Mercurial > repos > iuc > bbtools_bbnorm
changeset 0:1ef267476a17 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bbnorm.xml Tue May 30 09:02:11 2023 +0000 @@ -0,0 +1,392 @@ +<tool id="bbtools_bbnorm" name="BBTools: BBNorm" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>Normalise sequencing coverage</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="edam_ontology"/> + <expand macro="requirements"/> + <stdio> + <regex match="This table is (very|crazy|totally) full, which may reduce accuracy. Ideal load is under" source="stderr" level="fatal_oom" description="Too low memory - generated results might be inaccurate."/> + </stdio> + <command detect_errors="exit_code"><![CDATA[ +## bbtools recommends keeping a proper file extension to determine the input format +## so we hardcode them in the below block. +#if str($input_type_cond.input_type) == 'paired': + #set read1 = $input_type_cond.reads_collection['forward'] + #set read2 = $input_type_cond.reads_collection['reverse'] +#else: + #set read1 = $input_type_cond.read1 + #if str($input_type_cond.input_type) == 'PE_2files': + #set read2 = $input_type_cond.read2 + #end if +#end if + +#if $read1.ext.endswith('.gz'): + #set read1_file = 'forward.fastq.gz' +#else + #set read1_file = 'forward.fastq' +#end if +ln -s '${read1}' '${read1_file}' && + +#if $str($input_type_cond.input_type) in ['PE_2files', 'paired']: + #if $read2.ext.endswith('.gz'): + #set read2_file = 'reverse.fastq.gz' + #else + #set read2_file = 'reverse.fastq' + #end if + ln -s '${read2}' '${read2_file}' && +#end if + + +## As the program relies on a count-min-sketch algorithm, the potential hash collisions +## are ignored and translates to a decreased accuracy of the results. Therefore the allocated +## memory amount effects the numerical output: the more RAM the more accurate the results. +## Check if a memory cap was set. +if [[ "\${_JAVA_OPTIONS}" != *-Xmx* && "\${JAVA_TOOL_OPTIONS}" != *-Xmx* ]]; then + export _JAVA_OPTIONS="\${_JAVA_OPTIONS} -Xmx\${GALAXY_MEMORY_MB:-4096}m -Xms256m"; +fi && + +bbnorm.sh tmpdir="\$TMPDIR" t="\${GALAXY_SLOTS:-2}" + +#### Input parameters +#if str($input_type_cond.input_type) == 'single_end': + in='${read1_file}' + interleaved=f +#else: + #if str($input_type_cond.input_type) == 'PE_1file': + in='${read1_file}' + interleaved=t + #else: + in1='${read1_file}' + in2='${read2_file}' + interleaved=f + #end if +#end if + +#### Output options +out=normalised_R1.fastq +#if $str($input_type_cond.input_type) in ['PE_2files', 'paired']: + out2=normalised_R2.fastq +#end if +#if $output_options.save_discarded_reads: + outt=discarded.fastq +#end if +touppercase=t +#if $output_options.save_kmer_hists: + hist=kmer_hist_input.tabular + histout=kmer_hist_output.tabular +#end if + +#### Hashing parameters +k=$hashing_params.k +bits=$hashing_params.bits +hashes=$hashing_params.hashes +#if str($hashing_params.prefilter) == "true": + prefilter=t + prehashes=$hashing_params.prehashes + prefilterbits=$hashing_params.prefilterbits + prefiltersize=$hashing_params.prefiltersize +#end if +buildpasses=$hashing_params.buildpasses +minq=$hashing_params.minq +minprob=$hashing_params.minprob +rdk=$hashing_params.rdk + +### Normalization parameters +fixspikes=$norm_params.fixspikes +target=$target +maxdepth=$norm_params.maxdepth +mindepth=$norm_params.mindepth +minkmers=$norm_params.minkmers +percentile=$norm_params.percentile +uselowerdepth=$norm_params.uselowerdepth +deterministic=$norm_params.deterministic +passes=$norm_params.passes + +### Error detection parameters +hdp=$error_det_params.hdp +ldp=$error_det_params.ldp +tossbadreads=$error_det_params.tossbadreads +requirebothbad=$error_det_params.requirebothbad +errordetectratio=$error_det_params.errordetectratio +highthresh=$error_det_params.highthresh +lowthresh=$error_det_params.lowthresh + +### Error correction parameters +#if str($error_corr_params.ecc.ecc) == "true": + ecc=t + ecclimit=$error_corr_params.ecclimit + errorcorrectratio=$error_corr_params.errorcorrectratio + echighthresh=$error_corr_params.echighthresh + eclowthresh=$error_corr_params.eclowthresh + eccmaxqual=$error_corr_params.eccmaxqual + meo=$error_corr_params.meo + mue=$error_corr_params.mue + overlap=$error_corr_params.overlap +#end if +]]></command> + <inputs> + <conditional name="input_type_cond"> + <param name="input_type" type="select" label="Choose the category of inputs to be analyzed"> + <option value="single_end">Single-end reads</option> + <option value="PE_1file">Paired-end reads as a single, interleaved dataset</option> + <option value="PE_2files" selected="true">Paired-end reads as two separate datasets</option> + <option value="paired">Paired-end reads as a collection</option> + </param> + <when value="single_end"> + <param name="read1" type="data" format="fastqsanger,fastqsanger.gz" label="Single-end data"/> + </when> + <when value="PE_1file"> + <param name="read1" type="data" format="fastqsanger,fastqsanger.gz" label="Interleaved paired-end data"/> + </when> + <when value="PE_2files"> + <param name="read1" type="data" format="fastqsanger,fastqsanger.gz" label="Forward reads"/> + <param name="read2" type="data" format="fastqsanger,fastqsanger.gz" label="Reverse reads"/> + </when> + <when value="paired"> + <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of forward and reverse reads"/> + </when> + </conditional> + <param argument="target" type="integer" value="100" min="1" label="Target normalization depth" help="All depth parameters control kmer depth, not read depth. For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1))"/> + <section name="norm_params" title="Normalization parameters"> + <param argument="maxdepth" type="integer" value="-1" min="-1" label="Reads will not be downsampled when below this depth, even if they are above the target depth." help="All depth parameters control kmer depth, not read depth. For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1))"/> + <param argument="mindepth" type="integer" value="5" min="0" label="kmers with depth below this number will not be included when calculating the depth of a read." help="All depth parameters control kmer depth, not read depth. For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1))"/> + <param argument="minkmers" type="integer" value="15" min="0" label="Reads must have at least this many kmers over min depth to be retained."/> + <param argument="percentile" type="integer" value="54" min="1" max="100" label="Percentile to infer read depth" help="Read depth is by default inferred from the 54th percentile of kmer depth, but this may be changed to any number 1-100."/> + <param argument="uselowerdepth" type="boolean" checked="true" label="For pairs, use the depth of the lower read as the depth proxy."/> + <param argument="deterministic" type="boolean" checked="true" label="Generate random numbers deterministically" help="This would ensure identical output between multiple runs. May decrease speed with a huge number of threads."/> + <param argument="fixspikes" type="boolean" checked="false" label="Do a slower, high-precision bloom filter lookup of kmers that appear to have an abnormally high depth due to collisions."/> + <param argument="passes" type="integer" value="2" label="Number of passes to perform" help=" pass is the basic mode. 2 passes allows greater accuracy, error detection, better contol of output depth."/> + </section> + <section name="hashing_params" title="Hashing parameters"> + <param argument="k" type="integer" value="31" min="1" label="kmer length" help="Values under 32 are most efficient, but arbitrarily high values are supported."/> + <param argument="bits" type="select" label="Bits per cell in bloom filter" help="Maximum kmer depth recorded is 2^c bits. Large values decrease accuracy for a fixed amount of memory, so use the lowest number you can that will still capture highest-depth kmers."> + <option value="2">2</option> + <option value="4">4</option> + <option value="8">8</option> + <option value="16" selected="true">16</option> + <option value="32">32</option> + </param> + <param argument="hashes" type="integer" value="3" min="1" label="Number of times each kmer is hashed and stored." help="Higher is slower. Higher is more accurate if there is enough memory, but less accurate if there is not enough memory."/> + <conditional name="prefilter"> + <param argument="prefilter" type="select" label="Use a prefilter to eliminate low-depth kmers" help="True is slower, but generally more accurate; filters out low-depth kmers from the main hashtable. The prefilter is more memory-efficient because it uses 2-bit cells."> + <option value="true">Yes</option> + <option value="false" selected="true">No</option> + </param> + <when value="false"/> + <when value="true"> + <param argument="prehashes" type="integer" value="2" min="1" label="Number of hashes for the prefilter"/> + <param argument="prefilterbits" type="integer" value="2" min="1" label="Bits per cell in prefilter"/> + <param argument="prefiltersize" type="float" value="0.35" min="0" max="1" label="Fraction of memory to allocate for the prefilter."/> + </when> + </conditional> + <param argument="buildpasses" type="integer" value="1" min="1" label="Number of passes" help="More passes can sometimes increase accuracy by iteratively removing low-depth kmers"/> + <param argument="minq" type="integer" value="6" min="0" label="Ignore kmers containing bases with quality below this threshold"/> + <param argument="minprob" type="float" value="0.5" min="0" max="1" label="Ignore kmers with overall probability of correctness below this threshold"/> + <param argument="rdk" type="boolean" checked="true" label="Remove duplicate kmers" help="When true, a kmer's count will only be incremented once per read pair, even if that kmer occurs more than once."/> + </section> + <section name="error_det_params" title="Error detection parameters"> + <param argument="hdp" type="integer" value="90" min="0" max="100" label="highdepthpercentile" help="Position in sorted kmer depth array used as proxy of a read's high kmer depth."/> + <param argument="ldp" type="integer" value="25" min="0" max="100" label="lowdepthpercentile" help="Position in sorted kmer depth array used as proxy of a read's low kmer depth."/> + <param argument="tossbadreads" type="boolean" checked="false" label="Throw away reads detected as containing errors."