Mercurial > repos > iuc > rasusa
changeset 0:6a2965f39e3b draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rasusa.xml Wed Jul 10 17:01:03 2024 +0000 @@ -0,0 +1,309 @@ +<tool id="rasusa" name="rasusa" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05"> + <description>Randomly subsample reads to a specified coverage</description> + <macros> + <token name="@TOOL_VERSION@">2.0.0</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@FORMATS@">fastqsanger,fastqsanger.gz,fasta,fasta.gz</token> + <xml name="size_units"> + <option value="b">bases</option> + <option value="k">Kilo bases</option> + <option value="m">Mega bases</option> + <option value="g">Giga bases</option> + <option value="t">Tera bases</option> + </xml> + <xml name="params_fastq"> + <conditional name="subsample"> + <param name="type" type="select" label="Subsample reads based on"> + <option value="coverage">Coverage</option> + <option value="num_bases">Number of bases</option> + <option value="num_reads">Number of reads</option> + <option value="frac_reads" selected="true">Fraction of reads</option> + </param> + <when value="coverage"> + <param name="genome_size_unit" type="select" label="Specify genome size in"> + <expand macro="size_units" /> + </param> + <param name="genome_size" type="float" min="0" value="" label="Genome size to calculate coverage with respect to"/> + <param argument="--coverage" type="float" min="0" value="" label="The desired coverage to subsample the reads to"/> + </when> + <when value="num_bases"> + <param name="num_bases_unit" type="select" label="Specify number of bases in"> + <expand macro="size_units" /> + </param> + <param name="bases" type="float" min="0" value="" label="Explicitly set the number of bases required"/> + </when> + <when value="num_reads"> + <param argument="--num" type="integer" value="" min="1"/> + </when> + <when value="frac_reads"> + <param argument="--frac" type="float" value="0.1" min="0" max="1"/> + </when> + </conditional> + </xml> + <token name="@FASTQ_SUBSAMPLE_OPTIONS@"><![CDATA[ +#if str( $subsample.type ) == "coverage": +--genome-size '$subsample.genome_size$subsample.genome_size_unit' +--coverage $subsample.coverage +#elif str( $subsample.type ) == "num_bases": +--bases '$subsample.bases$subsample.num_bases_unit' +#elif str( $subsample.type ) == "num_reads": +--num $subsample.num +#elif str( $subsample.type ) == "frac_reads": +--frac $subsample.frac +#end if +#if $r1_ext.endswith(".gz") or $r2_ext.endswith(".gz") +--output-type g +#end if ]]> + </token> + </macros> + <xrefs> + <xref type='bio.tools'>rasusa</xref> + </xrefs> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">rasusa</requirement> + <requirement type="package" version="1.20">samtools</requirement> + </requirements> + + <command detect_errors="exit_code"><![CDATA[ +#if str( $input.input_selector ) == "aligned": +ln -s '$bam' 'input.bam' && +ln -s '$bam.metadata.bam_index' 'input.bam.bai' && +rasusa aln +--coverage $input.coverage +--step-size $input.step_size +#else: +rasusa reads +#end if + +#if $seed +-s $seed +#end if + +#if str( $input.input_selector ) == "paired": + #set r1_ext = $input.reads1.extension + #set r2_ext = $input.reads2.extension +-o 'paired_out1.$r1_ext' +-o 'paired_out2.$r2_ext' +@FASTQ_SUBSAMPLE_OPTIONS@ +'${input.reads1}' +'${input.reads2}' && +mv 'paired_out1.$r1_ext' '$paired_output1' && +mv 'paired_out2.$r2_ext' '$paired_output2' + +#elif str( $input.input_selector ) == "paired_collection": + #set r1_ext = $input.collection.forward.extension + #set r2_ext = $input.collection.reverse.extension +-o 'paired_out1.$r1_ext' +-o 'paired_out2.$r2_ext' +@FASTQ_SUBSAMPLE_OPTIONS@ +'${input.collection.forward}' +'${input.collection.reverse}' && +mv 'paired_out1.$r1_ext' '${collection_output.forward}' && +mv 'paired_out2.$r2_ext' '${collection_output.reverse}' + +#elif str( $input.input_selector ) == "single": + #set r1_ext = $input.reads.extension +-o 'single_out.$r1_ext' +@FASTQ_SUBSAMPLE_OPTIONS@ +'${input.reads}' && +mv 'single_out.$r1_ext' '$single_output' + +#elif str( $input.input_selector ) == "aligned": +'input.bam' | samtools sort --no-PG -@ 1 -T '\${TMPDIR:-.}' -O bam -o '$bam_output' - +#end if + ]]></command> + <inputs> + <conditional name="input"> + <param name="input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data"> + <option value="paired">Paired-end FASTQ</option> + <option value="single">Single-end FASTQ</option> + <option value="paired_collection">Paired FASTQ Collection</option> + <option value="aligned">BAM file of aligned reads</option> + </param> + <when value="paired"> + <param name="reads1" type="data" format="@FORMATS@" label="Select first set of reads" help="Specify dataset with forward reads"/> + <param name="reads2" type="data" format="@FORMATS@" label="Select second set of reads" help="Specify dataset with reverse reads"/> + <expand macro="params_fastq" /> + </when> + <when value="single"> + <param name="reads" type="data" format="@FORMATS@" label="Select fasta/fastq dataset" help="Specify dataset with single reads"/> + <expand macro="params_fastq" /> + </when> + <when