAGCGGTTGGCAACGATGT
+GGTGCGATCGCTAAAGATCACCGGGCCGGCGGCACCATCGTGGCGCAAGGGGCCTCGCCATATTGCCGGT
+AGGGGTCCGCGCGACACCTACGGATAACACGTCGATCGGCCCAGAACAAGGCGCTCCGGTCCCGGCCTGA
+GAGCCTCGAGGACGAAGCGGATCCGTATGCCGGACGTCGGGACGCACCAGGAAGAAAGATGTCCGACGCA
+CGGCGCGGTTAGATGGGTAAAAACGAGGCCAGAAGATCGGCCCTGGCGCCCGATCACGGTACAGTGGTGT
+GCGACCCCCTGCGGCGACTCAACCGCATGCACGCAACCCCTGAGGAGAGTATTCGGATCGTGGCTGCCCA
+GAAAAAGAAGGCCCAAGACGAATACGGCGCTGCGTCTATCACCATTCTCGAAGGGCTGGAGGCCGTCCGC
+AAACGTCCCGGCATGTACATTGGCTCGACCGGTGAGCGCGGTTTACACCATCTCATTTGGGAGGTGGTCG
+ACAACGCGGTCGACGAGGCGATGGCCGGTTATGCAACCACAGTGAACGTAGTGCTGCTTGAGGATGGCGG
+TGTCGAGGTCGCCGACGACGGCCGCGGCATTCCGGTCGCCACCCACGCCTCCGGCATACCGACCGTCGAC
+GTGGTGATGACACAACTACATGCCGGCGGCAAGTTCGACTCGGACGCGTATGCGATATCTGGTGGTCTGC
+ACGGCGTCGGCGTGTCGGTGGTTAACGCGCTATCCACCCGGCTCGAAGTCGAGATCAAGCGCGACGGGTA
+CGAGTGGTCTCAGGTTTATGAGAAGTCGGAACCCCTGGGCCTCAAGCAAGGGGCGCCGACCAAGAAGACG
+GGGTCAACGGTACGGTTCTGGGCCGACCCCGCTGTTTTCGAAACCACGGAATACGACTTCGAAACCGTCG
+CCCGCCGGCTGCAAGAGATGGCGTTCCTCAACAAGGGGCTGACCATCAACCTGACCGACGAGAGGGTGAC
+CCAAGACGAGGTCGTCGACGAAGTGGTCAGCGACGTCGCCGAGGCGCCGAAGTCGGCAAGTGAACGCGCA
+GCCGAATCCACTGCACCGCACAAAGTTAAGAGCCGCACCTTTCACTATCCGGGTGGCCTGGTGGACTTCG
+TGAAACACATCAACCGCACCAAGAACGCGATTCATAGCAGCATCGTGGACTTTTCCGGCAAGGGCACCGG
+GCACGAGGTGGAGATCGCGATGCAATGGAACGCCGGGTATTCGGAGTCGGTGCACACCTTCGCCAACACC
+ATCAACACCCACGAGGGCGGCACCCACGAAGAGGGCTTCCGCAGCGCGCTGACGTCGGTGGTGAACAAGT
+ACGCCAAGGACCGCAAGCTACTGAAGGACAAGGACCCCAACCTCACCGGTGACGATATCCGGGAAGGCCT
+GGCCGCTGTGATCTCGGTGAAGGTCAGCGAACCGCAGTTCGAGGGCCAGACCAAGACCAAGTTGGGCAAC
+ACCGAGGTCAAATCGTTTGTGCAGAAGGTCTGTAATGAACAGCTGACCCACTGGTTTGAAGCCAACCCCA
+CCGACTCGAAAGTCGTTGTGAACAAGGCTGTGTCCTCGGCGCAAGCCCGTATCGCGGCACGTAAGGCACG
+AGAGTTGGTGCGGCGTAAGAGCGCCACCGACATCGGTGGATTGCCCGGCAAGCTGGCCGATTGCCGTTCC
+ACGGATCCGCGCAAGTCCGAACTGTATGTCGTAGAAGGTGACTCGGCCGGCGGTTCTGCAAAAAGCGGTC
+GCGATTCGATGTTCCAGGCGATACTTCCGCTGCGCGGCAAGATCATCAATGTGGAGAAAGCGCGCATCGA
+CCGGGTGCTAAAGAACACCGAAGTTCAGGCGATCATCACGGCGCTGGGCACCGGGATCCACGACGAGTTC
+GATATCGGCAAGCTGCGCTACCACAAGATCGTGCTGATGGCCGACGCCGATGTTGACGGCCAACATATTT
+CCACGCTGTTGTTGACGTTGTTGTTCCGGTTCATGCGGCCGCTCATCGAGAACGGGCATGTGTTTTTGGC
+ACAACCGCCGCTGTACAAACTCAAGTGGCAGCGCAGTGACCCGGAATTCGCATACTCCGACCGCGAGCGC
diff -r 000000000000 -r fc029a9b4d07 test-data/SRX7529235_SRR10859038_1.fastq.gz
Binary file test-data/SRX7529235_SRR10859038_1.fastq.gz has changed
diff -r 000000000000 -r fc029a9b4d07 test-data/SRX7529235_SRR10859038_2.fastq.gz
Binary file test-data/SRX7529235_SRR10859038_2.fastq.gz has changed
diff -r 000000000000 -r fc029a9b4d07 test-data/adapters.fa.gz
Binary file test-data/adapters.fa.gz has changed
diff -r 000000000000 -r fc029a9b4d07 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 18:06:47 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 000000000000 -r fc029a9b4d07 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 18:06:47 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 000000000000 -r fc029a9b4d07 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 18:06:47 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 000000000000 -r fc029a9b4d07 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 18:06:47 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 000000000000 -r fc029a9b4d07 test-data/bbmerge/merged.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bbmerge/merged.fastq	Mon Feb 06 18:06:47 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 000000000000 -r fc029a9b4d07 test-data/bbmerge/unmerged.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bbmerge/unmerged.fastq	Mon Feb 06 18:06:47 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
diff -r 000000000000 -r fc029a9b4d07 test-data/bduk_output_dump1.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bduk_output_dump1.fasta	Mon Feb 06 18:06:47 2023 +0000
@@ -0,0 +1,100 @@
+>116
+GAGATGGAACTGTAACTGGAGTTCCTT
+>7
+TGCCTAAGTGACTAGAGTTCAGACGTG
+>28
+TGAACTCCAGTCAAATTCCTTTATCTC
+>141
