| Previous changeset 5:a9f4a217dcd6 (2021-07-02) Next changeset 7:addaf9d22850 (2023-08-07) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06 |
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modified:
dada2_filterAndTrim.xml macros.xml test-data/gentest.R |
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added:
README.rst test-data/F3D0_S188_L001_R1_001.fastq test-data/F3D0_S188_L001_R2_001.fastq test-data/filterAndTrim_F3D0_R1.fq test-data/filterAndTrim_F3D0_R2.fq |
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removed:
README.md |
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| diff -r a9f4a217dcd6 -r 34e55239e68b README.md --- a/README.md Fri Jul 02 20:12:35 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,63 +0,0 @@ -Wrappers for the core functionality of the dada2 package https://benjjneb.github.io/dada2/index.html. - -- assignTaxonomyAddspecies -- filterAndTrim -- learnErrors -- dada -- mergePairs -- makeSequenceTable -- plotComplexity -- plotQualityProfile -- removeBimeraDenovo -- seqCounts - -Installation -============ - -A conda release >=4.6 is needed so that the bioconductor-dada2 conda environment can be installed correctly. - -The dada2 wrappers can be installed via the toolshed. Since they use datatypes that have been introduced with Galaxy release 19.09 they won't work out of the box for older Galaxy releases. -In order to run the tools you may either upgrade Galaxy or execute the following two steps: - -1. `find GALAXY_ROOT/shed_tools/testtoolshed.g2.bx.psu.edu/repos/iuc/ -name "dada2_*xml" -exec sed -i -e 's/profile="19.09"/profile="YOUR_RELEASE"/' {} ;` (replace GALAXY_ROOT and YOUR_RELEASE appropriately) -2. insert the following lines in `config/datatypes.xml` (just before the line `</registration>`): -``` - <datatype extension="dada2_dada" type="galaxy.datatypes.binary:RData" subclass="true" display_in_upload="true" /> - <datatype extension="dada2_errorrates" type="galaxy.datatypes.binary:RData" subclass="true" display_in_upload="true" /> - <datatype extension="dada2_mergepairs" type="galaxy.datatypes.binary:RData" subclass="true" display_in_upload="true" /> - <datatype extension="dada2_sequencetable" type="galaxy.datatypes.tabular:Tabular" mimetype="application/text" subclass="true" display_in_upload="true" /> - <datatype extension="dada2_uniques" type="galaxy.datatypes.tabular:Tabular" mimetype="application/text" subclass="true" display_in_upload="true" /> -``` - -Datatypes -========= - -The dada2 Galaxy wrappers use a few extra data types to ensure that only inputs of the correct type can be used, these datatypes are available from Galaxy release 19.05, for earlier releases they need to be added manually. - -For the outputs of dada, learnErrors, and mergePairs the following datatypes are used that derive from Rdata (which contains the named list that is returned from the corresponding dada function): - -- dada2_dada (Rdata: named list, see docs for dada-class) -- dada2_errorrates (Rdata: named list, see docs for learnErrors) -- dada2_mergepairs (Rdata: named list, see docs for mergePairs) - -For the outputs of makeSequenceTable and removeBimeraDenovo the following data types are used which derive from tabular: - -- dada2_uniques --- in R a named integer vector (names are the unique sequences) --- in Galaxy written as a table (each row corresponding to a unique sequence, column 1: the sequence, column 2: the count) -- dada2_sequencetable --- in R a named integer matrix (rows = samples, columns = unique sequences) --- in Galaxy written as a table (rows = unique sequences, columns = samples) - -Note the difference between the R and Galaxy representations! The main motivation is that the dada2_sequencetable is analogous to OTU tables as produced for instance by qiime (and it seemed natural to extend this to the uniques which are essentially a sequencetables of single samples). - -Test data -========= - -Test data for `dada2_seqCounts` is generated using planemo's `--update_test_data` argument and manual -inspection of the test files. In addition a run of the pipeline (using collections) is executed -manually using `planemo serve` making sure that the entries of the tables are generated in a useful way. - -In order to have the Collection unzip tool available use `planemo s --galaxy_root GALAXY_ROOT --extra_tools GALAXY_ROOT/lib/galaxy/tools/` - -All test other test data is generated using the shell script (`gentest.sh`) in test-data |
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| diff -r a9f4a217dcd6 -r 34e55239e68b README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Fri Jun 30 07:56:47 2023 +0000 |
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| @@ -0,0 +1,68 @@ +Wrappers for the core functionality of the dada2 package https://benjjneb.github.io/dada2/index.html. + +- assignTaxonomyAddspecies +- filterAndTrim +- learnErrors +- dada +- mergePairs +- makeSequenceTable +- plotComplexity +- plotQualityProfile +- removeBimeraDenovo +- seqCounts + +Installation +============ + +A conda release >=4.6 is needed so that the bioconductor-dada2 conda environment can be installed correctly. + +The dada2 wrappers can be installed via the toolshed. Since they use datatypes that have been introduced with Galaxy release 19.09 they won't work out of the box for older Galaxy releases. +In order to run the tools you may either upgrade Galaxy or execute the following two steps: + + +1. ``find GALAXY_ROOT/shed_tools/testtoolshed.g2.bx.psu.edu/repos/iuc/ -name "dada2_*xml" -exec sed -i -e 's/profile="19.09"/profile="YOUR_RELEASE"/' {} ;`` (replace GALAXY_ROOT and YOUR_RELEASE appropriately) + +2. insert the following lines in ``config/datatypes.xml`` (just before the line ``</registration>``): + .. code-block:: + + <datatype extension="dada2_dada" type="galaxy.datatypes.binary:RData" subclass="true" display_in_upload="true" /> + <datatype extension="dada2_errorrates" type="galaxy.datatypes.binary:RData" subclass="true" display_in_upload="true" /> + <datatype