Mercurial > repos > triasteran > bowtie_remove_rrna_wrapper
changeset 5:f15caf1ebddd draft
Deleted selected files
| author | triasteran |
|---|---|
| date | Wed, 23 Feb 2022 13:29:59 +0000 |
| parents | de9c7fd47a62 |
| children | c0267c5fbc65 |
| files | bowtie_remove_rrna_wrapper/.hgignore bowtie_remove_rrna_wrapper/bowtie_indices.loc.sample bowtie_remove_rrna_wrapper/bowtie_remove_rrna_wrapper.xml bowtie_remove_rrna_wrapper/bowtie_wrapper.py bowtie_remove_rrna_wrapper/test-data/bowtie_in2.fastqsanger bowtie_remove_rrna_wrapper/test-data/bowtie_in5.fastqillumina bowtie_remove_rrna_wrapper/test-data/bowtie_in5.fastqsanger bowtie_remove_rrna_wrapper/test-data/bowtie_in5.fastqsolexa bowtie_remove_rrna_wrapper/test-data/bowtie_in6.fastqillumina bowtie_remove_rrna_wrapper/test-data/bowtie_in6.fastqsanger bowtie_remove_rrna_wrapper/test-data/bowtie_in6.fastqsolexa bowtie_remove_rrna_wrapper/test-data/bowtie_out10.sam bowtie_remove_rrna_wrapper/test-data/bowtie_out6.sam bowtie_remove_rrna_wrapper/test-data/bowtie_out7.sam bowtie_remove_rrna_wrapper/test-data/bowtie_out8_1.fastq bowtie_remove_rrna_wrapper/test-data/bowtie_out8_1.fastqillumina.sorted bowtie_remove_rrna_wrapper/test-data/bowtie_out8_1.fastqsolexa.sorted bowtie_remove_rrna_wrapper/test-data/bowtie_out8_2.fastq bowtie_remove_rrna_wrapper/test-data/bowtie_out8_2.fastqillumina.sorted bowtie_remove_rrna_wrapper/test-data/bowtie_out8_2.fastqsolexa.sorted bowtie_remove_rrna_wrapper/test-data/bowtie_out9.sam bowtie_remove_rrna_wrapper/test-data/phiX.fasta bowtie_remove_rrna_wrapper/tool-data/bowtie_indices.loc bowtie_remove_rrna_wrapper/tool_data_table_conf.xml.sample |
| diffstat | 24 files changed, 0 insertions(+), 2021 deletions(-) [+] |
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--- a/bowtie_remove_rrna_wrapper/.hgignore Wed Feb 23 12:22:25 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -syntax: glob -.idea
--- a/bowtie_remove_rrna_wrapper/bowtie_indices.loc.sample Wed Feb 23 12:22:25 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -Mouse_rRNA Mouse_rRNA Mouse_rRNA /home/DATA/galaxy/galaxy-dist/data/indexes/bowtie_rrna_indexes/Mouse_rRNA/bowtie_rrna_indexes/mouse_rRNA_index
--- a/bowtie_remove_rrna_wrapper/bowtie_remove_rrna_wrapper.xml Wed Feb 23 12:22:25 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,681 +0,0 @@ -<tool id="bowtie_remove_rrna_wrapper" name="Remove rRNA using Bowtie" version="0.1.0" python_template_version="2.7"> - <requirements> - <requirement type="package" version="1.3.1">bowtie</requirement> - </requirements> - <command detect_errors="exit_code"><![CDATA[ - python2 '__tool_directory__/bowtie_wrapper.py' - ## Set number of threads - --threads="\${GALAXY_SLOTS:-4}" - ## Outputs - --output="${output}" - #if str( $singlePaired.sPaired ) == "single" - #if $output_unmapped_reads_l - --output_unmapped_reads="${output_unmapped_reads_l}" - #end if - #if $output_suppressed_reads_l - --output_suppressed_reads="${output_suppressed_reads_l}" - #end if - --galaxy_input_format="${singlePaired.sInput1.ext}" - #else - #if $output_unmapped_reads_l and $output_unmapped_reads_r - --output_unmapped_reads_l="${output_unmapped_reads_l}" - --output_unmapped_reads_r="${output_unmapped_reads_r}" - #end if - #if $output_suppressed_reads_l and $output_suppressed_reads_l - --output_suppressed_reads_l="${output_suppressed_reads_l}" - --output_suppressed_reads_r="${output_suppressed_reads_r}" - #end if - --galaxy_input_format="${singlePaired.pInput1.ext}" - #end if - ## Inputs - --dataType="solexa" ##this indicates that nucleotide base space is used in the wrapper - --suppressHeader="${suppressHeader}" - --genomeSource="${refGenomeSource.genomeSource}" - #if $refGenomeSource.genomeSource == "history": - ##index already exists - #if $refGenomeSource.ownFile.extension.startswith( 'bowtie_' ): - ##user previously built - --ref="${refGenomeSource.ownFile.extra_files_path}/${refGenomeSource.ownFile.metadata.base_name}" - --do_not_build_index - #else: - ##build index on the fly - --ref="${refGenomeSource.ownFile}" - --indexSettings="${refGenomeSource.indexParams.indexSettings}" - #if $refGenomeSource.indexParams.indexSettings == "indexFull": - --iautoB="${refGenomeSource.indexParams.autoBehavior.autoB}" - #if $refGenomeSource.indexParams.autoBehavior.autoB == "set": - --ipacked="${refGenomeSource.indexParams.autoBehavior.packed}" - --ibmax="${refGenomeSource.indexParams.autoBehavior.bmax}" - --ibmaxdivn="${refGenomeSource.indexParams.autoBehavior.bmaxdivn}" - --idcv="${refGenomeSource.indexParams.autoBehavior.dcv}" - #end if - --inodc="${refGenomeSource.indexParams.nodc}" - --inoref="${refGenomeSource.indexParams.noref}" - --ioffrate="${refGenomeSource.indexParams.offrate}" - --iftab="${refGenomeSource.indexParams.ftab}" - --intoa="${refGenomeSource.indexParams.ntoa}" - --iendian="${refGenomeSource.indexParams.endian}" - --iseed="${refGenomeSource.indexParams.seed}" - --icutoff="${refGenomeSource.indexParams.cutoff}" - #end if - #end if - #else - ##use pre-built index - --ref="${refGenomeSource.index.fields.path}" - #end if - --paired="${singlePaired.sPaired}" - #if $singlePaired.sPaired == "single": - --input1="${singlePaired.sInput1}" - --params="${singlePaired.sParams.sSettingsType}" - #if $singlePaired.sParams.sSettingsType == "full": - --skip="${singlePaired.sParams.sSkip}" - --alignLimit="${singlePaired.sParams.sAlignLimit}" - --trimH="${singlePaired.sParams.sTrimH}" - --trimL="${singlePaired.sParams.sTrimL}" - --mismatchSeed="${singlePaired.sParams.sMismatchSeed}" - --mismatchQual="${singlePaired.sParams.sMismatchQual}" - --seedLen="${singlePaired.sParams.sSeedLen}" - --rounding="${singlePaired.sParams.sRounding}" - --maqSoapAlign="${singlePaired.sParams.sMaqSoapAlign}" - --reverseAlign="${singlePaired.sParams.sReverseAlign}"<!--Added by Claire for "norc"--> - --tryHard="${singlePaired.sParams.sTryHard}" - --valAlign="${singlePaired.sParams.sValAlign}" - --allValAligns="${singlePaired.sParams.sAllValAligns}" - --suppressAlign="${singlePaired.sParams.sSuppressAlign}" - --best="${singlePaired.sParams.sBestOption.sBest}" - #if $singlePaired.sParams.sBestOption.sBest == "doBest": - --maxBacktracks="${singlePaired.sParams.sBestOption.sdMaxBacktracks}" - --strata="${singlePaired.sParams.sBestOption.sdStrata}" - #else: - --maxBacktracks="${singlePaired.sParams.sBestOption.snMaxBacktracks}" - #end if - --offrate="${singlePaired.sParams.sOffrate}" - --seed="${singlePaired.sParams.sSeed}" - #end if - #else: - --input1="${singlePaired.pInput1}" - --input2="${singlePaired.pInput2}" - --maxInsert="${singlePaired.pMaxInsert}" - --mateOrient="${singlePaired.pMateOrient}" - --params="${singlePaired.pParams.pSettingsType}" - #if $singlePaired.pParams.pSettingsType == "full": - --skip="${singlePaired.pParams.pSkip}" - --alignLimit="${singlePaired.pParams.pAlignLimit}" - --trimH="${singlePaired.pParams.pTrimH}" - --trimL="${singlePaired.pParams.pTrimL}" - --mismatchSeed="${singlePaired.pParams.pMismatchSeed}" - --mismatchQual="${singlePaired.pParams.pMismatchQual}" - --seedLen="${singlePaired.pParams.pSeedLen}" - --rounding="${singlePaired.pParams.pRounding}" - --maqSoapAlign="${singlePaired.pParams.pMaqSoapAlign}" - --minInsert="${singlePaired.pParams.pMinInsert}" - --maxAlignAttempt="${singlePaired.pParams.pMaxAlignAttempt}" - --forwardAlign="${singlePaired.pParams.pForwardAlign}" - --reverseAlign="${singlePaired.pParams.pReverseAlign}" - --tryHard="${singlePaired.pParams.pTryHard}" - --valAlign="${singlePaired.pParams.pValAlign}" - --allValAligns="${singlePaired.pParams.pAllValAligns}" - --suppressAlign="${singlePaired.pParams.pSuppressAlign}" - --best="${singlePaired.pParams.pBestOption.pBest}" - #if $singlePaired.pParams.pBestOption.pBest == "doBest": - --maxBacktracks="${singlePaired.pParams.pBestOption.pdMaxBacktracks}" - --strata="${singlePaired.pParams.pBestOption.pdStrata}" - #else: - --maxBacktracks="${singlePaired.pParams.pBestOption.pnMaxBacktracks}" - #end if - --offrate="${singlePaired.pParams.pOffrate}" - --seed="${singlePaired.pParams.pSeed}" - #end if - #end if - ]]></command> - <inputs> - <conditional name="refGenomeSource"> - <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> - <option value="indexed">Use a built-in index</option> - <option value="history">Use one from the history</option> - </param> - <when value="indexed"> - <param name="index" type="select" label="Select the appropriate rRNA index" help="If the rRNA index for your organism is not listed, you will need to upload a fasta file of the rRNA sequences. "> - <options from_data_table="bowtie_rrna_indexes"> - <filter type="sort_by" column="2" /> - <validator type="no_options" message="No indexes are available" /> - </options> - </param> - </when> - <when value="history"> - <param name="ownFile" type="data" format="bowtie_base_index,fasta" label="Select the reference genome" /> - <conditional name="indexParams"> - <param name="indexSettings" type="select" label="Choose whether to use Default options for building indices or to Set your own" help="These settings are ignored when using a prebuilt index"> - <option value="indexPreSet">Default</option> - <option value="indexFull">Set your own</option> - </param> - <when value="indexPreSet" /> - <when value="indexFull"> - <conditional name="autoBehavior"> - <param name="autoB" type="select" label="Choose to use automatic or specified behavior for some parameters (-a)" help="Allows you to set --packed, --bmax, --bmaxdivn, and --dcv"> - <option value="auto">Automatic behavior</option> - <option value="set">Set values (sets --noauto and allows others to be set)</option> - </param> - <when value="auto" /> - <when value="set"> - <param name="packed" type="select" label="Whether or not to use a packed representation for DNA strings (--packed)"> - <option value="unpacked">Use regular representation</option> - <option value="packed">Use packed representation</option> - </param> - <param name="bmax" type="integer" value="-1" label="Maximum number of suffixes allowed in a block (--bmax)" help="-1 for not specified. Must be at least 1" /> - <param name="bmaxdivn" type="integer" value="4" label="Maximum number of suffixes allowed in a block as a fraction of the length of the reference (--bmaxdivn)" /> - <param name="dcv" type="integer" value="1024" label="The period for the difference-cover sample (--dcv)" /> - </when> - </conditional> - <param name="nodc" type="select" label="Whether or not to disable the use of the difference-cover sample (--nodc)" help="Suffix sorting becomes quadratic-time in the worst case (with a very repetitive reference)"> - <option value="dc">Use difference-cover sample</option> - <option value="nodc">Disable difference-cover sample</option> - </param> - <param name="noref" type="select" label="Whether or not to build the part of the reference index used only in paired-end alignment (-r)"> - <option value="ref">Build all index files</option> - <option value="noref">Do not build paired-end alignment index files</option> - </param> - <param name="offrate" type="integer" value="5" label="How many rows get marked during annotation of some or all of the Burrows-Wheeler rows (-o)" /> - <param name="ftab" type="integer" value="10" label="The size of the lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query (-t)" help="ftab is 4^(n+1) bytes" /> - <param name="ntoa" type="select" label="Whether or not to convert Ns in the reference sequence to As (--ntoa)"> - <option value="no">Do not convert Ns</option> - <option value="yes">Convert Ns to As</option> - </param> - <param name="endian" type="select" label="Endianness to use when serializing integers to the index file (--big/--little)" help="Little is most appropriate for Intel- and AMD-based architecture"> - <option value="little">Little</option> - <option value="big">Big</option> - </param> - <param name="seed" type="integer" value="-1" label="Seed for the pseudorandom number generator (--seed)" help="Use -1 to use default" /> - <param name="cutoff" type="integer" value="-1" label="Number of first bases of the reference sequence to index (--cutoff)" help="Use -1 to use default" /> - </when> <!-- indexFull --> - </conditional> <!-- indexParams --> - </when> <!-- history --> - </conditional> <!-- refGenomeSource --> - <conditional name="singlePaired"> - <param name="sPaired" type="select" label="Is this library mate-paired?"> - <option value="single">Single-end</option> - <option value="paired">Paired-end</option> - </param> - <when value="single"> - <param name="sInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="FASTQ file" help="Must have ASCII encoded quality scores"/> - <conditional name="sParams"> - <param name="sSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"> - <option value="preSet">Commonly used</option> - <option value="full" selected="true">Full parameter list</option> - </param> - <when value="preSet" /> - <when value="full"> - <param name="sSkip" type="integer" value="0" label="Skip the first n reads (-s)" /> - <param name="sAlignLimit" type="integer" value="-1" label="Only align the first n reads (-u)" help="-1 for off" /> - <param name="sTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" /> - <param name="sTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" /> - <param name="sMismatchSeed" type="integer" value="2" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" /> - <param name="sMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" /> - <param name="sSeedLen" type="integer" value="25" label="Seed length (-l)" help="Minimum value is 5" /> - <param name="sRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)"> - <option value="round">Round to nearest 10</option> - <option value="noRound">Do not round to nearest 10</option> - </param> - <param name="sMaqSoapAlign" type="integer" value="3" label="Number of mismatches for SOAP-like alignment policy (-v)" help="-1 for default MAQ-like alignment policy" /> - <param name="sReverseAlign" type="select" label="Choose whether or not to align against the reverse-complement reference strand (--norc)"> <!