| Previous changeset 5:8a0473eb465e (2022-06-17) Next changeset 7:28a0b1446d2b (2023-12-20) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78 |
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modified:
maxbin2.xml |
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added:
test-data/4/out.001.fasta test-data/4/out.002.fasta test-data/4/out.abund1 test-data/4/out.log test-data/4/out.marker test-data/4/out.marker.pdf test-data/4/out.noclass test-data/4/out.summary test-data/4/out.tooshort test-data/test4_contigs.fasta test-data/test4_reads.fastqsanger test-data/test4_reads.fastqsanger.gz |
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| diff -r 8a0473eb465e -r 2bc40bfbcfb4 maxbin2.xml --- a/maxbin2.xml Fri Jun 17 17:27:40 2022 +0000 +++ b/maxbin2.xml Mon Oct 16 07:46:13 2023 +0000 |
| [ |
| b'@@ -1,8 +1,5 @@\n-<tool id="maxbin2" name="MaxBin2" version="@MAXBIN_VERSION@+galaxy3">\n+<tool id="maxbin2" name="MaxBin2" version="@MAXBIN_VERSION@+galaxy4">\n <description>clusters metagenomic contigs into bins</description>\n- <xrefs>\n- <xref type="bio.tools">masigpro</xref>\n- </xrefs>\n <macros>\n <token name="@MAXBIN_VERSION@">2.2.7</token>\n <xml name="contig">\n@@ -19,19 +16,40 @@\n <param argument="--reassembly" type="boolean" truevalue="-reassembly" falsevalue="" checked="false" label="Reassembly" help="Reassembly option is still highly experimental. To use this function, you need to feed MaxBin interleaved paired-end fastq or fasta file." />\n </xml>\n </macros>\n+ <xrefs>\n+ <xref type="bio.tools">maxbin</xref>\n+ </xrefs>\n <requirements>\n <requirement type="package" version="@MAXBIN_VERSION@">maxbin2</requirement>\n </requirements>\n <version_command><![CDATA[run_MaxBin.pl -version | head -n 1]]></version_command>\n <command detect_errors="exit_code"><![CDATA[\n ## generate read or abundance files\n+#import re\n #if $assembly.inputs.type == \'reads\'\n #if $assembly.type == \'individual\'\n-echo \'$assembly.inputs.reads\' >> reads_list &&\n+ ## uncompress .gz reads files if necessary\n+ #set $e = $assembly.inputs.reads\n+ #set $identifier = re.sub(\'[^\\s\\w\\-\\\\.]\', \'_\', str($e.element_identifier))\n+ #if $e.ext.endswith(".gz")\n+gunzip -c \'$e\' > \'$identifier\' &&\n+echo \'$identifier\' >> reads_list &&\n+ #else \n+ln -s \'$e\' \'$identifier\' &&\n+echo \'$identifier\' >> reads_list &&\n+ #end if\n #else\n- #for $r in $assembly.inputs.reads\n+ #for $i, $r in enumerate($assembly.inputs.reads)\n #if $r\n-echo \'$r\' >> reads_list &&\n+ #set $identifier = re.sub(\'[^\\s\\w\\-\\\\.]\', \'_\', str($r.element_identifier))\n+ #set $newid = $identifier + \'_\' + str($i)\n+ #if $r.ext.endswith(".gz")\n+gunzip -c \'$r\' > \'$newid\' && \n+echo \'$newid\' >> reads_list &&\n+ #else\n+ln -s \'$r\' \'$newid\' &&\n+echo \'$newid\' >> reads_list &&\n+ #end if\n #end if\n #end for\n #end if\n@@ -94,7 +112,7 @@\n <conditional name="inputs">\n <expand macro="input_type"/>\n <when value="reads">\n- <param argument="-reads" type="data" format="fasta,fastq" label="Reads file"/>\n+ <param argument="-reads" type="data" format="fasta,fastq,fastq.gz,fasta.gz" label="Reads file"/>\n <expand macro="reads_extra_params"/>\n </when>\n <when value="abund">\n@@ -344,6 +362,129 @@\n </assert_contents>\n </output>\n </test>\n+ <!-- test w contigs and reads in fastqsanger format as input -->\n+ <test expect_num_outputs="4">\n+ <param name="contig" value="test4_contigs.fasta" ftype="fasta" />\n+ <conditional name="assembly">\n+ <param name="type" value="individual"/>\n+ <conditional name="inputs">\n+ <param name="type" value="reads"/>\n+ <param name="reads" value="test4_reads.fastqsanger" ftype="fastqsanger"/>\n+ <param name="output_abundances" value="false"/>\n+ <param name="reassembly" value=""/>\n+ </conditional>\n+ </conditional>\n+ <section name="adv">\n+ <param name="min_contig_length" value="1000"/>\n+ <param name="max_iteration" value="50"/>\n+ <param name="prob_threshold" value="0.5"/>\n+ </section>\n+ <section name="output">\n+ <param name="plotmarker" value=""/>\n+ <param name="marker" value="false"/>\n+ <param name="markers" value="false" />\n+ <param name="log" value="fa'..b'e="output">\n+ <param name="plotmarker" value=""/>\n+ <param name="marker" value="false"/>\n+ <param name="markers" value="false" />\n+ <param name="log" value="false"/>\n+ <param name="markerset" value="107"/>\n+ </section>\n+ <output_collection name="bins" type="list" count="2">\n+ <element name="001" file="4/out.001.fasta" ftype="fasta"/>\n+ <element name="002" file="4/out.002.fasta" ftype="fasta"/>\n+ </output_collection>\n+ <output name="summary" file="4/out.summary" ftype="tabular" />\n+ <output name="noclass" file="4/out.noclass" ftype="fasta" />\n+ <output name="toshort" file="4/out.tooshort" ftype="fasta" />\n+ </test>\n+ <!-- test w co-assembled contigs and multiple reads as .gz and optional outputs -->\n+ <test expect_num_outputs="9">\n+ <param name="contig" value="test4_contigs.fasta" ftype="fasta" />\n+ <conditional name="assembly">\n+ <param name="type" value="coassembly"/>\n+ <conditional name="inputs">\n+ <param name="type" value="reads"/>\n+ <param name="reads" value="test4_reads.fastqsanger.gz,test4_reads.fastqsanger.gz" ftype="fasta"/>\n+ <param name="output_abundances" value="true"/>\n+ <param name="reassembly" value=""/>\n+ </conditional>\n+ </conditional>\n+ <section name="adv">\n+ <param name="min_contig_length" value="1000"/>\n+ <param name="max_iteration" value="50"/>\n+ <param name="prob_threshold" value="0.5"/>\n+ </section>\n+ <section name="output">\n+ <param name="plotmarker" value="true"/>\n+ <param name="marker" value="true"/>\n+ <param name="markers" value="true" />\n+ <param name="log" value="true"/>\n+ <param name="markerset" value="107"/>\n+ </section>\n+ <output_collection name="bins" type="list" count="2">\n+ <element name="001" file="4/out.001.fasta" ftype="fasta"/>\n+ <element name="002" file="4/out.002.fasta" ftype="fasta"/>\n+ </output_collection>\n+ <output name="summary" ftype="tabular">\n+ <assert_contents>\n+ <has_text text="Completeness"/>\n+ <has_text text="out.001.fasta"/>\n+ </assert_contents>\n+ </output>\n+ <output name="noclass" file="4/out.noclass" ftype="fasta" />\n+ <output name="toshort" file="4/out.tooshort" ftype="fasta" />\n+ <output name="log" ftype="txt" >\n+ <assert_contents>\n+ <has_text text="Input contig"/>\n+ <has_text text="Elapsed time"/>\n+ <has_text text="Yielded 2 bins for contig (scaffold) file"/>\n+ </assert_contents>\n+ </output>\n+ <output name="abundout" file="4/out.abund1" ftype="tabular" />\n+ <output name="marker" file="4/out.marker" ftype="tabular" />\n+ <output name="plot" file="4/out.marker.pdf" ftype="pdf" compare="sim_size" />\n+ <output_collection name="markers" type="list" count="2">\n+ <element name="001" ftype="fasta">\n+ <assert_contents>\n+ <has_text text=">out.001.Methyltransf_5"/>\n+ </assert_contents>\n+ </element>\n+ <element name="002" ftype="fasta">\n+ <assert_contents>\n+ <has_text text=">out.002.Methyltransf_5"/>\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n+ </test>\n </tests>\n <help><![CDATA[\n MaxBin is a software that clusters metagenomic contigs into different bins,\n' |
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| diff -r 8a0473eb465e -r 2bc40bfbcfb4 test-data/4/out.001.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/4/out.001.fasta Mon Oct 16 07:46:13 2023 +0000 |