extension="dada2_mergepairs" type="galaxy.datatypes.binary:RData" subclass="true" display_in_upload="true" /> + <datatype extension="dada2_sequencetable" type="galaxy.datatypes.tabular:Tabular" mimetype="application/text" subclass="true" display_in_upload="true" /> + <datatype extension="dada2_uniques" type="galaxy.datatypes.tabular:Tabular" mimetype="application/text" subclass="true" display_in_upload="true" /> + + +Datatypes +========= + +The dada2 Galaxy wrappers use a few extra data types to ensure that only inputs of the correct type can be used, these datatypes are available from Galaxy release 19.05, for earlier releases they need to be added manually. + +For the outputs of dada, learnErrors, and mergePairs the following datatypes are used that derive from Rdata (which contains the named list that is returned from the corresponding dada function): + +- dada2_dada (Rdata: named list, see docs for dada-class) +- dada2_errorrates (Rdata: named list, see docs for learnErrors) +- dada2_mergepairs (Rdata: named list, see docs for mergePairs) + + +For the outputs of makeSequenceTable and removeBimeraDenovo the following data types are used which derive from tabular: + +- dada2_uniques + - in R a named integer vector (names are the unique sequences) + - in Galaxy written as a table (each row corresponding to a unique sequence, column 1: the sequence, column 2: the count) +- dada2_sequencetable + - in R a named integer matrix (rows = samples, columns = unique sequences) + - in Galaxy written as a table (rows = unique sequences, columns = samples) + + +Note the difference between the R and Galaxy representations! The main motivation is that the dada2_sequencetable is analogous to OTU tables as produced for instance by qiime (and it seemed natural to extend this to the uniques which are essentially a sequencetables of single samples). + +Test data +========= + +Test data for ``dada2_seqCounts`` is generated using planemo's ``--update_test_data`` argument and manual +inspection of the test files. In addition a run of the pipeline (using collections) is executed +manually using ``planemo serve`` making sure that the entries of the tables are generated in a useful way. + +In order to have the Collection unzip tool available use ``planemo s --galaxy_root GALAXY_ROOT --extra_tools GALAXY_ROOT/lib/galaxy/tools/`` + +All test other test data is generated using the shell script (``gentest.sh``) in test-data |
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| diff -r a9f4a217dcd6 -r 34e55239e68b dada2_filterAndTrim.xml --- a/dada2_filterAndTrim.xml Fri Jul 02 20:12:35 2021 +0000 +++ b/dada2_filterAndTrim.xml Fri Jun 30 07:56:47 2023 +0000 |
| [ |
| @@ -3,6 +3,7 @@ <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements"/> <expand macro="stdio"/> <expand macro="version_command"/> @@ -11,6 +12,11 @@ ]]></command> <configfiles> <configfile name="dada2_script"><![CDATA[ +#if $paired_cond.paired_select == "paired" + #set $compress_output = str($paired_cond.reads.forward.ext.endswith('gz')).upper() +#else + #set $compress_output = str($paired_cond.reads.ext.endswith('gz')).upper() +#end if truncQ <- c($trim.truncQ) truncLen <- c($trim.truncLen) trimLeft <- c($trim.trimLeft) @@ -75,7 +81,7 @@ library(dada2, quietly=T) -ftout <- filterAndTrim(fwd, filt.fwd, rev, filt.rev, compress = TRUE, +ftout <- filterAndTrim(fwd, filt.fwd, rev, filt.rev, compress = $compress_output, truncQ = truncQ, truncLen = truncLen, trimLeft = trimLeft, trimRight = trimRight, maxLen = maxLen, minLen = minLen, maxN = maxN, minQ = minQ, maxEE = maxEE, rm.lowcomplex = $rmlowcomplex, rm.phix = $rmPhiX, orient.fwd = orientFwd) @@ -110,10 +116,10 @@ <param name="output_statistics" truevalue="TRUE" falsevalue="FALSE" type="boolean" checked="true" label="Output statistics" help="Create extra table with the number of reads pre and post filtering" /> </inputs> <outputs> - <collection name="paired_output" type="paired" format_source="reads['forward']"> + <collection name="paired_output" type="paired" format_source="reads['forward']" label="${tool.name} on ${on_string}: Paired reads" > <filter>paired_cond['paired_select'] == "paired"</filter> </collection> - <data name="output_single" format_source="reads" > + <data name="output_single" format_source="reads" label="${tool.name} on ${on_string}: Reads" > <filter>paired_cond['paired_select'] == "single"</filter> </data> <data name="output_fwd" format_source="reads" label="${tool.name} on ${on_string}: Forward reads" > @@ -224,6 +230,28 @@ <param name="output_statistics" value="FALSE" /> <output_collection name="paired_output" type="paired" count="2"/> </test> + <!-- paired data in paired collection with uncompressed input --> + <test expect_num_outputs="4"> + <conditional name="paired_cond"> + <param name="paired_select" value="paired"/> + <param name="reads"> + <collection type="paired"> + <element name="forward" value="F3D0_S188_L001_R1_001.fastq" ftype="fastqsanger"/> + <element name="reverse" value="F3D0_S188_L001_R2_001.fastq" ftype="fastqsanger"/> + </collection> + </param> + </conditional> + <output_collection name="paired_output" type="paired" count="2"> + <element name="forward" value="filterAndTrim_F3D0_R1.fq" ftype="fastqsanger" /> + <element name="reverse" value="filterAndTrim_F3D0_R2.fq" ftype="fastqsanger" /> + </output_collection> + <output name="outtab" value="F3D0_S188_L001_R1_001.tab" ftype="tabular" lines_diff="2"> + <assert_contents> + <has_text text="745" /> + <has_text text="750" /> + </assert_contents> + </output> + </test> <!-- test failure in case all reads are filtered --> <test expect_exit_code="1" expect_failure="true"> |
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| diff -r a9f4a217dcd6 -r 34e55239e68b macros.xml --- a/macros.xml Fri Jul 02 20:12:35 2021 +0000 +++ b/macros.xml Fri Jun 30 07:56:47 2023 +0000 |
| [ |
| @@ -6,9 +6,14 @@ <yield/> </requirements> </xml> - + <xml name="bio_tools"> + <xrefs> + <xref type="bio.tools">dada2</xref> + <xref type="bioconductor">dada2</xref> + </xrefs> + </xml> <token name="@DADA2_VERSION@">1.20</token> - <token name="@WRAPPER_VERSION@">0</token> + <token name="@WRAPPER_VERSION@">1</token> <xml name="version_command"> <version_command><![CDATA[ |