/> + <param argument="requirebothbad" type="boolean" checked="false" label="Only toss bad pairs if both reads are bad."/> + <param argument="errordetectratio" type="integer" value="125" min="0" label="Error detection ratio" help="Reads with a ratio of at least this much between their high and low depth kmers will be classified as error reads."/> + <param argument="highthresh" type="integer" value="12" min="0" label="Threshold for high kmer" help="A high kmer at this or above are considered non-error."/> + <param argument="lowthresh" type="integer" value="3" min="0" label="Threshold for low kmer" help="Kmers at this and below are always considered errors."/> + </section> + + <section name="error_corr_params" title="Error correction parameters"> + <conditional name="ecc"> + <param argument="ecc" type="select" label="What should be done with detected errors?" help="Tadpole is now preferred for error correction, as it does a better job."> + <option value="true" >Correct errors when possible</option> + <option value="false" selected="true">Do not attempt to correct errors</option> + </param> + <when value="false"/> + <when value="true"> + <param argument="ecclimit" type="integer" value="3" min="1" label="Correct up to this many errors per read." help="If more are detected, the read will remain unchanged."/> + <param argument="errorcorrectratio" type="integer" value="140" min="0" label="Depth ratio" help="Adjacent kmers with a depth ratio of at least this much between will be classified as an error."/> + <param argument="echighthresh" type="integer" value="22" min="0" label="Threshold for high kmer" help="A kmer at this or above may be considered non-error."/> + <param argument="eclowthresh" type="integer" value="2" min="0" label="Threshold for low kmer." help="kmers at this depth or below will be considered as errors."/> + <param argument="eccmaxqual" type="integer" value="127" min="0" label="Do not correct bases with quality above this value."/> + <param argument="meo" type="boolean" checked="false" label="Marks errors by reducing quality value of suspected errors; does not correct anything."/> + <param argument="mue" type="boolean" checked="true" label="Mark errors only on uncorrectable reads."/> + <param argument="overlap" type="boolean" checked="false" label="Correct errors by read overlap."/> + </when> + </conditional> + </section> + + <section name="output_options" title="Output options"> + <param name="save_discarded_reads" type="boolean" checked="false" label="Save the reads that were eliminated from the input datasets to the history"/> + <param name="save_kmer_hists" type="boolean" checked="false" label="Save the kmer histograms (in tabular format) for the input and output datasets to the history"/> + </section> + </inputs> + <outputs> + <data name="output_normalised_R1" format_source="read1" from_work_dir="normalised_R1.fastq" label="${tool.name} on ${on_string} (normalised R1 reads)"> + <filter>input_type_cond['input_type'] != 'paired'</filter> + </data> + <data name="output_normalised_R2" format_source="read2" from_work_dir="normalised_R2.fastq" label="${tool.name} on ${on_string} (normalised R2 reads)"> + <filter>input_type_cond['input_type'] == 'PE_2files'</filter> + </data> + <collection name="output_pair" type="paired" format_source="reads_collection" label="${tool.name} on ${on_string} (normalised reads)"> + <filter>input_type_cond['input_type'] == 'paired'</filter> + <data name="forward" from_work_dir="normalised_R1.fastq" label="${tool.name} on ${on_string} (normalised R1 reads)"/> + <data name="reverse" from_work_dir="normalised_R2.fastq" label="${tool.name} on ${on_string} (normalised R2 reads)"/> + </collection> + <data name="output_discarded" format="fastqsanger" from_work_dir="discarded.fastq" label="${tool.name} on ${on_string} (discarded reads)"> + <filter>output_options['save_discarded_reads'] is True</filter> + </data> + <data name="kmer_hist_input" format="tabular" from_work_dir="kmer_hist_input.tabular" label="${tool.name} on ${on_string} (kmer histogram input)"> + <filter>output_options['save_kmer_hists'] is True</filter> + </data> + <data name="kmer_hist_output" format="tabular" from_work_dir="kmer_hist_output.tabular" label="${tool.name} on ${on_string} (kmer histogram output)"> + <filter>output_options['save_kmer_hists'] is True</filter> + </data> + </outputs> + <tests> + <!-- Single end sequencing --> + <test expect_num_outputs="1"> + <param name="input_type" value="single_end"/> + <param name="read1" ftype="fastqsanger" value="bbnorm/input_R1.fastq"/> + <param name="target" value="4"/> + <section name="norm_params"> + <param name="deterministic" value="true"/> + <param name="mindepth" value="0"/> + </section> + <output name="output_normalised_R1" ftype="fastqsanger" value="bbnorm/normalised_R1.fastq"/> + </test> + <!-- Single end sequencing, compressed --> + <test expect_num_outputs="1"> + <param name="input_type" value="single_end"/> + <param name="read1" ftype="fastqsanger.gz" value="bbnorm/input_R1.fastq.gz"/> + <param name="target" value="4"/> + <section name="norm_params"> + <param name="deterministic" value="true"/> + <param name="mindepth" value="0"/> + </section> + <output name="output_normalised_R1" ftype="fastqsanger.gz" value="bbnorm/normalised_R1.fastq"/> + </test> + <!-- PE as an interleaved file --> + <test expect_num_outputs="4"> + <param name="input_type" value="PE_1file"/> + <param name="read1" ftype="fastqsanger" value="bbnorm/input_interleaved.fastq"/> + <param name="target" value="4"/> + <section name="norm_params"> + <param name="deterministic" value="true"/> + <param name="mindepth" value="0"/> + </section> + <section name="output_options"> + <param name="save_discarded_reads" value="true"/> + <param name="save_kmer_hists" value="true"/> + </section> + <output name="output_normalised_R1" ftype="fastqsanger" value="bbnorm/normalised_interleaved.fastq"/> + <output name="output_discarded" ftype="fastqsanger" value="bbnorm/discarded.fastq"/> + <output name="kmer_hist_input" ftype="tabular" file="bbnorm/kmer_hist_input.tabular"/> + <output name="kmer_hist_output" ftype="tabular" file="bbnorm/kmer_hist_output.tabular"/> + </test> + <!-- PE as 2 files --> + <test expect_num_outputs="2"> + <param name="input_type" value="PE_2files"/> + <param name="read1" ftype="fastqsanger" value="bbnorm/input_R1.fastq"/> + <param name="read2" ftype="fastqsanger" value="bbnorm/input_R2.fastq"/> + <param name="target" value="4"/> + <section name="norm_params"> + <param name="deterministic" value="true"/> + <param name="mindepth" value="0"/> + </section> + <output name="output_normalised_R1" ftype="fastqsanger" value="bbnorm/normalised_R1.fastq"/> + <output name="output_normalised_R2" ftype="fastqsanger" value="bbnorm/normalised_R2.fastq"/> + </test> + <!-- Paired end collection --> + <test expect_num_outputs="3"> + <param name="input_type" value="paired"/> + <param name="reads_collection"> + <collection type="paired"> + <element name="forward" ftype="fastqsanger" value="bbnorm/input_R1.fastq"/> + <element name="reverse" ftype="fastqsanger" value="bbnorm/input_R2.fastq"/> + </collection> + </param> + <param name="target" value="4"/> + <section name="norm_params"> + <param name="deterministic" value="true"/> + <param name="mindepth" value="0"/> + </section> + <output_collection name="output_pair" type="paired" count="2"> + <element name="forward" ftype="fastqsanger" value="bbnorm/normalised_R1.fastq"/> + <element name="reverse" ftype="fastqsanger" value="bbnorm/normalised_R2.fastq"/> + </output_collection> + </test> + </tests> + <help> +**What it does** + +BBNorm downsamples a provided sequencing output, while paying attention to potential heteregeneities in sequencing depth obtained from the wet-lab workflow. The reads corresponding to regions with low coverage will be kept as is, whereas some of the reads contributing to an above-threshold coverage depth will be subsampled. The resulting data set is expected to be smaller in size, whereas the genome regions with low coverage levels will still be represented in the subsampled dataset. This provides a more uniform coverage depth against all genomic coordinates while the computational resources needed for subsequent steps such as assembly can be substantially reduced without losing coverage anywhere. + +----- + +**If the target sequencing depth is 2X, a Martian genome sequencing result is expected to be down-sampled as follows:** + +input.fastq:: + + @read_header_1 + AAAAATTTTTCCCCCGGGGGAAATTT + + + FFFFFFFFFFFFFFFEFFFFFF,FFE + @read_header_2 + TTTTTCCCCCGGGGGAAATTTCCCGGG + + + FFFFFFFFFFFFFFFEFFFFFFEFFDD + @read_header_3 + TTTTTCCCCCGGGGGAAATTTCCCGGG + + + FFFFFFFFFFFCEFFEFFFFFFEFFEE + @read_header_4 + TTTTTCCCCCGGGGGAAATTTCCCGGG + + + FFFFFDDFFFFFFFFEFFFFFFEFFEF + @read_header_5 + TTTTTCCCCCGGGGGAAATTTCCCGGG + + + FFFFFEFFFFEEFFFEFFFFFFDFFFF + @read_header_6 + AAAAATTTTTCCCCCGGGGGAAATTT + + + FFFFFFFFFFFFFFFEFFFFFFEFFD + + +output.fastq:: + + @read_header_1 + AAAAATTTTTCCCCCGGGGGAAATTT + + + FFFFFFFFFFFFFFFEFFFFFF,FFE + @read_header_2 + TTTTTCCCCCGGGGGAAATTTCCCGGG + + + FFFFFFFFFFFFFFFEFFFFFFEFFDD + @read_header_3 + TTTTTCCCCCGGGGGAAATTTCCCGGG + + + FFFFFFFFFFFCEFFEFFFFFFEFFEE + @read_header_6 + AAAAATTTTTCCCCCGGGGGAAATTT + + + FFFFFFFFFFFFFFFEFFFFFFEFFD + + +**Indications** + +BBNorm is mainly intended for use in assembly pipelines out of short reads. It might be useful when there is too much data that increases computation time or a highly skewed coverage distribution by subsampling from the existing data. As opposed to keeping a randomly selected subset of reads, such as retaining the first n-many elements, this is a weighted resampling that tries to reduce coverage around coordinates of very high sequencing depth. + + +**Contraindications** + +* The data already has a roughly uniform coverage that does not need to be normalised further. +* You do not have any excess data to discard: BBnorm does not increase data quantity by imputation or by repeatedly sampling with replacement. +* Your pipeline reports results that rely on quantification of abundance (ex: differential expression profiling or ChIP-Seq) +* You want to do variant discovery. Reduction of sequencing depth might bias significance levels, or even obscure the existence of rare variants altogether. +* The sequencing platform has a very high error rate (ex: ONT) that might mislead this algorithm. + + </help> + <expand macro="citations"/> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue May 30 09:02:11 2023 +0000 @@ -0,0 +1,107 @@ +<macros> + <token name="@TOOL_VERSION@">39.01</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">22.01</token> + <xml name="edam_ontology"> + <edam_topics> + <edam_topic>topic_0622</edam_topic> <!