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| b'@@ -0,0 +1,3675 @@\n+>k141_99\n+GGCAATGGCGTCGTCGTGCTGCAAGGTAAGCCCAATACTGTCCAGACCGTTCATCATGCAGTGGCGGCGG\n+AAGGCATCGATGGTAAAGCGATAGGTTTTCTCTCCCGCTTTCACCTCTTGCGCTTCCAGATCCACGTCGA\n+AATGGATCCCCGGATTAGCTTTCACCAGCGCAAACAGTTCGTCCACTTCTGCATCGCTTAATTTCACCGG\n+CAGCAGCTGGTTGTTAAAGCTATTGCCGTAGAAGATGTCAGCAAAACTCGGCGCAATCACCACTTTAAAA\n+CCGTAGTCGGTCAATGCCCAGGGCGCGTGCTCACGCGAAGAGCCACAGCCGAAGTTTTCTCGTGCCAGCA\n+AAATGGAAGCGCCCTGATACTGCGGGAAGTTCAGCACGAAGTCCGGGTTTGGCTGTTGGCCTTTTTCATC\n+CAGAAAACGCCAGTCGTTAAACAGATGCGCGCCAAAACCCGTACGGGTCACTTTCTGCAAAAACTGTTTC\n+GGGATGATTGCATCGGTATCGACATTGGCGGCATCCAGCGGAACCACCAGGCCTGTGTGTTTGATAAATT\n+TCTCTGCCATGGTGTGCTCCTTATTTAATGTTGCGAATGTCGGCGAAATGTCCGGTCACAGCAGCAGCGG\n+CAGCCATTGCCGGGCTGACCAGATGCGTGCGCCCGCCGCGCCCCTGGCGGCCTTCAAAGTTACGGTTGCT\n+GGTGGAGGCACAACGTTCGCCCGGATTCAGACGGTCGTTGTTCATCGCCAGACACATTGAGCAGCCAGGC\n+AAGCGCCATTCAAAACCGGCTTCAATAAAGATTTTATCCAGACCTTCCGCTTCCGCCTGGGCTTTTACCG\n+GGCCAGAGCCGGGAACCACCAGTGCCTGCACGCCTGGCGCGACTTTTCGCCCTTTGGCGATCTCCGCTGC\n+CGCGCGTAAATCTTCAATGCGCGAGTTGGTACAGGAACCGATAAACACTTTGTCGATAGCCACTTCGGTC\n+AGCGGAATACCCGGTTTCAGCCCCATATAGGCCAGCGCTTTTTCTGCCGACGCGCGTTCAACCGGATCGG\n+CAAACGAAGCCGGATCGGGAATATTGTCGTTCACGGAAATCACCTGGCCGGGATTGGTGCCCCAGGTGAC\n+CTGCGGTGAAATTTCTTCTGCTTGCAGAGTGACAACGGTATCGAAAGTTGCGCCTTCGTCGGTTTGCAGG\n+GTTTTCCAGTAGGCAACGGCGTCGTCGAAATCTTTGCCTTTCGGCGCATGCAGACGGCCTTTGACATAGT\n+TAAAGGTGGTTTCGTCCGGTGCAACCAGACCGGCTTTTGCGCCCATTTCGATTGCCATATTGCACAGGGT\n+CATACGACCTTCCATGCTTAAATCACGGATTGCTTCGCCGCAAAACTCCACCACATGCCCGGTGCCGCCT\n+GCGCTACCGGTTTTACCGATAATTGCCAGCACGATATCTTTTGCGGTAATGCCCGGCGCGGCTTTGCCCT\n+GGACTTCAATTTTCATGGTTTTTGCGCGGCCCTGTTTCAGGGTTTGCGTTGCCAGTACGTGTTCAACTTC\n+GGAAGTGCCGATACCAAAGGCCAGTGCGCCAAACGCGCCGTGGGTGGCGGTATGCGAGTCGCCGCAGACA\n+ATGGTCATCCCCGGCAAGGTGACGCCCTGTTCCGGCCCCATTACGTGGACGATCCCCTGATACGGGTGAT\n+TCAGGTCATACAGTTCGACGCCAAATTCTTTGCAGTTTTTGATCAGTTCCTGCATCTGGATACGCGCCAT\n+TTCACCGCAGGCATTAATGTCTTTGGTCTGGGTAGAGACGTTGTGATCCATGGTAGCGAAGGTTTTGCCC\n+GGCTGACGTACCGGGCGACCGTGGGCGCGCAGACCATCGAACGCCTGCGGTGAGGTCACTTCATGCACCA\n+GGTGGCGGTCGATATATAACAGTGGGGTTTCGTTTTCGGCTTCGTACACAACGTGAGCGTCGAACAATTT\n+TTCGTATAACGTCTTAGCCATGATTACACCCCTTCTGCTACATAGCGGGCAATGATATCGCCCATTTCAT\n+CGGTACTAACGGCGGCAGCGCCACGGGCTAAATCCCCGGTGCGAATGCCTTCTTCTAATGCGCGGTTAAT\n+GGCGCGTTCAATGGCGCAAGCCGCATCATCGGCATCCAGGCTGTAACGCAGCAGCAGTGCCAGCGAAAGG\n+ATTTGTGCAATCGGGTTGGCGATGTTTTTGCCTGCGATATCTGGTGCCGAGCCGCCCGCCGGTTCATACA\n+GTCCAAAACCTTGCTCGTTCAGGCTGGCGGAAGGCAACATCCCCATCGAGCCAGTGATCATTGCGCACTC\n+GTCAGACAGAATGTCGCCAAACAGGTTGGAGCACAGCAGAACGTCAAACTGTGATGGATCTTTAATCAGC\n+TGCATGGTGGCGTTGTCGATGTACATATGCGCCAGTTCGACATCCGGGTATTCCGTGGCGATCTCGTTAA\n+CGATCTCCCGCCATAAAATAGAGGATTGCAGCACGTTGGCTTTATCGATCGACGTCACTTTGTGGCGACG\n+CTTGCGAGCAGATTCAAACGCGATGCGGGCGATACGTTCGATCTCAAAACGGTGATACACCTCGGTATCA\n+AAGGCTTTTTCATATTGTCCGCTACCTTCGCGGCCTTTTGGCTGACCGAAATAGATGCCGCCGGTCAGTT\n+CGCGCACACACAGGATGTCGAAGCCGTTTGCGGCAATGTCTGCACGCAGCGGACAGAATGCTTCCAGCCC\n+CTGATACAGTTTTGCCGGGCGCAGGTTGCTGAATAATTTGAAGTGCTTACGCAGAGGCAGCAGCGCGCCG\n+CGTTCTGGTTGCTGGTCTGGTGGTAAATGTTCCCACTTCGGGCCGCCTACCGAGCCAAACAGCACGGCAT\n+CGGCTTGCTCACAACCTTCAACCGTCGCAGGCGGCAGTGGTTGCCCGTGGTTATCAATGGCTGCGCCGCC\n+TACATCGTAATGGCTGGTGGTGATGCGCATCGCAAAGCGGTTGCGCACGGCATCCAGCACTTTCAGCGCC\n+TGGGTCATCACTTCCGGACCAATACCGTCCCCCGGCAATACGGCAATATGGTAATTCTTCGACATCACAC\n+GGTTTCCTTGTTGTTTTCGTTGTGTTGAGCTTTGCGTTGCAACTCTTTTTCGACTTCTGCGGCACGCCAG\n+ATATTGTTCAGAACGTGCACCATGGCTTTGGCAGATGACTCGACAATATCGGTAGCCAGGCCGACGCCGT\n+GGAAGCGGCGACCGTTGTAGTTAGCGACGATATCCACCTGACCCAGCGCATCTTTACCGTGGCCTTTGGC\n+GGTCAGGCTGTATTTCACCAGTTCGACGTTATATTCAGTGATGCGGTTAATTGCCTGATAGACGGCATCG\n+ACCGGACCGTTACCGTTGGCGGCTTCTGCTTTGACTTCTTCGCCACAGGCCAGTTTGACGGCGGCGGTGG\n+CGATATCGTTAGAGCCAGACTGCACGCTGAAGTAATCCAGACGGAAATGCTCCGGCTCTTCTTGCTGCTT\n+ACCGATGAAGGCCAGCGCCTCCAGATCGTAATCAAACACCTGACCTTTTTTGTCCGCCAGCTTCAGGAAA\n+GCATCGTACAAATTGTCTAAATTATATTCACTTTCTTTATACCCCATCTCATCCATGCGATGTTTCACCG\n+CCGCACGCCCCGAACGAGAGGTCAGATTCAGCTGGATTTGGTTCAGACCAATAGATTCTGGTGTCATGAT\n+TTCGTAGTTTTCGCGGTTTTTCAGCACGCCATCCTGGTGTATACCGGAGGAGTGTGCGAATGCGCCGCTG\n+CCAACAATGGCTTTGTTTGCCGGGATCGGCATATTACAAATCTGGCTAACTAACTGGCTGGTGCGCCATA\n+TCTCCTGGT'..b'AGCTGCGTATATTGCA\n+ACAGCCGTATGCTGTTTGGTCTGGCACAACAGGGTAATGCGCCAAAAGCGCTGGCGTCTGTCGATAAACG\n+TGGTGTACCAGTAAATACCATTCTGGTGTCTGCACTGGTAACGGCGTTGTGCGTACTGATTAACTACCTT\n+GCCCCAGAGTCCGCTTTCGGACTGTTAATGGCGCTGGTGGTATCTGCACTGGTAATCAACTGGGCGATGA\n+TTAGCCTGGCGCATATGAAATTCCGTCGCGCCAAGCAGGAACAAGGCGTGGTAACTCGCTTCCCTGCTCT\n+GCTTTATCCGCTGGGTAACTGGATCTGCCTGCTGTTTATGGCGGCGGTACTGGTGATTATGCTGATGACC\n+CCAGGAATGGCGATTTCGGTATACCTGATCCCGGTATGGCTGATCGTGTTAGGTATCGGCTATCTGTTTA\n+AAGAGAAAACCGCCAAAGCCGTAAAAGCGCATTAATCTCTCTACGCCCTCACCCGTACAGGGTGAGGGCA\n+ATAATCTTTACACCAACGCCCCGTAAATCGTCAGTAGTGCAATCACCACCACGACCACGAACGAGGTTTT\n+CTTCGCCATTGAAACCGCTGCCTTCGGCGTCTCCACCTTATCGACATGCGGTTCACGCGCCAGAGAGAAC\n+TGCGCCAGACGCGTTAACACCTGATACTGCGAAGTATGGAAATCACCCAGCGAAGCAAACCAGGCCGGTA\n+ACGCTTTCTCACCATGACCGATCAAGGCATATACCACACCCGCAAGACGAACCGGCACCCAATCCAGTAC\n+ATGAAGCACGGCATCAATGCCGGACTGTAAACGATGATGCGGCGTCTGATATCGCGCCAGCCAGTATTGC\n+CATGCACGCAAAAACGCATACCCCATCAGCGTAACGGGTCCCCAGGTTCCCCCCACAATCAGCCAGAACA\n+GCGGTGCAAGATAAAAACGAAAGTTAATCCACAGCAATGCATTTTGCAGCTCACGCAAATACTCACGTTC\n+GTCGCAGCCTGCCGGGACGCCGTGAATCATGGTGAGTTCGCCAGCCATCGTGGCACGGGCATGGCTATCA\n+TTACGTGAAGCAGCTGTCAGATAAGCATGATAATGAAGACGAACTTTACCTGCGCCAATACACAGCAAAC\n+CAATCAGCAGCCACACCAGTAGCGTGGGAACGTTGAACAATACTCCCTGCAATGCGCGTAACAGTAAAAA\n+AGTCACGCCCATCGCAATAATGGTCATGCCTAACGTGCGCCCGAGAGAAAAATGTTTCACCCGCCGAAAG\n+AACGCTTCAAGACGATGATCAAGCTGCCAGTGCTCGCCCAACTTAAACAGGCGCTCGAAAATTAACACCA\n+GTAAGGTTGTAAATAGCGTCATGTTGTCTCCTTGCTGACCAGCACACGAAACCGTGCCCAATCAAATGCA\n+GGACCGGGATCGGTTTTCCGATCCGGCGCAATATCACAATGGCCCGTCATGTTTTTAGCGATATCCGGAT\n+AGCAATCAATCAGTGCCCGCGTAACCGCCGCAAGCTGTTGATACTGCGCATCGGTATACGCCAGCGTATC\n+GGTGCCTTCAAGCTCAATCCCAATAGAAAAATCATTGCAGCGTTCGCGCCCCTGATACTGAGAGACTCCC\n+GCATGCCATGCACGTTTATCGAAAGGAACATACTGGACTATTTCACCATCACGGCGAATCAAACAGTGAG\n+CGGAGACGCGCAAATGGGCGATCTCAGCAAAGAAAGGATGTGCCTGCGGATCAATAGTTCCAGTGAATAA\n+TGCGTCGATCCACGGACCGCCAAACTCGCCTGGCGGCAGGCTAATATTGTGCACCACCAGCAGGGTGGGT\n+GTTTCGTCATCCGGGCGGCAATCGTAATGTGGTGAGGGAACGCGGCGCGCGCCAACCAGCCACCCCTGTT\n+CTAACAACATGCAGGATCTCCTTATATGTGGTGCTAATACCCGGTTCAGAGTAGCATGTTTCTACCTTAT\n+GATTCGTTAGCTATCTGGAGTTTTAACATGCCGCCTCGCCGCTATAACCCTGACACCCGACGTGACGAGC\n+TGCTGGAACGCATTAATCTCGATATCCCCGGCGCGGTGGCCCAGGCGCTGCGGGAAGATTTAGGCGGAAC\n+AGTCGATGCCAACAATGATATTACGGCAAAACTTTTACCGGAAAATTCTCGCTCTCATGCCACGGTGATC\n+ACCCGCGAGAATGGCGTCTTTTGCGGCAAACGCTGGGTTGAAGAGGTGTTTATTCAACTGGCAGGCGACG\n+ATGTCACCATAATCTGGCATGTGGATGACGGCGATGTCATCAATGCCAATCAATCCTTGTTCGAACTTGA\n+AGGCCCATCCCGCGTGCTGTTAACGGGCGAACGCACTGCGCTTAATTTTGTGCAAACCCTTTCAGGAGTT\n+GCCAGTAAGGTACGCCACTATGTCGAATTGCTGGAAGGCACCAACACGCAGTTGTTGGATACGCGCAAAA\n+CCTTACCCGGCCTGCGTTCAGCTCTGAAATACGCGGTACTTTGCGGCGGCGGAGCGAATCACCGTCTGGG\n+GCTTTCTGATGCCTTCCTGATCAAAGAAAACCATATTATTGCCTCCGGCTCAGTGCGCCAGGCGGTCGAA\n+AAAGCGTCCTGGCTGCACCCGGATGCGCCAGTAGAAGTCGAAGTAGAGAATCTGGAAGAACTTGATGAAG\n+CCCTGAAAGCAGGAGCCGATATCATCATGCTGGATAACTTCGAAACAGAACAGATGCGCGAAGCCGTCAA\n+ACGCACCAACGGCAAGGCGCTACTGGAAGTGTCTGGCAACGTCACTGACAAAACACTGCGTGAATTTGCC\n+GAAACGGGCGTGGACTTTATCTCCGTCGGTGCGCTAACTAAACACGTACAAGCACTCGACCTTTCAATGC\n+GTTTTCGCTAATAGTTGACAGATTTATCCGCTCCATCGCGGGCGGATAATCTCCCCTTCCCCAACTTTCT\n+TCGTAACGCCTCGCAAATTTCTTGTCTTTCGCTGCAACGAAATCAAAAACCTCGGAATCTGCTTTCCCGT\n+TTCGTTTTTTGCCCCTCGCCTGTGCTGATGGCGTTTGCCAAAGTAGCGCCAACCAAATCAAGGAGCGAAA\n+CAGATGGACAAGCAACGCGGTTTTACACTTATCGAACTGATGGTGGTTATTGGCATCATTGCCATTTTAA\n+GCGCCATTGGTATTCCCGCTTATCAAAACTACCTGCGCAAAGCCGCACTCACCGACATGCTACAAACCTT\n+TGTGCCTTACCGTACCGCCGTAGAGTTGTGCGCGCTGGAACATGGTGGATTAGATACCTGCGACGGTGGC\n+AGCAATGGCATTCCCTCGCCTACCACCACCCGCTATGTTTCAGCCATGAGTGTGGCAAAGGGCGTGGTGT\n+CGCTGACCGGGCAAGAAAGTCTCAATGGGCTAAGCGTCGTCATGACACCGGGTTGGGATAACGCAAACGG\n+CGTCACCGGCTGGACGCGCAACTGCAATATTCAAAGTGACAGCGCATTGCAGCAAGCCTGCGAAGATGTC\n+TTCCGCTTTGATGACGCCAACTAAGGAGCGGCAATGAATATTCCACAGCTCACTGCCCTGTGTCTGCGTT\n+ATCATGGAGTCTTGCTGGATGCCAGCGAAGAGGTGGTTCATGTTGCGGTAGTCGATGCACCTTCGCATGA\n+GCTACTGGACGCATTGCATTTCGCTACCACCAAACGTATTGAGATCACCTGCTGGACGCGCCAACAAATG\n+GAAGGTCACGCCAGTCGCACACAACAGACATTGCCCGTAGCTGTTCAGGAGAAGCATCAGCCCAAAGCAG\n+AGTTGCTAACTCGAACGTTACAATCTGCGCTGGAACAACGCGCGTCTGATATTCATATCGAACCAGCGGA\n+CAATGCCTACCGCATCCGCT\n' |