value="paired_collection"> + <param name="collection" format="@FORMATS@" type="data_collection" collection_type="paired" label="Select a paired collection"/> + <expand macro="params_fastq" /> + </when> + <when value="aligned"> + <param name="bam" format="sam,bam" type="data" label="Select BAM file(s) with alignments"/> + <param argument="--coverage" type="integer" min="0" optional="true" value="" label="The desired depth of coverage to subsample the alignment to"/> + <param type="integer" argument="--step-size" value="100" label="When a region has less than the desired coverage, the step size to move along the chromosome to find more reads." + help="The lowest of the step and the minimum end coordinate of the reads in the region will be used. This parameter can have a significant impact on the runtime of the subsampling process."/> + </when> + </conditional> + <param type="integer" argument="--seed" optional="true" label="Random seed to use"/> + </inputs> + <outputs> + <data name="paired_output1" label="${tool.name} on ${on_string}: paired-end r1" format_source="reads1"> + <filter>input['input_selector'] == "paired"</filter> + </data> + <data name="paired_output2" label="${tool.name} on ${on_string}: paired-end R2" format_source="reads2"> + <filter>input['input_selector'] == "paired"</filter> + </data> + <data name="single_output" label="${tool.name} on ${on_string}: single-end" format_source="reads"> + <filter>input['input_selector'] == 'single'</filter> + </data> + <collection name="collection_output" type="paired" label="${tool.name} on ${on_string}: paired-collection"> + <filter>input['input_selector'] == "paired_collection"</filter> + <data name="forward" label="${tool.name} on ${input.collection.forward.name}: paired-end r1" format_source="collection['forward']"/> + <data name="reverse" label="${tool.name} on ${input.collection.reverse.name}: paired-end R2" format_source="collection['reverse']"/> + </collection> + <data name="bam_output" label="${tool.name} on ${on_string}: BAM" format="bam"> + <filter>input['input_selector'] == 'aligned'</filter> + </data> + </outputs> + <tests> + <test expect_num_outputs="1"> + <!-- test 1: single-end fastq by coverage in bases --> + <conditional name="input"> + <param name="input_selector" value="single"/> + <param name="reads" value="r1.fastq.gz"/> + </conditional> + <conditional name="subsample"> + <param name="type" value="coverage"/> + <param name="genome_size_unit" value="b"/> + <param name="genome_size" value="1000"/> + <param name="coverage" value="1"/> + </conditional> + <param name="seed" value="1"/> + <output name="single_output" value="single_by_coverage_b.fastq.gz" ftype="fastqsanger.gz"/> + </test> + <test expect_num_outputs="2"> + <!-- test 2: paired-end fastq by coverage in kb --> + <conditional name="input"> + <param name="input_selector" value="paired"/> + <param name="reads1" value="r1.fastq.gz"/> + <param name="reads2" value="r2.fastq.gz"/> + </conditional> + <conditional name="subsample"> + <param name="type" value="coverage"/> + <param name="genome_size_unit" value="k"/> + <param name="genome_size" value="1"/> + <param name="coverage" value="1"/> + </conditional> + <param name="seed" value="1"/> + <output name="paired_output1" value="paired1_by_coverage_k.fastq.gz" ftype="fastqsanger.gz"/> + <output name="paired_output2" value="paired2_by_coverage_k.fastq.gz" ftype="fastqsanger.gz"/> + </test> + <test expect_num_outputs="3"> + <!-- test 3: paired-collection fastq by coverage in mb --> + <conditional name="input"> + <param name="input_selector" value="paired_collection"/> + <param name="collection"> + <collection type="paired"> + <element name="forward" value="r1.fastq.gz"/> + <element name="reverse" value="r2.fastq.gz"/> + </collection> + </param> + </conditional> + <conditional name="subsample"> + <param name="type" value="coverage"/> + <param name="genome_size_unit" value="m"/> + <param name="genome_size" value="0.001"/> + <param name="coverage" value="1"/> + </conditional> + <param name="seed" value="1"/> + <output_collection name="collection_output" type="paired"> + <element name="forward" file="paired1_by_coverage_m.fastq.gz" ftype="fastqsanger.gz"/> + <element name="reverse" file="paired2_by_coverage_m.fastq.gz" ftype="fastqsanger.gz"/> + </output_collection> + </test> + <test expect_num_outputs="1"> + <!-- test 4: single-end fasta by coverage in gb --> + <conditional name="input"> + <param name="input_selector" value="single"/> + <param name="reads" value="r1.fasta.gz"/> + </conditional> + <conditional name="subsample"> + <param name="type" value="coverage"/> + <param name="genome_size_unit" value="g"/> + <param name="genome_size" value="0.001"/> + <param name="coverage" value="0.001"/> + </conditional> + <param name="seed" value="1"/> + <output name="single_output" value="single_end_by_coverage_g.fasta" ftype="fasta.gz"/> + </test> + <test expect_num_outputs="2"> + <!