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| diff -r a9f4a217dcd6 -r 34e55239e68b test-data/F3D0_S188_L001_R1_001.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/F3D0_S188_L001_R1_001.fastq Fri Jun 30 07:56:47 2023 +0000 |
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| b'@@ -0,0 +1,3000 @@\n+@M00967:43:000000000-A3JHG:1:1101:18327:1699 1:N:0:188\n+NACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAG\n++\n+#>>AABABBFFFGGGGGGGGGGGGGGGGHHHHHHHGGGHHHHHGHGGGGGGGHGGGGGGHHHHHHHHHHGGGGGHHHHGHGGGGGGHHBGHGDGGGGGHHHGGGGHHHHHHHHGGGGGHG@DHHGHEGGGGGGBFGGEGGGGGGGG.DFEFFFFFFFDCFFFFFFFFFFFFFFFFFFFFFFFFFFDFDFFFEFFCFF?FDFFFFFFFFAFFFFFFFFFFFBDDFFFFFEFADFFFFFBAFFFA?EFFFBFF\n+@M00967:43:000000000-A3JHG:1:1101:14069:1827 1:N:0:188\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAG\n++\n+3AA?ABBDBFFBEGGEGGGGAFFGGGGGHHHCGGGGGGHFGHGGCFDEFGGGHGGGEGF1GGFGHHHHHGGEGGHHHHHFGGGGGGHHHHHGGGGCDDGHHGGGFHHHHHHHHCD@CCHGGGGHEHGGG@GFGGGGGGG@BGGGEGCEBFFFBFFB;9@EFFFEFFFFFFFFFFFFAFBBBFFFFFBBBFFFFBBBFFFFFFFFFFFBBBBBBBFFFFFFFFFDDFAFFFFF.AF9/FBBBBB.EAFFE?F\n+@M00967:43:000000000-A3JHG:1:1101:18044:1900 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1:N:0:188\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGAAGATCAAGTCAGCGGTAAAATTGAGAGGCTCAACCTCTTCGAGCCGTTGAAACTGGTTTTCTTGAGTGAGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCTCAACTGACGCTCATGCACGAAAGTGTGGGTATCGAACAG\n++\n+BCBCCCCCCFFFGGGGGGGGGGHGGGGGHHHHHHHGGGHHHHHGHGGGGGGGGGGGGGHHHHHHHHHHHGGGGGHHHHHHHHHGGHHHHHHHHGHHHGHGGGGGGHHHHHHHGHHGHHHGHHHHHHHGGGGGHHHHHHGGGGGHHGGGGHGHHHHGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGFFFFFFFFFFFFFFFFFFFFFFFFAFFFFFFFFAFFFFFFFFFFFFFFBFFFFFFFFFFEFFFF\n+@M00967:43:000000000-A3JHG:1:1101:16780:2259 1:N:0:188\n+TACGTAGGTGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGTGTAGGCGGGGACGCAAGTCAGATGTGAAAACCACGGGCTCAACCTGTGGCCTGCATTTGAAACTGTGTTTCTTGAGTACTGGAGAGGCAGACGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGTCTGCTGGACAGCAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACG\n++\n+BBCCBFFCDFCFGGGGGGGGGGHGGGGGHHHHHHHHGGHFHHHGGGEGGHHHGGGGGGGEFGGGHHHHFHHHHGHHHHG/FGGGFGHFHHHGA?CGEHGGGHGHHFBGHHHGGHHHHDGHHFHFHHHHHEC0DDDEDAFFDDEGHHHHHEHHHHHEGGAFFGGGGBDGGGGGGFFFGGFFG.FFFFFFFFFFFFFFFDEFF@=FFFFFF.AFFEFFFFFFFDFFFBFF.:;F-@FFBDAFAAC.;9?FFE.\n+@M00967:43:000000000-A3JHG:1:1101:19378:2540 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1:N:0:188\n+TACGTAGGGGGCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGTAGACGGTAATGCAAGTCTGGAGTGAAAGGCGGGGGCCCAACCCCCGGACTGCTCTGGAAACTGTGTAACTGGAGTGCAGGAGAGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAAAACCAGTGGCGAAGGCGGCCTGCTGGACTGTAACTGACGTTGGGGGCCGAAAGGGTGGGGGGCAAAAA\n++\n+ABBBAFFAABBBGGGGGGGGGGHGGGGGGHHHHHHBEEHHHFHGHGGGEFAFHGGAGGHHHFHHGHHHHFHHFHHHHAAEGGGGGGGGHGGGGGCG?DGHHHHHHHHHHHHHHHFHHHGHHGHFFGGFGEEGGGGGDDA?D9D?F/BBB/9BBFFBBF.DEBFFBFFDDB./9B//BFBBD.B/.9DFFFFE.-9>-D.;B=9.99/BF.A/.9/B/;99/:9A..-9----9;@A.9.9-@--;-9::..\n+@M00967:43:000000000-A3JHG:1:1103:11662:24827 1:N:0:188\n+TACGTAGGGGGCGAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGCGTGGCAAGTCAGATGTGAAAACCCGGGGCCCAACCCCGGGACTGCATTTGAAACTGCCATGCTGGAGTGCCGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGGAGGCGGCTTGCTGGACGGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACA\n++\n+CCCCDFFCCCDCGGGGGGGGGGHGGGGGHHHHHHHHGCGHHHHGHGGGGEGGGGGGGCEGGHHGHHGHHHHHHHHHHGGGGGGGGGGGHGGGDGGGGGHHHFGHHHHHHHHHGHHHHGGGGGGGGGGGGGGGGGGGGGFFFFFFFFFFFFFFFFFFFFDFFFFFFFFDFFFFFFFFFFFFFFFFFFFFFFFFFFAACFDFFCFFFFFEF9ADFFEFFFFFEA.AFFFFFFFF;FDAFF:.DFB.@AAFF?.\n+@M00967:43:000000000-A3JHG:1:1103:25476:25068 1:N:0:188\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGAAGATCAAGTCAGCGGTAAAATTGAGAGGCTCAACCTCTTCGAGCCGTTGAAACTGGTTTTCTTGAGTGAGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCTCAACTGACGCTCATGCACGAAAGTGTGGGTATCGAACAG\n++\n+>AAABBB2AFFFGGGGGEGCGGHGGGFGHHHHHHHEFFHGHGHGCFGGGGGGGGGGGGHGHHHHHHHHHGGGGGHHHHHHHHHGGHHHHHHHHHHHHHHGGGGGGGHHHHHGHHHGHHHHHHHHHHHGGGGGHHHHHFGGGGAGHGGGGGGHHHGGGGGGGGGFFFGGGGGGGGGGGGGGGGGGGGGBFFFFF<BBFFFFFFFFFED?BBBBFFFFFFEFD?D?DFFFFFFFFB?/FFFFFDFFFAAFF;F\n' |
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| diff -r a9f4a217dcd6 -r 34e55239e68b test-data/F3D0_S188_L001_R2_001.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/F3D0_S188_L001_R2_001.fastq Fri Jun 30 07:56:47 2023 +0000 |
| b |
| b'@@ -0,0 +1,3000 @@\n+@M00967:43:000000000-A3JHG:1:1101:18327:1699 2:N:0:188\n+CCTGTTTGATCCCCGCACTTTCGTGCCTCAGCGTCAGTAGGGCGCCGGTATGCTGCCTTCGCAATCGGGGTTCTGCGTGATATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTCAACGGCTGTACGGGGTTGAGCCCCGCAATTTTACCGCTGACTTGGCAGGCCGCCTACGCACCCTTTAAACCCAATAAATCCGGATAACGCCCGCCTCCTCCGT\n++\n+BABBBFFFFFFFFGEGGGGGGGGHGGHHHHHGGGGGGHHHGGHGGGGGGEGHHGHHHHHHHG11EHEGCGGGHHHHGFGEHHHHGHHHHHHHHHFHHGGGCGHHHHHGGGGGGFHG@EGHHHHHHGFGGGGGGAGDGGGGGGFGHHGHHECDGGGGFGGGDFG:D-FFGGGGFCFBDFBFFFF.;--.BBFFFF/9B.;>-@DDF.-9B@DFFF/FFF/AFAB/B/B/FFF.AAFBA--@=F-.AA.;B..\n+@M00967:43:000000000-A3JHG:1:1101:14069:1827 2:N:0:188\n+CCTGTTTGATCCCCGCACTTTCGTGCCTCAGCGTCAGTAGGGCGCCGGTATGCTGCCTTCGCAATCGGGGTTCTGCGTGATATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTCAACGGCTGTACGGGGTTGAGCCCCGCAATTTTACCGCTGACTTGGCAGGCCGCCTACGCACCCTTTAAACCCAATAAATCCGGGTAAAGCTCGCATCCTCCGG\n++\n+BABBBFFFFFFFGGGGGGGGGGGHGGHHHHHHGGGGGHHHHFHGGGGGGFGHHGHHHHGHGGGGGHGGCGGGHHHHGGGDBGHHHFHHHHHHGHHHHGGGGGHHHEHGGGGGHHHGGGGHGHHHHGGGGGGHHEHGGGGG@FCCGHHHHGHGGGAGFBCEFGGGADGFGFGGFF;ADFFFFFBDFA>.BFFEFFFFFAFF;D..FFAA;BFEFFBBFFFF?EFFFFB/FDC-99B9FB/;AF-ABFFFF.