# HG changeset patch
# User bgruening
# Date 1715680172 0
# Node ID 76ea9d4604bc16ac65daa95f8363ea23aaef36c6

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep commit fd696b8f2ce44287b6ad19fe52277cfdbd7e94fb

diff -r 000000000000 -r 76ea9d4604bc README.md
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Tue May 14 09:49:32 2024 +0000
@@ -0,0 +1,18 @@
+# SeqPrep Tool Documentation
+
+> [!CAUTION]
+> This is a modified version of the 1.2 release. Made for use with the MGnify pipeline.
+
+## Overview
+
+SeqPrep is a bioinformatics tool primarily used for processing paired-end Illumina reads. It excels in merging overlapping reads and trimming adapter sequences, making it a valuable asset in genomic sequence analysis. Its efficient handling of paired-end data ensures high-quality preparation for downstream analysis.
+
+## Key Features
+
+- **Read Merging**: Seamlessly merges overlapping paired-end Illumina reads into longer, single reads.
+- **Adapter Trimming**: Efficiently trims adapter sequences from read ends to improve data quality.
+- **Quality Control**: Offers options for quality score cutoff and minimum read length, enhancing the integrity of output data.
+
+## Usage
+
+For a detailed tutorial on how to use SeqPrep, please refer to the [SeqPrep Tutorial](https://github.com/jstjohn/SeqPrep/tree/master).
diff -r 000000000000 -r 76ea9d4604bc macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue May 14 09:49:32 2024 +0000
@@ -0,0 +1,36 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.2</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <xml name="requirements">
+        <requirements>
+            <container type="docker">rz9082/seqprep:v1.2-mgnify-v5.0</container>
+        </requirements>
+    </xml>
+    <xml name="biotools">
+        <xrefs>
+            <xref type="bio.tools">seqprep</xref>
+        </xrefs>
+    </xml>
+    <xml name="creators">
+        <creator>
+            <person givenName="John" familyName="St. John" url="https://github.com/jstjohn" />
+            <person givenName="Lionel" familyName="Guy" />
+            <person givenName="John" familyName="Chilton" url="https://github.com/jmchilton" />
+            <person givenName="Albert" familyName="Ratschinski" url="https://github.com/Alby-Git" />
+            <person givenName="Rand" familyName="Zoabi" url="https://github.com/RZ9082" />
+        </creator>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+        @online{seqpre,
+          author = {St John, John},
+          title = {seqprep},
+          year = 2016,
+          url = {https://github.com/jstjohn/SeqPrep},
+          urldate = {2016-10-04}
+        }
+            </citation>
+        </citations>
+    </xml>
+</macros>
diff -r 000000000000 -r 76ea9d4604bc mgnify_seqprep.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mgnify_seqprep.xml	Tue May 14 09:49:32 2024 +0000
@@ -0,0 +1,347 @@
+<tool id="mgnify_seqprep" name="Merging paired-end Illumina reads (SeqPrep, modified for use with MGnify piplines)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
+    <description>Merge and Trim Adapter Sequences from Paired-End Illumina Reads</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="biotools"/>
+    <expand macro="requirements"/>
+    <expand macro="creators"/>
+    <command detect_errors="exit_code"><![CDATA[
+    SeqPrep
+        -f '${input1}'
+        -r '${input2}'
+        -1 '${output1}'
+        -2 '${output2}'
+
+        #if $merge_reads
+            -s '${merged}'
+        #end if
+
+        ## General Arguments ##
+        #if $general_options.first_read_discarded
+            -3 '${general_options.first_read_discarded}'
+        #end if
+        #if $general_options.second_read_discarded
+            -4 '${general_options.second_read_discarded}'
+        #end if
+        #if $general_options.phred64
+            -6 '${general_options.phred64}'
+        #end if
+        #if $general_options.quality_cutoff
+            -q '${general_options.quality_cutoff}'
+        #end if
+        #if $general_options.min_length
+            -L '${general_options.min_length}'
+        #end if
+
+        ## Additional Adapter/Primer Trimming Arguments ##
+        #if $trimming_options.adapter_a
+            -A '${trimming_options.adapter_a}'
+        #end if
+        #if $trimming_options.adapter_b
+            -B '${trimming_options.adapter_b}'
+        #end if
+        #if $trimming_options.adapter_overlap
+            -O '${trimming_options.adapter_overlap}'
+        #end if
+        #if $trimming_options.max_mismatch_fraction
+            -M '${trimming_options.max_mismatch_fraction}'
+        #end if
+        #if $trimming_options.min_match_fraction
+            -N '${trimming_options.min_match_fraction}'
+        #end if
+        #if $trimming_options.adapter_bandwidth
+            -b '${trimming_options.adapter_bandwidth}'
+        #end if
+        #if $trimming_options.gap_open
+            -Q '${trimming_options.gap_open}'
+        #end if
+        #if $trimming_options.gap_extend
+            -t '${trimming_options.gap_extend}'
+        #end if
+        #if $trimming_options.gap_end
+            -e '${trimming_options.gap_end}'
+        #end if
+        #if $trimming_options.local_alignment_score
+            -Z '${trimming_options.local_alignment_score}'
+        #end if
+        #if $trimming_options.read_alignment_bandwidth
+            -w '${trimming_options.read_alignment_bandwidth}'
+        #end if
+        #if $trimming_options.read_alignment_gap_open
+            -W '${trimming_options.read_alignment_gap_open}'
+        #end if
+        #if $trimming_options.read_alignment_gap_extend
+            -p '${trimming_options.read_alignment_gap_extend}'
+        #end if
+        #if $trimming_options.read_alignment_gap_end
+            -P '${trimming_options.read_alignment_gap_end}'
+        #end if
+        #if $trimming_options.read_alignment_max_gap_fraction
+            -X '${trimming_options.read_alignment_max_gap_fraction}'
+        #end if
+
+        ## Additional Arguments for Merging ##
+        #if $merging_options.maximum_quality_score
+            -y '${merging_options.maximum_quality_score}'
+        #end if
+        #if $merging_options.print_overhang
+            -g '${merging_options.print_overhang}'
+        #end if
+        #if $merging_options.min_base_pair_overlap
+            -o '${merging_options.min_base_pair_overlap}'
+        #end if
+        #if $merging_options.max_mismatch_fraction
+            -m '${merging_options.max_mismatch_fraction}'
+        #end if
+        #if $merging_options.min_match_fraction
+            -n '${merging_options.min_match_fraction}'
+        #end if
+    ]]></command>
+    <inputs>
+        <param name="input1" type="data" format="fastq" label="First Read Input" help="Select the FASTQ file containing the first set of paired-end reads." />
+        <param name="input2" type="data" format="fastq" label="Second Read Input" help="Select the FASTQ file containing the second set of paired-end reads." />
+        <param name="merge_reads" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Merge Reads" help="Enable this to merge overlapping reads from the provided paired-end FASTQ files." />        
+
+        <!-- Section for General Arguments -->
+        <section name="general_options" title="General Arguments (Optional)" expanded="false">
+            <param name="first_read_discarded" argument="-3" type="text" optional="true" label="First Read Discarded FASTQ Filename" help="first read discarded fastq filename" />
+            <param name="second_read_discarded" argument="-4" type="text" optional="true" label="Second Read Discarded FASTQ Filename" help="second read discarded fastq filename" />
+            <param name="phred64" argument="-6" type="boolean" truevalue="-6" falsevalue="" checked="false" label="Input Sequence is in Phred+64 Format" help="Input sequence is in phred+64 rather than phred+33 format, the output will still be phred+33"/>
+            <param name="quality_cutoff" argument="-q" type="integer" optional="true" value="13" label="Quality Score Cutoff" help="Quality score cutoff for mismatches to be counted in overlap" />
+            <param name="min_length" argument="-L" type="integer" optional="true" value="30" label="Minimum Length of Reads" help="Minimum length of a trimmed or merged read to print it" />
+        </section>
+
+        <!-- Section for Additional Adapter/Primer Trimming Arguments -->
+        <section name="trimming_options" title="Additional Adapter/Primer Trimming Arguments" expanded="false">
+            <param name="adapter_a" argument="-A" label="Adapter Sequence A" type="text" optional="true" value="AGATCGGAAGAGCGGTTCAG" help="Forward read primer/adapter sequence to trim as it would appear at the end of a read" />
+            <param name="adapter_b" argument="-B" label="Adapter Sequence B" type="text" optional="true" value="AGATCGGAAGAGCGTCGTGT" help="Reverse read primer/adapter sequence to trim as it would appear at the end of a read" />
+            <param name="adapter_overlap" argument="-O" label="Minimum Overall Base Pair Overlap with Adapter" type="integer" value="10" optional="true" help="minimum overall base pair overlap with adapter sequence to trim" />
+            <param name="max_mismatch_fraction" argument="-M" label="Maximum Fraction of Good Quality Mismatching Bases" type="float" value="0.02" optional="true" help="maximum fraction of good quality mismatching bases for primer/adapter overlap" />
+            <param name="min_match_fraction" argument="-N" label="Minimum Fraction of Matching Bases" type="float" value="0.87" optional="true" help="minimum fraction of matching bases for primer/adapter overlap" />
+            <param name="adapter_bandwidth" argument="-b" label="Adapter Alignment Band-width" type="integer" value="50" optional="true" />
+            <param name="gap_open" argument="-Q" label="Adapter Alignment Gap-Open" type="integer" value="8" optional="true" />
+            <param name="gap_extend" argument="-t" label="Adapter Alignment Gap-Extension" type="integer" value="2" optional="true" />
+            <param name="gap_end" argument="-e" label="Adapter Alignment Gap-End" type="integer" value="2" optional="true" />
+            <param name="local_alignment_score" argument="-Z" label="Minimum Local Alignment Score Cutoff" type="integer" value="26" optional="true" help="Adapter alignment minimum local alignment score cutoff [roughly (2*num_hits) - (num_gaps*gap_open) - (num_gaps*gap_close) - (gap_len*gap_extend) - (2*num_mismatches)]" />
+            <param name="read_alignment_bandwidth" argument="-w" label="Read Alignment Band-width" type="integer" value="50" optional="true" />