-- test 5: paired-end fastq by number of bases --> + <conditional name="input"> + <param name="input_selector" value="paired"/> + <param name="reads1" value="r1.fastq"/> + <param name="reads2" value="r2.fastq"/> + </conditional> + <conditional name="subsample"> + <param name="type" value="num_bases"/> + <param name="num_bases_unit" value="k"/> + <param name="bases" value="2"/> + </conditional> + <param name="seed" value="1"/> + <output name="paired_output1" value="paired1_by_num_bases_k.fastq" ftype="fastqsanger"/> + <output name="paired_output2" value="paired2_by_num_bases_k.fastq" ftype="fastqsanger"/> + </test> + <test expect_num_outputs="2"> + <!-- test 6: paired-end fasta by number of reads --> + <conditional name="input"> + <param name="input_selector" value="paired"/> + <param name="reads1" value="r1.fasta.gz"/> + <param name="reads2" value="r2.fasta.gz"/> + </conditional> + <conditional name="subsample"> + <param name="type" value="num_reads"/> + <param name="num" value="5"/> + </conditional> + <param name="seed" value="1"/> + <output name="paired_output1" value="paired1_by_num_reads.fasta.gz" ftype="fasta.gz"/> + <output name="paired_output2" value="paired2_by_num_reads.fasta.gz" ftype="fasta.gz"/> + </test> + <test expect_num_outputs="3"> + <!-- test 7: paired-collection fasta by fraction reads --> + <conditional name="input"> + <param name="input_selector" value="paired_collection"/> + <param name="collection"> + <collection type="paired"> + <element name="forward" value="r1.fasta"/> + <element name="reverse" value="r2.fasta"/> + </collection> + </param> + </conditional> + <conditional name="subsample"> + <param name="type" value="frac_reads"/> + <param name="frac" value="0.6"/> + </conditional> + <param name="seed" value="1"/> + <output_collection name="collection_output" type="paired"> + <element name="forward" file="paired1_by_frac_reads.fasta" ftype="fasta"/> + <element name="reverse" file="paired2_by_frac_reads.fasta" ftype="fasta"/> + </output_collection> + </test> + <test expect_num_outputs="1"> + <!-- test 8: bam input --> + <conditional name="input"> + <param name="input_selector" value="aligned"/> + <param name="bam" value="input.bam" /> + </conditional> + <param name="coverage" value="1"/> + <param name="seed" value="1"/> + <output name="bam_output" value="output.bam" ftype="bam"/> + </test> + </tests> + <help><![CDATA[ + +Randomly subsample reads to a specified coverage. Rasusa provides a random subsample of a read file (FASTA or FASTQ), with two ways of +specifying the size of the subset: + +* takes a genome size and the desired coverage +* takes a target number of bases (nucleotides) or fraction of reads to be sampled + ]]></help> + <citations> + <citation type="doi">10.21105/joss.03941</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/paired1_by_frac_reads.fasta Wed Jul 10 17:01:03 2024 +0000 @@ -0,0 +1,12 @@ +>MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 1:N:0:NAAGGCGATAGATCGC +CATCACTACCGCTCAGGAATNTGACGGCAGTCTTAGCGGCGCTCTAGTGCGGGAGGCCGTATCTTGGAATAAGGTGTCGTCAAATGCAAGGCAGGTAACCCTACACGCCGAGGTTACCACTATACTCCCGTTTCTATATTCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATATCGGTTGCCGTCTTCTGCTTGAAAAAAAAAAACAAACAAGAGAAGACGACGTACTGCACCACCA +>MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 1:N:0:NAAGGCGATAGATCGC +GAGCAGTCGGGCTCAGCGCTNTGCAAATTCTAGTTAGAAACTCACAGTTCTGACAAGCCTTAGGTCAGTGTGATTGGCGGTTAGTCAACTCGGAGAAAGCGTCTTTTCCCGACTTGAATGGTTTGTCCCGACAGTTCGTTGACTGGGGTTTCGTCAGCCTTGAGCGGGGTTCCATCCATCTTTATCGCGCCTTGGGAAAGTAGTCGGCGGGCTTCGGGGTTGGGTGAGGGCAATCCTTGTTCGGTCAAAA +>MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 1:N:0:NAAGGCGATAGATCGC +GGTATCCCCCGGCAGTGAGGATGGAGCCATGGTCTGCATCATACTCACCGTAGGTGAGAATATCCACGTCCTTCGACTCCTGGGTGCCGTCTATGGTGCCCTCTGTTACCAGGCAGTGACGGAGGACATGGTGAGGTTTCAGTACCTCTGGCCCGGCCTGGGTCACAGGGTCAGACTGGGTGACCTTCATGAAGCGTCTGGTGACGTAGCTGTGATAGTCCAGCTTGGCAACCTCTGCTGGTTGCAGAGG +>MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 1:N:0:NAAGGCGATAGATCGC +AAAATAATCCTAAAAAATAACCTCTATGCCGCCGAACGCTCCGCCTCTATCTTCGTAAAAACTATCTTCTCCTCCTCACCTCCATAATCAAGCATCAAGCGATCGCCCTCCGCCAACTCACCCCGCAAAATCTTATCCGCTAGCGGATTCTCAATCTCCGTCTGAATGACCCGCCTCAGCGGCCGCGCCCCATAAACCGAATCAAATCCACGCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAA +>MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 1:N:0:TAAGGCGATAGATCGC +GTGCAGGGGGTGTGGTCAATCCACACTGTTGCTGAGGTGATTGGGTCTCCGGGGTCAACTCCATGAGGTAGCAGACCAGTGCCAGAGATAGTGACCACAGTGTTGGCCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAGACTTTTAAAAAACCGATCTACACCTTGACAGGCTATTAAAGGAAACTGGCCTGGTATCACAG +>MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 1:N:0:TAAGGCGATAGATCGC +TCTCAGATGAGCATGCAGCAGCCCAGACTCGCCCCACGCAGTTTGCCAACCACAAGGCCATCCTCGGCCTGTCAGCCTGCCCCTCCCTCCCTCACCAGCTAGCCTCCTATGCCGCGGTAGGGGGCTCAAAGAGATTCAGACACAGCCACGTAATCATGTTACTTGCCCATTCCCCCCTCCCTCCTCCTCCTCTCCCCCCCTCTCTTCCCCTCTCCCCTCCCCTCCTCCCCTCCTGTCCCTTATACACATC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/paired1_by_num_bases_k.fastq Wed Jul 10 17:01:03 2024 +0000 @@ -0,0 +1,16 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 1:N:0:NAAGGCGATAGATCGC +CATCACTACCGCTCAGGAATNTGACGGCAGTCTTAGCGGCGCTCTAGTGCGGGAGGCCGTATCTTGGAATAAGGTGTCGTCAAATGCAAGGCAGGTAACCCTACACGCCGAGGTTACCACTATACTCCCGTTTCTATATTCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATATCGGTTGCCGTCTTCTGCTTGAAAAAAAAAAACAAACAAGAGAAGACGACGTACTGCACCACCA ++ +?