Mercurial > repos > iuc > bbtools_bbduk
changeset 0:132af91f11b9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bbduk.xml Thu Nov 11 16:36:50 2021 +0000 @@ -0,0 +1,356 @@ +<tool id="bbtools_bbduk" name="BBTools: BBduk" version="@WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>decontamination using kmers</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +#import os +#import re + +#if str($input_type_cond.input_type) in ['single', 'pair']: + #set read1 = $input_type_cond.read1 + #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier)) + ## bbduk uses the file extension to determine the input format. + #set ext = $read1_identifier + '.fastq' + #if $read1.ext.endswith('.gz'): + #set ext = $ext + '.gz' + #end if + #set read1_file = $read1_identifier + $ext + ln -s '${read1}' '${read1_file}' && + #if str($input_type_cond.input_type) == 'pair': + #set read2 = $input_type_cond.read2 + #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier)) + #set read2_file = $read2_identifier + $ext + ln -s '${read2}' '${read2_file}' && + #end if +#else: + #set read1 = $input_type_cond.reads_collection['forward'] + #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.name)) + ## bbduk uses the file extension to determine the input format. + #set ext = $read1_identifier + '.fastq' + #if $read1.ext.endswith('.gz'): + #set ext = $ext + '.gz' + #end if + #set read1_file = $read1_identifier + $ext + ln -s '${read1}' '${read1_file}' && + #set read2 = $input_type_cond.reads_collection['reverse'] + #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.name)) + #set read2_file = $read2_identifier + $ext + ln -s '${read2}' '${read2_file}' && +#end if + +#if str($reference_type_cond.reference_type) == 'files': + #set refs = list() + #for ref in $reference_type_cond.reference: + ## bbduk looks at the file extension. + #set ref_name = str($os.path.basename($ref.file_name)) + '.fa' + #if $ref.ext.endswith('.gz'): + gunzip -c '$ref' > '$ref_name' && + #else: + ln -s '$ref' '$ref_name' && + #end if + $refs.append(str($ref_name)) + #end for + #set refs = ','.join($refs) +#else if str($reference_type_cond.reference_type) == 'keywords': + #set refs = str($reference_type_cond.reference) +#end if + +bbduk.sh +in='${read1_file}' + +#if str($input_type_cond.input_type) in ['pair', 'paired']: + in2='${read2_file}' +#end if +#if str($outputs_select).find('outu') >= 0: + out='${outputu}' + #if str($input_type_cond.input_type) in ['pair', 'paired']: + out2='${outputu2}' + #end if +#end if +#if str($outputs_select).find('outm') >= 0: + outm='${outputm}' + #if str($input_type_cond.input_type) in ['pair', 'paired']: + outm2='${outputm2}' + #end if +#end if +#if str($outputs_select).find('outs') >= 0: + outs='${outputs}' +#end if + +#if str($reference_type_cond.reference_type) != 'no_reference': + ref='$refs' + #if str($reference_type_cond.ktrim_cond.ktrim_select) == 'yes': + ktrim='${reference_type_cond.ktrim_cond.ktrim}' + minlength=$reference_type_cond.ktrim_cond.minlength + #end if +#end if + +k=$advanced_options.k +rcomp='${advanced_options.rcomp}' +maskmiddle='${advanced_options.maskmiddle}' +minkmerhits='${advanced_options.minkmerhits}' +minkmerfraction=$advanced_options.minkmerfraction +mincovfraction=$advanced_options.mincovfraction +hammingdistance=$advanced_options.hammingdistance +qhdist=$advanced_options.qhdist +editdistance=$advanced_options.editdistance +forbidn='${advanced_options.forbidn}' +trimfailures='${advanced_options.trimfailures}' +findbestmatch='${advanced_options.findbestmatch}' +skipr1='${advanced_options.skipr1}' +skipr2='${advanced_options.skipr2}' + +#if str($output_stats_cond.output_stats) == 'yes': + #if str($output_stats_cond.output_stats_select).find('stats') >= 0: + stats='${output_stats}' + #end if + #if str($output_stats_cond.output_stats_select).find('ref') >= 0: + refstats='${output_ref}' + #end if + #if str($output_stats_cond.output_stats_select).find('rpkm') >= 0: + rpkm='${output_rpkm}' + #end if + #if str($output_stats_cond.output_stats_select).find('dump') >= 0: + dump='${output_dump}' + #end if +#end if +#if str($output_hists_cond.output_hists) == 'yes': + #if str($output_hists_cond.output_hists_select).find('bhist') >= 0: + bhist='${output_bhist}' + #end if + #if str($output_hists_cond.output_hists_select).find('quhist') >= 0: + qhist='${output_quhist}' + #end if + #if str($output_hists_cond.output_hists_select).find('quchist') >= 0: + qchist='${output_quchist}' + #end if + #if str($output_hists_cond.output_hists_select).find('aqhist') >= 0: + aqhist='${output_aqhist}' + #end if + #if str($output_hists_cond.output_hists_select).find('bqhist') >= 0: + bqhist='${output_bqhist}' + #end if + #if str($output_hists_cond.output_hists_select).find('lhist') >= 0: + lhist='${output_lhist}' + #end if + #if str($output_hists_cond.output_hists_select).find('phist') >= 0: + phist='${output_phist}' + #end if + #if str($output_hists_cond.output_hists_select).find('gchist') >= 0: + gchist='${output_gchist}' + #end