+            <param name="read_alignment_gap_open" argument="-W" label="Read Alignment Gap-Open" type="integer" value="26" optional="true" />
+            <param name="read_alignment_gap_extend" argument="-p" label="Read Alignment Gap-Extension" type="integer" value="9" optional="true" />
+            <param name="read_alignment_gap_end" argument="-P" label="Read Alignment Gap-End" type="integer" value="5" optional="true" help="read alignment maximum fraction gap cutoff" />
+            <param name="read_alignment_max_gap_fraction" argument="-X" label="Read Alignment Maximum Fraction Gap Cutoff" type="float" value="0.125" optional="true" />
+        </section>
+
+        <!-- Section for Optional Arguments for Merging: -->
+        <section name="merging_options" title="Optional Arguments for Merging" expanded="false">
+            <param name="maximum_quality_score" argument="-y" label="Maximum Quality Score in Output" type="text" optional="true" help="Maximum quality score in output (phred 33), default = ']'"/>
+            <param name="print_overhang" argument="-g" type="boolean" truevalue="-g" falsevalue="" checked="false" label="Print Overhang When Adapters Are Present and Stripped" help="Use this if reads are different lengths"/>
+            <param name="min_base_pair_overlap" argument="-o" type="integer" optional="true" value="15" label="Minimum Overall Base Pair Overlap" help="Minimum overall base pair overlap to merge two reads"/>
+            <param name="max_mismatch_fraction" argument="-m" type="float" optional="true" value="0.02" label="Maximum Fraction of Good Quality Mismatching Bases" help="Maximum fraction of good quality mismatching bases to overlap reads"/>
+            <param name="min_match_fraction" argument="-n" type="float" optional="true" value="0.9" label="Minimum Fraction of Matching Bases" help="Minimum fraction of matching bases to overlap reads"/>
+        </section>
+    </inputs>
+    <outputs>
+        <data format="fastq.gz" name="output1" label="${tool.name} on ${on_string}: First Read Output">
+            <filter>output_all</filter>
+        </data>
+        <data format="fastq.gz" name="output2" label="${tool.name} on ${on_string}: Second Read Output">
+            <filter>output_all</filter>
+        </data>
+        <data format="fastq.gz" name="merged" label="${tool.name} on ${on_string}: Merged Reads">
+            <filter>merge_reads</filter>
+        </data>
+    </outputs>
+    <tests>
+        <!-- Test default inputs #1 -->
+        <test expect_num_outputs="3">
+            <param name="input1" value="input1.fq" />
+            <param name="input2" value="input2.fq" />
+            <param name="merge_reads" value="true" />
+
+            <!-- Section for General Arguments -->
+            <section name="general_options" >
+                <param name="quality_cutoff" value="13" />
+                <param name="min_length" value="30" />
+            </section>
+
+            <!-- Section for Additional Adapter/Primer Trimming Arguments -->
+            <section name="trimming_options">
+                <param name="adapter_a" value="AGATCGGAAGAGCGGTTCAG" />
+                <param name="adapter_b" value="AGATCGGAAGAGCGTCGTGT" />
+                <param name="adapter_overlap" value="10" /> 
+                <param name="max_mismatch_fraction" value="0.02" />
+                <param name="min_match_fraction" value="0.87" />
+                <param name="adapter_bandwidth" value="50" />
+                <param name="gap_open" value="8" />
+                <param name="gap_extend" value="2" />
+                <param name="gap_end" value="2" />
+                <param name="local_alignment_score" value="26" />
+                <param name="read_alignment_bandwidth" value="50" />
+                <param name="read_alignment_gap_open" value="26" />
+                <param name="read_alignment_gap_extend" value="9" />
+                <param name="read_alignment_gap_end" value="5" />
+                <param name="read_alignment_max_gap_fraction" value="0.125" />
+            </section>
+            <output name="output1" file="output1.fq.gz" />
+            <output name="output2" file="output2.fq.gz" />
+            <output name="merged" file="merged_output.fq.gz" />
+        </test>
+    
+        <!-- Without Merging, Two Outputs #2 -->
+        <test expect_num_outputs="2">
+            <param name="input1" value="input1.fq" />
+            <param name="input2" value="input2.fq" />
+            <param name="merge_reads" value="false" />
+
+            <!-- Section for General Arguments -->
+            <section name="general_options" >
+                <param name="quality_cutoff" value="13" />
+                <param name="min_length" value="30" />
+            </section>  
+
+            <!-- Section for Additional Adapter/Primer Trimming Arguments -->
+            <section name="trimming_options">
+                <param name="adapter_a" value="AGATCGGAAGAGCGGTTCAG" />
+                <param name="adapter_b" value="AGATCGGAAGAGCGTCGTGT" />
+                <param name="adapter_overlap" value="10" /> 
+                <param name="max_mismatch_fraction" value="0.02" />
+                <param name="min_match_fraction" value="0.87" />
+                <param name="adapter_bandwidth" value="50" />
+                <param name="gap_open" value="8" />
+                <param name="gap_extend" value="2" />
+                <param name="gap_end" value="2" />
+                <param name="local_alignment_score" value="26" />
+                <param name="read_alignment_bandwidth" value="50" />
+                <param name="read_alignment_gap_open" value="26" />
+                <param name="read_alignment_gap_extend" value="9" />
+                <param name="read_alignment_gap_end" value="5" />
+                <param name="read_alignment_max_gap_fraction" value="0.125" />
+            </section>
+            <output name="output1" file="outputNoMerge1.fq.gz" />
+            <output name="output2" file="outputNoMerge2.fq.gz" />
+        </test>
+        <!-- Test with Empty Input Files #3 -->
+        <test expect_num_outputs="3">
+            <param name="input1" value="empty1.fq" />
+            <param name="input2" value="empty2.fq" />
+            <param name="merge_reads" value="true" />
+
+            <!-- Section for General Arguments -->
+            <section name="general_options" >
+                <param name="quality_cutoff" value="13" />
+                <param name="min_length" value="30" />
+            </section>  
+
+            <!-- Section for Additional Adapter/Primer Trimming Arguments -->
+            <section name="trimming_options">
+                <param name="adapter_a" value="AGATCGGAAGAGCGGTTCAG" />
+                <param name="adapter_b" value="AGATCGGAAGAGCGTCGTGT" />
+                <param name="adapter_overlap" value="10" /> 
+                <param name="max_mismatch_fraction" value="0.02" />
+                <param name="min_match_fraction" value="0.87" />
+                <param name="adapter_bandwidth" value="50" />
+                <param name="gap_open" value="8" />
+                <param name="gap_extend" value="2" />
+                <param name="gap_end" value="2" />
+                <param name="local_alignment_score" value="26" />
+                <param name="read_alignment_bandwidth" value="50" />
+                <param name="read_alignment_gap_open" value="26" />
+                <param name="read_alignment_gap_extend" value="9" />
+                <param name="read_alignment_gap_end" value="5" />
+                <param name="read_alignment_max_gap_fraction" value="0.125" />
+            </section>
+            <output name="output1" file="empty_output1.fq.gz" />
+            <output name="output2" file="empty_output2.fq.gz" />
+            <output name="merged" file="empty_merged_output.fq.gz" />
+        </test>
+
+        <!-- Advanced Functional Tests -->
+        <!-- General Arguments Test #4 -->
+        <test expect_num_outputs="2">
+            <param name="input1" value="input1.fq" />
+            <param name="input2" value="input2.fq" />
+            <param name="merge_reads" value="false" />
+
+            <param name="quality_cutoff" value="15" />
+            <param name="min_length" value="25" />
+            <output name="output1" file="output1_general_args.fq.gz" />
+            <output name="output2" file="output2_general_args.fq.gz" />
+        </test>
+
+        <!-- Adapter/Primer Trimming Arguements Test #5 -->
+        <test expect_num_outputs="2">
+            <param name="input1" value="input1.fq" />
+            <param name="input2" value="input2.fq" />
+            <param name="merge_reads" value="false" />
+            <section name="trimming_options">
+                <param name="adapter_a" value="ACTGACTG" />
+                <param name="adapter_b" value="GTGACTGA" />
+                <param name="adapter_overlap" value="12" />
+                <param name="max_mismatch_fraction" value="0.03" />
+                <param name="min_match_fraction" value="0.85" />
+                <param name="adapter_bandwidth" value="55" />
+                <param name="gap_open" value="10" />
+                <param name="gap_extend" value="3" />
+                <param name="gap_end" value="3" />
+                <param name="local_alignment_score" value="28" />
+            </section>
+            <output name="output1" file="output1_adapter_trim.fq.gz" />
+            <output name="output2" file="output2_adapter_trim.fq.gz" />
+        </test>
+        <!-- Test with gzipped input files #6 -->
+        <test expect_num_outputs="3">
+            <param name="input1" value="input1.fastq.gz" />
+            <param name="input2" value="input2.fastq.gz" />
+            <param name="merge_reads" value="true" />
+            <output name="output1" file="output1_from_gzipped.fq.gz" />
+            <output name="output2" file="output2_from_gzipped.fq.gz" />
+            <output name="merged" file="merged_output_from_gzipped.fq.gz" />
+        </test>
+    </tests>
+    <help><![CDATA[
+.. class:: warningmark
+
+**Caution**
+-----------
+::
+
+    This is a modified version of the 1.2 release. Made for use with the MGnify pipeline.
+
+    Difference in `utils.h`:
+
+::
+    
+    -#define MAX_SEQ_LEN (256)
+    +#define MAX_SEQ_LEN (1024)
+
+**SeqPrep**
+-----------
+::
+
+    SeqPrep is a versatile tool designed for merging overlapping paired-end Illumina reads into a single, longer read.
+    Additionally, it offers the functionality to trim adapter sequences from reads, making it a needful tool for preprocessing Illumina sequencing data.