--Added by Claire--> - <option value="noReverse">Do not align against the reverse-complement reference strand</option> - <option value="reverse">Align against the reverse-complement reference strand</option> - </param> - <param name="sTryHard" type="select" label="Whether or not to try as hard as possible to find valid alignments when they exist (-y)" help="Tryhard mode is much slower than regular mode"> - <option value="noTryHard">Do not try hard</option> - <option value="doTryHard">Try hard</option> - </param> - <param name="sValAlign" type="integer" value="1" label="Report up to n valid alignments per read (-k)" /> - <param name="sAllValAligns" type="select" label="Whether or not to report all valid alignments per read (-a)"> - <option value="noAllValAligns">Do not report all valid alignments</option> - <option value="doAllValAligns">Report all valid alignments</option> - </param> - <param name="sSuppressAlign" type="integer" value="-1" label="Suppress all alignments for a read if more than n reportable alignments exist (-m)" help="-1 for no limit" /> - <param name="sMaxFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads with a number of valid alignments exceeding the limit set with the -m option to a file (--max)" /> - <param name="sUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Write all reads that could not be aligned to a file (--un)" /> - <conditional name="sBestOption"> - <param name="sBest" type="select" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)" help="Removes all strand bias. Only affects which alignments are reported by Bowtie. Runs slower with best option"> - <option value="noBest">Do not use best</option> - <option value="doBest">Use best</option> - </param> - <when value="noBest"> - <param name="snMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> - </when> - <when value="doBest"> - <param name="sdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> - <param name="sdStrata" type="select" label="Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable (--strata)"> - <option value="noStrata">Do not use strata option</option> - <option value="doStrata">Use strata option</option> - </param> - </when> - </conditional> <!-- bestOption --> - <param name="sOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" /> - <param name="sSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" /> - </when> <!-- full --> - </conditional> <!-- sParams --> - </when> <!-- single --> - <when value="paired"> - <param name="pInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/> - <param name="pInput2" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file"> - <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()"> - <column name="name" index="0"/> - <column name="value" index="0"/> - <filter type="param_value" ref="pInput1" ref_attribute="ext" column="0"/> - </options> - </param> - <param name="pMaxInsert" type="integer" value="1000" label="Maximum insert size for valid paired-end alignments (-X)" /> - <param name="pMateOrient" type="select" label="The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand (--fr/--rf/--ff)"> - <option value="fr">FR (for Illumina)</option> - <option value="rf">RF</option> - <option value="ff">FF (for SOLiD)</option> - </param> - <conditional name="pParams"> - <param name="pSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"> - <option value="preSet">Commonly used</option> - <option value="full">Full parameter list</option> - </param> - <when value="preSet" /> - <when value="full"> - <param name="pSkip" type="integer" value="0" label="Skip the first n pairs (-s)" /> - <param name="pAlignLimit" type="integer" value="-1" label="Only align the first n pairs (-u)" help="-1 for off" /> - <param name="pTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" /> - <param name="pTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" /> - <param name="pMismatchSeed" type="integer" value="2" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" /> - <param name="pMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" /> - <param name="pSeedLen" type="integer" value="25" label="Seed length (-l)" help="Minimum value is 5" /> - <param name="pRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)"> - <option value="round">Round to nearest 10</option> - <option value="noRound">Do not round to nearest 10</option> - </param> - <param name="pMaqSoapAlign" type="integer" value="-1" label="Number of mismatches for SOAP-like alignment policy (-v)" help="-1 for default MAQ-like alignment policy" /> - <param name="pMinInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" /> - <param name="pMaxAlignAttempt" type="integer" value="100" label="Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate (--pairtries)" /> - <param name="pForwardAlign" type="select" label="Choose whether or not to attempt to align the forward reference strand (--nofw)"> - <option value="forward">Align against the forward reference strand</option> - <option value="noForward">Do not align against the forward reference strand</option> - </param> - <param name="pReverseAlign" type="select" label="Choose whether or not to align against the reverse-complement reference strand (--norc)"> - <option value="reverse">Align against the reverse-complement reference strand</option> - <option value="noReverse">Do not align against the reverse-complement reference strand</option> - </param> - <param name="pTryHard" type="select" label="Whether or not to try as hard as possible to find valid alignments when they exist (-y)" help="Tryhard mode is much slower than regular mode"> - <option value="noTryHard">Do not try hard</option> - <option value="doTryHard">Try hard</option> - </param> - <param name="pValAlign" type="integer" value="1" label="Report up to n valid arguments per pair (-k)" /> - <param name="pAllValAligns" type="select" label="Whether or not to report all valid alignments per pair (-a)"> - <option value="noAllValAligns">Do not report all valid alignments</option> - <option value="doAllValAligns">Report all valid alignments</option> - </param> - <param name="pSuppressAlign" type="integer" value="-1" label="Suppress all alignments for a pair if more than n reportable alignments exist (-m)" help="-1 for no limit" /> - <param name="pMaxFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads with a number of valid alignments exceeding the limit set with the -m option to a file (--max)" /> - <param name="pUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (--un)" /> - <conditional name="pBestOption"> - <param name="pBest" type="select" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)" help="Removes all strand bias. Only affects which alignments are reported by Bowtie. Runs slower with best option"> - <option value="noBest">Do not use best</option> - <option value="doBest">Use best</option> - </param> - <when value="noBest"> - <param name="pnMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> - </when> - <when value="doBest"> - <param name="pdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> - <param name="pdStrata" type="select" label="Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable (--strata)"> - <option value="noStrata">Do not use strata option</option> - <option value="doStrata">Use strata option</option> - </param> - </when> - </conditional> - <param name="pOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" /> - <param name="pSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" /> - </when> <!-- full --> - </conditional> <!-- pParams --> - </when> <!-- paired --> - </conditional> <!-- singlePaired --> - <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file" help="Bowtie produces SAM with several lines of header information by default" /> - </inputs> - <outputs> - <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads"> - <actions> - <conditional name="refGenomeSource.genomeSource"> - <when value="indexed"> - <action type="metadata" name="dbkey"> - <option type="from_data_table" name="bowtie_indexes" column="1" offset="0"> - <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> - <filter type="param_value" ref="refGenomeSource.index" column="0"/> - </option> - </action> - </when> - <when value="history"> - <action type="metadata" name="dbkey"> - <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> - </action> - </when> - </conditional> - </actions> - </data> - <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)"> - <filter>(( - singlePaired['sPaired'] == "single" and - singlePaired['sParams']['sSettingsType'] == "full" and - singlePaired['sParams']['sMaxFile'] is True - ) or ( - singlePaired['sPaired'] == "paired" and - singlePaired['pParams']['pSettingsType'] == "full" and - singlePaired['pParams']['pMaxFile'] is True - )) - </filter> - <actions> - <conditional name="singlePaired.sPaired"> - <when value="single"> - <action type="format"> - <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" /> - </action> - </when> - <when value="paired"> - <action type="format"> - <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" /> - </action> - </when> - </conditional> - </actions> - </data> - <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)"> - <filter>singlePaired['sPaired'] == "paired"</filter> - <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter> - <filter>singlePaired['pParams']['pMaxFile'] is True</filter> - <actions> - <conditional name="singlePaired.sPaired"> - <when value="single"> - <action type="format"> - <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" /> - </action> - </when> - <when value="paired"> - <action type="format"> - <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" /> - </action> - </when> - </conditional> - </actions> - </data> - <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)"> - <filter> - (( - singlePaired['sPaired'] == "single" and - singlePaired['sParams']['sSettingsType'] == "full" and - singlePaired['sParams']['sUnmappedFile'] is True - ) or ( - singlePaired['sPaired'] == "paired" and - singlePaired['pParams']['pSettingsType'] == "full" and - singlePaired['pParams']['pUnmappedFile'] is True - )) - </filter> - <actions> - <conditional name="singlePaired.sPaired"> - <when value="single"> - <action type="format"> - <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" /> - </action> - </when> - <when value="paired"> - <action type="format"> - <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" /> - </action> - </when> - </conditional> - </actions> - </data> - <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)"> - <filter>singlePaired['sPaired'] == "paired"</filter> - <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter> - <filter>singlePaired['pParams']['pUnmappedFile'] is True</filter> - <actions> - <conditional name="singlePaired.sPaired"> - <when value="single"> - <action type="format"> - <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" /> - </action> - </when> - <when value="paired"> - <action type="format"> - <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" /> - </action> - </when> - </conditional> - </actions> - </data> - </outputs> - <tests> - <test> - <!-- - Bowtie command: - bowtie -q -p 4 -S +sam-nohead chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out6_u.sam - sort bowtie_out6_u.sam > bowtie_out6.sam - -p is the number of threads. You need to replace the + with 2 dashes. - chrM_base needs to be the base location/name of the index files. - --> - <param name="genomeSource" value="indexed" /> - <!-- this is the backwards-compatible "unique value" for this index, not an actual path --> - <param name="index" value="equCab2chrM" /> - <param name="sPaired" value="single" /> - <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" /> - <param name="sSettingsType" value="preSet" /> - <param name="suppressHeader" value="true" /> - <output name="output" ftype="sam" file="bowtie_out6.sam" sort="True" /> - </test> - <test> - <!