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| diff -r 8a0473eb465e -r 2bc40bfbcfb4 test-data/4/out.002.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/4/out.002.fasta Mon Oct 16 07:46:13 2023 +0000 |
| b |
| b'@@ -0,0 +1,6447 @@\n+>k141_199\n+TTATTGTCTTTTACCAAGTGTTCAGGTGATAAGTCTTTCACATCGCTGAACGCCAAACCAGTAAAAACGC\n+AAAAAATGAAAACGTCCCGTACCTGTTCTACTCGCTTAATGGTGAACTCTTTGGCGAGAATAATTTTAAT\n+CTCGTCCATTGTCAGAAATTCAGGATCAGTTTCTTCCAGTTTGAAACGGTAGTAAGCAAAGGGATCTTTC\n+TTTATCCAGTCGTTTTCTAAAGCAATGCGGATAATCTTCTTCAAGTTCTTTAGTCGGGTGATAGCAGAGT\n+TCTGCGCACAACCTTTTTCAATCTTCAAGAAAGCATCGAACTTAGAAATGAAGTTGGCTTCCAAGTTGTT\n+CAGAGCAATATCCGATAGCTGATATTCTTTCTTAATAAATTCCTCTAAATATCGGGTAGTGGTTTCATAC\n+CGTTGAACGGTCTTACTAACGAAGTCTTTGCCGATCAGCTTACGGCTGTGTTCGTTATGCTCCTTGAATA\n+CCTGCAATAGCGTTTTGTTATCTTCATCCACACCATAAAACAACTTTCTCACAAGATCAACAGTGATAAC\n+CTTGCCGGAAGTTTCCAGTTCTCTATAAATTTGGTGTACGTGCGAGCGTGTGATTTCTAAGTAGTGGTTC\n+AGTTCCACCGACATACGGTCTTTGCCTTTTGAATTTTCTTTTGCCTGATTCCATAGATTTACGGGACAGC\n+TTCTTTTGATAGAAATATCTACCATGCAGCCGTTTACGGTGATTCTCATGCACACGGGTGCTTCTCCGTT\n+CTTTAATAATTTGCCTTTCTTGATGAAGAACAATACAGAAAATGATTTTCGAGCCATTTTTACATCGTTT\n+TTAAAGTTACAAAACTATGTATTCTCTTCCAAAGTAAGTCTATGCAAAATGCTATGAATCAGTGAGAAAG\n+ATGCGAATTCGTGGGACTTTTTTGAACTAAATTTTAGTCCCACGATTTATCCACCAATAATATGCTTGAA\n+ACGGCTGTTTTCTGCCACCTGCCGGAAAAAAGAAATCCCTGATAATGTCTGATTATCAGGGATTTGCTTG\n+ATTTTTCTTTTGTTTTCAGTGATCCGGTTTGGCGTTCAGCGATGTGAAAGACTTATCACCTGAACACTTG\n+GTAAAAGACAATAAAGGGGAACTTTGGATAAGGAAGAACCGCCAAAAGACTAAAATCATGTGTAACATTC\n+CTGTGCTACCTGTAGCAGTTTCAATACTTGAAAAGTATAAAAATGTGGCAGAATGCACTGGAAAACTATT\n+GCCTGTATTGAGCAATCAGCGCATGAACAGTTATTTGAAAGAAATTGCCGATGTGTGCGGAATTCATAAA\n+AATCTTAGCACTCATACCGCCCGTCATAGCTATGCCACAAGCATTTGCCTTGCAAATGGCGTGAGTATGG\n+AGAATGTTGCTAAGATGTTAGGTCATGCAGATACTAGCATAACAAAACACTATGCAAGGGTATTGGATCA\n+GAATATTTTCAAGGATATGCAAAAAGTAAATAGCTGTTTATCAGAATTAACTATATAATAAAGGTAATAG\n+GCAATATAGAAAAAGGATTGGGAAGAATGAATTTCATTTTCTCAACCTTTTTCTTTTAAGGTAAGTTTTC\n+CAAAACTTCAATATGAAGCATTGACAAAGGTAAGTTCCGCATTTAGCCTGTTCAAGTCCGAGCCTTCGGT\n+TTGAATAAAAACCTTCCTCTCCATTTCATTCCGAGCGTATTTTTATCCAAAGACTTGCACAGACTAAATA\n+CTTCACTGGAAAAGTCAATGATTCAAATTAAATTCCGAAAAACAATGTTTTTGGCTTGACAGGTTACTCT\n+TTCCAACTTTCAAAGTAGTGCTTTTGGAGCAGTTTATCAATATCACTCTGACGGTAGATGATTTTACCTT\n+TTATCTGGATAAAGGGGATTAGACCTGTATCTCGCCATTCTTGCAGGGTTCGCAAACTGACATTCAGTTT\n+CTTGGAAACTTCATGGTTGGAAAGAAAGCGCTCCCCATTCAGATGGGGCTTGTAATGCTTTACAATGGAT\n+TTAATACCGTTCAGCATCGAATCAAGCGAAGAAATAAATTCTTTGACTTGCGGAGTATCTTTATTTATTA\n+GTTCCATGATTGAAAGATTGTTTTATTGAAATATTGATTTCAAGATTGCTATATGGCTGGTTAGTTACGC\n+AGATAGTCACCAAGTGATGAAATGCTAAGTACATCTTTTACCGGATCATAATCTATATAGAGCAGTTTGG\n+ATGCTGTGGCAATAAAATACTGGCTACCATCTTGTTGTATCTCATAAGTAGCGGGTGAAGCTTGTTTAGT\n+GGTTTCCGATACATATATAATAGAAAGAAGGTACTCTTTATCGCTCCGATAAATGATTATCGTAGGATTC\n+AGATTAACGCTTTCCCATGTGCCGACAATGGAAAACAGGTTAAAAGACGGATAATCTTTTTTAATTCTTT\n+TCATAAGACGTGGTTTGTTTGGGTGATTGATTCTGTATTTCACTGTCCGCAATAATTCTTTCAATATCGG\n+AAGACTTATAATAAATCTTGCTGCCGATTTGAGAATAAGCCAGCCGTCCACTACTTCGGTAATATTGCAG\n+TGTTCGTTTACTAAAACCTAACAACAGGCACACCTCTTGACTATCCAGCCAGTTTTCTACTTTCTGGGTA\n+TGAGTATTGCACAAACTTTCTATTCGTTTGGCAAACTCGGTGAACCGTTCGCAGATATACGAAAAAGTTC\n+TTTTTTCAATGGTTACTACTTCCATACTTTTAATTTTTAATGGTTTATAAAACGTGTTGATTCTATTTTC\n+ATCGGCAAATGAAAGAAGAATCAAGAGACGTTTTAAAAACTGTCTGGAAGTGGTGAGATTTGACTATTGC\n+TGGCTTCTTATTGAAATAAGAAAACAGATAAATAGTATATATGTTATCGCTGAAATATATTAGATTAAGA\n+ATAGATACGCATCATATTGCCTTATTATTTTTTCTGAAACTTGAAGGACTACAGCCTTTGTTTTTTCTAA\n+AGAATTTACTCAAATGGCTTTCATCGGTAAATCCTAGTTCTTCGGCAATCTCATTTATTCTCATTTGACT\n+ATGTAACAATCTGCTTTCGACCAATTTTAGTTTATAGCTTAATATGTATTGCTGCATTGTTTCGTTGGTG\n+TGCTTTTTTATATAACGTCCCAAGTAACTTTCAGATATACCAAGATGCTGACTGATTTCTTTTGCTCTAA\n+TTTTACCTGTTTGATAGATATTTGCTTGGATATATTGAAGAATATCGAGAGACTTATCATCTGAACATTC\n+ATCGACTTGTTGAGGTAAAAACATAGCTATATTTCTTGCCACAACAATAATTATAGTATTTATCAACTGC\n+GTGATAATCTCTTTACTATACAGATTCCGATTTACATACTCCCGAATAATTGCTTCAATCATTGGTTTCA\n+CTAATAACTTATCCACCTTATTTCTAAGGATGCAACCCGGTTGATGATTTGCATGTTGTAAAATAAATTC\n+TAATCTCTGGATGTTCTCTGAACCAAATATGGCTGAATGTATATAGATGTCATTAAACTTGATGTTAATG\n+AATTTTGTAGTTGTGTGAATCTCAAAGGAATGAGAATCATTTGGAGTTATCAAGAACAAGTGTCCATCAT\n+GATATGGGAACATACTATTGTTAATCCATTGAATACCTGTTCCTGTTAAGATGTAGACTAGTTCAAAAAA\n+AGTATGCTCATGCTCAGTTAATAACGATTCACTATGCTCGTTAAAGCTGAGCTCAAATGGTTGATGAAGA\n+TTTTCTTTTTTCATACCTCAAATATAACACATAAAGCGGAATTATACCAATATAGCGAAAATATATACCC\n+ATATTTAG'..b'TCGCGCATCGGAGATATTGGCCATGGCAACCGGATTATCTTCGAGTATGAATTCCG\n+GATTGTCGGATGTATATACTTTCACCTGCCCCTTGATGAGAGGAGTCGTTTCCCATTTAAGAATACAGTT\n+TCCTATATTATTCTCTTCGCAAACCACCGAAATGTTAGGAGACATGTCTGTGCACGAAGGCAGAATAAGT\n+AAAATAGTTAGTAAATTGAACAGGTTCTTGTACATAGTTTGTATTTGTCTGAAAGCACTAATTGCAAAGA\n+TAGGAATTCTCGTTACATGGTATAATTACTTTGCGATAATTAGGCAACGTTAATAGTAATTAGCTACGAA\n+TTGCAGGCTACAAGCTACAGGTAACCGTGCCGGATGACTGTACATTCATTCGCAGTTTGTAGCCCGTAGC\n+TTATTGCTTTCAACGGTAGTTGGCCGCAAACTCCCCGGATATGGAGTTGTTGAAACTTTTGCAGACTTCG\n+GCTGCAAAGTCTTGTCCGCATTGTATCACTTTATCCCAGGTCTCTTCACTCAGGTGTTGCAAGTCACGGT\n+ACCGGACGTCGTACTTTAGCATGCCGTAGATCAGCCCGGCATTAAAATTGTCTCCTGCACCGATAGTGCT\n+GACTGCCTCTAATGGCGCGACAGGATACTCTTTGGATATTGCGTTCGTACGCAGTGAGATTCTTTCGGCT\n+CCAGCTGTGCAAAGGAAGAGCGGACAATAGAACTTTATCTTGTCCTTGTAGATTTTTTCTACGTCTTTGA\n+TTCCGTACATATAATAGAAGTCTTCCAAAGAGCCTCTTACAATGTCGGCATATTCCAGGTTCTCGATAAT\n+GGTCGGAGTCAGTTTCATCGCTTCATTCTTGTGTGAGGATCGGAAATTGGGATCGTAGTATACAATCGCT\n+CTTTTCTCTTTTGCTATGTCCAGCAGTTCCAATATCTTATCACGCAATACCGGATTGAGAGCATAATATG\n+AACCGATGACAATGATGTCGTCTTCATTGATGGACGGGAATAAAACGTCCAGCCGCTGTTTGGGGTAGTC\n+TTTATAGAAGATATATTCTGCATCGCTGTGTTCGTTGAGGAAAGCCAGGGATACGGGCGATTTGCCGTCC\n+GGAAACACGTTGACGTGATCCGTCGGGATGTGATTGTCACGCATGAATTGCAGAATGATGTTTCCTACAT\n+GGTCATTCCCTGTTTCACTGATGAAGCATACATTGACTCCCATGCGTCCCAAAGAAACGATGCCGTTGAA\n+TACAGAGCCTCCGGGAACGGCTGCCGAAGGCTGGTCGTTCCGGAAGATGATATCGAGTATAGTCTCTCCG\n+ATGCCGATTACTTTACGCATAGTTTTCTTGATTTTTCGCCCAAGTAACCACCGTGATGGCGTTTGGAGTA\n+TTCTTCAATAGTAAATTCGGTCCTTTTCATGGTTTGCACTACGAGAATATCGCCGATGACGGTCATTACC\n+GTAGTCGAAGTGGTCGGAGTCATCCCCAGGGTACAAACTTCGGCAGGATGTCCTGTGCTCAGGCATACAT\n+CCGATTCGCTGGCAAGCGGACTGTCCGGATTGCCGGTGATGACAATGAAACGGGTTCCGGCATCTACGGC\n+AAATCCGCAATAAGCCACCTTCGAAGAAGAGGGTTCATGAATAATGCGAAGTCCATTGGACAGGGTATGT\n+ATATTATATTGCATTTCTGCACGGGTACTTAACTGCTTCATTCTTACTATTAAGTTAGGTTGAGGACACA\n+AAAATACAATAAAACTTATTGTCGTTTATAGAAAATTGCAGATATTTGTAAGCTATAACATCAATAACCC\n+TTATGGAGAAGATAGGAATTTTCTGTTCCGCATCCGGCAGCATCGACCCGATATACTTCGATGCCGCCCA\n+TCAGATTGGCGAATGGATGGGGAAAAACGGCAAGACACTTATCTATGGTGGTGCCAACCTCGGACTCATG\n+GAATGCGTGGCCAAAGCAGTCAAAGAAAACGGGGGACATGTCATCGGTGTAGTACCTTCCAAACTGGAAG\n+AAAACGGCAAAGTGAGTACATACCCCGATGAGATAATCGCCACACACGACCTGAGCGACCGCAAGGATAT\n+CATCCTGCAACAATCGGATGTATTGGTGGCCCTTCCCGGCGGCATAGGCACGCTGGATGAGGTATTTCAT\n+GTCATGGCAGCCGCTTCCATCGGCTATCATCAGAAGAAAGTGATCTTCTACAATGCAGATGGTTTCTACA\n+ACCCACTGCTCGCCGTGCTCAGCGAATTACAGACAAGAGGATTCACCCGTCACCCTCTGTCCTCCTATTA\n+TGAAGTAGCAAACACATTTAATGAATTAACAATTAAGATATAATGATTGAATCTATTCAAGAACTCCTGC\n+AAAAGGAAGCACAAGCTGTGCTGAATATTCCTGTGACTGATGCCTACGAAAAGGCCGTTGAATTAATAGT\n+GGAACAAATACACAGAAAAAAAGGCAAACTTGTAACTTCCGGCATGGGTAAAGCCGGACAAATAGCGATG\n+AACATCGCCACTACGTTTTGTTCGACCGGAATTCCCTCTGTCTTCCTGCACCCCAGCGAGGCACAACACG\n+GCGATCTGGGCATCCTGCAAGAGAACGACCTGTTATTATTGATTTCAAATTCAGGTAAAACCCGTGAAAT\n+CGTAGAGTTAACCCAGCTGGCCCACAACCTGAATCCGGGTCT\n+>k141_1208\n+ATTTTTTTCCTGAAGCGGAAAACATTACTACAGTACCTTGAACCTTGGTTTTAACATTCTCGAAATGCTC\n+TGAGAGTATATGTGTTAAGCCTTCTTCGGAATCTTTTGTGTTTGAAAAGATGCCTTTCTGATTGTAAATG\n+CGCATCAGTTTTTGACCGAAGCTATTGTGCACAACTCCATCGCCAAGAATTGTGGCTCCGTATAGAGTTC\n+CATCGTCAGTTAAGGCCTGCGCCGCATTGCGTATTACACAGCTTTTTGTAGATATATTTCCAGGCAGGCA\n+GTGAAGAAGGTAAGACATGGAAATGGAATCAAATTGACCATGTAACGCCGCGGGATAAGGTTCAAAAACA\n+TCATGGCTAATTTTATGTTTAATTTTTGATTCCCCAGCCCTTGTAGATGCCGCGTTCAGGCTAGCTTCGT\n+TCAAATCCATTAAAGATATCAGACTACTCTCAGGTACGTGAGTAAGGTAAAACCCAGTTCCAACACCAAT\n+ATCCAGATGGTTGTTACCTAAATGTTCCAGAAAGTGTGGAAGAAGGTGTTCCTTTGTAGGACATCCCCAT\n+GCAAGCCGATTTGATACTCCCAAAACCCACCAGTCATAAAGCTTTAGGGTAAGTGGTGTGTAAATTCTAG\n+CCCCATCATCTGTGTTTTTTTATTAATTTCACCATGTTATAGTTTTATTTGTGAATTAAATCAATTATGG\n+CAATGAATTACAAGGGGTTAAATGCTGCCGCAGCATAGCGATATTGAAATAGCCTGGTATGCTTCAATAC\n+AGCAGGAGCCGAATGGCTGGAAGACCGTCACCACACAGTTCTACATCCAGGAATTCAGTGAGTATATTGC\n+GCCACTGCAGGATGCTGTAGATCTGGAAATCGCAACGGAGGAAGAAACCTCATTGCTGGAAGCCTGGAAA\n+AAATATCGGGTGTTGCTGAACCGTGTTGATACATCAACTGCACCTGATATTGAGTGGCCTACGAACCCTG\n+TCAGGGAGTAATCATTGGGATTATGCCGCAGCACGTCTTAAGCAAGAACATGCTGCGGTTGGATGCTATT\n+TTTTTCCTGAAGCGGAAAACATTACTACAGTACCTTGAACCTTGGTTTTAACATTCTCGAAATGCTCTGA\n+GAGTATATGTGTTAAGCCTTCTTCGGAATCTTTTGTGTTTGAAAAGATGCCTTTCTGATTGTAAATGC\n' |