-- Genomics --> + <edam_topic>topic_0091</edam_topic> <!-- Bioinformatics --> + </edam_topics> + <edam_operations> + <edam_operation>operation_0496</edam_operation> <!-- Global alignment --> + <edam_operation>operation_0491</edam_operation> <!-- Pairwise sequence alignment --> + </edam_operations> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">bbmap</requirement> + <requirement type="package" version="1.16.1">samtools</requirement> <!-- automatic solving installs 1.6 in some cases, instead --> + </requirements> + </xml> + <macro name="dbKeyActionsBBMap"> + <expand macro="dbKeyActions"> + <option type="from_data_table" name="fasta_indexes" column="1" offset="0"> + <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> + <filter type="param_value" ref="ref_source_cond.reference" column="1"/> + </option> + </expand> + </macro> + <macro name="dbKeyActions"> + <actions> + <conditional name="ref_source_cond.ref_source"> + <when value="cached"> + <action type="metadata" name="dbkey"> + <yield/> + </action> + </when> + <when value="history"> + <action type="metadata" name="dbkey"> + <option type="from_param" name="ref_source_cond.reference" param_attribute="dbkey"/> + </action> + </when> + </conditional> + </actions> + </macro> + <macro name="input_type_cond"> + <conditional name="input_type_cond"> + <param name="input_type" type="select" label="Choose the category of the files to be analyzed"> + <option value="single" selected="true">Single dataset</option> + <option value="pair">Dataset pair</option> + <option value="paired">List of dataset pairs</option> + </param> + <when value="single"> + <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Fastq file"/> + </when> + <when value="pair"> + <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Forward reads fastq file"/> + <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Reverse reads fastq file"/> + </when> + <when value="paired"> + <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of fastqsanger paired read files"/> + </when> + </conditional> + </macro> + <macro name="reference_source_cond"> + <conditional name="ref_source_cond"> + <param name="ref_source" type="select" label="Select reference genome source; a cached reference or one from the history"> + <option value="cached" selected="True">Use a cached reference</option> + <option value="history">Use a reference from the history</option> + </param> + <when value="cached"> + <param name="reference" type="select" label="Using reference genome"> + <options from_data_table="fasta_indexes"> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="A built-in reference genome is not available"/> + </options> + </param> + </when> + <when value="history"> + <param name="reference" type="data" format="fasta" label="Using reference genome"/> + </when> + </conditional> + </macro> + <macro name="ktrim_cond"> + <conditional name="ktrim_cond"> + <param name="ktrim_select" type="select" label="Trim reads to remove bases matching reference kmers?"> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param argument="ktrim" type="select" label="Select trimming position"> + <option value="r">Trim to the right</option> + <option value="l">Trim to the left</option> + </param> + <param argument="minlength" type="integer" value="10" label="Minimum read length" help="Trimmed reads shorter than this will be discarded, pairs will be discarded if both are shorter."/> + </when> + </conditional> + </macro> + <xml name="citations"> + <citations> + <citation type="doi"> + https://doi.org/10.1371/journal.pone.0185056 + </citation> + </citations> + </xml> +</macros> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Tue May 30 09:02:11 2023 +0000 @@ -0,0 +1,18 @@ + +================= +IMPORTANT NOTE REGARDING SYSTEM CONFIGURATION +================= + +All of the Galaxy wrappers contained herein call the respective bbtools' shell wrapper, which calls the underlying java-based tool. Unlike a C-based program, java will grab a pre-determined amount of memory at the very beginning of the execution. + +Some of the algorithms (e.g. bbnorm) utilise a hash table, and potential collusions can decrease the numeric accuracy of the output. This problem is expected to become more pronounced if the fraction of the memory occupied w.r.t. allocated memory becomes high, i.e. when the available memory is low and/or the input file is big. If the tool generates a warning to stderr, and will be caught by the Galaxy wrapper resulting in a failed job. However, `count min sketch <https://en.wikipedia.org/wiki/Count%E2%80%93min_sketch>` does not run out of memory, this is a gradual effect, and will NOT trigger a fatal error unless the load reaches this critically high level. You can read more about the implications of this at the `BBtools manual <https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbnorm-guide/>` + +If you are administering a heteregenous computing environment with multiple nodes of very different quantities of physically available RAM, it is recommended to define a global cap on the RAM to be used to avoid introducing run-to-run bias by exporting an environmental variable, by something like: +export _JAVA_OPTIONS="-Xmx2048m -Xms256m" + +The tool currently considers the following limits, in the given priority order: +1) _JAVA_OPTIONS +2) JAVA_TOOL_OPTIONS +3) GALAXY_MEMORY_MB +4) 4 GB +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_002945v4.fasta Tue May 30 09:02:11 2023 +0000 @@ -0,0 +1,101 @@ +>NC_002945.4 Mycobacterium bovis AF2122/97 genome assembly, chromosome: Mycobacterium_bovis_AF2122/97 +TTGACCGATGACCCCGGTTCAGGCTTCACCACAGTGTGGAACGCGGTCGTCTCCGAACTTAACGGCGACC +CTAAGGTTGACGACGGACCCAGCAGTGATGCTAATCTCAGCGCTCCGCTGACCCCTCAGCAAAGGGCTTG +GCTCAATCTCGTCCAGCCATTGACCATCGTCGAGGGGTTTGCTCTGTTATCCGTGCCGAGCAGCTTTGTC +CAAAACGAAATCGAGCGCCATCTGCGGGCCCCGATTACCGACGCTCTCAGCCGCCGACTCGGACATCAGA +TCCAACTCGGGGTCCGCATCGCTCCGCCGGCGACCGACGAAGCCGACGACACTACCGTGCCGCCTTCCGA +AAATCCTGCTACCACATCGCCAGACACCACAACCGACAACGACGAGATTGATGACAGCGCTGCGGCACGG +GGCGATAACCAGCACAGTTGGCCAAGTTACTTCACCGAGCGCCCGCGCAATACCGATTCCGCTACCGCTG +GCGTAACCAGCCTTAACCGTCGCTACACCTTTGATACGTTCGTTATCGGCGCCTCCAACCGGTTCGCGCA +CGCCGCCGCCTTGGCGATCGCAGAAGCACCCGCCCGCGCTTACAACCCCCTGTTCATCTGGGGCGAGTCC +GGTCTCGGCAAGACACACCTGCTACACGCGGCAGGCAACTATGCCCAACGGTTGTTCCCGGGAATGCGGG +TCAAATATGTCTCCACCGAGGAATTCACCAACGACTTCATTAACTCGCTCCGCGATGACCGCAAGGTCGC +ATTCAAACGCAGCTACCGCGACGTAGACGTGCTGTTGGTCGACGACATCCAATTCATTGAAGGCAAAGAG +GGTATTCAAGAGGAGTTCTTCCACACCTTCAACACCTTGCACAATGCCAACAAGCAAATCGTCATCTCAT +CTGACCGCCCACCCAAGCAGCTCGCCACCCTCGAGGACCGGCTGAGAACCCGCTTTGAGTGGGGGCTGAT +CACTGACGTACAACCACCCGAGCTGGAGACCCGCATCGCCATCTTGCGCAAGAAAGCACAGATGGAACGG +CTCGCGATCCCCGACGATGTCCTCGAACTCATCGCCAGCAGTATCGAACGCAATATCCGTGAACTCGAGG +GCGCGCTGATCCGGGTCACCGCGTTCGCCTCATTGAACAAAACACCAATCGACAAAGCGCTGGCCGAGAT +TGTGCTTCGCGATCTGATCGCCGACGCCAACACCATGCAAATCAGCGCGGCGACGATCATGGCTGCCACC +GCCGAATACTTCGACACTACCGTCGAAGAGCTTCGCGGGCCCGGCAAGACCCGAGCACTGGCCCAGTCAC +GACAGATTGCGATGTACCTGTGTCGTGAGCTCACCGATCTTTCGTTGCCCAAAATCGGCCAAGCGTTCGG +CCGTGATCACACAACCGTCATGTACGCCCAACGCAAGATCCTGTCCGAGATGGCCGAGCGCCGTGAGGTC +TTTGATCACGTCAAAGAACTCACCACTCGCATCCGTCAGCGCTCCAAGCGCTAGCACGGCGTGTTCTTCC +GACAACGTTCTTAAAAAAACTTCTCTCTCCCAGGTCACACCAGTCACAGAGATTGGCTGTGAGTGTCGCT +GTGCACAAACCGCGCACAGACTCATACAGTCCCGGCGGTTCCGTTCACAACCCACGCCTCATCCCCACCG +ACCCAACACACACCCCACAGTCATCGCCACCGTCATCCACAACTCCGACCGACGTCGACCTGCACCAAGA +CCAGACTGTCCCCAAACTGCACACCCTCTAATACTGTTACCGAGATTTCTTCGTCGTTTGTTCTTGGAAA +GACAGCGCTGGGGATCGTTCGCTGGATACCACCCGCATAACTGGCTCGTCGCGGTGGGTCAGAGGTCAAT +GATGAACTTTCAAGTTGACGTGAGAAGCTCTACGGTTGTTGTTCGACTGCTGTTGCGGCCGTCGTGGCGG +GTCACGCGTCATGGGCGTTCGTCGTTGGCAGTCCCCACGCTAGCGGGGCGCTAGCCACGGGATCGAACTC +ATCGTGAGGTGAAAGGGCGCAATGGACGCGGCTACGACAAGAGTTGGCCTCACCGACTTGACGTTTCGTT +TGCTACGAGAGTCTTTCGCCGATGCGGTGTCGTGGGTGGCTAAAAATCTGCCAGCCAGGCCCGCGGTGCC +GGTGCTCTCCGGCGTGTTGTTGACCGGCTCGGACAACGGTCTGACGATTTCCGGATTCGACTACGAGGTT +TCCGCCGAGGCCCAGGTTGGCGCTGAAATTGTTTCTCCTGGAAGCGTTTTAGTTTCTGGCCGATTGTTGT +CCGATATTACCCGGGCGTTGCCTAACAAGCCCGTAGGCGTTCATGTCGAAGGTAACCGGGTCGCATTGAC +CTGCGGTAACGCCAGGTTTTCGCTACCGACGATGCCAGTCGAGGATTATCCGACGCTGCCGACGCTGCCG +GAAGAGACCGGATTGTTGCCTGCGGAATTATTCGCCGAGGCAATCAGTCAGGTCGCTATCGCCGCCGGCC +GGGACGACACGCTGCCTATGTTGACCGGCATCCGGGTCGAAATCCTCGGTGAGACGGTGGTTTTGGCCGC +TACCGACAGGTTTCGCCTGGCTGTTCGAGAACTGAAGTGGTCGGCGTCGTCGCCAGATATCGAAGCGGCT +GTGCTGGTCCCGGCCAAGACGCTGGCCGAGGCCGCCAAAGCGGGCATCGGCGGCTCTGACGTTCGTTTGT +CGTTGGGTACTGGGCCGGGGGTGGGCAAGGATGGCCTGCTCGGTATCAGTGGGAACGGCAAGCGCAGCAC +CACGCGACTTCTTGATGCCGAGTTCCCGAAGTTTCGGCAGTTGCTACCAACCGAACACACCGCGGTGGCC +ACCATGGACGTGGCCGAGTTGATCGAAGCGATCAAGCTGGTTGCGTTGGTAGCTGATCGGGGCGCGCAGG +TGCGCATGGAGTTCGCTGATGGCAGCGTGCGGCTTTCTGCGGGTGCCGATGATGTTGGACGAGCCGAGGA +AGATCTTGTTGTTGACTATGCCGGTGAACCATTGACGATTGCGTTTAACCCAACCTATCTAACGGACGGT +TTGAGTTCGTTGCGCTCGGAGCGAGTGTCTTTCGGGTTTACGACTGCGGGTAAGCCTGCCTTGCTACGTC +CGGTGTCCGGGGACGATCGCCCTGTGGCGGGTCTGAATGGCAACGGTCCGTTCCCGGCGGTGTCGACGGA +CTATGTCTATCTGTTGATGCCGGTTCGGTTGCCGGGCTGAGCACTTGGCGCCCGGGTAGGTGTACGTCCG +TCATTTGGGGCTGCGTGACTTCCGGTCCTGGGCATGTGTAGATCTGGAATTGCATCCAGGGCGGACGGTT +TTTGTTGGGCCTAACGGTTATGGTAAGACGAATCTTATTGAGGCACTGTGGTATTCGACGACGTTAGGTT +CGCACCGCGTTAGCGCCGATTTGCCGTTGATCCGGGTAGGTACCGATCGTGCGGTGATCTCCACGATCGT +GGTGAACGACGGTAGAGAATGTGCCGTCGACCTCGAGATCGCCACGGGGCGAGTCAACAAAGCGCGATTG +AATCGATCATCGGTCCGAAGTACACGTGATGTGGTCGGAGTGCTTCGAGCTGTGTTGTTTGCCCCTGAGG +ATCTGGGGTTGGTTCGTGGGGATCCCGCTGACCGGCGGCGCTATCTGGATGATCTGGCGATCGTGCGTAG +GCCTGCGATCGCTGCGGTACGAGCCGAATATGAGAGGGTGGTGCGCCAGCGGACGGCGTTATTGAAGTCC +GTACCTGGAGCACGGTATCGGGGTGACCGGGGTGTGTTTGACACTCTTGAGGTATGGGACAGTCGTTTGG +CGGAGCACGGGGCTGAACTGGTGGCCGCCCGCATCGATTTGGTCAACCAGTTGGCACCGGAAGTGAAGAA +GGCATACCAGCTGTTGGCGCCGGAATCGCGATCGGCGTCTATCGGTTATCGGGCCAGCATGGATGTAACC +GGTCCCAGCGAGCAGTCAGATACCGATCGGCAATTGTTAGCAGCTCGGCTGTTGGCGGCGCTGGCGGCCC +GTCGGGATGCCGAACTCGAGCGTGGGGTTTGTCTAGTTGGTCCGCACCGTGACGACCTAATACTGCGACT +AGGCGATCAACCCGCGAAAGGATTTGCTAGCCATGGGGAGGCGTGGTCGTTGGCGGTGGCACTGCGGTTG +GCGGCCTATCAACTGTTACGCGTTGATGGTGGTGAGCCGGTGTTGTTGCTCGACGACGTGTTCGCCGAAC +TGGATGTCATGCGCCGTCGAGCGTTGGCGACGGCGGCCGAGTCCGCCGAACAGGTGTTGGTGACTGCCGC +GGTGCTCGAGGATATTCCCGCCGGCTGGGACGCCAGGCGGGTGCACATCGATGTGCGTGCCGATGACACC +GGATCGATGTCGGTGGTTCTGCCATGACGGGTTCTGTTGACCGGCCCGACCAGAATCGCGGTGAGCGATT +AATGAAGTCACCAGGGTTGGATTTGGTCAGGCGCACCCTGGACGAAGCTCGTGCTGCTGCCCGCGCGCGC +GGACAAGACGCCGGTCGAGGGCGGGTCGCTTCCGTTGCGTCGGGTCGGGTGGCCGGACGGCGACGAAGCT +GGTCGGGTCCGGGGCCCGACATTCGTGATCCACAACCGCTGGGTAAGGCCGCTCGTGAGCTGGCAAAGAA +ACGCGGCTGGTCGGTGCGGGTCGCCGAGGGTATGGTGCTCGGCCAGTGGTCTGCGGTGGTCGGCCACCAG +ATCGCCGAACATGCACGCCCGACTGCGCTAAACGACGGGGTGTTGAGCGTGATTGCGGAGTCGACGGCGT +GGGCGACGCAGTTGAGGATCATGCAGGCCCAGCTTCTGGCCAAGATCGCCGCAGCGGTTGGCAACGATGT +GGTGCGATCGCTAAAGATCACCGGGCCGGCGGCACCATCGTGGCGCAAGGGGCCTCGCCATATTGCCGGT +AGGGGTCCGCGCGACACCTACGGATAACACGTCGATCGGCCCAGAACAAGGCGCTCCGGTCCCGGCCTGA +GAGCCTCGAGGACGAAGCGGATCCGTATGCCGGACGTCGGGACGCACCAGGAAGAAAGATGTCCGACGCA +CGGCGCGGTTAGATGGGTAAAAACGAGGCCAGAAGATCGGCCCTGGCGCCCGATCACGGTACAGTGGTGT +GCGACCCCCTGCGGCGACTCAACCGCATGCACGCAACCCCTGAGGAGAGTATTCGGATCGTGGCTGCCCA +GAAAAAGAAGGCCCAAGACGAATACGGCGCTGCGTCTATCACCATTCTCGAAGGGCTGGAGGCCGTCCGC +AAACGTCCCGGCATGTACATTGGCTCGACCGGTGAGCGCGGTTTACACCATCTCATTTGGGAGGTGGTCG +ACAACGCGGTCGACGAGGCGATGGCCGGTTATGCAACCACAGTGAACGTAGTGCTGCTTGAGGATGGCGG +TGTCGAGGTCGCCGACGACGGCCGCGGCATTCCGGTCGCCACCCACGCCTCCGGCATACCGACCGTCGAC +GTGGTGATGACACAACTACATGCCGGCGGCAAGTTCGACTCGGACGCGTATGCGATATCTGGTGGTCTGC +ACGGCGTCGGCGTGTCGGTGGTTAACGCGCTATCCACCCGGCTCGAAGTCGAGATCAAGCGCGACGGGTA +CGAGTGGTCTCAGGTTTATGAGAAGTCGGAACCCCTGGGCCTCAAGCAAGGGGCGCCGACCAAGAAGACG +GGGTCAACGGTACGGTTCTGGGCCGACCCCGCTGTTTTCGAAACCACGGAATACGACTTCGAAACCGTCG +CCCGCCGGCTGCAAGAGATGGCGTTCCTCAACAAGGGGCTGACCATCAACCTGACCGACGAGAGGGTGAC +CCAAGACGAGGTCGTCGACGAAGTGGTCAGCGACGTCGCCGAGGCGCCGAAGTCGGCAAGTGAACGCGCA +GCCGAATCCACTGCACCGCACAAAGTTAAGAGCCGCACCTTTCACTATCCGGGTGGCCTGGTGGACTTCG +TGAAACACATCAACCGCACCAAGAACGCGATTCATAGCAGCATCGTGGACTTTTCCGGCAAGGGCACCGG +GCACGAGGTGGAGATCGCGATGCAATGGAACGCCGGGTATTCGGAGTCGGTGCACACCTTCGCCAACACC +ATCAACACCCACGAGGGCGGCACCCACGAAGAGGGCTTCCGCAGCGCGCTGACGTCGGTGGTGAACAAGT +ACGCCAAGGACCGCAAGCTACTGAAGGACAAGGACCCCAACCTCACCGGTGACGATATCCGGGAAGGCCT +GGCCGCTGTGATCTCGGTGAAGGTCAGCGAACCGCAGTTCGAGGGCCAGACCAAGACCAAGTTGGGCAAC +ACCGAGGTCAAATCGTTTGTGCAGAAGGTCTGTAATGAACAGCTGACCCACTGGTTTGAAGCCAACCCCA +CCGACTCGAAAGTCGTTGTGAACAAGGCTGTGTCCTCGGCGCAAGCCCGTATCGCGGCACGTAAGGCACG +AGAGTTGGTGCGGCGTAAGAGCGCCACCGACATCGGTGGATTGCCCGGCAAGCTGGCCGATTGCCGTTCC +ACGGATCCGCGCAAGTCCGAACTGTATGTCGTAGAAGGTGACTCGGCCGGCGGTTCTGCAAAAAGCGGTC +GCGATTCGATGTTCCAGGCGATACTTCCGCTGCGCGGCAAGATCATCAATGTGGAGAAAGCGCGCATCGA +CCGGGTGCTAAAGAACACCGAAGTTCAGGCGATCATCACGGCGCTGGGCACCGGGATCCACGACGAGTTC +GATATCGGCAAGCTGCGCTACCACAAGATCGTGCTGATGGCCGACGCCGATGTTGACGGCCAACATATTT +CCACGCTGTTGTTGACGTTGTTGTTCCGGTTCATGCGGCCGCTCATCGAGAACGGGCATGTGTTTTTGGC +ACAACCGCCGCTGTACAAACTCAAGTGGCAGCGCAGTGACCCGGAATTCGCATACTCCGACCGCGAGCGC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bbmerge/input_R1.fastq Tue May 30 09:02:11 2023 +0000 @@ -0,0 +1,40 @@ +@A00604:500:HKMVNDSX3:2:1101:8196:1000 1:N:0:ATCGTCTC+NTAACCGA +NATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGTGGAATCGCAGCCGAACCTGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:20419:1000 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF,,,F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:20853:1000 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGGCCGCGGACATCTCGGTGGGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFF:FF,FFFFFFFFFFFFFFFFF:FFFFFF:FF:FFFFF +@A00604:500:HKMVNDSX3:2:1101:20943:1000 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGTAAGTCATGGAGATTGTGTCTATATAAAAAGTGGTAGTGAAATCTGCATTATAAGATGACACTATCTCAAAGTGTATATCAATGAAGAGGATTGGTCATCCAGAAGTAGCACTGGAA ++ +FFFFFFFFFFFFFFFFFFFF:FFFFFF:FFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:29460:1000 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGTCGATTCGGCCGCAGACGGGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FF,FFFFFFFFFFFFF:FFFFFFFFFF:FFFFFF:FFFFFFFF:FFFFFFFFF,FFFFFFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:12979:1016 1:N:0:ATCGTCTC+NTAACCGA +ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACTGCGCACTGCAGGTGCCATCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:17517:1016 1:N:0:ATCGTCTC+NTAACCGA +ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGATGAAACTATGGGACCCTCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF,FF:FFFFFFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:25310:1016 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCAAAGCCCCGGTAGGGCCGGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFF:FFFFFF:FFFFFFF:FFFF:F:FF:FFFFF::FFFFFFFF::FFF:FFF:FFFFFFFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:7346:1031 1:N:0:ATCGTCTC+GTAACCGA +ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGGACTCGCCCACCTATGTCCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFFFFF:FF +@A00604:500:HKMVNDSX3:2:1101:8919:1031 1:N:0:ATCGTCTC+GTAACCGA +GATCTCATTCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCTCACCGGTTCTGCAGTAAGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAA ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:F
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bbmerge/input_R2.fastq Tue May 30 09:02:11 2023 +0000 @@ -0,0 +1,40 @@ +@A00604:500:HKMVNDSX3:2:1101:8196:1000 2:N:0:ATCGTCTC+NTAACCGA +ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACAGGTTCGGCTGCGATTCCACGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF +@A00604:500:HKMVNDSX3:2:1101:20419:1000 2:N:0:ATCGTCTC+NTAACCGA +ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:20853:1000 2:N:0:ATCGTCTC+NTAACCGA +ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACCCACCGAGATGTCCGCGGCCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF,FFFFFFFFFFFFFFFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:20943:1000 2:N:0:ATCGTCTC+NTAACCGA +ACTCGGTGCCACTTTTTCAACCAAGAGGGGCTAAAAATTTTCAAAGGTTACCTATATGATCAGATAAGTTCTGTTGGAAAGAAAATCAATTGATATGACATTGTCAGTCAACTGACATGGATTTTCTCATGACCTAACATGATATATTAAC ++ +FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:29460:1000 2:N:0:ATCGTCTC+NTAACCGA +ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACCCGTCTGCGGCCGAATCGACGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFF:FFFFFFFFFFFFFFF:F:FFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:12979:1016 2:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGATGGCACCTGCAGTGCGCAGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:17517:1016 2:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGAGGGTCCCATAGTTTCATCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:25310:1016 2:N:0:ATCGTCTC+NTAACCGA +ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACCGGCCCTACCGGGGCTTTGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF +@A00604:500:HKMVNDSX3:2:1101:7346:1031 2:N:0:ATCGTCTC+GTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGGACATAGGTGGGCGAGTCCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFF:FFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFF:FFF +@A00604:500:HKMVNDSX3:2:1101:8919:1031 2:N:0:ATCGTCTC+GTAACCGA +ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACTTACTGCAGAACCGGTGAGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FFFFF
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bbmerge/input_interleaved.fastq Tue May 30 09:02:11 2023 +0000 @@ -0,0 +1,80 @@ +@A00604:500:HKMVNDSX3:2:1101:8196:1000 1:N:0:ATCGTCTC+NTAACCGA +NATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGTGGAATCGCAGCCGAACCTGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:8196:1000 2:N:0:ATCGTCTC+NTAACCGA +ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACAGGTTCGGCTGCGATTCCACGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF +@A00604:500:HKMVNDSX3:2:1101:20419:1000 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF,,,F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:20419:1000 2:N:0:ATCGTCTC+NTAACCGA +ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:20853:1000 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGGCCGCGGACATCTCGGTGGGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFF:FF,FFFFFFFFFFFFFFFFF:FFFFFF:FF:FFFFF +@A00604:500:HKMVNDSX3:2:1101:20853:1000 2:N:0:ATCGTCTC+NTAACCGA +ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACCCACCGAGATGTCCGCGGCCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF,FFFFFFFFFFFFFFFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:20943:1000 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGTAAGTCATGGAGATTGTGTCTATATAAAAAGTGGTAGTGAAATCTGCATTATAAGATGACACTATCTCAAAGTGTATATCAATGAAGAGGATTGGTCATCCAGAAGTAGCACTGGAA ++ +FFFFFFFFFFFFFFFFFFFF:FFFFFF:FFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:20943:1000 2:N:0:ATCGTCTC+NTAACCGA +ACTCGGTGCCACTTTTTCAACCAAGAGGGGCTAAAAATTTTCAAAGGTTACCTATATGATCAGATAAGTTCTGTTGGAAAGAAAATCAATTGATATGACATTGTCAGTCAACTGACATGGATTTTCTCATGACCTAACATGATATATTAAC ++ +FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:29460:1000 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGTCGATTCGGCCGCAGACGGGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FF,FFFFFFFFFFFFF:FFFFFFFFFF:FFFFFF:FFFFFFFF:FFFFFFFFF,FFFFFFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:29460:1000 2:N:0:ATCGTCTC+NTAACCGA +ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACCCGTCTGCGGCCGAATCGACGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFF:FFFFFFFFFFFFFFF:F:FFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:12979:1016 1:N:0:ATCGTCTC+NTAACCGA +ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACTGCGCACTGCAGGTGCCATCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:12979:1016 2:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGATGGCACCTGCAGTGCGCAGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:17517:1016 1:N:0:ATCGTCTC+NTAACCGA +ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGATGAAACTATGGGACCCTCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF,FF:FFFFFFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:17517:1016 2:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGAGGGTCCCATAGTTTCATCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:25310:1016 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCAAAGCCCCGGTAGGGCCGGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFF:FFFFFF:FFFFFFF:FFFF:F:FF:FFFFF::FFFFFFFF::FFF:FFF:FFFFFFFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:25310:1016 2:N:0:ATCGTCTC+NTAACCGA +ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACCGGCCCTACCGGGGCTTTGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF +@A00604:500:HKMVNDSX3:2:1101:7346:1031 1:N:0:ATCGTCTC+GTAACCGA +ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGGACTCGCCCACCTATGTCCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFFFFF:FF +@A00604:500:HKMVNDSX3:2:1101:7346:1031 2:N:0:ATCGTCTC+GTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGGACATAGGTGGGCGAGTCCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFF:FFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFF:FFF +@A00604:500:HKMVNDSX3:2:1101:8919:1031 1:N:0:ATCGTCTC+GTAACCGA +GATCTCATTCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCTCACCGGTTCTGCAGTAAGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAA ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:F +@A00604:500:HKMVNDSX3:2:1101:8919:1031 2:N:0:ATCGTCTC+GTAACCGA +ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACTTACTGCAGAACCGGTGAGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTT ++ +FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FFFFF