-\n+@M00967:43:000000000-A3JHG:1:1101:18044:1900 2:N:0:188\n+CCTGTTTGCTCCCCACGCTTTCGCGCCTCAGCGTCAGTCTTGGCCCAGAGAATCGCCTTCGCCACTGGTGTTCCTCCTAATATCTACGCATTTCACCGCTACACTAGGAATTCCATTCTCCTCTTCCATACTCAAGTCTAACAGTATCAGTGGCAGGCTGAGGGTTGAGCCCTCAGTTTTCACCACTGACTTATTAAACCGCCTACGCGCCCTTTAAGCCCAGTGATTCCGGACAAAGCCCGCCTCCCCCG\n++\n+>AAABFFFFFFFGGGGGGGGGGGGGGGGGGHGGGGGGHHGHGGCEGEGGGHHFHFGGGGHHGGGGBFHHGHGGHGHGHEHH4FHHHGGGGGGHHHFHGGGGGHH3FHGFGGHHHFFHDFHFHHHHHHHFHHHHDFG2FFFHHHHFHHHHHGHHGHGG/000<CDDHC01<CE/<.C=DDGDDGHBC/CCGHBCGF00CGB-;:E.CFGAAFG?CF009:9E..;//BB/:/9.9-.::B.9---9:..9D-\n+@M00967:43:000000000-A3JHG:1:1101:13234:1983 2:N:0:188\n+CCTGTTCGATACCCACACTTTCGTGCATGAGCGTCAGTTGAGCGCCGGTATGCTGCCTTCGCAATCGGAGTTCTGCGTGATATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCTCACTCAAGAAAACCAGTTTCAACGGCTCGAAGAGGTTGAGCCTCTCAATTTTACCGCTGCCTTGATCTTCCGCCTGCGCCCCCTTTAAACCCAATAAATCCGGATAACGCTCGCATCCTCCGT\n++\n+ABBBBFFBBFBBGGGGGGGGGGGHGGHGGHHHGGGGGHHHHHHGGGGGGGGHHHHHHHHHHGGGGHGGGGGHHGHHGGGGHHHHHGHHHHHHHHHHHGGGGGHHHHGGGGGGHHHGGGGHHHHFHGGGHGHHGHHHHHHHHDGHGHHHFHHGGGFDC<C.AGHC/C/C0GG//:GBB0CF9009??-..9;/0;;B90;.;D.C.B9.:-@-:F/BF//;EE./;::/9.@.A.B:.9.9;-999B99/.;\n+@M00967:43:000000000-A3JHG:1:1101:16780:2259 2:N:0:188\n+CCTGTTTGCTCCCCACGCTTTCGCGCCTCAGCGTCAGTTGCTGTCCAGCAGACCGCCTTCGCCACTGGTGTTCCTCCTAATATCTACGCATTTCACCGCTACACTAGGAATTCCGTCTGCCTCTCCAGTACTCAAGAAACACAGTTTCAAATGCAGGCCACAGGTTGAGCCCGTGGTTTTCACATCTGACTTGCGTCCCCGCCTACACGCCCTTTACACCCAGTAAATCCGGATAACGCTTGCCACCTACG\n++\n+>AABAFFFFFFFGGGGGGGGGGGGGGGGGHHHGGGGGGHHHGFHHHHHHHHBGHGGGGGHHGGGGFHHFHHEFHHHHHEHHFHHHFFGGGGGHHFHHGGGGGFHHHHHHHHHHHHHHHGHHHHHHHFHHHHHHHHHEHHHHHHHHHHHGGGHHHHGGGGHGFHHHFG<CFHGGCDC.EHGHHGFHHGG0CGHHHCD@BFGF?B?DGGGDCEFFFFFFFFB?EFFFF/BFFD;?FFFBD=AEEFB/FFFFF?\n+@M00967:43:000000000-A3JHG:1:1101:19378:2540 2:N:0:188\n+CCTGTTCGATACCCACACTTTCGTGCATGAGCGTCAGTTGAGCGCCGGTATGCTGCCTTCGCAATCGGAGTTCTGCGTGATATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCTCACTCAAGAAAACCAGTTTCAACGGCTCGAAGAGGTTGAGCCTCTCAATTTTACCGCTGACTTGATCTTTCGCCTGCGCACCCTTTAAACCCAATAAATCCGGATAACGCTCGCATCCTCCG\n++\n+BCCCCFFCCFCCGGGGGGGGGGGHGGHGHHHHGGGGGHHHHHHGGGGGCEFHHHHHHHHHHGGGGHGGGGGHHHHHGGGGHEHHHHHHHHHHHHHHHGGGGGHHHHHGGGGGHHHGGGGHHHHHHGGGHGHHHHHHBCGHHGHHFGHHHHHGGGGGC-C...;;CC/;0C/:0:0<0;BFB0:A??-9/0;90;9CF0;9?D...--@-@9.BB0BBB9AEEF0FF009.=...0B.-.9--;.@B0:B;\n+@M00967:43:000000000-A3JHG:1:1101:17674:2779 2:N:0:188\n+CCTGTTCGATACCCACGCTTCCGTGCATGAGCGTCAGTTGCGCGCCGGTAGGCTGCATTCGCAATCGGAGTTCTGCGCGCTATCTATTCATCTTACCGCTACACCACGCCTTCCGCCTACTTCTCGCGCACTCAAGGCTCCCAGTTCCAACCACGGGACGGGGCTGAGCCCCGCGAATTTCCCCCTGACTTGACAGTCCGCCCGCGACCCCTTTAAAACTAAACACTCCGCATTACGCTAGCACCCTCCT\n++\n+1>AA>1BA1D>A1BGEAAE00B0BCEC221BFEAEE?D211AAEAE?/>///B@0>0@FG2/EFC1A//>/BB21B//>/>//0B2B2BGF222B>CBBC/><FGG/<C/?EHCEGC/.><<111F.C@-<</<C0/./;C:/0/:0<CGG....--.99A-A-;--;B/AB--;--9;///9--;-;B///9//99//9---9----;---9///9/B/////:9//------;9;----9//99-A9;\n+@M00967:43:000000000-A3JHG:1'..b'FADDFFFFFFBFFFFFFFFBBFFFD?ADFFDFFAEFBFFFFFF.\n+@M00967:43:000000000-A3JHG:1:1103:6627:24281 2:N:0:188\n+CCTGTTCGATCCCCGCACTTTCGTGCCTCAGCGTCAGTAGGGCGCCGGCAGGCTGCCTTCGCAATCGGGGTTCTGCGTGATATCTATGCATTTCACCGCTACACCACGCATTCCGCCTTCTTCTCGCCCACTCAAGGCCCCCAGTTTCAACGGCCGGACGGGGTTGAGCCCCGAATTTTTACCGCTGACTTAAAAGCCCGCCTACGCACCCTTTAAACCCAATAAAACCGGTTAACGCTCGCATCCTCCGT\n++\n+3AAABFFBBFFAGG2E?FFGGGGFGGAHGCHFEGGGGHHHHABEGGGG0E0FGHHGGFHHHGGGGHGCFGGGHHHHGGGDHHHHHGHHGGHHHHHHHGG/CDFFHHHGGGGGHHGG/C.FFHGHGGGGGGGGGHHHF.<<@CGGHGGHGHFGGGFGG@?@GGFFFFF///ADA-;AEFFF.B/:BCBABBF/9/9FFFF@>=A.9DFA-BDFFFFB/FF.E9.FB//:9@D-.:B9.-::---.;//9;..\n+@M00967:43:000000000-A3JHG:1:1103:24233:24298 2:N:0:188\n+CCTGTTCGATACCCACGCTTTCGTGCCTCAGCGTCAGTAGGGCGCCGGTATGCTGCCTTCGCAATCGGAGTTCTGCGTGATATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCAAGAACGCCAGTTTCAACGGCTCGACGGCGTTGAGCACCGCTTTTTTACCGCTGACTTGGCATCCCGCCTACGCACCCTTTAAACCCAATAAATCCGGATAACGCTCGCATCCTCCGT\n++\n+BBBBBFFBBFBBGGGGGGGGGGGHGGHHHHHGGGGGGHHHHGHGEGGGGGGHHGHHHHHHHGGGGHGGCGGFHHHHGGGGHGHHGGHHHHHHHHHHHGGGGGHHHHHGGGGGHHHGCGGHGHHHHGGGGGGHHHHHHHHGGGGGHHHHHHHGGGGGGCFG?BFGBFFGGFGGFFAFFFFFFFFDFACFFFFFFFBBFFFFFFFFFFF?F-AAFFBFFFFDFFFFFFFFFAC...BBFFDFCFF.BBBFFA9\n+@M00967:43:000000000-A3JHG:1:1103:20946:24435 2:N:0:188\n+CCTGTTCGATACCCACACTTTCGTGCATGAGCGTCAGTTGAGCGCCGGTATGCTGCCTTCGCAATCGGAGTTCTGCGTGATATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCTCACTCAAGAAAACCAGTTTCAACGGCTCGAAGAGGTTGAGCCTCTCAATTTTACCGCTGACTTGATCTTCCGCCTGCGCACCCTTTAAAACCAATAAATCCGGATAACGCTCGCATCCTCC\n++\n+>ABAAFFBBBBBGGGGGGGGGGGHGGHHHHHHGGDGGHHGHGHGGGGCGGFHHHHGHHHHHGGGFHGGGGGHHHHHCEGEFHHHHGHGFGHHHHHHHGGGGGHHHHHGGGGGHHHGGGGHHHHHHGGGGGFHHHHHDHHHHGEHHHHHHHHGGGCG<-C..CGGGFFHHHCG/:0C9BFFFFGAA?-.;BGGBBFB;BFAGFC.ADA;-9A9FF/BF/;DFFFEFFEBFDB...;/9@.;---:-9/99\n+@M00967:43:000000000-A3JHG:1:1103:24627:24453 2:N:0:188\n+CCTGTTCGATACCCACGCTTTCGTGCATGAGCGTCAGTTGCGCGCCGGTAGGCTGCCTTCGCAATCGGAGTTCTGCGTGATATCTATGCATTTCACCGCTACACCACGCATTCCGCCTACTTCTCGCGCACTCAAGGCTCCCAGTTTCAACGGCGGAACGGGGTTGAGCCCCGCGATTTGACCGCTGACTTGAGAGTCCGCCTGCGCACCCTTTAAACCCAATAAATCCGGATAACGCCCGCATCCTCCGT\n++\n+AABBBFFABFBBGGGGFGGGGGGHGGHGHHHHGGGGGHHHGEGGGGGGGGGGHHHGHHHHHGGGGHGGGGFHHHGHGEGFHHHHHHHHHHHHHHHHHGGGGGHHHGHGGGGGHHHGGGGHHHHEHGGGGGGGHHHHGHFGGGHHHHHGHHHGGGGG-B?9DEG9@CBFFFFFDAD-@EFFBFFFFDCDFFFBBF.BB9B.BDAE9-99@>FEFEFFFFFFFAFFFF/;B.>.::B/.--;-:-:@F;BFD:\n+@M00967:43:000000000-A3JHG:1:1103:8261:24679 2:N:0:188\n+CCTGTTTGCTCCCCACGCTTTCGAGCCTCAACGTCAGTTACAGTCCAGCAGGCCGCCTTCGCCACTGGTGTTCCTCCTAATATCTACGCATTTCACCGCTACACTAGGAATTCCGCCTGCCTCTCCTGCACTCCAGTTACACAGTTTCCAGAGCAGTCCGGGGGTTGGGCCCCCGCCTTTCACTCCAGACTTGCATTACCGTCTACGCTACCTTTACACCCAGTAATTCCGGATAACGCTTGCCCCCTACG\n++\n+AABBBFFF5FDFEGGGEFGGGGGGHGGHGHBGGHHGGHGGHHGHHGHHHHFEGGGGGGGHHGGGGFGHDBCEHGHHHHGHFHHHHHHGGGGFHHHHHFGEEGHHHHHHHHHHHHHGGFEGFHHHHGHHHHGHHHHGDGHHHHHHHHHG1GDHHHHGDGHDCFFGGGGC?AACG?GGGG.BCFGGGGFFFEFFFFFFFFFFFE?FE/AB..;BFFFEFFFFFEE9BB//BB/BDDDFFFFFEA9BBABF.9.\n+@M00967:43:000000000-A3JHG:1:1103:11662:24827 2:N:0:188\n+CCTGTTTGCTCCCCACGCTTTCGAGCCTCAGCGTCAGTTACCGTCCAGCAAGCCGCCTCCGCCACTGGTGTTCCTCCTAATATCTACGCATTTCACCGCTACACTAGGAATTCCACTTGCCTCTCCGGCACTCCAGCATGGCAGTTTCAAATGCAGTCCCGGGGTTGGGCCCCGGGTTTTCACATCTGACTTGCCACGCCGCCTGCGCTCCCTTTACACCCAGTAAATCCGGATAACGCCCGCCCCCCACG\n++\n+A>ABBFFFFFFFGGGGGGGGGGGGHGGGGHFHGGFGGHHHHHGGGGGGFHGHHGGGG?>FFGGGGFHHFGHFHHHHHHHGHHHGHHHFGGGGHHHHHGGGGGHHGHHHHHHHHHHHFHGHHFHHHHBFGGGHHHHHHFGFFHFGHHHHGHHHGGHHHCGHGGGGCCGGGFHGFFG-.;CEFB000;CFFGGGFFFGGADF=FA...9=-;AFFFFFFFBFD?ABFFFFFFFFFFFFFB;---@C=FB--A-\n+@M00967:43:000000000-A3JHG:1:1103:25476:25068 2:N:0:188\n+CCTGNTCGATACCCACANNNNNGNNNNNNNNNNNCAGTNNNNCGNNNNNNNNNTGCCTTCGCAATCGGANNNNNNCGTGNTATCTNTNNNNNNNNNNNNNNNNNNNNNNNNNCCGCATACTTCTCGCTCACNCAAGAANNCNNNNNNNNNNNGNNNNAAGAGGNTNNGCCTNNNANTTTTACCGCCTAATTGATCTTCCGCCCGCGCACCCTTTAAACCCAATAAATACGGGTAACGCNCCNNNCCCNCN\n++\n+>AAA#>>>AAADEFFGG#####A###########BBAF####BA#########BBBCFHHFGGGGHF?C######?BBF#??FFG#>#########################?<?FFG?GHHHHGFEECE1#??FEFF##<###########<####..:.:;#:##.:..###9#.;;CEBB.?-../0;090000/;-;A---9---9AA/F/:9/9AA9-/9:;/:-A-9-;9;9#9-###9;9#9#\n' |