-- - Bowtie command: - bowtie-build -f test-data/phiX.fasta phiX_base - bowtie -q -X 1000 +ff -p 4 -S +sam-nohead -n 2 -e 70 -l 28 +pairtries 100 +maxbts 800 +best +un bowtie_out8_u.fastq phiX_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > bowtie_out7_u.sam - sort bowtie_out7_u.sam > bowtie_out7.sam - sort bowtie_out8_u_1.sam > bowtie_out8_1.sam - sort bowtie_out8_u_2.sam > bowtie_out8_2.sam - Then also need to modify bowtie_out8_1.sam and bowtie_out8_2.sam so that all @ lines come before sequence lines. - -p is the number of threads. You need to replace the + with 2 dashes. - The two unmapped output files will be named bowtie_out8_1.fastq and bowtie_out8_2.fastq. - chrM_base is the index files' location/base name. - --> - <param name="genomeSource" value="history" /> - <param name="ownFile" value="phiX.fasta" /> - <param name="indexSettings" value="indexPreSet" /> - <param name="sPaired" value="paired" /> - <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" /> - <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" /> - <param name="pMaxInsert" value="1000" /> - <param name="pMateOrient" value="ff" /> - <param name="pSettingsType" value="full" /> - <param name="pSkip" value="0" /> - <param name="pAlignLimit" value="-1" /> - <param name="pTrimH" value="0" /> - <param name="pTrimL" value="0" /> - <param name="pMismatchSeed" value="2" /> - <param name="pMismatchQual" value="70" /> - <param name="pSeedLen" value="25" /> - <param name="pRounding" value="round" /> - <param name="pMaqSoapAlign" value="-1" /> - <param name="pMinInsert" value="0" /> - <param name="pMaxAlignAttempt" value="100" /> - <param name="pForwardAlign" value="forward" /> - <param name="pReverseAlign" value="reverse" /> - <param name="pTryHard" value="noTryHard" /> - <param name="pValAlign" value="1" /> - <param name="pAllValAligns" value="noAllValAligns" /> - <param name="pSuppressAlign" value="-1" /> - <param name="pUnmappedFile" value="true" /> - <param name="pMaxFile" value="false" /> - <param name="pBest" value="doBest" /> - <param name="pdMaxBacktracks" value="800" /> - <param name="pdStrata" value="noStrata" /> - <param name="pOffrate" value="-1" /> - <param name="pSeed" value="-1" /> - <param name="suppressHeader" value="true" /> - <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" /> - <output name="output_unmapped_reads_l" ftype="fastqsanger" file="bowtie_out8_1.fastq" sort="True" /> - <output name="output_unmapped_reads_r" ftype="fastqsanger" file="bowtie_out8_2.fastq" sort="True" /> - </test> - <!-- start testing of non-sanger variant fastq reads --> - <test> - <param name="genomeSource" value="history" /> - <param name="ownFile" value="phiX.fasta" /> - <param name="indexSettings" value="indexPreSet" /> - <param name="sPaired" value="paired" /> - <param name="pInput1" ftype="fastqillumina" value="bowtie_in5.fastqillumina" /> - <param name="pInput2" ftype="fastqillumina" value="bowtie_in6.fastqillumina" /> - <param name="pMaxInsert" value="1000" /> - <param name="pMateOrient" value="ff" /> - <param name="pSettingsType" value="full" /> - <param name="pSkip" value="0" /> - <param name="pAlignLimit" value="-1" /> - <param name="pTrimH" value="0" /> - <param name="pTrimL" value="0" /> - <param name="pMismatchSeed" value="2" /> - <param name="pMismatchQual" value="70" /> - <param name="pSeedLen" value="25" /> - <param name="pRounding" value="round" /> - <param name="pMaqSoapAlign" value="-1" /> - <param name="pMinInsert" value="0" /> - <param name="pMaxAlignAttempt" value="100" /> - <param name="pForwardAlign" value="forward" /> - <param name="pReverseAlign" value="reverse" /> - <param name="pTryHard" value="noTryHard" /> - <param name="pValAlign" value="1" /> - <param name="pAllValAligns" value="noAllValAligns" /> - <param name="pSuppressAlign" value="-1" /> - <param name="pUnmappedFile" value="true" /> - <param name="pMaxFile" value="false" /> - <param name="pBest" value="doBest" /> - <param name="pdMaxBacktracks" value="800" /> - <param name="pdStrata" value="noStrata" /> - <param name="pOffrate" value="-1" /> - <param name="pSeed" value="-1" /> - <param name="suppressHeader" value="true" /> - <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" /> - <output name="output_unmapped_reads_l" ftype="fastqillumna" file="bowtie_out8_1.fastqillumina.sorted" sort="True" /> - <output name="output_unmapped_reads_r" ftype="fastqillumna" file="bowtie_out8_2.fastqillumina.sorted" sort="True" /> - </test> - <test> - <param name="genomeSource" value="history" /> - <param name="ownFile" value="phiX.fasta" /> - <param name="indexSettings" value="indexPreSet" /> - <param name="sPaired" value="paired" /> - <param name="pInput1" ftype="fastqsolexa" value="bowtie_in5.fastqsolexa" /> - <param name="pInput2" ftype="fastqsolexa" value="bowtie_in6.fastqsolexa" /> - <param name="pMaxInsert" value="1000" /> - <param name="pMateOrient" value="ff" /> - <param name="pSettingsType" value="full" /> - <param name="pSkip" value="0" /> - <param name="pAlignLimit" value="-1" /> - <param name="pTrimH" value="0" /> - <param name="pTrimL" value="0" /> - <param name="pMismatchSeed" value="2" /> - <param name="pMismatchQual" value="70" /> - <param name="pSeedLen" value="25" /> - <param name="pRounding" value="round" /> - <param name="pMaqSoapAlign" value="-1" /> - <param name="pMinInsert" value="0" /> - <param name="pMaxAlignAttempt" value="100" /> - <param name="pForwardAlign" value="forward" /> - <param name="pReverseAlign" value="reverse" /> - <param name="pTryHard" value="noTryHard" /> - <param name="pValAlign" value="1" /> - <param name="pAllValAligns" value="noAllValAligns" /> - <param name="pSuppressAlign" value="-1" /> - <param name="pUnmappedFile" value="true" /> - <param name="pMaxFile" value="false" /> - <param name="pBest" value="doBest" /> - <param name="pdMaxBacktracks" value="800" /> - <param name="pdStrata" value="noStrata" /> - <param name="pOffrate" value="-1" /> - <param name="pSeed" value="-1" /> - <param name="suppressHeader" value="true" /> - <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" /> - <output name="output_unmapped_reads_l" ftype="fastqsolexa" file="bowtie_out8_1.fastqsolexa.sorted" sort="True" /> - <output name="output_unmapped_reads_r" ftype="fastqsolexa" file="bowtie_out8_2.fastqsolexa.sorted" sort="True" /> - </test> - <!-- end testing of non-sanger variant fastq reads --> - <test> - <!-- - Bowtie command: - bowtie -q -p 4 -S +sam-nohead -n 2 -e 70 -l 25 +maxbts 125 -y -k 1 chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out9_u.sam - sort bowtie_out9_u.sam > bowtie_out9.sam - -p is the number of threads. You need to replace the + with 2 dashes. - chrM_base is the index files' location/base name. - --> - <param name="genomeSource" value="indexed" /> - <!-- this is the backwards-compatible "unique value" for this index, not an actual path --> - <param name="index" value="equCab2chrM" /> - <param name="sPaired" value="single" /> - <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" /> - <param name="sSettingsType" value="full" /> - <param name="sSkip" value="0" /> - <param name="sAlignLimit" value="-1" /> - <param name="sTrimH" value="0" /> - <param name="sTrimL" value="0" /> - <param name="sMismatchSeed" value="2" /> - <param name="sMismatchQual" value="70" /> - <param name="sSeedLen" value="25" /> - <param name="sRounding" value="round" /> - <param name="sMaqSoapAlign" value="-1" /> - <param name="sTryHard" value="doTryHard" /> - <param name="sValAlign" value="1" /> - <param name="sAllValAligns" value="noAllValAligns" /> - <param name="sSuppressAlign" value="-1" /> - <param name="sUnmappedFile" value="false" /> - <param name="sMaxFile" value="false" /> - <param name="sBest" value="noBest" /> - <param name="snMaxBacktracks" value="125" /> - <param name="sOffrate" value="-1" /> - <param name="sSeed" value="-1" /> - <param name="suppressHeader" value="true" /> - <output name="output" ftype="sam" file="bowtie_out9.sam" sort="True" /> - </test> - <test> - <!-- - Bowtie command: - bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base - bowtie -q -X 1000 +ff -p 4 -S +sam-nohead phiX_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > bowtie_out10_u.sam - sort bowtie_out10_u.sam > bowtie_out10.sam - -p is the number of threads. You need to replace the + with 2 dashes. - chrM_base is the index files' location/base name. - --> - <param name="genomeSource" value="history" /> - <param name="ownFile" value="phiX.fasta" /> - <param name="indexSettings" value="indexFull" /> - <param name="autoB" value="auto" /> - <param name="nodc" value="dc" /> - <param name="noref" value="ref" /> - <param name="offrate" value="5" /> - <param name="ftab" value="10" /> - <param name="ntoa" value="no" /> - <param name="endian" value="little" /> - <param name="seed" value="-1" /> - <param name="cutoff" value="-1" /> - <param name="sPaired" value="paired" /> - <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" /> - <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" /> - <param name="pMaxInsert" value="1000" /> - <param name="pMateOrient" value="ff" /> - <param name="pSettingsType" value="preSet" /> - <param name="suppressHeader" value="true" /> - <output name="output" ftype="sam" file="bowtie_out10.sam" sort="True" /> - </test> - </tests> - <help> - <![CDATA[ - Bowtie is a short read aligner. - ]]> - </help> - <citations> - <citation type="bibtex"> -@misc{githubbowtie, - author = {LastTODO, FirstTODO}, - year = {TODO}, - title = {bowtie}, - publisher = {GitHub}, - journal = {GitHub repository}, - url = {https://github.com/BenLangmead/bowtie}, -}</citation> - </citations> -</tool>
--- a/bowtie_remove_rrna_wrapper/bowtie_wrapper.py Wed Feb 23 12:22:25 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,469 +0,0 @@ -#!/usr/bin/env python - -""" -Runs Bowtie on single-end or paired-end data. -For use with Bowtie v. 0.12.7 - -usage: bowtie_wrapper.py [options] - -t, --threads=t: The number of threads to run - -o, --output=o: The output file - --output_unmapped_reads=: File name for unmapped reads (single-end) - --output_unmapped_reads_l=: File name for unmapped reads (left, paired-end) - --output_unmapped_reads_r=: File name for unmapped reads (right, paired-end) - --output_suppressed_reads=: File name for suppressed reads because of max setting (single-end) - --output_suppressed_reads_l=: File name for suppressed reads because of max setting (left, paired-end) - --output_suppressed_reads_r=: File name for suppressed reads because of max setting (right, paired-end) - -i, --input1=i: The (forward or single-end) reads file in Sanger FASTQ format - -I, --input2=I: The reverse reads file in Sanger FASTQ format - -4, --dataType=4: The type of data (SOLiD or Solexa) - -2, --paired=2: Whether the data is single- or paired-end - -g, --genomeSource=g: The type of reference provided - -r, --ref=r: The reference genome to use or index - -s, --skip=s: Skip the first n reads - -a, --alignLimit=a: Only align the first n reads - -T, --trimH=T: Trim n bases from high-quality (left) end of each read before alignment - -L, --trimL=L: Trim n bases from low-quality (right) end of each read before alignment - -m, --mismatchSeed=m: Maximum number of mismatches permitted in the seed - -M, --mismatchQual=M: Maximum permitted total of quality values at mismatched read positions - -l, --seedLen=l: Seed length - -n, --rounding=n: Whether or not to round to the nearest 10 and saturating at 30 - -P, --maqSoapAlign=P: Choose MAQ- or SOAP-like alignment policy - -w, --tryHard=: Whether or not to try as hard as possible to find valid alignments when they exist - -v, --valAlign=v: Report up to n valid arguments per read - -V, --allValAligns=V: Whether or not to report all valid alignments per read - -G, --suppressAlign=G: Suppress all alignments for a read if more than n reportable alignments exist - -b, --best=b: Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions - -B, --maxBacktracks=B: Maximum number of backtracks permitted when aligning a read - -R, --strata=R: Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable - -j, --minInsert=j: Minimum insert size for valid paired-end alignments - -J, --maxInsert=J: Maximum insert size for valid paired-end alignments - -O, --mateOrient=O: The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand - -A, --maxAlignAttempt=A: Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate - -f, --forwardAlign=f: Whether or not to attempt to align the forward reference strand - -E, --reverseAlign=E: Whether or not to attempt to align the reverse-complement reference strand - -F, --offrate=F: Override the offrate of the index to n - -8, --snpphred=8: SNP penalty on Phred scale - -6, --snpfrac=6: Fraction of sites expected to be SNP sites - -7, --keepends=7: Keep extreme-end nucleotides and qualities - -S, --seed=S: Seed for pseudo-random number generator - -C, --params=C: Whether to use default or specified parameters - -u, --iautoB=u: Automatic or specified behavior - -K, --ipacked=K: Whether or not to use a packed representation for DNA strings - -Q, --ibmax=Q: Maximum number of suffixes allowed in a block - -Y, --ibmaxdivn=Y: Maximum number of suffixes allowed in a block as a fraction of the length of the reference - -D, --idcv=D: The period for the difference-cover sample - -U, --inodc=U: Whether or not to disable the use of the difference-cover sample - -y, --inoref=y: Whether or not to build the part of the reference index used only in paired-end alignment - -z, --ioffrate=z: How many rows get marked during annotation of some or all of the Burrows-Wheeler rows - -W, --iftab=W: The size of the lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query - -X, --intoa=X: Whether or not to convert Ns in the reference sequence to As - -N, --iendian=N: Endianness to use when serializing integers to the index file - -Z, --iseed=Z: Seed for the pseudorandom number generator - -c, --icutoff=c: Number of first bases of the reference sequence to index - -x, --indexSettings=x: Whether or not indexing options are to be set - -H, --suppressHeader=H: Suppress header - --do_not_build_index: Flag to specify that provided file is already indexed and to just use 'as is' -""" - -import optparse, os, shutil, subprocess, sys, tempfile - -#Allow more than Sanger encoded variants -DEFAULT_ASCII_ENCODING = '--phred33-quals' -GALAXY_FORMAT_TO_QUALITY_SCORE_ENCODING_ARG = { 'fastqsanger':'--phred33-quals', 'fastqillumina':'--phred64-quals', 'fastqsolexa':'--solexa-quals' } -#FIXME: Integer quality scores are supported only when the '--integer-quals' argument is specified to bowtie; this is not currently able to be set in the tool/wrapper/config - -def stop_err( msg ): - sys.stderr.write( '%s\n' % msg ) - sys.exit() - -def __main__(): - #Parse Command Line - parser = optparse.OptionParser() - parser.add_option( '-t', '--threads', dest='threads', help='The number of threads to run' ) - parser.add_option( '-o', '--output', dest='output', help='The output file' ) - parser.add_option( '', '--output_unmapped_reads', dest='output_unmapped_reads', help='File name for unmapped reads (single-end)' ) - parser.add_option( '', '--output_unmapped_reads_l', dest='output_unmapped_reads_l', help='File name for unmapped reads (left, paired-end)' ) - parser.add_option( '', '--output_unmapped_reads_r', dest='output_unmapped_reads_r', help='File name for unmapped reads (right, paired-end)' ) - parser.add_option( '', '--output_suppressed_reads', dest='output_suppressed_reads', help='File name for suppressed reads because of max setting (single-end)' ) - parser.add_option( '', '--output_suppressed_reads_l', dest='output_suppressed_reads_l', help='File name for suppressed reads because of max setting (left, paired-end)' ) - parser.add_option( '', '--output_suppressed_reads_r', dest='output_suppressed_reads_r', help='File name for suppressed reads because of max setting (right, paired-end)' ) - parser.add_option( '-4', '--dataType', dest='dataType', help='The type of data (SOLiD or Solexa)' ) - parser.add_option( '-i', '--input1', dest='input1', help='The (forward or single-end) reads file in Sanger FASTQ format' ) - parser.add_option( '-I', '--input2', dest='input2', help='The reverse reads file in Sanger FASTQ format' ) - parser.add_option( '-2', '--paired', dest='paired', help='Whether the data is single- or paired-end' ) - parser.add_option( '-g', '--genomeSource', dest='genomeSource', help='The type of reference provided' ) - parser.add_option( '-r', '--ref', dest='ref', help='The reference genome to use or index' ) - parser.add_option( '-s', '--skip', dest='skip', help='Skip the first n reads' ) - parser.add_option( '-a', '--alignLimit', dest='alignLimit', help='Only align the first n reads' ) - parser.add_option( '-T', '--trimH', dest='trimH', help='Trim n bases from high-quality (left) end of each read before alignment' ) - parser.add_option( '-L', '--trimL', dest='trimL', help='Trim n bases from low-quality (right) end of each read before alignment' ) - parser.add_option( '-m', '--mismatchSeed', dest='mismatchSeed', help='Maximum number of mismatches permitted in the seed' ) - parser.add_option( '-M', '--mismatchQual', dest='mismatchQual', help='Maximum permitted total of quality values at mismatched read positions' ) - parser.add_option( '-l', '--seedLen', dest='seedLen', help='Seed length' ) - parser.add_option( '-n', '--rounding', dest='rounding', help='Whether or not to round to the nearest 10 and saturating at 30' ) - parser.add_option( '-P', '--maqSoapAlign', dest='maqSoapAlign', help='Choose MAQ- or SOAP-like alignment policy' ) - parser.add_option( '-w', '--tryHard', dest='tryHard', help='Whether or not to try as hard as possible to find valid alignments when they exist' ) - parser.add_option( '-v', '--valAlign', dest='valAlign', help='Report up to n valid arguments per read' ) - parser.add_option( '-V', '--allValAligns', dest='allValAligns', help='Whether or not to report all valid alignments per read' ) - parser.add_option( '-G', '--suppressAlign', dest='suppressAlign', help='Suppress all alignments for a read if more than n reportable alignments exist' ) - parser.add_option( '-b', '--best', dest='best', help="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions" ) - parser.add_option( '-B', '--maxBacktracks', dest='maxBacktracks', help='Maximum number of backtracks permitted when aligning a read' ) - parser.add_option( '-R', '--strata', dest='strata', help='Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable' ) - parser.add_option( '-j', '--minInsert', dest='minInsert', help='Minimum insert size for valid paired-end alignments' ) - parser.add_option( '-J', '--maxInsert', dest='maxInsert', help='Maximum insert size for valid paired-end alignments' ) - parser.add_option( '-O', '--mateOrient', dest='mateOrient', help='The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand' ) - parser.add_option( '-A', '--maxAlignAttempt', dest='maxAlignAttempt', help='Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate' ) - parser.add_option( '-f', '--forwardAlign', dest='forwardAlign', help='Whether or not to attempt to align the forward reference strand' ) - parser.add_option( '-E', '--reverseAlign', dest='reverseAlign', help='Whether or not to attempt to align the reverse-complement reference strand' ) - parser.add_option( '-F', '--offrate', dest='offrate', help='Override the offrate of the index to n' ) - parser.add_option( '-S', '--seed', dest='seed', help='Seed for pseudo-random number generator' ) - parser.add_option( '-8', '--snpphred', dest='snpphred', help='SNP penalty on Phred scale' ) - parser.add_option( '-6', '--snpfrac', dest='snpfrac', help='Fraction of sites expected to be SNP sites' ) - parser.add_option( '-7', '--keepends', dest='keepends', help='Keep extreme-end nucleotides and qualities' ) - parser.add_option( '-C', '--params', dest='params', help='Whether to use default or specified parameters' ) - parser.add_option( '-u', '--iautoB', dest='iautoB', help='Automatic or specified behavior' ) - parser.add_option( '-K', '--ipacked', dest='ipacked', help='Whether or not to use a packed representation for DNA strings' ) - parser.add_option( '-Q', '--ibmax', dest='ibmax', help='Maximum number of suffixes allowed in a block' ) - parser.add_option( '-Y', '--ibmaxdivn', dest='ibmaxdivn', help='Maximum number of suffixes allowed in a block as a fraction of the length of the reference' ) - parser.add_option( '-D', '--idcv', dest='idcv', help='The period for the difference-cover sample' ) - parser.add_option( '-U', '--inodc', dest='inodc', help='Whether or not to disable the use of the difference-cover sample' ) - parser.add_option( '-y', '--inoref', dest='inoref', help='Whether or not to build the part of the reference index used only in paired-end alignment' ) - parser.add_option( '-z', '--ioffrate', dest='ioffrate', help='How many rows get marked during annotation of some or all of the Burrows-Wheeler rows' ) - parser.add_option( '-W', '--iftab', dest='iftab', help='The size of the lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query' ) - parser.add_option( '-X', '--intoa', dest='intoa', help='Whether or not to convert Ns in the reference sequence to As' ) - parser.add_option( '-N', '--iendian', dest='iendian', help='Endianness to use when serializing integers to the index file' ) - parser.add_option( '-Z', '--iseed', dest='iseed', help='Seed for the pseudorandom number generator' ) - parser.add_option( '-c', '--icutoff', dest='icutoff', help='Number of first bases of the reference sequence to index' ) - parser.add_option( '-x', '--indexSettings', dest='index_settings', help='Whether or not indexing options are to be set' ) - parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' ) - parser.add_option( '--galaxy_input_format', dest='galaxy_input_format', default="fastqsanger", help='galaxy input format' ) - parser.add_option( '--do_not_build_index', dest='do_not_build_index', action="store_true", default=False, help='Flag to specify that provided file is already indexed, use as is' ) - (options, args) = parser.parse_args() - stdout = '' - - # make temp directory for placement of indices and copy reference file there if necessary - tmp_index_dir = tempfile.mkdtemp() - # get type of data (solid or solexa) - if options.dataType == 'solid': - colorspace = '-C' - else: - colorspace = '' - # index if necessary - if options.genomeSource == 'history' and not options.do_not_build_index: - # set up commands - if options.index_settings =='indexPreSet': - indexing_cmds = '%s' % colorspace - else: - try: - if options.iautoB and options.iautoB == 'set': - iautoB = '--noauto' - else: - iautoB = '' - if options. ipacked and options.ipacked == 'packed': - ipacked = '--packed' - else: - ipacked = '' - if options.ibmax and int( options.ibmax ) >= 1: - ibmax = '--bmax %s' % options.ibmax - else: - ibmax = '' - if options.ibmaxdivn and int( options.ibmaxdivn ) >= 0: - ibmaxdivn = '--bmaxdivn %s' % options.ibmaxdivn - else: - ibmaxdivn = '' - if options.idcv and int( options.idcv ) > 0: - idcv = '--dcv %s' % options.idcv - else: - idcv = '' - if options.inodc and options.inodc == 'nodc': - inodc = '--nodc' - else: - inodc = '' - if options.inoref and options.inoref == 'noref': - inoref = '--noref' - else: - inoref = '' - if options.iftab and int( options.iftab ) >= 0: - iftab = '--ftabchars %s' % options.iftab - else: - iftab = '' - if options.intoa and options.intoa == 'yes': - intoa = '--ntoa' - else: - intoa = '' - if options.iendian and options.iendian == 'big': - iendian = '--big' - else: - iendian = '--little' - if options.iseed and int( options.iseed ) > 0: - iseed = '--seed %s' % options.iseed - else: - iseed = '' - if options.icutoff and int( options.icutoff ) > 0: - icutoff = '--cutoff %s' % options.icutoff - else: - icutoff = '' - indexing_cmds = '%s %s %s %s %s %s %s --offrate %s %s %s %s %s %s %s' % \ - ( iautoB, ipacked, ibmax, ibmaxdivn, idcv, inodc, - inoref, options.ioffrate, iftab, intoa, iendian, - iseed, icutoff, colorspace ) - except ValueError, e: - # clean up temp dir - if os.path.exists( tmp_index_dir ): - shutil.rmtree( tmp_index_dir ) - stop_err( "Something is wrong with the indexing parameters and the indexing and alignment could not be run. Make sure you don't have any non-numeric values where they should be numeric.\n" + str( e ) ) - ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir ) - ref_file_name = ref_file.name - ref_file.close() - os.symlink( options.ref, ref_file_name ) - cmd1 = 'bowtie-build %s -f %s %s' % ( indexing_cmds, ref_file_name, ref_file_name ) - try: - tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name - tmp_stderr = open( tmp, 'wb' ) - proc = subprocess.Popen( args=cmd1, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno() ) - returncode = proc.wait() - tmp_stderr.close() - # get stderr, allowing for case where it's very large - tmp_stderr = open( tmp, 'rb' ) - stderr = '' - buffsize = 1048576 - try: - while True: - stderr += tmp_stderr.read( buffsize ) - if not stderr or len( stderr ) % buffsize != 0: - break - except OverflowError: - pass - tmp_stderr.close() - if returncode != 0: - raise Exception, stderr - except Exception, e: - # clean up temp dir - if os.path.exists( tmp_index_dir ): - shutil.rmtree( tmp_index_dir ) - stop_err( 'Error indexing reference sequence\n' + str( e ) ) - stdout += 'File indexed. ' - else: - ref_file_name = options.ref - # set up aligning and generate aligning command options - # automatically set threads in both cases - tmp_suppressed_file_name = None - tmp_unmapped_file_name = None - if options.suppressHeader == 'true': - suppressHeader = '--sam-nohead' - else: - suppressHeader = '' - if options.maxInsert and int( options.maxInsert ) > 0: - maxInsert = '-X %s' % options.maxInsert - else: - maxInsert = '' - if options.mateOrient: - mateOrient = '--%s' % options.mateOrient - else: - mateOrient = '' - quality_score_encoding = GALAXY_FORMAT_TO_QUALITY_SCORE_ENCODING_ARG.get( options.galaxy_input_format, DEFAULT_ASCII_ENCODING ) - if options.params == 'preSet': - aligning_cmds = '-q %s %s -p %s -S %s %s %s ' % \ - ( maxInsert, mateOrient, options.threads, suppressHeader, colorspace, quality_score_encoding ) - else: - try: - if options.skip and int( options.skip ) > 0: - skip = '-s %s' % options.skip - else: - skip = '' - if options.alignLimit and int( options.alignLimit ) >= 0: - alignLimit = '-u %s' % options.alignLimit - else: - alignLimit = '' - if options.trimH and int( options.trimH ) > 0: - trimH = '-5 %s' % options.trimH - else: - trimH = '' - if options.trimL and int( options.trimL ) > 0: - trimL = '-3 %s' % options.trimL - else: - trimL = '' - if options.maqSoapAlign != '-1' and int( options.maqSoapAlign ) >= 0: - maqSoapAlign = '-v %s' % options.maqSoapAlign - else: - maqSoapAlign = '' - if options.mismatchSeed and (options.mismatchSeed == '0' or options.mismatchSeed == '1' \ - or options.mismatchSeed == '2' or options.mismatchSeed == '3'): - mismatchSeed = '-n %s' % options.mismatchSeed - else: - mismatchSeed = '' - if options.mismatchQual and int( options.mismatchQual ) >= 0: - mismatchQual = '-e %s' % options.mismatchQual - else: - mismatchQual = '' - if options.seedLen and int( options.seedLen ) >= 5: - seedLen = '-l %s' % options.seedLen - else: - seedLen = '' - if options.rounding == 'noRound': - rounding = '--nomaqround' - else: - rounding = '' - if options.minInsert and int( options.minInsert ) > 0: - minInsert = '-I %s' % options.minInsert - else: - minInsert = '' - if options.maxAlignAttempt and int( options.maxAlignAttempt ) >= 0: - maxAlignAttempt = '--pairtries %s' % options.maxAlignAttempt - else: - maxAlignAttempt = '' - if options.forwardAlign == 'noForward': - forwardAlign = '--nofw' - else: - forwardAlign = '' - if options.reverseAlign == 'noReverse': - reverseAlign = '--norc' - else: - reverseAlign = '' - if options.maxBacktracks and int( options.maxBacktracks ) > 0 and \ - ( options.mismatchSeed == '2' or