if + #if str($output_hists_cond.output_hists_select).find('enthist') >= 0: + enthist='${output_enthist}' + #end if +#end if +t=\${GALAXY_SLOTS:-4} +]]></command> + <inputs> + <expand macro="input_type_cond"/> + <conditional name="reference_type_cond"> + <param name="reference_type" type="select" label="Choose the reference type" help="Optional, no reference is the default"> + <option value="no_reference" selected="true">No reference</option> + <option value="files">files</option> + <option value="keywords">keywords</option> + </param> + <when value="no_reference"/> + <when value="files"> + <param name="reference" type="data" format="fasta,fasta.gz" multiple="true" optional="false" label="Select one or more fasta file"/> + <expand macro="ktrim_cond"/> + </when> + <when value="keywords"> + <param name="reference" type="select" multiple="true" optional="false" label="Select one or more keywords"> + <option value="adapters">adapters</option> + <option value="artifacts">artifacts</option> + <option value="phix">phix</option> + <option value="lambda">lambda</option> + <option value="pjet">pjet</option> + <option value="mtst">mtst</option> + <option value="kapa">kapa</option> + </param> + <expand macro="ktrim_cond"/> + </when> + </conditional> + <section name="advanced_options" title="Advanced options" expanded="false"> + <param argument="k" type="integer" value="27" min="1" label="Kmer length used for finding contaminants"/> + <param argument="rcomp" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Look for reverse-complements of kmers in addition to forward kmers?"/> + <param argument="maskmiddle" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Treat the middle base of a kmer as a wildcard to increase sensitivity in the presence of errors?"/> + <param argument="minkmerhits" type="integer" value="1" min="1" label="Reads need at least this many matching kmers to be considered as matching the reference"/> + <param argument="minkmerfraction" type="float" value="0" min="0" label="A read needs at least this fraction of its total kmers to hit a ref in order to be considered a match"/> + <param argument="mincovfraction" type="float" value="0" min="0" label="A read needs at least this fraction of its total bases to be covered by ref kmers to be considered a match"/> + <param argument="hammingdistance" type="integer" value="0" min="0" label="Maximum Hamming distance for ref kmers (subs only)"/> + <param argument="qhdist" type="integer" value="0" min="0" label="Hamming distance for query kmers"/> + <param argument="editdistance" type="integer" value="0" min="0" label="Maximum edit distance from ref kmers (subs and indels)"/> + <param argument="forbidn" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Do not match kmers comntaining N?"/> + <param argument="trimfailures" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Trim failed reads to 1bp instead of discarding them?"/> + <param argument="findbestmatch" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Associate read with sequence sharing most kmers if multiple matches?"/> + <param argument="skipr1" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Don't do kmer-based operations on read 1?"/> + <param argument="skipr2" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Don't do kmer-based operations on read 2?"/> + </section> + <param name="outputs_select" type="select" multiple="true" optional="false" label="Specify outputs"> + <option value="outu">Unmatched</option> + <option value="outm">Matched</option> + <option value="outs">Single</option> + </param> + <conditional name="output_stats_cond"> + <param name="output_stats" type="select" label="Output statistics?"> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param name="output_stats_select" type="select" multiple="true" optional="false" label="Specify statistics outputs"> + <option value="stats">Statistics about which contamininants were detected</option> + <option value="ref">Statistics on a per-reference-file basis</option> + <option value="rpkm">RPKM for each reference sequence (for RNA-seq)</option> + <option value="dump">kmer tables in fasta format</option> + </param> + </when> + </conditional> + <conditional name="output_hists_cond"> + <param name="output_hists" type="select" label="Output histograms?"> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param name="output_hists_select" type="select" multiple="true" optional="false" label="Specify statistics outputs"> + <option value="bhist">Base composition histogram by position</option> + <option value="quhist">Quality histogram by position</option> + <option value="quchist">Count of bases with each quality value</option> + <option value="aqhist">Histogram of average read quality</option> + <option value="bqhist">Quality histogram designed for box plots</option> + <option value="lhist">Read length histogram</option> + <option value="phist">Polymer length histogram</option> + <option value="gchist">Read GC content