| b |
| diff -r 8a0473eb465e -r 2bc40bfbcfb4 test-data/4/out.abund1 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/4/out.abund1 Mon Oct 16 07:46:13 2023 +0000 |
| b |
| b'@@ -0,0 +1,500 @@\n+k141_100\t0.370508982035928\n+k141_101\t0.427843803056027\n+k141_102\t0.245136186770428\n+k141_103\t0.518518518518518\n+k141_1035\t0.00643136053900926\n+k141_1036\t0.828947368421053\n+k141_1037\t0.076271186440678\n+k141_1038\t0.157795867251096\n+k141_1039\t0.402555910543131\n+k141_104\t0.375558867362146\n+k141_1040\t0\n+k141_1041\t0.45\n+k141_1042\t0.0776818742293465\n+k141_1043\t0.126126126126126\n+k141_1044\t0.0102090422946038\n+k141_1045\t0.473684210526316\n+k141_1047\t0.0960731986275257\n+k141_1048\t0\n+k141_1049\t0.30526953361599\n+k141_105\t0.613138686131387\n+k141_1050\t0.382397572078907\n+k141_1051\t0.338255033557047\n+k141_1052\t0.431506849315068\n+k141_1053\t0.4921875\n+k141_1054\t0.715909090909091\n+k141_1055\t0.243478260869565\n+k141_1056\t0.622222222222222\n+k141_1057\t0.49802371541502\n+k141_1058\t0.101204819277108\n+k141_1059\t0\n+k141_106\t0.257668711656442\n+k141_1060\t0.724137931034483\n+k141_1061\t0.540772532188841\n+k141_1062\t0.379518072289157\n+k141_1063\t0\n+k141_1064\t0.36734693877551\n+k141_1065\t0.268943436499466\n+k141_1066\t0.0342717258261934\n+k141_1067\t0.454054054054054\n+k141_1068\t0.295081967213115\n+k141_1069\t0.812903225806452\n+k141_107\t0.199683042789223\n+k141_1070\t0\n+k141_1071\t0.815533980582524\n+k141_1072\t0.672\n+k141_1073\t0.696132596685083\n+k141_1074\t0.0395977372721559\n+k141_1075\t0.810289389067524\n+k141_1076\t0.785046728971963\n+k141_1077\t0.0356687898089172\n+k141_1078\t0.752238805970149\n+k141_1079\t0.561247216035635\n+k141_108\t0.586046511627907\n+k141_1080\t0.663157894736842\n+k141_1081\t0.763636363636364\n+k141_1082\t0.518518518518518\n+k141_1083\t0.810289389067524\n+k141_1084\t0.23977164605138\n+k141_1085\t0\n+k141_1086\t0.466666666666667\n+k141_1087\t0.545454545454545\n+k141_1088\t0.115915363385465\n+k141_109\t1.07843137254902\n+k141_110\t0.521739130434783\n+k141_111\t0.50501002004008\n+k141_112\t0.0453972257250946\n+k141_113\t0.681081081081081\n+k141_114\t0.311111111111111\n+k141_1144\t0.0147394279698193\n+k141_1145\t0.705882352941177\n+k141_1146\t0.472795497185741\n+k141_1147\t0\n+k141_1148\t0.0435609334485739\n+k141_1149\t0.0136874694476128\n+k141_115\t0.785046728971963\n+k141_1150\t0.243008678881389\n+k141_1151\t0\n+k141_1152\t0.571428571428571\n+k141_1153\t0.288990825688073\n+k141_1154\t0\n+k141_1155\t0.747774480712166\n+k141_1156\t0\n+k141_1157\t0.316185696361355\n+k141_1158\t0\n+k141_1159\t0.826229508196721\n+k141_116\t0\n+k141_1160\t0.485549132947977\n+k141_1161\t0\n+k141_1162\t0.326848249027237\n+k141_1163\t0\n+k141_1164\t0.6\n+k141_1165\t0.4375\n+k141_1166\t0.242540904716073\n+k141_1167\t0.170963364993216\n+k141_1168\t0\n+k141_1169\t0.266666666666667\n+k141_117\t0\n+k141_1170\t0.619164619164619\n+k141_1171\t0.43979057591623\n+k141_1172\t0.62531017369727\n+k141_1173\t0.13614262560778\n+k141_1174\t0.278145695364238\n+k141_1175\t0.457350272232305\n+k141_1176\t0.818181818181818\n+k141_1177\t0.394984326018809\n+k141_1178\t0.292004634994206\n+k141_1179\t0.0637007077856421\n+k141_118\t0.104564315352697\n+k141_1180\t0.241379310344828\n+k141_1181\t0.276923076923077\n+k141_1182\t0.917883211678832\n+k141_1183\t0.0356637418624399\n+k141_1184\t0\n+k141_1185\t0\n+k141_1186\t0.756756756756757\n+k141_1187\t0.28\n+k141_1188\t0.649484536082474\n+k141_1189\t0.628428927680798\n+k141_119\t0.348547717842324\n+k141_1190\t0.156424581005587\n+k141_1191\t0.250996015936255\n+k141_1192\t0.080846968238691\n+k141_1193\t0\n+k141_1194\t0.728323699421965\n+k141_1195\t0.668435013262599\n+k141_1196\t0.295081967213115\n+k141_1197\t0\n+k141_1198\t0.285067873303167\n+k141_1199\t0\n+k141_120\t0.0738786279683377\n+k141_1200\t0.137554585152838\n+k141_1201\t0.0296052631578947\n+k141_1202\t0.4921875\n+k141_1203\t0.0394366197183099\n+k141_1204\t0.543103448275862\n+k141_1205\t0.381240544629349\n+k141_1206\t0\n+k141_1207\t0.644501278772379\n+k141_1208\t0\n+k141_199\t0.035264483627204\n+k141_200\t0.660550458715596\n+k141_201\t0.132492113564669\n+k141_202\t0.0912052117263844\n+k141_203\t0.0755848830233953\n+k141_204\t0.329842931937173\n+k141_205\t0.818181818181818\n+k141_206\t0.200636942675159\n+k141_207\t0.53276955602537\n+k141_208\t0.444444444444444\n+k141_209\t0.566292134831461\n+k141_210\t0.420701168614357\n+k141_211\t0.476370510396975\n+k141_212\t0.0797973400886637\n+k141_213\t0.5260'..b'75\n+k141_655\t0\n+k141_656\t0.647814910025707\n+k141_657\t0.73469387755102\n+k141_658\t0.0632847815168257\n+k141_659\t0.158790170132325\n+k141_660\t0.0751117734724292\n+k141_661\t0.256880733944954\n+k141_662\t0.395604395604396\n+k141_663\t0.464088397790055\n+k141_664\t0.831683168316832\n+k141_665\t0.45\n+k141_666\t0.679245283018868\n+k141_667\t0.684782608695652\n+k141_668\t0.0763173834039976\n+k141_669\t0.67379679144385\n+k141_670\t0.601431980906921\n+k141_672\t0\n+k141_673\t0.756756756756757\n+k141_674\t0.571428571428571\n+k141_675\t0.670212765957447\n+k141_676\t0.705882352941177\n+k141_677\t0.722063037249284\n+k141_678\t0.724137931034483\n+k141_679\t0\n+k141_680\t0.411092985318108\n+k141_681\t0.276619099890231\n+k141_682\t0\n+k141_683\t0.39873417721519\n+k141_684\t1.21153846153846\n+k141_685\t0.775384615384615\n+k141_686\t0\n+k141_687\t0\n+k141_688\t0.292004634994206\n+k141_689\t0.754491017964072\n+k141_690\t0.62531017369727\n+k141_691\t0.613138686131387\n+k141_692\t0.417218543046358\n+k141_693\t0.401913875598086\n+k141_694\t0.112\n+k141_695\t0.260330578512397\n+k141_696\t0\n+k141_697\t0.346629986244842\n+k141_698\t0.561247216035635\n+k141_699\t0.143671607753706\n+k141_700\t0.310727496917386\n+k141_701\t0.224199288256228\n+k141_702\t0.537313432835821\n+k141_703\t0\n+k141_704\t0.613138686131387\n+k141_705\t0.42\n+k141_706\t0.679245283018868\n+k141_707\t0.173673328738801\n+k141_708\t0.692307692307692\n+k141_709\t0.0254519745480255\n+k141_710\t0.761329305135952\n+k141_711\t0.478178368121442\n+k141_712\t0.0670926517571885\n+k141_713\t0.364161849710983\n+k141_714\t0.152542372881356\n+k141_715\t0.626865671641791\n+k141_716\t0.619164619164619\n+k141_717\t0.252252252252252\n+k141_718\t0.310727496917386\n+k141_719\t0.794303797468354\n+k141_720\t0.639593908629442\n+k141_722\t0\n+k141_723\t0.350974930362117\n+k141_724\t0.473684210526316\n+k141_725\t0.478178368121442\n+k141_818\t0.770642201834862\n+k141_819\t0\n+k141_820\t0\n+k141_821\t0.583333333333333\n+k141_822\t0.402555910543131\n+k141_823\t0.773006134969325\n+k141_824\t0.464944649446494\n+k141_825\t0.759036144578313\n+k141_826\t0.519587628865979\n+k141_827\t0.50501002004008\n+k141_828\t0.380090497737557\n+k141_829\t0.580645161290323\n+k141_830\t0.580645161290323\n+k141_831\t0.810289389067524\n+k141_832\t0.679245283018868\n+k141_833\t0.0452342487883683\n+k141_834\t0.0905172413793103\n+k141_835\t0.0887323943661972\n+k141_836\t0.0179922890189919\n+k141_837\t0\n+k141_838\t0.48742746615087\n+k141_839\t0.0691927512355848\n+k141_840\t0.0425675675675676\n+k141_841\t0\n+k141_842\t0.266949152542373\n+k141_843\t0.392523364485981\n+k141_844\t0.0456852791878173\n+k141_845\t0.375