+GCATACGAGATGTATAGGTGACTGGAG
+>3
+GTTCAGCAGGAATACCGAGACCGATCT
+>126
+GGTAGCATCTCGTATGCCGTCTTCTGC
+>123
+GCCAAGGAACTCCAGTCACGTTTCGAT
+>126
+ATACGAGATGCTAACGTGACTGGAGTT
+>18
+CCGTATCTCGTATACCGTCTTCTGCTT
+>26
+TCTGAACTCCAGTAACGAGTGGATATC
+>17
+GAAGACGGCATACAAGATTGTTGACTG
+>22
+TGAACTCCAGTCAAGTGAAACGATCTC
+>50
+ACGCTACGCTATCACGTATGCCGTCTT
+>103
+TCGGGTGCCAAGGAACTCCAGTCACAT
+>141
+ATACATCTCGTATACCGTCTTCTGCTT
+>113
+TCGGGTGCCAAGGAACTCCAGTCACGG
+>84
+GAGATTACTACGCATCTCGTGGGCTCG
+>122
+CGTGGCCATCTCGAATGCCGTCTTCTG
+>139
+TCCAGTCACCGGAATATCTCGTATGCC
+>42
+CAGAAGACGGCATACGAGATTCGCCTT
+>107
+TGTGTGACTGGAGATCCTTGGCACCCG
+>140
+CATACGAGATAGCAAGGTGACTGGAGT
+>6
+GGTGACTGGAGTTAAGACGTGTGCTCT
+>30
+TCTCTTATACACAACTCCGAGCCCACG
+>122
+CAGTCACGTGGCCATCTCGTATGCCGT
+>19
+GTCACATGTCAGAATCTCGTATGCCGT
+>41
+GCGTGTAGATCTCAGTGGTCGCCGTAT
+>1
+GTGACTGGAGTTCAGACGTGTGCTCTT
+>15
+GTCTGAACTCCAGACACGGCTACATCT
+>4
+TCCGATCTCAAGCAGAAGACGGCATAC
+>119
+GAAGACGGCATACAAGATCTCTACGTG
+>129
+GTCACATTCCTATATCGTATGCCGTCT
+>107
+GATCACTGTGTGAATGGAGTTCCTTGG
+>9
+ATACGAGATCACTATGTGACTGGAGTT
+>24
+CTGAACTCCAGTCACGTTTCGGAATCT
+>116
+TGGAACTGTGACTAGAGTTCCTTGGCA
+>13
+GAAGACGGCATACAAGATCTGATCGTG
+>30
+TCTTATACACATCACCGAGCCCACGAG
+>49
+CAGAGAGGATCTCATATGCCGTCTTCT
+>133
+TCGTGGTGACTGGAGTTCCTTGGCACC
+>8
+CAGTCACTGACCAATCTCGTATGCCGT
+>33
+TCTAGTGTAGATCACGGTGGTCGCCGT
+>21
+TGCGGACGTGACTAGAGTTCAGACGTG
+>37
+GACGACTCCTTACATGTAGATCTCGGT
+>124
+GTACGGTGACTGGAGTTCCTTGGCACC
+>69
+TACACTTATGCGAACGTCGGCAGCGTC
+>149
+GCATACGAGATCTACGAGTGACTGGAG
+>124
+GAGATCGTACGGTAACTGGAGTTCCTT
+>105
+GCCAAGGAACTCCAGTCACTTAGGCAT
+>150
+CAGTCACTCGGCAATCTCGTATGCCGT
diff -r 000000000000 -r fc029a9b4d07 test-data/bduk_output_quhist1.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bduk_output_quhist1.tabular	Mon Feb 06 18:06:47 2023 +0000
@@ -0,0 +1,101 @@
+#BaseNum	Read1_linear	Read1_log	Read2_linear	Read2_log
+1	16.400	4.332	32.940	32.694
+2	24.580	19.293	32.680	30.545
+3	29.880	28.913	32.720	32.218
+4	35.400	35.023	35.740	28.139
+5	35.610	35.076	35.980	34.688
+6	36.070	35.819	36.130	35.232
+7	36.030	35.134	35.750	28.304
+8	36.210	35.891	35.760	30.427
+9	37.770	36.724	37.550	36.174
+10	37.770	36.627	37.890	36.829
+11	38.130	34.528	37.720	35.825
+12	38.120	37.610	37.930	36.724
+13	37.600	29.816	37.860	33.975
+14	39.600	38.822	39.490	29.436
+15	39.240	37.118	39.430	34.527
+16	39.370	37.815	39.670	29.527
+17	39.230	35.062	39.310	34.199
+18	39.410	38.456	39.700	38.264
+19	39.470	38.621	38.680	28.791
+20	39.170	36.390	39.340	38.126
+21	39.340	38.280	39.320	37.141
+22	38.870	32.580	38.480	25.015
+23	39.370	37.125	38.850	32.436
+24	38.940	36.347	39.200	37.110
+25	38.560	36.248	39.000	28.586
+26	38.810	33.655	38.460	29.005
+27	38.930	35.395	38.560	25.539
+28	39.090	37.259	38.190	23.947
+29	38.610	25.879	38.730	30.749
+30	38.540	33.271	38.520	32.796
+31	38.840	33.517	38.040	30.447
+32	38.730	36.053	38.530	27.397
+33	38.340	34.385	38.880	35.605
+34	38.470	28.217	38.430	32.167
+35	37.350	30.035	38.560	26.684
+36	37.380	20.434	38.900	32.524
+37	37.810	32.591	38.450	34.632
+38	38.150	33.133	38.750	35.749
+39	37.660	31.924	38.420	26.003
+40	38.040	34.153	38.730	36.080
+41	37.970	35.596	39.020	37.708
+42	37.240	31.069	39.380	33.973
+43	37.740	29.175	38.840	35.607
+44	38.070	34.040	38.400	23.939
+45	37.690	30.131	38.160	26.507
+46	37.160	26.236	37.990	32.407
+47	37.820	35.168	37.330	29.388
+48	37.920	35.623	37.850	31.413
+49	38.150	34.322	37.830	27.255
+50	38.250	34.017	38.260	36.442
+51	38.060	36.455	36.270	30.125
+52	37.240	34.726	37.000	33.291
+53	37.700	32.804	37.210	34.667
+54	37.740	33.699	37.520	34.736
+55	37.780	33.713	37.880	35.604
+56	37.470	31.063	37.880	35.326
+57	36.680	26.593	36.810	22.646
+58	36.390	26.714	37.140	31.327
+59	35.960	29.732	36.900	20.404
+60	35.500	27.738	36.440	21.355
+61	35.800	28.761	36.200	20.579
+62	34.880	22.760	36.570	21.483
+63	35.560	30.716	36.180	21.372
+64	35.460	30.521	35.970	20.108