histogram</option> + <option value="enthist">Read entropy histogram</option> + </param> + </when> + </conditional> + </inputs> + <outputs> + <data name="outputu" format="fastqsanger" label="${tool.name} on ${on_string} (Unmatched)"> + <filter>str(outputs_select).find('outu') >= 0</filter> + <filter>'outu' in outputs_select</filter> + </data> + <data name="outputu2" format="fastqsanger" label="${tool.name} on ${on_string} (Unmatched)"> + <filter>'outu' in outputs_select and input_type_cond['input_type'] != 'single'</filter> + </data> + <data name="outputm" format="fastqsanger" label="${tool.name} on ${on_string} (Matched)"> + <filter>'outm' in outputs_select</filter> + </data> + <data name="outputm2" format="fastqsanger" label="${tool.name} on ${on_string} (Matched)"> + <filter>'outm' in outputs_select and input_type_cond['input_type'] != 'single'</filter> + </data> + <data name="outputs" format="fastqsanger" label="${tool.name} on ${on_string} (Single)"> + <filter>'outs' in outputs_select</filter> + </data> + <data name="output_stats" format="tabular" label="${tool.name} on ${on_string} (Detected contaminates stats)"> + <filter>output_stats_cond['output_stats'] == 'yes' and 'stats' in output_stats_cond['output_stats_select']</filter> + </data> + <data name="output_ref" format="tabular" label="${tool.name} on ${on_string} (Per reference file stats)"> + <filter>output_stats_cond['output_stats'] == 'yes' and 'ref' in output_stats_cond['output_stats_select']</filter> + </data> + <data name="output_rpkm" format="tabular" label="${tool.name} on ${on_string} (RPKM for each ref seq)"> + <filter>output_stats_cond['output_stats'] == 'yes' and 'rpkm' in output_stats_cond['output_stats_select']</filter> + </data> + <data name="output_dump" format="fasta" label="${tool.name} on ${on_string} (kmer tables)"> + <filter>output_stats_cond['output_stats'] == 'yes' and 'dump' in output_stats_cond['output_stats_select']</filter> + </data> + <data name="output_bhist" format="tabular" label="${tool.name} on ${on_string} (Base composition py poition)"> + <filter>output_hists_cond['output_hists'] == 'yes' and 'bhist' in output_hists_cond['output_hists_select']</filter> + </data> + <data name="output_quhist" format="tabular" label="${tool.name} on ${on_string} (Quality by position)"> + <filter>output_hists_cond['output_hists'] == 'yes' and 'quhist' in output_hists_cond['output_hists_select']</filter> + </data> + <data name="output_quchist" format="tabular" label="${tool.name} on ${on_string} (Bases w/ each quality value)"> + <filter>output_hists_cond['output_hists'] == 'yes' and 'quchist' in output_hists_cond['output_hists_select']</filter> + </data> + <data name="output_aqhist" format="tabular" label="${tool.name} on ${on_string} (average read quality)"> + <filter>output_hists_cond['output_hists'] == 'yes' and 'aqhist' in output_hists_cond['output_hists_select']</filter> + </data> + <data name="output_bqhist" format="tabular" label="${tool.name} on ${on_string} (Quality for box plots)"> + <filter>output_hists_cond['output_hists'] == 'yes' and 'bqhist' in output_hists_cond['output_hists_select']</filter> + </data> + <data name="output_lhist" format="tabular" label="${tool.name} on ${on_string} (Read length)"> + <filter>output_hists_cond['output_hists'] == 'yes' and 'lhist' in output_hists_cond['output_hists_select']</filter> + </data> + <data name="output_phist" format="tabular" label="${tool.name} on ${on_string} (Polymer length)"> + <filter>output_hists_cond['output_hists'] == 'yes' and 'phist' in output_hists_cond['output_hists_select']</filter> + </data> + <data name="output_gchist" format="tabular" label="${tool.name} on ${on_string} (Read GC content)"> + <filter>output_hists_cond['output_hists'] == 'yes' and 'gchist' in output_hists_cond['output_hists_select']</filter> + </data> + <data name="output_enthist" format="tabular" label="${tool.name} on ${on_string} (Read entropy)"> + <filter>output_hists_cond['output_hists'] == 'yes' and 'enthist' in output_hists_cond['output_hists_select']</filter> + </data> + </outputs> + <tests> + <!-- Single read --> + <test expect_num_outputs="1"> + <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/> + <param name="reference" value="adapters.fa.gz" ftype="fasta.gz"/> + <param name="reference_type" value="files"/> + <param name="outputs_select" value="outu"/> + <output name="outputu" file="bduk_outputu1.fastqsanger" ftype="fastqsanger" compare="contains"/> + </test> + <!-- Paired reads in separate datasets --> + <test expect_num_outputs="4"> + <param name="input_type" value="pair"/> + <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/> + <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz"/> + <param name="reference_type" value="files"/> + <param name="reference" value="adapters.fa.gz" ftype="fasta.gz"/> + <param name="outputs_select" value="outu"/> + <param name="output_stats" value="yes"/> + <param name="output_stats_select" value="dump"/> + <param name="output_hists" value="yes"/> + <param name="output_hists_select" value="quhist"/> + <output name="outputu" file="bduk_outputu1.fastqsanger" ftype="fastqsanger" compare="contains"/> + <output name="outputu2" file="bduk_outputu2.fastqsanger" ftype="fastqsanger" compare="contains"/> + <output name="output_dump" file="bduk_output_dump1.fasta" ftype="fasta" compare="contains"/> + <output name="output_quhist" file="bduk_output_quhist1.tabular" ftype="tabular"/> + </test> + <!