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bbmerge/insert_length_hist.tabular Tue May 30 09:02:11 2023 +0000 @@ -0,0 +1,8 @@ +#Mean 165.889 +#Median 166 +#Mode 166 +#STDev 0.314 +#PercentOfPairs 90.000 +#InsertSize Count +165 1 +166 8
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bbmerge/merged.fastq Tue May 30 09:02:11 2023 +0000 @@ -0,0 +1,36 @@ +@A00604:500:HKMVNDSX3:2:1101:8196:1000 1:N:0:ATCGTCTC+NTAACCGA +NATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGTGGAATCGCAGCCGAACCTGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGT ++ +!FFFFFFFFFFFFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFFFFFFFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:20419:1000 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGT ++ +FFFFFFFFFFFFFFFJJJJJJJJJJJJJJJJJJJJHHHJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFFFFFFFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:20853:1000 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGGCCGCGGACATCTCGGTGGGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGT ++ +FFFFFFFFFFFFFFFJJJJJJJJJJJJJJJJJJJJJHJJJJJHJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFFFFFFFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:29460:1000 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGTCGATTCGGCCGCAGACGGGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGT ++ +FFFFFFFFFFFFFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHJJJJJJJJJJJJFFFFFFFFFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:12979:1016 1:N:0:ATCGTCTC+NTAACCGA +ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACTGCGCACTGCAGGTGCCATCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC ++ +FFFFFFFFFFFFFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFFFFFFFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:17517:1016 1:N:0:ATCGTCTC+NTAACCGA +ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGATGAAACTATGGGACCCTCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC ++ +FFFFFFFFFFFFFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJH<JJJJJJJJJJJJJJJFFFFFFFFFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:25310:1016 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCAAAGCCCCGGTAGGGCCGGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGT ++ +FFFFFFFFFFFFFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFFFFFFFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:7346:1031 1:N:0:ATCGTCTC+GTAACCGA +ACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGGACTCGCCCACCTATGTCCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC ++ +FFFFFFFFFFFFFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHJJJJJJJHJJJJJJJHJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFFFFFFFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:8919:1031 1:N:0:ATCGTCTC+GTAACCGA +GATCTCATTCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCTCACCGGTTCTGCAGTAAGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGT ++ +FFFFFFFFFFFFFFJJJJJHJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFFFFFFFFFFFF
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bbmerge/unmerged.fastq Tue May 30 09:02:11 2023 +0000 @@ -0,0 +1,8 @@ +@A00604:500:HKMVNDSX3:2:1101:20943:1000 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGTAAGTCATGGAGATTGTGTCTATATAAAAAGTGGTAGTGAAATCTGCATTATAAGATGACACTATCTCAAAGTGTATATCAATGAAGAGGATTGGTCATCCAGAAGTAGCACTGGAA ++ +FFFFFFFFFFFFFFFFFFFF:FFFFFF:FFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@A00604:500:HKMVNDSX3:2:1101:20943:1000 2:N:0:ATCGTCTC+NTAACCGA +ACTCGGTGCCACTTTTTCAACCAAGAGGGGCTAAAAATTTTCAAAGGTTACCTATATGATCAGATAAGTTCTGTTGGAAAGAAAATCAATTGATATGACATTGTCAGTCAACTGACATGGATTTTCTCATGACCTAACATGATATATTAAC ++ +FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFFFFFFFF
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bbnorm/discarded.fastq Tue May 30 09:02:11 2023 +0000 @@ -0,0 +1,32 @@ +@read1:duplicateA 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read1:duplicateA 2:N:0:ATCGTCTC+NTAACCGA +TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read5:duplicateA 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read5:duplicateA 2:N:0:ATCGTCTC+NTAACCGA +TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read7:duplicateB 1:N:0:ATCGTCTC+NTAACCGA +AAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAACGCGCGAGTCGGCATGCTGATGCACGATGCTAGCTGAGCATGCTAGTCGAGCAGTCGT ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read7:duplicateB 2:N:0:ATCGTCTC+NTAACCGA +ACGACTGCTCGACTAGCATGCTCAGCTAGCATCGTGCATCAGCATGCCGACTCGCGCGTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTT ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read8:duplicateB 1:N:0:ATCGTCTC+NTAACCGA +AAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAACGCGCGAGTCGGCATGCTGATGCACGATGCTAGCTGAGCATGCTAGTCGAGCAGTCGT ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read8:duplicateB 2:N:0:ATCGTCTC+NTAACCGA +ACGACTGCTCGACTAGCATGCTCAGCTAGCATCGTGCATCAGCATGCCGACTCGCGCGTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTT ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bbnorm/input_R1.fastq Tue May 30 09:02:11 2023 +0000 @@ -0,0 +1,40 @@ +@read1:duplicateA 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read2:duplicateA 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read3:duplicateA 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read4:duplicateA 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read5:duplicateA 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read6:duplicateA 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read7:duplicateB 1:N:0:ATCGTCTC+NTAACCGA +AAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAACGCGCGAGTCGGCATGCTGATGCACGATGCTAGCTGAGCATGCTAGTCGAGCAGTCGT ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read8:duplicateB 1:N:0:ATCGTCTC+NTAACCGA +AAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAACGCGCGAGTCGGCATGCTGATGCACGATGCTAGCTGAGCATGCTAGTCGAGCAGTCGT ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read9:duplicateC 1:N:0:ATCGTCTC+NTAACCGA +ACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAACGCGCGAGTCGGCATGCTGATGCACGATGCTAGCTGAGCATGCTAGTCGAGCAGTCGTAGCGCGCGCGCTATCGCGATCGCGATCGGCATCGGAGCTACGGAATA ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read10:duplicateC 1:N:0:ATCGTCTC+NTAACCGA +ACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAACGCGCGAGTCGGCATGCTGATGCACGATGCTAGCTGAGCATGCTAGTCGAGCAGTCGTAGCGCGCGCGCTATCGCGATCGCGATCGGCATCGGAGCTACGGAATA ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bbnorm/input_R2.fastq Tue May 30 09:02:11 2023 +0000 @@ -0,0 +1,40 @@ +@read1:duplicateA 2:N:0:ATCGTCTC+NTAACCGA +TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read2:duplicateA 2:N:0:ATCGTCTC+NTAACCGA +TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read3:duplicateA 2:N:0:ATCGTCTC+NTAACCGA +TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read4:duplicateA 2:N:0:ATCGTCTC+NTAACCGA +TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read5:duplicateA 2:N:0:ATCGTCTC+NTAACCGA +TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read6:duplicateA 2:N:0:ATCGTCTC+NTAACCGA +TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read7:duplicateB 2:N:0:ATCGTCTC+NTAACCGA +ACGACTGCTCGACTAGCATGCTCAGCTAGCATCGTGCATCAGCATGCCGACTCGCGCGTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTT ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read8:duplicateB 2:N:0:ATCGTCTC+NTAACCGA +ACGACTGCTCGACTAGCATGCTCAGCTAGCATCGTGCATCAGCATGCCGACTCGCGCGTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTT ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read9:duplicateC 2:N:0:ATCGTCTC+NTAACCGA +TATTCCGTAGCTCCGATGCCGATCGCGATCGCGATAGCGCGCGCGCTACGACTGCTCGACTAGCATGCTCAGCTAGCATCGTGCATCAGCATGCCGACTCGCGCGTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGT ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read10:duplicateC 2:N:0:ATCGTCTC+NTAACCGA +TATTCCGTAGCTCCGATGCCGATCGCGATCGCGATAGCGCGCGCGCTACGACTGCTCGACTAGCATGCTCAGCTAGCATCGTGCATCAGCATGCCGACTCGCGCGTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGT ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bbnorm/input_interleaved.fastq Tue May 30 09:02:11 2023 +0000 @@ -0,0 +1,80 @@ +@read1:duplicateA 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read1:duplicateA 2:N:0:ATCGTCTC+NTAACCGA +TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read2:duplicateA 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read2:duplicateA 2:N:0:ATCGTCTC+NTAACCGA +TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read3:duplicateA 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read3:duplicateA 2:N:0:ATCGTCTC+NTAACCGA +TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read4:duplicateA 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read4:duplicateA 2:N:0:ATCGTCTC+NTAACCGA +TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read5:duplicateA 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read5:duplicateA 2:N:0:ATCGTCTC+NTAACCGA +TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read6:duplicateA 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read6:duplicateA 2:N:0:ATCGTCTC+NTAACCGA +TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read7:duplicateB 1:N:0:ATCGTCTC+NTAACCGA +AAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAACGCGCGAGTCGGCATGCTGATGCACGATGCTAGCTGAGCATGCTAGTCGAGCAGTCGT ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read7:duplicateB 