+65	35.090	25.249	35.450	20.127
+66	35.240	31.736	35.330	20.499
+67	35.230	25.003	35.410	21.618
+68	34.870	25.901	35.400	21.693
+69	34.560	24.095	35.200	21.684
+70	34.670	29.988	34.730	21.372
+71	35.010	32.741	34.710	21.582
+72	33.750	21.148	34.060	18.014
+73	34.130	29.634	34.040	18.342
+74	34.080	21.493	33.840	17.025
+75	33.590	20.367	33.380	16.366
+76	31.930	18.529	33.300	17.088
+77	32.400	18.486	32.360	15.307
+78	32.840	18.708	32.170	15.246
+79	33.190	18.732	32.130	15.504
+80	32.680	17.826	32.770	15.850
+81	32.690	17.578	32.640	15.552
+82	32.510	16.664	32.800	15.822
+83	31.640	15.134	32.350	15.209
+84	31.220	15.026	32.320	15.547
+85	31.270	14.413	32.170	15.387
+86	31.310	14.436	32.520	15.576
+87	32.130	14.923	32.070	15.354
+88	31.610	14.417	31.780	15.361
+89	31.240	14.665	32.290	15.854
+90	31.130	14.606	31.730	15.508
+91	31.350	14.867	32.120	14.926
+92	31.270	14.282	32.040	14.910
+93	31.790	14.879	31.770	14.676
+94	31.010	13.468	31.380	14.768
+95	30.280	12.737	31.220	14.847
+96	30.310	12.852	31.050	14.129
+97	30.390	12.411	31.160	13.935
+98	30.150	12.394	30.960	13.893
+99	30.300	11.964	30.610	13.166
+100	29.860	11.945	30.460	12.397
diff -r 000000000000 -r fc029a9b4d07 test-data/bduk_outputu1.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bduk_outputu1.fastqsanger	Mon Feb 06 18:06:47 2023 +0000
@@ -0,0 +1,102 @@
+@XXXXXXXXXX:7:1101:1582:1835#/1
+NGCTTCAGTTGGTACAGGTGTGTCACCCGTAGTTTGTAGGCTTGGAAGCCTGTAAGCTGTAGGGAACGTGGCAAGAACCAGATCTGGCCTTCCATATCTC
++
+!1=DDDDDAFFDDEFFG@AGHBCFHIFIEGIC?DBFGIFF?FGDFIBFFII8BCFIEEF.@FFIIEFFCE=??B@>A@@@BBBAD>A:?BBBBB@>>>B:
+@XXXXXXXXXX:7:1101:1610:1859#/1
+NTTATGTGTTACGTGAATCTCCTGAAGACAGCAGAAACTAGGTTGGTGAATTCTTATCCATTCTGCCATTCTGTATCTTTTAAGTGGAGCATTTAGGCTA
++
+!1=DDFDFHHHHHHJJIJJJJJJJJJJJIJIIJJJIJIJJJJIJJJIIJJJIJJJIIJJJJIIJJJJGIJJJIHJHHHHHHHFFFFFFDDDEEDEDDCDD
+@XXXXXXXXXX:7:1101:1743:1871#/1
+NCGGGATGGAGGCAGGGCAAGCGGATGCAGGCCCAGCCCTGCCCTTACAGGTAGCTGGAAGTGACGAAGGAGTGGGGCCCCCGGACTCTGCTCAGGTGGA
++
+!1=DDDFFHHHHHIJJJEGGGIHIGIIGGGIIIJEHHHGGCCHIIIFHHFHADDCDDC@CECECCDDB7?BB9?BA>9<@DDB>>9>CD>:>CA9A:A@A
+@XXXXXXXXXX:7:1101:1536:1878#/1
+NGGCCTTTTTGGACAGGTGGTGTGTGGTGGCCTTGGTATGTGCTTTCTCGTGTTACATCGCGCCATCATTGGTATATGGTTAGTGTGTTGGTTAGTAGGC
++
+!1=DDDFEHHHHCGGIJFHIECHEFHIGGGGIJI<BBFGEIFGIIJIIJJJEGGEGGIHCCBHBFFCCEDEEC@CDDDC3>:95>@ABCAA<?C?>CDCC
+@XXXXXXXXXX:7:1101:2990:100153#/1
+GCCAGGAGTGACTGTGTTGTTCTTTGCTTTATATACATAAGCGCATCTCTTGCCCAAATAGAATTCTGTTTCATCTCGGGCGTAAACACCTTCAATTTTA
++
+@@@DDDFDBFHDFH<EHGIHGCHEGHGIIGIIEGFEIGGIIIIII<GICCE@4?BBFHGHAEGIHHIICDHEEEAAHFBEDD@B@B@><@D>CDDDDCCB
+@XXXXXXXXXX:7:1101:1624:1906#/1
+NCCAGGTTTAAGGCATTACATCGAGGGGCTGAACTTGAGACAGTCCCTGAAAATGTAAGAACAGGAGCTAGAACTTGCTTATGGGAAGGGCCTAGGGAGA
++
+!1=DDFFFHHHHHJJJJJIJJJJJJJJJJJJJJJJJIJJIJIIJJJJJJJGIJJIIJIECGIHHHHFFFFEECEECEDDDDDDCDCDDDDDDDDDDDDD@
+@XXXXXXXXXX:7:1101:1666:1926#/1
+NGCAAACTGGTCAGGACCTGGAGCTGCTTGCCTGGCCTTGGCACAAGAGGCCGACATATGCCCAGCCCCTAGGAGTGACAGATCCGTCCTCTGTGGGAAC
++
+!1BDFFFFHHHHHJJJJJJJJJJJJJJJJJJJIJIJJJJJJIJJJJJJJJJJJJJJJHHHHHHFFFFDDDDDDCCDBDDDDDDDDDDDDDDDDDDDDBCD
+@XXXXXXXXXX:7:1101:2921:100163#/1
+CTCCGGATGCCAAAGGATCTGACAGTGTATCTAGCTTTGGAAAACACAGGGGTCTGCCCTGTGAGCTGCTCCAACACCTTGGCTGCTCGCGTCAGTCTGT
++
+CCBFFFFFHHHHHJJJIJIIIJJJJHIFFHGIIHEIJIIIIIJIIGIIIICHHHHIJIIEHHJIHHFHHFFFFFFBDDDDDCDDDDDDDDD@B@@CCDDD
+@XXXXXXXXXX:7:1101:1513:1929#/1
+NCACTATCAAGGTTAGTGTCTATATCTACTTGAGANAAAATACTGAAAATTCAGTGTATGAAGCCAAATCCTGATTTAACAAGTTATTGGTAGTATAAGT
++
+!1:ABDDDDFFF:ACGFGFHHFIFAHEEHDFI@F8!1:CFEFFIGEFGIII>GIFICGGII@FFFIEFEADGIIEIFFFFFFFEEDDDDBDAC>>;;BA5
+@XXXXXXXXXX:7:1101:2759:100170#/1
+CTGCTCATCACATTCCAGATGCCATCACAGGCAATGACCATGAATTCATGGTCGTCAGTGAGAGTCAGCACCTTGATGTCAGGAAGGGCTGAAATCATCT
++
+CCCFFFFFHHHHHJJJJJIJJJJJJJJJJJJJJJJJJJJJJJJIJJJIJJJIJJJJJJHIIJJJIJJJJJJJHHHHHHHFFFFFEEDDDDDBCDDDDDDD
+@XXXXXXXXXX:7:1101:1708:1937#/1
+NGGTCGGTGTCCTTTTTTGGCGTCAAACTTATAGAGGGAAGCAGGGAATCTACCCAACCAAAGCCAATGAACAGTCAGTCAGTCCATCTAGTTAAGGTTC
++