\n+k141_846\t0\n+k141_910\t0.271551724137931\n+k141_911\t0.355430183356841\n+k141_912\t0.110043668122271\n+k141_913\t0.754491017964072\n+k141_914\t0.679245283018868\n+k141_915\t0.282511210762332\n+k141_916\t0.25\n+k141_917\t0.103067484662577\n+k141_918\t0.035876993166287\n+k141_919\t0.21105527638191\n+k141_920\t0.278453038674033\n+k141_921\t0.073900293255132\n+k141_922\t0.526096033402923\n+k141_923\t0.666666666666667\n+k141_924\t0.722063037249284\n+k141_925\t0.696132596685083\n+k141_926\t0.0364794441227562\n+k141_927\t0.288329519450801\n+k141_928\t0.451612903225806\n+k141_929\t0.56\n+k141_930\t0.63\n+k141_931\t0.794952681388013\n+k141_932\t0.127465857359636\n+k141_933\t0.8\n+k141_934\t0.724137931034483\n+k141_935\t0\n+k141_936\t0.37444279346211\n+k141_937\t0.424242424242424\n+k141_938\t0.301075268817204\n+k141_939\t0.684782608695652\n+k141_940\t0.39873417721519\n+k141_941\t0.0897755610972569\n+k141_942\t0.752238805970149\n+k141_943\t0.150089338892198\n+k141_944\t0.362589928057554\n+k141_945\t0\n+k141_946\t0.780185758513932\n+k141_947\t0.295081967213115\n+k141_948\t0.27968923418424\n+k141_949\t0.316582914572864\n+k141_950\t0.326848249027237\n+k141_951\t0.235514018691589\n+k141_952\t0\n+k141_953\t0\n+k141_954\t0.454873646209386\n+k141_955\t0.763636363636364\n+k141_956\t0.355430183356841\n+k141_957\t0.777777777777778\n+k141_958\t0.686648501362398\n+k141_959\t0.50199203187251\n+k141_960\t0.65625\n+k141_961\t0.782608695652174\n+k141_962\t1.25373134328358\n+k141_963\t0.595744680851064\n+k141_964\t0.298932384341637\n+k141_965\t0.571428571428571\n+k141_966\t0.805111821086262\n+k141_967\t0.010816843370391\n+k141_99\t0.0172875077176374\n' |
| b |
| diff -r 8a0473eb465e -r 2bc40bfbcfb4 test-data/4/out.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/4/out.log Mon Oct 16 07:46:13 2023 +0000 |
| [ |
| @@ -0,0 +1,64 @@ +MaxBin 2.2.7 +Input contig: /tmp/tmpc9eyur_0/files/f/d/a/dataset_fda5399c-97b7-4ad2-bbe6-0f90e5e51369.dat +out header: out +Min contig length: 1000 +Max iteration: 50 +Probability threshold: 0.5 +Thread: 1 +Located reads file [test4_reads.fastqsanger_0] +Located reads file [test4_reads.fastqsanger_1] +Running Bowtie2 on reads file [test4_reads.fastqsanger_0]...this may take a while... +Running Bowtie2 on reads file [test4_reads.fastqsanger_1]...this may take a while... +Searching against 107 marker genes to find starting seed contigs for [/tmp/tmpc9eyur_0/files/f/d/a/dataset_fda5399c-97b7-4ad2-bbe6-0f90e5e51369.dat]... +Try harder to dig out marker genes from contigs. +Done data collection. Running MaxBin... +Command: /home/gitpod/miniconda3/envs/__maxbin2@2.2.7/opt/MaxBin-2.2.7/src/MaxBin -fasta out.contig.tmp -abund out.contig.tmp.reads.abund1 -abund2 out.contig.tmp.reads.abund2 -seed out.seed -out out -min_contig_length 1000 -max_run 50 -prob_threshold 0.5 +Minimum contig length set to 1000. +Reading seed list... +Looking for seeds in sequences. + k141_99 [0.017288] [0.017288] + k141_239 [0.015466] [0.015466] +Get 2 seeds. + +Start EM process. +Iteration 1 +Iteration 2 +Iteration 3 +Iteration 4 +Iteration 5 +Iteration 6 +Iteration 7 +Iteration 8 + +EM finishes successfully. + +Classifying sequences based on the EM result. +Minimum probability for binning: 0.50 +Ignoring 0 bins without any sequences. +Number of unclassified sequences: 0 (0.00%) +Elapsed time: 0 days 00:00:01 + +Deleting intermediate files. + + +========== Job finished ========== +Yielded 2 bins for contig (scaffold) file /tmp/tmpc9eyur_0/files/f/d/a/dataset_fda5399c-97b7-4ad2-bbe6-0f90e5e51369.dat + +Here are the output files for this run. +Please refer to the README file for further details. + +Summary file: out.summary +Genome abundance info file: out.abundance +Marker counts: out.marker +Marker genes for each bin: out.marker_of_each_gene.tar.gz +Bin files: out.001.fasta - out.002.fasta +Unbinned sequences: out.noclass +Marker plot: out.marker.pdf + +Store abundance information of reads file [test4_reads.fastqsanger_0] in [out.abund1]. +Store abundance information of reads file [test4_reads.fastqsanger_1] in [out.abund2]. + + +========== Elapsed Time ========== +0 hours 0 minutes and 3 seconds. + |
| b |
| diff -r 8a0473eb465e -r 2bc40bfbcfb4 test-data/4/out.marker --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/4/out.marker Mon Oct 16 07:46:13 2023 +0000 |
| b |
| @@ -0,0 +1,3 @@ + Total marker Unique marker PGK Ribosomal_L23 Ribosomal_L5 Ribosomal_L3 Ribosomal_L6 Ribosomal_S17 Ribosomal_S9 Ribosomal_S8 Ribosomal_S11 Ribosomal_S13 Ribosomal_L10 Ribosomal_L4 tRNA-synt_1d GrpE Methyltransf_5 TIGR00001 TIGR00002 TIGR00009 TIGR00012 TIGR00019 TIGR00029 TIGR00043 TIGR00059 TIGR00060 TIGR00061 TIGR00062 TIGR00064 TIGR00082 TIGR00086 TIGR00092 TIGR00115 TIGR00116 TIGR00152 TIGR00158 TIGR00165 TIGR00166 TIGR00168 TIGR00234 TIGR00337 TIGR00344 TIGR00362 TIGR00389 TIGR00392 TIGR00396 TIGR00409 TIGR00414 TIGR00418 TIGR00420 TIGR00422 TIGR00435 TIGR00436 TIGR00442 TIGR00459 TIGR00460 TIGR00468 TIGR00472 TIGR00487 TIGR00496 TIGR00575 TIGR00631 TIGR00663 TIGR00755 TIGR00810 TIGR00855 TIGR00922 TIGR00952 TIGR00959 TIGR00963 TIGR00964 TIGR00967 TIGR00981 TIGR01009 TIGR01011 TIGR01017 TIGR01021 TIGR01024 TIGR01029 TIGR01030 TIGR01031 TIGR01032 TIGR01044 TIGR01049 TIGR01050 TIGR01059 TIGR01063 TIGR01066 TIGR01067 TIGR01071 TIGR01079 TIGR01164 TIGR01169 TIGR01171 TIGR01391 TIGR01393 TIGR01632 TIGR01953 TIGR02012 TIGR02013 TIGR02027 TIGR02191 TIGR02350 TIGR02387 TIGR02397 TIGR02432 TIGR02729 TIGR03263 TIGR03594 +out.001.fasta 5 4 1 1 2 1 +out.002.fasta 7 7 1 1 1 1 1 1 1 |
| b |
| diff -r 8a0473eb465e -r 2bc40bfbcfb4 test-data/4/out.marker.pdf |
| b |
| Binary file test-data/4/out.marker.pdf has changed |
| b |
| diff -r 8a0473eb465e -r 2bc40bfbcfb4 test-data/4/out.summary --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/4/out.summary Mon Oct 16 07:46:13 2023 +0000 |
| b |
| @@ -0,0 +1,3 @@ +Bin name Abundance Completeness Genome size GC content +out.001.fasta 0.08 3.7% 248903 52.2 +out.002.fasta 0.03 6.5% 445717 43.2 |
| b |
| diff -r 8a0473eb465e -r 2bc40bfbcfb4 test-data/4/out.tooshort --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/4/out.tooshort Mon Oct 16 07:46:13 2023 +0000 |
| b |
| b'@@ -0,0 +1,3293 @@\n+>k141_910 flag=1 multi=4.3596 len=928\n+GGCAATGGCCTCTCTTCCTATCCGCACCCGAAACTGATGCCGGAATTCTGGCAGTTCCCGACCGTATCTA\n+TGGGTCTGGGTCCGATTGGTGCTATTTACCAGGCTAAATTCCTGAAATATCTGGAACACCGTGGCCTGAA\n+AGATACCTCTAAACAAACCGTTTACGCGTTCCTCGGTGACGGTGAAATGGACGAACCGGAATCCAAAGGT\n+GCGATCACCATCGCTACCCGTGAAAAACTGGATAACCTGGTCTTCGTTATCAACTGTAACCTGCAGCGTC\n+TTGACGGCCCGGTCACCGGTAACGGCAAGATCATCAACGAACTGGAAGGCATCTTCGAAGGTGCTGGCTG\n+GAACGTGATCAAAGTGATGTGGGGTAGCCGTTGGGATGAACTGCTGCGTAAGGATACCAGCGGTAAACTG\n+ATCCAGCTGATGAACGAAACCGTTGACGGCGACTACCAGACCTTCAAATCGAAAGATGGTGCGTACGTTC\n+GTGAACACTTCTTCGGTAAATATCCTGAAACCGCAGCACTGGTTGCAGACTGGACTGACGAGCAGATCTG\n+GGCACTGAACCGTGGTGGTCACGATCCGAAGAAAATCTACGCTGCATTCAAGAAAGCGCAGGAAACCAAA\n+GGCAAAGCGACAGTAATCCTTGCTCATACCATTAAAGGTTACGGCATGGGCGACGCGGCTGAAGGTAAAA\n+ACATCGCGCACCAGGTTAAGAAAATGAACATGGACGGTGTGCGTCATATCCGCGACCGTTTCAATGTGCC\n+GGTGTCTGATGCAGATATCGAAAAACTGCCGTGACTTGTTCTTCAGCATCACGTTCAGAGCACGAACGAA\n+AGCGATAGTGGTAGAGATCTCTTTGCTCTGCTCTTCCAACAGCGCGCCGAAGTCTTGCAGGCTCGGCAGC\n+TCAAGCTTCTCGGTGAAG\n+>k141_818 flag=1 multi=1.9677 len=327\n+TAAAGTTTTTCTTTAGTTCGGACTTATTGACTATATTAATTGTTTGTTCAAGGCCTCTGAGATTTTTCTC\n+AAGATGGTGATGCAGATTTAACCCTGTTGTCGTCGGCGCGATACCTTTTCCTGATCACATGAGTAAGGAA\n+AATACGCTACAACAGGCCGTGGGGTTGCCCGATCAGAAAACGCTTAATATCATTATGGGGAATAAATAAA\n+AGGTAATTCATGGATGGTTGAACTATATCCCTGCTTTTCAACCATCCTAAAAAAGCATGAATTGCTCGCT\n+CTGCCCTAAGTGGCTGTGCTATTTTAGAAAAACTTAATCCTGAGTTA\n+>k141_335 flag=1 multi=3.2506 