| Next changeset 1:8c1bba8d544a (2021-10-04) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican commit 48a91cdf44f4d7e332b852bb2ced6cd180147fdc" |
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added:
amplican.xml macros.xml test-data/R1_001.fastq test-data/R1_001.fastq.gz test-data/R1_002.fastq test-data/R1_002.fastq.gz test-data/R2_001.fastq test-data/R2_001.fastq.gz test-data/R2_002.fastq test-data/R2_002.fastq.gz test-data/RunParameters.txt test-data/alignments.txt test-data/barcode_reads_filtered.csv test-data/config.csv test-data/config_gzip.csv test-data/config_summary.csv test-data/events_filtered_shifted.csv test-data/events_filtered_shifted_normalized.csv test-data/output_html.html test-data/raw_events.csv test-data/unassigned_reads.csv |
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| diff -r 000000000000 -r 71adaaace336 amplican.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/amplican.xml Wed Sep 22 21:01:40 2021 +0000 |
| [ |
| b'@@ -0,0 +1,438 @@\n+<tool id=\'amplican\' name=\'AmpliCan\' version=\'@TOOL_VERSION@+galaxy@SUFFIX_VERSION@\' profile=\'20.01\'>\n+ <description>analysis tool for genome editing </description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro=\'requirements\' />\n+ <expand macro="bio_tools"/>\n+ <command detect_errors=\'exit_code\'><![CDATA[\n+ #import re\n+ mkdir ./fastq_folder ./output_folder\n+ #for $i in $fastq_files\n+ #if str($i.element_identifier) != re.sub(\'[^\\w\\-_\\.]\', \'_\', str($i.element_identifier))\n+ && echo "Please rename your datasets; only underscore (_) and alphanumeric characters are allowed."\n+ && exit 1\n+ #else \n+ && ln -s \'${i}\' ./fastq_folder/\'${i.element_identifier}\'\n+ #end if\n+ #end for\n+ && Rscript \'$amplican_script\'\n+ #if \'knit_reports\' in $output_options.outputs\n+ && mv ./output_folder/reports/amplicon_report.html \'${output_html.extra_files_path}\'\n+ && mv ./output_folder/reports/barcode_report.html \'${output_html.extra_files_path}\'\n+ && mv ./output_folder/reports/group_report.html \'${output_html.extra_files_path}\'\n+ && mv ./output_folder/reports/guide_report.html \'${output_html.extra_files_path}\'\n+ && mv ./output_folder/reports/id_report.html \'${output_html.extra_files_path}\'\n+ #end if\n+ ]]> </command>\n+ <configfiles>\n+ <configfile name="amplican_script"><![CDATA[\n+ ## Setup R error handling to go to stderr\n+ options(\n+ show.error.messages = F,\n+ error = function() {\n+ cat(geterrmessage(), file = stderr())\n+ q("no", 1, F)\n+ }\n+ )\n+ # we need that to not crash galaxy with an UTF8 error on German LC settings.\n+ Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")\n+\n+ suppressPackageStartupMessages({\n+ library("amplican")\n+ })\n+ #full analysis\n+ amplicanPipeline(\n+ \'${config_file}\',\n+ \'fastq_folder\',\n+ \'output_folder\',\n+ #if \'knit_reports\' in $output_options.outputs\n+ knit_reports = TRUE,\n+ #else\n+ knit_reports = FALSE,\n+ #end if\n+ #if $output_options.write_alignment_format == \'fasta\'\n+ write_alignments_format = "fasta",\n+ #else if $output_options.write_alignment_format == \'txt\'\n+ write_alignments_format = "txt",\n+ #else\n+ write_alignments_format = "None",\n+ #end if\n+ average_quality = $quality_options.average_quality,\n+ min_quality = $quality_options.min_quality,\n+ use_parallel = FALSE,\n+ scoring_matrix = Biostrings::nucleotideSubstitutionMatrix(\n+ match = $alignment_options.scoring_matrix.match_scoring,\n+ mismatch = $alignment_options.scoring_matrix.mismatch_scoring,\n+ baseOnly = $alignment_options.scoring_matrix.base_only,\n+ type = "$alignment_options.scoring_matrix.scoring_type"\n+ ),\n+ gap_opening = $alignment_options.gap_opening,\n+ gap_extension = $alignment_options.gap_extension,\n+ fastqfiles = $advanced_options.fastq_use,\n+ primer_mismatch = $alignment_options.primer_mismatch,\n+ donor_mismatch = $alignment_options.donor_mismatch,\n+ PRIMER_DIMER = $advanced_options.primer_dimer,\n+ event_filter = $advanced_options.event_filter,\n+ cut_buffer = $advanced_options.cut_buffer,\n+ promiscuous_consensus = $advanced_options.promiscuous_consensus,\n+ normalize = c("guideRNA", "Group")\n+ )\n+ ]]></configfile>\n+ </configfiles>\n+ <inputs>\n+ <param name="config_file" type="data" for'..b' </assert_contents>\n+ </output>\n+ <output name="alignments_fasta" ftype="fasta">\n+ <assert_contents>\n+ <has_size value="16146" delta="300" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <!-- Test gzip files -->\n+ <test expect_num_outputs="2">\n+ <param name="config_file" value="config_gzip.csv" />\n+ <param name="fastq_files" value="R1_001.fastq.gz,R1_002.fastq.gz,R2_001.fastq.gz,R2_002.fastq.gz" />\n+ <section name="output_options">\n+ <param name="write_alignment_format" value="fasta"/>\n+ <param name="outputs" value="config_summary"/>\n+ </section>\n+ <output name="config_summary" ftype="csv">\n+ <assert_contents>\n+ <has_size value="2896" delta="300" />\n+ </assert_contents>\n+ </output>\n+ <output name="alignments_fasta" ftype="fasta">\n+ <assert_contents>\n+ <has_size value="16146" delta="300" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+.. class:: infomark\n+\n+**Purpose**\n+\n+AmpliCan is an analysis tool for genome editing that unites highly precise quantification and \n+visualization of genuine genome editing events. ampliCan features nuclease-optimized alignments, \n+filtering of experimental artifacts, event-specific normalization, and off-target read detection \n+and quantifies insertions, deletions, HDR repair, as well as targeted base editing. It is \n+scalable to thousands of amplicon sequencing-based experiments from any genome editing experiment, \n+including CRISPR. It enables automated integration of controls and accounts for biases at every \n+step of the analysis.\n+\n+----\n+\n+.. class:: infomark\n+\n+**Config file details**\n+\n+Columns of the config file:\n+\n+- ID - should be a unique identifier of your experiments.\n+- Barcode - use this to group experiments with the same barcode.\n+- Forward_Reads, Reverse_Reads - put names of your files in these fields, you can put here files compressed to .gz, we will unpack them for you.\n+- Group - use this field if you want to group ID by other criteria, here for instance we will group by person that performed experiment, on later stage it is possible to generate report with breakdown using this field.\n+- guideRNA - put your guideRNA in 5\xe2\x80\x99 to 3\xe2\x80\x99 fashion here, if he has to be reverse complemented to be found in the amplicon put \xe2\x80\x9c1\xe2\x80\x9d into Direction field, we will use this field to make sure your guideRNA is inside the amplicon and during plotting of the results.\n+- Forward_Primer, Reverse_Primer - make sure these primers are correct for each of your IDs, Forward_Primer should be found in the amplicon as is, on the left side of the guide, Reverse_Primer reverse complement should be found on the amplicon on the right side of the guide.\n+- Direction - here \xe2\x80\x9c0\xe2\x80\x9d means guide does not requires to be reverse complemented to be matched to the amplicon, \xe2\x80\x9c1\xe2\x80\x9d means it should be reverse complemented, this field is also used when plotting deletions, mismatches and insertions.\n+- Amplicon - insert amplicon sequence as lower case letters, by putting UPPER CASE letters you can specify expected cut site, you should specify at least one cut site, here for example we specify in uppercase letter PAM sequence of the corresponding guideRNA.\n+- Donor - insert donor template if you have designed HDR experiments or used base editors, otherwise leave empty, but keep the column. amplican will estimate HDR efficiency based on the events from aligning donor and amplicon sequences, donor and reads and reads and amplicon.\n+\n+If you have only forward primers leave column Reverse_Primer empty, leave empty also the Reverse_Reads column. You can still use amplican like normal. \n+\n+ ]]> </help>\n+ <expand macro="citations" />\n+</tool>\n' |