+!1=BDDDDFDHHHIJJIJIJGIJIGGIJIGAGFHGHIGA=FCDFGHJJHEHFHHEFFFDABCDCDCCCDCDDDDDACDDCDDCAAACCDDDDDDACCACD
+@XXXXXXXXXX:7:1101:2981:100211#/1
+GGGGTCAGTGGGAAAGGTGTCAATGGGACTTCGGTCTCCATGCCGAAACACCAAAGTCACAAACTTCAACTCCTTGGCTAGTACACTTCGGTCTAGCCAG
++
+@@CFDDDFFFFHHEIGGHIIIIJJIIDHIGGIJFGBHIIIGGGGGGGIIJJHJGIG=DECEEEFFFFCDCCE@CC@?CDCBDDCDCCCCBB?B@>CACAB
+@XXXXXXXXXX:7:1101:1688:1946#/1
+NCCGCCTTCTTTCTCTACTTCGTGACCTTTTGTGGTCCCGAGACCTGCTGCATCTTCTGTCTGATGTTCGGCTTGAGTGTCTACTTCCTGAACGACTTCT
++
+!1:BDAAD<DDDDIEE>DBEEFEEFIIIIIEADEC?C>DD<?D@?@BDDDEEDIEIEDE=CEE>CE?CCC6=?###########################
+@XXXXXXXXXX:7:1101:2767:100225#/1
+CGCCTGGTGTCAATGCGCACATCTGGAGTTCCCATCTCCTTCATGGCAAATTTCCGAATCTCTTTGAGTGCCCGAGGTGCACGCTTCTTGAAGCCCACTC
++
+@@@FDFFFGHHHFJJIJIIIIJIJIJIGHBD@DFGGGJIFIJJJJIIIIIGHIIGIJFIJJIJIG@EECCHEEDCAD>ACCCDDDDDACCAC@CDDDDDD
+@XXXXXXXXXX:7:1101:1536:1959#/1
+NGATACTGTTGGGTCAGGACCAGGGCCTGCACCACCGAAATTCTGTCTTTTACAAACTGGACCAAGCGGTTGAGAATACAGGGGCCGAAGAGTAGGATTA
++
+!4:BB?DDHHDHAE?ECB@=GGI=<;CG@B;<D@DG:@FFABFBG<=FFGFHIIGGH@>==AEC?DECA<;8;3<AC>CCCC8&-5>@@59?4::>>>CC
+@XXXXXXXXXX:7:1101:2797:100234#/1
+GTGCTGGTCTCTCTCCACGATCTCTTACGTGCTAGCAGGGTGAACAAGGACGCCTCGCTGTCATTGCACTCACGCCACAGGAGCCTGGCACATTTCCGCT
++
++:?BDD8DFFFB8ED;@GF8A3?FH?B<)11?@FG<E<;@F629?BF@?2=A;4C6BE7-,7@;@;@A>;@CBB?=88?5(95983?(8<><AA######
+@XXXXXXXXXX:7:1101:1552:1976#/1
+NTGATGAGTTTGCTAATACAATGCCAGTCAGGCCACCTACGGTGAAAAGAAAGATGAATCCTAGGGCTCAGAGCACTGCAGCAGATCATTTCATATTGCT
++
+!1=DDFFFFHFHGJJJJIJJJJJJJJJJJIIJFGHGIIIJIJGHIEIIJJJHIGIIJGJIIJJJBHIIJHHHHHDEFCECEEEEDDDDDEFEEEEEEEDD
+@XXXXXXXXXX:7:1101:1748:1978#/1
+NCGCTGAGCAGGGCAGGCAGTGGTGGAGGCAGCCCCCCAAGACCCCATCTCTATCACAGTGAGAGCATCTGAACTCCAAAGCCACGACAGAACAGCTCCC
++
+!1=DFFFFHHHHHIJJJJIJIJJFHJIIJIJJGJJIIJAHGGGHHHHFFFFFFEEDECE@CDDCDDDCDDDACCCCDDDDCDDDDDDDDBDDCCC@ACDD
+@XXXXXXXXXX:7:1101:2779:100239#/1
+TGGGTGCTCTCCTTGGTCAGCTGCTGCTCGAACAGAGCACTTCTAGATACAGAGTTGGACCCAGACACAGCAGGGGTGGCCATGGCGGCTGGGAAAGACC
++
+@@@?DD?DFHHFFHIEEHIBGI9CFHFGCB::CGIGHG@BF<FHFHD@DDDBBDBFGH<C;C;==;C;;?H;;?<>88=@?C##################
+@XXXXXXXXXX:7:1101:1593:1980#/1
+NGGCACCAGAAGCATGAGCATAGGCAGAGCCATTTCCACCATGCTGACGGCAGGCAAGAAGAAGACAAAAATGAACCCCTTTCATGCTTGTTTAGAAATG
++
+!1=DFFFFHHHHGJJJJJJJJIJJIJJJIGJIIJJJJGIIIJJJJJIIJJJJJJIIJHHHHHFFFFFEEDDDDDDDDDDDDDDDEDDDEDDDDDDDDDDD
+@XXXXXXXXXX:7:1101:2946:100242#/1
+TGGGGATGTTGTTAAAAAAAATACAGGCTCCCCCACAACTGGGGTGCCTGGGGGGAACTTGGTCTGCTTCAGCCCAAGAGGAATCAAAAGATCAAAAGCA
++
+@@@FFDDDHHHHHJIIGIJIGEGIIJJIIJJGJJEECDEA=FHI-=?B?CEDDDD5583:AC3::94:CAACCDBABD8?BA?CCDDDDD@CCACCDCBD
+@XXXXXXXXXX:7:1101:1987:1781#/1
+NTTAGCAGGTCCTCGTAGCGTTTCCGCAACTCTCGGAATCTGGAGTCTTCGGAGTGCAACTCTGAGGGTCCCGGGAAACTTGCGCGGCTCGCCTCGGCCA
++
+!1=DDFFFHHHHHJJJJJIJJJJIJJJJJJJJJJJJJJJGJJJJIIHIJJJIJHHGHFFFFFFCEEDDDDDDDDDBDDDDDDDDDDDDDDBBDDD9B?B<
+@XXXXXXXXXX:7:1101:3046:100006#/1
+CTGTACAGCATGGATGTGGACAGGGAAAACAGCAAGTGCACACAGTGGGACAGGCCACAGGACAGGCTGGGAGTGAATAAAGAGTTCACACTGCTTCCCT
++
+CCCFFFFFHHHHHJJJIJJJJJJJJJJJJJJJIJJJFHIJJIIJIGGHIJJJJJJIJJIIJJJHHHHFFFD=C;?CDCDDD@>?>@CACDACCDDCDDDD
+@XXXXXXXXXX:7:1101:1900:1788#/1
+NCCCGCTGCCCACGCCACTGTCCCGGCGCTGCCCTGGGCGCGGAATGCGCGTTAGGCAATCCCCGGTCTGCGCGTCCCACACGCAGATGTGGCCTGCCAG
++
+!1=DFFFFGHHGHJJJIJJIJJJJGIIJJJIIJJIJJJIHFFDDDDDDDDDBDDDDDDDDDDDDBD@BDDDB>BB<BBDDDDDDDDDDDECDDBDDDDC@
+@XXXXXXXXXX:7:1101:3214:100027#/1
+GGCTGAGGTACTGAATGAGGAACAGCAGGAGGTAACGTCTGAGGGTGCGGCTGGGGAACGGTTTGCACAGGGGTGGCTGTAGGAGCAGGAGGTGAAACAC
++
+@@@FFDFF?DFHHIIIIIIGIIGHGIIGIIII?FHHGDFGIGGIC6?FHIIFIHHH59;=B559=33:55<(830588<((>:(98<CB02&28>CA>98
+@XXXXXXXXXX:7:1101:1848:1879#/1
+NCTTCTTCTTCCTCATGTTTTTTGATCAACTGCTCCACTTCTTTTTGTTTGAGAACTCTGATTACTGTCTTTCCATTCTCTCTTGTTAGTGTTGCAATTT
diff -r 000000000000 -r fc029a9b4d07 test-data/bduk_outputu2.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bduk_outputu2.fastqsanger	Mon Feb 06 18:06:47 2023 +0000
@@ -0,0 +1,102 @@
+@XXXXXXXXXX:7:1101:1582:1835#/2
+GCAATGATGGGGCCGCTCCCGGGGCCACACCTGCTTCTGGATCCGCTGCTTCCAAGTTCCTTTGCCTCCCTCCTGGCATCACTGTCTGCGACTCAGGCCG