len=564\n+GCGTGGGCCATCACCAGCTTTTTCTCTTCGTCGATTTGCAGCAGAGGCTGGCGCCGCAGCCAGTTAAGCA\n+GCTCGTCGGCATCCGGCGCTTCCAGCAGCGGTGTCAGGCGATCTTTCGGTTTATTGTGGAATTCGCTGAA\n+TACCGATTCCCAGTCATCCGGCTCGTAATCCGGGAAATGGGTGTTGCCTTCCACTTCTGCGTCGATATGC\n+GTCAGATACAGTTTTTGCGCTTTTGGCAAGAACTGTTCATAAACGCGACCGCCGCCAATCACCATGATTT\n+CTGGTACGTCACCACACGCCGCGATGGCTTCATCCACCGACTTCACCCACGTTACGCGATCGTCCGTACC\n+CGGTTGACTGCTGAGGATAATATTTTTGCGTCCTGGCAACGGACGACCGATTGATTCCCAGGTATGGCGG\n+CCCATAATCACGGGTTTATTTAAGGTGTTGCGTTTAAACCAGGCGAGATCGGCAGGCAGGTTCCACGGCA\n+TGGCGTTTTCCATGCCGATAACGCGATCTACCGCTAACGCCGCAATCAGACTGATCATTGAGATTTCCCG\n+ATAA\n+>k141_819 flag=1 multi=5.0000 len=306\n+AAACTATGGAACAGGCGATGCGCTTGCTGGCTCCGCGTGTTCAGCCGGGCGATATGGTTCTGCTCTCCCC\n+AGCCTGTGCCAGCCTTGATCAGTTCAAGAACTTTGAACAACGAGGCAATGAGTTTGCCCGTCTGGCGAAG\n+GAGTTAGGTTGATGCGTTTATCTCTCCCTCGCCTGAAAATGCCGCGCCTGCCAGGATTCAGTATCCTGGT\n+CTGGATCTCCACGGCGCTAAAGGGCTGGGTGATGGGCTCGCGGGAAAAAGATACCGACAGCCTGATCATG\n+TACGATCGCACCTTACTGTGGCTGAC\n+>k141_336 flag=1 multi=5.3434 len=473\n+CTATCGGCATACAACGTTCCGTCAGCCAATGTCAGTTGAACAGCCGGGAAGCTATTCAGAAATTCAGTCT\n+GAGAACCGTCCTGACGGATCAGGTTCAGTAATTCCTTTTCTGTCAGTGAAAAGTAACCGGGTTTATCACT\n+AAACTGAATATTGATGAAGGATCTATGGTCAAAAAAGGACAGGTACTGTTCGTCATCGATCCGGTGCAGT\n+ATGAATCTGCCGCCCGTGCAGCAAAAGCCGCTGTAGCCACAGCTAAAGCGAATGTTTCTACTCAGGAAAT\n+CACTGTAAAAAACAAACGTGAATTAAACAAGAAAAACATCATCAGCGACTATGATCTGGAAATGGCTGAA\n+AATACACTTGCATCTGCAAAAGCTCAATTGGCATCTGCCGAAGCCCAGCTGATCAGCGCTAACCAAAATC\n+TGGCATACACACGCGTAACAAGCCCTTCGGACGGTGTAGCCGGAACAATCCCT\n+>k141_911 flag=1 multi=5.0000 len=709\n+ATGACGAAAGCGCCTGGCGGCACCGTCGTTTCATAAATCTTATAGCCACCTTGCGTAATAGTGACTTTGG\n+CGTTGGTATTGGCAACGCCATGAATGATAGGCGCAAAGCTGGCTAAAGTCGGAGGCAACATGCGGCTGTC\n+ACTGTATAAACGAATGCCTCGGATACTGACGGAATCAAAGGTTTCGCCCGTCGTATAAGACTCACCAAGA\n+ATGAGTTGAGAACGCAGCGAGGCGATATCACGCTGAACATACCGATTCTTAAAATCATAATTACTGCCAG\n+AATCGGTCATCCAGTTGTAGTTGCCCGAGGCACGCAGTCGCCATGCACCTAAATTCATCCCACCGTTAAA\n+TGCAGCATAAATGCTTTCATTTTTTCGACCAGGGGTTTCACTATGATATCCGTTGAGGTTGTATGACAGA\n+AGGTAACCCCGCTATACCGGGTGTTTACGACGTCAGTGTTTATGTAAACGACCAACCAATCATTAACCAA\n+AGTATTACATTTGTCGCAATTGAAGGAAAAAAGAACGCCCAGGCTTGTATCACATTAAAGAATTTATTGC\n+AGTTTCATATTAATTCTCCCGATATAAATAACGAAAAAGCCGTTCTGCTTGCCAGGGATGAAACGCTCGG\n+CAATTGCCTCAATTTGACGGAAATTATCCCTCAGGCTTCTGTTCGTTATGACGTTAACGATCAACGTCTG\n+GATATAGAC\n+>k141_337 flag=1 multi=1.1094 len=333\n+CATAAAGTGACGGAATTTATTGATGATATGGCGGCGGCGTATGCGTGGGCGGATGTCGTCGTTTGCCGCT\n+CCGGTGCGTTAACGGTGAGTGAAATCGCCGCGGCAGGACTACCGGCGTTGTTTGTGCCGTTTCAACATAA\n+AGACCGCCTGCAATACTGGAATGCGCTACCGCTGGAAAAAGCGGGCGCAGCCAAAATTATCGAGCAGATA\n+CGAATGAAATCAATTTCGATGCCATGTTTTGGCACTAAGTCCGCTTCCATACGGTCGGCAGTCCCCAGCC\n+AGCGAACTT'..b'GAAGGCCGTGCTGAAGCGGTGACTTGCGCCGTTATGCAGGAGCTAAAGCGAAT\n+CGTCGCACCGCTGTCGTGATAGTTCACTTCGGTCGCTTTCAACCAGCGTCCGTGACAGTTCGGATTAATA\n+TGATCTTCCATTGATACCGCAACCGCGTCCGGCAGTTTTGCCAGCCAGCGGCGGCCCACTTCATCGTCGG\n+CGTTAATAATCGCCTGACCGCAATGATGCTCAGAATAAAGCAGCCATTTCGCGGCTTCGTAGTGTTCCAT\n+ATCACCATGATAATCAAGGTGATCGCGGCTTAAGTTGGTAAAGACCGACGCCGCAAATTTCAATGCCGCC\n+ACACGGTGCTGTACCAGCCCGTGGGAGGAAACTTCCATTGCGCAAAACGTCGCGCCCTGATCCACCAGCC\n+CCGCCAGCTCATGCTGAACATCGACTGCCGAACCGGTTGTAT\n+>k141_725 flag=1 multi=2.9637 len=527\n+AGCCAAATCATCAGTACCAGTCCTACACACGCCAGTGCGCCCCAGGTAATTTGATCAAATACTTCAATAT\n+ATGCATTGATGGAGTAGTTGATCGCCCCGGAAGCATCAAACGAAGCCTGCGATGTCTGATCGGCAATCAC\n+GCCCGCCAGATAGTTCGCGATCGCGCCAGAAAGCAGCATGTAGATGCCGGTTAATACGCCGGTCACACCG\n+GGGATTTCAATGCGCGTAATTTGCGACATGGCAACCGGGTCGATAAACAGTTCCGCAAAGCCCATCACCG\n+CCAGGCCTAATACCATCAGTGGCAGAGAAGAGTGACCATACATTGCGGACCAGCGGGCGCTTAAGGTCAG\n+AATGCAGAATCCGGCGCTCATCAGGCCAAGGCCAAGAGCAAATTTCCCCCACTTATCAGGCCTACGTATT\n+TCCTGCAATTTATTGAATTTGCACAAATTTGTAGGCTGGATAAGGCGTTCACGCCGCATCCGGCATCTGG\n+GCTCGATTGCCTGACGCGTCTGTTATTTCCCCTTCCG\n+>k141_1202 flag=1 multi=3.6523 len=512\n+AATCCTATGCTAATAAATCTACTTCGAACAGTTATGAAGTGTGAGGCTTGTGGTAATACCATGATTGTTC\n+ATGCGGTATCTGGAAGTTTGCATGGCTATTATGTTTGTCCGATGAGAAGATTACATTATTATCCGTATTA\n+ATTATGATTTTTTCGAATGTTTTATAGGCAAGTGTACGGCATAACTCTCGTCCATTTTTACTGGTTAAGT\n+CAATAGCATAAAAATCACTGAATGAATTTACACCTTTACTCTTCAAAGTTTTCAATGATACCGAAGCCCT\n+TCGTAATTCCTTATCTAATAGTCTTATTTTCTCTGCTATAGCGGTAACTTCAGGCGCGACAGACAATGCA\n+ACGATTAAATTATTAATTTTCATCTGAAGCTCAATAATTTTTAACTCTAAAGTTTCATTAGCATCTTTCT\n+TGTTTTCAACTGGTTGAATTTTGCTACAATTAAAAAGCAATTCATTAATGATATTATAATCAACCAAATC\n+TCTTTTTATTGATGGCCTGTCA\n+>k141_1204 flag=1 multi=3.4644 len=464\n+GCGCGTACAGTCGATGCCCGAAATTAACGATGCCGACAAAACCGTTAAATTACGTGTGAACGTTGATGCG\n+GGTAACCGTTTCTACGTGCGTAAGATCCGTTTTGAAGGTAACGATACCTCGAAAGAAGCTACCGGTGTTG\n+CGCTCTTTTACCTTGTAGACGACATCAACCTGGTCCGGGCTACCCGGAACACGTTGGGTATCGGTATCGA\n+CAGTTTCAAAGAAGCCCAGACGATTCAGACGCTCCTTACCCTGATCGACCAGATCGCTCCCCAGCCATGC\n+ACCTTCCATCTGACGCATTTCGCGACGCAGGACGGCATCTTTCGAGGTATCGTTACCTTCAAAACGGATC\n+TTACGCACGTAGAAACGGTTACCCGCATCAACGTTCACACGTAATTTAACGGTTTTGTCGGCATCGTTAA\n+TTTCGGGCATCGACTGTACGCGCGGATAGGCATAACCATAGCGA\n+>k141_1205 flag=1 multi=3.9462 len=661\n+TGCGTAAACTGGGTATGAAGCCAGGCGAAGCCATTGAACACCCGTGGGTGACTAAAGCGATTGCCAACGC\n+CCAGCGTAAAGTTGAAAGCCGTAACTTCGACATTCGTAAGCAACTGCTGGAATATGATGACGTGGCTAAC\n+GATCAGCGTCGCGCCATTTACTCCCAGCGTAACGAACTGTTGGATGTCAGCGATGTGAGCGAAACCATTA\n+ACAGCATTCGTGAAGATGTGTTCAAAGCGACCATTGATGCCTACATTCCACCACAGTCGCTGGAAGAAAT\n+GTGGGATATTCCGGGGCTGCAGGAACGTCTGAAGAACGATTTCGACCTCGATTTGCCAATTGCCGAGTGG\n+CTGGATAAAGAACCAGAACTGCATGAAGAGACGCTGCGTGAGCGCATTCTGGCGCAGTCCATCGAAGTGT\n+ATCAGCGTAAAGAAGAAGTGGTTGGTGCTGAGATGATGCGTCACTTCGAGAAAGGCGTCATGCTGCAAAC\n+GCTTGACTCCCTGTGGAAAGAGCACCTGGCAGCGATGGACTATCTCGTTGTCAGCTGATCGACCTCGGAG\n+AATGGGCTGCTGAAGAAAAACGAATCCCCAGCAGTGGCGATCTTTCCGAAAGCGATGACTGGAGCGAAGA\n+ACCAAAGCAGTGACATTTGTCTGATGCCGCA\n+>k141_1206 flag=1 multi=5.0000 len=649\n+AGCGGGACAACAAACGCAAACACCAGCGAATGGGTAAACCCGCGATGACCAAAAACATTGCCGTAAGCAA\n+CGCCAAATTTAAACGACAATACGTCGGCGTCGGGCAGCATCGCCAGGATGATTCCGGCAAATAACAGACG\n+CGGAGGGATGACTTTCGAACCCAACCCTAAACCAATGCATAGGGGAACGGCGGCGTGCGTAATAACGGTT\n+GGCATGATGGTCGCTTCGGCAAAATGTCGATGCTATCAGCATGGATGAACGGGGCGTAGAGGGCAAAAGT\n+CTGAAAAGAGAACCGGCCTGTTGATACAGGCCGGGAAAGGGATCAGGCAACAACCTGTACGCTGTGACCT\n+GCAAAACTCACTGTCTGACCGGCGACGATTTTGCAGCGTTTGCGCGTTTCAACCGCACCGTCGACTTTCA\n+CCTGGCCTTCGGCAATCGCGATTTTCGCCTGCGCGCCGCTTTCGCTCCAGCCTTCCAGTTTCAGCAAGTC\n+GCACAGCTCAACGTGCGGATGTTTACCTAAAGAAAATGTCGCCATGTTACTCATCCTGTGGATCATGATA\n+TTCAACGCACGCCTGTAGCGTGTTTTCAATCAGCGTGGCAACCGTCATCGGGCCAACGCCGCCGGGAACA\n+GGCGTAATGTATGAGGCGC\n+>k141_1207 flag=1 multi=2.0000 len=391\n+TGAAGAGAACCCGCATCAGCTGCAGCAGCTTATCCGCCTGCCGGGGCAGCAGTATGATGAGGAGTCCGGC\n+CTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACACAAATAACGCGGCCTT\n+ACCTCTTTAAACTTCCCTTTTAAACAGTTCTCCACACAACTATTATCGGTTTCAACGAGGTCACAACGGC\n+CAGCAGCTTCTTTTGTATCATTACTTGCTTTACCTGGCCCCCATAGACCATCTCCTTTTGATTCTCCCCG\n+TTGGTCTTGGCCACCACAAGTATAGTCCCCTTTACCATCTGGGACACAAAGATATTGATGATAGAACGGA\n+TTCCCCCATATATCTGGACCGCTTCTTTCACCAGTTCCGCC\n' |
| b |
| diff -r 8a0473eb465e -r 2bc40bfbcfb4 test-data/test4_contigs.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test4_contigs.fasta Mon Oct 16 07:46:13 2023 +0000 |
| b |