options.mismatchSeed == '3' ): - maxBacktracks = '--maxbts %s' % options.maxBacktracks - else: - maxBacktracks = '' - if options.tryHard == 'doTryHard': - tryHard = '-y' - else: - tryHard = '' - if options.valAlign and int( options.valAlign ) >= 0: - valAlign = '-k %s' % options.valAlign - else: - valAlign = '' - if options.allValAligns == 'doAllValAligns': - allValAligns = '-a' - else: - allValAligns = '' - if options.suppressAlign and int( options.suppressAlign ) >= 0: - suppressAlign = '-m %s' % options.suppressAlign - else: - suppressAlign = '' - if options.best == 'doBest': - best = '--best' - else: - best = '' - if options.strata == 'doStrata': - strata = '--strata' - else: - strata = '' - if options.offrate and int( options.offrate ) >= 0: - offrate = '-o %s' % options.offrate - else: - offrate = '' - if options.seed and int( options.seed ) >= 0: - seed = '--seed %s' % options.seed - else: - seed = '' - if options.paired == 'paired': - if options.output_unmapped_reads_l and options.output_unmapped_reads_r: - tmp_unmapped_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir, suffix='.fastq' ) - tmp_unmapped_file_name = tmp_unmapped_file.name - tmp_unmapped_file.close() - output_unmapped_reads = '--un %s' % tmp_unmapped_file_name - else: - output_unmapped_reads = '' - if options.output_suppressed_reads: - tmp_suppressed_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir, suffix='.fastq' ) - tmp_suppressed_file_name = tmp_suppressed_file.name - tmp_suppressed_file.close() - output_suppressed_reads = '--max %s' % tmp_suppressed_file_name - else: - output_suppressed_reads = '' - else: - if options.output_unmapped_reads: - output_unmapped_reads = '--un %s' % options.output_unmapped_reads - else: - output_unmapped_reads = '' - if options.output_suppressed_reads: - output_suppressed_reads = '--max %s' % options.output_suppressed_reads - else: - output_suppressed_reads = '' - snpfrac = '' - if options.snpphred and int( options.snpphred ) >= 0: - snpphred = '--snpphred %s' % options.snpphred - else: - snpphred = '' - if options.snpfrac and float( options.snpfrac ) >= 0: - snpfrac = '--snpfrac %s' % options.snpfrac - if options.keepends and options.keepends == 'doKeepends': - keepends = '--col-keepends' - else: - keepends = '' - aligning_cmds = '-q %s %s -p %s -S %s %s %s %s %s %s %s %s %s %s %s %s ' \ - '%s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s ' % \ - ( maxInsert, mateOrient, options.threads, suppressHeader, - colorspace, skip, alignLimit, trimH, trimL, maqSoapAlign, - mismatchSeed, mismatchQual, seedLen, rounding, minInsert, - maxAlignAttempt, forwardAlign, reverseAlign, maxBacktracks, - tryHard, valAlign, allValAligns, suppressAlign, best, - strata, offrate, seed, snpphred, snpfrac, keepends, - output_unmapped_reads, output_suppressed_reads, - quality_score_encoding ) - except ValueError, e: - # clean up temp dir - if os.path.exists( tmp_index_dir ): - shutil.rmtree( tmp_index_dir ) - stop_err( 'Something is wrong with the alignment parameters and the alignment could not be run\n' + str( e ) ) - try: - # have to nest try-except in try-finally to handle 2.4 - try: - # prepare actual mapping commands - if options.paired == 'paired': - cmd2 = 'bowtie %s %s -1 %s -2 %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.input2, options.output ) - else: - cmd2 = 'bowtie %s %s %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.output ) - # align - tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name - tmp_stderr = open( tmp, 'wb' ) - proc = subprocess.Popen( args=cmd2, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno() ) - returncode = proc.wait() - tmp_stderr.close() - # get stderr, allowing for case where it's very large - tmp_stderr = open( tmp, 'rb' ) - stderr = '' - buffsize = 1048576 - try: - while True: - stderr += tmp_stderr.read( buffsize ) - if not stderr or len( stderr ) % buffsize != 0: - break - except OverflowError: - pass - tmp_stderr.close() - if returncode != 0: - raise Exception, stderr - # get suppressed and unmapped reads output files in place if appropriate - if options.paired == 'paired' and tmp_suppressed_file_name and \ - options.output_suppressed_reads_l and options.output_suppressed_reads_r: - try: - left = tmp_suppressed_file_name.replace( '.fastq', '_1.fastq' ) - right = tmp_suppressed_file_name.replace( '.fastq', '_1.fastq' ) - shutil.move( left, options.output_suppressed_reads_l ) - shutil.move( right, options.output_suppressed_reads_r ) - except Exception, e: - sys.stdout.write( 'Error producing the suppressed output file.\n' ) - if options.paired == 'paired' and tmp_unmapped_file_name and \ - options.output_unmapped_reads_l and options.output_unmapped_reads_r: - try: - left = tmp_unmapped_file_name.replace( '.fastq', '_1.fastq' ) - right = tmp_unmapped_file_name.replace( '.fastq', '_2.fastq' ) - shutil.move( left, options.output_unmapped_reads_l ) - shutil.move( right, options.output_unmapped_reads_r ) - except Exception, e: - sys.stdout.write( 'Error producing the unmapped output file.\n' ) - # check that there are results in the output file - if os.path.getsize( options.output ) == 0: - raise Exception, 'The output file is empty, there may be an error with your input file or settings.' - except Exception, e: - stop_err( 'Error aligning sequence. ' + str( e ) ) - finally: - # clean up temp dir - if os.path.exists( tmp_index_dir ): - shutil.rmtree( tmp_index_dir ) - stdout += 'Sequence file aligned.\n' - sys.stdout.write( stdout ) - -if __name__=="__main__": __main__()
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_in2.fastqsanger Wed Feb 23 12:22:25 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,104 +0,0 @@ -@HWI-EAS91_1_30788AAXX:1:1:1513:715/1 -GTTTTTTGGGCATAGATGTTTAGTTGTGGTAGTCAG -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIDI?II-+I -@HWI-EAS91_1_30788AAXX:1:1:1698:516/1 -GTTGTTAGGGAGAGGAGTTGAACCTCTGAGTGTAAA -+ -IIIIIII""IIIIIIIIIIIIIIIIIII5IIIII9I -@HWI-EAS91_1_30788AAXX:1:1:1491:637/1 -GCTAGCAGGATGGATCCGGCAATTGGGGCTTCTACA -+ -IIIIIII""IIIIIIIIIIIIFIIIIIIIIIIIABD -@HWI-EAS91_1_30788AAXX:1:1:1711:249/1 -GGAAGTAGGGGCCTGCGTTCAGGCGTTCTGTTTGGT -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII -@HWI-EAS91_1_30788AAXX:1:1:1634:211/1 -GAAGCAGGGGCTTGATACTGACACTTCGTCGACGTA -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF -@HWI-EAS91_1_30788AAXX:1:1:1218:141/1 -GTTAAATATTGGGAGTGGGGGGGGGGGGGAGTTTTG -+ -IIIIIII""IIIIIIIIIIIIIIIIIIII1IIII+I -@HWI-EAS91_1_30788AAXX:1:1:1398:854/1 -GTGAAGAGGAGGGGATTTATTAGTACGGGAAGGGTG -+ -IIIIIII""IIIIIBIIIIIIIIIIIIIIA=IIIII -@HWI-EAS91_1_30788AAXX:1:1:1310:991/1 -GAATAGTGGTAGTATTATTCCTTCTAGGCATAGGAG -+ -IIIIIII""IIIIIIIIII4IIIIIIDII:IEI2:I -@HWI-EAS91_1_30788AAXX:1:1:1716:413/1 -GATCCAAGGCTTTATCAACACCTATTCTGATTCTTC -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII -@HWI-EAS91_1_30788AAXX:1:1:1630:59/1 -GGAGCGGGGGGTTGGTAAGGTTGGGGTCGAGTATGA -+ -IIIIIII""IIIIIIIIIIIIIIIIIIII;IIHIIF -@HWI-EAS91_1_30788AAXX:1:1:1601:805/1 -GAAAACAGGAAAACAATCCAGTCACTTACCCTATGC -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIII@III -@HWI-EAS91_1_30788AAXX:1:1:1663:724/1 -GTTTGCCGGCGCCATCCTACGCTCCATTCCCAACAA -+ -IIIIIII""IIII8IIIIIIHIIII6IIIII1CI=3 -@HWI-EAS91_1_30788AAXX:1:1:1454:975/1 -GCTAGGCGGGAGTGGTAAAAGGCTCAGAAGAAGCCA -+ -IIIIIII""IIIIIIIIIIIIIIIIEIG;IIIIIII -@HWI-EAS91_1_30788AAXX:1:1:1461:255/1 -GTACACCGGCGCCTGAGCCCTACTAATAACTCTCAT -+ -IIIIIII""IIIIII9IIIIIIEI(II9.I4III,I -@HWI-EAS91_1_30788AAXX:1:1:1775:764/1 -GCATCCCGGTAGATCTAATTTTCTAAATCTGTCAAC -+ -IIIIIII""III@IIII+IIIIII8H8IIIIIIICI -@HWI-EAS91_1_30788AAXX:1:1:1269:520/1 -GGAGTATGGAATAAGTGATTTTAGATCGGTTTGTCG -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII -@HWI-EAS91_1_30788AAXX:1:1:1303:1162/1 -GAGCAAGGGCAGGAGGAGGAGTCCTAGGATGTCTTT -+ -IIIIIII""IIIIFII4*IGIAI(IAII49',3I6I -@HWI-EAS91_1_30788AAXX:1:1:1090:409/1 -GTTTGTTGGGAATGGAGCGTAGGATGGCGTAGGCAA -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIII:IIA8I -@HWI-EAS91_1_30788AAXX:1:1:1336:1000/1 -GGTAAATGGGAAATATTAAGTTTCTGTTTCTAGATC -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIII9II -@HWI-EAS91_1_30788AAXX:1:1:1199:1376/1 -GTTTTCTGGAAAACCTTCACCTATTTATGGGGGTTT -+ -IIIIIII""IIIIIIIIIIIII;III3IIG&:/III -@HWI-EAS91_1_30788AAXX:1:1:1598:1148/1 -GATCAATGGTTTGGATCAATAAGTGATTATATATTT -+ -IIIIIII""IIIIIDIIIIII?IIICII=IHIIIII -@HWI-EAS91_1_30788AAXX:1:1:1723:1459/1 -GAAACCCGGACGTTTGGATGGGCCCGGAGCGAGGAT -+ -IIIIIII""IIIIIIIIDIIIIIIIII9HII-II=I -@HWI-EAS91_1_30788AAXX:1:1:1442:1346/1 -TATCAAGGGGCTGCTTCGAATCCGAAGTGGTGGCTG -+ -IIIIIII""IIIIIDIIIII1I(I4II<?<-II*,& -@HWI-EAS91_1_30788AAXX:1:1:850:117/1 -GTATGACGGTAAAGAAAATTATTACGAATGCATGGG -+ -IIIIIII""IIIIIIEIEIIIIIIIIEBIDD9I;:? -@HWI-EAS91_1_30788AAXX:1:1:795:325/1 -GGGTACTGGGAAGTGGAATGGTGTGAGTCCAAGTTT -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIII65IIII -@HWI-EAS91_1_30788AAXX:1:1:873:453/1 -GAGTAGGGGGATTGCTAGAGTTACTTCGTATGAGAT -+ -IIIIIII""IIIIIIIIIIIIIIIII@IIIIIII=I
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_in5.fastqillumina Wed Feb 23 12:22:25 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,72 +0,0 @@ -@Dummy:1:1:1761:343/1 -TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA -+ -hhhhhhhAAhhhhhhhhhhh^hOhhhhghhhfhhhhhOhh^hAAhhhhhh -@Dummy:1:1:1578:331/1 -TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC -+ -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh -@Dummy:1:1:1647:512/1 -TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA -+ -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh -@Dummy:1:1:1570:620/1 -GAGTAACAAAGTaaaGTTTGGAccGTTTTTGTCTCGTGCTCGTCGCTGCG -+ -hhhhhhhAAhhhhhhhhhhhhhahhhhhhhhhhhhAhhhhhhhOOOhhhh -@Dummy:1:1:1599:330/1 -AGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTC -+ -hhhhhhhAAhhhhhhhhhhhhhhhhhhh[hhh_hhAhhhhhhhOOOhhhh -@Dummy:1:1:1652:270/1 -AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGacTTTGCATTGTTTAATTG -+ -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhUhhAhhhhhhhOOOhhhh -@Dummy:1:1:1746:351/1 -CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT -+ -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh -@Dummy:1:1:1582:633/1 -CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC -+ -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh -@Dummy:1:1:1598:534/1 -GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA -+ -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh -@Dummy:1:1:1572:324/1 -AAGGTGCTTaaaTTCgtGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC -+ -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhJVhOThAhhhhhhhOOOhhhh -@Dummy:1:1:1749:466/1 -TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT -+ -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh -@Dummy:1:1:1629:446/1 -AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT -+ -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh -@Dummy:1:1:1763:587/1 -AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT -+ -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh -@Dummy:1:1:1616:363/1 -TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG -+ -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhchhhAhhhhhhhOOOhhhh -@Dummy:1:1:1768:715/1 -ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT -+ -hhhhhhhAAhhhhhhhhhhhhhchhhhhhhhhhhhAhhhhhhhOOOhhhh -@Dummy:1:1:1572:270/1 -TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA -+ -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh -@Dummy:1:1:1673:514/1 -ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT -+ -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhPAhhhhhhhOOOhhhh -@Dummy:1:1:1634:330/1 -GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG -+ -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhWhhAhhhhhhhOOOhhhh
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_in5.fastqsanger Wed Feb 23 12:22:25 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,72 +0,0 @@ -@Dummy:1:1:1761:343/1 -TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA -+ -IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIII0II?I""IIIIII -@Dummy:1:1:1578:331/1 -TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII -@Dummy:1:1:1647:512/1 -TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII -@Dummy:1:1:1570:620/1 -GAGTAACAAAGTaaaGTTTGGAccGTTTTTGTCTCGTGCTCGTCGCTGCG -+ -IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII"IIIIIII000IIII -@Dummy:1:1:1599:330/1 -AGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTC -+ -IIIIIII""IIIIIIIIIIIIIIIIIII<III@II"IIIIIII000IIII -@Dummy:1:1:1652:270/1 -AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGacTTTGCATTGTTTAATTG -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II"IIIIIII000IIII -@Dummy:1:1:1746:351/1 -CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII -@Dummy:1:1:1582:633/1 -CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII -@Dummy:1:1:1598:534/1 -GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII -@Dummy:1:1:1572:324/1 -AAGGTGCTTaaaTTCgtGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC -+ -IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I"IIIIIII000IIII -@Dummy:1:1:1749:466/1 -TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII -@Dummy:1:1:1629:446/1 -AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII -@Dummy:1:1:1763:587/1 -AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII -@Dummy:1:1:1616:363/1 -TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII"IIIIIII000IIII -@Dummy:1:1:1768:715/1 -ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT -+ -IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII"IIIIIII000IIII -@Dummy:1:1:1572:270/1 -TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII -@Dummy:1:1:1673:514/1 -ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1"IIIIIII000IIII -@Dummy:1:1:1634:330/1 -GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II"IIIIIII000IIII