<,<?BBBBBBBBBBBFFFF#6ACECCEC78CE=CGHEH7CHCHFGHADGHHHCCCHHE<DFHFFFFDFFFFFFDFDFDDEEEEEEEEECAEEEE;?BEEEBEEBCE;C;48;)?AACCEEE?AA?:?E88AEE:CE?AAEEEE:?***0:*??AAEEEEEEA?.8;E################################################################################## +@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 1:N:0:NAAGGCGATAGATCGC +GAGCAGTCGGGCTCAGCGCTNTGCAAATTCTAGTTAGAAACTCACAGTTCTGACAAGCCTTAGGTCAGTGTGATTGGCGGTTAGTCAACTCGGAGAAAGCGTCTTTTCCCGACTTGAATGGTTTGTCCCGACAGTTCGTTGACTGGGGTTTCGTCAGCCTTGAGCGGGGTTCCATCCATCTTTATCGCGCCTTGGGAAAGTAGTCGGCGGGCTTCGGGGTTGGGTGAGGGCAATCCTTGTTCGGTCAAAA ++ +5====>/<@@@@@@>@CCCE#66>ACEEEEGGGGGGGFFFEFDFFFFF=CDEFFFFEDEFFFFFC=AEBF-AA@CE;ECD5<5<==C==DEEE)83CD==@+4@DEE*<D1<)1@;888*90;*1988@)2)'4;=EE################################################################################################################ +@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 1:N:0:NAAGGCGATAGATCGC +GGTATCCCCCGGCAGTGAGGATGGAGCCATGGTCTGCATCATACTCACCGTAGGTGAGAATATCCACGTCCTTCGACTCCTGGGTGCCGTCTATGGTGCCCTCTGTTACCAGGCAGTGACGGAGGACATGGTGAGGTTTCAGTACCTCTGGCCCGGCCTGGGTCACAGGGTCAGACTGGGTGACCTTCATGAAGCGTCTGGTGACGTAGCTGTGATAGTCCAGCTTGGCAACCTCTGCTGGTTGCAGAGG ++ +??,<?BBBDDDDDDD<FFF@FC;FFFBEFHHHCDDHHGHHHDGHHHFHHEA?EEAEEHDEFHHHHHFECFHHHFHDHEEHHCFH7CEFHDEHHCFHHFHHF=FFFDFDFFFFEEEEDDEFEEE<BBCEBCE,==AE1::AAEECEE*?*AAEFF??>D?)8):A8?EC?8***0*00:8?*)0*1:?CACC:AA?;)?EEFAEECE88*)1A*10*1:*1?:AC::A)*::*8ACEEE?########### +@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 1:N:0:TAAGGCGATAGATCGC +TCTCAGATGAGCATGCAGCAGCCCAGACTCGCCCCACGCAGTTTGCCAACCACAAGGCCATCCTCGGCCTGTCAGCCTGCCCCTCCCTCCCTCACCAGCTAGCCTCCTATGCCGCGGTAGGGGGCTCAAAGAGATTCAGACACAGCCACGTAATCATGTTACTTGCCCATTCCCCCCTCCCTCCTCCTCCTCTCCCCCCCTCTCTTCCCCTCTCCCCTCCCCTCCTCCCCTCCTGTCCCTTATACACATC ++ +=,,<=>>>@@@@@9@@CCEE@EE+++6C8-++CECE+>DCC>@@EFFFFEEEDEE55+ACEF;-C+>EE++CBA--5A++CDC+4<<+=DE=CDEE@+@9D:D+4;@###############################################################################################################################################
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/paired2_by_frac_reads.fasta Wed Jul 10 17:01:03 2024 +0000 @@ -0,0 +1,12 @@ +>MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 2:N:0:NAAGGCGATAGATCGC +GAATATAGAAACGGGAGTATAGTGGTAACCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAGNNCGCCGCTAAGACTGCCGTCAAATTCCTGAGCGGTAGTGATGCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGTAGATCTCGGGGGGCGCCGGCACATTCAAAAAAAAAAAACAGGAAAATGACATAGGCGTGTGTGA +>MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 2:N:0:NAAGGCGATAGATCGC +GTCCACGTGAAATCCCGAGCGTCCCTCTCCCTCCCGAGAACCCGGTCTATATCCCACGATTTTTGACCGAACAAGGATTGACCTCATCCAACTCCGAAGCCCGCCGCCTACTTTCCCAAGGCGCGATAAAGATTGATGGAACCCCGCCCAAGGCTGACGAAATCCCCGCCAACGAACTGTCGGGCCGACCCATTCAAGTGGGGAAAAAAACCTTTCCCCGGGTTGACAAACCGCCAAACAACCTCACCAA +>MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 2:N:0:NAAGGCGATAGATCGC +TCTCCTCAGTACGGGGGAGGAGGTTCGCTCGGCGGACGTGCGGCCCTACGCCAGACTCTACCACATGGTTCAGCAGGAGCTGGAGCACCGCGCTGTGTCCGGGGACTGGGAATACACCATCAGCCCCGGCGAGGAGTGGCAAGAGACGGAGCCTCTGCAACCAGCAGAGGTTGCCAAGCTGGACTATCACAGCTACGTCACCAGACGCTTCATGAAGGTCACCCAGTCTGACCCTGTGAACCAGGCCGGG +>MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 2:N:0:NAAGGCGATAGATCGC +GCGTGGATTTGATTCGGTTTATGGGGCGCGGCCGCTGAGGCGGGTCATTCAGACGGAGATTGAGAATCCGCTAGCGGATAAGATTTTGCGGGGGGAGTTGGCGGAGGGCGATCGCTTGATGCTTGATTATGGAGGGGAGGGGGAGAAGATAGGTTTTACGAAAATAGAGGCGGAGGGGTCGGCGGCATAGAGGGTAATTTTTTGGGTTTTTTTCTGTGTCTTATACACAACTGAACGTGCCGACGAGCGG +>MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 2:N:0:TAAGGCGATAGATCGC +GGCCAACACTGTGGTCACTATCTCTGGCACTGGTCTGCTACCACATGGAGTTGACACCGGAGACCCAATCACCACAGCAACAGTGTGGATTGACCACACCCCCTGCACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGTAGATCTCCGTGGGCGCCGCATCATTAAAAAAAAAAAAAAAAAACATAACTCTCAAACGCGAATAGAGCAAGAAACAGACAGCTAAAGTACAAACAAT +>MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 2:N:0:TAAGGCGATAGATCGC +GAGGGGAGGAGGGGAAGGGAGAGGGGAAGAGAGGAGAGGAGAGGAGGAGGAGAGAAGGGGGAATGAGCAAGTAACATAATTACATAGCTGTGTCTGAATCTCTTTGAGCACCCTACCTCGGCATAGGAGGCTAGCTGGTGAGGGAGGGAGGGGCAGACTGACAGGCCGAGGATGGCCTTGTGGTTGGCAAACTCCGTGGGGCGAGTCTGGGCTGCTGCATGCGCATCTGAGACTGGCTCTTGTACACATC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/paired2_by_num_bases_k.fastq Wed Jul 10 17:01:03 2024 +0000 @@ -0,0 +1,16 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 2:N:0:NAAGGCGATAGATCGC +GAATATAGAAACGGGAGTATAGTGGTAACCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAGNNCGCCGCTAAGACTGCCGTCAAATTCCTGAGCGGTAGTGATGCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGTAGATCTCGGGGGGCGCCGGCACATTCAAAAAAAAAAAACAGGAAAATGACATAGGCGTGTGTGA ++ +??AAABBBDDDDDEDDGGCFGGHHIFFHHH################################################################66?=##466@@EEEGCGGC>CE<EGEEGEGCEGEGGGG88<?1?C?EGCE?EEC?CC?CCEGGCGGCGC8?CCAC<AA'2228>*0*1C:?