2:N:0:ATCGTCTC+NTAACCGA +ACGACTGCTCGACTAGCATGCTCAGCTAGCATCGTGCATCAGCATGCCGACTCGCGCGTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTT ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read8:duplicateB 1:N:0:ATCGTCTC+NTAACCGA +AAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAACGCGCGAGTCGGCATGCTGATGCACGATGCTAGCTGAGCATGCTAGTCGAGCAGTCGT ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read8:duplicateB 2:N:0:ATCGTCTC+NTAACCGA +ACGACTGCTCGACTAGCATGCTCAGCTAGCATCGTGCATCAGCATGCCGACTCGCGCGTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTT ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read9:duplicateC 1:N:0:ATCGTCTC+NTAACCGA +ACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAACGCGCGAGTCGGCATGCTGATGCACGATGCTAGCTGAGCATGCTAGTCGAGCAGTCGTAGCGCGCGCGCTATCGCGATCGCGATCGGCATCGGAGCTACGGAATA ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read9:duplicateC 2:N:0:ATCGTCTC+NTAACCGA +TATTCCGTAGCTCCGATGCCGATCGCGATCGCGATAGCGCGCGCGCTACGACTGCTCGACTAGCATGCTCAGCTAGCATCGTGCATCAGCATGCCGACTCGCGCGTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGT ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read10:duplicateC 1:N:0:ATCGTCTC+NTAACCGA +ACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAACGCGCGAGTCGGCATGCTGATGCACGATGCTAGCTGAGCATGCTAGTCGAGCAGTCGTAGCGCGCGCGCTATCGCGATCGCGATCGGCATCGGAGCTACGGAATA ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read10:duplicateC 2:N:0:ATCGTCTC+NTAACCGA +TATTCCGTAGCTCCGATGCCGATCGCGATCGCGATAGCGCGCGCGCTACGACTGCTCGACTAGCATGCTCAGCTAGCATCGTGCATCAGCATGCCGACTCGCGCGTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGT ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bbnorm/kmer_hist_input.tabular Tue May 30 09:02:11 2023 +0000 @@ -0,0 +1,6 @@ +#Depth Raw_Count Unique_Kmers +2 188 94 +4 472 118 +6 708 118 +8 752 94 +10 300 30
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bbnorm/kmer_hist_output.tabular Tue May 30 09:02:11 2023 +0000 @@ -0,0 +1,4 @@ +#Depth Raw_Count Unique_Kmers +2 424 212 +4 848 212 +6 180 30
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bbnorm/normalised_R1.fastq Tue May 30 09:02:11 2023 +0000 @@ -0,0 +1,24 @@ +@read2:duplicateA 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read3:duplicateA 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read4:duplicateA 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read6:duplicateA 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read9:duplicateC 1:N:0:ATCGTCTC+NTAACCGA +ACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAACGCGCGAGTCGGCATGCTGATGCACGATGCTAGCTGAGCATGCTAGTCGAGCAGTCGTAGCGCGCGCGCTATCGCGATCGCGATCGGCATCGGAGCTACGGAATA ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read10:duplicateC 1:N:0:ATCGTCTC+NTAACCGA +ACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAACGCGCGAGTCGGCATGCTGATGCACGATGCTAGCTGAGCATGCTAGTCGAGCAGTCGTAGCGCGCGCGCTATCGCGATCGCGATCGGCATCGGAGCTACGGAATA ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bbnorm/normalised_R2.fastq Tue May 30 09:02:11 2023 +0000 @@ -0,0 +1,24 @@ +@read2:duplicateA 2:N:0:ATCGTCTC+NTAACCGA +TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read3:duplicateA 2:N:0:ATCGTCTC+NTAACCGA +TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read4:duplicateA 2:N:0:ATCGTCTC+NTAACCGA +TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read6:duplicateA 2:N:0:ATCGTCTC+NTAACCGA +TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read9:duplicateC 2:N:0:ATCGTCTC+NTAACCGA +TATTCCGTAGCTCCGATGCCGATCGCGATCGCGATAGCGCGCGCGCTACGACTGCTCGACTAGCATGCTCAGCTAGCATCGTGCATCAGCATGCCGACTCGCGCGTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGT ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read10:duplicateC 2:N:0:ATCGTCTC+NTAACCGA +TATTCCGTAGCTCCGATGCCGATCGCGATCGCGATAGCGCGCGCGCTACGACTGCTCGACTAGCATGCTCAGCTAGCATCGTGCATCAGCATGCCGACTCGCGCGTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGT ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bbnorm/normalised_interleaved.fastq Tue May 30 09:02:11 2023 +0000 @@ -0,0 +1,48 @@ +@read2:duplicateA 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read2:duplicateA 2:N:0:ATCGTCTC+NTAACCGA +TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read3:duplicateA 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read3:duplicateA 2:N:0:ATCGTCTC+NTAACCGA +TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read4:duplicateA 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read4:duplicateA 2:N:0:ATCGTCTC+NTAACCGA +TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read6:duplicateA 1:N:0:ATCGTCTC+NTAACCGA +GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read6:duplicateA 2:N:0:ATCGTCTC+NTAACCGA +TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read9:duplicateC 1:N:0:ATCGTCTC+NTAACCGA +ACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAACGCGCGAGTCGGCATGCTGATGCACGATGCTAGCTGAGCATGCTAGTCGAGCAGTCGTAGCGCGCGCGCTATCGCGATCGCGATCGGCATCGGAGCTACGGAATA ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read9:duplicateC 2:N:0:ATCGTCTC+NTAACCGA +TATTCCGTAGCTCCGATGCCGATCGCGATCGCGATAGCGCGCGCGCTACGACTGCTCGACTAGCATGCTCAGCTAGCATCGTGCATCAGCATGCCGACTCGCGCGTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGT ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read10:duplicateC 1:N:0:ATCGTCTC+NTAACCGA +ACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAACGCGCGAGTCGGCATGCTGATGCACGATGCTAGCTGAGCATGCTAGTCGAGCAGTCGTAGCGCGCGCGCTATCGCGATCGCGATCGGCATCGGAGCTACGGAATA ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF +@read10:duplicateC 2:N:0:ATCGTCTC+NTAACCGA +TATTCCGTAGCTCCGATGCCGATCGCGATCGCGATAGCGCGCGCGCTACGACTGCTCGACTAGCATGCTCAGCTAGCATCGTGCATCAGCATGCCGACTCGCGCGTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGT ++ +EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bduk_output_dump1.fasta Tue May 30 09:02:11 2023 +0000 @@ -0,0 +1,100 @@ +>116 +GAGATGGAACTGTAACTGGAGTTCCTT +>7 +TGCCTAAGTGACTAGAGTTCAGACGTG +>28 +TGAACTCCAGTCAAATTCCTTTATCTC +>141 +GCATACGAGATGTATAGGTGACTGGAG +>3 +GTTCAGCAGGAATACCGAGACCGATCT +>126 +GGTAGCATCTCGTATGCCGTCTTCTGC +>123 +GCCAAGGAACTCCAGTCACGTTTCGAT +>126 +ATACGAGATGCTAACGTGACTGGAGTT +>18 +CCGTATCTCGTATACCGTCTTCTGCTT +>26 +TCTGAACTCCAGTAACGAGTGGATATC +>17 +GAAGACGGCATACAAGATTGTTGACTG +>22 +TGAACTCCAGTCAAGTGAAACGATCTC +>50 +ACGCTACGCTATCACGTATGCCGTCTT +>103 +TCGGGTGCCAAGGAACTCCAGTCACAT +>141 +ATACATCTCGTATACCGTCTTCTGCTT +>113 +TCGGGTGCCAAGGAACTCCAGTCACGG +>84 +GAGATTACTACGCATCTCGTGGGCTCG +>122 +CGTGGCCATCTCGAATGCCGTCTTCTG +>139 +TCCAGTCACCGGAATATCTCGTATGCC +>42 +CAGAAGACGGCATACGAGATTCGCCTT +>107 +TGTGTGACTGGAGATCCTTGGCACCCG +>140 +CATACGAGATAGCAAGGTGACTGGAGT +>6 +GGTGACTGGAGTTAAGACGTGTGCTCT +>30 +TCTCTTATACACAACTCCGAGCCCACG +>122 +CAGTCACGTGGCCATCTCGTATGCCGT +>19 +GTCACATGTCAGAATCTCGTATGCCGT +>41 +GCGTGTAGATCTCAGTGGTCGCCGTAT +>1 +GTGACTGGAGTTCAGACGTGTGCTCTT +>15 +GTCTGAACTCCAGACACGGCTACATCT +>4 +TCCGATCTCAAGCAGAAGACGGCATAC +>119 +GAAGACGGCATACAAGATCTCTACGTG +>129 +GTCACATTCCTATATCGTATGCCGTCT +>107 +GATCACTGTGTGAATGGAGTTCCTTGG +>9 +ATACGAGATCACTATGTGACTGGAGTT +>24 +CTGAACTCCAGTCACGTTTCGGAATCT +>116 +TGGAACTGTGACTAGAGTTCCTTGGCA +>13 +GAAGACGGCATACAAGATCTGATCGTG +>30 +TCTTATACACATCACCGAGCCCACGAG +>49 +CAGAGAGGATCTCATATGCCGTCTTCT +>133 +TCGTGGTGACTGGAGTTCCTTGGCACC +>8 +CAGTCACTGACCAATCTCGTATGCCGT +>33 +TCTAGTGTAGATCACGGTGGTCGCCGT +>21 +TGCGGACGTGACTAGAGTTCAGACGTG +>37 +GACGACTCCTTACATGTAGATCTCGGT +>124 +GTACGGTGACTGGAGTTCCTTGGCACC +>69 +TACACTTATGCGAACGTCGGCAGCGTC +>149 +GCATACGAGATCTACGAGTGACTGGAG +>124 +GAGATCGTACGGTAACTGGAGTTCCTT +>105 +GCCAAGGAACTCCAGTCACTTAGGCAT +>150 +CAGTCACTCGGCAATCTCGTATGCCGT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bduk_output_quhist1.tabular Tue May 30 09:02:11 2023 +0000 @@ -0,0 +1,101 @@ +#BaseNum Read1_linear Read1_log Read2_linear Read2_log +1 16.400 4.332 32.940 32.694 +2 24.580 19.293 32.680 30.545 +3 29.880 28.913 32.720 32.218 +4 35.400 35.023 35.740 28.139 +5 35.610 35.076 35.980 34.688 +6 36.070 35.819 36.130 35.232 +7 36.030 35.134 35.750 28.304 +8 36.210 35.891 35.760 30.427 +9 37.770 36.724 37.550 36.174 +10 37.770 36.627 37.890 36.829 +11 38.130 34.528 37.720 35.825 +12 38.120 37.610 37.930 36.724 +13 37.600 29.816 37.860 33.975 +14 39.600 38.822 39.490 29.436 +15 39.240 37.118 39.430 34.527 +16 39.370 37.815 39.670 29.527 +17 39.230 35.062 39.310 34.199 +18 39.410 38.456 39.700 38.264 +19 39.470 38.621 38.680 28.791 +20 39.170 36.390 39.340 38.126 +21 39.340 38.280 39.320 37.141 +22 38.870 32.580 38.480 25.015 +23 39.370 37.125 38.850 32.436 +24 38.940 36.347 39.200 37.110 +25 38.560 36.248 39.000 28.586 +26 38.810 33.655 38.460 29.005 +27 38.930 35.395 38.560 25.539 +28 39.090 37.259 38.190 23.947 +29 38.610 25.879 38.730 30.749 +30 38.540 33.271 38.520 32.796 +31 38.840 33.517 38.040 30.447 +32 38.730 36.053 38.530 27.397 +33 38.340 34.385 38.880 35.605 +34 38.470 28.217 38.430 32.167 +35 37.350 30.035 38.560 26.684 +36 37.380 20.434 38.900 32.524 +37 37.810 32.591 38.450 34.632 +38 38.150 33.133 38.750 35.749 +39 37.660 31.924 38.420 26.003 +40 38.040 34.153 38.730 36.080 +41 37.970 35.596 39.020 37.708 +42 37.240 31.069 39.380 33.973 +43 37.740 29.175 38.840 35.607 +44 38.070 34.040 38.400 23.939 +45 37.690 30.131 38.160 26.507 +46 37.160 26.236 37.990 32.407 +47 37.820 35.168 37.330 29.388 +48 37.920 35.623 37.850 31.413 +49 38.150 34.322 37.830 27.255 +50 38.250 34.017 38.260 36.442 +51 38.060 36.455 36.270 30.125 +52 37.240 34.726 37.000 33.291 +53 37.700 32.804 37.210 34.667 +54 37.740 33.699 37.520 34.736 +55 37.780 33.713 37.880 35.604 +56 37.470 31.063 37.880 35.326 +57 36.680 26.593 36.810 22.646 +58 36.390 26.714 37.140 31.327 +59 35.960 29.732 36.900 20.404 +60 35.500 27.738 36.440 21.355 +61 35.800 28.761 36.200 20.579 +62 34.880 22.760 36.570 21.483 +63 35.560 30.716 36.180 21.372 +64 35.460 30.521 35.970 20.108 +65 35.090 25.249 35.450 20.127 +66 35.240 31.736 35.330 20.499 +67 35.230 25.003 35.410 21.618 +68 34.870 25.901 35.400 21.693 +69 34.560 24.095 35.200 21.684 +70 34.670 29.988 34.730 21.372 +71 35.010 32.741 34.710 21.582 +72 33.750 21.148 34.060 18.014 +73 34.130 29.634 34.040 18.342 +74 34.080 21.493 33.840 17.025 +75 33.590 20.367 33.380 16.366 +76 31.930 18.529 33.300 17.088 +77 32.400 18.486 32.360 15.307 +78 32.840 18.708 32.170 15.246 +79 33.190 18.732 32.130 15.504 +80 32.680 17.826 32.770 15.850 +81 32.690 17.578 32.640 15.552 +82 32.510 16.664 32.800 15.822 +83 31.640 15.134 32.350 15.209 +84 31.220 15.026 32.320 15.547 +85 31.270 14.413 32.170 15.387 +86 31.310 14.436 32.520 15.576 +87 32.130 14.923 32.070 15.354 +88 31.610 14.417 31.780 15.361 +89 31.240 14.665 32.290 15.854 +90 31.130 14.606 31.730 15.508 +91 31.350 14.867 32.120 14.926 +92 31.270 14.282 32.040 14.910 +93 31.790 14.879 31.770 14.676 +94 31.010 13.468 31.380 14.768 +95 30.280 12.737 31.220 14.847 +96 30.310 12.852 31.050 14.129 +97 30.390 12.411 31.160 13.935 +98 30.150 12.394 30.960 13.893 +99 30.300 11.964 30.610 13.166 +100 29.860 11.945 30.460 12.397