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| diff -r 000000000000 -r 71adaaace336 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Sep 22 21:01:40 2021 +0000 |
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| @@ -0,0 +1,19 @@ +<macros> + <token name="@TOOL_VERSION@">1.14.0</token> + <token name="@SUFFIX_VERSION@">0</token> + <xml name="bio_tools"> + <xrefs> + <xref type="bio.tools">amplican</xref> + </xrefs> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">bioconductor-amplican</requirement> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1101/gr.244293.118</citation> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r 71adaaace336 test-data/R1_001.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/R1_001.fastq Wed Sep 22 21:01:40 2021 +0000 |
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| @@ -0,0 +1,80 @@ +@ID_1_valid_cut_biggest_1 +AAGCTGACGGCTAAATGAAAAATGTCAAACGTCTGTTCCAGAAAAAAAAAAAAAAAAAAAATTCCCACACCAATGGGGAAAGGAGTCCTGCCAGATGACCATCCCAACTGTGTTGCAGCAGCCAGATCCAGGTGTGTTTGCGCTTGTGTAATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_1_valid_cut_biggest_2 +AAGCTGACGGCTAAATGAAAAATGTCAAACGTCTGTTCCAGAAAAAAAAAAAAAAAAAAAATTCCCACACCAATGGGGAAAGGAGTCCTGCCAGATGACCATCCCAACTGTGTTGCAGCAGCCAGATCCAGGTGTGTTTGCGCTTGTGTAATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_1_valid_cut_biggest_3 +AAGCTGACGGCTAAATGAAAAATGTCAAACGTCTGTTCCAGAAAAAAAAAAAAAAAAAAAATTCCCACACCAATGGGGAAAGGAGTCCTGCCAGATGACCATCCCAACTGTGTTGCAGCAGCCAGATCCAGGTGTGTTTGCGCTTGTGTAATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_1_valid_cut_medium_1 +AAGCTGACGGCTAAATGAAAAATGTCAAACGTCTGTTAAAAAAAAAAAAAAAAAAAACACACCAATGGGGAAAGGAGTCCTGCCAGATGACCATCCCAACTGTGTTGCAGCAGCCAGATCCAGGTGTGTTTGCGCTTGTGTAATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_1_valid_cut_medium_2 +AAGCTGACGGCTAAATGAAAAATGTCAAACGTCTGTTAAAAAAAAAAAAAAAAAAAACACACCAATGGGGAAAGGAGTCCTGCCAGATGACCATCCCAACTGTGTTGCAGCAGCCAGATCCAGGTGTGTTTGCGCTTGTGTAATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_1_valid_cut_small +AAGCTGACGGCTAAATGAAAAATGTCAAACGTCAATGGGGAAAGGAGTCCTGCCAGATGACCATCCCAACTGTGTTGCTGCAGCCAAATCCAGGTGTGTTTGCGCTTGTGTAATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@primer_dimer +AAGCTGACGGCTAAATGAAAAAGCCTCGTGTGTTTGCGCTTGTGTAATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@bad_quality32 +AAGCTGACGGCTAAATGAAAAATATCTGAAACATCTGTTCCAGGTGCTGCGTATGCCAGGGCAGAGAAGAAGGTCAGGGAAGGTCACTGGAGGTCACTGGGATACCCTTTCTTCCCACACCAATGGGGAAAGGAGTCCTGCCAGATGACCA ++ +9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 +@bad_quality32 +AAGCTGACGGCTAAATGAAAAATATCTGAAACATCTGTTCCAGGTGCTGCGTATGCCAGGGCAGAGAAGAAGGTCAGGGAAGGTCACTGGAGGTCACTGGGATACCCTTTCTTCCCACACCAATGGGGAAAGGAGTCCTGCCAGATGACCA ++ +9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 +@bad_bases +AAGCTGACGGCTAAATNNNAAATATCTGAAACATCTGTTCCAGGTGCTGCGTATGCCAGGGCAGAGAAGAAGGTCAGGGAAGGTCACTGGAGGTCACTGGGATACCCTTTCTTCCCACACCAATGGGGAAAGGAGTCCTGCCAGATGACCA ++ +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +@bad_bases +AAGCTNGCGGCTAAATGAAAAATATCTGAAACATCTGTTCCAGGTGCTGCGTATGCCAGGGCAGAGAAGAAGGTCAGGGAAGGTCACTGGAGGTCACTGGGATACCCTTTCTTCCCACACCANNNGGGAAAGGAGTCCTGCCAGATGACCA ++ +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +@next_id_nocut6_bad_alphabet +AAATACTGTCTTGTGACCAAACCTTCTTAAGGTGCTGTTTTGATGATNNNCTTTATTGTGCTTTTGTAGTTGTGCCCCTTGTGTTGGCAGAGGGTCAGCAGACCAGTAAGTCTTCTCAATTTCTTTTATTTATGTATATGTAGTGATAAAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@next_id_nocut7_bad_quality +AAATACTGTCTTGTGACCAAACCTTCTTAAGGTGCTGTTTTGATGATAAACTTTATTGTGCTTTTGTAGTTGTGCCCCTTGTGTTGGCAGAGGGTCAGCAGACCAGTAAGTCTTCTCAATTTCTTTTATTTATGTATATGTAGTGATAAAA ++ +9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 +@next_id_nocut8_bad_quality +AAATACTGTCTTGTGACCAAACCTTCTTAAGGTGCTGTTTTGATGATAAACTTTATTGTGCTTTTGTAGTTGTGCCCCTTGTGTTGGCAGAGGGTCAGCAGACCAGTAAGTCTTCTCAATTTCTTTTATTTATGTATATGTAGTGATAAAA ++ +9999999999999999999999999999999999999999999999999999999999999999IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_2_valid_cut_biggest_1 +AAATACTGTCTTGTGACCAAACCTTCTTAAGGTGCTATTTTGATAATAAACTTTATTGTGCTTTTGTAGTTGTGCCCCTGGTCAGCAGACCAGTAAGTCTTCTCAATTTCTTTTATTTATGTGTAGTGATAAAAAAATGTTAAATTAAAATTAAATGTTTTTTTTTGCCTTGCATTTTGCAGCAGAGGATGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_2_valid_cut_biggest_2 +AAATACTGTCTTGTGACCAAACCTTCTTAAGGTGCTATTTTGATAATAAACTTTATTGTGCTTTTGTAGTTGTGCCCCTGGTCAGCAGACCAGTAAGTCTTCTCAATTTCTTTTATTTATGTGTAGTGATAAAAAAATGTTAAATTAAAATTAAATGTTTTTTTTTGCCTTGCATTTTGCAGCAGAGGATGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_2_valid_cut_biggest_3 +AAATACTGTCTTGTGACCAAACCTTCTTAAGGTGCTATTTTGATAATAAACTTTATTGTGCTTTTGTAGTTGTGCCCCTGGTCAGCAGACCAGTAAGTCTTCTCAATTTCTTTTATTTATGTGTAGTGATAAAAAAATGTTAAATTAAAATTAAATGTTTTTTTTTGCCTTGCATTTTGCAGCAGAGGATGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_2_valid_cut_medium_1 +AAATACTGTCTTGTGACCAAACCTTCTTAAGGTGCTATTTTGATAATAAACTTTATTGTGCTTTTGTAGTTGTGCCCCTTGTGTTGGCAGAGACCAGTAAGTCTTCTCAATTTCTTTTATTTATGTGTAGTGATAAAAAAATGTTAAATTAAAATTAAATGTTTTTTTTTGCCTTGCATTTTGCAGCAGAGGATGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_2_valid_cut_medium_2 +AAATACTGTCTTGTGACCAAACCTTCTTAAGGTGCTATTTTGATAATAAACTTTATTGTGCTTTTGTAGTTGTGCCCCTTGTGTTGGCAGAGACCAGTAAGTCTTCTCAATTTCTTTTATTTATGTGTAGTGATAAAAAAATGTTAAATTAAAATTAAATGTTTTTTTTTGCCTTGCATTTTGCAGCAGAGGATGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_2_valid_cut_small +AAATACTGTCTTGTGACCAAACCTTCTTAAGGTGCTATTTTGATAATAAACTTTATTGTGCTTTTGTAGTTGTGCCCCTTGTGTTGGCAGAGGGTCAGCAGTAAGTCTTCTCAATTTCTTTTATTTATGTGTAGTGATAAAAAAATGTTAAATTAAAATTAAATGTTTTTTTTTGCCTTGCATTTTGCAGCAGAGGATGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII |
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| diff -r 000000000000 -r 71adaaace336 test-data/R1_001.fastq.gz |
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| Binary file test-data/R1_001.fastq.gz has changed |
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| diff -r 000000000000 -r 71adaaace336 test-data/R1_002.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/R1_002.fastq Wed Sep 22 21:01:40 2021 +0000 |