################################################################# +@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 2:N:0:NAAGGCGATAGATCGC +GTCCACGTGAAATCCCGAGCGTCCCTCTCCCTCCCGAGAACCCGGTCTATATCCCACGATTTTTGACCGAACAAGGATTGACCTCATCCAACTCCGAAGCCCGCCGCCTACTTTCCCAAGGCGCGATAAAGATTGATGGAACCCCGCCCAAGGCTGACGAAATCCCCGCCAACGAACTGTCGGGCCGACCCATTCAAGTGGGGAAAAAAACCTTTCCCCGGGTTGACAAACCGCCAAACAACCTCACCAA ++ +????9B???AD9?BDDEEDDDDHHHHHFHFHFFHHHHHHHHHEHH>CEGHHFGHHGHH=FHHHHC+CGEBCC<CF@,4CF@CFBFFFFDF?B4BD@@D)>CE6BB)).).:AAAEE?A?A################################################################################################################################## +@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 2:N:0:NAAGGCGATAGATCGC +TCTCCTCAGTACGGGGGAGGAGGTTCGCTCGGCGGACGTGCGGCCCTACGCCAGACTCTACCACATGGTTCAGCAGGAGCTGGAGCACCGCGCTGTGTCCGGGGACTGGGAATACACCATCAGCCCCGGCGAGGAGTGGCAAGAGACGGAGCCTCTGCAACCAGCAGAGGTTGCCAAGCTGGACTATCACAGCTACGTCACCAGACGCTTCATGAAGGTCACCCAGTCTGACCCTGTGAACCAGGCCGGG ++ +A??A?BBBDDDDDDDDGGGGGGHEFHHGEHHHIHEHHHHHDHBEHGFFFEGGDEEDGGGGGEGGEECE?EGCEGEGGGCEEEGGCEEGG4D;;4AGGGGGG8>GGA?EGGGEEGEEGGGCGGEGEGGGGD8<AADECECEGG?CCC:8CC''8:C:?CCE*?)0CC0:*?:C:?CCC8?CCEC9*::CCCC?C*::.CEGGEC99C4')).00*:C:?*10:CC########################## +@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 2:N:0:TAAGGCGATAGATCGC +GAGGGGAGGAGGGGAAGGGAGAGGGGAAGAGAGGAGAGGAGAGGAGGAGGAGAGAAGGGGGAATGAGCAAGTAACATAATTACATAGCTGTGTCTGAATCTCTTTGAGCACCCTACCTCGGCATAGGAGGCTAGCTGGTGAGGGAGGGAGGGGCAGACTGACAGGCCGAGGATGGCCTTGTGGTTGGCAAACTCCGTGGGGCGAGTCTGGGCTGCTGCATGCGCATCTGAGACTGGCTCTTGTACACATC ++ +?????@9@B?B?BBBBEEEFB@@EEHEC?BF-CE@DDEH,5+5C,>@+CE+<?=E-CFECEHHDBD,?DFF,4DDDBF;=B;;BBD;D,B4=BEEEEECB,,BB;?C?CEEEE*;;C:AC?C;?CC:AEEE?E8ACE:0:A?AA8A4.??8?8248)8:ACEEE?E)4;?;?##############################################################################
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/r1.fasta Wed Jul 10 17:01:03 2024 +0000 @@ -0,0 +1,20 @@ +>MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 1:N:0:NAAGGCGATAGATCGC +AGATAGCCGAAGATAAAGAGNTCATAACCGTAAAGGCCAGAGACGAGAACCACTCGCAGGCAAGGTTTGCAAGCCTCGCCAAGAATATTATAGACCCGCTTGCCAACGACTGGCATTACATCACCGTAAAGAAGGTAGGCAAGAATCACTGGATCAGCATAACAGATGAGGGTAGAGACGCCGTATCGTTTCTGGGCTAGGTTATCTGGGCCGCCTTCTTGCGTCGGCGCACAGTCACAAAGGAAATGCC +>MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 1:N:0:NAAGGCGATAGATCGC +ATATATTCATCCGCCATTATNAGAGTCCGATTACTTTAGAACAGTGCCGCGAATCCTTCGTCAACTGTAATCCAAGCGACATTGGTTCGATTAGCACGCATGAGGCACGAGATCTACGCGTATCTCTGGTAGATACACCAGGAGGGATGAGAGTTGAGCGAGTTAGCTGTGGCCAGAGAGATGGGTCTAATCGTAGTCTACAACTGGGAGTCACATGCCACTACCGACTAATCTGGTCGCCGAACGGGAG +>MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 1:N:0:NAAGGCGATAGATCGC +CATCACTACCGCTCAGGAATNTGACGGCAGTCTTAGCGGCGCTCTAGTGCGGGAGGCCGTATCTTGGAATAAGGTGTCGTCAAATGCAAGGCAGGTAACCCTACACGCCGAGGTTACCACTATACTCCCGTTTCTATATTCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATATCGGTTGCCGTCTTCTGCTTGAAAAAAAAAAACAAACAAGAGAAGACGACGTACTGCACCACCA +>MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 1:N:0:NAAGGCGATAGATCGC +GAGCAGTCGGGCTCAGCGCTNTGCAAATTCTAGTTAGAAACTCACAGTTCTGACAAGCCTTAGGTCAGTGTGATTGGCGGTTAGTCAACTCGGAGAAAGCGTCTTTTCCCGACTTGAATGGTTTGTCCCGACAGTTCGTTGACTGGGGTTTCGTCAGCCTTGAGCGGGGTTCCATCCATCTTTATCGCGCCTTGGGAAAGTAGTCGGCGGGCTTCGGGGTTGGGTGAGGGCAATCCTTGTTCGGTCAAAA +>MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 1:N:0:NAAGGCGATAGATCGC +GGTATCCCCCGGCAGTGAGGATGGAGCCATGGTCTGCATCATACTCACCGTAGGTGAGAATATCCACGTCCTTCGACTCCTGGGTGCCGTCTATGGTGCCCTCTGTTACCAGGCAGTGACGGAGGACATGGTGAGGTTTCAGTACCTCTGGCCCGGCCTGGGTCACAGGGTCAGACTGGGTGACCTTCATGAAGCGTCTGGTGACGTAGCTGTGATAGTCCAGCTTGGCAACCTCTGCTGGTTGCAGAGG +>MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 1:N:0:NAAGGCGATAGATCGC +AAAATAATCCTAAAAAATAACCTCTATGCCGCCGAACGCTCCGCCTCTATCTTCGTAAAAACTATCTTCTCCTCCTCACCTCCATAATCAAGCATCAAGCGATCGCCCTCCGCCAACTCACCCCGCAAAATCTTATCCGCTAGCGGATTCTCAATCTCCGTCTGAATGACCCGCCTCAGCGGCCGCGCCCCATAAACCGAATCAAATCCACGCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAA +>MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 1:N:0:NAAGGCGATAGATCGC +GTAGTATTCTCATATCACAAGTCCCCAAACTGCATAAGGTGTGGAGTGGAGTGTCTCCCACTGCATTTTGTTGGTTTGGGTTGCATTTTTTGTGGCACAAAATTATCTTTAAACACTCTAAGCTCATATTTGCACATGCAACATGAATTGGAGCATTTCTTTTGCAGTCAACTGCCAGTACATTAACTCCACTCTGTAATAGTAAATCCTGTCTCTTATCCACATCTCCGAGCCCACGAGAATAAGGCGA +>MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 1:N:0:NAAGGCGATAGATCGC +CTTCCCCACGGCCCAGACACAAGAGACGACCTCCATAAATCTTTTAGAGGGTGACCGCATCTCCGACGCAAACCAGGACGCCGATACCCTCGTGGTGGTGTTCGACCGTACGGATGGCGCAGACACCGACGGCACTAGTGCCACGGTATCAGGTACCACCATAACGTATGATTCGGGCACGCTCAAGGGCCAGCGTGACGGAATCGATAGAATACACTACACGGTGACTGATGGGGCCAGCCAAACCTGT +>MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 1:N:0:TAAGGCGATAGATCGC +GTGCAGGGGGTGTGGTCAATCCACACTGTTGCTGAGGTGATTGGGTCTCCGGGGTCAACTCCATGAGGTAGCAGACCAGTGCCAGAGATAGTGACCACAGTGTTGGCCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAGACTTTTAAAAAACCGATCTACACCTTGACAGGCTATTAAAGGAAACTGGCCTGGTATCACAG +>MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 1:N:0:TAAGGCGATAGATCGC +TCTCAGATGAGCATGCAGCAGCCCAGACTCGCCCCACGCAGTTTGCCAACCACAAGGCCATCCTCGGCCTGTCAGCCTGCCCCTCCCTCCCTCACCAGCTAGCCTCCTATGCCGCGGTAGGGGGCTCAAAGAGATTCAGACACAGCCACGTAATCATGTTACTTGCCCATTCCCCCCTCCCTCCTCCTCCTCTCCCCCCCTCTCTTCCCCTCTCCCCTCCCCTCCTCCCCTCCTGTCCCTTATACACATC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/r1.fastq Wed Jul 10 17:01:03 2024 +0000 @@ -0,0 +1,40 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 1:N:0:NAAGGCGATAGATCGC +AGATAGCCGAAGATAAAGAGNTCATAACCGTAAAGGCCAGAGACGAGAACCACTCGCAGGCAAGGTTTGCAAGCCTCGCCAAGAATATTATAGACCCGCTTGCCAACGACTGGCATTACATCACCGTAAAGAAGGTAGGCAAGAATCACTGGATCAGCATAACAGATGAGGGTAGAGACGCCGTATCGTTTCTGGGCTAGGTTATCTGGGCCGCCTTCTTGCGTCGGCGCACAGTCACAAAGGAAATGCC ++ +?????BBB@BBBB?BBFFFF#66EAFHHHCEFEDFGHHHHF@DFHACEEF@FDFHHHHEEEHHHF?FGEHFHDEFGHHCEHEFHHHHFFFCFDFFFFBEEEEEEEEEEEB?EEEEEEEEEEEBBEE?CE?:ACCC*??CAAEECE:?ECA:?A*?EEEE?EEEE?0AAC/?8)00**0:8'8;48*?8/8?AEEEE8:A*8*0:**0**:?C?480?EE?A############################# +@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 1:N:0:NAAGGCGATAGATCGC +ATATATTCATCCGCCATTATNAGAGTCCGATTACTTTAGAACAGTGCCGCGAATCCTTCGTCAACTGTAATCCAAGCGACATTGGTTCGATTAGCACGCATGAGGCACGAGATCTACGCGTATCTCTGGTAGATACACCAGGAGGGATGAGAGTTGAGCGAGTTAGCTGTGGCCAGAGAGATGGGTCTAATCGTAGTCTACAACTGGGAGTCACATGCCACTACCGACTAATCTGGTCGCCGAACGGGAG ++ +?????BBBDDDDADDDE@FF#66CFCFHHBEHHIIIHIIHHFHHGHHHHHHHHHHIHIHIFHHHHHHEGFHIHHIIIHHHHHHHHCFHHHHHHHFFFFFFEEEEFFEFEEBBEEEFFE@E8;EEFFFEF*:AEEEEEFFFEAAEA?A?ACAEF?CEEFED2<.?AAECEAEFEEE8??A8?CAAE1?EEE?AE*888AEEEEFEEFFA8A8?ACEAEEEAE?C:??ED2<E:C*:?*:8?ED<>8.)8?< +@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 1:N:0:NAAGGCGATAGATCGC +CATCACTACCGCTCAGGAATNTGACGGCAGTCTTAGCGGCGCTCTAGTGCGGGAGGCCGTATCTTGGAATAAGGTGTCGTCAAATGCAAGGCAGGTAACCCTACACGCCGAGGTTACCACTATACTCCCGTTTCTATATTCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATATCGGTTGCCGTCTTCTGCTTGAAAAAAAAAAACAAACAAGAGAAGACGACGTACTGCACCACCA ++ +?<,<?BBBBBBBBBBBFFFF#6ACECCEC78CE=CGHEH7CHCHFGHADGHHHCCCHHE<DFHFFFFDFFFFFFDFDFDDEEEEEEEEECAEEEE;?BEEEBEEBCE;C;48;)?AACCEEE?AA?:?E88AEE:CE?AAEEEE:?***0:*??AAEEEEEEA?.8;E################################################################################## +@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 1:N:0:NAAGGCGATAGATCGC +GAGCAGTCGGGCTCAGCGCTNTGCAAATTCTAGTTAGAAACTCACAGTTCTGACAAGCCTTAGGTCAGTGTGATTGGCGGTTAGTCAACTCGGAGAAAGCGTCTTTTCCCGACTTGAATGGTTTGTCCCGACAGTTCGTTGACTGGGGTTTCGTCAGCCTTGAGCGGGGTTCCATCCATCTTTATCGCGCCTTGGGAAAGTAGTCGGCGGGCTTCGGGGTTGGGTGAGGGCAATCCTTGTTCGGTCAAAA ++ +5====>/<@@@@@@>@CCCE#66>ACEEEEGGGGGGGFFFEFDFFFFF=CDEFFFFEDEFFFFFC=AEBF-AA@CE;ECD5<5<==C==DEEE)83CD==@+4@DEE*<D1<)1@;888*90;*1988@)2)'4;=EE################################################################################################################ +@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 1:N:0:NAAGGCGATAGATCGC +GGTATCCCCCGGCAGTGAGGATGGAGCCATGGTCTGCATCATACTCACCGTAGGTGAGAATATCCACGTCCTTCGACTCCTGGGTGCCGTCTATGGTGCCCTCTGTTACCAGGCAGTGACGGAGGACATGGTGAGGTTTCAGTACCTCTGGCCCGGCCTGGGTCACAGGGTCAGACTGGGTGACCTTCATGAAGCGTCTGGTGACGTAGCTGTGATAGTCCAGCTTGGCAACCTCTGCTGGTTGCAGAGG ++ +??,<?BBBDDDDDDD<FFF@FC;FFFBEFHHHCDDHHGHHHDGHHHFHHEA?EEAEEHDEFHHHHHFECFHHHFHDHEEHHCFH7CEFHDEHHCFHHFHHF=FFFDFDFFFFEEEEDDEFEEE<BBCEBCE,==AE1::AAEECEE*?*AAEFF??>D?)8):A8?EC?8***0*00:8?*)0*1:?CACC:AA?;)?EEFAEECE88*)1A*10*1:*1?:AC::A)*::*8ACEEE?########### +@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 1:N:0:NAAGGCGATAGATCGC +AAAATAATCCTAAAAAATAACCTCTATGCCGCCGAACGCTCCGCCTCTATCTTCGTAAAAACTATCTTCTCCTCCTCACCTCCATAATCAAGCATCAAGCGATCGCCCTCCGCCAACTCACCCCGCAAAATCTTATCCGCTAGCGGATTCTCAATCTCCGTCTGAATGACCCGCCTCAGCGGCCGCGCCCCATAAACCGAATCAAATCCACGCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAA ++ +?????BBBDDDDDDDDGGGGGGIIIHHFFHHHHHHHHHHEHHEHHHHHIIHHHHHFEHIIIHHIHHIHIHIIIIIHHHHHHHHHHHHHHHHDHHHHHHHHGEDFGGGGGGG;CEGEGCEGGGGG8>GGGGEGGEECEGGGGD8EDGGAEGEEGGCE:CGG8CEEGG???CEE<DG8CC*??>DG.8<AGGGGCEEG*C2<GCCECE*:?CE?CE9C:C:C:?C*1**010:*?E82'2<GCE######## +@MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 1:N:0:NAAGGCGATAGATCGC +GTAGTATTCTCATATCACAAGTCCCCAAACTGCATAAGGTGTGGAGTGGAGTGTCTCCCACTGCATTTTGTTGGTTTGGGTTGCATTTTTTGTGGCACAAAATTATCTTTAAACACTCTAAGCTCATATTTGCACATGCAACATGAATTGGAGCATTTCTTTTGCAGTCAACTGCCAGTACATTAACTCCACTCTGTAATAGTAAATCCTGTCTCTTATCCACATCTCCGAGCCCACGAGAATAAGGCGA ++ +55,,5?9BBBBB<<BBFFFFFFFHHFBEFHFHHHFDFCF0A9@>9D9DFG;FHHHHGHHFFFFHHHHECDCEFF>EFEEEE@CDFEFHHGHHHHEHDGHHFHDFHFHHHHFFHHH@FDD??DFFFFDBBEEBEEEEEEEEEEEEEEEEE,;?CEC;CEEEECB?CEEEEEEEECEEE?C?CE*0?***/:::?:*/?:A::**/:*:ACE?0:::A::***00::*/?C888??EEE############# +@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 1:N:0:NAAGGCGATAGATCGC +CTTCCCCACGGCCCAGACACAAGAGACGACCTCCATAAATCTTTTAGAGGGTGACCGCATCTCCGACGCAAACCAGGACGCCGATACCCTCGTGGTGGTGTTCGACCGTACGGATGGCGCAGACACCGACGGCACTAGTGCCACGGTATCAGGTACCACCATAACGTATGATTCGGGCACGCTCAAGGGCCAGCGTGACGGAATCGATAGAATACACTACACGGTGACTGATGGGGCCAGCCAAACCTGT ++ +?????BBBDBDDDDDDFFFFFFHIHIHHHHHHIHIFGGHFHHHHIIFHIHH?EEGHHHHHH-EGEHHCEHHHHH@FDFFEFF5@EEEFFEFE;AECCE;AEEEEEA?8?AEDDEEDFFDE2>>EEFF<<<2>D?DEEE*:C?AA<>8AEFCEE:?C?EEE?CEFEE0?:E?ACEECD8>EE>)8>E:CEEEEEED.)?AE??A?:A?*??:C0?CCE?AAA:88.88?::C:C?*8)4A?A######### +@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 1:N:0:TAAGGCGATAGATCGC +GTGCAGGGGGTGTGGTCAATCCACACTGTTGCTGAGGTGATTGGGTCTCCGGGGTCAACTCCATGAGGTAGCAGACCAGTGCCAGAGATAGTGACCACAGTGTTGGCCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAGACTTTTAAAAAACCGATCTACACCTTGACAGGCTATTAAAGGAAACTGGCCTGGTATCACAG ++ +=5===<>+5<5<+5=@CC;8CEEEEE;-8ACFDE.7C87CF-A>E>E=FFE**>>5AEDAEED-5-5AADC=D+=DDE<++3+CCD9DCD+=@3:DEEEEDD<@D*9DE99;@;@EE@;@@EEE7@@8@:@@@;9EE'449?