| b'@@ -0,0 +1,1000 @@\n+>k141_910 flag=1 multi=4.3596 len=928\n+GGCAATGGCCTCTCTTCCTATCCGCACCCGAAACTGATGCCGGAATTCTGGCAGTTCCCGACCGTATCTATGGGTCTGGGTCCGATTGGTGCTATTTACCAGGCTAAATTCCTGAAATATCTGGAACACCGTGGCCTGAAAGATACCTCTAAACAAACCGTTTACGCGTTCCTCGGTGACGGTGAAATGGACGAACCGGAATCCAAAGGTGCGATCACCATCGCTACCCGTGAAAAACTGGATAACCTGGTCTTCGTTATCAACTGTAACCTGCAGCGTCTTGACGGCCCGGTCACCGGTAACGGCAAGATCATCAACGAACTGGAAGGCATCTTCGAAGGTGCTGGCTGGAACGTGATCAAAGTGATGTGGGGTAGCCGTTGGGATGAACTGCTGCGTAAGGATACCAGCGGTAAACTGATCCAGCTGATGAACGAAACCGTTGACGGCGACTACCAGACCTTCAAATCGAAAGATGGTGCGTACGTTCGTGAACACTTCTTCGGTAAATATCCTGAAACCGCAGCACTGGTTGCAGACTGGACTGACGAGCAGATCTGGGCACTGAACCGTGGTGGTCACGATCCGAAGAAAATCTACGCTGCATTCAAGAAAGCGCAGGAAACCAAAGGCAAAGCGACAGTAATCCTTGCTCATACCATTAAAGGTTACGGCATGGGCGACGCGGCTGAAGGTAAAAACATCGCGCACCAGGTTAAGAAAATGAACATGGACGGTGTGCGTCATATCCGCGACCGTTTCAATGTGCCGGTGTCTGATGCAGATATCGAAAAACTGCCGTGACTTGTTCTTCAGCATCACGTTCAGAGCACGAACGAAAGCGATAGTGGTAGAGATCTCTTTGCTCTGCTCTTCCAACAGCGCGCCGAAGTCTTGCAGGCTCGGCAGCTCAAGCTTCTCGGTGAAG\n+>k141_818 flag=1 multi=1.9677 len=327\n+TAAAGTTTTTCTTTAGTTCGGACTTATTGACTATATTAATTGTTTGTTCAAGGCCTCTGAGATTTTTCTCAAGATGGTGATGCAGATTTAACCCTGTTGTCGTCGGCGCGATACCTTTTCCTGATCACATGAGTAAGGAAAATACGCTACAACAGGCCGTGGGGTTGCCCGATCAGAAAACGCTTAATATCATTATGGGGAATAAATAAAAGGTAATTCATGGATGGTTGAACTATATCCCTGCTTTTCAACCATCCTAAAAAAGCATGAATTGCTCGCTCTGCCCTAAGTGGCTGTGCTATTTTAGAAAAACTTAATCCTGAGTTA\n+>k141_335 flag=1 multi=3.2506 len=564\n+GCGTGGGCCATCACCAGCTTTTTCTCTTCGTCGATTTGCAGCAGAGGCTGGCGCCGCAGCCAGTTAAGCAGCTCGTCGGCATCCGGCGCTTCCAGCAGCGGTGTCAGGCGATCTTTCGGTTTATTGTGGAATTCGCTGAATACCGATTCCCAGTCATCCGGCTCGTAATCCGGGAAATGGGTGTTGCCTTCCACTTCTGCGTCGATATGCGTCAGATACAGTTTTTGCGCTTTTGGCAAGAACTGTTCATAAACGCGACCGCCGCCAATCACCATGATTTCTGGTACGTCACCACACGCCGCGATGGCTTCATCCACCGACTTCACCCACGTTACGCGATCGTCCGTACCCGGTTGACTGCTGAGGATAATATTTTTGCGTCCTGGCAACGGACGACCGATTGATTCCCAGGTATGGCGGCCCATAATCACGGGTTTATTTAAGGTGTTGCGTTTAAACCAGGCGAGATCGGCAGGCAGGTTCCACGGCATGGCGTTTTCCATGCCGATAACGCGATCTACCGCTAACGCCGCAATCAGACTGATCATTGAGATTTCCCGATAA\n+>k141_819 flag=1 multi=5.0000 len=306\n+AAACTATGGAACAGGCGATGCGCTTGCTGGCTCCGCGTGTTCAGCCGGGCGATATGGTTCTGCTCTCCCCAGCCTGTGCCAGCCTTGATCAGTTCAAGAACTTTGAACAACGAGGCAATGAGTTTGCCCGTCTGGCGAAGGAGTTAGGTTGATGCGTTTATCTCTCCCTCGCCTGAAAATGCCGCGCCTGCCAGGATTCAGTATCCTGGTCTGGATCTCCACGGCGCTAAAGGGCTGGGTGATGGGCTCGCGGGAAAAAGATACCGACAGCCTGATCATGTACGATCGCACCTTACTGTGGCTGAC\n+>k141_336 flag=1 multi=5.3434 len=473\n+CTATCGGCATACAACGTTCCGTCAGCCAATGTCAGTTGAACAGCCGGGAAGCTATTCAGAAATTCAGTCTGAGAACCGTCCTGACGGATCAGGTTCAGTAATTCCTTTTCTGTCAGTGAAAAGTAACCGGGTTTATCACTAAACTGAATATTGATGAAGGATCTATGGTCAAAAAAGGACAGGTACTGTTCGTCATCGATCCGGTGCAGTATGAATCTGCCGCCCGTGCAGCAAAAGCCGCTGTAGCCACAGCTAAAGCGAATGTTTCTACTCAGGAAATCACTGTAAAAAACAAACGTGAATTAAACAAGAAAAACATCATCAGCGACTATGATCTGGAAATGGCTGAAAATACACTTGCATCTGCAAAAGCTCAATTGGCATCTGCCGAAGCCCAGCTGATCAGCGCTAACCAAAATCTGGCATACACACGCGTAACAAGCCCTTCGGACGGTGTAGCCGGAACAATCCCT\n+>k141_911 flag=1 multi=5.0000 len=709\n+ATGACGAAAGCGCCTGGCGGCACCGTCGTTTCATAAATCTTATAGCCACCTTGCGTAATAGTGACTTTGGCGTTGGTATTGGCAACGCCATGAATGATAGGCGCAAAGCTGGCTAAAGTCGGAGGCAACATGCGGCTGTCACTGTATAAACGAATGCCTCGGATACTGACGGAATCAAAGGTTTCGCCCGTCGTATAAGACTCACCAAGAATGAGTTGAGAACGCAGCGAGGCGATATCACGCTGAACATACCGATTCTTAAAATCATAATTACTGCCAGAATCGGTCATCCAGTTGTAGTTGCCCGAGGCACGCAGTCGCCATGCACCTAAATTCATCCCACCGTTAAATGCAGCATAAATGCTTTCATTTTTTCGACCAGGGGTTTCACTATGATATCCGTTGAGGTTGTATGACAGAAGGTAACCCCGCTATACCGGGTGTTTACGACGTCAGTGTTTATGTAAACGACCAACCAATCATTAACCAAAGTATTACATTTGTCGCAATTGAAGGAAAAAAGAACGCCCAGGCTTGTATCACATTAAAGAATTTATTGCAGTTTCATATTAATTCTCCCGATATAAATAACGAAAAAGCCGTTCTGCTTGCCAGGGATGAAACGCTCGGCAATTGCCTCAATTTGACGGAAATTATCCCTCAGGCTTCTGTTCGTTATGACGTTAACGATCAACGTCTGGATATAGAC\n+>k141_337 flag=1 multi=1.1094 len=333\n+CATAAAGTGACGGAATTTATTGATGATATGGCGGCGGCGTATGCGTGGGCGGATGTCGTCGTTTGCCGCTCCGGTGCGTTAACGGTGAGTGAAATCGCCGCGGCAGGACTACCGGCGTTGTTTGTGCCGTTTCAACATAAAGACCGCCTGCAATACTGGAATGCGCTACCGCTGGAAAAAGCGGGCGCAGCCAAAATTATCGAGCAGATACGAATGAAATCAATTTCGATGCCATGTTTTGGCACTAAGTCCGCTTCCATACGGTCGGCAGTCCCCAGCCAGCGAACTTGCCAACCCTGAGCCATTAGATGGTGCGCAACCGCCAGTCCCGGG\n+>k141_199 flag=1 multi=6.9623 len=7146\n+TTATTGTCTTTT'..b'CGGCTGGACGCGCAACTGCAATATTCAAAGTGACAGCGCATTGCAGCAAGCCTGCGAAGATGTCTTCCGCTTTGATGACGCCAACTAAGGAGCGGCAATGAATATTCCACAGCTCACTGCCCTGTGTCTGCGTTATCATGGAGTCTTGCTGGATGCCAGCGAAGAGGTGGTTCATGTTGCGGTAGTCGATGCACCTTCGCATGAGCTACTGGACGCATTGCATTTCGCTACCACCAAACGTATTGAGATCACCTGCTGGACGCGCCAACAAATGGAAGGTCACGCCAGTCGCACACAACAGACATTGCCCGTAGCTGTTCAGGAGAAGCATCAGCCCAAAGCAGAGTTGCTAACTCGAACGTTACAATCTGCGCTGGAACAACGCGCGTCTGATATTCATATCGAACCAGCGGACAATGCCTACCGCATCCGCT\n+>k141_1204 flag=1 multi=3.4644 len=464\n+GCGCGTACAGTCGATGCCCGAAATTAACGATGCCGACAAAACCGTTAAATTACGTGTGAACGTTGATGCGGGTAACCGTTTCTACGTGCGTAAGATCCGTTTTGAAGGTAACGATACCTCGAAAGAAGCTACCGGTGTTGCGCTCTTTTACCTTGTAGACGACATCAACCTGGTCCGGGCTACCCGGAACACGTTGGGTATCGGTATCGACAGTTTCAAAGAAGCCCAGACGATTCAGACGCTCCTTACCCTGATCGACCAGATCGCTCCCCAGCCATGCACCTTCCATCTGACGCATTTCGCGACGCAGGACGGCATCTTTCGAGGTATCGTTACCTTCAAAACGGATCTTACGCACGTAGAAACGGTTACCCGCATCAACGTTCACACGTAATTTAACGGTTTTGTCGGCATCGTTAATTTCGGGCATCGACTGTACGCGCGGATAGGCATAACCATAGCGA\n+>k141_1205 flag=1 multi=3.9462 len=661\n+TGCGTAAACTGGGTATGAAGCCAGGCGAAGCCATTGAACACCCGTGGGTGACTAAAGCGATTGCCAACGCCCAGCGTAAAGTTGAAAGCCGTAACTTCGACATTCGTAAGCAACTGCTGGAATATGATGACGTGGCTAACGATCAGCGTCGCGCCATTTACTCCCAGCGTAACGAACTGTTGGATGTCAGCGATGTGAGCGAAACCATTAACAGCATTCGTGAAGATGTGTTCAAAGCGACCATTGATGCCTACATTCCACCACAGTCGCTGGAAGAAATGTGGGATATTCCGGGGCTGCAGGAACGTCTGAAGAACGATTTCGACCTCGATTTGCCAATTGCCGAGTGGCTGGATAAAGAACCAGAACTGCATGAAGAGACGCTGCGTGAGCGCATTCTGGCGCAGTCCATCGAAGTGTATCAGCGTAAAGAAGAAGTGGTTGGTGCTGAGATGATGCGTCACTTCGAGAAAGGCGTCATGCTGCAAACGCTTGACTCCCTGTGGAAAGAGCACCTGGCAGCGATGGACTATCTCGTTGTCAGCTGATCGACCTCGGAGAATGGGCTGCTGAAGAAAAACGAATCCCCAGCAGTGGCGATCTTTCCGAAAGCGATGACTGGAGCGAAGAACCAAAGCAGTGACATTTGTCTGATGCCGCA\n+>k141_1206 flag=1 multi=5.0000 len=649\n+AGCGGGACAACAAACGCAAACACCAGCGAATGGGTAAACCCGCGATGACCAAAAACATTGCCGTAAGCAACGCCAAATTTAAACGACAATACGTCGGCGTCGGGCAGCATCGCCAGGATGATTCCGGCAAATAACAGACGCGGAGGGATGACTTTCGAACCCAACCCTAAACCAATGCATAGGGGAACGGCGGCGTGCGTAATAACGGTTGGCATGATGGTCGCTTCGGCAAAATGTCGATGCTATCAGCATGGATGAACGGGGCGTAGAGGGCAAAAGTCTGAAAAGAGAACCGGCCTGTTGATACAGGCCGGGAAAGGGATCAGGCAACAACCTGTACGCTGTGACCTGCAAAACTCACTGTCTGACCGGCGACGATTTTGCAGCGTTTGCGCGTTTCAACCGCACCGTCGACTTTCACCTGGCCTTCGGCAATCGCGATTTTCGCCTGCGCGCCGCTTTCGCTCCAGCCTTCCAGTTTCAGCAAGTCGCACAGCTCAACGTGCGGATGTTTACCTAAAGAAAATGTCGCCATGTTACTCATCCTGTGGATCATGATATTCAACGCACGCCTGTAGCGTGTTTTCAATCAGCGTGGCAACCGTCATCGGGCCAACGCCGCCGGGAACAGGCGTAATGTATGAGGCGC\n+>k141_1207 flag=1 multi=2.0000 len=391\n+TGAAGAGAACCCGCATCAGCTGCAGCAGCTTATCCGCCTGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACACAAATAACGCGGCCTTACCTCTTTAAACTTCCCTTTTAAACAGTTCTCCACACAACTATTATCGGTTTCAACGAGGTCACAACGGCCAGCAGCTTCTTTTGTATCATTACTTGCTTTACCTGGCCCCCATAGACCATCTCCTTTTGATTCTCCCCGTTGGTCTTGGCCACCACAAGTATAGTCCCCTTTACCATCTGGGACACAAAGATATTGATGATAGAACGGATTCCCCCATATATCTGGACCGCTTCTTTCACCAGTTCCGCC\n+>k141_1208 flag=3 multi=5.0048 len=1188\n+ATTTTTTTCCTGAAGCGGAAAACATTACTACAGTACCTTGAACCTTGGTTTTAACATTCTCGAAATGCTCTGAGAGTATATGTGTTAAGCCTTCTTCGGAATCTTTTGTGTTTGAAAAGATGCCTTTCTGATTGTAAATGCGCATCAGTTTTTGACCGAAGCTATTGTGCACAACTCCATCGCCAAGAATTGTGGCTCCGTATAGAGTTCCATCGTCAGTTAAGGCCTGCGCCGCATTGCGTATTACACAGCTTTTTGTAGATATATTTCCAGGCAGGCAGTGAAGAAGGTAAGACATGGAAATGGAATCAAATTGACCATGTAACGCCGCGGGATAAGGTTCAAAAACATCATGGCTAATTTTATGTTTAATTTTTGATTCCCCAGCCCTTGTAGATGCCGCGTTCAGGCTAGCTTCGTTCAAATCCATTAAAGATATCAGACTACTCTCAGGTACGTGAGTAAGGTAAAACCCAGTTCCAACACCAATATCCAGATGGTTGTTACCTAAATGTTCCAGAAAGTGTGGAAGAAGGTGTTCCTTTGTAGGACATCCCCATGCAAGCCGATTTGATACTCCCAAAACCCACCAGTCATAAAGCTTTAGGGTAAGTGGTGTGTAAATTCTAGCCCCATCATCTGTGTTTTTTTATTAATTTCACCATGTTATAGTTTTATTTGTGAATTAAATCAATTATGGCAATGAATTACAAGGGGTTAAATGCTGCCGCAGCATAGCGATATTGAAATAGCCTGGTATGCTTCAATACAGCAGGAGCCGAATGGCTGGAAGACCGTCACCACACAGTTCTACATCCAGGAATTCAGTGAGTATATTGCGCCACTGCAGGATGCTGTAGATCTGGAAATCGCAACGGAGGAAGAAACCTCATTGCTGGAAGCCTGGAAAAAATATCGGGTGTTGCTGAACCGTGTTGATACATCAACTGCACCTGATATTGAGTGGCCTACGAACCCTGTCAGGGAGTAATCATTGGGATTATGCCGCAGCACGTCTTAAGCAAGAACATGCTGCGGTTGGATGCTATTTTTTTCCTGAAGCGGAAAACATTACTACAGTACCTTGAACCTTGGTTTTAACATTCTCGAAATGCTCTGAGAGTATATGTGTTAAGCCTTCTTCGGAATCTTTTGTGTTTGAAAAGATGCCTTTCTGATTGTAAATGC\n' |
| b |
| diff -r 8a0473eb465e -r 2bc40bfbcfb4 test-data/test4_reads.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test4_reads.fastqsanger Mon Oct 16 07:46:13 2023 +0000 |
| b |