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| @@ -0,0 +1,84 @@ +@ID_3_valid_cut_biggest_1 +AAGCTGACGGCTAAATGAAAAATGTCAAACATCTGTTCCAGGTGCTGCGTATGCCAGGGCAGAGGTGGAGGTCACTGGGATACCCTTTCTTCCCACACCAATGGGGAAAGGAGTCCTGCCAGATGACCATCCCAACTGTGTTGCTGCATTTTTGATCCAGGTGTGTTTGCGCTTGTGTAATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_3_valid_cut_biggest_2 +AAGCTGACGGCTAAATGAAAAATGTCAAACATCTGTTCCAGGTGCTGCGTATGCCAGGGCAGAGGTGGAGGTCACTGGGATACCCTTTCTTCCCACACCAATGGGGAAAGGAGTCCTGCCAGATGACCATCCCAACTGTGTTGCTGCATTTTTGATCCAGGTGTGTTTGCGCTTGTGTAATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_3_valid_cut_biggest_3 +AAGCTGACGGCTAAATGAAAAATGTCAAACATCTGTTCCAGGTGCTGCGTATGCCAGGGCAGAGGTGGAGGTCACTGGGATACCCTTTCTTCCCACACCAATGGGGAAAGGAGTCCTGCCAGATGACCATCCCAACTGTGTTGCTGCATTTTTGATCCAGGTGTGTTTGCGCTTGTGTAATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_3_valid_cut_biggest_4 +AAGCTGACGGCTAAATGAAAAATGTCAAACATCTGTTCCAGGTGCTGCGTATGCCAGGGCAGAGGTGGAGGTCACTGGGATACCCTTTCTTCCCACACCAATGGGGAAAGGAGTCCTGCCAGATGACCATCCCAACTGTGTTGCTGCATTTTTGATCCAGGTGTGTTTGCGCTTGTGTAATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_3_valid_cut_biggest_5 +AAGCTGACGGCTAAATGAAAAATGTCAAACATCTGTTCCAGGTGCTGCGTATGCCAGGGCAGAGGTGGAGGTCACTGGGATACCCTTTCTTCCCACACCAATGGGGAAAGGAGTCCTGCCAGATGACCATCCCAACTGTGTTGCTGCATTTTTGATCCAGGTGTGTTTGCGCTTGTGTAATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_3_valid_cut_medium_1 +AAGCTGACGGCTAAATGAAAAATGTCAAACATCTGTTCCAGGTGCTGCGTATGCCAGGGCAGTGGTCAGGGAACAGGTCACTGGGATACCCTTTCTTCCCACACCAATGGGGAAAGGAGTCCTGCCAGATGACCATCCCAACTGTGTTGCTGCAGCCAGATCCAGGTGTGTTTGCGCTTGTGTAATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_3_valid_cut_medium_2 +AAGCTGACGGCTAAATGAAAAATGTCAAACATCTGTTCCAGGTGCTGCGTATGCCAGGGCAGTGGTCAGGGAACAGGTCACTGGGATACCCTTTCTTCCCACACCAATGGGGAAAGGAGTCCTGCCAGATGACCATCCCAACTGTGTTGCTGCAGCCAGATCCAGGTGTGTTTGCGCTTGTGTAATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_3_PD_1 +AAGCTGACGGCTAAATGAAAGGTGTGTTTGCGCTTGTGTAATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_3_not_valid_insertion_deletion +AAGCTGACGGCTAAATGAAAAATGTTGCTGCGTATGCCAGGGCAGAGGAGGTGGTCCCCCCCCCCCCCCCCCAGGGAACTGGTGGAGGTCACTGGGATACCCTTTCTTCCCACACCAATGGGGAAAGGAGTCCTGCCAGATGACCATCCCAACTGTGTTGCTGCAGCCAGATCCAGGTGTGTTTGCGCTTGTGTAATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_4_not_valid_insertion_deletion_1 +GCTGGCAACATTCCTACCAGTAATTTACGTAAAAAAGTAACTTGTGCTTGCATTGTGTAACAACTGACTGCTGTTAAAGGCCGGAAGTCTAAGAACTCACATGAAAGAGGGTATAATCCTGCCTCAGCGCTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_4_not_valid_insertion_deletion_2 +GCTGGCAACATTCCTACCAGTAATTTACGTAAAAAAGTAACTTGTGCTTGCATTGTGTAACAACTGACTGCTGTTAAAGGCCGGAAGTCTAAGAACTCACATGAAAGAGGGTATAATCCTGCCTCAGCGCTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_4_not_valid_insertion_deletion_3 +GCTGGCAACATTCCTACCAGTAATTTACGTAAAAAAGTAACTTGTGCTTGCATTGTGTAACAACTGACTGCTGTTAAAGGCCGGAAGTCTAAGAACTCACATGAAAGAGGGTATAATCCTGCCTCAGCGCTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_4_not_valid_insertion_deletion_4 +GCTGGCAACATTCCTACCAGTAATTTACGTAAAAAAGTAACTTGTGCTTGCATTGTGTAACAACTGACTGCTGTTAAAGGCCGGAAGTCTAAGAACTCACATGAAAGAGGGTATAATCCTGCCTCAGCGCTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_4_not_valid_insertion_deletion_medium_1 +GCTGGCAACATTCCTACCAGTAATTTACGTAAAAATCTAATGTAACTTGTGCTTGCATTGTGTTTACAGGAAACCAGTCCCTGCAACATTGGGGGGGGAAAGGCCGGAAGTCTAAGAACTCACATCAGCAGGTGTCAAGAGTGCATGTAGAGGGTATAATCCTGCCTCAGCGCTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_4_not_valid_insertion_deletion_medium_2 +GCTGGCAACATTCCTACCAGTAATTTACGTAAAAATCTAATGTAACTTGTGCTTGCATTGTGTTTACAGGAAACCAGTCCCTGCAACATTGGGGGGGGAAAGGCCGGAAGTCTAAGAACTCACATCAGCAGGTGTCAAGAGTGCATGTAGAGGGTATAATCCTGCCTCAGCGCTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_4_not_valid_insertion_deletion_small_1 +GCTGGCAACATTCCTACCAGTAATTTACGTAAAAAAATGCTATAAAATGTGCTAATGTAACTTGTGCTTGCATTGTGTTTACAGGAAACCAGTCCCACCACACGTGCATCGTACTGCAACATTAAAGGCCGGAAGTCTAAGAACTCACATCAGCAGGTGTCAAGTGTCCTTGGAGAGGGTATAATCCTGCCTCAGCGCTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_5_perfect1 +ACTGGCAACATTCCTACCAGTAATTTACGTAAAAAAATGCTATAAAATGTGTAGCTCTCCAGTCTAATGTAACTTGTGCTTGCATTGTGTTTACAGGAAACCAGTCCCTGCAACATTAAAGGCCGGAAGTCTAAGAACTCACATCAGCAGGTGTCAAGTGTGCATGAAGAGGGTATAATCCTGCCTCAGCCAGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_5_perfect2 +ACTGGCAACATTCCTACCAGTAATTTACGTAAAAAAATGCTATAAAATGTGTAGCTCTCCAGTCTAATGTAACTTGTGCTTGCATTGTGTTTACAGGAAACCAGTCCCTGCAACATTAAAGGCCGGAAGTCTAAGAACTCACATCAGCAGGTGTCAAGTGTGCATGAAGAGGGTATAATCCTGCCTCAGCCAGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_5_perfect3 +ACTGGCAACATTCCTACCAGTAATTTACGTAAAAAAATGCTATAAAATGTGTAGCTCTCCAGTCTAATGTAACTTGTGCTTGCATTGTGTTTACAGGAAACCAGTCCCTGCAACATTAAAGGCCGGAAGTCTAAGAACTCACATCAGCAGGTGTCAAGTGTGCATGAAGAGGGTATAATCCTGCCTCAGCCAGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_5_perfectHDR1 +ACTGGCAACATTCCTACCAGTAATTTACGTAAAAAAATGCTATAAAATGTGTAGCTCTCCAGTCTAATGTAACTTGTGCTTGCATTGTGTTTACAGGAAACCAGTCCCTGCAACATTAAAAGCCGGAAGTCTAAGAACTCACATCAGCAGGTGTCAAGTGTGCATGAAGAGGGTATAATCCTGCCTCAGCCAGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_5_perfectHDR2 +ACTGGCAACATTCCTACCAGTAATTTACGTAAAAAAATGCTATAAAATGTGTAGCTCTCCAGTCTAATGTAACTTGTGCTTGCATTGTGTTTACAGGAAACCAGTCCCTGCAACATTAAAAGCCGGAAGTCTAAGAACTCACATCAGCAGGTGTCAAGTGTGCATGAAGAGGGTATAATCCTGCCTCAGCCAGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII |
| b |
| diff -r 000000000000 -r 71adaaace336 test-data/R1_002.fastq.gz |
| b |
| Binary file test-data/R1_002.fastq.gz has changed |
| b |
| diff -r 000000000000 -r 71adaaace336 test-data/R2_001.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/R2_001.fastq Wed Sep 22 21:01:40 2021 +0000 |
| b |
| @@ -0,0 +1,80 @@ +@ID_1_valid_cut_biggest_1 +AATTACACAAGCGCAAACACACCTGGATCTGGCTGCTGCAACACAGTTGGGATGGTCATCTGGCAGGACTCCTTTCCCCATTGGTGTGGGAATTTTTTTTTTTTTTTTTTTTCTGGAACAGACGTTTGACATTTTTCATTTAGCCGTCAGCTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_1_valid_cut_biggest_2 +AATTACACAAGCGCAAACACACCTGGATCTGGCTGCTGCAACACAGTTGGGATGGTCATCTGGCAGGACTCCTTTCCCCATTGGTGTGGGAATTTTTTTTTTTTTTTTTTTTCTGGAACAGACGTTTGACATTTTTCATTTAGCCGTCAGCTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_1_valid_cut_biggest_3 +AATTACACAAGCGCAAACACACCTGGATCTGGCTGCTGCAACACAGTTGGGATGGTCATCTGGCAGGACTCCTTTCCCCATTGGTGTGGGAATTTTTTTTTTTTTTTTTTTTCTGGAACAGACGTTTGACATTTTTCATTTAGCCGTCAGCTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_1_valid_cut_medium_1 +AATTACACAAGCGCAAACACACCTGGATCTGGCTGCTGCAACACAGTTGGGATGGTCATCTGGCAGGACTCCTTTCCCCATTGGTGTGTTTTTTTTTTTTTTTTTTTTAACAGACGTTTGACATTTTTCATTTAGCCGTCAGCTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_1_valid_cut_medium_2 +AATTACACAAGCGCAAACACACCTGGATCTGGCTGCTGCAACACAGTTGGGATGGTCATCTGGCAGGACTCCTTTCCCCATTGGTGTGTTTTTTTTTTTTTTTTTTTTAACAGACGTTTGACATTTTTCATTTAGCCGTCAGCTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_1_valid_cut_small +AATTACACAAGCGCAAACACACCTGGATTTGGCTGCAGCAACACAGTTGGGATGGTCATCTGGCAGGACTCCTTTCCCCATTGACGTTTGACATTTTTCATTTAGCCGTCAGCTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@primer_dimer +AATTACACAAGCGCAAACACACGAGGCTTTTTCATTTAGCCGTCAGCTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@bad_quality32 +TGGTCATCTGGCAGGACTCCTTTCCCCATTGGTGTGGGAAGAAAGGGTATCCCAGTGACCTCCAGTGACCTTCCCTGACCTTCTTCTCTGCCCTGGCATACGCAGCACCTGGAACAGATGTTTCAGATATTTTTCATTTAGCCGTCAGCTT ++ +9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 +@bad_quality32 +AAGCTGACGGCTAAATGAAAAATATCTGAAACATCTGTTCCAGGTGCTGCGTATGCCAGGGCAGAGAAGAAGGTCAGGGAAGGTCACTGGAGGTCACTGGGATACCCTTTCTTCCCACACCAATGGGGAAAGGAGTCCTGCCAGATGACCA ++ +9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 +@bad_bases +TGGTCATCTGGCAGGACTCCTTTCCCCATTGGTGTGGGAAGAAAGGGTATCCCAGTGACCTCCAGTGACCTTCCCTGACCTTCTTCTCTGCCCTGGCATACGCAGCACCTGGAACAGATGTTTCAGATATTTTTCATTTAGCCGTCAGCTT ++ +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +@bad_bases +TGGTCATCNNNNAGGACTCCTTTCCCCATTGGTGTGGGAAGNNNGGGTATCCCAGTGACCTCCAGTGACCTTCCCTGACCTTCTTCTCTGCCCTGGCATACGCAGCACCTGGAACAGATGTTTCAGATATTTTTCATTTAGCCGTCAGNNN ++ +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +@next_id_nocut6_bad_alphabet +AAATACTGTCTTGTGACCAAACCTTCTTAAGGTGCTGTTTTGATGATNNNCTTTATTGTGCTTTTGTAGTTGTGCCCCTTGTGTTGGCAGAGGGTCAGCAGACCAGTAAGTCTTCTCAATTTCTTTTATTTATGTATATGTAGTGATAAAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@next_id_nocut7_bad_quality +TGGTCATCTGGCAGGACTCCTTTCCCCATTGGTGTGGGAAGAAAGGGTATCCCAGTGACCTCCAGTGACCTTCCCTGACCTTCTTCTCTGCCCTGGCATACGCAGCACCTGGAACAGATGTTTCAGATATTTTTCATTTAGCCGTCAGCTT ++ +9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 +@next_id_nocut8_bad_quality +TGGTCATCTGGCAGGACTCCTTTCCCCATTGGTGTGGGAAGAAAGGGTATCCCAGTGACCTCCAGTGACCTTCCCTGACCTTCTTCTCTGCCCTGGCATACGCAGCACCTGGAACAGATGTTTCAGATATTTTTCATTTAGCCGTCAGCTT ++ +9999999999999999999999999999999999999999999999999999999999999999IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_2_valid_cut_biggest_1 +ATCATCCTCTGCTGCAAAATGCAAGGCAAAAAAAAACATTTAATTTTAATTTAACATTTTTTTATCACTACACATAAATAAAAGAAATTGAGAAGACTTACTGGTCTGCTGACCAGGGGCACAACTACAAAAGCACAATAAAGTTTATTATCAAAATAGCACCTTAAGAAGGTTTGGTCACAAGACAGTATTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_2_valid_cut_biggest_2 +ATCATCCTCTGCTGCAAAATGCAAGGCAAAAAAAAACATTTAATTTTAATTTAACATTTTTTTATCACTACACATAAATAAAAGAAATTGAGAAGACTTACTGGTCTGCTGACCAGGGGCACAACTACAAAAGCACAATAAAGTTTATTATCAAAATAGCACCTTAAGAAGGTTTGGTCACAAGACAGTATTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_2_valid_cut_biggest_3 +ATCATCCTCTGCTGCAAAATGCAAGGCAAAAAAAAACATTTAATTTTAATTTAACATTTTTTTATCACTACACATAAATAAAAGAAATTGAGAAGACTTACTGGTCTGCTGACCAGGGGCACAACTACAAAAGCACAATAAAGTTTATTATCAAAATAGCACCTTAAGAAGGTTTGGTCACAAGACAGTATTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_2_valid_cut_medium_1 +ATCATCCTCTGCTGCAAAATGCAAGGCAAAAAAAAACATTTAATTTTAATTTAACATTTTTTTATCACTACACATAAATAAAAGAAATTGAGAAGACTTACTGGTCTCTGCCAACACAAGGGGCACAACTACAAAAGCACAATAAAGTTTATTATCAAAATAGCACCTTAAGAAGGTTTGGTCACAAGACAGTATTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_2_valid_cut_medium_2 +ATCATCCTCTGCTGCAAAATGCAAGGCAAAAAAAAACATTTAATTTTAATTTAACATTTTTTTATCACTACACATAAATAAAAGAAATTGAGAAGACTTACTGGTCTCTGCCAACACAAGGGGCACAACTACAAAAGCACAATAAAGTTTATTATCAAAATAGCACCTTAAGAAGGTTTGGTCACAAGACAGTATTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@ID_2_valid_cut_small +ATCATCCTCTGCTGCAAAATGCAAGGCAAAAAAAAACATTTAATTTTAATTTAACATTTTTTTATCACTACACATAAATAAAAGAAATTGAGAAGACTTACTGCTGACCCTCTGCCAACACAAGGGGCACAACTACAAAAGCACAATAAAGTTTATTATCAAAATAGCACCTTAAGAAGGTTTGGTCACAAGACAGTATTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII |
| b |
| diff -r 000000000000 -r 71adaaace336 test-data/R2_001.fastq.gz |
| b |
| Binary file test-data/R2_001.fastq.gz has changed |
| b |
| diff -r 000000000000 -r 71adaaace336 test-data/R2_002.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/R2_002.fastq Wed Sep 22 21:01:40 2021 +0000 |
| b |
| b'@@ -0,0 +1,84 @@\n+@ID_3_valid_cut_biggest_1\n+AATTACACAAGCGCAAACACACCTGGATCAAAAATGCAGCAACACAGTTGGGATGGTCATCTGGCAGGACTCCTTTCCCCATTGGTGTGGGAAGAAAGGGTATCCCAGTGACCTCCACCTCTGCCCTGGCATACGCAGCACCTGGAACAGATGTTTGACATTTTTCATTTAGCCGTCAGCTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@ID_3_valid_cut_biggest_2\n+AATTACACAAGCGCAAACACACCTGGATCAAAAATGCAGCAACACAGTTGGGATGGTCATCTGGCAGGACTCCTTTCCCCATTGGTGTGGGAAGAAAGGGTATCCCAGTGACCTCCACCTCTGCCCTGGCATACGCAGCACCTGGAACAGATGTTTGACATTTTTCATTTAGCCGTCAGCTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@ID_3_valid_cut_biggest_3\n+AATTACACAAGCGCAAACACACCTGGATCAAAAATGCAGCAACACAGTTGGGATGGTCATCTGGCAGGACTCCTTTCCCCATTGGTGTGGGAAGAAAGGGTATCCCAGTGACCTCCACCTCTGCCCTGGCATACGCAGCACCTGGAACAGATGTTTGACATTTTTCATTTAGCCGTCAGCTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@ID_3_valid_cut_biggest_4\n+AATTACACAAGCGCAAACACACCTGGATCAAAAATGCAGCAACACAGTTGGGATGGTCATCTGGCAGGACTCCTTTCCCCATTGGTGTGGGAAGAAAGGGTATCCCAGTGACCTCCACCTCTGCCCTGGCATACGCAGCACCTGGAACAGATGTTTGACATTTTTCATTTAGCCGTCAGCTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@ID_3_valid_cut_biggest_5\n+AATTACACAAGCGCAAACACACCTGGATCAAAAATGCAGCAACACAGTTGGGATGGTCATCTGGCAGGACTCCTTTCCCCATTGGTGTGGGAAGAAAGGGTATCCCAGTGACCTCCACCTCTGCCCTGGCATACGCAGCACCTGGAACAGATGTTTGACATTTTTCATTTAGCCGTCAGCTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@ID_3_valid_cut_medium_1\n+AATTACACAAGCGCAAACACACCTGGATCTGGCTGCAGCAACACAGTTGGGATGGTCATCTGGCAGGACTCCTTTCCCCATTGGTGTGGGAAGAAAGGGTATCCCAGTGACCTGTTCCCTGACCACTGCCCTGGCATACGCAGCACCTGGAACAGATGTTTGACATTTTTCATTTAGCCGTCAGCTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@ID_3_valid_cut_medium_2\n+AATTACACAAGCGCAAACACACCTGGATCTGGCTGCAGCAACACAGTTGGGATGGTCATCTGGCAGGACTCCTTTCCCCATTGGTGTGGGAAGAAAGGGTATCCCAGTGACCTGTTCCCTGACCACTGCCCTGGCATACGCAGCACCTGGAACAGATGTTTGACATTTTTCATTTAGCCGTCAGCTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@ID_3_PD_1\n+AATTACACAAGCGCAAACACACCTTTCATTTAGCCGTCAGCTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@ID_3_not_valid_insertion_deletion\n+AATTACACAAGCGCAAACACACCTGGATCTGGCTGCAGCAACACAGTTGGGATGGTCATCTGGCAGGACTCCTTTCCCCATTGGTGTGGGAAGAAAGGGTATCCCAGTGACCTCCACCAGTTCCCTGGGGGGGGGGGGGGGGGACCACCTCCTCTGCCCTGGCATACGCAGCAACATTTTTCATTTAGCCGTCAGCTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@ID_4_not_valid_insertion_deletion_1\n+GAGCGCTGAGGCAGGATTATACCCTCTTTCATGTGAGTTCTTAGACTTCCGGCCTTTAACAGCAGTCAGTTGTTGCAGGGACTGGTTTCCTGTAAACACAATGCAAGCACAAGTTACTTTTTTACGTAAATTACTGGTAGGAATGTTGCCAGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@ID_4_not_valid_insertion_deletion_2\n+GAGCGCTGAGGCAGGATTATACCCTCTTTCATGTGAGTTCTTAGACTTCCGGCCTTTAACAGCAGTCAGTTGTTGCAGGGACTGGTTTCCTGTAAACACAATGCAAGCACAAGTTACTTTTTTACGTAAATTACTGGTAGGAATGTTGCCAGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII'..b'sertion_deletion_3\n+GAGCGCTGAGGCAGGATTATACCCTCTTTCATGTGAGTTCTTAGACTTCCGGCCTTTAACAGCAGTCAGTTGTTGCAGGGACTGGTTTCCTGTAAACACAATGCAAGCACAAGTTACTTTTTTACGTAAATTACTGGTAGGAATGTTGCCAGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@ID_4_not_valid_insertion_deletion_4\n+GAGCGCTGAGGCAGGATTATACCCTCTTTCATGTGAGTTCTTAGACTTCCGGCCTTTAACAGCAGTCAGTTGTTGCAGGGACTGGTTTCCTGTAAACACAATGCAAGCACAAGTTACTTTTTTACGTAAATTACTGGTAGGAATGTTGCCAGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@ID_4_not_valid_insertion_deletion_medium_1\n+GAGCGCTGAGGCAGGATTATACCCTCTACATGCACTCTTGACACCTGCTGATGTGAGTTCTTAGACTTCCGGCCTTTCCCCCCCCAATGTTGCAGGGACTGGTTTCCTGTAAACACAATGCAAGCACAAGTTACATTAGATTTTTACGTAAATTACTGGTAGGAATGTTGCCAGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@ID_4_not_valid_insertion_deletion_medium_2\n+GAGCGCTGAGGCAGGATTATACCCTCTACATGCACTCTTGACACCTGCTGATGTGAGTTCTTAGACTTCCGGCCTTTCCCCCCCCAATGTTGCAGGGACTGGTTTCCTGTAAACACAATGCAAGCACAAGTTACATTAGATTTTTACGTAAATTACTGGTAGGAATGTTGCCAGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@ID_4_not_valid_insertion_deletion_small_1\n+GAGCGCTGAGGCAGGATTATACCCTCTCCAAGGACACTTGACACCTGCTGATGTGAGTTCTTAGACTTCCGGCCTTTAATGTTGCAGTACGATGCACGTGTGGTGGGACTGGTTTCCTGTAAACACAATGCAAGCACAAGTTACATTAGCACATTTTATAGCATTTTTTTACGTAAATTACTGGTAGGAATGTTGCCAGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@ID_5_perfect1\n+ACTGGCTGAGGCAGGATTATACCCTCTTCATGCACACTTGACACCTGCTGATGTGAGTTCTTAGACTTCCGGCCTTTAATGTTGCAGGGACTGGTTTCCTGTAAACACAATGCAAGCACAAGTTACATTAGACTGGAGAGCTACACATTTTATAGCATTTTTTTACGTAAATTACTGGTAGGAATGTTGCCAGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@ID_5_perfect2\n+ACTGGCTGAGGCAGGATTATACCCTCTTCATGCACACTTGACACCTGCTGATGTGAGTTCTTAGACTTCCGGCCTTTAATGTTGCAGGGACTGGTTTCCTGTAAACACAATGCAAGCACAAGTTACATTAGACTGGAGAGCTACACATTTTATAGCATTTTTTTACGTAAATTACTGGTAGGAATGTTGCCAGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@ID_5_perfect3\n+ACTGGCTGAGGCAGGATTATACCCTCTTCATGCACACTTGACACCTGCTGATGTGAGTTCTTAGACTTCCGGCCTTTAATGTTGCAGGGACTGGTTTCCTGTAAACACAATGCAAGCACAAGTTACATTAGACTGGAGAGCTACACATTTTATAGCATTTTTTTACGTAAATTACTGGTAGGAATGTTGCCAGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@ID_5_perfectHDR1\n+ACTGGCTGAGGCAGGATTATACCCTCTTCATGCACACTTGACACCTGCTGATGTGAGTTCTTAGACTTCCGGCTTTTAATGTTGCAGGGACTGGTTTCCTGTAAACACAATGCAAGCACAAGTTACATTAGACTGGAGAGCTACACATTTTATAGCATTTTTTTACGTAAATTACTGGTAGGAATGTTGCCAGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@ID_5_perfectHDR2\n+ACTGGCTGAGGCAGGATTATACCCTCTTCATGCACACTTGACACCTGCTGATGTGAGTTCTTAGACTTCCGGCTTTTAATGTTGCAGGGACTGGTTTCCTGTAAACACAATGCAAGCACAAGTTACATTAGACTGGAGAGCTACACATTTTATAGCATTTTTTTACGTAAATTACTGGTAGGAATGTTGCCAGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n' |