++
+@@@DDDADHFHGFEGIGIIIGEGFD@FHA@GIGIJJIJJEAHHEBEDACEAC@CDDDC@@CCCCDCD@AD9?BCCDDCCDDDDDDDDCC99BBDDCACBB
+@XXXXXXXXXX:7:1101:1610:1859#/2
+CAATAACACAGTCCAAAATATATGTATGTATGTATATATATATGCAGGCAACAAATAGCACAATGAATAAAATAGTACTTCATCTCAGTACTAACATTGA
++
+C@BFFFFFHHGHDIIJJJJJJIIJHIJJHIJIJJIGIJIJJJJJFIIJJIIIIIJJJIJJJJJJJJIJJJIJJJJEGIIJJIJHHHHHCDFFFFFFEEEE
+@XXXXXXXXXX:7:1101:1743:1871#/2
+GCTTCCAAGGGACAAAGTCCTGCCCTTGGGTGTGGAAGACACCGTGGACAAGCTCAAGATGCTGGAAGGCCGCAAGACCAGCATCCGCAAGTCAGTGCAG
++
+CCCFFFFFHHHHHJJJJJIIJHEHJIJJJIEDGIIIJIGGGIJIGEIIIIJIIIIIHGHHHHFFFFFFFDB>B@BDDCDDDDDDDCB?@BDCCDDDDDDD
+@XXXXXXXXXX:7:1101:1536:1878#/2
+TGCCTATCATATAGTAAAACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTAGCCATGTGATTTCACTTCCACTCC
++
+@@@DFFFFHGFHGIJJJJJJJAFDHICDFHGIJIIJEEIJGIJGHJIJJIFAAAFGBGGFFFHGHFDFDFBCBDDDD<ACDDDCADEDDDDCD:>CDDCC
+@XXXXXXXXXX:7:1101:2990:100153#/2
+TGGAGGCCTGCTGGGAACGGGACTTCTAAAAGGAACTATGTCTGGAAGGCTGTGGTCCAAGGCCATTTTTGCTGGCTATAAGCGGGGTCTCCGGAACCAA
++
+@@@DDDDFHHFDHJJIGGHIJHIJJJJJGGGHJEGIIJJJIJJJIJJII?=FFHIHGGIJIHHHHFFC@BBCCEDDDDDECCDBDBD09CDDDDBBB??1
+@XXXXXXXXXX:7:1101:1624:1906#/2
+GGCTGGTCTGTCCCCTCTGCATCTGGGGCTCCTCCTGGCCCTTCTCCCGCTGCCTGTCCTGCCTCCTGGCCCTGCAGCAGCACCTTGCCCAGTGATCTTT
++
+CCCFFFFFHGHHHJJJJJJJIJJJIJJJIJIJJIJJIJIJJJJJJGGIJJFGIJGHHIFHHHHHFFDFDEEDDDD?CDDDDDDDDDCCDCDDCCCDCCCD
+@XXXXXXXXXX:7:1101:1666:1926#/2
+GGCTGTGGGAACTCTAGCTGCTGTCAGCCCCTCCTGTAGGAGCTGGCCCTGCCCAGGCTCCTGACTTCCCTCAGGAAGTCTTTCTGTCTTTCTCCATCAG
++
+CCCFFFFFHHFHHJJIJJJJJJIJJJJJJJJJJJJJJJJIIJJJJIJJJJIJJIJJIIJJJIHCHHGHFFFFBEE>@B>CDDDCDDDDDDDDDACDDCCD
+@XXXXXXXXXX:7:1101:2921:100163#/2
+GAAAAGGAGAACCCCATGCGGGAACTTCGCATCCGCAAACTCTGTCTCAACATCTGTGTTGGGGAGAGTGGAGACAGACTGACGCGAGCAGCCAAGGTGT
++
+CCCFFFFFHHGHHJJIJJJJJJIIJJJIIIGDHIGIJJJIJJ>HHGEHHGEHFFFFCDEEDCBDDDBB>C@DDCDDDDDDDDDDB@BD@BDDDBDDD:@@
+@XXXXXXXXXX:7:1101:1513:1929#/2
+AAAATGAGGGCCCGTAACAGAACCAGTGTGTGTATAACGAAAACCATGTATAAAATGGGCCTATCACCCTTGTCAGAGATATAAATTACCACATTTGCCT
++
+?@@;;D>DFH:;?EFD:F<FE?;CBF:DCG?FD4?FIGHIGIJJGFGIFG@FGGDHIHIGHHGFFFFFECEDADCDACA>CAADACDDCDCC<ACDDDDD
+@XXXXXXXXXX:7:1101:2759:100170#/2
+GGTCACCATGGATGGGCGAGTCAACGGGGGCCTCAACCTCTCCAGAGCCATTGGGGACCACTTCTATAAGAGAAACAAGAACCTGCCACCTGAGGAACAG
++
+CC@FFFFFHHHHHJJJJJIJGIIJJJJJJIJJGGHHCEFFFFEEEEDDDDDDDDDDDDDDDDDDDDEEDDDDCDDDDDDDDDDDDDDDDDDDDCDC?ABD
+@XXXXXXXXXX:7:1101:1708:1937#/2
+GAATACTTTGTGTTTACCCACTGCCCCCTGACCACTGCTGAAGGCAGAAAGGGACGATCACCTACAGTACCTGGTTTGGGTCTTTATTCTCTCATTCTAG
++
+B@BFFFFFHHCFHIJIHGIGIIJJGGIJJGIIIGIGGIJJEIGIHHJJJJIHIIJJIJHHHGFBEFFCCEEDCD;@A?BB?ACCCCCCCCACD@DADA@C
+@XXXXXXXXXX:7:1101:2981:100211#/2
+TTCCTCCTAACTCCTGCCAGAAACAGCTCTCCTCAACATGAGAGCTGCACCCCTCCTCCTGGCCAGGGCAGCAAGCCTTAGCCTTGGCTTCTTGTTTCTG
++
+@@BFFFFFHBDHHIHIIIIGGGADGGIGIEHIIIIJJIIIE<BHAHHHIGFGIJJJJIIHIBDGGEAEFFF;>CCABCDCDDCACDCCAA?@CD4:<@AC
+@XXXXXXXXXX:7:1101:1688:1946#/2
+GAGAAAGGGAAGAAAGAGAAAGGAAAAGACGAAGGGAAGAGGAAGAAAGAGAAAAAGAAAGGGCTCGTGACAGAGAAAGAAGAAAGAGAAGTCGTTCACG
++
+BB@ADFFFHDDHAGGHGHGGHEHGIJJIIJIIJJJJ<FH;FGDEGEGHGIFHEGIJFFHHFDFFEDDBDDDDCCCACCDABDDDDDCCCCDCCD@B?CDD
+@XXXXXXXXXX:7:1101:2767:100225#/2
+TGCAGAATGGCTCCCGCAAAGAAGGGTGGCGAGAAGAAAAAGGGCCGTTCTGCCATCAACGAAGTGGTAACCCGAGAATACACCATCAACATTCACAAGC
++
+@@@FFFFF<FFHHGGIJIIGGGIII>):?FF:FGGGIJIJIHCHHHFBCE;ACDDDDDCA@<@DBDDCDDCDDDDDDDDD@CCCDAA@>ACC>>A@@C1<
+@XXXXXXXXXX:7:1101:1536:1959#/2
+GAGACAAAAATTGTTTGAATCAGGACAAGGGAGGTTTGAGGGACTGTTTAACAGGTCCCCATGGTTCACGACCCTGATATCCACCATTATGGGCCCTCTG
++
+@8@1:?:=DD>D<CE+A:+C?+AF++++281)?D):?HD=FG6((?88=CFFCHG7=@HH@9?3.)7772?3,9;A(((5>;5>BBAA:>CCD?8@BD9A
+@XXXXXXXXXX:7:1101:2797:100234#/2
+GGAAACGCTGGAGAAGACAGTGTTGCTAGTCTGTTCCTGTTCGTGAGAATGCTTTGAATGGAGGCTCACTGTGCTGCGGCGGCTGCGGCCGTAGCGGGCG
++
+B1=+:A+0A::A2+2A2A3A<+2<?9<*119:9:1CC:DDFF<)800//9/>8E=<)/8@@@6C(6==737==>>@########################
+@XXXXXXXXXX:7:1101:1552:1976#/2
+TGTGAGCACACCATATATTTACAGTAGGAATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCACCGGCGTCAAAGT
++