| b'@@ -0,0 +1,1948 @@\n+@NC_006347.1_63\n+AAGCCTTGGCCGGAAATATTTTATTTTGCTTTGTCGGCTACACAGTCCGAACTGCGTGATTCGCTAATGATAGGTGATAGTTGGGAAGCGGATATTACAGGTGCCAATGGCATAGGGATGCATCAGATCAGTCATACCATGGGTGATGGTCAAAAAGACAGGCATTGTTCCCAAGGGGTTAGTCAACGTAAAGAAAGAGGTAAAACAGAGTAAAGCGAAAGGTAAGAGAGTGTCCATAGTTGTATTTTTATG\n++\n+BBBBBFFFFFFFFFFFFFBFFFFFFBFBFFFFFFFF<FFFFFFFFFFFFFFFFFFFFFB/FFFFFFFFFFFFFFF<FBFFFFFFFFFFBFF<FFFFBFFFFFFFFFFFFF<F/FFFFF</FFFFFFBBBBBFFFFFF<FFFFFF/FFFFFF/FFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFF/FFFFFFFFFFFFFFFFF<FFFFFFFFBFFFFFFFF/FFFFF7BBFFBFFFF\n+@NC_006347.1_193\n+GGAGGAGTAAAACCCTATACCGTAAGTAGCAATTCTGATATCCTCAAAGTGAATATGGATAAGCTTTCGGATGCTTTCAACTACGAAACACTGGGCGTTGGTGATGCGGAAGTGACTATTACCGATCTTATCTCACTCAAAGCCGGAGGTGTAGGCCTCAACCTGACACAGGCAGACTATGTATTCATTATCGATCCTTGGTGGAACCCGGCAGCCGAATCACAGGCCATCGCCCGAGCCCACCGTATCGGA\n++\n+BBBBBFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFF/FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF<FFF/FFFFFFFFFF<FFFFFFFFFFFFFFFFFFF/BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF<<FFFFFFFBFFFFFFFFFFFFFFFFFFFFF<FFFFFFFFFFFFFF<F<FFFFFFFFFFFFBF/FFFFFFFFFFFFFFFFFFF/FF/FFF\n+@NC_006347.1_656\n+GTTATACTTTACCAATTGCTTGTTGCTACAGCGGGAGAGACTTATGAATTCACTTCTTGTTGGAGTACGCCAACCACTACCGTATATACTTTCGTCAAGACGTGTACAAGGATCAACAGCACCATACTCCACATCATGGAAGATCGGTCCTTCGACCAATGTGGTAGCCGCCAACACAAATAATACGGCGGCATTCAGTCCGAACACGACCCTGAATACAACCATACGCATGGTTCCATTTGCAGGGGCCAG\n++\n+BBBBBFFFFFFFFBFFFFFFFFFFFFFFBFFFBFFFFFFFFFBFFFFFFFFFFFFFFF/FF<FFBFFFFFFBFFF<FFFFFFFFFFFFF/FFFFFBFFFFFFFFFFFFFFFFBFFFFFFFFFFBFFBBBBBFFFBBFFFFFFFFFFFFFFFFF/<FFFFFFFFFFFFFFFFFFFFFFFF/FFBFFFFFFFFFFFFFFFFFF/FFFB<FFFFF/FFFFFFFFFBFFBFFFFFFFFFFFFFFFFFF7FF<FF/F\n+@NC_006347.1_1720\n+CATTACCGTAGTCGAAGTGGTCGGAGTCATCCCCAGGGTACAAACTTCGGCAGGATGTCCTGTGCTCAGGCATACATCCGATTCGCTGGCAAGCGGACTGTCCGGATTGCCGGTGATGACAATGAAACGGGTTCCGGCATCTACGGCAAATCCGCAATAAGCCACCTTCGAAGAAGAGGGTTCATGAATAATGCGAAGTCCATTGGACAGGGTATGTATATTATATTGCATTTCTGCACGGGTACTTAACTG\n++\n+/BBBBFFFFFFFBFFFFFFFFFF<FFFFFFFFFFFFFFFFFFBFFFFFFFF/FFFBFFFFFFF/FFFBFFFFFFFFFFFFFFFFFFFFFF<FFF/F<FFBFBFFFFFF<FFFFFFFFF7F7FBBFF/BBBBFF<FFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFBFFFFFFFF<FFFFFFFFFFFFFFFFBFFFFFFFF<FFFF<FFFFFFFFFFFFFFFFFFFFFFFFFF<FF/FFFFFF/FFFFF/FF\n+@NC_006347.1_2535\n+CAGGTAGCACAGGAATGTTACACATGATTTTAGTCTTTTGGCGGTTCTTCCTTATCCAAAGTTCCCCTTTATTGTCTTTTACCAAGTGTTCAGGTGATAAGTCTTTCACATCGCTGAACGCCAAACCGGATCACTGAAAACAAAAGAAAAATCAAGCAAATCCCTGATAATCAGACATTATCAGGGATTTCTTTTTTCCGGCAGGTGGCAGAAAACAGCCGTTTCAAGCATATTATTGGTGGATAAATCGTG\n++\n+BBBBBFFFFFFFFFFFBFFFFFFFFFFFFF<FFFFFFFFF/FF/<FFFFFFFFF/FFFFFFFFFFFFFBFFF/FFFFFFFFFFFFFFFFFFFFFFFF<FFFFFFFFFFFBFF<FFF7FFBFFFFFFBBBBBFBFFFFFFFFFFFF<FFFFFFFFFFFFFFFFFFFFFFF/FFFFFFFFFFFBFFFFFFFFFFFBBFFFFFFFFFFFFFFFFFFFFF/FFFFFFFFFFFBFFFFBFBBF/FFFF<FFFFFF7F\n+@NC_006347.1_3006\n+GAACTGTTACTGCGTTTGAAAGCTAATCATCTGGCTCCGGCAATGCATCCCGTATCTACCGCTTTTTATCAGATTCCCGAGAATAAGCTCGTAGCAGATACGTTTGCCATTGTTATGGGCTCCAGCCGATATCATAAGCCATATCGAGAAAAAACGATACTTGTGCCTCAGCCCCTTTCAGGTCTCCACAGTTTGCCAACCAGATACGGTCGGCCGTAGTATCATACGCTTTGCGAAGCTCTTCATACATTA\n++\n+BBBBBFFBFFFFFFFFFFFFFFFFFFF<FFFBFFFFFFFFFFFFF/FFFFFFFFFFFFFFFFFFF<FFFFF</FFFFFFFFFFF<FFFFFF<BFFFFFFFFFFBFFFF/FFBFFFFFFFFFB7FFFBBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFBFFFFF<FFFFFFFFFFF/FFFFFFFFFFFFF7FBFFFFFFFFFFFFFFFBFFFFFFFFFFFFB\n+@NC_006347.1_3200\n+AGCAGACAATCATCAATATACTCGTTTTTTTTTTCTCTTTTCCAATTCATAAATAATTAGCACAAATGTACGAAATGTGTTCGTAATCGCAAATTATTTATTATGAAAGATATAGAATTTATCAAGCCAAACAAGGCTTTAAGTGGTAATAATCCCTTTTCTACTTGTGAAACAAGGTATATTCCAAGTCTGAAACGGAAATGCCAAGCCCTTTGGGTTTTAGAAGATTTCTTCTTTTTCGCTTACAAGAAG\n++\n+BBBBBFFFFFFFFFFFF<FFFFFFFFFFBFFFFFFFFFFFFFFFFFFF/FFFBFFFFFF<FFFFFFFFFFFFFFBFFFBFBFFFFFBFFFFFFF<FF/F/FFFFB/FFF<FFFFFFFF<BFF/FF/BB<</BFF/FF<FFF7FB<FFFF//BFBF<FF//<F<F/</<F/<FFFFFF/BF//FB/<FBFB/F/F///B<FBFFF//<<B/BB//F/FBF7<FB<B/FFFF/F/B7BF7F/BB/<B7/F/BBF\n+@NC_006347.1_4206\n+TTCGCCCGTATTCGTCTCTATTCCTTTCACTTCTCCCTGTTCGATGATCAATGCATCCATCCGTGTCTTGAAGTGTACTTCGCCTCCACATTCAATAATCGTATTGCGCATATTCTCTATCACCCGCCGCAGGTTATTGTGGTAGGTGCAGGCCCCGGAGGACTGTTTGCCGCATTACGGCTGATAGAACTGGGGCTGCGTCCTGTCGTCGTGGAGCGTGGCAAGGATGTGCGCGAACGTAAGAAAGACCTG\n+'..b'AGGAGATAATAGCCGAATCGGGCT\n++\n+BBBBBFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFF/FFFFFFF<FFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBBFFFFF<FFFF//FFFBFFF/FBB/BBF///FF/<F</BB</FF//FF<F<F///FF////7BB/F//BF/</FF//FFB<///<<//F/<<BF/</F/FB/<FF/FF<77/F</FF</7/7B</<FB/B/B//<F/FFF/77</<F/\n+@NC_006347.1_12312\n+CCGTGAGGTGAAGAAGCTAATCTTAGACTAAACCATCTGAAAATCAATATCTTTAAGAAGTAAGATTTCTGTCCTCAAAAGCTTTGTTTTAACACAGAGTTAAAGCTTGTTCTTTGGATGTGAATACCATCGTGCTTGAAGTTCCACCACAGGCCCCCCCTTTCTTTATCATACGACTCTTTCCAGACATGGTAGAATCCCGAAGAGGCATGTGCCAGGTATTTCGGGTCATTCGTGATTTCGTAAGCACGT\n++\n+BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFF/FFFB/FFFFFFFFFFFFFFFFFF//FFFFBFFFFFFBFFFFFFFFF<FFFFF//FBBBBBFF/FFFBFFFFBFFFFFFFFFFBFFFFFBFFFFFFFFFFFFFFFFFFFFFFF<FFFFFFFFFFBBF<FFFFFFFFFFF7FFFFFFFFFFFFFFFFFBFFFFFFFFFFFFF<FFFBFFFFF/\n+@NC_006347.1_13121\n+TTGTAGGTGTACTTGTAGTTCCCCTCGACCACGAAGCGGTTGTCGGTGAACTCCAATCCCTCTTTGAGTATCCTTTCGCTCACCACCTTTATCGGAAAACCGTAAAGTTCACCGACCTGCGTGTACCTGTTCGGGCTCTACCTCTATGCTCGGAACGGGTGTGAACGCCCAGAAACGGTGTGTGGCTATCCATCATCTCGATACGCCGTGGCGACCGTCCGACTTGCAACAGCGTGACGGACGCGGAGTTAG\n++\n+BBBBBFFFFFFFBFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFBFFFFFFFFF/FFFF/FFFF<F<FFFFF/F<FBF/FFBBFFBFBFBFFFFFFFFFFFFBBBBBFFFFFFFFFFFFFBFFFFFFFFFFFFF<FFFFFFFFBF7FFFFFFFFFBFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/BFFF/F<FBFF/FFFF/FFBF\n+@NC_006347.1_13826\n+GCAGGAACAGCAAGTCAAGATAGCCACGCTCCAGCAAAGCCTCGAACGGTATAAGTCTTACGATGAAATGAGCCGGAAAATTATCCCGGAACTGAAAGTACTCTATCCGTCGGTGACGGCTTTGTCTGTATCCATCCAATGTGATGGGAGCCACGTATTCGGGACGATAGGGCACGTTGTCGGGTGAATAGTCGGCAGGACGGTTGTCTTTACCGGCATAGATACGAAAGACGCAGAAATCGCCAGTATGAC\n++\n+BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFF<FFFFFFFFFFFFFFFFFFFFFFBFFFFFFF/FF</FBFBFFFFBFFFFFFFFFFFFFFFFFFFFF7FFFFFFFFFFFFF7FFFFFBF<FFF/BBBBBFFFFF/FF<FFFFFFFFFFFF<BF/<FFFFFFFFFFFFFFFFFFFFFFFFFF/FFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF<FFF<FF<FFFFFBFFFFFFFFFFFFBFFF\n+@NC_006347.1_13843\n+TCTTATTTATTTTCGCCAGTTCCGATTTTACGGATTCAGGGGCTTCGGATGGGTTGATATGTGCCTTATCTATATATCCGAACGCCAATATTACAACTTCACTCTTTTTCAGTGAATAACGTTTGCCTTTAGCGTGTTACAAGAACACGCTGTAATGACACCTGTAATAAGTATTTTCTTTGTAATGCTTATTATCAGGTATTTATCTATTCATATTTCTATAAAAAAGTAATTACCATGCCAAACAGCAGT\n++\n+BBBBBBFFFFFFFFFFFFFFFFFFFFFFFFF<FFFF<FFFFBFFFF<FFFFFFFFFBFFFFFFFFFFFFBFFFFFFFFFFFFBFFFFFF/FBFFFFFFFFF7FFF<FFBFBFFFFFFFFFFFFF/FB<BBBFFFFF<BFFBBFF<FFFFFFFFFFFF<FFFFFFFFFFFFFFFFF/<FFFFFFFFFBFFFFFFF/FFFFFF<FFFF7FFFFFFFFFFFF/FFFF<FF/FFFFBFFFFFFFFFFFFFFBFFF/\n+@NC_006347.1_13966\n+TTTTACGGCAGTAGTGACCGCCACCCCGTTATTTACGGGCTGTAGAGCACTGCTTTTCTGGGTACCGAATACCAAAAACAACAGGCATAACATTAGTAGTTTGATGTATGCTGCCATAATTGGCGGACAGCCAACTTCTTTATCCGGTACAAATACAGATTCCACAGATTAACACAGATTCCCCACTAGGACAATCAATCTCTGCTAATCTGTGGAAGCAATAGTATATCGACAAATATACAAGGTTTGTAC\n++\n+BBBBBBFFFFFFFFFFFFFF<FFFFFFFFFFF<FFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/FFFFFFFFFFFFFFFBF/FFB<FFF<FFFF<FFFFBFFFFFBFFBBBBBFFFFFFFFFFBFFFFFFFFFFFBFFFFFFFFFFFFFFFFFBBFF/FFFFFFFFF/FFFFFFFFFFBFFFFFFFFBFFFFFFFFF/F/BFFFFFFFFBBBFFFBFF/FFFBFBFBFF/FFFF\n+@NC_006347.1_14109\n+GCCGGGGATGGTAATTTCCTCTTTTTCCTCGCCATAGACGGCACGCCATCCGGTTTGCTTCACGACGCTGCCTTTTACGGTAAACTCCACTCCGGCACATTCCGCCGTGACAGTGGTCACATCCTTTCTACCTCGCCGCCAAAGCGCGGAGCGAATCCGACTGGCTCGTGGGCATCAACGGCACACAGGCGTTATCCATCGCCGCCGGACACGGCACGTATTCCGTGGGGCGGGTGCAGACACCAACGTTGG\n++\n+B<BBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBBFFFFF<FFFFBFFFFFFFFFFFFFFFFFFFFFBFFFF<FFFFFBFFFFFFFF/FFFF/FFFFF/BFFFFFFFF<BBBBBFFFFFFFFFFFFFF<FFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFF<FFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFBFFF7\n+@NC_006347.1_14401\n+AAGAAGGATTCAAGACTCCGGTGGGAAAGTTACCGTTGGACAAACAACTGGAGAATTCATGGGAAAAACAGATGGAAATTGATATGAATGGCAATCCATACTGGTATATTGCCACATCAAGAGTGATTTATCCAGTTCCTTAGCCAATTCCGGTGATTTTTTAGCCAATTCTTCGCTAAGTGCTTTGACAGCTACTTTGTTTGCAGCTTCCAGGCTATAACCGATGGTTACCATTACCTCTACATTTTTGTA\n++\n+BBBBBFFFFFFFFFFFFBFFFFFFFF<FFFFFFFFFFFFFFFFFFFFBFFFFBFBFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF<FF/FFBBFFFBFFFFFFFFFFBBBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFBBFFFFFFFFFFFFBF<FFFFF/FFFFFFFFFFFFFFFFFFFFF/FBFFFFFFFFFF<F<FFF/\n' |
| b |
| diff -r 8a0473eb465e -r 2bc40bfbcfb4 test-data/test4_reads.fastqsanger.gz |
| b |
| Binary file test-data/test4_reads.fastqsanger.gz has changed |