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_in5.fastqsolexa Wed Feb 23 12:22:25 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,72 +0,0 @@ -@Dummy:1:1:1761:343/1 -TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA -+ -hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhhhOhh^h;;hhhhhh -@Dummy:1:1:1578:331/1 -TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC -+ -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh -@Dummy:1:1:1647:512/1 -TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA -+ -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh -@Dummy:1:1:1570:620/1 -GAGTAACAAAGTaaaGTTTGGAccGTTTTTGTCTCGTGCTCGTCGCTGCG -+ -hhhhhhh;;hhhhhhhhhhhhhahhhhhhhhhhhh;hhhhhhhOOOhhhh -@Dummy:1:1:1599:330/1 -AGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTC -+ -hhhhhhh;;hhhhhhhhhhhhhhhhhhh[hhh_hh;hhhhhhhOOOhhhh -@Dummy:1:1:1652:270/1 -AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGacTTTGCATTGTTTAATTG -+ -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhUhh;hhhhhhhOOOhhhh -@Dummy:1:1:1746:351/1 -CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT -+ -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh -@Dummy:1:1:1582:633/1 -CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC -+ -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh -@Dummy:1:1:1598:534/1 -GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA -+ -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh -@Dummy:1:1:1572:324/1 -AAGGTGCTTaaaTTCgtGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC -+ -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhJVhOTh;hhhhhhhOOOhhhh -@Dummy:1:1:1749:466/1 -TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT -+ -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh -@Dummy:1:1:1629:446/1 -AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT -+ -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh -@Dummy:1:1:1763:587/1 -AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT -+ -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh -@Dummy:1:1:1616:363/1 -TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG -+ -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhchhh;hhhhhhhOOOhhhh -@Dummy:1:1:1768:715/1 -ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT -+ -hhhhhhh;;hhhhhhhhhhhhhchhhhhhhhhhhh;hhhhhhhOOOhhhh -@Dummy:1:1:1572:270/1 -TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA -+ -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh -@Dummy:1:1:1673:514/1 -ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT -+ -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhP;hhhhhhhOOOhhhh -@Dummy:1:1:1634:330/1 -GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG -+ -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhWhh;hhhhhhhOOOhhhh
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_in6.fastqillumina Wed Feb 23 12:22:25 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,72 +0,0 @@ -@Dummy:1:1:1761:343/2 -TTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGG -+ -hhhhhhhAAhhhhhhhOhh^hAAhhhhhhhhhhhh^hOhhhhghhhfhhh -@Dummy:1:1:1578:331/2 -AAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCT -+ -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh -@Dummy:1:1:1647:512/2 -TTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTG -+ -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh -@Dummy:1:1:1570:620/2 -CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT -+ -hhhhhhhAAhhhhhhhhhhhhhahhhhhhhhhhhh^hOhhhhghhhfhhh -@Dummy:1:1:1599:330/2 -TTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCA -+ -hhhhhhhAAhhhhhhhhhhhhhhhhhhh[hhh_hh^hOhhhhghhhfhhh -@Dummy:1:1:1652:270/2 -GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG -+ -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhUhh^hOhhhhghhhfhhh -@Dummy:1:1:1746:351/2 -CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT -+ -hhhhhhhAAhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhhhhhhhhhh -@Dummy:1:1:1582:633/2 -TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT -+ -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh -@Dummy:1:1:1598:534/2 -TTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCC -+ -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh -@Dummy:1:1:1572:324/2 -GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT -+ -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhJVhOTh^hOhhhhghhhfhhh -@Dummy:1:1:1749:466/2 -GCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG -+ -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh -@Dummy:1:1:1629:446/2 -CAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGA -+ -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh -@Dummy:1:1:1763:587/2 -CATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTC -+ -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh -@Dummy:1:1:1616:363/2 -GTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGG -+ -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhchhh^hOhhhhghhhfhhh -@Dummy:1:1:1768:715/2 -AGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATA -+ -hhhhhhhAAhhhhhhhhhhhhhchhhhhhhhhhhh^hOhhhhghhhfhhh -@Dummy:1:1:1572:270/2 -ACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATG -+ -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh -@Dummy:1:1:1673:514/2 -GCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATG -+ -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhP^hOhhhhghhhfhhh -@Dummy:1:1:1634:330/2 -TCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTAT -+ -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhWhh^hOhhhhghhhfhhh
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_in6.fastqsanger Wed Feb 23 12:22:25 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,72 +0,0 @@ -@Dummy:1:1:1761:343/2 -TTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGG -+ -IIIIIII""IIIIIII0II?I""IIIIIIIIIIII?I0IIIIHIIIGIII -@Dummy:1:1:1578:331/2 -AAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCT -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII -@Dummy:1:1:1647:512/2 -TTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTG -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII -@Dummy:1:1:1570:620/2 -CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT -+ -IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII?I0IIIIHIIIGIII -@Dummy:1:1:1599:330/2 -TTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCA -+ -IIIIIII""IIIIIIIIIIIIIIIIIII<III@II?I0IIIIHIIIGIII -@Dummy:1:1:1652:270/2 -GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II?I0IIIIHIIIGIII -@Dummy:1:1:1746:351/2 -CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT -+ -IIIIIII""IIIIIIIIIIIIIIIIII?I0IIIIHIIIGIIIIIIIIIII -@Dummy:1:1:1582:633/2 -TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII -@Dummy:1:1:1598:534/2 -TTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCC -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII -@Dummy:1:1:1572:324/2 -GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT -+ -IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I?I0IIIIHIIIGIII -@Dummy:1:1:1749:466/2 -GCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII -@Dummy:1:1:1629:446/2 -CAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGA -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII -@Dummy:1:1:1763:587/2 -CATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTC -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII -@Dummy:1:1:1616:363/2 -GTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGG -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII?I0IIIIHIIIGIII -@Dummy:1:1:1768:715/2 -AGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATA -+ -IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII?I0IIIIHIIIGIII -@Dummy:1:1:1572:270/2 -ACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATG -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII -@Dummy:1:1:1673:514/2 -GCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATG -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1?I0IIIIHIIIGIII -@Dummy:1:1:1634:330/2 -TCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTAT -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II?I0IIIIHIIIGIII
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_in6.fastqsolexa Wed Feb 23 12:22:25 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,72 +0,0 @@ -@Dummy:1:1:1761:343/2 -TTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGG -+ -hhhhhhh;;hhhhhhhOhh^h;;hhhhhhhhhhhh^hOhhhhghhhfhhh -@Dummy:1:1:1578:331/2 -AAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCT -+ -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh -@Dummy:1:1:1647:512/2 -TTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTG -+ -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh -@Dummy:1:1:1570:620/2 -CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT -+ -hhhhhhh;;hhhhhhhhhhhhhahhhhhhhhhhhh^hOhhhhghhhfhhh -@Dummy:1:1:1599:330/2 -TTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCA -+ -hhhhhhh;;hhhhhhhhhhhhhhhhhhh[hhh_hh^hOhhhhghhhfhhh -@Dummy:1:1:1652:270/2 -GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG -+ -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhUhh^hOhhhhghhhfhhh -@Dummy:1:1:1746:351/2 -CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT -+ -hhhhhhh;;hhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhhhhhhhhhh -@Dummy:1:1:1582:633/2 -TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT -+ -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh -@Dummy:1:1:1598:534/2 -TTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCC -+ -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh -@Dummy:1:1:1572:324/2 -GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT -+ -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhJVhOTh^hOhhhhghhhfhhh -@Dummy:1:1:1749:466/2 -GCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG -+ -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh -@Dummy:1:1:1629:446/2 -CAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGA -+ -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh -@Dummy:1:1:1763:587/2 -CATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTC -+ -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh -@Dummy:1:1:1616:363/2 -GTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGG -+ -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhchhh^hOhhhhghhhfhhh -@Dummy:1:1:1768:715/2 -AGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATA -+ -hhhhhhh;;hhhhhhhhhhhhhchhhhhhhhhhhh^hOhhhhghhhfhhh -@Dummy:1:1:1572:270/2 -ACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATG -+ -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh -@Dummy:1:1:1673:514/2 -GCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATG -+ -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhP^hOhhhhghhhfhhh -@Dummy:1:1:1634:330/2 -TCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTAT -+ -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhWhh^hOhhhhghhhfhhh
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_out10.sam Wed Feb 23 12:22:25 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,36 +0,0 @@ -Dummy:1:1:1570:620 141 * 0 0 * * 0 0 CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII?I0IIIIHIIIGIII XM:i:0 -Dummy:1:1:1570:620 77 * 0 0 * * 0 0 GAGTAACAAAGTAAAGTTTGGACCGTTTTTGTCTCGTGCTCGTCGCTGCG IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII"IIIIIII000IIII XM:i:0 -Dummy:1:1:1572:270 131 phiX174 3577 255 50M = 3518 -109 ACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1572:270 67 phiX174 3518 255 50M = 3577 109 TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1572:324 141 * 0 0 * * 0 0 GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I?I0IIIIHIIIGIII XM:i:0 -Dummy:1:1:1572:324 77 * 0 0 * * 0 0 AAGGTGCTTAAATTCGTGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I"IIIIIII000IIII XM:i:0 -Dummy:1:1:1578:331 131 phiX174 268 255 50M = 209 -109 AAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1578:331 67 phiX174 209 255 50M = 268 109 TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1582:633 141 * 0 0 * * 0 0 TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XM:i:0 -Dummy:1:1:1582:633 77 * 0 0 * * 0 0 CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XM:i:0 -Dummy:1:1:1598:534 131 phiX174 1772 255 50M = 1717 -105 TTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1598:534 67 phiX174 1717 255 50M = 1772 105 GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1599:330 131 phiX174 868 255 50M = 803 -115 TTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCA IIIIIII""IIIIIIIIIIIIIIIIIII<III@II?