| b |
| diff -r a9f4a217dcd6 -r 34e55239e68b test-data/filterAndTrim_F3D0_R1.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filterAndTrim_F3D0_R1.fq Fri Jun 30 07:56:47 2023 +0000 |
| b |
| b'@@ -0,0 +1,2980 @@\n+@M00967:43:000000000-A3JHG:1:1101:14069:1827 1:N:0:188\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAG\n++\n+3AA?ABBDBFFBEGGEGGGGAFFGGGGGHHHCGGGGGGHFGHGGCFDEFGGGHGGGEGF1GGFGHHHHHGGEGGHHHHHFGGGGGGHHHHHGGGGCDDGHHGGGFHHHHHHHHCD@CCHGGGGHEHGGG@GFGGGGGGG@BGGGEGCEBFFFBFFB;9@EFFFEFFFFFFFFFFFFAFBBBFFFFFBBBFFFFBBBFFFFFFFFFFFBBBBBBBFFFFFFFFFDDFAFFFFF.AF9/FBBBBB.EAFFE?F\n+@M00967:43:000000000-A3JHG:1:1101:18044:1900 1:N:0:188\n+TACGGAGGATGCGAGCGTTGTCCGGAATCACTGGGCGTAAAGGGCGCGTAGGCGGTTTAATAAGTCAGTGGTGAAAACTGAGGGCTCAACCCTCAGCCTGCCACTGATACTGTTAGACTTGAGTATGGAAGAGGAGAATGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGATTCTCTGGGCCAAGACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACA\n++\n+BA@BBBABBFFFGGGGGGGGGGHGGGGGHHHHGHHHGGGGHHHGGGGGGGGGHGGGGGGFHFHHHFHHHHHHGFHHHHHHFHGGFGHHGGHGGHHFHHHHHHHHHHHHHHGHHHGHDHHHHHHHHHGHDGFFHHHDHHHHHHHHHHHHFHHHDGHHGGGGGHHHHHGGGGEGGGGGBF0BGGGGGGGGFFFGGGDGFFFFBCFBFFBFFBEEFFEFFFFFFFFBDA9EEFFF>DFFFFDDFFFADDFFFF.\n+@M00967:43:000000000-A3JHG:1:1101:13234:1983 1:N:0:188\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGAAGATCAAGTCAGCGGTAAAATTGAGAGGCTCAACCTCTTCGAGCCGTTGAAACTGGTTTTCTTGAGTGAGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCTCAACTGACGCTCATGCACGAAAGTGTGGGTATCGAACAG\n++\n+BCBCCCCCCFFFGGGGGGGGGGHGGGGGHHHHHHHGGGHHHHHGHGGGGGGGGGGGGGHHHHHHHHHHHGGGGGHHHHHHHHHGGHHHHHHHHGHHHGHGGGGGGHHHHHHHGHHGHHHGHHHHHHHGGGGGHHHHHHGGGGGHHGGGGHGHHHHGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGFFFFFFFFFFFFFFFFFFFFFFFFAFFFFFFFFAFFFFFFFFFFFFFFBFFFFFFFFFFEFFFF\n+@M00967:43:000000000-A3JHG:1:1101:16780:2259 1:N:0:188\n+TACGTAGGTGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGTGTAGGCGGGGACGCAAGTCAGATGTGAAAACCACGGGCTCAACCTGTGGCCTGCATTTGAAACTGTGTTTCTTGAGTACTGGAGAGGCAGACGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGTCTGCTGGACAGCAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACG\n++\n+BBCCBFFCDFCFGGGGGGGGGGHGGGGGHHHHHHHHGGHFHHHGGGEGGHHHGGGGGGGEFGGGHHHHFHHHHGHHHHG/FGGGFGHFHHHGA?CGEHGGGHGHHFBGHHHGGHHHHDGHHFHFHHHHHEC0DDDEDAFFDDEGHHHHHEHHHHHEGGAFFGGGGBDGGGGGGFFFGGFFG.FFFFFFFFFFFFFFFDEFF@=FFFFFF.AFFEFFFFFFFDFFFBFF.:;F-@FFBDAFAAC.;9?FFE.\n+@M00967:43:000000000-A3JHG:1:1101:19378:2540 1:N:0:188\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGAAGATCAAGTCAGCGGTAAAATTGAGAGGCTCAACCTCTTCGAGCCGTTGAAACTGGTTTTCTTGAGTGAGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCTCAACTGACGCTCATGCACGAAAGTGTGGGTATCGAACAG\n++\n+CCCCCCCCCFFFGGGGGGGGGGHGGGGGHHHHHHGGGGHHHHHGFFGGGGGGGGGGGGHHHGHHHHHHHGGGGGHHHHHHHHHGGHHGGHHHHHHHHHHGGGGGGGHHHHHHHHHGHHHHHHHHHHHGGGGGGHHHHHGGGGGHHGGGGHGHHHHGCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEFFFFFFDFFFFFFADFFFFFFFFAFFFFFFFFF\n+@M00967:43:000000000-A3JHG:1:1101:17674:2779 1:N:0:188\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGACTCTCAAGTCAGCGGTCAAATCGCGGGGCTCAACCCCGTTCCGCCGTTGAAACTGGGAGCCTTGAGTGCGCGAGAAGTAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCCTACCGGCGCGCAACTGACGCTCATGCACGAAAGCGTGGGTATCGAACAG\n++\n+ABB@BABDAFFFGGGGGGGGGGHGGGGGHHGHHGHGGGHFDHHGHEGCGGGGGGGFEECGHHHHHHHHHGGGGGHHHGGGGGGGGGHGHGHGGGGHHHGGGGDGGEHHHGFHHGGGFHHGHFHFHCGGGGGGGFGGGGGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF?FFFFFFFFFFFFFAFEFFFFFFFFFFBFFDFFFFFFFFFDBF/AEFFFF\n+@M00967:43:000000000-A3JHG:1:1101:18089:2781 1:N:0:188\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGCGCCAAGTCTGGAGTGAAATGCCGCAGCTTAACTGCGGAACTGCTTTGGAAACTGGCGGACTAGAGTGCGGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCGGTGGCGAAGGCGGCTTACTGGACCGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACA\n++\n+BBBBBFFBBBBBGGGGFGGGGGHGGCGGHHHHHHHHFEFHHHGGGGGGGGGGHGGGFGGGGGGHHHHHHBGHHGHHHHHHGGGGGHHHHHHHHGGGGGHHHHHHHHHGHHHHHHGGGGGHHHHHHHGGGGGGGGFGHHHGGGGGGGGGGGGGGGGGGGGAGGGGGBDFFFFFFFFFFFFFFFFFFFFFFAFFFFFFFFFFFFAFFFFFFFFFFF?FFEFFBDFF?EFFFFFFDFFFFFDFFFFFFFFFF?.\n+@M00967:43:000000000-A3J'..b'FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEFFFFFF\n+@M00967:43:000000000-A3JHG:1:1103:16873:24153 1:N:0:188\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGCGCCAAGTCTGGAGTGAAATGCCGCAGCTTAACTGCGGAACTGCTTTGGAAACTGGCGGACTAGAGTGCGGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCGGTGGCGAAGGCGGCTTACTGGACCGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACA\n++\n+BBBBBFFBBBBB?GGGGGGGGDHGGGGGHHHHHHHGGEHHHHFGFGGGEGGGHGGEG@E?EGGHHHGHFBHHHHHHHHHHGGCEGHHHHHDHFEGGGGHHHFHHHHGDGHHHEEGC?DGHHHHGHHGGCDGCGG;A/GFCCDGGGGGGFGGGGGGGGGGGGGGGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFC=BFA/FFFFFFFFFFFFFFFFFFFFFFFFFEF;FFFFF9DFFFAFFFFFF.\n+@M00967:43:000000000-A3JHG:1:1103:6627:24281 1:N:0:188\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGCTTTTAAGTCAGCGGTCAAAATTCGGGGCTCAACCCCGTCCGGCCGTTGAAACTGGGGGCCTTGAGTGGGCGAGAAGAAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCCTTCCGGCGCCCTACTGACGCTAAGGCACGAAGGGGCGGGGATCGACCAG\n++\n+BAABBBBBBFFFGGFGGGEGGGFGGGGGHHHHGHHEFGHHHHHGHGGGFGEGHGGGGGHHHHHFHHGHFEGE/?GHEGH?FGGG?//F2?FFCG?CD@/C-CCGAGH000DGHGCG-CCH0:0CEA.9--?DFFFGF9??DBA/;DDDCFFEBFBD;9-EFBB9B//9//BBBF/99.9>BFFFF?9;B?EBDF--9.;AA9B/B/D---@C-9B.BFB/?....;/9.:9.A.:.---;9-9..9.