| b |
| diff -r 000000000000 -r 71adaaace336 test-data/R2_002.fastq.gz |
| b |
| Binary file test-data/R2_002.fastq.gz has changed |
| b |
| diff -r 000000000000 -r 71adaaace336 test-data/RunParameters.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RunParameters.txt Wed Sep 22 21:01:40 2021 +0000 |
| b |
| @@ -0,0 +1,17 @@ +Config file: /tmp/tmpg3fcuksp/files/f/0/2/dataset_f0207835-503b-4340-b985-c28af77332e6.dat +Average Quality: 0 +Minimum Quality: 20 +Write Alignments: txt +Fastq files Mode: 0 +Gap Opening: 25 +Gap Extension: 0 +Consensus: TRUE +Normalize: guideRNA, Group +PRIMER DIMER buffer: 30 +Cut buffer: 5 +Scoring Matrix: +,A,C,G,T +A,5,-4,-4,-4 +C,-4,5,-4,-4 +G,-4,-4,5,-4 +T,-4,-4,-4,5 |
| b |
| diff -r 000000000000 -r 71adaaace336 test-data/alignments.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alignments.txt Wed Sep 22 21:01:40 2021 +0000 |
| b |
| b'@@ -0,0 +1,112 @@\n+ID: ID_1 read_id: 1 Count: 3\n+AAGCTGACGGCTAAATGAAAAATGTCAAACGTCTGTTCCAG------------------------------------------------------------------AAAAAAAAAAAAAAAAAAAATTCCCACACCAATGGGGAAAGGAGTCCTGCCAGATGACCATCCCAACTGTGTTGCAGCAGCCAGATCCAGGTGTGTTTGCGCTTGTGTAATT\n+AAGCTGACGGCTAAATGAAAAATGTCAAACATCTGTTCCAGGTGCTGCGTATGCCAGGGCAGAGGAGGTGGTCAGGGAACTGGTGGAGGTCACTGGGATACCCTTTC--------------------TTCCCACACCAATGGGGAAAGGAGTCCTGCCAGATGACCATCCCAACTGTGTTGCTGCAGCCAGATCCAGGTGTGTTTGCGCTTGTGTAATT\n+\n+AAGCTGACGGCTAAATGAAAAATGTCAAACGTCTGTTCCAG------------------------------------------------------------------AAAAAAAAAAAAAAAAAAAATTCCCACACCAATGGGGAAAGGAGTCCTGCCAGATGACCATCCCAACTGTGTTGCAGCAGCCAGATCCAGGTGTGTTTGCGCTTGTGTAATT\n+AAGCTGACGGCTAAATGAAAAATGTCAAACATCTGTTCCAGGTGCTGCGTATGCCAGGGCAGAGGAGGTGGTCAGGGAACTGGTGGAGGTCACTGGGATACCCTTTC--------------------TTCCCACACCAATGGGGAAAGGAGTCCTGCCAGATGACCATCCCAACTGTGTTGCTGCAGCCAGATCCAGGTGTGTTTGCGCTTGTGTAATT\n+\n+ID: ID_1 read_id: 2 Count: 2\n+AAGCTGACGGCTAAATGAAAAATGTCAAACGTCTGTT--------------------------------------------------------------------------AAAAAAAAAAAAAAAAAAAACACACCAATGGGGAAAGGAGTCCTGCCAGATGACCATCCCAACTGTGTTGCAGCAGCCAGATCCAGGTGTGTTTGCGCTTGTGTAATT\n+AAGCTGACGGCTAAATGAAAAATGTCAAACATCTGTTCCAGGTGCTGCGTATGCCAGGGCAGAGGAGGTGGTCAGGGAACTGGTGGAGGTCACTGGGATACCCTTTCTTCC--------------------CACACCAATGGGGAAAGGAGTCCTGCCAGATGACCATCCCAACTGTGTTGCTGCAGCCAGATCCAGGTGTGTTTGCGCTTGTGTAATT\n+\n+AAGCTGACGGCTAAATGAAAAATGTCAAACGTCTGTT--------------------------------------------------------------------------AAAAAAAAAAAAAAAAAAAACACACCAATGGGGAAAGGAGTCCTGCCAGATGACCATCCCAACTGTGTTGCAGCAGCCAGATCCAGGTGTGTTTGCGCTTGTGTAATT\n+AAGCTGACGGCTAAATGAAAAATGTCAAACATCTGTTCCAGGTGCTGCGTATGCCAGGGCAGAGGAGGTGGTCAGGGAACTGGTGGAGGTCACTGGGATACCCTTTCTTCC--------------------CACACCAATGGGGAAAGGAGTCCTGCCAGATGACCATCCCAACTGTGTTGCTGCAGCCAGATCCAGGTGTGTTTGCGCTTGTGTAATT\n+\n+ID: ID_1 read_id: 3 Count: 1\n+AAGCTGACGGCTAAATGAAAAAG------------------------------------------------------------------------------------------------------------------------------------------------------CCTCGTGTGTTTGCGCTTGTGTAATT\n+AAGCTGACGGCTAAATGAAAAATGTCAAACATCTGTTCCAGGTGCTGCGTATGCCAGGGCAGAGGAGGTGGTCAGGGAACTGGTGGAGGTCACTGGGATACCCTTTCTTCCCACACCAATGGGGAAAGGAGTCCTGCCAGATGACCATCCCAACTGTGTTGCTGCAGCCAGATCCAGGTGTGTTTGCGCTTGTGTAATT\n+\n+AAGCTGACGGCTAAATGAAAAAG------------------------------------------------------------------------------------------------------------------------------------------------------CCTCGTGTGTTTGCGCTTGTGTAATT\n+AAGCTGACGGCTAAATGAAAAATGTCAAACATCTGTTCCAGGTGCTGCGTATGCCAGGGCAGAGGAGGTGGTCAGGGAACTGGTGGAGGTCACTGGGATACCCTTTCTTCCCACACCAATGGGGAAAGGAGTCCTGCCAGATGACCATCCCAACTGTGTTGCTGCAGCCAGATCCAGGTGTGTTTGCGCTTGTGTAATT\n+\n+ID: ID_1 read_id: 4 Count: 1\n+AAGCTGACGGCTAAATGAAAAATGTCAAACGTC------------------------------------------------------------------------------------AATGGGGAAAGGAGTCCTGCCAGATGACCATCCCAACTGTGTTGCTGCAGCCAAATCCAGGTGTGTTTGCGCTTGTGTAATT\n+AAGCTGACGGCTAAATGAAAAATGTCAAACATCTGTTCCAGGTGCTGCGTATGCCAGGGCAGAGGAGGTGGTCAGGGAACTGGTGGAGGTCACTGGGATACCCTTTCTTCCCACACCAATGGGGAAAGGAGTCCTGCCAGATGACCATCCCAACTGTGTTGCTGCAGCCAGATCCAGGTGTGTTTGCGCTTGTGTAATT\n+\n+AAGCTGACGGCTAAATGAAAAATGTCAAACGTC------------------------------------------------------------------------------------AATGGGGAAAGGAGTCCTGCCAGATGACCATCCCAACTGTGTTGCTGCAGCCAAATCCAGGTGTGTTTGCGCTTGTGTAATT\n+AAGCTGACGGCTAAATGAAAAATGTCAAACATCTGTTCCAGGTGCTGCGTATGCCAGGGCAGAGGAGGTGGTCAGGGAACTGGTGGAGGTCACTGGGATACCCTTTCTTCCCACACCAATGGGGAAAGGAGTCCTGCCAGATGACCATCCCAACTGTGTTGCTGCAGCCAGATCCAGGTGTGTTTGCGCTTGTGTAATT\n+\n+ID: ID_2 read_id: 1 Count: 3\n+TGACCAAACCTTCTTAAGGTGCTATTTTGATAATAAACTTTATTGTGCTTTTGTAGTTGTGCCCCT-------------GGTCAGCAGACCAGTAAGTCTTCTCAATTTCTTTTATTTATGTGTAGTGATAAAAAAATGTTAAATTAAAATTAAATGTTTTTTTTTGCCTTGCATTTTGCAGCAGAG\n+TGACCAAACCTTCTTAAGGTGCTATTTTGATAATAAACTTTATTGTGCTTTTGTAGTTGTGCCCCTTGTGTTGGCAGAGGGTCAGCAGACCAGTAAGTCTTCTCAATTTCTTTTATTTATGTGTAGTGATAAAAAAATGTTAAATTAAAATTAAATGTTTTTTTTTGCCTTGCATTTTGCAGCAGAG\n+\n+TGACCAAACCTTCTTAAGGTGCTATTTTGATAATAAACTTTATTGTGCTTTTGTAGTT'..b'CAGCGCTC\n+GCTGGCAACATTCCTACCAGTAATTTACGTAAAAAAATGCTATAAAATGTGTAGCTCTCCAGTCTAATGTAACTTGTGCTTGCATTGTGTTTACAGGAAACCAGTCCCTGCAACATTAAAGGCCGGAAGTCTAAGAACTCACATCAGCAGGTGTCAAGTGTGCATGAAGAGGGTATAATCCTGCCTCAGCGCTC\n+\n+GCTGGCAACATTCCTACCAGTAATTTACGTAAAAAA--------------------------------GTAACTTGTGCTTGCATTGTGTTTACAGGAAACCAGTCCCTGCAACAACTGACTGCTGTTAAAGGCCGGAAGTCTAAGAACTCACATGA--------------------AAGAGGGTATAATCCTGCCTCAGCGCTC\n+GCTGGCAACATTCCTACCAGTAATTTACGTAAAAAAATGCTATAAAATGTGTAGCTCTCCAGTCTAATGTAACTTGTGCTTGCATTGTGTTTACAGGAAACCAGTCCCTGCAACA-----------TTAAAGGCCGGAAGTCTAAGAACTCACATCAGCAGGTGTCAAGTGTGCATGAAGAGGGTATAATCCTGCCTCAGCGCTC\n+\n+ID: ID_4 read_id: 2 Count: 2\n+GCTGGCAACATTCCTACCAGTAATTTACGTAAAAA---------------------------TCTAATGTAACTTGTGCTTGCATTGTGTTTACAGGAAACCAGTCCCTGCAACATTGGGGGGGGAAAGGCCGGAAGTCTAAGAACTCACATCAGCAGGTGTCAAGAGTGCATGTAGAGGGTATAATCCTGCCTCAGCGCTC\n+GCTGGCAACATTCCTACCAGTAATTTACGTAAAAAAATGCTATAAAATGTGTAGCTCTCCAGTCTAATGTAACTTGTGCTTGCATTGTGTTTACAGGAAACCAGTCCCTGCAACATT--------AAAGGCCGGAAGTCTAAGAACTCACATCAGCAGGTGTCAAGTGTGCATGAAGAGGGTATAATCCTGCCTCAGCGCTC\n+\n+GCTGGCAACATTCCTACCAGTAATTTACGTAAAAA---------------------------TCTAATGTAACTTGTGCTTGCATTGTGTTTACAGGAAACCAGTCCCTGCAACATTGGGGGGGGAAAGGCCGGAAGTCTAAGAACTCACATCAGCAGGTGTCAAGAGTGCATGTAGAGGGTATAATCCTGCCTCAGCGCTC\n+GCTGGCAACATTCCTACCAGTAATTTACGTAAAAAAATGCTATAAAATGTGTAGCTCTCCAGTCTAATGTAACTTGTGCTTGCATTGTGTTTACAGGAAACCAGTCCCTGCAACATT--------AAAGGCCGGAAGTCTAAGAACTCACATCAGCAGGTGTCAAGTGTGCATGAAGAGGGTATAATCCTGCCTCAGCGCTC\n+\n+ID: ID_4 read_id: 3 Count: 