+
+**Usage**
+=========
+::
+
+    To utilize SeqPrep, start by selecting your input FASTQ files: one for the first set of reads and another for the second set.
+    SeqPrep provides several options to customize your data processing:
+
+    - Adapter Sequences: You can provide specific sequences for adapter trimming if they are known. SeqPrep will remove these sequences from the reads.
+    - Quality Score Cutoff: Set a threshold for the quality score. Reads with quality scores below this threshold can be discarded or trimmed.
+    - Minimum Read Length: Define the minimum length for reads to be retained after trimming. Reads shorter than this length will be discarded.
+
+    If the merging feature is enabled, SeqPrep will combine overlapping reads into longer sequences, thereby enhancing the data quality for downstream analysis.
+
+**Outputs**
+===========
+::
+
+    SeqPrep generates outputs in gzipped FASTQ format.
+
+    See more details on `SeqPrep GitHub repository <https://github.com/jstjohn/SeqPrep>`_.
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
diff -r 000000000000 -r 76ea9d4604bc test-data/empty1.fq
diff -r 000000000000 -r 76ea9d4604bc test-data/empty2.fq
diff -r 000000000000 -r 76ea9d4604bc test-data/empty_merged_output.fq.gz
Binary file test-data/empty_merged_output.fq.gz has changed
diff -r 000000000000 -r 76ea9d4604bc test-data/empty_output1.fq.gz
Binary file test-data/empty_output1.fq.gz has changed
diff -r 000000000000 -r 76ea9d4604bc test-data/empty_output2.fq.gz
Binary file test-data/empty_output2.fq.gz has changed
diff -r 000000000000 -r 76ea9d4604bc test-data/input1.fastq.gz
Binary file test-data/input1.fastq.gz has changed
diff -r 000000000000 -r 76ea9d4604bc test-data/input1.fq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input1.fq	Tue May 14 09:49:32 2024 +0000
@@ -0,0 +1,240 @@
+@SimSeq_1/229/1
+TAGGAGGCTTGGGGTTAGGAATTGGTCAAATAGGTTTATGTTCAAGGTCAGGGTCATGTTTTAATAGTTATGGCTTTGTAAGGGGTTGGGCTGCTTGTGA
++
+E=AGEFGGGFFEDDGGGECGDADF>DEF?EECAFFEBF:=B2EGGEGF#ABAF7BGFC:FC??:D:?FCD<A??EB5E:G##EEDAB;###.#@EE?BD#
+@SimSeq_2/49/1
+AAAGAAATTAGGTTTAAATTCCAAGCCGAGGGCCTTCAAAGCCCTAAATAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGAAAAAAAAAAAAAA
++
+F?A?BEEDAGAGFFGBFDE>E=G;FD=ED<CFGDGEGFG7DF5DFGBEGBCBEFCBCEDC+CEBE7D##?,=#5BD+D#:?EGC::#5,#E5=9+D#EF#
+@SimSeq_3/149/1
+GAAAATTAATAGCACTATCGTCCATTGCCCAAATAGCATGAATTATCGTAATTATTAAATACGCACCATCACTAGCCATCCTAACCTTCTACATCTGCTC
++
+EDGBGFEEG>:FGD=GG5F?CFEEEFED,?:?D:GFGDEEFDEEDEDFFAEAE@?E>BGEFE3EA@1GED#=#-5:CEAC#?4DBGE?F#FAFD#C#C#G
+@SimSeq_4/197/1
+CGGGGGCCTAACTGGGATTGTCCTAGCCAACTCCTCACTAGACATTGTCCTCCACGACACGTATTATGTAGTGGCCCACTTCCACTACGTACTCTCAATA
++
+GDEGGDEGFGGDEGCFE>F>E;G>F@CFGGGFBGEDGDEC@GGEFG>ACBEFGGEE?F?@(G7GEFCG#E#B@A?CE;FE?G:3#7:B?=,F;D@>A##D
+@SimSeq_5/40/1
+ACCCCTCTCAGAGGAGGATGGAGCATGGTGGTATTGCGGCAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGAAAAAAAAAAAAAAAAAAAAAGA
++
+CFGGD>AFGGGFGEEDGGE?EFDGEGBFEBED+FBG5GGFE:BEAADABEF@?EEEBBF;+DDEDD3=E#F2#)G*#C>>F3>E#@C#?4<G#-BE:?#7
+@SimSeq_6/190/1
+TAACTAAATATTTGTGAGATCGAAGCTCGCCTGTTTATTGAGGTTTTAGCTTAATTAAAGTTTCTGAGTTGCACTTTGAAGATGCCGGATAGAGTCCTGC
++
+DFD:DAE?GE0FDCAFF:GE>DFF;G6G@FGGEEGFD@EGAED=G7E1G:EFGEFD>BGD@:DE?#;(G3=8#:DDBD6#AG##E#@E:8BGG#/DG#<B
+@SimSeq_7/178/1
+TAAATCCCATTCCACCCCTACTTCACCATAAAAGACGCCCTAGGAGCAGCACTAGCTGCCTCCTCACTACTCATCTTAGCTCTCTACCTACCAGCCCTAT
++
+:BFCBD@GGFEFGF>AGDDF5EGGFAGGD@DFFDD@G??GF>BEBDE4EGAEFADFE@G:A#GFD=C#BBG#BGF#CEC=F>8:#E<FG5E>E=5DE#:#
+@SimSeq_8/18/1
+AATCCTCCCTCCCCTTATAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+@A8GG?DDFEFCBGGGADFE<7EEFDG>>EGGEDBGAEDG:G8DFF@FG5GECCCEF*=BC=,DC?C>CE#D:BD0#=3ED@F#E(AF5GAE4GGF@:,=
+@SimSeq_9/103/1
+GTTGTCCGGTTACTTTAATAGTCAGGCAGGGGTTATTGGTTTCGTCTATGAGGTATAGGGTGCGTAGTGATGGTAGGGCAATTGAGATAAGGACAAAGGC
++
+F;GFDE@?;GF?:5E:CGCGD?@D=GFCEEDC7=EAD#F5G:EGACFDE:*C:FA=BA*<AF;EG=D=CEE7B54C@?C9:=FFB@AG:#E#AB-#DC#F
+@SimSeq_a/334/1
+TTCAAGAAGTAGAAGTAATCTGAACCGTCCTACCAGCCATTGTCCTTATCTCAATTGCCCTACCAGCACTACGCACCCTATACCTCAGAGACGAAACCAA
++
+GG?>AGFGEEFFDGFGCFGDFEGC?F:DEBEGGAGEGEE>EEGAFB)F>EBD-FAA>GG?GFG3B#B6G:EG6;>DEG#2G?GC?D##)GB=#D###ED#
+@SimSeq_b/247/1
+TAACAATAAGGGAGATTCAAACGATTAGGAAGGTTGTTAGTCAAGGTTCTGGGTTTAGTTGTGGCATGGTCACTAAGGGGGAGGGGGTAATACTAGTCCC
++
+G?DGG?B;GC?GEA?E7AACD@EEDE:GE:=GF??6EEGDFGFFBDFBG0EF.DB@D@EE5A@#E2#8ADA6DEE=@3EDEC#C:CCB#EF?FD=#??5#
+@SimSeq_c/0/1
+AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+DFBCGCG7B?BG=CEEEFGGEDBGFAEEGGEFADGFD#:ED>/GG:G:BDDFAD:=EG5@EGDBDE>>8D,BDB3F@BGB#BDD#BB:EE:AD:#DD##>
+@SimSeq_d/127/1
+TTAAGGCTTAAGTAGATGGGGCAGGTTCCTATGCTGAGTCAATGTCAAGTGAATGAGAGGGGAACTATGTTGTTGTAAGTTAATAAAATAAGGGGAGGGA
++
+BFGCCG?E?EG2EBEGGGGCDGFED:FGDDGDGEEF+CGADDGG=G=ADG?=BE5=EGA:F3DAD>ADE@8DG#E#:A#29BF?AEFEED>=;E#DCC?:
+@SimSeq_e/84/1
+CCCCTGTTGTATTTCAACTATAAAAACCCATGACCCACCAACTACGAAAATCCCACCCAATCATTAAACTCATCAACCGCTCCCAGATCGGAAGAGCGGT
++
+BEEFFCFGGGEBG?GE9G>GFEGGCGFEFGBE<EFG>GEGEG@FGBFDE?F-;GF#D#E;@BD?=:??G#DDCF?DGEDDAGBCAC6#F?C#F#475#B#
+@SimSeq_f/64/1
+CTCAGGATTCTTTTCCAAAGACGCTATTATTGAAGCACTAAACACCTCTTATATTAACGCCTGTAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACC
++
+ADG9EGGFDC=DGGGF=DFBDGAGG;B5GGDFA=CCFFBGGF<B85DFGAFGAE#1:DCGE?#EB??584F*?BEDAGDFB#D#EG85?EE,E=E6#C:A
+@SimSeq_10/154/1