<<E;=E<<;8(6;?############################################################################################## +@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 1:N:0:TAAGGCGATAGATCGC +TCTCAGATGAGCATGCAGCAGCCCAGACTCGCCCCACGCAGTTTGCCAACCACAAGGCCATCCTCGGCCTGTCAGCCTGCCCCTCCCTCCCTCACCAGCTAGCCTCCTATGCCGCGGTAGGGGGCTCAAAGAGATTCAGACACAGCCACGTAATCATGTTACTTGCCCATTCCCCCCTCCCTCCTCCTCCTCTCCCCCCCTCTCTTCCCCTCTCCCCTCCCCTCCTCCCCTCCTGTCCCTTATACACATC ++ +=,,<=>>>@@@@@9@@CCEE@EE+++6C8-++CECE+>DCC>@@EFFFFEEEDEE55+ACEF;-C+>EE++CBA--5A++CDC+4<<+=DE=CDEE@+@9D:D+4;@###############################################################################################################################################
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/r2.fasta Wed Jul 10 17:01:03 2024 +0000 @@ -0,0 +1,20 @@ +>MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 2:N:0:NAAGGCGATAGATCGC +GCCGATATGCAGATGCCGTTGATTGCTGCCAGCATAGCAGCCATTGCCGGCATATCCTTTGTGACTGTGCGCCGACGCAAGAAGGCGGCCCAGATAACCTAGCCCAGAAACGATACGGCGTCTCTACCCTCATCTGTTATGCTGATCCAGTGATTCTTGCCTACCTTCTTTACGGTGATGTAATGCCAGTCGTTGGCAAGCGGGTCTATAATATTCTTGGCGAGGCTTGCAAACCTGGCCTGCGAGTGGT +>MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 2:N:0:NAAGGCGATAGATCGC +GATGACATCAGCACAGGTTCCGCTTCCGCTGTCGCAACGACGTGGCTGCCATCGATTATATTCAATTCTGAGTGCTGCCGTAGGGCTAGATGTAAGACTCACGTTCGGCGACCAGATTAGTCGGTAGTGGCATGTGACTCCCCGTTGTAGACTACGATTAGACCCATCTCTCTGGCCACAGCTAACTCGCTCAACTCTCATCCCTCCTGGGGTATCTACCAGCGATACGCGTAGAACTCGTGCCTCATGC +>MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 2:N:0:NAAGGCGATAGATCGC +GAATATAGAAACGGGAGTATAGTGGTAACCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAGNNCGCCGCTAAGACTGCCGTCAAATTCCTGAGCGGTAGTGATGCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGTAGATCTCGGGGGGCGCCGGCACATTCAAAAAAAAAAAACAGGAAAATGACATAGGCGTGTGTGA +>MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 2:N:0:NAAGGCGATAGATCGC +GTCCACGTGAAATCCCGAGCGTCCCTCTCCCTCCCGAGAACCCGGTCTATATCCCACGATTTTTGACCGAACAAGGATTGACCTCATCCAACTCCGAAGCCCGCCGCCTACTTTCCCAAGGCGCGATAAAGATTGATGGAACCCCGCCCAAGGCTGACGAAATCCCCGCCAACGAACTGTCGGGCCGACCCATTCAAGTGGGGAAAAAAACCTTTCCCCGGGTTGACAAACCGCCAAACAACCTCACCAA +>MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 2:N:0:NAAGGCGATAGATCGC +TCTCCTCAGTACGGGGGAGGAGGTTCGCTCGGCGGACGTGCGGCCCTACGCCAGACTCTACCACATGGTTCAGCAGGAGCTGGAGCACCGCGCTGTGTCCGGGGACTGGGAATACACCATCAGCCCCGGCGAGGAGTGGCAAGAGACGGAGCCTCTGCAACCAGCAGAGGTTGCCAAGCTGGACTATCACAGCTACGTCACCAGACGCTTCATGAAGGTCACCCAGTCTGACCCTGTGAACCAGGCCGGG +>MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 2:N:0:NAAGGCGATAGATCGC +GCGTGGATTTGATTCGGTTTATGGGGCGCGGCCGCTGAGGCGGGTCATTCAGACGGAGATTGAGAATCCGCTAGCGGATAAGATTTTGCGGGGGGAGTTGGCGGAGGGCGATCGCTTGATGCTTGATTATGGAGGGGAGGGGGAGAAGATAGGTTTTACGAAAATAGAGGCGGAGGGGTCGGCGGCATAGAGGGTAATTTTTTGGGTTTTTTTCTGTGTCTTATACACAACTGAACGTGCCGACGAGCGG +>MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 2:N:0:NAAGGCGATAGATCGC +GAGTTACTATTACAGAGTGGAGCTAATGTACTGGCAGTTGACTGCAAAAGAAATGCTCCAATTCATGTTGCATGTGCAAATATGAGCTTAGAGTGTTTAAAGATAATTTTGTGCCACAAAAAATGCAACCCAAACCAACAAAATGCAGTGGGAGACACTCCACTCCACACCTTATGCAGTTTGGGGACTTGTGATATGAGAATACTACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGAACAAG +>MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 2:N:0:NAAGGCGATAGATCGC +GTATTGCTGGCACCATCAGTCACCGTGTAGTGTATTCTATCGATTCCGTCACGCTGGCCCTTGAGCGTGCCCGAATCATACGTTATGGTGGTACCTGATACCGTGGCACTAGTGCCGTCGGTGTCTGCGCCATCCGTACGGTCGAACACCACCACGAGGGTATCGGCGTCCTGGTTTGCGTCGGGGATGCGGTCACCCTCTAAAAGATTTATGGAGGTCGTCTCTTGTGTCTGGGCCGGGGGGAAGATGT +>MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 2:N:0:TAAGGCGATAGATCGC +GGCCAACACTGTGGTCACTATCTCTGGCACTGGTCTGCTACCACATGGAGTTGACACCGGAGACCCAATCACCACAGCAACAGTGTGGATTGACCACACCCCCTGCACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGTAGATCTCCGTGGGCGCCGCATCATTAAAAAAAAAAAAAAAAAACATAACTCTCAAACGCGAATAGAGCAAGAAACAGACAGCTAAAGTACAAACAAT +>MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 2:N:0:TAAGGCGATAGATCGC +GAGGGGAGGAGGGGAAGGGAGAGGGGAAGAGAGGAGAGGAGAGGAGGAGGAGAGAAGGGGGAATGAGCAAGTAACATAATTACATAGCTGTGTCTGAATCTCTTTGAGCACCCTACCTCGGCATAGGAGGCTAGCTGGTGAGGGAGGGAGGGGCAGACTGACAGGCCGAGGATGGCCTTGTGGTTGGCAAACTCCGTGGGGCGAGTCTGGGCTGCTGCATGCGCATCTGAGACTGGCTCTTGTACACATC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/r2.fastq Wed Jul 10 17:01:03 2024 +0000 @@ -0,0 +1,40 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 2:N:0:NAAGGCGATAGATCGC +GCCGATATGCAGATGCCGTTGATTGCTGCCAGCATAGCAGCCATTGCCGGCATATCCTTTGTGACTGTGCGCCGACGCAAGAAGGCGGCCCAGATAACCTAGCCCAGAAACGATACGGCGTCTCTACCCTCATCTGTTATGCTGATCCAGTGATTCTTGCCTACCTTCTTTACGGTGATGTAATGCCAGTCGTTGGCAAGCGGGTCTATAATATTCTTGGCGAGGCTTGCAAACCTGGCCTGCGAGTGGT ++ +??A??ABBDDDDDDDDFFEEEFHIIIIHHIIHIFHIIHHHFHHIIIIIHHHFHHIIIIIIFFFHHIIHGDEHHAAEHHHHFHHHHD=EBBEEEEEFFFFEEEECEFFEEFFF8*??AA?;>DEEEFFFF*?8AECFEFFFFFFEAEEECFFFCEEEFFFFFFEEFEACEEC?CAACEFEEEFE?0?EACAAAEEAACEEA*.48.'0*1::A?CAA?CC::4''4'00'8:?A8?E############## +@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 2:N:0:NAAGGCGATAGATCGC +GATGACATCAGCACAGGTTCCGCTTCCGCTGTCGCAACGACGTGGCTGCCATCGATTATATTCAATTCTGAGTGCTGCCGTAGGGCTAGATGTAAGACTCACGTTCGGCGACCAGATTAGTCGGTAGTGGCATGTGACTCCCCGTTGTAGACTACGATTAGACCCATCTCTCTGGCCACAGCTAACTCGCTCAACTCTCATCCCTCCTGGGGTATCTACCAGCGATACGCGTAGAACTCGTGCCTCATGC ++ +?????BBBDDDDDDDDGFFGGGHHHHIHHHHHHHIHHHHIHBCEEHFFHHHIIHFHHHIIIIIIIHIFBGFGFHHHHIHE@EEEHHFFHHFF?CFHHHHHGGGGGGGGGGGGGGGGGGGECGGG;EE:CEGGG?