1\n+GCTGGCAACATTCCTACCAGTAATTTACGTAAAAAAATGCTATAAAATGTG------------CTAATGTAACTTGTGCTTGCATTGTGTTTACAGGAAACCAGTCCCACCACACGTGCATCGTACTGCAACATTAAAGGCCGGAAGTCTAAGAACTCACATCAGCAGGTGTCAAGTGTCCTTGGAGAGGGTATAATCCTGCCTCAGCGCTC\n+GCTGGCAACATTCCTACCAGTAATTTACGTAAAAAAATGCTATAAAATGTGTAGCTCTCCAGTCTAATGTAACTTGTGCTTGCATTGTGTTTACAGGAAACCAGTCCC------------------TGCAACATTAAAGGCCGGAAGTCTAAGAACTCACATCAGCAGGTGTCAAGTGTGCATGAAGAGGGTATAATCCTGCCTCAGCGCTC\n+\n+ACTGGCAACATTCCTACCAGTAATTTACGTAAAAAAATGCTATAAAATGTG------------CTAATGTAACTTGTGCTTGCATTGTGTTTACAGGAAACCAGTCCCACCACACGTGCATCGTACTGCAACATTAAAGGCCGGAAGTCTAAGAACTCACATCAGCAGGTGTCAAGTGTCCTTGGAGAGGGTATAATCCTGCCTCAGCGCTC\n+GCTGGCAACATTCCTACCAGTAATTTACGTAAAAAAATGCTATAAAATGTGTAGCTCTCCAGTCTAATGTAACTTGTGCTTGCATTGTGTTTACAGGAAACCAGTCCC------------------TGCAACATTAAAGGCCGGAAGTCTAAGAACTCACATCAGCAGGTGTCAAGTGTGCATGAAGAGGGTATAATCCTGCCTCAGCGCTC\n+\n+ID: ID_5 read_id: 1 Count: 3\n+ACTGGCAACATTCCTACCAGTAATTTACGTAAAAAAATGCTATAAAATGTGTAGCTCTCCAGTCTAATGTAACTTGTGCTTGCATTGTGTTTACAGGAAACCAGTCCCTGCAACATTAAAGGCCGGAAGTCTAAGAACTCACATCAGCAGGTGTCAAGTGTGCATGAAGAGGGTATAATCCTGCCTCAGCCAGT\n+ACTGGCAACATTCCTACCAGTAATTTACGTAAAAAAATGCTATAAAATGTGTAGCTCTCCAGTCTAATGTAACTTGTGCTTGCATTGTGTTTACAGGAAACCAGTCCCTGCAACATTAAAGGCCGGAAGTCTAAGAACTCACATCAGCAGGTGTCAAGTGTGCATGAAGAGGGTATAATCCTGCCTCAGCCAGT\n+\n+ACTGGCAACATTCCTACCAGTAATTTACGTAAAAAAATGCTATAAAATGTGTAGCTCTCCAGTCTAATGTAACTTGTGCTTGCATTGTGTTTACAGGAAACCAGTCCCTGCAACATTAAAGGCCGGAAGTCTAAGAACTCACATCAGCAGGTGTCAAGTGTGCATGAAGAGGGTATAATCCTGCCTCAGCCAGT\n+ACTGGCAACATTCCTACCAGTAATTTACGTAAAAAAATGCTATAAAATGTGTAGCTCTCCAGTCTAATGTAACTTGTGCTTGCATTGTGTTTACAGGAAACCAGTCCCTGCAACATTAAAGGCCGGAAGTCTAAGAACTCACATCAGCAGGTGTCAAGTGTGCATGAAGAGGGTATAATCCTGCCTCAGCCAGT\n+\n+ID: ID_5 read_id: 2 Count: 2\n+ACTGGCAACATTCCTACCAGTAATTTACGTAAAAAAATGCTATAAAATGTGTAGCTCTCCAGTCTAATGTAACTTGTGCTTGCATTGTGTTTACAGGAAACCAGTCCCTGCAACATTAAAAGCCGGAAGTCTAAGAACTCACATCAGCAGGTGTCAAGTGTGCATGAAGAGGGTATAATCCTGCCTCAGCCAGT\n+ACTGGCAACATTCCTACCAGTAATTTACGTAAAAAAATGCTATAAAATGTGTAGCTCTCCAGTCTAATGTAACTTGTGCTTGCATTGTGTTTACAGGAAACCAGTCCCTGCAACATTAAAGGCCGGAAGTCTAAGAACTCACATCAGCAGGTGTCAAGTGTGCATGAAGAGGGTATAATCCTGCCTCAGCCAGT\n+\n+ACTGGCAACATTCCTACCAGTAATTTACGTAAAAAAATGCTATAAAATGTGTAGCTCTCCAGTCTAATGTAACTTGTGCTTGCATTGTGTTTACAGGAAACCAGTCCCTGCAACATTAAAAGCCGGAAGTCTAAGAACTCACATCAGCAGGTGTCAAGTGTGCATGAAGAGGGTATAATCCTGCCTCAGCCAGT\n+ACTGGCAACATTCCTACCAGTAATTTACGTAAAAAAATGCTATAAAATGTGTAGCTCTCCAGTCTAATGTAACTTGTGCTTGCATTGTGTTTACAGGAAACCAGTCCCTGCAACATTAAAGGCCGGAAGTCTAAGAACTCACATCAGCAGGTGTCAAGTGTGCATGAAGAGGGTATAATCCTGCCTCAGCCAGT\n+\n' |
| b |
| diff -r 000000000000 -r 71adaaace336 test-data/barcode_reads_filtered.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/barcode_reads_filtered.csv Wed Sep 22 21:01:40 2021 +0000 |
| b |
| @@ -0,0 +1,3 @@ +Barcode,experiment_count,read_count,bad_base_quality,bad_average_quality,bad_alphabet,filtered_read_count,unique_reads,unassigned_reads,assigned_reads +barcode_1,2,20,0,0,3,17,10,3,7 +barcode_2,3,21,0,0,0,21,9,0,9 |
| b |
| diff -r 000000000000 -r 71adaaace336 test-data/config.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/config.csv Wed Sep 22 21:01:40 2021 +0000 |
| b |
| @@ -0,0 +1,6 @@ +ID,Barcode,Forward_Reads,Reverse_Reads,Group,Control,guideRNA,Forward_Primer,Reverse_Primer,Direction,Amplicon,Donor +ID_1,barcode_1,R1_001.fastq,R2_001.fastq,Betty,0,AGGTGGTCAGGGAACTGG,AAGCTGACGGCTAAATGA,AATTACACAAGCGCAAACACAC,0,aagctgacggctaaatgaaaaatgtcaaacatctgttccaggtgctgcgtatgccagggcagaggAGGTGGTCAGGGAACTGGtggaggtcactgggataccctttcttcccacaccaatggggaaaggagtcctgccagatgaccatcccaactgtgttgctgcagccagatccaggtgtgtttgcgcttgtgtaatt, +ID_2,barcode_1,R1_001.fastq,R2_001.fastq,Tom,0,TGACCCTCTGCCAACACAAGGGG,TGACCAAACCTTCTTAAGGTGC,CTCTGCTGCAAAATGCAAGG,1,aaatactgtcttgtgaccaaaccttcttaaggtgctattttgataataaactttattgtgcttttgtagttgtgCCCCTTGTGTTGGCAGAGGGTCAgcagaccagtaagtcttctcaatttcttttatttatgtgtagtgataaaaaaatgttaaattaaaattaaatgtttttttttgccttgcattttgcagcagaggatgat, +ID_3,barcode_2,R1_002.fastq,R2_002.fastq,Tom,0,AGGTGGTCAGGGAACTGG,AAGCTGACGGCTAAATGA,AATTACACAAGCGCAAACACAC,0,aagctgacggctaaatgaaaaatgtcaaacatctgttccaggtgctgcgtatgccagggcagaggAGGTGGTCAGGGAACTGGtggaggtcactgggataccctttcttcccacaccaatggggaaaggagtcctgccagatgaccatcccaactgtgttgctgcagccagatccaggtgtgtttgcgcttgtgtaatt, +ID_4,barcode_2,R1_002.fastq,R2_002.fastq,Betty,1,GTCCCTGCAACATTAAAGGCCGG,GCTGGCAACATTCCTACCAGT,GAGCGCTGAGGCAGGATTAT,0,gctggcaacattcctaccagtaatttacgtaaaaaaatgctataaaatgtgtagctctccagtctaatgtaacttgtgcttgcattgtgtttacaggaaaccaGTCCCTGCAACATTAAAGGCCGGaagtctaagaactcacatcagcaggtgtcaagtgtgcatgaagagggtataatcctgcctcagcgctc, +ID_5,barcode_2,R1_002.fastq,R2_002.fastq,Betty,0,GTCCCTGCAACATTAAAGGCCGG,ACTGGCAACATTCCTACCAGT,ACTGGCTGAGGCAGGATTAT,0,actggcaacattcctaccagtaatttacgtaaaaaaatgctataaaatgtgtagctctccagtctaatgtaacttgtgcttgcattgtgtttacaggaaaccaGTCCCTGCAACATTAAAGGCCGGaagtctaagaactcacatcagcaggtgtcaagtgtgcatgaagagggtataatcctgcctcagccagt,actggcaacattcctaccagtaatttacgtaaaaaaatgctataaaatgtgtagctctccagtctaatgtaacttgtgcttgcattgtgtttacaggaaaccaGTCCCTGCAACATTAAAAGCCGGaagtctaagaactcacatcagcaggtgtcaagtgtgcatgaagagggtataatcctgcctcagccagt |
| b |
| diff -r 000000000000 -r 71adaaace336 test-data/config_gzip.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/config_gzip.csv Wed Sep 22 21:01:40 2021 +0000 |
| b |
| @@ -0,0 +1,6 @@ +ID,Barcode,Forward_Reads,Reverse_Reads,Group,Control,guideRNA,Forward_Primer,Reverse_Primer,Direction,Amplicon,Donor +ID_1,barcode_1,R1_001.fastq.gz,R2_001.fastq.gz,Betty,0,AGGTGGTCAGGGAACTGG,AAGCTGACGGCTAAATGA,AATTACACAAGCGCAAACACAC,0,aagctgacggctaaatgaaaaatgtcaaacatctgttccaggtgctgcgtatgccagggcagaggAGGTGGTCAGGGAACTGGtggaggtcactgggataccctttcttcccacaccaatggggaaaggagtcctgccagatgaccatcccaactgtgttgctgcagccagatccaggtgtgtttgcgcttgtgtaatt, +ID_2,barcode_1,R1_001.fastq.gz,R2_001.fastq.gz,Tom,0,TGACCCTCTGCCAACACAAGGGG,TGACCAAACCTTCTTAAGGTGC,CTCTGCTGCAAAATGCAAGG,1,aaatactgtcttgtgaccaaaccttcttaaggtgctattttgataataaactttattgtgcttttgtagttgtgCCCCTTGTGTTGGCAGAGGGTCAgcagaccagtaagtcttctcaatttcttttatttatgtgtagtgataaaaaaatgttaaattaaaattaaatgtttttttttgccttgcattttgcagcagaggatgat, +ID_3,barcode_2,R1_002.fastq.gz,R2_002.fastq.gz,Tom,0,AGGTGGTCAGGGAACTGG,AAGCTGACGGCTAAATGA,AATTACACAAGCGCAAACACAC,0,aagctgacggctaaatgaaaaatgtcaaacatctgttccaggtgctgcgtatgccagggcagaggAGGTGGTCAGGGAACTGGtggaggtcactgggataccctttcttcccacaccaatggggaaaggagtcctgccagatgaccatcccaactgtgttgctgcagccagatccaggtgtgtttgcgcttgtgtaatt, +ID_4,barcode_2,R1_002.fastq.gz,R2_002.fastq.gz,Betty,1,GTCCCTGCAACATTAAAGGCCGG,GCTGGCAACATTCCTACCAGT,GAGCGCTGAGGCAGGATTAT,0,gctggcaacattcctaccagtaatttacgtaaaaaaatgctataaaatgtgtagctctccagtctaatgtaacttgtgcttgcattgtgtttacaggaaaccaGTCCCTGCAACATTAAAGGCCGGaagtctaagaactcacatcagcaggtgtcaagtgtgcatgaagagggtataatcctgcctcagcgctc, +ID_5,barcode_2,R1_002.fastq.gz,R2_002.fastq.gz,Betty,0,GTCCCTGCAACATTAAAGGCCGG,ACTGGCAACATTCCTACCAGT,ACTGGCTGAGGCAGGATTAT,0,actggcaacattcctaccagtaatttacgtaaaaaaatgctataaaatgtgtagctctccagtctaatgtaacttgtgcttgcattgtgtttacaggaaaccaGTCCCTGCAACATTAAAGGCCGGaagtctaagaactcacatcagcaggtgtcaagtgtgcatgaagagggtataatcctgcctcagccagt,actggcaacattcctaccagtaatttacgtaaaaaaatgctataaaatgtgtagctctccagtctaatgtaacttgtgcttgcattgtgtttacaggaaaccaGTCCCTGCAACATTAAAAGCCGGaagtctaagaactcacatcagcaggtgtcaagtgtgcatgaagagggtataatcctgcctcagccagt |
| b |
| diff -r 000000000000 -r 71adaaace336 test-data/config_summary.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/config_summary.csv Wed Sep 22 21:01:40 2021 +0000 |
| b |