+CACATTCGTAAGGGGATAATTTTTCTGGGTCGGGTGATGTTTTGGCAGTCAGTAGGTGTAGGGCGACTACGATTGAAACGGTGATTGAGGATATTGTGAG
++
+FFEGGCG?ABFBDFGFGGBBGFEG?#DA?9GDGBCCGFEF=DBF#FDG>FEGCD#EA'BF==DGD6#3A@B5?GC#F.G:,DFGCEFF?:5;:A7#C#F=
+@SimSeq_11/66/1
+TGCTCGAACCCATAAGAAACTTATGGTTAGTAGGAGAGCCTTGCTTATTAGGGCAATGGTGAATAGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGA
++
+GG;EBGGEGEDCDGGFDED?,DDG?GDGEFGFFD@G;EA@EAEGG)GCDA#CEF7ADAGB=EBEGF#A?G?<ACCCFEDD?#F:B>E#FAA##9G###?>
+@SimSeq_12/241/1
+ATGCCGGATAGAGTCCTGCAAACCTTAAATCAAGAAATGGGGGGTTGTTTACTCCCATTTAGGGCTTTGAAGGCCCTCGGCTTGGAATTTACACCTAATT
++
+DGDDE8EGGGGGDGGEEDDE4EDEDCDF?EDBGF?=-AGGB:GFCBGE=?AFBGFAD9B@DAE:F0@>D@C=B=CGC=G#D7??FADBCC#:#:#>DB3E
+@SimSeq_13/221/1
+TACCTGCTTTTATCCTTTTACTATCTCTACTTCATATAACCGCCCACCCGGTCGGTTTTAAAAAAATGATAATTAAACTAGCATTTTTCACCAGCCTCCC
++
+G=DG;DGE<5A>GEGGDAEDFEGCBEEFGF?GF=CFCGAF=CFEEAG>@FFG?=GGEF7FCGE#A@B?E=FB@AB,C5AD@G,@BB@)F1D#F##GB#C#
+@SimSeq_14/154/1
+CACTCAATATTTAACCGAGAGAGATCCGCGCAGGAACTGCTAATTCCTAGCCCCCAGGACTAACAGCCTGGCCCTCTCGTCGTGGGCTCGGTAAGTGAAG
++
+GDEBAFE=GBDG=G@GGGE?DE?FCGGDEG:GAC??BGDBEF=BGC:?FEEFAFB?-#CDFCDECEGA=E;FCEBEG#BEGDGDCEDAA###E5;:###E
+@SimSeq_15/76/1
+GGTTGTTAGTCAAGGTTCTGGGTTTAGTTGTGGCATGGTCACTAAGGGGGAGGGGGTAATACTAGTCCCCTAATCCAGATCGGAAGAGCGGTTCAGCAGG
++
+GEGDGGEDA=GFG@=FGGGG=GDBFGGF@EAEGEEG:GFDGDBGCGDEEEDDGGG7CF@:@A=AA1@A?EAEECFEEDDCFDBEDEDBD###F>=BA@E#
+@SimSeq_16/55/1
+TTTATGGTTCAGGCACGGATCCTAAGTCATTGGTGGTAGTCCAAACATTGATATTAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGAAAAAAAA
++
+ADGFBFCCF?DGDEGDFDDFDGEGGE@CDFD=DEBFC-G:EGBF?B+EGBDAGEAE?DEFCBF'?=@E5E=FGBE;=AFECA15FDBA#EE,:5B=#DEB
+@SimSeq_17/122/1
+CCCCAATAACAGGCCTCATCTCCTGAACAGACACCCTACTATGACTATCAATTCTACTAGCTTTCCGAGTAAAAATCCCCCTCTATGGTTTACATCTATG
++
+GGDGCEGGFGGDEGGCGCGDAGC7GFBDAC=GCEDD;AEGDG?2A>E=G*CE>D:GDG:EG?D->A#>DE1BBE2DEBDCDBEF8?F6??D#C:CE##FE
+@SimSeq_18/188/1
+TTTGTAGTTGTATTCGGTAGTGGTTTGTTAATTATTGAGGGTGGAAGTTTTATGCCTTTAGTGGTGTTATTAGTTTATTTAGGGGGGTTATTGGTGGTGT
++
+FG=DFDFGGGGFGGE=DGD=BGDEGEFG;FB=C=EEAFGCEA5EBDGEGBDF?AEAEAFC>BAE:#EG=BDG##E=GG@#CEFA;?#DCE@-#BC6D###
+@SimSeq_19/46/1
+ANACCACAAACGCCAATATGCGTAACAAACCCCAGCAAAGAACCCCAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGAAAAAAAAAAAAAAAAA
++
+D#DGFEF>GDG3GEF?EEGCGFGGGGD?EGGG:GGGDGG:EECFFG-3ECDD@E5>?#F@@DA#F8@:;:GBG9CEE9C>DEDB7DCE:#?:EEF#55A#
+@SimSeq_1a/16/1
+GTGATATAAAGGAGGTAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+DAGG>GGGAECFDEFBFDBE?GBDEFGCGGGE5CBCGBGEB?DDAG?A=BGA#0=E?GBDFF#CG>E??A=?;C=CAE=?#DE;?#DF>5EBF?B#E##<
+@SimSeq_1b/116/1
+TGGAGGATACAGATGAAAATGCTAGAGTATCGCTTGATGAAAAGTGCATTATTAAGAAGAGTCTTGTTAGAATCTGAATTAATAGGGTTAGGCCTAGTAG
++
+7B9BG;6GDGGGFFGBGD==DGGGAEGEBGDG@@FFDFEGFE?;?EBA#?>FED4AB:DD?DE0B0F@B@FEE;EE?E??C:F5EA#=9ABE7C#GB-##
+@SimSeq_1c/138/1
+TTGTGTTTGCTTTTTGTGTTGGGTTTACTGATGATCCATTTGGGGGGTTTTGAGGAGTGGGGGTGTCTAAGTGGGTCGTATTTTTTTGATGGGCGGGGTT
++
+E<GFCDGGFDG2@DGE;FGFFEE,:GGGDGGDGBGEFD?GG==@EFE??EA>ECFDED@?EDFB??FEBFAF>A?,:DGA:#,FC#G;#C??A##:E>#D
+@SimSeq_1d/195/1
+TTGGGCAGTCAGTAGGTTTAGGGCGACTACGATTGAAACGGTGATTGAGGATATTGTGAGTATGATAAATAGGTTAATTGCTTTTCCACGGGTGGGATAA
++
+FC5GFGGCDG:EG6EFED=?:FCD@GGEDBF>DGEFDFDDFE?3AACCGCEF?DDDGADBE7CADB?BBB@B???E#BF@>#GFE:C#FAD@B#BDB#C#
+@SimSeq_1e/0/1
+AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAA
++
+AEEGD=GFBFG=FADFGDEGGEB8@CBGFEFBGGGEGAGAFGDD=DAFFBEDEBDF7EBGA?GGB@?EBA#DEF@D.B<ECDAC@B??###F-##@2#D?
+@SimSeq_1f/145/1
+ACTGCCCTACACTTCCTCCTTCCATTCGCCCTATTGGCTTCACTCATCACCCACCTGATCTTCCTCCATGAACGAGGATCATTTAACCCCCTAGGAATTA
++
+?GE?6AGFDDF8A?GDGFDEDBBEEF;EEDCF?BFFDD7#EGGADF>GDBDDDFG:CFGC7C?DEG@E6@GBABF<3:EBE#EAC=#BCA##B#CG;##A
+@SimSeq_20/104/1
+TTAGCATTGTAGCAGGTTTAGGTTTTTGAGGCTCGCCGTATTATGAGTTCGAGCAGAGGCGACTAATAAGGCAAGGCCAACTCCTGCTTGACAAGCGGAT
++
+DGCEBCD-GGGECEEF?DACFEEADGDGAG7AEFFGC?EDECG0A?:#-DG7GGDEE>??BFC==*GE@:>=AD#C@@F?GA;@CAE?A##BAFEB##:C
+@SimSeq_21/50/1
+AGAAACTTATGGTTAGTAGGAGAGCCTTGCTTATTAGGGCAATGGTGAATAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGAAAAAAAAAAAAA
++
+EE/DDGGFFEG=GG=EBCE9EB:EEABBD?FD;G::FC@#GE?GEG?D=GCA?FAECGE6AAE-D?A0DF:5>C<A#EACFBE#DDDD#D>E5>#DEB##
+@SimSeq_22/0/1
+AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+@GFGGDFDGGFD?EEGGGGBCEDDCCDFF@GB;EEGGG7DD5EGFAG6EDGEAFGAABCG.B:EBEGE:F5@-D?6C2=F:#GCC#6@5=E?=D=E#A##
+@SimSeq_23/196/1
+TAAATTTTACCTTCTTCCCACAACACTTCCTAGGACTATCTGGGATACCTCGACGATACTCGGACTACCCAGACGCATACACCCTCTGAAACCGAACATC
++
+EEDG@CGGFGDGFDDAGGFDGDCGFDCAGE<AGGEGDGBG@G4BDEE-?EDG?E9C>E@?CDGG,BEBGFGC=#A@C>D#ADDG5C9E#,#BA#56@=:A
+@SimSeq_24/0/1
+ATATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+F3GFGG;:CCGGGDAGE@AGD?AC>0E@FE@DFG=GBEDFFGEGFGGEEE#FBF@G3GEEDB#B:DE?A><5:D=EB=BFGDAG@GEBAG#5#ADDF#D5
+@SimSeq_25/224/1
+CTAAACAGAATAATATAGAAGATGTTATTCCATGGGCAATCATTAGGATTATTGACCCTATCGGGGTTAGTTGGTTTCGGGTGAGAATTGCAGCTGTTAC
++
+G?EGDEGGFDFDFFEGFDABFGBCF5G=G>FF<F5DD7BBGG?>FG<F?EFBEEAFDE#EGGCECDC)#DG#E@5D?E7F>#DE:>#DF##=BB?=#G@#
+@SimSeq_26/97/1
+GATAACTGCAACCATGGAAATTAAGGATCCAATTGATGATGTTAGGTTTCAGAGGGTGTATGCGTCTGGGTAGTCCGAGTATCGTCGAGGTATCCCAAGA
++
+>GGAGFGBEDFGGGDFGFGA*GDFD=DGDEDCGG>FFEE5E=DDGCCCE?GDE3=CGDFGGC?>#DEFCE8DFEED#BFCBD?DA#D#A#AA#FB#9#?E
+@SimSeq_27/144/1
+ATAGGTGATTAAAGAAGCTAATAATTTTTAGGTCTGAATCTATATATAATTCGGTGAATTCTATAATTGATCATGTGACAAACAGTGCTGTGGGGACGAA
++
+E;GGA?GDD?GEGFGDEGAGGAB:CE@FE:BEFEFFF8GGDGG;?G@D=G?G??6AF#AD#FB??=#=EF3;#E@E>:DB?B?;F#D#?:C#E#E??C#?