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bduk_outputu1.fastqsanger Tue May 30 09:02:11 2023 +0000 @@ -0,0 +1,102 @@ +@XXXXXXXXXX:7:1101:1582:1835#/1 +NGCTTCAGTTGGTACAGGTGTGTCACCCGTAGTTTGTAGGCTTGGAAGCCTGTAAGCTGTAGGGAACGTGGCAAGAACCAGATCTGGCCTTCCATATCTC ++ +!1=DDDDDAFFDDEFFG@AGHBCFHIFIEGIC?DBFGIFF?FGDFIBFFII8BCFIEEF.@FFIIEFFCE=??B@>A@@@BBBAD>A:?BBBBB@>>>B: +@XXXXXXXXXX:7:1101:1610:1859#/1 +NTTATGTGTTACGTGAATCTCCTGAAGACAGCAGAAACTAGGTTGGTGAATTCTTATCCATTCTGCCATTCTGTATCTTTTAAGTGGAGCATTTAGGCTA ++ +!1=DDFDFHHHHHHJJIJJJJJJJJJJJIJIIJJJIJIJJJJIJJJIIJJJIJJJIIJJJJIIJJJJGIJJJIHJHHHHHHHFFFFFFDDDEEDEDDCDD +@XXXXXXXXXX:7:1101:1743:1871#/1 +NCGGGATGGAGGCAGGGCAAGCGGATGCAGGCCCAGCCCTGCCCTTACAGGTAGCTGGAAGTGACGAAGGAGTGGGGCCCCCGGACTCTGCTCAGGTGGA ++ +!1=DDDFFHHHHHIJJJEGGGIHIGIIGGGIIIJEHHHGGCCHIIIFHHFHADDCDDC@CECECCDDB7?BB9?BA>9<@DDB>>9>CD>:>CA9A:A@A +@XXXXXXXXXX:7:1101:1536:1878#/1 +NGGCCTTTTTGGACAGGTGGTGTGTGGTGGCCTTGGTATGTGCTTTCTCGTGTTACATCGCGCCATCATTGGTATATGGTTAGTGTGTTGGTTAGTAGGC ++ +!1=DDDFEHHHHCGGIJFHIECHEFHIGGGGIJI<BBFGEIFGIIJIIJJJEGGEGGIHCCBHBFFCCEDEEC@CDDDC3>:95>@ABCAA<?C?>CDCC +@XXXXXXXXXX:7:1101:2990:100153#/1 +GCCAGGAGTGACTGTGTTGTTCTTTGCTTTATATACATAAGCGCATCTCTTGCCCAAATAGAATTCTGTTTCATCTCGGGCGTAAACACCTTCAATTTTA ++ +@@@DDDFDBFHDFH<EHGIHGCHEGHGIIGIIEGFEIGGIIIIII<GICCE@4?BBFHGHAEGIHHIICDHEEEAAHFBEDD@B@B@><@D>CDDDDCCB +@XXXXXXXXXX:7:1101:1624:1906#/1 +NCCAGGTTTAAGGCATTACATCGAGGGGCTGAACTTGAGACAGTCCCTGAAAATGTAAGAACAGGAGCTAGAACTTGCTTATGGGAAGGGCCTAGGGAGA ++ +!1=DDFFFHHHHHJJJJJIJJJJJJJJJJJJJJJJJIJJIJIIJJJJJJJGIJJIIJIECGIHHHHFFFFEECEECEDDDDDDCDCDDDDDDDDDDDDD@ +@XXXXXXXXXX:7:1101:1666:1926#/1 +NGCAAACTGGTCAGGACCTGGAGCTGCTTGCCTGGCCTTGGCACAAGAGGCCGACATATGCCCAGCCCCTAGGAGTGACAGATCCGTCCTCTGTGGGAAC ++ +!1BDFFFFHHHHHJJJJJJJJJJJJJJJJJJJIJIJJJJJJIJJJJJJJJJJJJJJJHHHHHHFFFFDDDDDDCCDBDDDDDDDDDDDDDDDDDDDDBCD +@XXXXXXXXXX:7:1101:2921:100163#/1 +CTCCGGATGCCAAAGGATCTGACAGTGTATCTAGCTTTGGAAAACACAGGGGTCTGCCCTGTGAGCTGCTCCAACACCTTGGCTGCTCGCGTCAGTCTGT ++ +CCBFFFFFHHHHHJJJIJIIIJJJJHIFFHGIIHEIJIIIIIJIIGIIIICHHHHIJIIEHHJIHHFHHFFFFFFBDDDDDCDDDDDDDDD@B@@CCDDD +@XXXXXXXXXX:7:1101:1513:1929#/1 +NCACTATCAAGGTTAGTGTCTATATCTACTTGAGANAAAATACTGAAAATTCAGTGTATGAAGCCAAATCCTGATTTAACAAGTTATTGGTAGTATAAGT ++ +!1:ABDDDDFFF:ACGFGFHHFIFAHEEHDFI@F8!1:CFEFFIGEFGIII>GIFICGGII@FFFIEFEADGIIEIFFFFFFFEEDDDDBDAC>>;;BA5 +@XXXXXXXXXX:7:1101:2759:100170#/1 +CTGCTCATCACATTCCAGATGCCATCACAGGCAATGACCATGAATTCATGGTCGTCAGTGAGAGTCAGCACCTTGATGTCAGGAAGGGCTGAAATCATCT ++ +CCCFFFFFHHHHHJJJJJIJJJJJJJJJJJJJJJJJJJJJJJJIJJJIJJJIJJJJJJHIIJJJIJJJJJJJHHHHHHHFFFFFEEDDDDDBCDDDDDDD +@XXXXXXXXXX:7:1101:1708:1937#/1 +NGGTCGGTGTCCTTTTTTGGCGTCAAACTTATAGAGGGAAGCAGGGAATCTACCCAACCAAAGCCAATGAACAGTCAGTCAGTCCATCTAGTTAAGGTTC ++ +!1=BDDDDFDHHHIJJIJIJGIJIGGIJIGAGFHGHIGA=FCDFGHJJHEHFHHEFFFDABCDCDCCCDCDDDDDACDDCDDCAAACCDDDDDDACCACD +@XXXXXXXXXX:7:1101:2981:100211#/1 +GGGGTCAGTGGGAAAGGTGTCAATGGGACTTCGGTCTCCATGCCGAAACACCAAAGTCACAAACTTCAACTCCTTGGCTAGTACACTTCGGTCTAGCCAG ++ +@@CFDDDFFFFHHEIGGHIIIIJJIIDHIGGIJFGBHIIIGGGGGGGIIJJHJGIG=DECEEEFFFFCDCCE@CC@?CDCBDDCDCCCCBB?B@>CACAB +@XXXXXXXXXX:7:1101:1688:1946#/1 +NCCGCCTTCTTTCTCTACTTCGTGACCTTTTGTGGTCCCGAGACCTGCTGCATCTTCTGTCTGATGTTCGGCTTGAGTGTCTACTTCCTGAACGACTTCT ++ +!1:BDAAD<DDDDIEE>DBEEFEEFIIIIIEADEC?C>DD<?D@?@BDDDEEDIEIEDE=CEE>CE?CCC6=?########################### +@XXXXXXXXXX:7:1101:2767:100225#/1 +CGCCTGGTGTCAATGCGCACATCTGGAGTTCCCATCTCCTTCATGGCAAATTTCCGAATCTCTTTGAGTGCCCGAGGTGCACGCTTCTTGAAGCCCACTC ++ +@@@FDFFFGHHHFJJIJIIIIJIJIJIGHBD@DFGGGJIFIJJJJIIIIIGHIIGIJFIJJIJIG@EECCHEEDCAD>ACCCDDDDDACCAC@CDDDDDD +@XXXXXXXXXX:7:1101:1536:1959#/1 +NGATACTGTTGGGTCAGGACCAGGGCCTGCACCACCGAAATTCTGTCTTTTACAAACTGGACCAAGCGGTTGAGAATACAGGGGCCGAAGAGTAGGATTA ++ +!4:BB?DDHHDHAE?ECB@=GGI=<;CG@B;<D@DG:@FFABFBG<=FFGFHIIGGH@>==AEC?DECA<;8;3<AC>CCCC8&-5>@@59?4::>>>CC +@XXXXXXXXXX:7:1101:2797:100234#/1 +GTGCTGGTCTCTCTCCACGATCTCTTACGTGCTAGCAGGGTGAACAAGGACGCCTCGCTGTCATTGCACTCACGCCACAGGAGCCTGGCACATTTCCGCT ++ ++:?BDD8DFFFB8ED;@GF8A3?FH?B<)11?@FG<E<;@F629?BF@?2=A;4C6BE7-,7@;@;@A>;@CBB?=88?5(95983?(8<><AA###### +@XXXXXXXXXX:7:1101:1552:1976#/1 +NTGATGAGTTTGCTAATACAATGCCAGTCAGGCCACCTACGGTGAAAAGAAAGATGAATCCTAGGGCTCAGAGCACTGCAGCAGATCATTTCATATTGCT ++ +!1=DDFFFFHFHGJJJJIJJJJJJJJJJJIIJFGHGIIIJIJGHIEIIJJJHIGIIJGJIIJJJBHIIJHHHHHDEFCECEEEEDDDDDEFEEEEEEEDD +@XXXXXXXXXX:7:1101:1748:1978#/1 +NCGCTGAGCAGGGCAGGCAGTGGTGGAGGCAGCCCCCCAAGACCCCATCTCTATCACAGTGAGAGCATCTGAACTCCAAAGCCACGACAGAACAGCTCCC ++ +!1=DFFFFHHHHHIJJJJIJIJJFHJIIJIJJGJJIIJAHGGGHHHHFFFFFFEEDECE@CDDCDDDCDDDACCCCDDDDCDDDDDDDDBDDCCC@ACDD +@XXXXXXXXXX:7:1101:2779:100239#/1 +TGGGTGCTCTCCTTGGTCAGCTGCTGCTCGAACAGAGCACTTCTAGATACAGAGTTGGACCCAGACACAGCAGGGGTGGCCATGGCGGCTGGGAAAGACC ++ +@@@?DD?DFHHFFHIEEHIBGI9CFHFGCB::CGIGHG@BF<FHFHD@DDDBBDBFGH<C;C;==;C;;?H;;?<>88=@?C################## +@XXXXXXXXXX:7:1101:1593:1980#/1 +NGGCACCAGAAGCATGAGCATAGGCAGAGCCATTTCCACCATGCTGACGGCAGGCAAGAAGAAGACAAAAATGAACCCCTTTCATGCTTGTTTAGAAATG ++ +!1=DFFFFHHHHGJJJJJJJJIJJIJJJIGJIIJJJJGIIIJJJJJIIJJJJJJIIJHHHHHFFFFFEEDDDDDDDDDDDDDDDEDDDEDDDDDDDDDDD +@XXXXXXXXXX:7:1101:2946:100242#/1 +TGGGGATGTTGTTAAAAAAAATACAGGCTCCCCCACAACTGGGGTGCCTGGGGGGAACTTGGTCTGCTTCAGCCCAAGAGGAATCAAAAGATCAAAAGCA ++ +@@@FFDDDHHHHHJIIGIJIGEGIIJJIIJJGJJEECDEA=FHI-=?B?CEDDDD5583:AC3::94:CAACCDBABD8?BA?CCDDDDD@CCACCDCBD +@XXXXXXXXXX:7:1101:1987:1781#/1 +NTTAGCAGGTCCTCGTAGCGTTTCCGCAACTCTCGGAATCTGGAGTCTTCGGAGTGCAACTCTGAGGGTCCCGGGAAACTTGCGCGGCTCGCCTCGGCCA ++ +!1=DDFFFHHHHHJJJJJIJJJJIJJJJJJJJJJJJJJJGJJJJIIHIJJJIJHHGHFFFFFFCEEDDDDDDDDDBDDDDDDDDDDDDDDBBDDD9B?B< +@XXXXXXXXXX:7:1101:3046:100006#/1 +CTGTACAGCATGGATGTGGACAGGGAAAACAGCAAGTGCACACAGTGGGACAGGCCACAGGACAGGCTGGGAGTGAATAAAGAGTTCACACTGCTTCCCT ++ +CCCFFFFFHHHHHJJJIJJJJJJJJJJJJJJJIJJJFHIJJIIJIGGHIJJJJJJIJJIIJJJHHHHFFFD=C;?CDCDDD@>?>@CACDACCDDCDDDD +@XXXXXXXXXX:7:1101:1900:1788#/1 +NCCCGCTGCCCACGCCACTGTCCCGGCGCTGCCCTGGGCGCGGAATGCGCGTTAGGCAATCCCCGGTCTGCGCGTCCCACACGCAGATGTGGCCTGCCAG ++ +!1=DFFFFGHHGHJJJIJJIJJJJGIIJJJIIJJIJJJIHFFDDDDDDDDDBDDDDDDDDDDDDBD@BDDDB>BB<BBDDDDDDDDDDDECDDBDDDDC@ +@XXXXXXXXXX:7:1101:3214:100027#/1 +GGCTGAGGTACTGAATGAGGAACAGCAGGAGGTAACGTCTGAGGGTGCGGCTGGGGAACGGTTTGCACAGGGGTGGCTGTAGGAGCAGGAGGTGAAACAC ++ +@@@FFDFF?DFHHIIIIIIGIIGHGIIGIIII?FHHGDFGIGGIC6?FHIIFIHHH59;=B559=33:55<(830588<((>:(98<CB02&28>CA>98 +@XXXXXXXXXX:7:1101:1848:1879#/1 +NCTTCTTCTTCCTCATGTTTTTTGATCAACTGCTCCACTTCTTTTTGTTTGAGAACTCTGATTACTGTCTTTCCATTCTCTCTTGTTAGTGTTGCAATTT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bduk_outputu2.fastqsanger Tue May 30 09:02:11 2023 +0000 @@ -0,0 +1,102 @@ +@XXXXXXXXXX:7:1101:1582:1835#/2 +GCAATGATGGGGCCGCTCCCGGGGCCACACCTGCTTCTGGATCCGCTGCTTCCAAGTTCCTTTGCCTCCCTCCTGGCATCACTGTCTGCGACTCAGGCCG ++ +@@@DDDADHFHGFEGIGIIIGEGFD@FHA@GIGIJJIJJEAHHEBEDACEAC@CDDDC@@CCCCDCD@AD9?BCCDDCCDDDDDDDDCC99BBDDCACBB +@XXXXXXXXXX:7:1101:1610:1859#/2 +CAATAACACAGTCCAAAATATATGTATGTATGTATATATATATGCAGGCAACAAATAGCACAATGAATAAAATAGTACTTCATCTCAGTACTAACATTGA ++ +C@BFFFFFHHGHDIIJJJJJJIIJHIJJHIJIJJIGIJIJJJJJFIIJJIIIIIJJJIJJJJJJJJIJJJIJJJJEGIIJJIJHHHHHCDFFFFFFEEEE +@XXXXXXXXXX:7:1101:1743:1871#/2 +GCTTCCAAGGGACAAAGTCCTGCCCTTGGGTGTGGAAGACACCGTGGACAAGCTCAAGATGCTGGAAGGCCGCAAGACCAGCATCCGCAAGTCAGTGCAG ++ +CCCFFFFFHHHHHJJJJJIIJHEHJIJJJIEDGIIIJIGGGIJIGEIIIIJIIIIIHGHHHHFFFFFFFDB>B@BDDCDDDDDDDCB?@BDCCDDDDDDD +@XXXXXXXXXX:7:1101:1536:1878#/2 +TGCCTATCATATAGTAAAACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTAGCCATGTGATTTCACTTCCACTCC ++ +@@@DFFFFHGFHGIJJJJJJJAFDHICDFHGIJIIJEEIJGIJGHJIJJIFAAAFGBGGFFFHGHFDFDFBCBDDDD<ACDDDCADEDDDDCD:>CDDCC +@XXXXXXXXXX:7:1101:2990:100153#/2 +TGGAGGCCTGCTGGGAACGGGACTTCTAAAAGGAACTATGTCTGGAAGGCTGTGGTCCAAGGCCATTTTTGCTGGCTATAAGCGGGGTCTCCGGAACCAA ++ +@@@DDDDFHHFDHJJIGGHIJHIJJJJJGGGHJEGIIJJJIJJJIJJII?=FFHIHGGIJIHHHHFFC@BBCCEDDDDDECCDBDBD09CDDDDBBB??1 +@XXXXXXXXXX:7:1101:1624:1906#/2 +GGCTGGTCTGTCCCCTCTGCATCTGGGGCTCCTCCTGGCCCTTCTCCCGCTGCCTGTCCTGCCTCCTGGCCCTGCAGCAGCACCTTGCCCAGTGATCTTT ++ +CCCFFFFFHGHHHJJJJJJJIJJJIJJJIJIJJIJJIJIJJJJJJGGIJJFGIJGHHIFHHHHHFFDFDEEDDDD?CDDDDDDDDDCCDCDDCCCDCCCD +@XXXXXXXXXX:7:1101:1666:1926#/2 +GGCTGTGGGAACTCTAGCTGCTGTCAGCCCCTCCTGTAGGAGCTGGCCCTGCCCAGGCTCCTGACTTCCCTCAGGAAGTCTTTCTGTCTTTCTCCATCAG ++ +CCCFFFFFHHFHHJJIJJJJJJIJJJJJJJJJJJJJJJJIIJJJJIJJJJIJJIJJIIJJJIHCHHGHFFFFBEE>@B>CDDDCDDDDDDDDDACDDCCD +@XXXXXXXXXX:7:1101:2921:100163#/2 +GAAAAGGAGAACCCCATGCGGGAACTTCGCATCCGCAAACTCTGTCTCAACATCTGTGTTGGGGAGAGTGGAGACAGACTGACGCGAGCAGCCAAGGTGT ++ +CCCFFFFFHHGHHJJIJJJJJJIIJJJIIIGDHIGIJJJIJJ>HHGEHHGEHFFFFCDEEDCBDDDBB>C@DDCDDDDDDDDDDB@BD@BDDDBDDD:@@ +@XXXXXXXXXX:7:1101:1513:1929#/2 +AAAATGAGGGCCCGTAACAGAACCAGTGTGTGTATAACGAAAACCATGTATAAAATGGGCCTATCACCCTTGTCAGAGATATAAATTACCACATTTGCCT ++ +?@@;;D>DFH:;?EFD:F<FE?;CBF:DCG?FD4?FIGHIGIJJGFGIFG@FGGDHIHIGHHGFFFFFECEDADCDACA>CAADACDDCDCC<ACDDDDD +@XXXXXXXXXX:7:1101:2759:100170#/2 +GGTCACCATGGATGGGCGAGTCAACGGGGGCCTCAACCTCTCCAGAGCCATTGGGGACCACTTCTATAAGAGAAACAAGAACCTGCCACCTGAGGAACAG ++ +CC@FFFFFHHHHHJJJJJIJGIIJJJJJJIJJGGHHCEFFFFEEEEDDDDDDDDDDDDDDDDDDDDEEDDDDCDDDDDDDDDDDDDDDDDDDDCDC?ABD +@XXXXXXXXXX:7:1101:1708:1937#/2 +GAATACTTTGTGTTTACCCACTGCCCCCTGACCACTGCTGAAGGCAGAAAGGGACGATCACCTACAGTACCTGGTTTGGGTCTTTATTCTCTCATTCTAG ++ +B@BFFFFFHHCFHIJIHGIGIIJJGGIJJGIIIGIGGIJJEIGIHHJJJJIHIIJJIJHHHGFBEFFCCEEDCD;@A?BB?ACCCCCCCCACD@DADA@C +@XXXXXXXXXX:7:1101:2981:100211#/2 +TTCCTCCTAACTCCTGCCAGAAACAGCTCTCCTCAACATGAGAGCTGCACCCCTCCTCCTGGCCAGGGCAGCAAGCCTTAGCCTTGGCTTCTTGTTTCTG ++ +@@BFFFFFHBDHHIHIIIIGGGADGGIGIEHIIIIJJIIIE<BHAHHHIGFGIJJJJIIHIBDGGEAEFFF;>CCABCDCDDCACDCCAA?@CD4:<@AC +@XXXXXXXXXX:7:1101:1688:1946#/2 +GAGAAAGGGAAGAAAGAGAAAGGAAAAGACGAAGGGAAGAGGAAGAAAGAGAAAAAGAAAGGGCTCGTGACAGAGAAAGAAGAAAGAGAAGTCGTTCACG ++ +BB@ADFFFHDDHAGGHGHGGHEHGIJJIIJIIJJJJ<FH;FGDEGEGHGIFHEGIJFFHHFDFFEDDBDDDDCCCACCDABDDDDDCCCCDCCD@B?CDD +@XXXXXXXXXX:7:1101:2767:100225#/2 +TGCAGAATGGCTCCCGCAAAGAAGGGTGGCGAGAAGAAAAAGGGCCGTTCTGCCATCAACGAAGTGGTAACCCGAGAATACACCATCAACATTCACAAGC ++ +@@@FFFFF<FFHHGGIJIIGGGIII>):?FF:FGGGIJIJIHCHHHFBCE;ACDDDDDCA@<@DBDDCDDCDDDDDDDDD@CCCDAA@>ACC>>A@@C1< +@XXXXXXXXXX:7:1101:1536:1959#/2 +GAGACAAAAATTGTTTGAATCAGGACAAGGGAGGTTTGAGGGACTGTTTAACAGGTCCCCATGGTTCACGACCCTGATATCCACCATTATGGGCCCTCTG ++ +@8@1:?:=DD>D<CE+A:+C?