| @@ -0,0 +1,6 @@ +ID,Barcode,Forward_Reads_File,Reverse_Reads_File,Group,guideRNA,Found_Guide,Control,Forward_Primer,Reverse_Primer,Direction,Amplicon,Donor,fwdPrPosEnd,rvePrPos,Reads,PRIMER_DIMER,Low_Score,Reads_Filtered,Reads_Del,Reads_In,Reads_Edited,Reads_Frameshifted,HDR +ID_1,barcode_1,/tmp/tmpg3fcuksp/job_working_directory/000/6/working/fastq_folder/R1_001.fastq,/tmp/tmpg3fcuksp/job_working_directory/000/6/working/fastq_folder/R2_001.fastq,Betty,AGGTGGTCAGGGAACTGG,TRUE,FALSE,AAGCTGACGGCTAAATGA,AATTACACAAGCGCAAACACAC,FALSE,aagctgacggctaaatgaaaaatgtcaaacatctgttccaggtgctgcgtatgccagggcagaggAGGTGGTCAGGGAACTGGtggaggtcactgggataccctttcttcccacaccaatggggaaaggagtcctgccagatgaccatcccaactgtgttgctgcagccagatccaggtgtgtttgcgcttgtgtaatt,"",18,178,7,1,0,6,6,0,6,2,0 +ID_2,barcode_1,/tmp/tmpg3fcuksp/job_working_directory/000/6/working/fastq_folder/R1_001.fastq,/tmp/tmpg3fcuksp/job_working_directory/000/6/working/fastq_folder/R2_001.fastq,Tom,TGACCCTCTGCCAACACAAGGGG,TRUE,FALSE,TGACCAAACCTTCTTAAGGTGC,CTCTGCTGCAAAATGCAAGG,TRUE,aaatactgtcttgtgaccaaaccttcttaaggtgctattttgataataaactttattgtgcttttgtagttgtgCCCCTTGTGTTGGCAGAGGGTCAgcagaccagtaagtcttctcaatttcttttatttatgtgtagtgataaaaaaatgttaaattaaaattaaatgtttttttttgccttgcattttgcagcagaggatgat,"",35,181,6,0,0,6,6,0,6,4,0 +ID_3,barcode_2,/tmp/tmpg3fcuksp/job_working_directory/000/6/working/fastq_folder/R1_002.fastq,/tmp/tmpg3fcuksp/job_working_directory/000/6/working/fastq_folder/R2_002.fastq,Tom,AGGTGGTCAGGGAACTGG,TRUE,FALSE,AAGCTGACGGCTAAATGA,AATTACACAAGCGCAAACACAC,FALSE,aagctgacggctaaatgaaaaatgtcaaacatctgttccaggtgctgcgtatgccagggcagaggAGGTGGTCAGGGAACTGGtggaggtcactgggataccctttcttcccacaccaatggggaaaggagtcctgccagatgaccatcccaactgtgttgctgcagccagatccaggtgtgtttgcgcttgtgtaatt,"",18,178,9,1,0,8,7,1,8,1,0 +ID_4,barcode_2,/tmp/tmpg3fcuksp/job_working_directory/000/6/working/fastq_folder/R1_002.fastq,/tmp/tmpg3fcuksp/job_working_directory/000/6/working/fastq_folder/R2_002.fastq,Betty,GTCCCTGCAACATTAAAGGCCGG,TRUE,TRUE,GCTGGCAACATTCCTACCAGT,GAGCGCTGAGGCAGGATTAT,FALSE,gctggcaacattcctaccagtaatttacgtaaaaaaatgctataaaatgtgtagctctccagtctaatgtaacttgtgcttgcattgtgtttacaggaaaccaGTCCCTGCAACATTAAAGGCCGGaagtctaagaactcacatcagcaggtgtcaagtgtgcatgaagagggtataatcctgcctcagcgctc,"",21,175,7,0,0,7,4,7,7,2,0 +ID_5,barcode_2,/tmp/tmpg3fcuksp/job_working_directory/000/6/working/fastq_folder/R1_002.fastq,/tmp/tmpg3fcuksp/job_working_directory/000/6/working/fastq_folder/R2_002.fastq,Betty,GTCCCTGCAACATTAAAGGCCGG,TRUE,FALSE,ACTGGCAACATTCCTACCAGT,ACTGGCTGAGGCAGGATTAT,FALSE,actggcaacattcctaccagtaatttacgtaaaaaaatgctataaaatgtgtagctctccagtctaatgtaacttgtgcttgcattgtgtttacaggaaaccaGTCCCTGCAACATTAAAGGCCGGaagtctaagaactcacatcagcaggtgtcaagtgtgcatgaagagggtataatcctgcctcagccagt,actggcaacattcctaccagtaatttacgtaaaaaaatgctataaaatgtgtagctctccagtctaatgtaacttgtgcttgcattgtgtttacaggaaaccaGTCCCTGCAACATTAAAAGCCGGaagtctaagaactcacatcagcaggtgtcaagtgtgcatgaagagggtataatcctgcctcagccagt,21,175,5,0,0,5,0,0,2,0,2 |
| b |
| diff -r 000000000000 -r 71adaaace336 test-data/events_filtered_shifted.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/events_filtered_shifted.csv Wed Sep 22 21:01:40 2021 +0000 |
| b |
| @@ -0,0 +1,84 @@ +seqnames,start,end,width,strand,originally,replacement,type,read_id,score,counts,readType,overlaps,consensus +ID_1,42,61,20,+,"",AAAAAAAAAAAAAAAAAAAA,insertion,1,597,3,FALSE,FALSE,TRUE +ID_1,46,65,20,+,"",AAAAAAAAAAAAAAAAAAAA,insertion,2,557,2,FALSE,FALSE,TRUE +ID_1,-24,41,66,+,"","",deletion,1,597,3,FALSE,TRUE,TRUE +ID_1,-28,45,74,+,"","",deletion,2,557,2,FALSE,TRUE,TRUE +ID_1,-32,51,84,+,"","",deletion,4,532,1,FALSE,TRUE,TRUE +ID_1,-35,-35,1,+,A,G,mismatch,1,597,3,FALSE,FALSE,TRUE +ID_1,97,97,1,+,T,A,mismatch,1,597,3,FALSE,FALSE,TRUE +ID_1,-35,-35,1,+,A,G,mismatch,2,557,2,FALSE,FALSE,TRUE +ID_1,97,97,1,+,T,A,mismatch,2,557,2,FALSE,FALSE,TRUE +ID_1,-35,-35,1,+,A,G,mismatch,4,532,1,FALSE,FALSE,TRUE +ID_1,105,105,1,+,G,A,mismatch,4,532,1,FALSE,FALSE,TRUE +ID_1,42,61,20,-,"",AAAAAAAAAAAAAAAAAAAA,insertion,1,597,3,FALSE,FALSE,FALSE +ID_1,46,65,20,-,"",AAAAAAAAAAAAAAAAAAAA,insertion,2,557,2,FALSE,FALSE,FALSE +ID_1,-24,41,66,-,"","",deletion,1,597,3,FALSE,TRUE,FALSE +ID_1,-28,45,74,-,"","",deletion,2,557,2,FALSE,TRUE,FALSE +ID_1,-32,51,84,-,"","",deletion,4,532,1,FALSE,TRUE,FALSE +ID_1,-35,-35,1,-,A,G,mismatch,1,597,3,FALSE,FALSE,FALSE +ID_1,97,97,1,-,T,A,mismatch,1,597,3,FALSE,FALSE,FALSE +ID_1,-35,-35,1,-,A,G,mismatch,2,557,2,FALSE,FALSE,FALSE +ID_1,97,97,1,-,T,A,mismatch,2,557,2,FALSE,FALSE,FALSE +ID_1,-35,-35,1,-,A,G,mismatch,4,532,1,FALSE,FALSE,FALSE +ID_1,105,105,1,-,G,A,mismatch,4,532,1,FALSE,FALSE,FALSE +ID_2,5,17,13,-,"","",deletion,1,845,3,FALSE,TRUE,FALSE +ID_2,-4,4,9,-,"","",deletion,2,865,2,FALSE,TRUE,FALSE +ID_2,-9,-5,5,-,"","",deletion,3,885,1,FALSE,TRUE,FALSE +ID_2,5,17,13,+,"","",deletion,1,845,3,FALSE,TRUE,TRUE +ID_2,-4,4,9,+,"","",deletion,2,865,2,FALSE,TRUE,TRUE +ID_2,-9,-5,5,+,"","",deletion,3,885,1,FALSE,TRUE,TRUE +ID_3,105,105,1,+,"",T,insertion,1,819,5,FALSE,FALSE,TRUE +ID_3,8,23,16,+,"",CCCCCCCCCCCCCCCC,insertion,3,860,1,FALSE,TRUE,TRUE +ID_3,0,17,18,+,"","",deletion,1,819,5,FALSE,TRUE,TRUE +ID_3,-3,2,6,+,"","",deletion,2,885,2,FALSE,TRUE,TRUE +ID_3,15,20,6,+,"","",deletion,2,885,2,FALSE,TRUE,TRUE +ID_3,-40,-24,17,+,"","",deletion,3,860,1,FALSE,FALSE,TRUE +ID_3,101,101,1,+,G,T,mismatch,1,819,5,FALSE,FALSE,TRUE +ID_3,102,102,1,+,C,T,mismatch,1,819,5,FALSE,FALSE,TRUE +ID_3,103,103,1,+,C,T,mismatch,1,819,5,FALSE,FALSE,TRUE +ID_3,104,104,1,+,A,T,mismatch,1,819,5,FALSE,FALSE,TRUE +ID_3,105,105,1,-,"",T,insertion,1,819,5,FALSE,FALSE,FALSE +ID_3,8,23,16,-,"",CCCCCCCCCCCCCCCC,insertion,3,860,1,FALSE,TRUE,FALSE +ID_3,0,17,18,-,"","",deletion,1,819,5,FALSE,TRUE,FALSE +ID_3,-3,2,6,-,"","",deletion,2,885,2,FALSE,TRUE,FALSE +ID_3,15,20,6,-,"","",deletion,2,885,2,FALSE,TRUE,FALSE +ID_3,-40,-24,17,-,"","",deletion,3,860,1,FALSE,FALSE,FALSE +ID_3,101,101,1,-,G,T,mismatch,1,819,5,FALSE,FALSE,FALSE +ID_3,102,102,1,-,C,T,mismatch,1,819,5,FALSE,FALSE,FALSE +ID_3,103,103,1,-,C,T,mismatch,1,819,5,FALSE,FALSE,FALSE +ID_3,104,104,1,-,A,T,mismatch,1,819,5,FALSE,FALSE,FALSE +ID_4,14,21,8,+,"",GGGGGGGG,insertion,2,767,2,FALSE,TRUE,TRUE +ID_4,5,22,18,+,"",ACCACACGTGCATCGTAC,insertion,3,833,1,FALSE,TRUE,TRUE +ID_4,-67,-36,32,+,"","",deletion,1,497,4,FALSE,FALSE,TRUE +ID_4,-13,-6,8,+,"","",deletion,1,497,4,FALSE,FALSE,FALSE +ID_4,10,11,2,+,"","",deletion,1,497,4,FALSE,TRUE,TRUE +ID_4,43,62,20,+,"","",deletion,1,497,4,FALSE,FALSE,TRUE +ID_4,-68,-42,27,+,"","",deletion,2,767,2,FALSE,FALSE,TRUE +ID_4,-52,-41,12,+,"","",deletion,3,833,1,FALSE,FALSE,TRUE +ID_4,-2,-2,1,+,C,A,mismatch,1,497,4,FALSE,TRUE,TRUE +ID_4,0,0,1,+,G,C,mismatch,1,497,4,FALSE,TRUE,TRUE +ID_4,41,41,1,+,C,G,mismatch,1,497,4,FALSE,FALSE,TRUE +ID_4,55,55,1,+,T,A,mismatch,2,767,2,FALSE,FALSE,TRUE +ID_4,63,63,1,+,A,T,mismatch,2,767,2,FALSE,FALSE,TRUE +ID_4,58,58,1,+,G,C,mismatch,3,833,1,FALSE,FALSE,TRUE +ID_4,60,60,1,+,A,T,mismatch,3,833,1,FALSE,FALSE,TRUE +ID_4,63,63,1,+,A,G,mismatch,3,833,1,FALSE,FALSE,TRUE +ID_4,2,2,1,+,C,G,mismatch,1,497,4,FALSE,TRUE,TRUE +ID_4,3,3,1,+,C,A,mismatch,1,497,4,FALSE,TRUE,TRUE +ID_4,8,8,1,+,A,T,mismatch,1,497,4,FALSE,TRUE,TRUE +ID_4,9,9,1,+,A,G,mismatch,1,497,4,FALSE,TRUE,TRUE +ID_4,12,22,11,-,"",ACTGACTGCTG,insertion,1,626,4,FALSE,TRUE,TRUE +ID_4,14,21,8,-,"",GGGGGGGG,insertion,2,767,2,FALSE,TRUE,FALSE +ID_4,5,22,18,-,"",ACCACACGTGCATCGTAC,insertion,3,824,1,FALSE,TRUE,FALSE +ID_4,-67,-36,32,-,"","",deletion,1,626,4,FALSE,FALSE,FALSE +ID_4,43,62,20,-,"","",deletion,1,626,4,FALSE,FALSE,FALSE +ID_4,-68,-42,27,-,"","",deletion,2,767,2,FALSE,FALSE,FALSE +ID_4,-52,-41,12,-,"","",deletion,3,824,1,FALSE,FALSE,FALSE +ID_4,41,41,1,-,C,G,mismatch,1,626,4,FALSE,FALSE,FALSE +ID_4,55,55,1,-,T,A,mismatch,2,767,2,FALSE,FALSE,FALSE +ID_4,63,63,1,-,A,T,mismatch,2,767,2,FALSE,FALSE,FALSE +ID_4,58,58,1,-,G,C,mismatch,3,824,1,FALSE,FALSE,FALSE +ID_4,60,60,1,-,A,T,mismatch,3,824,1,FALSE,FALSE,FALSE +ID_4,63,63,1,-,A,G,mismatch,3,824,1,FALSE,FALSE,FALSE +ID_5,17,17,1,+,G,A,mismatch,2,961,2,TRUE,TRUE,TRUE +ID_5,17,17,1,-,G,A,mismatch,2,961,2,TRUE,TRUE,FALSE |