+@SimSeq_28/124/1
+TAATTATGGAATTTGCTGGGGTGAAGTTTTCAGGGTCCCCTAATAGGGCTGGTAGGTAGAGAGCTAAGATGAGTAGTGAGGAGGCAGCTAGTGCTGCTCC
++
+D9AFG:D=GGGCG@AGGBGFCEGD?GEEEGFE@E?ECBGEECFDBFEF;DFE:AB@4?FEEEAFGAE::>5DCEEEA:D?C@#G@GCE#BCAD;E8=?D#
+@SimSeq_29/224/1
+TGATGAGTGAAGCCAATAGGGCGAATGGAAGGAGGAAGTGTAGGGCAGTGAAGCGTGTAAGTGTTGCGTTGTCAACAGAGGGGCCGCCTCAAATTCATGG
++
+EGGGCGEGDDCGGGGDACDA;GFEG:FCGGDEC=:GFF>BAEDFEEGF;CE>E@CE>GCB=CA#:C>F(A;B85B7CCE=BA6##A>>E@:5@B#BDE#B
+@SimSeq_2a/120/1
+CGAGCGGAGATGGTATGGGGAGGGGGGACCACATGGCGAGAGCAAGTATTAAGGCAGCTGTTGGGGCCAGGATGAAAAGGGTAGGGGTGGCAAGCAGGGG
++
+E7GFGDEGB;CDGGFFDEDFAGEDEG>BFDFGE=BEGGCG>?FDBCFADGD#9AB@EEDGFBAG:1DD:@BGAB>5BD=E5#=@#CCB#A?##7=?E###
+@SimSeq_2b/140/1
+AAGTTGCTTTTTCTGCGAGGAGTTGGTTGATTGTTAATCATTTTGGTATAAAGCCGGCTAGGGGTGGGAGGCCGGATAGTGATAGGAGGGAAATTATCGG
++
+GE-GFGGGGGEFFEF=CG=FACEEEDFGE7EG@BC#EGDBAEA?FGCEC>4-C;G>ED@#9E@DG:DD@>CE??CEA:65@C#E##5AE)G<AE##:##=
+@SimSeq_2c/0/1
+AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAA
++
+DGF=D>DCGGGGDDFGG??GFCGGEE??FEB=DFG??EGDF>DDDA?.GFEEG3AEDC@GEC=?C:EE=?BC?F#1ED.DE=D695EGBFE;.#E;BA#>
+@SimSeq_2d/200/1
+CAAGCCGTAGTTGCTGCTTGACTGCTATAGACTACGTGGGAGGTTCGGATTAGCAGGAAAATGCCTGCTACTACTATGGTGCTTGAGTGGAGTAGAGCTG
++
+G?F=EGBEEDDDGFF=GADDEGGFGEB=G9BGFDGCGFBDFG?BG=?DC=3:AGDG#.BD<DCBGG>9CEE@F>6EF>ADAFFC5D@F@ABCB>##<A:G
+@SimSeq_2e/53/1
+CTCGCTGCTATATCATGAATGATCCTAAACAACATCAGTCTGGACATCCAAGAAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGAAAAAAAAAA
++
+<GGG@GFABBDFGGFDGFFEEEEEG5ED=FBGDEDEGCG=?GD5EGD?G:ACF??@BAC:EFGF>F4>##CB5B:#2A?=;?=3B6C;@@#AD:>@5#B#
+@SimSeq_2f/212/1
+ACTATCTGGGATACCTCGACGATACTCGGACTACCCAGACGCATACACCCTCTGAAACCTAACATCATCAATTGGATCCTTAATTTCCATGGTTGCAGTT
++
+G6DEEGGDFDD98GEGFF5?AFEF?CGDEGCB=EFFACCAAGGADFGEE1CFD=FFGEGBGDDC@:G#G:#BE##7#DG#CAD#?DC#G@@A6>B#BFC#
+@SimSeq_30/65/1
+GCGCTGCGAGCTTGGCTGTGTTCGATATGGTTAGTTGGGGGGTGTTGGATGGTAATATAGAGGATAGATCGGAAGAGCGGTTCGGCAGGAATGCCGAGAC
++
+G)DGGEBEGGGGGGDEEEBGBGFGAECE7GEG'EFGG:5AAA>C5FD:?FD<AGFEG:EF=GEFF4=ECD@#AFA;#GDA#?6#DD?>DB>EE?=#F?##
+@SimSeq_31/205/1
+ATTTCTTTTAGCCTAGAGAGTATTCTTGTTTAGTAATTGCTTTCATTAGTGTGGTTGATAGTAGGAGAGTGGTGGTCGCTATGGTGAGGAGGTTGATGGT
++
+DFFFFGEFDEA?CGFFGEF;EGFGGDEFAEEGDEG=FE9G=EGGEGF9=CCG=G?DF#ECEFD?CEE@35B#CG?AG=B5F<CE>=9#C:#F#>DFAAA#
+@SimSeq_32/111/1
+TTCACTGTATTCTACATTAAATCCGGATACTAGTTCCGATTCTCCTTCTGTTAAGTCAAAGGGGGCGCGGTTTGTTTCTGCTAGTGTGGAAGTCTACCAT
++
+D7GGD@GGGFCFECGGGEBEE-GDACDBCF1EDGGGE<5G:E=?F)A?AGEED@BEABB=>8B==5:>C=,?@?E:BE-D2F?C6BDDF6F?C#:#BG?#
+@SimSeq_33/123/1
+GTCCCCTCTGTTGACAACGCAACACTTACACGCTTCACTGCCCTACACTTCCTCCTTCCATTCGCCCTATTGGCTTCACTCATCACCCACCTGATCTTCC
++
+B8EGCDFDGFBEEGCEGBEDE>?EGBEFFDGF45?FAGA?G,G?G-DEECEF>=ECEDECGAD#GAEFF?5EDC;?=GC>?ABFB?E9#CF*#5D##G#B
+@SimSeq_34/23/1
+TAATAGGGTTAGGCCTAGTAGTGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAT
++
+FEF3DDGEFEFDFDGDBDFCGFGBFEGDGGADFCDEEAGDD9GGGBEGB>CCFCEEG,BFG5GD#5BEDCFDADE=AD##G#FBF5AE@)E9B###-###
+@SimSeq_35/203/1
+TCGTAGTCGCCCTAAACCTACTGACTGCCAAAACATCACCCGACCCAGAAAAATTATCCCCTTACGAATGTGGATTCGACCCCCTCGGCTCTGCTCGCTT
++
+F-,F6DFGDF7GEFGDF?D;GCEGCGBGG7B==D=G:FGGDE<GFFBAFEG?E?EEEFDBCAF#EGABEEAC<=*>G#D,DCFEEE##=A;=DEECCD##
+@SimSeq_36/0/1
+AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAATAAAAAAA
++
+FG:FGFEEGEGGGG??EGEFDEFDD?GFGF=G>GGFEEFFE-EBGEED5E<EAEEEEDG?E5FB8D5=B9=EA4DE#CC@DC#:#=>AA2?G#B###BE#
+@SimSeq_37/282/1
+CTTCTGAGTACCAGAAGTTCTCCAAGGAATATCCACAACTGCCGCAAGCTTCCTATTAACCTGACAAAAACTAGGACCATTAATTATACTATTCCTAATT
++
+FD=E?F=G9GFGGFEEG=BC=GEEBDDAGBFDFG=GGDGCDABECGC*GCGG#B>D:CGDF>#EE5G4DBBC94CCE8FE?*#DAFEFC5/D<@#5BB##
+@SimSeq_38/212/1
+GCCAGCGCTTTTCCTTTAGCCACGGGAGTGTGGTGAGGTTTGGTCTTGTTGGGATGGAGGGACTTAGGGGTAACATAGGTGGGTTCAACTATTTTGTTCT
++
+DGGEFA:GCGE:DGBGEDAFGEGE@?GDEG+>;BCEDFE>EGEBGDGACCEFGBF=6?@DBCFF=#EDCE1F::<62D>#2#?6EEE?EEA?AC#BB?DC
+@SimSeq_39/149/1
+AGACCAAACCTCACCACCCTCCCGTGGCTAAAGGAAAAGCGCTGGCCTTGTAAGACCGAAGTGGACGGAACCAACCCTCCCGTGAGTACACCAGCACCCT
++
+FGEBEE==G?:GG>FGCFEDEFACGEDEEADFF5FE)D5F;GFDFEF,EGEBG@EE,AADGGE5B>GF:DEC::E?EC5G##36BGD@#7=?#@)#,+ED
+@SimSeq_3a/195/1
+ATCGGAACTAGTATCCGGATTTAATGTAGAATACAGTGCAAGCCCTTTCGCACTTTTTTTCCTAGCTGAATATGCCAACATTAGATTAATAAATACACTC
++
+FCGG?D-DEFFCEG?EDEGG??FGFE>DGDGEDFBFG4:EEEGGGGGDGGGFEBECDDEF%DA9?GAGF=CB#:13?BEA;C#-ED=A##CC:#=D#A#1
+@SimSeq_3b/93/1
+TCCCTCGTATTTTACATAATCTTCGCCCTATTATTCCCTAAACTATACTACCCAAACACCTCAGACGTTCAAGAAGTAGAAGTAATCTGAACCAGATCGG
++
+FFF,FGGGFDE?FDGDAGCDAGCF1D?DCDGFEF;B8GBDBG?DBG=?FEEAGFC5:F'D?FBEBE.?:D-#EC??@?#=#GDD#:C?E?D?#A:#D#A#
+@SimSeq_3c/122/1
+TTGATAGTTTTTGGCTCATTCGCAGGGTTGTGGTTGGGAAGAAGTGGTGGAATAGGTGGTTGAAGTAGGTTAGTTTAGTTAGGAAGGGCGGTTGGGTGTC
++
+GGGG@AD>CD<?:G?GGGEAGFGGG@FBE:GGBBED=GFEEGA>E?AD<@E>=CF?5#D?DF@B?#B>:='C?B#;EE:G#>B9AE#5AA;?EF5##@1C
diff -r 000000000000 -r 76ea9d4604bc test-data/input2.fastq.gz
Binary file test-data/input2.fastq.gz has changed
diff -r 000000000000 -r 76ea9d4604bc test-data/input2.fq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input2.fq	Tue May 14 09:49:32 2024 +0000
@@ -0,0 +1,240 @@
+@SimSeq_1/229/2
+GGACTAGTATTACCCCCTCCCCCTTAGTGACCATGCCAAAACTAAACCCAGAACCTTGACTAACAACCTTCCTAATCGTTTGAATCTCCCTTATTGTTAT
++
+BECAFFGCG#5AFGEBB5EBD@ED:=FF?=:GGCD:G?-:AEECECEGABF57F-FFEAFF#EEEAC=A5CEDDDCA#-A#@C=#@?##E#A=@E#>#BD
+@SimSeq_2/49/2
+ATTTAGGGCTTTGAAGGCCCTCGGCTTGGAATTTAAACCTAATTTCTTTAGATCGGAAGAGCGTCGTGTAGGGACGGAGTGTAAAAAAAAAAAAAAAAAA
++
+=AFGG2=CFE6FG:?GEGGADBECGFEEFC>BB96E>5>DDB55=D?:-A=CDFGC4DDCAFA?G#C=#FCD8?#6AFF,EDA#BA##5;D6C#/#-A-A