-- Collection of Paired reads --> + <test expect_num_outputs="2"> + <param name="input_type" value="paired"/> + <param name="reads_collection"> + <collection type="paired"> + <element name="forward" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/> + <element name="reverse" value="13-1941-6_S4_L001_R2_600000.fastq.gz"/> + </collection> + </param> + <param name="reference_type" value="keywords"/> + <param name="reference" value="adapters,artifacts,phix,lambda,pjet,mtst,kapa"/> + <param name="outputs_select" value="outu"/> + <output name="outputu" file="bduk_outputu1.fastqsanger" ftype="fastqsanger" compare="contains"/> + <output name="outputu2" file="bduk_outputu2.fastqsanger" ftype="fastqsanger" compare="contains"/> + </test> + </tests> + <help> +**What it does** + +BBDuk was developed to combine most common data-quality-related trimming, filtering, and masking operations into a single +high-performance tool. It is capable of quality-trimming and filtering, adapter-trimming, contaminant-filtering via kmer +matching, sequence masking, GC-filtering, length filtering, entropy-filtering, format conversion, histogram generation, +subsampling, quality-score recalibration, kmer cardinality estimation, and various other operations in a single pass. +Specifically, any combination of operations is possible in a single pass with the exception of kmer-based operations (kmer +trimming, kmer masking, or kmer filtering). At most 1 kmer-based operation can be done in a single pass. + +**Options** + + * **Reference** - if a reference is specified, BBDuk will operate on kmers in one of 4 modes: right-trimming, left-trimming, masking, or filtering. The default is filtering - any read matching a reference kmer will be discarded. + + * **Trim reads to remove bases matching reference kmers** - When trimming to the right, once a reference kmer is matched in a read, that kmer and all the bases to the right will be trimmed, leaving only the bases to the left. When trimming to the left, trimming will be done to the left instead. + +**Outputs** + + * **Unmatched** - All the reads that pass all filtering criteria. Reads will be at least as long as **Minimum read length** after any trimming operations and reads will not match any reference kmer if kmer-filtering is being performed. A read’s average quality will be at least as high as the specified **Minimum average quality**. + * **Matched** - Reads failing any filter criteria (such as matching a reference kmer). By default, if either read in a pair fails, both will be included in *Matched*. + * **Single** - Singleton reads whose mate was trimmed shorter than the value of **Minimum read length**. + </help> + <expand macro="citations"/> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Nov 11 16:36:50 2021 +0000 @@ -0,0 +1,96 @@ +<macros> + <token name="@WRAPPER_VERSION@">1.0.0</token> + <token name="@VERSION_SUFFIX@">1.0.0</token> + <token name="@PROFILE@">20.09</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="38.92">bbmap</requirement> + </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="Read1 fastq file"/> + </when> + <when value="pair"> + <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/> + <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Read2 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/test-data/NC_002945v4.fasta Thu Nov 11 16:36:50 2021 +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/bduk_output_dump1.fasta Thu Nov 11 16:36:50 2021 +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 Thu Nov 11 16:36:50 2021 +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 Thu Nov 11 16:36:50 2021 +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 Thu Nov 11 16:36:50 2021 +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 Thu Nov 11 16:36:50 2021 +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 Thu Nov 11 16:36:50 2021 +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 Thu Nov 11 16:36:50 2021 +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 Thu Nov 11 16:36:50 2021 +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 Thu Nov 11 16:36:50 2021 +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 Thu Nov 11 16:36:50 2021 +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 Thu Nov 11 16:36:50 2021 +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 Thu Nov 11 16:36:50 2021 +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 Thu Nov 11 16:36:50 2021 +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 Thu Nov 11 16:36:50 2021 +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>