+CCCFFFFFHHHHHIIGIGGIHJIGHHJIECGGGHJIJJJJJJJJJGHIJJGGHGIIEHIIJDIJFHFFFFF@CCCEECDDDDDCDDDB@BDDBBBDDCD>
+@XXXXXXXXXX:7:1101:1748:1978#/2
+CAAGGAGCTGTTCTGTCGTGGCTTTGGAATTCAGATGCTCTCACTGTGATAGAGATGGGGTCTTGGGGGGCTGGGAGCTGTTCTGTCGTGGCTTTGGAGT
++
+B@@FFFFFHHHHHJJIIJHIJIJJJJJIIJJIJJJJJIJJJJIJJJGHFGGHHIIIJIJJ@GIIJJIHFDDDDDDABBDCCDDEDDDB?BDDDDCCDCDA
+@XXXXXXXXXX:7:1101:2779:100239#/2
+GCTGTGGTTACCTGTCCCCTGCCCCTGGCCTCCAGCCAGCTGCCAGTGGCCCCTCAGCTGCCTGTGGTGAGGCAATACTTAGCTAGGTTCTTAGACGGCC
++
+?<?BBDDEFADA?ECCFFGEHDIDB;;FBG>GDHFGGGAFEHE?F@8?>F;CFCEADEEG@EEHAEFBDEEED7A>CACDECD>C@A(5>>C@>A#####
+@XXXXXXXXXX:7:1101:1593:1980#/2
+GGCTGTTCTCGAACTCCTGACCTCAGGTGATCTGCCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACTGCGCCTAGCCGTCACATTTC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJJJFHIIJJJJJIIJJJJJJJJJJJJJJJIHIJJJJJHIJJJJJJJHEEEFEEEEDECDDDDDDDDDBDDDCDDEE
+@XXXXXXXXXX:7:1101:2946:100242#/2
+AATCCCTTCACCCCAGTTGCCAAACAGACCCCCCACCCCCTGGATTTTCCTTCTCCCTCCATCCCTTGACGGTTCTGGCCTTCCCAAACTGCTTTTGATC
++
+C@CFFFFFHHHFFHBHHHEIJJIIIJIIJCGGIIGIHHIJIG@D;DCE>>?AEEFF@@DB(.;>?;CC@>=',5<CC>ADCDCCDA>B?CDD>ACCC0>C
+@XXXXXXXXXX:7:1101:1987:1781#/2
+GCCGCAACCTGCACAGCCATGCCCGGGCAAGAACTCAGGACGCTGAATGGCTCTCAGATGCTCCTGGTGTTGCTGGTGCTCTCGTGGCTGCCGCATGGGG
++
+CCCFFFFFHHHHHJJJJJJIJJJJJJJJJJJJJJJJJJIIJIJJJJJHHHHHFFFFFFEEEEEEDDDCCBDDDDDDDDDDDDDDDDDDDDDD<@BBDBBD
+@XXXXXXXXXX:7:1101:3046:100006#/2
+GACGAGATGGAGTTCACCGAGGCCGAGAGCAACATGAATGACCTGGTGTCCGAGTACCAGCAGTACCAGGATGCCACAGCCGAGGAGGAGGGCGAGTTCG
++
+CCCFFFFFHHHHFIJJJJJIIJIJJIHIIIJJJIIJJJGIJJJIJJIJHGEHFFFEEEEEDDDDDDDDDDDCDDDDDDDDDDDDDDDDBDDBDD<B9@CB
+@XXXXXXXXXX:7:1101:1900:1788#/2
+CGGCTATGCGCCACCCGAGACGGAGATCGTGCCGCTTGTGCTGCGCGGCCACCTCATGGACATCGAGTGCCTGGCCAGCGACGGCATGCTGCTGGTGAGC
++
+CCCFFFFFGHHHHJJJJJJHHJJIFHIJJHHIIIJJJIIIJJJJJHFDDD@@DDDDCDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDCDD<?C@C
+@XXXXXXXXXX:7:1101:3214:100027#/2
+CACAACAACTGCTACTTCAGTTGCGCAGACAGTATCAACACCCACAACACAAGATCAGACCCCAAGTTCTGCTGTTTCAGTTGCCACGCCTACAGTTAGT
++
+@CCFFFFFGFHHHIIJJJIIHIIIIIJ<GIIG?DHIJJGIIJBHJJJJJIGCGGHHJJHHHHFDEF;ACEEEDDDDDCEDDDDCDCDDDDDDDCCDDDD>
+@XXXXXXXXXX:7:1101:1848:1879#/2
+GGAGAAATGACCTTGAAGTCAGCACTTGCTTTAGCTATCAAAGTACTAAATAAGACCATGGATGTTAGTAAACTCTCTGCTGAAAAAGTGGAAATTGCAA
diff -r 000000000000 -r fc029a9b4d07 test-data/cv_input.bam
Binary file test-data/cv_input.bam has changed
diff -r 000000000000 -r fc029a9b4d07 test-data/cv_output.gff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cv_output.gff	Mon Feb 06 18:06:47 2023 +0000
@@ -0,0 +1,18 @@
+##gff-version
+#BBMapVersion
+#ploidy	2
+#rarity	1.00000
+#minAlleleFraction	0.1000
+#reads	2207
+#pairedReads	0
+#properlyPairedReads	0
+#readLengthAvg
+#properPairRate	0.0000
+#totalQualityAvg
+#mapqAvg
+#reference
+#seqid	source	type	start	end	score	strand	phase	attributes
+NC_002945.4	.	sequence_variant_obs	976327	976327
+NC_002945.4	.	sequence_variant_obs	1501932	1501932
+NC_002945.4	.	sequence_variant_obs	3380579	3380579
+NC_002945.4	.	sequence_variant_obs	3646293	3646293
diff -r 000000000000 -r fc029a9b4d07 test-data/cv_output.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cv_output.txt	Mon Feb 06 18:06:47 2023 +0000
@@ -0,0 +1,18 @@
+#fileformat
+#BBMapVersion
+#ploidy	2
+#rarity	1.00000
+#minAlleleFraction	0.1000
+#reads	2207
+#pairedReads	0
+#properlyPairedReads	0
+#readLengthAvg
+#properPairRate
+#totalQualityAvg
+#mapqAvg
+#reference
+#scaf	start	stop	type	call	r1p	r1m	r2p	r2m	paired	lengthSum	mapq	mapqMax	baseq	baseqMax	edist	edistMax	id	idMax	cov	minusCov	nearbyVarCount	flagged	contigEndDist	phredScore	readCount	alleleFraction	revisedAF	strandRatio	baseqAvg	mapqAvg	edistAvg	identityAvg	edistScore	identityScore	qualityScore	pairedScore	biasScore	coverageScore	homopolymerScore	score
+0	976326	976327	SUB	T
+0	1501931	1501932	SUB	C
+0	3380578	3380579	SUB	G
+0	3646292	3646293	SUB	A
diff -r 000000000000 -r fc029a9b4d07 test-data/cv_output.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cv_output.vcf	Mon Feb 06 18:06:47 2023 +0000