+@SimSeq_3/149/2
+GGTTGTTGATATTTTGTCTAGTGTTAACAGTGTAGCGGAGATGGTGGTGGAGTAGATGTAGAAGGTTAGGATGGCTAGTGATGGTGGGTATTTAATAACT
++
+GFGEBB=EB@FCDEDGFC#FGD5GGCGGF<BBFFAG?:ECD@BCE:BD9@??B-DADGG7DABADED###:#ABC#ECB?B#F#DF#E##69@8##-#,B
+@SimSeq_4/197/2
+TTACAAATTGGATTTTAGTTCATGTTGGGTGAAGGGTAAATCCTGTAAAGAGTGGGAATCAGTGGGTGAATCCGCTCATGATAGCGAAGACTGCTCCTAT
++
+DFGGGDGF6EGDG;BFB?EEGGG>=E:GBGDGB=G.C?GEDCF#E:E5CB#DBGFDE>CFFC=F7D?8ED=DDCE#9BC@B;#B8#A2;#AECE??C@#E
+@SimSeq_5/40/2
+GCCGCAATACCACCATGCTCCATCCTCCTCTGAGAGGGGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTATAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+GBCEGF:CE0D5FGED7FCAFCBFCG;EAFA#A##FDDCG:8GFADCBCAEDFC#EDFGEDCEDGFDC;D?-D?B?FA7AD#C5#7CA#>###?A;;###
+@SimSeq_6/190/2
+GCTAAAAGAAATTAGGTTTAAATTCCAAGCCGAGGGCCTTCAAAGACCTAAATGGGAGTAAACAACCCCCCATTTCTTGATTTAAGGTTTGCAGGACTCT
++
+GDF=E:EEB=;A>EAEGE@FCGGAGFDEGEGE#:DDGF?BC/DEC#F??=GDD#FDE9@1FGE?EFCDGAGA#EDAB=7FED59=AE+#9##C57>A#B#
+@SimSeq_7/178/2
+ATAGGAAGTACCATTCGGGTTTGATGTGTGTTGGGGTAATTATGGAATTTGCTGGGGTGAAGTTTTCAGGGTCCCCTAATAGGGCTGGTAGGTAGAGGGC
++
+DDEGGGG?D>G@?:GEF>GCGEG=FE;D@GFFE=EC5>=A:GAB?GA?E@D?E7?BDDG:GEA#CGB@;7AEB>;DBCC#CEA2B@:CB#>C##BC###@
+@SimSeq_8/18/2
+ATAAGGGGAGGGAGGCTTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAA
++
+AFDG2D?EG?E;?FDG4EFGGD:EEABFEFG??GDEE3G0#DEFE?CDGBGCCFFF,#GBBEG:?C#AF;?GG?E5C>#AGD-3###4#E#A#>#DB?/:
+@SimSeq_9/103/2
+CCAGCCATTGTCCTTATCTCAATTGCCCTACCATCACTACGCACCCTATACCTCATAGACGAAACCAATAACCCCTGCCTGACTATTAAAGTAAGCGGAC
++
+FEG?GGAG:GEAGEF;GDGEG?:EAGB#EAEEG?>#EC57C:F:4FGC-#<EFEAGGD#EEE8GGGFCA-9A:AG5FD'DAGB5A#@G4AEB#CA<#>#:
+@SimSeq_a/334/2
+CCAATGGATGGGATTGCCCATGAGTGTAGTACATCTGCTGCTGTAATTAGTACTCGGATGGTTGAGTTAGTTGGGGTGATTAGGCGGTGGTCAACTTCGA
++
+F:CBBDG9?@AGDE<FEEG?GCAD#EDE5FF5FF#G&BDEGDGD>?C:>CCFF;FADGGEDC??B-CEBBDBBC#:#0DDB##+E#?5#AFB:D?#####
+@SimSeq_b/247/2
+TCTGAGATCTGCGGGGCAAACCACAGCTTCATACCTATCACCATAGAAACCATCCCACTAAACCACTTCCAACTCTGATTAGAATATTCTATTCTCTCCT
++
+DGGGED6BGDGGB=FFAEDGFDGEG056AGGFECECGDG8FD:DFFG=FDBD-BDEB>E>AF;##GCC?GB5CDG7:E#A#;#A#@?@C###GA?G#?D#
+@SimSeq_c/0/2
+ATATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+FFGFG=G:GE=C86GFB:D?GGF?=E-AGG:DE;EG*EEF?G.DGBCD6CGFCD2#=GECE=?F;AEE#5;GD5>8DE7#A;E,=5D5@###C#5#FF#C
+@SimSeq_d/127/2
+TAATTAAACTAGCATTTTTCACAAGCCTCCCTCCCCTTATTTTATTAACTTACAACAACATAGTTGCCCTCTCATTCACTTGACATTGACTCTGCATAGG
++
+DBGFFBABGGDGEEAEE?FBADGC:DFGBCE?BEDAD@CF7EEBC=>A?F5:-5EBEBFDCGGE;#?:?CB=G=3'AD<::7AD?E7E:=*C###FDE##
+@SimSeq_e/84/2
+GGGAGCGGTTGATGAGTTTAATGATTGGGTGGGATTTTCGTAGTTGGTGGGTCATGGGTTTTTATAGTTGAAATACAACAGGGGAGATCGGAAGAGCGTC
++
+CEFEEEGEFFDGEGE9GB,AFDE?C>@DDEDFGAFGDGGBED:G)E4E?C>D(EEF#F=GC9D#E>===ECD;###:GC#F<C#?<B######B###=B#
+@SimSeq_f/64/2
+ACAGGCGTTAATATAAGAGGTGTTTAGTGCTTCAATAATAGCGTCTTTGGAAAAGAATCCTGAGAGATCGTAAGAGCGTCGTGTAGGGAAGGAGCGTAAA
++
+;GDGEGEGC9BGGEGEEGE-ADDAGEFCG=A9A;G;FFFDEE<AFABEFCG@:B=@7=EFC:A??DEGGD#:>=CAGE##EABF>##EBC##A4##C4;>
+@SimSeq_10/154/2
+CACTAGACCCCCAATTATCCCACCAGGGGAAAAGCAATTAACCTATTTATCATACTCACAATATCCTCAATCACCGTTTCAATCGTAGTCGCCCTAAAGC
++
+DFGAFDGGE9=?;:BB>B>:BCCB?DEFD-G?FB@=E9GG:E;E5B)==DEC-GDG9GAG6F;CE:57#A?::DE,EB>BF<ABC=##;B#DC##?##+C
+@SimSeq_11/66/2
+CTATTCACCATTGCCCTAATAAGCAAGGCTCTCCTACTAACCATAAGTTTCTTATGGGTTCGAGCAAGATCGGACGAGCGTCGTGTAGGGAAAGCGTTTA
++
+EEGAEFGFF*GGB;D;GA6B@GFCCEF?EDECGG4EB7?EED#EAAA?<B>2DBC=FA=@BDC9E=BG=E:DCB#GDEA?CD?##C#?5##E#:#7F#@=
+@SimSeq_12/241/2
+ACACAACCCGCCTCTGACGAAAATCTACCCCCCAGAGTAACTTTACCATCAACCTCCTCACCATAGCGACCACCACTCTCCGACTATCAACGACACTACT
++
+FA=DEDGAGGGG=GCFGGGEDF:CG3GCEF@GBGDAG?G6=FEF=GBG?G5@#GEABDDD-@E;#GA9AF=A#F#?AE#:E*?BED8?DE#?#D=##A#C
+@SimSeq_13/221/2
+GAAGAAGATTGAGAAGGTGTCGAGTTTAAGGCTTAAGTAGATGGGGCAGGTTCCTATGCTGAGTCAATGTCAAGTGAATGAGAGGGGAACTATGGTGTTG
++
+FBGGEGGEGDCAEADD?EE=EFGBEGGFFE@G?EGEDGEFGC3BDECBB#CD?FED=D55#F#FA6@<@BFDD@;ECB:?#D:###C#5A###=#@##A#
+@SimSeq_14/154/2
+GTAAGGGGAAGTAGTCTCCTATTTTTAGGTTTACATTCTAATGTTTTGTTTAAACTATACTTACCGAGCCCACGACGAGAGGGCCAGGCTGGTAGTCCTG
++
+#<GGAD#DFGA>=GFGGGGAEGB5DEGEDE*6CDE'EADGG?CAGDF=D54G-<CDDCFECEFGGDA#EE#6=FGEG##-D#5G##A#>FA#B5###B?#
+@SimSeq_15/76/2
+GGATTAGGGGACTAGTATTACCCCCTCCCCCTTAGTGACCATGCCACAACTAAACCCAGAACCTTGACTAACAACCAGATCGGAACTGCGTCGTGTAGGC
++
+DC?D@EGFDGGGCAGDAAGAD;DFGBABDBCDB>FCFFDAGB;FEB=F#,DFD5CF-ECEFF>?G#C#@GGEEGD#-#B?D?;<-#1BG7?59####D?#
+@SimSeq_16/55/2
+AATATCAATGTTTGGACTACCACCAATGACTTAGGATCCGTGCCTGAACCATAAAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAAAAAAAAACAA
++
+EFGGGGEC:GFGFG-BGAFDAGG=G>C9E@GEGAEABCECAAD76CFDAC:FC?5GE??FC=EBCG#ADDG=:FAFE=BBAB6A0;#D#B:F:#><D=#A
+@SimSeq_17/122/2
+TTCTACATGAGCCTTGGGGAGTCATAGATGTAAACCATAGAGGGGGAGTTTTACTAGGAAAGCTAGTAGAATTGATAGCCATAGTAGGGTGTCTGTTCAG
++
+GGFEG3GE>DEBG;GDGCEGDFE=C?CG:;GABEAG?#BF<7=FG5.-9>DA?=AE<7FE###?=#EED:=GF#EGF##2>C:F4F?EE=B#E=#CB###
+@SimSeq_18/188/2
+GCCCATCAAAAAAATACGACCCACTTAGACACCCCCACTCCTCAAAACCCCCCAAATGGATCATCAGTAAACCCAACACAAAAAGCAAACACCACCAAGA
++
+FGG2CDGC5GGGGEGF6?DGGG:8EEFE>4CBFFDE>3BFD=E=?B>@DC?E4;G(/F#@>G;:04D#E>:A>E=?#FFBDBB?-#8D#AE;#?#=###C
+@SimSeq_19/46/2
+GTGGTTCTTTGCTGGGGTTTGTTACGCATATTGGCGTTTGTGGTGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAAAAAAAAAAAAAAAAAAAAA
++
+>?G4GFD-B7EGGG=D>(=#FFG>E9BGDEFG?DCDEGCGECCD67@7EFEE-FE#?ECAA;:A9GFA#CAF:EA#?DCEAG55#?#.#BC#F5EC4@##
+@SimSeq_1a/16/2
+ACCTCCTTTATATCACAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACA
++
+@GEAEGECGFAGFG:1FAG=GF@FEBG:C5FGDEEBGFGB#?EEFDG5GCF-=GEC#*@GD75DD@BD?;2A7;G@-G#?GF5F?#BB#F#A7EG##B#?