+AF++++281)?D):?HD=FG6((?88=CFFCHG7=@HH@9?3.)7772?3,9;A(((5>;5>BBAA:>CCD?8@BD9A +@XXXXXXXXXX:7:1101:2797:100234#/2 +GGAAACGCTGGAGAAGACAGTGTTGCTAGTCTGTTCCTGTTCGTGAGAATGCTTTGAATGGAGGCTCACTGTGCTGCGGCGGCTGCGGCCGTAGCGGGCG ++ +B1=+:A+0A::A2+2A2A3A<+2<?9<*119:9:1CC:DDFF<)800//9/>8E=<)/8@@@6C(6==737==>>@######################## +@XXXXXXXXXX:7:1101:1552:1976#/2 +TGTGAGCACACCATATATTTACAGTAGGAATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCACCGGCGTCAAAGT ++ +CCCFFFFFHHHHHIIGIGGIHJIGHHJIECGGGHJIJJJJJJJJJGHIJJGGHGIIEHIIJDIJFHFFFFF@CCCEECDDDDDCDDDB@BDDBBBDDCD> +@XXXXXXXXXX:7:1101:1748:1978#/2 +CAAGGAGCTGTTCTGTCGTGGCTTTGGAATTCAGATGCTCTCACTGTGATAGAGATGGGGTCTTGGGGGGCTGGGAGCTGTTCTGTCGTGGCTTTGGAGT ++ +B@@FFFFFHHHHHJJIIJHIJIJJJJJIIJJIJJJJJIJJJJIJJJGHFGGHHIIIJIJJ@GIIJJIHFDDDDDDABBDCCDDEDDDB?BDDDDCCDCDA +@XXXXXXXXXX:7:1101:2779:100239#/2 +GCTGTGGTTACCTGTCCCCTGCCCCTGGCCTCCAGCCAGCTGCCAGTGGCCCCTCAGCTGCCTGTGGTGAGGCAATACTTAGCTAGGTTCTTAGACGGCC ++ +?<?BBDDEFADA?ECCFFGEHDIDB;;FBG>GDHFGGGAFEHE?F@8?>F;CFCEADEEG@EEHAEFBDEEED7A>CACDECD>C@A(5>>C@>A##### +@XXXXXXXXXX:7:1101:1593:1980#/2 +GGCTGTTCTCGAACTCCTGACCTCAGGTGATCTGCCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACTGCGCCTAGCCGTCACATTTC ++ +CCCFFFFFHHHHHJJJJJJJJJJJJJJFHIIJJJJJIIJJJJJJJJJJJJJJJIHIJJJJJHIJJJJJJJHEEEFEEEEDECDDDDDDDDDBDDDCDDEE +@XXXXXXXXXX:7:1101:2946:100242#/2 +AATCCCTTCACCCCAGTTGCCAAACAGACCCCCCACCCCCTGGATTTTCCTTCTCCCTCCATCCCTTGACGGTTCTGGCCTTCCCAAACTGCTTTTGATC ++ +C@CFFFFFHHHFFHBHHHEIJJIIIJIIJCGGIIGIHHIJIG@D;DCE>>?AEEFF@@DB(.;>?;CC@>=',5<CC>ADCDCCDA>B?CDD>ACCC0>C +@XXXXXXXXXX:7:1101:1987:1781#/2 +GCCGCAACCTGCACAGCCATGCCCGGGCAAGAACTCAGGACGCTGAATGGCTCTCAGATGCTCCTGGTGTTGCTGGTGCTCTCGTGGCTGCCGCATGGGG ++ +CCCFFFFFHHHHHJJJJJJIJJJJJJJJJJJJJJJJJJIIJIJJJJJHHHHHFFFFFFEEEEEEDDDCCBDDDDDDDDDDDDDDDDDDDDDD<@BBDBBD +@XXXXXXXXXX:7:1101:3046:100006#/2 +GACGAGATGGAGTTCACCGAGGCCGAGAGCAACATGAATGACCTGGTGTCCGAGTACCAGCAGTACCAGGATGCCACAGCCGAGGAGGAGGGCGAGTTCG ++ +CCCFFFFFHHHHFIJJJJJIIJIJJIHIIIJJJIIJJJGIJJJIJJIJHGEHFFFEEEEEDDDDDDDDDDDCDDDDDDDDDDDDDDDDBDDBDD<B9@CB +@XXXXXXXXXX:7:1101:1900:1788#/2 +CGGCTATGCGCCACCCGAGACGGAGATCGTGCCGCTTGTGCTGCGCGGCCACCTCATGGACATCGAGTGCCTGGCCAGCGACGGCATGCTGCTGGTGAGC ++ +CCCFFFFFGHHHHJJJJJJHHJJIFHIJJHHIIIJJJIIIJJJJJHFDDD@@DDDDCDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDCDD<?C@C +@XXXXXXXXXX:7:1101:3214:100027#/2 +CACAACAACTGCTACTTCAGTTGCGCAGACAGTATCAACACCCACAACACAAGATCAGACCCCAAGTTCTGCTGTTTCAGTTGCCACGCCTACAGTTAGT ++ +@CCFFFFFGFHHHIIJJJIIHIIIIIJ<GIIG?DHIJJGIIJBHJJJJJIGCGGHHJJHHHHFDEF;ACEEEDDDDDCEDDDDCDCDDDDDDDCCDDDD> +@XXXXXXXXXX:7:1101:1848:1879#/2 +GGAGAAATGACCTTGAAGTCAGCACTTGCTTTAGCTATCAAAGTACTAAATAAGACCATGGATGTTAGTAAACTCTCTGCTGAAAAAGTGGAAATTGCAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cv_output.gff Tue May 30 09:02:11 2023 +0000 @@ -0,0 +1,18 @@ +##gff-version +#BBMapVersion +#ploidy 2 +#rarity 1.00000 +#minAlleleFraction 0.1000 +#reads 2207 +#pairedReads 0 +#properlyPairedReads 0 +#readLengthAvg +#properPairRate 0.0000 +#totalQualityAvg +#mapqAvg +#reference +#seqid source type start end score strand phase attributes +NC_002945.4 . sequence_variant_obs 976327 976327 +NC_002945.4 . sequence_variant_obs 1501932 1501932 +NC_002945.4 . sequence_variant_obs 3380579 3380579 +NC_002945.4 . sequence_variant_obs 3646293 3646293
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cv_output.txt Tue May 30 09:02:11 2023 +0000 @@ -0,0 +1,18 @@ +#fileformat +#BBMapVersion +#ploidy 2 +#rarity 1.00000 +#minAlleleFraction 0.1000 +#reads 2207 +#pairedReads 0 +#properlyPairedReads 0 +#readLengthAvg +#properPairRate +#totalQualityAvg +#mapqAvg +#reference +#scaf start stop type call r1p r1m r2p r2m paired lengthSum mapq mapqMax baseq baseqMax edist edistMax id idMax cov minusCov nearbyVarCount flagged contigEndDist phredScore readCount alleleFraction revisedAF strandRatio baseqAvg mapqAvg edistAvg identityAvg edistScore identityScore qualityScore pairedScore biasScore coverageScore homopolymerScore score +0 976326 976327 SUB T +0 1501931 1501932 SUB C +0 3380578 3380579 SUB G +0 3646292 3646293 SUB A
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cv_output.vcf Tue May 30 09:02:11 2023 +0000 @@ -0,0 +1,60 @@ +##fileformat=VCFv4.2 +##BBMapVersion= +##ploidy=2 +##rarity=1.00000 +##minallelefraction=0.10000 +##reads=2207 +##pairedReads=0 +##properlyPairedReads=0 +##readLengthAvg= +##properPairRate=0.00000 +##totalQualityAvg= +##mapqAvg=43.348 +##reference= +##contig=<ID=NC_002945.4,length=7000> +##FILTER=<ID=FAIL,Description="Fail"> +##FILTER=<ID=PASS,Description="Pass"> +##INFO=<ID=SN,Number=1,Type=Integer,Description="Scaffold Number"> +##INFO=<ID=STA,Number=1,Type=Integer,Description="Start"> +##INFO=<ID=STO,Number=1,Type=Integer,Description="Stop"> +##INFO=<ID=TYP,Number=1,Type=String,Description="Type"> +##INFO=<ID=R1P,Number=1,Type=Integer,Description="Read1 Plus Count"> +##INFO=<ID=R1M,Number=1,Type=Integer,Description="Read1 Minus Count"> +##INFO=<ID=R2P,Number=1,Type=Integer,Description="Read2 Plus Count"> +##INFO=<ID=R2M,Number=1,Type=Integer,Description="Read2 Minus Count"> +##INFO=<ID=AD,Number=1,Type=Integer,Description="Allele Depth"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> +##INFO=<ID=MCOV,Number=1,Type=Integer,Description="Minus Coverage"> +##INFO=<ID=PPC,Number=1,Type=Integer,Description="Paired Count"> +##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Fraction"> +##INFO=<ID=RAF,Number=1,Type=Float,Description="Revised Allele Fraction"> +##INFO=<ID=LS,Number=1,Type=Integer,Description="Length Sum"> +##INFO=<ID=MQS,Number=1,Type=Integer,Description="MAPQ Sum"> +##INFO=<ID=MQM,Number=1,Type=Integer,Description="MAPQ Max"> +##INFO=<ID=BQS,Number=1,Type=Integer,Description="Base Quality Sum"> +##INFO=<ID=BQM,Number=1,Type=Integer,Description="Base Quality Max"> +##INFO=<ID=EDS,Number=1,Type=Integer,Description="End Distance Sum"> +##INFO=<ID=EDM,Number=1,Type=Integer,Description="End Distance Max"> +##INFO=<ID=IDS,Number=1,Type=Integer,Description="Identity Sum"> +##INFO=<ID=IDM,Number=1,Type=Integer,Description="Identity Max"> +##INFO=<ID=NVC,Number=1,Type=Integer,Description="Nearby Variation Count"> +##INFO=<ID=FLG,Number=1,Type=Integer,Description="Flagged"> +##INFO=<ID=CED,Number=1,Type=Integer,Description="Contig End Distance"> +##INFO=<ID=HMP,Number=1,Type=Integer,Description="Homopolymer Count"> +##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias"> +##INFO=<ID=DP4,Number=4,Type=Integer,Description="Ref+, Ref-, Alt+, Alt-"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Allele Depth"> +##FORMAT=<ID=AF,Number=1,Type=Float,Description="Allele Fraction"> +##FORMAT=<ID=RAF,Number=1,Type=Float,Description="Revised Allele Fraction"> +##FORMAT=<ID=NVC,Number=1,Type=Integer,Description="Nearby Variation Count"> +##FORMAT=<ID=FLG,Number=1,Type=Integer,Description="Flagged"> +##FORMAT=<ID=SB,Number=1,Type=Float,Description="Strand Bias"> +##FORMAT=<ID=SC,Number=1,Type=Float,Description="Score"> +##FORMAT=<ID=PF,Number=1,Type=String,Description="Pass Filter"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT +NC_002945.4 976327 . N T 22.21 PASS SN=0;STA=976326;STO=976327;TYP=SUB;R1P=2;R1M=0;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1.0000;RAF=1.0000;LS=292;MQS=77;MQM=40;BQS=48;BQM=24;EDS=111;EDM=65;IDS=1930;IDM=972;NVC=0;FLG=0;CED=0;HMP=0;SB=0.9980 GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF 1/1:2:2:1.0000:1.0000:0:0:0.9980:22.21:PASS +NC_002945.4 1501932 . N C 27.20 PASS SN=0;STA=1501931;STO=1501932;TYP=SUB;R1P=0;R1M=2;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1.0000;RAF=1.0000;LS=292;MQS=88;MQM=44;BQS=64;BQM=39;EDS=74;EDM=38;IDS=1986;IDM=993;NVC=0;FLG=0;CED=0;HMP=0;SB=0.9980 GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF 1/1:2:2:1.0000:1.0000:0:0:0.9980:27.20:PASS +NC_002945.4 3380579 . N G 27.85 PASS SN=0;STA=3380578;STO=3380579;TYP=SUB;R1P=0;R1M=2;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1.0000;RAF=1.0000;LS=289;MQS=87;MQM=44;BQS=75;BQM=38;EDS=105;EDM=63;IDS=1986;IDM=993;NVC=0;FLG=0;CED=0;HMP=0;SB=0.9980 GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF 1/1:2:2:1.0000:1.0000:0:0:0.9980:27.85:PASS +NC_002945.4 3646293 . N A 23.34 PASS SN=0;STA=3646292;STO=3646293;TYP=SUB;R1P=1;R1M=1;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1.0000;RAF=1.0000;LS=291;MQS=86;MQM=44;BQS=76;BQM=38;EDS=44;EDM=31;IDS=1986;IDM=993;NVC=0;FLG=0;CED=0;HMP=0;SB=1.0000 GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF 1/1:2:2:1.0000:1.0000:0:0:1.0000:23.34:PASS
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cv_qualityhist_output.tabular Tue May 30 09:02:11 2023 +0000 @@ -0,0 +1,46 @@ +#BaseQualityHist +#Vars +#Mean +#Median +#Mode +#Quality AvgCount MaxCount +0 0 0 +1 0 0 +2 0 0 +3 0 0 +4 0 0 +5 0 0 +6 0 0 +7 0 0 +8 0 0 +9 0 0 +10 0 0 +11 0 0 +12 0 0 +13 0 0 +14 0 0 +15 0 0 +16 0 0 +17 0 0 +18 0 0 +19 0 0 +20 0 0 +21 0 0 +22 0 0 +23 0 0 +24 1 1 +25 0 0 +26 0 0 +27 0 0 +28 0 0 +29 0 0 +30 0 0 +31 0 0 +32 1 0 +33 0 0 +34 0 0 +35 0 0 +36 0 0 +37 1 0 +38 1 2 +39 0 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cv_scorehist_output.tabular Tue May 30 09:02:11 2023 +0000 @@ -0,0 +1,34 @@ +#ScoreHist +#Vars +#Mean +#Median +#Mode +#Quality Count +0 0 +1 0 +2 0 +3 0 +4 0 +5 0 +6 0 +7 0 +8 0 +9 0 +10 0 +11 0 +12 0 +13 0 +14 0 +15 0 +16 0 +17 0 +18 0 +19 0 +20 0 +21 0 +22 1 +23 1 +24 0 +25 0 +26 0 +27 2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cv_zygosityhist_output.tabular Tue May 30 09:02:11 2023 +0000 @@ -0,0 +1,8 @@ +#ZygoHist +#Vars +#Mean +#HomozygousFraction +#Zygosity Count +0 0 +1 0 +2 4
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fasta_indexes.loc Tue May 30 09:02:11 2023 +0000 @@ -0,0 +1,1 @@ +89 89 Mycobacterium_AF2122 ${__HERE__}/NC_002945v4.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Tue May 30 09:02:11 2023 +0000 @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue May 30 09:02:11 2023 +0000 @@ -0,0 +1,8 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Location of SAMTools indexes for FASTA files --> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/fasta_indexes.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Tue May 30 09:02:11 2023 +0000 @@ -0,0 +1,6 @@ +<tables> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/fasta_indexes.loc" /> + </table> +</tables>