@@ -0,0 +1,60 @@
+##fileformat=VCFv4.2
+##BBMapVersion=
+##ploidy=2
+##rarity=1.00000
+##minallelefraction=0.10000
+##reads=2207
+##pairedReads=0
+##properlyPairedReads=0
+##readLengthAvg=
+##properPairRate=0.00000
+##totalQualityAvg=
+##mapqAvg=43.348
+##reference=
+##contig=<ID=NC_002945.4,length=7000>
+##FILTER=<ID=FAIL,Description="Fail">
+##FILTER=<ID=PASS,Description="Pass">
+##INFO=<ID=SN,Number=1,Type=Integer,Description="Scaffold Number">
+##INFO=<ID=STA,Number=1,Type=Integer,Description="Start">
+##INFO=<ID=STO,Number=1,Type=Integer,Description="Stop">
+##INFO=<ID=TYP,Number=1,Type=String,Description="Type">
+##INFO=<ID=R1P,Number=1,Type=Integer,Description="Read1 Plus Count">
+##INFO=<ID=R1M,Number=1,Type=Integer,Description="Read1 Minus Count">
+##INFO=<ID=R2P,Number=1,Type=Integer,Description="Read2 Plus Count">
+##INFO=<ID=R2M,Number=1,Type=Integer,Description="Read2 Minus Count">
+##INFO=<ID=AD,Number=1,Type=Integer,Description="Allele Depth">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=MCOV,Number=1,Type=Integer,Description="Minus Coverage">
+##INFO=<ID=PPC,Number=1,Type=Integer,Description="Paired Count">
+##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Fraction">
+##INFO=<ID=RAF,Number=1,Type=Float,Description="Revised Allele Fraction">
+##INFO=<ID=LS,Number=1,Type=Integer,Description="Length Sum">
+##INFO=<ID=MQS,Number=1,Type=Integer,Description="MAPQ Sum">
+##INFO=<ID=MQM,Number=1,Type=Integer,Description="MAPQ Max">
+##INFO=<ID=BQS,Number=1,Type=Integer,Description="Base Quality Sum">
+##INFO=<ID=BQM,Number=1,Type=Integer,Description="Base Quality Max">
+##INFO=<ID=EDS,Number=1,Type=Integer,Description="End Distance Sum">
+##INFO=<ID=EDM,Number=1,Type=Integer,Description="End Distance Max">
+##INFO=<ID=IDS,Number=1,Type=Integer,Description="Identity Sum">
+##INFO=<ID=IDM,Number=1,Type=Integer,Description="Identity Max">
+##INFO=<ID=NVC,Number=1,Type=Integer,Description="Nearby Variation Count">
+##INFO=<ID=FLG,Number=1,Type=Integer,Description="Flagged">
+##INFO=<ID=CED,Number=1,Type=Integer,Description="Contig End Distance">
+##INFO=<ID=HMP,Number=1,Type=Integer,Description="Homopolymer Count">
+##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Ref+, Ref-, Alt+, Alt-">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Allele Depth">
+##FORMAT=<ID=AF,Number=1,Type=Float,Description="Allele Fraction">
+##FORMAT=<ID=RAF,Number=1,Type=Float,Description="Revised Allele Fraction">
+##FORMAT=<ID=NVC,Number=1,Type=Integer,Description="Nearby Variation Count">
+##FORMAT=<ID=FLG,Number=1,Type=Integer,Description="Flagged">
+##FORMAT=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
+##FORMAT=<ID=SC,Number=1,Type=Float,Description="Score">
+##FORMAT=<ID=PF,Number=1,Type=String,Description="Pass Filter">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	
+NC_002945.4	976327	.	N	T	22.21	PASS	SN=0;STA=976326;STO=976327;TYP=SUB;R1P=2;R1M=0;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1.0000;RAF=1.0000;LS=292;MQS=77;MQM=40;BQS=48;BQM=24;EDS=111;EDM=65;IDS=1930;IDM=972;NVC=0;FLG=0;CED=0;HMP=0;SB=0.9980	GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF	1/1:2:2:1.0000:1.0000:0:0:0.9980:22.21:PASS
+NC_002945.4	1501932	.	N	C	27.20	PASS	SN=0;STA=1501931;STO=1501932;TYP=SUB;R1P=0;R1M=2;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1.0000;RAF=1.0000;LS=292;MQS=88;MQM=44;BQS=64;BQM=39;EDS=74;EDM=38;IDS=1986;IDM=993;NVC=0;FLG=0;CED=0;HMP=0;SB=0.9980	GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF	1/1:2:2:1.0000:1.0000:0:0:0.9980:27.20:PASS
+NC_002945.4	3380579	.	N	G	27.85	PASS	SN=0;STA=3380578;STO=3380579;TYP=SUB;R1P=0;R1M=2;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1.0000;RAF=1.0000;LS=289;MQS=87;MQM=44;BQS=75;BQM=38;EDS=105;EDM=63;IDS=1986;IDM=993;NVC=0;FLG=0;CED=0;HMP=0;SB=0.9980	GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF	1/1:2:2:1.0000:1.0000:0:0:0.9980:27.85:PASS