---;\n+@M00967:43:000000000-A3JHG:1:1103:24233:24298 1:N:0:188\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGCCAAGTCAGCGGTAAAAAAGCGGTGCTCAACGCCGTCGAGCCGTTGAAACTGGCGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAG\n++\n+CBBCCCCBBFFFGGGGGGGGGGHGGGGGHFHHHHHGGGHHHHHGFGGGGGGGHGGGGCGGHHHHHHHHHGGGGGHHHGGHGGFGGHHHHHGGGGGGGGGGGGGGGHHHHHHHHGDGGGHHHHHHGHGGGGGGGGGGGGGGGGEGGGGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFF..:AFFFFFDFFFAFFFFFFE9F\n+@M00967:43:000000000-A3JHG:1:1103:20946:24435 1:N:0:188\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGAAGATCAAGTCAGCGGTAAAATTGAGAGGCTCAACCTCTTCGAGCCGTTGAAACTGGTTTTCTTGAGTGAGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCTCAACTGACGCTCATGCACGAAAGTGTGGGTATCGAACAG\n++\n+BCCCCCCCCFFFGGGGGGGGGGHGGGGGHHHHHHHGGGHHHHHGHGGGGGGGGGGGGGHHHHHHHHHHHGGGGGHHHHHHHHHGGHHHHHHHHHHHHHHGGGGGGHHHHHHHHHHGHHHHHHHHHHHGGGGGHHHHHHGGGGGHHGGGGHGHHHHGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFFFFFFFFFEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@M00967:43:000000000-A3JHG:1:1103:24627:24453 1:N:0:188\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGACTCTCAAGTCAGCGGTCAAATCGCGGGGCTCAACCCCGTTCCGCCGTTGAAACTGGGAGCCTTGAGTGCGCGAGAAGTAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCCTACCGGCGCGCAACTGACGCTCATGCACGAAAGCGTGGGTATCGAACAG\n++\n+CCCCCCCBCFFFGGGGGGGGGGHGGGGGHGHHHHHGGGHHHHHGHGGGGGGGGGGGGGHHHHHHHHHHHCFGGGHHGHGGGGGGGGHHHHHGGGGHHHGGGGGGGHHHHHHHHHGGGHHHHHHHHGGGGGGGGGGGGGGGGFFFFFFFFFFFFEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFAAFFFFFFFFFFFFFFFFFFFFFDDDDFFFFFF9BFFFFFFFF\n+@M00967:43:000000000-A3JHG:1:1103:8261:24679 1:N:0:188\n+TACGTAGGGGGCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGTAGACGGTAATGCAAGTCTGGAGTGAAAGGCGGGGGCCCAACCCCCGGACTGCTCTGGAAACTGTGTAACTGGAGTGCAGGAGAGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAAAACCAGTGGCGAAGGCGGCCTGCTGGACTGTAACTGACGTTGGGGGCCGAAAGGGTGGGGGGCAAAAA\n++\n+ABBBAFFAABBBGGGGGGGGGGHGGGGGGHHHHHHBEEHHHFHGHGGGEFAFHGGAGGHHHFHHGHHHHFHHFHHHHAAEGGGGGGGGHGGGGGCG?DGHHHHHHHHHHHHHHHFHHHGHHGHFFGGFGEEGGGGGDDA?D9D?F/BBB/9BBFFBBF.DEBFFBFFDDB./9B//BFBBD.B/.9DFFFFE.-9>-D.;B=9.99/BF.A/.9/B/;99/:9A..-9----9;@A.9.9-@--;-9::..\n+@M00967:43:000000000-A3JHG:1:1103:11662:24827 1:N:0:188\n+TACGTAGGGGGCGAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGCGTGGCAAGTCAGATGTGAAAACCCGGGGCCCAACCCCGGGACTGCATTTGAAACTGCCATGCTGGAGTGCCGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGGAGGCGGCTTGCTGGACGGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACA\n++\n+CCCCDFFCCCDCGGGGGGGGGGHGGGGGHHHHHHHHGCGHHHHGHGGGGEGGGGGGGCEGGHHGHHGHHHHHHHHHHGGGGGGGGGGGHGGGDGGGGGHHHFGHHHHHHHHHGHHHHGGGGGGGGGGGGGGGGGGGGGFFFFFFFFFFFFFFFFFFFFDFFFFFFFFDFFFFFFFFFFFFFFFFFFFFFFFFFFAACFDFFCFFFFFEF9ADFFEFFFFFEA.AFFFFFFFF;FDAFF:.DFB.@AAFF?.\n' |
| b |
| diff -r a9f4a217dcd6 -r 34e55239e68b test-data/filterAndTrim_F3D0_R2.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filterAndTrim_F3D0_R2.fq Fri Jun 30 07:56:47 2023 +0000 |
| b |
| b'@@ -0,0 +1,2980 @@\n+@M00967:43:000000000-A3JHG:1:1101:14069:1827 2:N:0:188\n+CCTGTTTGATCCCCGCACTTTCGTGCCTCAGCGTCAGTAGGGCGCCGGTATGCTGCCTTCGCAATCGGGGTTCTGCGTGATATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTCAACGGCTGTACGGGGTTGAGCCCCGCAATTTTACCGCTGACTTGGCAGGCCGCCTACGCACCCTTTAAACCCAATAAATCCGGGTAAAGCTCGCATCCTCCGG\n++\n+BABBBFFFFFFFGGGGGGGGGGGHGGHHHHHHGGGGGHHHHFHGGGGGGFGHHGHHHHGHGGGGGHGGCGGGHHHHGGGDBGHHHFHHHHHHGHHHHGGGGGHHHEHGGGGGHHHGGGGHGHHHHGGGGGGHHEHGGGGG@FCCGHHHHGHGGGAGFBCEFGGGADGFGFGGFF;ADFFFFFBDFA>.BFFEFFFFFAFF;D..FFAA;BFEFFBBFFFF?EFFFFB/FDC-99B9FB/;AF-ABFFFF.-\n+@M00967:43:000000000-A3JHG:1:1101:18044:1900 2:N:0:188\n+CCTGTTTGCTCCCCACGCTTTCGCGCCTCAGCGTCAGTCTTGGCCCAGAGAATCGCCTTCGCCACTGGTGTTCCTCCTAATATCTACGCATTTCACCGCTACACTAGGAATTCCATTCTCCTCTTCCATACTCAAGTCTAACAGTATCAGTGGCAGGCTGAGGGTTGAGCCCTCAGTTTTCACCACTGACTTATTAAACCGCCTACGCGCCCTTTAAGCCCAGTGATTCCGGACAAAGCCCGCCTCCCCCG\n++\n+>AAABFFFFFFFGGGGGGGGGGGGGGGGGGHGGGGGGHHGHGGCEGEGGGHHFHFGGGGHHGGGGBFHHGHGGHGHGHEHH4FHHHGGGGGGHHHFHGGGGGHH3FHGFGGHHHFFHDFHFHHHHHHHFHHHHDFG2FFFHHHHFHHHHHGHHGHGG/000<CDDHC01<CE/<.C=DDGDDGHBC/CCGHBCGF00CGB-;:E.CFGAAFG?CF009:9E..;//BB/:/9.9-.::B.9---9:..9D-\n+@M00967:43:000000000-A3JHG:1:1101:13234:1983 2:N:0:188\n+CCTGTTCGATACCCACACTTTCGTGCATGAGCGTCAGTTGAGCGCCGGTATGCTGCCTTCGCAATCGGAGTTCTGCGTGATATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCTCACTCAAGAAAACCAGTTTCAACGGCTCGAAGAGGTTGAGCCTCTCAATTTTACCGCTGCCTTGATCTTCCGCCTGCGCCCCCTTTAAACCCAATAAATCCGGATAACGCTCGCATCCTCCGT\n++\n+ABBBBFFBBFBBGGGGGGGGGGGHGGHGGHHHGGGGGHHHHHHGGGGGGGGHHHHHHHHHHGGGGHGGGGGHHGHHGGGGHHHHHGHHHHHHHHHHHGGGGGHHHHGGGGGGHHHGGGGHHHHFHGGGHGHHGHHHHHHHHDGHGHHHFHHGGGFDC<C.AGHC/C/C0GG//:GBB0CF9009??-..9;/0;;B90;.;D.C.B9.:-@-:F/BF//;EE./;::/9.@.A.B:.9.9;-999B99/.;\n+@M00967:43:000000000-A3JHG:1:1101:16780:2259 2:N:0:188\n+CCTGTTTGCTCCCCACGCTTTCGCGCCTCAGCGTCAGTTGCTGTCCAGCAGACCGCCTTCGCCACTGGTGTTCCTCCTAATATCTACGCATTTCACCGCTACACTAGGAATTCCGTCTGCCTCTCCAGTACTCAAGAAACACAGTTTCAAATGCAGGCCACAGGTTGAGCCCGTGGTTTTCACATCTGACTTGCGTCCCCGCCTACACGCCCTTTACACCCAGTAAATCCGGATAACGCTTGCCACCTACG\n++\n+>AABAFFFFFFFGGGGGGGGGGGGGGGGGHHHGGGGGGHHHGFHHHHHHHHBGHGGGGGHHGGGGFHHFHHEFHHHHHEHHFHHHFFGGGGGHHFHHGGGGGFHHHHHHHHHHHHHHHGHHHHHHHFHHHHHHHHHEHHHHHHHHHHHGGGHHHHGGGGHGFHHHFG<CFHGGCDC.EHGHHGFHHGG0CGHHHCD@BFGF?B?DGGGDCEFFFFFFFFB?EFFFF/BFFD;?FFFBD=AEEFB/FFFFF?\n+@M00967:43:000000000-A3JHG:1:1101:19378:2540 2:N:0:188\n+CCTGTTCGATACCCACACTTTCGTGCATGAGCGTCAGTTGAGCGCCGGTATGCTGCCTTCGCAATCGGAGTTCTGCGTGATATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCTCACTCAAGAAAACCAGTTTCAACGGCTCGAAGAGGTTGAGCCTCTCAATTTTACCGCTGACTTGATCTTTCGCCTGCGCACCCTTTAAACCCAATAAATCCGGATAACGCTCGCATCCTCCG\n++\n+BCCCCFFCCFCCGGGGGGGGGGGHGGHGHHHHGGGGGHHHHHHGGGGGCEFHHHHHHHHHHGGGGHGGGGGHHHHHGGGGHEHHHHHHHHHHHHHHHGGGGGHHHHHGGGGGHHHGGGGHHHHHHGGGHGHHHHHHBCGHHGHHFGHHHHHGGGGGC-C...;;CC/;0C/:0:0<0;BFB0:A??-9/0;90;9CF0;9?D...--@-@9.BB0BBB9AEEF0FF009.=...0B.-.9--;.@B0:B;\n+@M00967:43:000000000-A3JHG:1:1101:17674:2779 2:N:0:188\n+CCTGTTCGATACCCACGCTTCCGTGCATGAGCGTCAGTTGCGCGCCGGTAGGCTGCATTCGCAATCGGAGTTCTGCGCGCTATCTATTCATCTTACCGCTACACCACGCCTTCCGCCTACTTCTCGCGCACTCAAGGCTCCCAGTTCCAACCACGGGACGGGGCTGAGCCCCGCGAATTTCCCCCTGACTTGACAGTCCGCCCGCGACCCCTTTAAAACTAAACACTCCGCATTACGCTAGCACCCTCCT\n++\n+1>AA>1BA1D>A1BGEAAE00B0BCEC221BFEAEE?D211AAEAE?/>///B@0>0@FG2/EFC1A//>/BB21B//>/>//0B2B2BGF222B>CBBC/><FGG/<C/?EHCEGC/.><<111F.C@-<</<C0/./;C:/0/:0<CGG....