+@SimSeq_1b/116/2
+ATTAAACTTTGGATCACTACTAGGCCTAACCCTATTAATTCAGATTCTAACAGGATTCTTCTTAATAATGCACTTTTCCTCAAGCGATACTCTACCATTT
++
+;E2GFG;;FFGG?:EG<BGE;#C>D-6EEA/7GDD=EA=GDG4E=FF?=?EE:?7GBEE@DG:-E#GA=55>:?E:F5#<>):*#?C#=<#=>B##:5?:
+@SimSeq_1c/138/2
+ACCACAAACGCCAATATGCGTAACAAACCCCAGCAAAGAACCCCGCCCATCAAAAAAATACGACCCACTTAGACACCCCCACTACTCAAAACCCCCTAAA
++
+AGGAFGDGGGGFG;EDGEGCCGDGA@E;=GGEGFB-G=G=DFG:GGE?A:@E:DEDDBD5G#AGF:GD:EBG#F@E>G1F#EF#F#A:>##>A#B#>4##
+@SimSeq_1d/195/2
+TCGTCTGACTTTTCCTCTATATCTCGATCTACTGATGAGGATCGTGCTTTTCTAGTACAAACAATACAAGTGACTTCCAATCACTAGACCCCCAATTATC
++
+F?D8GGGEGFDFGDEF=FE.=EFCEEABC+?FGE=C?DFC'.GBF=GG7F*B#:>BEA5??A?:5#EC==#.2G?DA.A?#EF#1AC#B##=F?EA###A
+@SimSeq_1e/0/2
+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+GGGG0DFGGGAEC=<E?DGAEGFAAED?=GBFFDBDDC-3G<F-=55<:ECF=5;D>@#AEDEB?DAED:D:-#DDE#AE:A:=E+8#DA-#.E@#?#8#
+@SimSeq_1f/145/2
+TTATGGTGAAGTAGGGGTGGAATGGGATTTTGTCAGCATTTGGGCTAATTCCTAGGGGGTTAAATGATCCTCGTTCAGGGAGGAAGATCAGGTGGGTGCT
++
+GAED=EGGEFGG<1D=6FAGE;GED)?DGG#EGE<B:GCAEGEE:GB#=E;C5G?#ADBCB@D#BDA-AG5CE:GEF#?EB#/>#####DGC#E+##:#A
+@SimSeq_20/104/2
+CCCTATCCGCTTGTGAAGCAGGAGTTGGCCTTGCCTTATTAGTCGCCTCTGCTCGAACTCATAATACGGCGAGCCTCACAAACCTACACCTGCTACCATG
++
+7FBGGGGFG@E5>GGGDEG5FAG>:DA5GFG?EAE;:GE>E>?F@CG6.D=B,A;#G#AG8A?CDADACCC?C;A#DD.AFBCAB##B-A#DF3#A##??
+@SimSeq_21/50/2
+ATTCACCATTGCCCTAATAAGCAAGGCTCTCCTACTAACCATAAGTTTCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAAAAAAAAAAAAAAAAC
++
+GD==GF=GGGADEEFG=D>@BGEBEC:E>D:GAFG#=GCGAF5FFG56G'=G?A=BE@DC#GCEFG?FG>>A:B@>.9#F2#AFFG##ECEB1-#?##3#
+@SimSeq_22/0/2
+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAA
++
+FFAFGCEF:EDDDD:<>CF?:B?FG:EC=<AAD#BF:FDG:5EE@ECECF1DF9BE?DE?GE5C@FE>BAEC5?;-=C@#E@##:?##?<=D##B#####
+@SimSeq_23/196/2
+TCGAGTGCTGTCACTTTTCGTTTTGATGTGAATGCTTCTCAGATAATAAATATTAGAAGGATAACTGCAACCATGGAAATTAAGGATCCAATTGATGATG
++
+@GCEDDGFGEE?BGFG?DGADDGG<G#GBDB=>:E?BD:GFGGGDEEGAC#E5AEDEG-:AB5=EF>:2;?:=EDC#B-@CC?C@######-?#B?GE##
+@SimSeq_24/0/2
+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAA
++
+FED=?GFBG>3ED=FDFFDGEGFAGC=:G@6FE5EF?EF@=AD#ADAEBFDE/FCE,?;DC-:CDACCD#DE>B5D4A#+.C+C###C>FC##A####D?
+@SimSeq_25/224/2
+CACAATCTACCCCCCAATTTTAGGCCTAGCGCTCTGGGGGGCACTTATGACAAGCCTCATCTGCTTGCGACAAACGGACCTAAAATCCCTAATCGCTGAC
++
+DGD=GEB?EFGDEEGFEBGC<EFBGFGEAFDABDDGCG-D<G=5BGED:CCF:.DEGABFA:EF?D6.6GB75:FF.?>E)E-==:#5#C:A?/B#B#>#
+@SimSeq_26/97/2
+TGGGATACCTCGACGATACTCGGACTACCCAGACGCATACACCCTCTGAAACCTAACATCAGCAATTGGATCCTTACTTTCCATGGTTGCGGTTATCCGA
++
+GFF#@CFG=EGEFBCF5GCDGEEF?=EBAEGEECGGB,5EG#C:DF>FFCEFDCEDE:EGC&=@@*FB<BE7#>=<#:=4#8#=C@E#=##>###AC#FA
+@SimSeq_27/144/2
+GCCCCATCTACTTAAGCCTTAAACTCGACACCTTCTCAATCTTCTTCGTCCCCACAGCACTGTTTGTCACATGATCAATTATAGAATTCACCGAATTAGA
++
+?GGAEGGGAEFGA;GDEGF;GCGDFG?E=D;FBDC8CBC=G:GEA)-?@DGAEAGDD#AG:EEDECEE=5B:#5,#6A=?DCF5E?=#=E#EA##:<##F
+@SimSeq_28/124/2
+TACTCCACCATAAAAGACGCCCTAGGAGCAGCACTAGCTGCCTCCTCACTACTCATCTTAGCTCTCTACCTACCAGCCCTATTAGGGGACCCTGGAACCT
++
+-G6A:@F:?GEG?EDGF?FGAGG8DEEGG<GAAE4FADE9?F?D#GD4;:EGB5E?GGAG#E;DEE?@DDE5<B=C=C#BE#6D?C#=GG@F#G##A##B
+@SimSeq_29/224/2
+TCTACTCCTAATAGCCACAGCATTTATAGGCTATGTTCTCCCATGAGGACAAATATCATTCTGAGGAGCAACCGTAATCACGAATCTACTTTCTGCCACA
++
+GGGGGC6,?@EFGDFF=G6DGBBGBDD-E#EBGFF#ECEGC35G@?DB=G@DGF@,BFAAGB5F-E=F:G=7DFBG=?A;ADA##DB:A#;###=E#C##
+@SimSeq_2a/120/2
+TTACCAAAGAGTTAACCCTTCCCCTGCTTGCCACCCCTACCCTTTTCATCCTGGCCCCAACAGCTGCCTTAATACGTGCTCACGCCATGTGGTCCCCCCT
++
+GGGGGEEFGEACDF-DG:B=?G@DD?FG-DDGBDCFFC@E>B::D::AF/?A;GBB2E:FBAF=9#?F@F#E:>G#@E,##6:C#%:##E#D#E#?#E##
+@SimSeq_2b/140/2
+CATTATTTCTTTTTCAAAATCCCCAATCACCACCACCATCCTGATAATTTCCCTCCTATCACTATCCGGCCTCCCACCCCTAGCCGGGTTTATACCAAAA
++
+GGGG=AFGFFDC?GGFGEGGCCF;=GCED=EEEG=DG?E#ECEGBEDE5?D9:EGF:D=:@GA0E*G2EGCBF@A@ECF?B##A:B5#C=DC#?DF;-##
+@SimSeq_2c/0/2
+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+FEEEGGGD>GEGGFGCGBE5DF5F7F>6GFG6D?FGGFEE@E>??FDA8=?ACE?;:,DGF?=FCBFA5?EBA:@E=#+:=#F65@C>#=###7E#:FA#
+@SimSeq_2d/200/2
+ATCCCTGCCATTGGCCTCGTCCTAGCAGCAACTGGAAAATCGGCCCAATTCGGTTTCCACCCATGACTCCCGGCAGCAATAGAAGGCCAGACACCAGTCT
++
+GBG:ED:>=G?G:EEDFGDFFGDBA<EGBED?BE@E:@BFGGG;::9AFGG@=EEGEFGD#:4D2ADCDEEAAFEBGGEC?A==0CEE###A#AD###:#
+@SimSeq_2e/53/2
+TCTTGGATGTCCAGACTGATGTTGTTTAGGATCATTCATGATATAGCAGCGAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTCAAAAAAAAAAATA
++
+AFD;G5CBFDGG=F=DEAGFFFGDD6BE6E5E;GGG$B=EFGGFE4?F?G3?GE5GE;6BGG;ADE=:E#DGGG#D)9B@E?D<:#1##D@.##?7#=#D
+@SimSeq_2f/212/2
+GATGAGATGGGGGGCAGTTGTTAAGTCACTCAATGTTGGTTATTGTTATTTCGAGTGCTGTCACTTTTCGTTTTGATGTGAATGCTTCTCAGATAATAAA
++