+NC_002945.4	3646293	.	N	A	23.34	PASS	SN=0;STA=3646292;STO=3646293;TYP=SUB;R1P=1;R1M=1;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1.0000;RAF=1.0000;LS=291;MQS=86;MQM=44;BQS=76;BQM=38;EDS=44;EDM=31;IDS=1986;IDM=993;NVC=0;FLG=0;CED=0;HMP=0;SB=1.0000	GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF	1/1:2:2:1.0000:1.0000:0:0:1.0000:23.34:PASS
diff -r 000000000000 -r fc029a9b4d07 test-data/cv_qualityhist_output.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cv_qualityhist_output.tabular	Mon Feb 06 18:06:47 2023 +0000
@@ -0,0 +1,46 @@
+#BaseQualityHist
+#Vars
+#Mean
+#Median
+#Mode
+#Quality	AvgCount	MaxCount
+0	0	0
+1	0	0
+2	0	0
+3	0	0
+4	0	0
+5	0	0
+6	0	0
+7	0	0
+8	0	0
+9	0	0
+10	0	0
+11	0	0
+12	0	0
+13	0	0
+14	0	0
+15	0	0
+16	0	0
+17	0	0
+18	0	0
+19	0	0
+20	0	0
+21	0	0
+22	0	0
+23	0	0
+24	1	1
+25	0	0
+26	0	0
+27	0	0
+28	0	0
+29	0	0
+30	0	0
+31	0	0
+32	1	0
+33	0	0
+34	0	0
+35	0	0
+36	0	0
+37	1	0
+38	1	2
+39	0	1
diff -r 000000000000 -r fc029a9b4d07 test-data/cv_scorehist_output.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cv_scorehist_output.tabular	Mon Feb 06 18:06:47 2023 +0000
@@ -0,0 +1,34 @@
+#ScoreHist
+#Vars
+#Mean
+#Median
+#Mode
+#Quality	Count
+0	0
+1	0
+2	0
+3	0
+4	0
+5	0
+6	0
+7	0
+8	0
+9	0
+10	0
+11	0
+12	0
+13	0
+14	0
+15	0
+16	0
+17	0
+18	0
+19	0
+20	0
+21	0
+22	1
+23	1
+24	0
+25	0
+26	0
+27	2
diff -r 000000000000 -r fc029a9b4d07 test-data/cv_zygosityhist_output.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cv_zygosityhist_output.tabular	Mon Feb 06 18:06:47 2023 +0000
@@ -0,0 +1,8 @@
+#ZygoHist
+#Vars
+#Mean
+#HomozygousFraction
+#Zygosity	Count
+0	0
+1	0
+2	4
diff -r 000000000000 -r fc029a9b4d07 test-data/fasta_indexes.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fasta_indexes.loc	Mon Feb 06 18:06:47 2023 +0000
@@ -0,0 +1,1 @@
+89	89	Mycobacterium_AF2122	${__HERE__}/NC_002945v4.fasta
diff -r 000000000000 -r fc029a9b4d07 tool-data/fasta_indexes.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/fasta_indexes.loc.sample	Mon Feb 06 18:06:47 2023 +0000
@@ -0,0 +1,29 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files.  You will need
+#to create these data files and then create a fasta_indexes.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The fasta_indexes.loc
+#file has this format (white space characters are TAB characters):
+#
+# <unique_build_id>	<dbkey>	<display_name>	<file_base_path>
+#
+#So, for example, if you had hg19 Canonical indexed stored in
+#
+# /depot/data2/galaxy/hg19/sam/,
+#
+#then the fasta_indexes.loc entry would look like this:
+#
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#
+#and your /depot/data2/galaxy/hg19/sam/ directory
+#would contain hg19canon.fa and hg19canon.fa.fai files.
+#
+#Your fasta_indexes.loc file should include an entry per line for
+#each index set you have stored.  The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file.  For example:
+#
+#hg18canon	hg18	Human (Homo sapiens): hg18 Canonical	/depot/data2/galaxy/hg18/sam/hg18canon.fa
+#hg18full	hg18	Human (Homo sapiens): hg18 Full	/depot/data2/galaxy/hg18/sam/hg18full.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/depot/data2/galaxy/hg19/sam/hg19full.fa
diff -r 000000000000 -r fc029a9b4d07 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Mon Feb 06 18:06:47 2023 +0000
@@ -0,0 +1,8 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<tables>
+    <!-- Location of SAMTools indexes for FASTA files -->
+    <table name="fasta_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/fasta_indexes.loc" />
+    </table>
+</tables>
diff -r 000000000000 -r fc029a9b4d07 tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Mon Feb 06 18:06:47 2023 +0000
@@ -0,0 +1,6 @@
+<tables>
+    <table name="fasta_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/fasta_indexes.loc" />
+    </table>
+</tables>