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1599:330 67 phiX174 803 255 50M = 868 115 AGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAGTGATGTAATGTC IIIIIII""IIIIIIIIIIIIIIIIIII<III@II"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1616:363 131 phiX174 2773 255 50M = 2718 -105 GTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAATGTTTATGTTGG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1616:363 67 phiX174 2718 255 50M = 2773 105 TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1629:446 131 phiX174 2355 255 50M = 2301 -104 CAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1629:446 67 phiX174 2301 255 50M = 2355 104 AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1634:330 131 phiX174 4473 255 50M = 4418 -105 TCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTAT IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1634:330 67 phiX174 4418 255 50M = 4473 105 GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1647:512 131 phiX174 451 255 50M = 401 -100 TTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1647:512 67 phiX174 401 255 50M = 451 100 TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1652:270 141 * 0 0 * * 0 0 GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II?I0IIIIHIIIGIII XM:i:0 -Dummy:1:1:1652:270 77 * 0 0 * * 0 0 AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGACTTTGCATTGTTTAATTG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II"IIIIIII000IIII XM:i:0 -Dummy:1:1:1673:514 131 phiX174 4072 255 50M = 4018 -104 GCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1673:514 67 phiX174 4018 255 50M = 4072 104 ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1746:351 141 * 0 0 * * 0 0 CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT IIIIIII""IIIIIIIIIIIIIIIIII?I0IIIIHIIIGIIIIIIIIIII XM:i:0 -Dummy:1:1:1746:351 77 * 0 0 * * 0 0 CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XM:i:0 -Dummy:1:1:1749:466 131 phiX174 2251 255 50M = 2201 -100 GCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1749:466 67 phiX174 2201 255 50M = 2251 100 TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1761:343 131 phiX174 69 255 50M = 5 -114 TTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGG IIIIIII""IIIIIII0II?I""IIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1761:343 67 phiX174 5 255 50M = 69 114 TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIII0II?I""IIIIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1763:587 131 phiX174 2566 255 50M = 2501 -115 CATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1763:587 67 phiX174 2501 255 50M = 2566 115 AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1768:715 131 phiX174 3173 255 50M = 3118 -105 AGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATA IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1768:715 67 phiX174 3118 255 50M = 3173 105 ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_out6.sam Wed Feb 23 12:22:25 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ -HWI-EAS91_1_30788AAXX:1:1:1090:409/1 16 chrM 15014 255 36M * 0 0 TTGCCTACGCCATCCTACGCTCCATTCCCAACAAAC I8AII:IIIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:0 MD:Z:36 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1199:1376/1 16 chrM 14023 255 36M * 0 0 AAACCCCCATAAATAGGTGAAGGTTTTCCAGAAAAC III/:&GII3III;IIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27G0A7 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1218:141/1 4 * 0 0 * * 0 0 GTTAAATATTGGGAGTGGGGGGGGGGGGGAGTTTTG IIIIIII""IIIIIIIIIIIIIIIIIIII1IIII+I XM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1269:520/1 16 chrM 11036 255 36M * 0 0 CGACAAACCGATCTAAAATCACTTATTCCATACTCC IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:1 MD:Z:27G8 NM:i:1 -HWI-EAS91_1_30788AAXX:1:1:1303:1162/1 16 chrM 14866 255 36M * 0 0 AAAGACATCCTAGGACTCCTCCTCCTGCCCTTGCTC I6I3,'94IIAI(IAIGI*4IIFIIII""IIIIIII XA:i:2 MD:Z:27A0T7 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1310:991/1 16 chrM 10002 255 36M * 0 0 CTCCTATGCCTAGAAGGAATAATACTACCACTATTC I:2IEI:IIDIIIIII4IIIIIIIIII""IIIIIII XA:i:1 MD:Z:27T8 NM:i:1 -HWI-EAS91_1_30788AAXX:1:1:1336:1000/1 16 chrM 11616 255 36M * 0 0 GATCTAGAAACAGAAACTTAATATTTCCCATTTACC II9IIIIIIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27T0T7 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1398:854/1 16 chrM 3921 255 36M * 0 0 CACCCTTCCCGTACTAATAAATCCCCTCCTCTTCAC IIIII=AIIIIIIIIIIIIIIBIIIII""IIIIIII XA:i:2 MD:Z:27T0A7 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1442:1346/1 16 chrM 9331 255 36M * 0 0 CAGCCACCACTTCGGATTCGAAGCAGCCCCTTGATA &,*II-<?<II4I(I1IIIIIDIIIII""IIIIIII XA:i:1 MD:Z:28G7 NM:i:1 -HWI-EAS91_1_30788AAXX:1:1:1454:975/1 16 chrM 8929 255 36M * 0 0 TGGCTTCTTCTGAGCCTTTTACCACTCCCGCCTAGC IIIIIII;GIEIIIIIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27A0A7 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1461:255/1 0 chrM 12988 255 36M * 0 0 GTACACCGGCGCCTGAGCCCTACTAATAACTCTCAT IIIIIII""IIIIII9IIIIIIEI(II9.I4III,I XA:i:2 MD:Z:7A0A27 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1491:637/1 16 chrM 10864 255 36M * 0 0 TGTAGAAGCCCCAATTGCCGGATCCATCCTGCTAGC DBAIIIIIIIIIIIFIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27A0G7 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1513:715/1 16 chrM 9563 255 36M * 0 0 CTGACTACCACAACTAAACATCTATGCCCAAAAAAC I+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27A0G7 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1598:1148/1 16 chrM 2334 255 36M * 0 0 AAATATATAATCACTTATTGATCCAAACCATTGATC IIIIIHI=IICIII?IIIIIIDIIIII""IIIIIII XA:i:0 MD:Z:36 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1601:805/1 0 chrM 12584 255 36M * 0 0 GAAAACAGGAAAACAATCCAGTCACTTACCCTATGC IIIIIII""IIIIIIIIIIIIIIIIIIIIIII@III XA:i:2 MD:Z:7A0C27 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1630:59/1 16 chrM 12387 255 36M * 0 0 TCATACTCGACCCCAACCTTACCAACCCCCCGCTCC FIIHII;IIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:1 MD:Z:27T8 NM:i:1 -HWI-EAS91_1_30788AAXX:1:1:1634:211/1 0 chrM 9350 255 36M * 0 0 GAAGCAGGGGCTTGATACTGACACTTCGTCGACGTA IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF XA:i:2 MD:Z:7C0C27 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1663:724/1 0 chrM 15012 255 36M * 0 0 GTTTGCCGGCGCCATCCTACGCTCCATTCCCAACAA IIIIIII""IIII8IIIIIIHIIII6IIIII1CI=3 XA:i:2 MD:Z:7T0A27 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1698:516/1 16 chrM 2735 255 36M * 0 0 TTTACACTCAGAGGTTCAACTCCTCTCCCTAACAAC I9IIIII5IIIIIIIIIIIIIIIIIII""IIIIIII XA:i:0 MD:Z:36 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1711:249/1 16 chrM 10617 255 36M * 0 0 ACCAAACAGAACGCCTGAACGCAGGCCCCTACTTCC IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:1 MD:Z:27T8 NM:i:1 -HWI-EAS91_1_30788AAXX:1:1:1716:413/1 0 chrM 6040 255 36M * 0 0 GATCCAAGGCTTTATCAACACCTATTCTGATTCTTC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII XA:i:2 MD:Z:7T0C27 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1723:1459/1 16 chrM 15787 255 36M * 0 0 ATCCTCGCTCCGGGCCCATCCAAACGTCCGGGTTTC I=II-IIH9IIIIIIIIIDIIIIIIII""IIIIIII XA:i:2 MD:Z:27G0G7 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1775:764/1 0 chrM 16613 255 36M * 0 0 GCATCCCGGTAGATCTAATTTTCTAAATCTGTCAAC IIIIIII""III@IIII+IIIIII8H8IIIIIIICI XA:i:2 MD:Z:7C0C27 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:795:325/1 16 chrM 4249 255 36M * 0 0 AAACTTGGACTCACACCATTCCACTTCCCAGTACCC IIII56IIIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27T0G7 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:850:117/1 16 chrM 5540 255 36M * 0 0 CCCATGCATTCGTAATAATTTTCTTTACCGTCATAC ?:;I9DDIBEIIIIIIIIEIEIIIIII""IIIIIII XA:i:2 MD:Z:27T0G7 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:873:453/1 16 chrM 3188 255 36M * 0 0 ATCTCATACGAAGTAACTCTAGCAATCCCCCTACTC I=IIIIIII@IIIIIIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27A0T7 NM:i:2
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_out7.sam Wed Feb 23 12:22:25 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,36 +0,0 @@ -Dummy:1:1:1570:620 141 * 0 0 * * 0 0 CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII?I0IIIIHIIIGIII XM:i:0 -Dummy:1:1:1570:620 77 * 0 0 * * 0 0 GAGTAACAAAGTAAAGTTTGGACCGTTTTTGTCTCGTGCTCGTCGCTGCG IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII"IIIIIII000IIII XM:i:0 -Dummy:1:1:1572:270 131 phiX174 3577 255 50M = 3518 -109 ACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1572:270 67 phiX174 3518 255 50M = 3577 109 TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1572:324 141 * 0 0 * * 0 0 GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I?I0IIIIHIIIGIII XM:i:0 -Dummy:1:1:1572:324 77 * 0 0 * * 0 0 AAGGTGCTTAAATTCGTGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I"IIIIIII000IIII XM:i:0 -Dummy:1:1:1578:331 131 phiX174 268 255 50M = 209 -109 AAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1578:331 67 phiX174 209 255 50M = 268 109 TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1582:633 141 * 0 0 * * 0 0 TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XM:i:0 -Dummy:1:1:1582:633 77 * 0 0 * * 0 0 CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XM:i:0 -Dummy:1:1:1598:534 131 phiX174 1772 255 50M = 1717 -105 TTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1598:534 67 phiX174 1717 255 50M = 1772 105 GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1599:330 131 phiX174 868 255 50M = 803 -115 TTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCA IIIIIII""IIIIIIIIIIIIIIIIIII<III@II?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1599:330 67 phiX174 803 255 50M = 868 115 AGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAGTGATGTAATGTC IIIIIII""IIIIIIIIIIIIIIIIIII<III@II"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1616:363 131 phiX174 2773 255 50M = 2718 -105 GTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAATGTTTATGTTGG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1616:363 67 phiX174 2718 255 50M = 2773 105 TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1629:446 131 phiX174 2355 255 50M = 2301 -104 CAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1629:446 67 phiX174 2301 255 50M = 2355 104 AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1634:330 131 phiX174 4473 255 50M = 4418 -105 TCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTAT IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1634:330 67 phiX174 4418 255 50M = 4473 105 GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1647:512 131 phiX174 451 255 50M = 401 -100 TTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1647:512 67 phiX174 401 255 50M = 451 100 TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1652:270 141 * 0 0 * * 0 0 GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II?I0IIIIHIIIGIII XM:i:0 -Dummy:1:1:1652:270 77 * 0 0 * * 0 0 AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGACTTTGCATTGTTTAATTG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II"IIIIIII000IIII XM:i:0 -Dummy:1:1:1673:514 131 phiX174 4072 255 50M = 4018 -104 GCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1673:514 67 phiX174 4018 255 50M = 4072 104 ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1746:351 141 * 0 0 * * 0 0 CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT IIIIIII""IIIIIIIIIIIIIIIIII?I0IIIIHIIIGIIIIIIIIIII XM:i:0 -Dummy:1:1:1746:351 77 * 0 0 * * 0 0 CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XM:i:0 -Dummy:1:1:1749:466 131 phiX174 2251 255 50M = 2201 -100 GCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1749:466 67 phiX174 2201 255 50M = 2251 100 TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1761:343 131 phiX174 69 255 50M = 5 -114 TTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGG IIIIIII""IIIIIII0II?I""IIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1761:343 67 phiX174 5 255 50M = 69 114 TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIII0II?I""IIIIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1763:587 131 phiX174 2566 255 50M = 2501 -115 CATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1763:587 67 phiX174 2501 255 50M = 2566 115 AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1768:715 131 phiX174 3173 255 50M = 3118 -105 AGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATA IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII?I0IIIIHIIIGIII XA:i:0 MD:Z:50 NM:i:0 -Dummy:1:1:1768:715 67 phiX174 3118 255 50M = 3173 105 ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_out8_1.fastq Wed Feb 23 12:22:25 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +0,0 @@ -+ -+ -+ -+ -+ -@Dummy:1:1:1570:620/1 -@Dummy:1:1:1572:324/1 -@Dummy:1:1:1582:633/1 -@Dummy:1:1:1652:270/1 -@Dummy:1:1:1746:351/1 -AAGGTGCTTaaaTTCgtGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC -AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGacTTTGCATTGTTTAATTG -CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC -CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT -GAGTAACAAAGTaaaGTTTGGAccGTTTTTGTCTCGTGCTCGTCGCTGCG -IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII"IIIIIII000IIII -IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I"IIIIIII000IIII -IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II"IIIIIII000IIII -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_out8_1.fastqillumina.sorted Wed Feb 23 12:22:25 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +0,0 @@ -+ -+ -+ -+ -+ -@Dummy:1:1:1570:620/1 -@Dummy:1:1:1572:324/1 -@Dummy:1:1:1582:633/1 -@Dummy:1:1:1652:270/1 -@Dummy:1:1:1746:351/1 -AAGGTGCTTaaaTTCgtGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC -AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGacTTTGCATTGTTTAATTG -CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC -CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT -GAGTAACAAAGTaaaGTTTGGAccGTTTTTGTCTCGTGCTCGTCGCTGCG -hhhhhhhAAhhhhhhhhhhhhhahhhhhhhhhhhhAhhhhhhhOOOhhhh -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhJVhOThAhhhhhhhOOOhhhh -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhUhhAhhhhhhhOOOhhhh -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhhAhhhhhhhOOOhhhh
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_out8_1.fastqsolexa.sorted Wed Feb 23 12:22:25 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +0,0 @@ -+ -+ -+ -+ -+ -@Dummy:1:1:1570:620/1 -@Dummy:1:1:1572:324/1 -@Dummy:1:1:1582:633/1 -@Dummy:1:1:1652:270/1 -@Dummy:1:1:1746:351/1 -AAGGTGCTTaaaTTCgtGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC -AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGacTTTGCATTGTTTAATTG -CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC -CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT -GAGTAACAAAGTaaaGTTTGGAccGTTTTTGTCTCGTGCTCGTCGCTGCG -hhhhhhh;;hhhhhhhhhhhhhahhhhhhhhhhhh;hhhhhhhOOOhhhh -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhJVhOTh;hhhhhhhOOOhhhh -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhUhh;hhhhhhhOOOhhhh -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh;hhhhhhhOOOhhhh
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_out8_2.fastq Wed Feb 23 12:22:25 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +0,0 @@ -+ -+ -+ -+ -+ -@Dummy:1:1:1570:620/2 -@Dummy:1:1:1572:324/2 -@Dummy:1:1:1582:633/2 -@Dummy:1:1:1652:270/2 -@Dummy:1:1:1746:351/2 -CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT -CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT -GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT -GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG -IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII?I0IIIIHIIIGIII -IIIIIII""IIIIIIIIIIIIIIIIII?I0IIIIHIIIGIIIIIIIIIII -IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I?I0IIIIHIIIGIII -IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II?I0IIIIHIIIGIII -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII -TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_out8_2.fastqillumina.sorted Wed Feb 23 12:22:25 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +0,0 @@ -+ -+ -+ -+ -+ -@Dummy:1:1:1570:620/2 -@Dummy:1:1:1572:324/2 -@Dummy:1:1:1582:633/2 -@Dummy:1:1:1652:270/2 -@Dummy:1:1:1746:351/2 -CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT -CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT -GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT -GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG -TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT -hhhhhhhAAhhhhhhhhhhhhhahhhhhhhhhhhh^hOhhhhghhhfhhh -hhhhhhhAAhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhhhhhhhhhh -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhJVhOTh^hOhhhhghhhfhhh -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhUhh^hOhhhhghhhfhhh -hhhhhhhAAhhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_out8_2.fastqsolexa.sorted Wed Feb 23 12:22:25 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +0,0 @@ -+ -+ -+ -+ -+ -@Dummy:1:1:1570:620/2 -@Dummy:1:1:1572:324/2 -@Dummy:1:1:1582:633/2 -@Dummy:1:1:1652:270/2 -@Dummy:1:1:1746:351/2 -CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT -CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT -GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT -GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG -TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT -hhhhhhh;;hhhhhhhhhhhhhahhhhhhhhhhhh^hOhhhhghhhfhhh -hhhhhhh;;hhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhhhhhhhhhh -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhJVhOTh^hOhhhhghhhfhhh -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhUhh^hOhhhhghhhfhhh -hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhh^hOhhhhghhhfhhh
--- a/bowtie_remove_rrna_wrapper/test-data/bowtie_out9.sam Wed Feb 23 12:22:25 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ -HWI-EAS91_1_30788AAXX:1:1:1090:409/1 16 chrM 15014 255 36M * 0 0 TTGCCTACGCCATCCTACGCTCCATTCCCAACAAAC I8AII:IIIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:0 MD:Z:36 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1199:1376/1 16 chrM 14023 255 36M * 0 0 AAACCCCCATAAATAGGTGAAGGTTTTCCAGAAAAC III/:&GII3III;IIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27G0A7 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1218:141/1 4 * 0 0 * * 0 0 GTTAAATATTGGGAGTGGGGGGGGGGGGGAGTTTTG IIIIIII""IIIIIIIIIIIIIIIIIIII1IIII+I XM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1269:520/1 16 chrM 11036 255 36M * 0 0 CGACAAACCGATCTAAAATCACTTATTCCATACTCC IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:1 MD:Z:27G8 NM:i:1 -HWI-EAS91_1_30788AAXX:1:1:1303:1162/1 16 chrM 14866 255 36M * 0 0 AAAGACATCCTAGGACTCCTCCTCCTGCCCTTGCTC I6I3,'94IIAI(IAIGI*4IIFIIII""IIIIIII XA:i:2 MD:Z:27A0T7 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1310:991/1 16 chrM 10002 255 36M * 0 0 CTCCTATGCCTAGAAGGAATAATACTACCACTATTC I:2IEI:IIDIIIIII4IIIIIIIIII""IIIIIII XA:i:1 MD:Z:27T8 NM:i:1 -HWI-EAS91_1_30788AAXX:1:1:1336:1000/1 16 chrM 11616 255 36M * 0 0 GATCTAGAAACAGAAACTTAATATTTCCCATTTACC II9IIIIIIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27T0T7 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1398:854/1 16 chrM 3921 255 36M * 0 0 CACCCTTCCCGTACTAATAAATCCCCTCCTCTTCAC IIIII=AIIIIIIIIIIIIIIBIIIII""IIIIIII XA:i:2 MD:Z:27T0A7 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1442:1346/1 16 chrM 9331 255 36M * 0 0 CAGCCACCACTTCGGATTCGAAGCAGCCCCTTGATA &,*II-<?<II4I(I1IIIIIDIIIII""IIIIIII XA:i:1 MD:Z:28G7 NM:i:1 -HWI-EAS91_1_30788AAXX:1:1:1454:975/1 16 chrM 8929 255 36M * 0 0 TGGCTTCTTCTGAGCCTTTTACCACTCCCGCCTAGC IIIIIII;GIEIIIIIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27A0A7 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1461:255/1 0 chrM 12988 255 36M * 0 0 GTACACCGGCGCCTGAGCCCTACTAATAACTCTCAT IIIIIII""IIIIII9IIIIIIEI(II9.I4III,I XA:i:2 MD:Z:7A0A27 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1491:637/1 16 chrM 10864 255 36M * 0 0 TGTAGAAGCCCCAATTGCCGGATCCATCCTGCTAGC DBAIIIIIIIIIIIFIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27A0G7 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1513:715/1 16 chrM 9563 255 36M * 0 0 CTGACTACCACAACTAAACATCTATGCCCAAAAAAC I+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27A0G7 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1598:1148/1 16 chrM 2334 255 36M * 0 0 AAATATATAATCACTTATTGATCCAAACCATTGATC IIIIIHI=IICIII?IIIIIIDIIIII""IIIIIII XA:i:0 MD:Z:36 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1601:805/1 0 chrM 12584 255 36M * 0 0 GAAAACAGGAAAACAATCCAGTCACTTACCCTATGC IIIIIII""IIIIIIIIIIIIIIIIIIIIIII@III XA:i:2 MD:Z:7A0C27 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1630:59/1 16 chrM 12387 255 36M * 0 0 TCATACTCGACCCCAACCTTACCAACCCCCCGCTCC FIIHII;IIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:1 MD:Z:27T8 NM:i:1 -HWI-EAS91_1_30788AAXX:1:1:1634:211/1 0 chrM 9350 255 36M * 0 0 GAAGCAGGGGCTTGATACTGACACTTCGTCGACGTA IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF XA:i:2 MD:Z:7C0C27 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1663:724/1 0 chrM 15012 255 36M * 0 0 GTTTGCCGGCGCCATCCTACGCTCCATTCCCAACAA IIIIIII""IIII8IIIIIIHIIII6IIIII1CI=3 XA:i:2 MD:Z:7T0A27 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1698:516/1 16 chrM 2735 255 36M * 0 0 TTTACACTCAGAGGTTCAACTCCTCTCCCTAACAAC I9IIIII5IIIIIIIIIIIIIIIIIII""IIIIIII XA:i:0 MD:Z:36 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1711:249/1 16 chrM 10617 255 36M * 0 0 ACCAAACAGAACGCCTGAACGCAGGCCCCTACTTCC IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:1 MD:Z:27T8 NM:i:1 -HWI-EAS91_1_30788AAXX:1:1:1716:413/1 0 chrM 6040 255 36M * 0 0 GATCCAAGGCTTTATCAACACCTATTCTGATTCTTC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII XA:i:2 MD:Z:7T0C27 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1723:1459/1 16 chrM 15787 255 36M * 0 0 ATCCTCGCTCCGGGCCCATCCAAACGTCCGGGTTTC I=II-IIH9IIIIIIIIIDIIIIIIII""IIIIIII XA:i:2 MD:Z:27G0G7 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:1775:764/1 0 chrM 16613 255 36M * 0 0 GCATCCCGGTAGATCTAATTTTCTAAATCTGTCAAC IIIIIII""III@IIII+IIIIII8H8IIIIIIICI XA:i:2 MD:Z:7C0C27 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:795:325/1 16 chrM 4249 255 36M * 0 0 AAACTTGGACTCACACCATTCCACTTCCCAGTACCC IIII56IIIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27T0G7 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:850:117/1 16 chrM 5540 255 36M * 0 0 CCCATGCATTCGTAATAATTTTCTTTACCGTCATAC ?:;I9DDIBEIIIIIIIIEIEIIIIII""IIIIIII XA:i:2 MD:Z:27T0G7 NM:i:2 -HWI-EAS91_1_30788AAXX:1:1:873:453/1 16 chrM 3188 255 36M * 0 0 ATCTCATACGAAGTAACTCTAGCAATCCCCCTACTC I=IIIIIII@IIIIIIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27A0T7 NM:i:2
--- a/bowtie_remove_rrna_wrapper/test-data/phiX.fasta Wed Feb 23 12:22:25 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,79 +0,0 @@ ->phiX174 -GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT -GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA -ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG -TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA -GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC -TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT -TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT -CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT -TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG -TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC -GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA -CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG -TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT -AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC -CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA -TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC -TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA -CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA -GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT -GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA -ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC -TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT -TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC -ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC -CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT -GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC -CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC -TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG -TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT -TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA -AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT -TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT -ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC -GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC -TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT -TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA -TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG -TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC -CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG -AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC -CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT -TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG -CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA -AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT -GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG -GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA -TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT -CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG -TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA -GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC -CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA -TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA -AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC -TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT -CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA -TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG -TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT -CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT -TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC -ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG -TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA -ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG -GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC -CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT -GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG -GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT -ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG -CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC -CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC -GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT -CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG -CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA -TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT -TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG -TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC -AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC -TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA -
--- a/bowtie_remove_rrna_wrapper/tool-data/bowtie_indices.loc Wed Feb 23 12:22:25 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -Mouse_rRNA Mouse_rRNA Mouse_rRNA /home/DATA/galaxy/galaxy-dist/data/indexes/bowtie_rrna_indexes/Mouse_rRNA/bowtie_rrna_indexes/mouse_rRNA_index
--- a/bowtie_remove_rrna_wrapper/tool_data_table_conf.xml.sample Wed Feb 23 12:22:25 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -<tables> - <!-- Locations of indexes in the Bowtie mapper format --> - <table name="bowtie_rrna_indexes" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/bowtie_indices.loc" /> - </table> -</tables> -