#################################################################################################################### +@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 2:N:0:NAAGGCGATAGATCGC +GAATATAGAAACGGGAGTATAGTGGTAACCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAGNNCGCCGCTAAGACTGCCGTCAAATTCCTGAGCGGTAGTGATGCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGTAGATCTCGGGGGGCGCCGGCACATTCAAAAAAAAAAAACAGGAAAATGACATAGGCGTGTGTGA ++ +??AAABBBDDDDDEDDGGCFGGHHIFFHHH################################################################66?=##466@@EEEGCGGC>CE<EGEEGEGCEGEGGGG88<?1?C?EGCE?EEC?CC?CCEGGCGGCGC8?CCAC<AA'2228>*0*1C:?################################################################# +@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 2:N:0:NAAGGCGATAGATCGC +GTCCACGTGAAATCCCGAGCGTCCCTCTCCCTCCCGAGAACCCGGTCTATATCCCACGATTTTTGACCGAACAAGGATTGACCTCATCCAACTCCGAAGCCCGCCGCCTACTTTCCCAAGGCGCGATAAAGATTGATGGAACCCCGCCCAAGGCTGACGAAATCCCCGCCAACGAACTGTCGGGCCGACCCATTCAAGTGGGGAAAAAAACCTTTCCCCGGGTTGACAAACCGCCAAACAACCTCACCAA ++ +????9B???AD9?BDDEEDDDDHHHHHFHFHFFHHHHHHHHHEHH>CEGHHFGHHGHH=FHHHHC+CGEBCC<CF@,4CF@CFBFFFFDF?B4BD@@D)>CE6BB)).).:AAAEE?A?A################################################################################################################################## +@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 2:N:0:NAAGGCGATAGATCGC +TCTCCTCAGTACGGGGGAGGAGGTTCGCTCGGCGGACGTGCGGCCCTACGCCAGACTCTACCACATGGTTCAGCAGGAGCTGGAGCACCGCGCTGTGTCCGGGGACTGGGAATACACCATCAGCCCCGGCGAGGAGTGGCAAGAGACGGAGCCTCTGCAACCAGCAGAGGTTGCCAAGCTGGACTATCACAGCTACGTCACCAGACGCTTCATGAAGGTCACCCAGTCTGACCCTGTGAACCAGGCCGGG ++ +A??A?BBBDDDDDDDDGGGGGGHEFHHGEHHHIHEHHHHHDHBEHGFFFEGGDEEDGGGGGEGGEECE?EGCEGEGGGCEEEGGCEEGG4D;;4AGGGGGG8>GGA?EGGGEEGEEGGGCGGEGEGGGGD8<AADECECEGG?CCC:8CC''8:C:?CCE*?)0CC0:*?:C:?CCC8?CCEC9*::CCCC?C*::.CEGGEC99C4')).00*:C:?*10:CC########################## +@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 2:N:0:NAAGGCGATAGATCGC +GCGTGGATTTGATTCGGTTTATGGGGCGCGGCCGCTGAGGCGGGTCATTCAGACGGAGATTGAGAATCCGCTAGCGGATAAGATTTTGCGGGGGGAGTTGGCGGAGGGCGATCGCTTGATGCTTGATTATGGAGGGGAGGGGGAGAAGATAGGTTTTACGAAAATAGAGGCGGAGGGGTCGGCGGCATAGAGGGTAATTTTTTGGGTTTTTTTCTGTGTCTTATACACAACTGAACGTGCCGACGAGCGG ++ +?????@?BDDDDDDDDFEEEFFHIIHEHHHHDHHHHHEHHHHHH8ADFFFDFFD1D;>1,;;;;3B,3B;;*:B;1;''0::0*1:A*:;>DD'4'8.::AA>D22>DA>''0..08?*:A*1?:*0?########################################################################################################################## +@MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 2:N:0:NAAGGCGATAGATCGC +GAGTTACTATTACAGAGTGGAGCTAATGTACTGGCAGTTGACTGCAAAAGAAATGCTCCAATTCATGTTGCATGTGCAAATATGAGCTTAGAGTGTTTAAAGATAATTTTGTGCCACAAAAAATGCAACCCAAACCAACAAAATGCAGTGGGAGACACTCCACTCCACACCTTATGCAGTTTGGGGACTTGTGATATGAGAATACTACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGAACAAG ++ +?????BBBDDDDDDDDGCFGFGIIIIIHFHIIIIHIHFG=EHHIGIIIIFHIHDGHGHHHIHIH=CGHGGHFHHHFHFGHHFH/ACDFGG?FE?CDFFHHHHHIIHFHHI>CEDGFHHHHHHHHDFHHFHHHFFAFFGGGGGGEDEG>>DACC;?EGG>CEEA>AEACCEE?:C::CC:::C:CE<C<9C:?C?*?CEECCC*:C?C?E:?:C:C:CCCCE:?C1*0*11.8C)2?'48>G######### +@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 2:N:0:NAAGGCGATAGATCGC +GTATTGCTGGCACCATCAGTCACCGTGTAGTGTATTCTATCGATTCCGTCACGCTGGCCCTTGAGCGTGCCCGAATCATACGTTATGGTGGTACCTGATACCGTGGCACTAGTGCCGTCGGTGTCTGCGCCATCCGTACGGTCGAACACCACCACGAGGGTATCGGCGTCCTGGTTTGCGTCGGGGATGCGGTCACCCTCTAAAAGATTTATGGAGGTCGTCTCTTGTGTCTGGGCCGGGGGGAAGATGT ++ +?????BBBDDDDDDDDGGGGGGIIHIIFHHHIHHIFHGHGGHHIHIIDEFFHEF@DFHIIHIIIGHACDCFFHHHIHIIHIHGHHHBGFGEEHHHHFHFFHHDFDCEGGFGGFGGG@DBEEEEGC>CEEGGGGGGE0?CDGGGD>EE2CE8CEGEE<>>>):CEEGDA'428CE:?9CC4828>'4<)0:>'04)1?E*8:1CC??):CCEECC**8)0548?C*:?:*010*:CC############## +@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 2:N:0:TAAGGCGATAGATCGC +GGCCAACACTGTGGTCACTATCTCTGGCACTGGTCTGCTACCACATGGAGTTGACACCGGAGACCCAATCACCACAGCAACAGTGTGGATTGACCACACCCCCTGCACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGTAGATCTCCGTGGGCGCCGCATCATTAAAAAAAAAAAAAAAAAACATAACTCTCAAACGCGAATAGAGCAAGAAACAGACAGCTAAAGTACAAACAAT ++ +55<?????DDDBBDDBFFFFFFCHHIIHHIIIIIIIHGHHIIIIHHGHIIHFHHIIIIHHHCDHIIIHFFHIIIIICFFHIHECGCGEHIH=FHHHHHHHHHHF;FFFFFDDFFFFFFFEFFFFEFEBDFAEEAEE@EEDD>DDD880:?#################################################################################################### +@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 2:N:0:TAAGGCGATAGATCGC +GAGGGGAGGAGGGGAAGGGAGAGGGGAAGAGAGGAGAGGAGAGGAGGAGGAGAGAAGGGGGAATGAGCAAGTAACATAATTACATAGCTGTGTCTGAATCTCTTTGAGCACCCTACCTCGGCATAGGAGGCTAGCTGGTGAGGGAGGGAGGGGCAGACTGACAGGCCGAGGATGGCCTTGTGGTTGGCAAACTCCGTGGGGCGAGTCTGGGCTGCTGCATGCGCATCTGAGACTGGCTCTTGTACACATC ++ +?????@9@B?B?BBBBEEEFB@@EEHEC?BF-CE@DDEH,5+5C,>@+CE+<?=E-CFECEHHDBD,?DFF,4DDDBF;=B;;BBD;D,B4=BEEEEECB,,BB;?C?CEEEE*;;C:AC?C;?CC:AEEE?E8ACE:0:A?AA8A4.??8?8248)8:ACEEE?E)4;?;?##############################################################################