--.99A-A-;--;B/AB--;--9;///9--;-;B///9//99//9---9----;---9///9/B/////:9//------;9;----9//99-A9;\n+@M00967:43:000000000-A3JHG:1:1101:18089:2781 2:N:0:188\n+CCTGTTTGCTCCCCACGCTTTCGAGCCTCAACGTCAGTTACGGTCCAGTAAGCCGCCTTCGCCACCGGTGTTCCTCCTAATATCTACGCATTTCACCGCTACACTAGGAATTCCGCTTACCCCTCCCGCACTCTAGTCCGCCAGTTTCCAAAGCAGTTCCGCAGTTAAGCTGCGGCATTTCACTCCAGACTTGGCGCACCGTCTACGCTCCCTTTACACCCAGTAAATCCGGATAACGCTTGCCCCCTACG\n++\n+AABBBFFFFFFFGGGGGGGGFGGGGGGHHHHHGHGGGHHGHGGHGGHHHHHHGHGGGGGHHGGGGHGGGGGGGHHHHHHHHHHHHHHGGGGGHHHHHGGGGGHHGHHHHHHGHHHGGGGFHGHGGGGFGGGGHFHGDGHGGGGFHHFHHHHHHHGHHHHHGGG@DGGHHHHHHGFGFGGGGFGGGGGGFEBBFFFGFDFFFFFFFBAB?ADFFFFFFFB9AAFFF/9BFF?B.;DFBD;.99EFFFF-9F;\n+@M00967:43:000000000-A3JHG:1'..b'DFF.FFBFFFFFFFBBFF00BADFFDF00;0;0.:;F?0::.\n+@M00967:43:000000000-A3JHG:1:1103:16873:24153 2:N:0:188\n+CCTGTTTGCTCCCCACGCTTTCGAGCCTCAACGTCAGTTACGGTCCAGTAAGCCGCCTTCGCCACCGGTGTTCCTCCTAATATCTACGCATTTCACCGCTACACTAGGAATTCCGCTTACCCCTCCCGCACTCTAGTCCGCCAGTTTCCAAAGCAGTTCCGCAGTTAAGCTGCGGCATTTCACTCCAGACTTGGCGCACCGTCTACGCTCCCTTTACACCCAGTAAATCCGGATAACGCTTGCCCCCTACG\n++\n+BBCCCFFFFFFFGGGGGGGGGGGGHGFHFH3GGHHGGHCAAFDHGGHHHGBFHGEGGGGHHGGGFHGGEGGGHGHHHHEHHHHGHHHGGGGGHHEHHGGEGGHHF3BFGHHHHHHF///FGBGGGGGGGGGGHHHH1=1<-EGGHFHHFHHDFGHFGHFHDA-AEGBHFHB0CEFAGGFGGGGBBF0FBEGGFFBDGGFFF.AF.FEFADDFFFFFFBFFFFFFFFBBFFFD?ADFFDFFAEFBFFFFFF.\n+@M00967:43:000000000-A3JHG:1:1103:6627:24281 2:N:0:188\n+CCTGTTCGATCCCCGCACTTTCGTGCCTCAGCGTCAGTAGGGCGCCGGCAGGCTGCCTTCGCAATCGGGGTTCTGCGTGATATCTATGCATTTCACCGCTACACCACGCATTCCGCCTTCTTCTCGCCCACTCAAGGCCCCCAGTTTCAACGGCCGGACGGGGTTGAGCCCCGAATTTTTACCGCTGACTTAAAAGCCCGCCTACGCACCCTTTAAACCCAATAAAACCGGTTAACGCTCGCATCCTCCGT\n++\n+3AAABFFBBFFAGG2E?FFGGGGFGGAHGCHFEGGGGHHHHABEGGGG0E0FGHHGGFHHHGGGGHGCFGGGHHHHGGGDHHHHHGHHGGHHHHHHHGG/CDFFHHHGGGGGHHGG/C.FFHGHGGGGGGGGGHHHF.<<@CGGHGGHGHFGGGFGG@?@GGFFFFF///ADA-;AEFFF.B/:BCBABBF/9/9FFFF@>=A.9DFA-BDFFFFB/FF.E9.FB//:9@D-.:B9.-::---.;//9;..\n+@M00967:43:000000000-A3JHG:1:1103:24233:24298 2:N:0:188\n+CCTGTTCGATACCCACGCTTTCGTGCCTCAGCGTCAGTAGGGCGCCGGTATGCTGCCTTCGCAATCGGAGTTCTGCGTGATATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCAAGAACGCCAGTTTCAACGGCTCGACGGCGTTGAGCACCGCTTTTTTACCGCTGACTTGGCATCCCGCCTACGCACCCTTTAAACCCAATAAATCCGGATAACGCTCGCATCCTCCGT\n++\n+BBBBBFFBBFBBGGGGGGGGGGGHGGHHHHHGGGGGGHHHHGHGEGGGGGGHHGHHHHHHHGGGGHGGCGGFHHHHGGGGHGHHGGHHHHHHHHHHHGGGGGHHHHHGGGGGHHHGCGGHGHHHHGGGGGGHHHHHHHHGGGGGHHHHHHHGGGGGGCFG?BFGBFFGGFGGFFAFFFFFFFFDFACFFFFFFFBBFFFFFFFFFFF?F-AAFFBFFFFDFFFFFFFFFAC...BBFFDFCFF.BBBFFA9\n+@M00967:43:000000000-A3JHG:1:1103:20946:24435 2:N:0:188\n+CCTGTTCGATACCCACACTTTCGTGCATGAGCGTCAGTTGAGCGCCGGTATGCTGCCTTCGCAATCGGAGTTCTGCGTGATATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCTCACTCAAGAAAACCAGTTTCAACGGCTCGAAGAGGTTGAGCCTCTCAATTTTACCGCTGACTTGATCTTCCGCCTGCGCACCCTTTAAAACCAATAAATCCGGATAACGCTCGCATCCTCC\n++\n+>ABAAFFBBBBBGGGGGGGGGGGHGGHHHHHHGGDGGHHGHGHGGGGCGGFHHHHGHHHHHGGGFHGGGGGHHHHHCEGEFHHHHGHGFGHHHHHHHGGGGGHHHHHGGGGGHHHGGGGHHHHHHGGGGGFHHHHHDHHHHGEHHHHHHHHGGGCG<-C..CGGGFFHHHCG/:0C9BFFFFGAA?-.;BGGBBFB;BFAGFC.ADA;-9A9FF/BF/;DFFFEFFEBFDB...;/9@.;---:-9/99\n+@M00967:43:000000000-A3JHG:1:1103:24627:24453 2:N:0:188\n+CCTGTTCGATACCCACGCTTTCGTGCATGAGCGTCAGTTGCGCGCCGGTAGGCTGCCTTCGCAATCGGAGTTCTGCGTGATATCTATGCATTTCACCGCTACACCACGCATTCCGCCTACTTCTCGCGCACTCAAGGCTCCCAGTTTCAACGGCGGAACGGGGTTGAGCCCCGCGATTTGACCGCTGACTTGAGAGTCCGCCTGCGCACCCTTTAAACCCAATAAATCCGGATAACGCCCGCATCCTCCGT\n++\n+AABBBFFABFBBGGGGFGGGGGGHGGHGHHHHGGGGGHHHGEGGGGGGGGGGHHHGHHHHHGGGGHGGGGFHHHGHGEGFHHHHHHHHHHHHHHHHHGGGGGHHHGHGGGGGHHHGGGGHHHHEHGGGGGGGHHHHGHFGGGHHHHHGHHHGGGGG-B?9DEG9@CBFFFFFDAD-@EFFBFFFFDCDFFFBBF.BB9B.BDAE9-99@>FEFEFFFFFFFAFFFF/;B.>.::B/.--;-:-:@F;BFD:\n+@M00967:43:000000000-A3JHG:1:1103:8261:24679 2:N:0:188\n+CCTGTTTGCTCCCCACGCTTTCGAGCCTCAACGTCAGTTACAGTCCAGCAGGCCGCCTTCGCCACTGGTGTTCCTCCTAATATCTACGCATTTCACCGCTACACTAGGAATTCCGCCTGCCTCTCCTGCACTCCAGTTACACAGTTTCCAGAGCAGTCCGGGGGTTGGGCCCCCGCCTTTCACTCCAGACTTGCATTACCGTCTACGCTACCTTTACACCCAGTAATTCCGGATAACGCTTGCCCCCTACG\n++\n+AABBBFFF5FDFEGGGEFGGGGGGHGGHGHBGGHHGGHGGHHGHHGHHHHFEGGGGGGGHHGGGGFGHDBCEHGHHHHGHFHHHHHHGGGGFHHHHHFGEEGHHHHHHHHHHHHHGGFEGFHHHHGHHHHGHHHHGDGHHHHHHHHHG1GDHHHHGDGHDCFFGGGGC?AACG?GGGG.BCFGGGGFFFEFFFFFFFFFFFE?FE/AB..;BFFFEFFFFFEE9BB//BB/BDDDFFFFFEA9BBABF.9.\n+@M00967:43:000000000-A3JHG:1:1103:11662:24827 2:N:0:188\n+CCTGTTTGCTCCCCACGCTTTCGAGCCTCAGCGTCAGTTACCGTCCAGCAAGCCGCCTCCGCCACTGGTGTTCCTCCTAATATCTACGCATTTCACCGCTACACTAGGAATTCCACTTGCCTCTCCGGCACTCCAGCATGGCAGTTTCAAATGCAGTCCCGGGGTTGGGCCCCGGGTTTTCACATCTGACTTGCCACGCCGCCTGCGCTCCCTTTACACCCAGTAAATCCGGATAACGCCCGCCCCCCACG\n++\n+A>ABBFFFFFFFGGGGGGGGGGGGHGGGGHFHGGFGGHHHHHGGGGGGFHGHHGGGG?>FFGGGGFHHFGHFHHHHHHHGHHHGHHHFGGGGHHHHHGGGGGHHGHHHHHHHHHHHFHGHHFHHHHBFGGGHHHHHHFGFFHFGHHHHGHHHGGHHHCGHGGGGCCGGGFHGFFG-.;CEFB000;CFFGGGFFFGGADF=FA...9=-;AFFFFFFFBFD?ABFFFFFFFFFFFFFB;---@C=FB--A-\n' |
| b |
| diff -r a9f4a217dcd6 -r 34e55239e68b test-data/gentest.R --- a/test-data/gentest.R Fri Jul 02 20:12:35 2021 +0000 +++ b/test-data/gentest.R Fri Jun 30 07:56:47 2023 +0000 |
| [ |
| @@ -1,5 +1,5 @@ -library(dada2, quietly = T) -library(ggplot2, quietly = T) +library(dada2, quietly = TRUE) +library(ggplot2, quietly = TRUE) sample_names <- c("F3D0_S188_L001", "F3D141_S207_L001") fwd <- c("F3D0_S188_L001_R1_001.fastq.gz", "F3D141_S207_L001_R1_001.fastq.gz") @@ -12,8 +12,8 @@ for (i in seq_len(fwd)) { ftout <- dada2::filterAndTrim(fwd[i], filt_fwd[i], rev[i], filt_rev[i]) - b <- paste(strsplit(fwd[i], ".", fixed = T)[[1]][1], "tab", sep = ".") - write.table(ftout, b, quote = F, sep = "\t", col.names = NA) + b <- paste(strsplit(fwd[i], ".", fixed = TRUE)[[1]][1], "tab", sep = ".") + write.table(ftout, b, quote = FALSE, sep = "\t", col.names = NA) } # In the test only the 1st data set is used @@ -21,7 +21,7 @@ t <- rbind(t, ftout[1, ]) colnames(t) <- colnames(ftout) rownames(t) <- rownames(ftout)[1] -write.table(t, "filterAndTrim.tab", quote = F, sep = "\t", col.names = NA) +write.table(t, "filterAndTrim.tab", quote = FALSE, sep = "\t", col.names = NA) names(fwd) <- sample_names names(rev) <- sample_names @@ -79,7 +79,7 @@ # make sequence table print("makeSequenceTable") seqtab <- makeSequenceTable(merged) -write.table(t(seqtab), file = "makeSequenceTable.tab", quote = F, sep = "\t", row.names = T, col.names = NA) +write.table(t(seqtab), file = "makeSequenceTable.tab", quote = FALSE, sep = "\t", row.names = TRUE, col.names = NA) reads_per_seqlen <- tapply(colSums(seqtab), factor(nchar(getSequences(seqtab))), sum) df <- data.frame(length = as.numeric(names(reads_per_seqlen)), count = reads_per_seqlen) @@ -92,7 +92,7 @@ # remove bimera print("removeBimera") seqtab_nochim <- dada2::removeBimeraDenovo(seqtab) -write.table(t(seqtab), file = "removeBimeraDenovo.tab", quote = F, sep = "\t", row.names = T, col.names = NA) +write.table(t(seqtab), file = "removeBimeraDenovo.tab", quote = FALSE, sep = "\t", row.names = TRUE, col.names = NA) # assign taxonomy/species tl <- "Level1,Level2,Level3,Level4,Level5" @@ -100,17 +100,17 @@ set.seed(42) print("assignTaxonomyAndSpecies") -taxa <- dada2::assignTaxonomy(seqtab_nochim, "reference.fa.gz", outputBootstraps = T, taxLevels = tl, multithread = 1) +taxa <- dada2::assignTaxonomy(seqtab_nochim, "reference.fa.gz", outputBootstraps = TRUE, taxLevels = tl, multithread = 1) taxa$tax <- dada2::addSpecies(taxa$tax, "reference_species.fa.gz") -write.table(taxa$tax, file = "assignTaxonomyAddspecies.tab", quote = F, sep = "\t", row.names = T, col.names = NA) +write.table(taxa$tax, file = "assignTaxonomyAddspecies.tab", quote = FALSE, sep = "\t", row.names = TRUE, col.names = NA) -write.table(taxa$boot, file = "assignTaxonomyAddspecies_boot.tab", quote = F, sep = "\t", row.names = T, col.names = NA) +write.table(taxa$boot, file = "assignTaxonomyAddspecies_boot.tab", quote = FALSE, sep = "\t", row.names = TRUE, col.names = NA) ## Generate extra test data for parameter testing print("alternatives") -dada2::filterAndTrim(fwd, c("filterAndTrim_single_F3D0_R1.fq.gz", "filterAndTrim_single_F3D141_R1.fq.gz"), rm.phix = T, orient.fwd = "TACGG") +dada2::filterAndTrim(fwd, c("filterAndTrim_single_F3D0_R1.fq.gz", "filterAndTrim_single_F3D141_R1.fq.gz"), rm.phix = TRUE, orient.fwd = "TACGG") dada2::filterAndTrim(fwd, c("filterAndTrim_single_trimmers_F3D0_R1.fq.gz", "filterAndTrim_single_trimmers_F3D141_R1.fq.gz"), truncQ = 30, truncLen = 2, trimLeft = 150, trimRight = 2) @@ -122,7 +122,7 @@ saveRDS(merged_nondef[[id]], file = paste("mergePairs_", id, "_nondefault.Rdata", sep = "")) } rb_dada_fwd <- dada2::removeBimeraDenovo(dada_fwd[["F3D0_S188_L001"]]) -write.table(rb_dada_fwd, file = "removeBimeraDenovo_F3D0_dada_uniques.tab", quote = F, sep = "\t", row.names = T, col.names = F) +write.table(rb_dada_fwd, file = "removeBimeraDenovo_F3D0_dada_uniques.tab", quote = FALSE, sep = "\t", row.names = TRUE, col.names = FALSE) rb_merged <- dada2::removeBimeraDenovo(merged, method = "pooled") saveRDS(rb_merged, file = "removeBimeraDenovo_F3D0_mergepairs.Rdata") @@ -134,22 +134,22 @@ print("seqCounts ft") samples <- list() -samples[["F3D0_S188_L001_R1_001.tab"]] <- read.table("F3D0_S188_L001_R1_001.tab", header = T, sep = "\t", row.names = 1) +samples[["F3D0_S188_L001_R1_001.tab"]] <- read.table("F3D0_S188_L001_R1_001.tab", header = TRUE, sep = "\t", row.names = 1) dname <- "filter" tdf <- samples[["F3D0_S188_L001_R1_001.tab"]] names(tdf) <- paste(dname, names(tdf)) tdf <- cbind(data.frame(samples = names(samples)), tdf) -write.table(tdf, "seqCounts_filter.tab", quote = F, sep = "\t", row.names = F, col.names = T) +write.table(tdf, "seqCounts_filter.tab", quote = FALSE, sep = "\t", row.names = FALSE, col.names = TRUE) samples <- list() -samples[["F3D0_S188_L001_R1_001.tab"]] <- read.table("F3D0_S188_L001_R1_001.tab", header = T, sep = "\t", row.names = 1) -samples[["F3D141_S207_L001_R1_001.tab"]] <- read.table("F3D141_S207_L001_R1_001.tab", header = T, sep = "\t", row.names = 1) +samples[["F3D0_S188_L001_R1_001.tab"]] <- read.table("F3D0_S188_L001_R1_001.tab", header = TRUE, sep = "\t", row.names = 1) +samples[["F3D141_S207_L001_R1_001.tab"]] <- read.table("F3D141_S207_L001_R1_001.tab", header = TRUE, sep = "\t", row.names = 1) dname <- "filter" tdf <- samples[["F3D0_S188_L001_R1_001.tab"]] tdf <- rbind(tdf, samples[["F3D141_S207_L001_R1_001.tab"]]) names(tdf) <- paste(dname, names(tdf)) tdf <- cbind(data.frame(samples = names(samples)), tdf) -write.table(tdf, "seqCounts_filter_both.tab", quote = F, sep = "\t", row.names = F, col.names = T) +write.table(tdf, "seqCounts_filter_both.tab", quote = FALSE, sep = "\t", row.names = FALSE, col.names = TRUE) print("seqCounts dada") samples <- list() @@ -158,7 +158,7 @@ dname <- "dadaF" tdf <- data.frame(samples = names(samples)) tdf[[dname]] <- sapply(samples, get_n) -write.table(tdf, "seqCounts_dadaF.tab", quote = F, sep = "\t", row.names = F, col.names = T) +write.table(tdf, "seqCounts_dadaF.tab", quote = FALSE, sep = "\t", row.names = FALSE, col.names = TRUE) print("seqCounts mp") samples <- list() @@ -167,20 +167,20 @@ dname <- "merge" tdf <- data.frame(samples = names(samples)) tdf[[dname]] <- sapply(samples, get_n) -write.table(tdf, "seqCounts_merge.tab", quote = F, sep = "\t", row.names = F, col.names = T) +write.table(tdf, "seqCounts_merge.tab", quote = FALSE, sep = "\t", row.names = FALSE, col.names = TRUE) print("seqCounts st") samples <- list() -samples <- t(as.matrix(read.table("makeSequenceTable.tab", header = T, sep = "\t", row.names = 1))) +samples <- t(as.matrix(read.table("makeSequenceTable.tab", header = TRUE, sep = "\t", row.names = 1))) dname <- "seqtab" tdf <- data.frame(samples = row.names(samples)) tdf[[dname]] <- rowSums(samples) -write.table(tdf, "seqCounts_seqtab.tab", quote = F, sep = "\t", row.names = F, col.names = T) +write.table(tdf, "seqCounts_seqtab.tab", quote = FALSE, sep = "\t", row.names = FALSE, col.names = TRUE) print("seqCounts rb") samples <- list() -samples <- t(as.matrix(read.table("removeBimeraDenovo.tab", header = T, sep = "\t", row.names = 1))) +samples <- t(as.matrix(read.table("removeBimeraDenovo.tab", header = TRUE, sep = "\t", row.names = 1))) dname <- "nochim" tdf <- data.frame(samples = row.names(samples)) tdf[[dname]] <- rowSums(samples) -write.table(tdf, "seqCounts_nochim.tab", quote = F, sep = "\t", row.names = F, col.names = T) +write.table(tdf, "seqCounts_nochim.tab", quote = FALSE, sep = "\t", row.names = FALSE, col.names = TRUE) |