| b |
| diff -r 000000000000 -r 71adaaace336 test-data/events_filtered_shifted_normalized.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/events_filtered_shifted_normalized.csv Wed Sep 22 21:01:40 2021 +0000 |
| b |
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| b |
| diff -r 000000000000 -r 71adaaace336 test-data/output_html.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_html.html Wed Sep 22 21:01:40 2021 +0000 |
| [ |
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| b |
| diff -r 000000000000 -r 71adaaace336 test-data/raw_events.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/raw_events.csv Wed Sep 22 21:01:40 2021 +0000 |
| b |
| @@ -0,0 +1,95 @@ +seqnames,start,end,width,strand,originally,replacement,type,read_id,score,counts,readType +ID_1,108,127,20,+,"",AAAAAAAAAAAAAAAAAAAA,insertion,1,597,3,FALSE +ID_1,112,131,20,+,"",AAAAAAAAAAAAAAAAAAAA,insertion,2,557,2,FALSE +ID_1,42,107,66,+,"","",deletion,1,597,3,FALSE +ID_1,38,111,74,+,"","",deletion,2,557,2,FALSE +ID_1,24,173,150,+,"","",deletion,3,193,1,FALSE +ID_1,34,117,84,+,"","",deletion,4,532,1,FALSE +ID_1,31,31,1,+,A,G,mismatch,1,597,3,FALSE +ID_1,163,163,1,+,T,A,mismatch,1,597,3,FALSE +ID_1,31,31,1,+,A,G,mismatch,2,557,2,FALSE +ID_1,163,163,1,+,T,A,mismatch,2,557,2,FALSE +ID_1,23,23,1,+,T,G,mismatch,3,193,1,FALSE +ID_1,31,31,1,+,A,G,mismatch,4,532,1,FALSE +ID_1,171,171,1,+,G,A,mismatch,4,532,1,FALSE +ID_1,176,176,1,+,A,T,mismatch,3,193,1,FALSE +ID_1,177,177,1,+,G,C,mismatch,3,193,1,FALSE +ID_1,108,127,20,-,"",AAAAAAAAAAAAAAAAAAAA,insertion,1,597,3,FALSE +ID_1,112,131,20,-,"",AAAAAAAAAAAAAAAAAAAA,insertion,2,557,2,FALSE +ID_1,42,107,66,-,"","",deletion,1,597,3,FALSE +ID_1,38,111,74,-,"","",deletion,2,557,2,FALSE +ID_1,24,173,150,-,"","",deletion,3,193,1,FALSE +ID_1,34,117,84,-,"","",deletion,4,532,1,FALSE +ID_1,31,31,1,-,A,G,mismatch,1,597,3,FALSE +ID_1,163,163,1,-,T,A,mismatch,1,597,3,FALSE +ID_1,31,31,1,-,A,G,mismatch,2,557,2,FALSE +ID_1,163,163,1,-,T,A,mismatch,2,557,2,FALSE +ID_1,23,23,1,-,T,G,mismatch,3,193,1,FALSE +ID_1,31,31,1,-,A,G,mismatch,4,532,1,FALSE +ID_1,171,171,1,-,G,A,mismatch,4,532,1,FALSE +ID_1,176,176,1,-,A,T,mismatch,3,193,1,FALSE +ID_1,177,177,1,-,G,C,mismatch,3,193,1,FALSE +ID_2,115,127,13,-,"","",deletion,1,845,3,FALSE +ID_2,106,114,9,-,"","",deletion,2,865,2,FALSE +ID_2,101,105,5,-,"","",deletion,3,885,1,FALSE +ID_2,115,127,13,+,"","",deletion,1,845,3,FALSE +ID_2,106,114,9,+,"","",deletion,2,865,2,FALSE +ID_2,101,105,5,+,"","",deletion,3,885,1,FALSE +ID_3,171,171,1,+,"",T,insertion,1,819,5,FALSE +ID_3,74,89,16,+,"",CCCCCCCCCCCCCCCC,insertion,3,860,1,FALSE +ID_3,66,83,18,+,"","",deletion,1,819,5,FALSE +ID_3,63,68,6,+,"","",deletion,2,885,2,FALSE +ID_3,81,86,6,+,"","",deletion,2,885,2,FALSE +ID_3,26,42,17,+,"","",deletion,3,860,1,FALSE +ID_3,21,176,156,+,"","",deletion,4,190,1,FALSE +ID_3,167,167,1,+,G,T,mismatch,1,819,5,FALSE +ID_3,168,168,1,+,C,T,mismatch,1,819,5,FALSE +ID_3,169,169,1,+,C,T,mismatch,1,819,5,FALSE +ID_3,170,170,1,+,A,T,mismatch,1,819,5,FALSE +ID_3,171,171,1,-,"",T,insertion,1,819,5,FALSE +ID_3,74,89,16,-,"",CCCCCCCCCCCCCCCC,insertion,3,860,1,FALSE +ID_3,66,83,18,-,"","",deletion,1,819,5,FALSE +ID_3,63,68,6,-,"","",deletion,2,885,2,FALSE +ID_3,81,86,6,-,"","",deletion,2,885,2,FALSE +ID_3,26,42,17,-,"","",deletion,3,860,1,FALSE +ID_3,21,176,156,-,"","",deletion,4,190,1,FALSE +ID_3,167,167,1,-,G,T,mismatch,1,819,5,FALSE +ID_3,168,168,1,-,C,T,mismatch,1,819,5,FALSE +ID_3,169,169,1,-,C,T,mismatch,1,819,5,FALSE +ID_3,170,170,1,-,A,T,mismatch,1,819,5,FALSE +ID_4,118,125,8,+,"",GGGGGGGG,insertion,2,767,2,FALSE +ID_4,109,126,18,+,"",ACCACACGTGCATCGTAC,insertion,3,833,1,FALSE +ID_4,37,68,32,+,"","",deletion,1,497,4,FALSE +ID_4,91,98,8,+,"","",deletion,1,497,4,FALSE +ID_4,114,115,2,+,"","",deletion,1,497,4,FALSE +ID_4,147,166,20,+,"","",deletion,1,497,4,FALSE +ID_4,36,62,27,+,"","",deletion,2,767,2,FALSE +ID_4,52,63,12,+,"","",deletion,3,833,1,FALSE +ID_4,102,102,1,+,C,A,mismatch,1,497,4,FALSE +ID_4,104,104,1,+,G,C,mismatch,1,497,4,FALSE +ID_4,145,145,1,+,C,G,mismatch,1,497,4,FALSE +ID_4,159,159,1,+,T,A,mismatch,2,767,2,FALSE +ID_4,167,167,1,+,A,T,mismatch,2,767,2,FALSE +ID_4,162,162,1,+,G,C,mismatch,3,833,1,FALSE +ID_4,164,164,1,+,A,T,mismatch,3,833,1,FALSE +ID_4,167,167,1,+,A,G,mismatch,3,833,1,FALSE +ID_4,106,106,1,+,C,G,mismatch,1,497,4,FALSE +ID_4,107,107,1,+,C,A,mismatch,1,497,4,FALSE +ID_4,112,112,1,+,A,T,mismatch,1,497,4,FALSE +ID_4,113,113,1,+,A,G,mismatch,1,497,4,FALSE +ID_4,116,126,11,-,"",ACTGACTGCTG,insertion,1,626,4,FALSE +ID_4,118,125,8,-,"",GGGGGGGG,insertion,2,767,2,FALSE +ID_4,109,126,18,-,"",ACCACACGTGCATCGTAC,insertion,3,824,1,FALSE +ID_4,37,68,32,-,"","",deletion,1,626,4,FALSE +ID_4,147,166,20,-,"","",deletion,1,626,4,FALSE +ID_4,36,62,27,-,"","",deletion,2,767,2,FALSE +ID_4,52,63,12,-,"","",deletion,3,824,1,FALSE +ID_4,145,145,1,-,C,G,mismatch,1,626,4,FALSE +ID_4,159,159,1,-,T,A,mismatch,2,767,2,FALSE +ID_4,167,167,1,-,A,T,mismatch,2,767,2,FALSE +ID_4,1,1,1,-,G,A,mismatch,3,824,1,FALSE +ID_4,162,162,1,-,G,C,mismatch,3,824,1,FALSE +ID_4,164,164,1,-,A,T,mismatch,3,824,1,FALSE +ID_4,167,167,1,-,A,G,mismatch,3,824,1,FALSE +ID_5,121,121,1,+,G,A,mismatch,2,961,2,TRUE +ID_5,121,121,1,-,G,A,mismatch,2,961,2,TRUE |
| b |
| diff -r 000000000000 -r 71adaaace336 test-data/unassigned_reads.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/unassigned_reads.csv Wed Sep 22 21:01:40 2021 +0000 |
| b |
| @@ -0,0 +1,4 @@ +Forward,Reverse,Total,BarcodeFrequency,Asigned,fwdPrInReadPos,forwardFound,rvePrInReadPos,reverseFound,Barcode +AAATACTGTCTTGTGACCAAACCTTCTTAAGGTGCTGTTTTGATGATAAACTTTATTGTGCTTTTGTAGTTGTGCCCCTTGTGTTGGCAGAGGGTCAGCAGACCAGTAAGTCTTCTCAATTTCTTTTATTTATGTATATGTAGTGATAAAA,TGGTCATCTGGCAGGACTCCTTTCCCCATTGGTGTGGGAAGAAAGGGTATCCCAGTGACCTCCAGTGACCTTCCCTGACCTTCTTCTCTGCCCTGGCATACGCAGCACCTGGAACAGATGTTTCAGATATTTTTCATTTAGCCGTCAGCTT,2,0.117647058823529,FALSE,14,TRUE,,FALSE,barcode_1 +AAGCTGACGGCTAAATGAAAAATATCTGAAACATCTGTTCCAGGTGCTGCGTATGCCAGGGCAGAGAAGAAGGTCAGGGAAGGTCACTGGAGGTCACTGGGATACCCTTTCTTCCCACACCAATGGGGAAAGGAGTCCTGCCAGATGACCA,AAGCTGACGGCTAAATGAAAAATATCTGAAACATCTGTTCCAGGTGCTGCGTATGCCAGGGCAGAGAAGAAGGTCAGGGAAGGTCACTGGAGGTCACTGGGATACCCTTTCTTCCCACACCAATGGGGAAAGGAGTCCTGCCAGATGACCA,1,0.0588235294117647,FALSE,,FALSE,,FALSE,barcode_1 +AAGCTGACGGCTAAATGAAAAATATCTGAAACATCTGTTCCAGGTGCTGCGTATGCCAGGGCAGAGAAGAAGGTCAGGGAAGGTCACTGGAGGTCACTGGGATACCCTTTCTTCCCACACCAATGGGGAAAGGAGTCCTGCCAGATGACCA,TGGTCATCTGGCAGGACTCCTTTCCCCATTGGTGTGGGAAGAAAGGGTATCCCAGTGACCTCCAGTGACCTTCCCTGACCTTCTTCTCTGCCCTGGCATACGCAGCACCTGGAACAGATGTTTCAGATATTTTTCATTTAGCCGTCAGCTT,1,0.0588235294117647,FALSE,,FALSE,,FALSE,barcode_1 |