+G0G:GGFFEFCGGGF,GGF:>DE@?G56G2GE?>DDEBEEG=DEECECF<>CDGA6C6DFGFFE??F9:FC18AE?#E=A?##:#BCCDGE##G>B#B#@
+@SimSeq_30/65/2
+ATCCTCTATATTACCATCCAACACCCCCCAACTAACCATATCGAACACAGCCAAGCTCGCAGCCCAGATCGGCAGAGCGTCGTGTAGGGAAAGAGTGTAA
++
+EDFFGE?GGE:FEDF;=7GFFGBGGDE=FBGFGGB?GEEG4AG=G5>EB#.EFDB:ED:CE<E?=#GEDA:=+#>#:AGDGB-69##A@-F?EGBECE6;
+@SimSeq_31/205/2
+CTATTCTTCTATCTCCGACTATGATACAACTCCTCATCAACTATGCCACCAAGCACTACCAACACAACCCGCCTCTGACGAAAATCTACCCCCCCAAGTA
++
+EDAE6GEFBG#EDDDEEGGEGA=FCCFEGAA=FDFA>EE5EA-EEG=FA?#>@C6CFEGA=?BEDF:8>DE/DE-:C#FBD>?BCED#DA-?AE##5C##
+@SimSeq_32/111/2
+TCAATAACAATATGGTATACTTCCACACTAGCAGAAACAAACCGCGCCCCCTTTGACTTAACAGAAGGAGAATCGGAACTAGTATCCGGATTTAATGTAG
++
+GGFGBBF=C=7AGEA2FECG(BF>8D?(DFEE?:AECG=FAGACE:A7FGGE?>?'#C-FEF7DFEA?A#A6CAD@D#?#?=#:#DB5#CFG##E>#@#7
+@SimSeq_33/123/2
+GTTAAATGATCCCCGTTCATGGAGGAAGATCAGGTGGGTGATGAGTGAAGCCAATAGGGCGAATGGAAGGAGGAAGTGTAGGGCAGTGAAGCGTGTAAGT
++
+DDGFGEFG?G>GAFBAFF=?D:GFAAAF4GA?EEBEC=BGEFCFEAEFD@?E=GB=CDEG=#G=?#D-:?EF;#;@E*A5C@,56#C7?G?#D9####?#
+@SimSeq_34/23/2
+CACTACTAGGCCTAACCCTATTAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAA
++
+?=EGF3EAGFFGFACEG=BFCGFADCFD7>EGA:EGBF@:>*CD:CC??-:EEDE:D=D:GF=D=EE#->C1BE1CG+:##D#:D)#E#C#*@C#?A###
+@SimSeq_35/203/2
+GTTGAGGGTGTGGATGGCTCATGTGAGTGGTAGTAGGATGGCAATTTCAAGGTCAAAAAGCAGGAATAGGATGCCTACTAGAAAGAACCGGATTGATAGG
++
+DEAEEGA-CFDFEGFGFBDA>AFGC>;AGDE2:AEA>FADFE;E=#GE@FCD:C@A5GGGDFFACB5E:C?#FCF=;E5C&@FF9#:CF:###C>F#?#C
+@SimSeq_36/0/2
+AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAG
++
+DG5F::GBDGCE?DGGEGD9DGD=A6EDBC>:EGEF=ADCA8GAFF:?@DFE:?G5E>5-GD=B?F5E5?.D5-#G?:F,?F4#/#>FD#=-A#B#@###
+@SimSeq_37/282/2
+TAGAAGGTTAGGATGGCTAGTGATGGTGCGTATTTAATAATTACGATAATTCATGCTATTTCGGCAATGGACGATAGTGCTATTAATTTTCGTACTTGAG
++
+EGEBGG?GBFDGGGACGF?F=6AACFC,GEG0EGDE#DGEFD:C=7D1E#DGD1FEGG=6GE#@@DCCCDCE@A2=##EF##C=A8E#A<#:##=#?#B#
+@SimSeq_38/212/2
+ACATGAATCGGAGGCCAACCAGTAAACCCCCCATATATTTTAATTGGCCAAACTGCCTCCCTATTCTACTTCATCATCATCCTAATCCTCATACCAATAG
++
+GDDCEGB==E?DEDEEFAAEAA?EEGCA>FFD-5;D@EF::FC5AE6G?GC?E=AFFEDABEE5EDE#.EBACD#BBAD#F@-#F-###?##:##?EF15
+@SimSeq_39/149/2
+GGCTTTGGGGGCCGAAGGTGCAAAGTTTTGTTTGCTTTCTTGATACCGGAGGGTGCTGGTGTACTCACGGGAGGGTTGGTTGCGTCCACTGCTGTCTTAC
++
+GGEFGA:EFDFD=GBAACGDGGG=G5AD6ECG:G?GEA@CB?A:5EB?A>BEAA?-G:AD5A9=DDB?A=E5AE#FEA5A##EA:D@C??-:D#BA###C
+@SimSeq_3a/195/2
+CTTATGGTTAGTAGGAGAGCCTTGCTTATTAGGGCAATGGTGAATAGTGCTGGGAGGAAGGTGGGGGTTGATGGGCTGAGACACAGGGTGGTGGTCAGTG
++
+G?GGGEGEGAGEGFG=-B8F?C=AEG>E8EA@E#GG=?FDG#D:=EBGE@EECCDEDFFB=;EFAB=:#>FAC##BCD##B#EDG#??G###@###GD>#
+@SimSeq_3b/93/2
+GGTTCAGATTACTTCTACTTCTTGAACGTCTGAGGTGTTTGGGTAGTATAGTTTAGGGAATAATAGGGCGAAGATTATGTAAAATACGAGGGAAGATCGG
++
+EFCFCDECEB=DDAGCE?GGACFGD:3EF?FED>F=AFCBDDEAFDG=GFA43=EF=BDEDGF?F#=EGC@B?#;-AC5=#AE6#?B#E#>#?:?####5
+@SimSeq_3c/122/2
+TAAATTCCCGCCCATTACCAACGACACCCAACCGCCCTTCCTAACTAAACTAACCTACTTCAACCCCCTATTCCACCACTTCTTGCCAACCACAACACTG
++
+-:E?DE>EG>BFFDDGGGBDEE=C:>DDG?FG8#8AA;5CAB?.F@B:AG==FA?C;D0-:=D##-BDEDEAC:F#:?C#GFGG-B>F#*#?C#E##>3#
diff -r 000000000000 -r 76ea9d4604bc test-data/merged_output.fq.gz
Binary file test-data/merged_output.fq.gz has changed
diff -r 000000000000 -r 76ea9d4604bc test-data/merged_output_from_gzipped.fq.gz
Binary file test-data/merged_output_from_gzipped.fq.gz has changed
diff -r 000000000000 -r 76ea9d4604bc test-data/output1.fq.gz
Binary file test-data/output1.fq.gz has changed
diff -r 000000000000 -r 76ea9d4604bc test-data/output1_adapter_trim.fq.gz
Binary file test-data/output1_adapter_trim.fq.gz has changed
diff -r 000000000000 -r 76ea9d4604bc test-data/output1_from_gzipped.fq.gz
Binary file test-data/output1_from_gzipped.fq.gz has changed
diff -r 000000000000 -r 76ea9d4604bc test-data/output1_general_args.fq.gz
Binary file test-data/output1_general_args.fq.gz has changed
diff -r 000000000000 -r 76ea9d4604bc test-data/output2.fq.gz
Binary file test-data/output2.fq.gz has changed
diff -r 000000000000 -r 76ea9d4604bc test-data/output2_adapter_trim.fq.gz
Binary file test-data/output2_adapter_trim.fq.gz has changed
diff -r 000000000000 -r 76ea9d4604bc test-data/output2_from_gzipped.fq.gz
Binary file test-data/output2_from_gzipped.fq.gz has changed
diff -r 000000000000 -r 76ea9d4604bc test-data/output2_general_args.fq.gz
Binary file test-data/output2_general_args.fq.gz has changed
diff -r 000000000000 -r 76ea9d4604bc test-data/outputNoMerge1.fq.gz
Binary file test-data/outputNoMerge1.fq.gz has changed
diff -r 000000000000 -r 76ea9d4604bc test-data/outputNoMerge2.fq.gz
Binary file test-data/outputNoMerge2.fq.gz has changed