| Previous changeset 13:675488238c96 (2022-03-25) Next changeset 15:72472698a2df (2023-03-02) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124 |
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modified:
macros.xml quast.xml test-data/test1_report.html test-data/test2.log test-data/test2_report.html test-data/test2_report.pdf test-data/test2_report.tab test-data/test3.log test-data/test3_report.html test-data/test3_report.pdf test-data/test5.tab test-data/test6.tab test-data/test7.tab |
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added:
test-data/meta_contigs_1.fasta test-data/meta_contigs_2.fasta test-data/meta_ref_1.fasta test-data/meta_ref_2.fasta test-data/meta_ref_3.fasta test-data/reads1.fastq.gz test-data/reads2.fastq.gz test-data/test10_missasembly.tab test-data/test10_tabular_report.tab test-data/test10_unalign.tab |
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| diff -r 675488238c96 -r 3061c8b029e5 macros.xml --- a/macros.xml Fri Mar 25 17:36:59 2022 +0000 +++ b/macros.xml Fri Aug 05 15:21:27 2022 +0000 |
| b |
| @@ -1,8 +1,12 @@ <macros> + <token name="@TOOL_VERSION@">5.2.0</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">21.01</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">quast</requirement> - <requirement type="package" version="0.69.8">circos</requirement> + <requirement type="package" version="0.7.17">bwa</requirement> + <requirement type="package" version="2.30.0">bedtools</requirement> </requirements> </xml> <xml name="bio_tools"> @@ -10,8 +14,6 @@ <xref type="bio.tools">quast</xref> </xrefs> </xml> - <token name="@TOOL_VERSION@">5.0.2</token> - <token name="@VERSION_SUFFIX@">5</token> <xml name="gene_thresholds"> <param name="gene_thresholds" argument="--gene-thresholds" type="text" value="0,300,1500,3000" label="Comma-separated list of thresholds (in bp) for gene lengths to find with a finding tool"/> </xml> @@ -23,4 +25,8 @@ <citation type="doi">10.1093/bioinformatics/btt086</citation> </citations> </xml> + <xml name="min_identity_macros" token_value=""> + <param argument="--min-identity" type="float" value="@VALUE@" min="80" max="100" label="Minimum IDY% considered as proper alignment" help="Alignments with IDY% worse than this value will be filtered. Note that all alignments + with IDY% less than 80.0% will be filtered regardless of this threshold. "/> + </xml> </macros> |
| b |
| diff -r 675488238c96 -r 3061c8b029e5 quast.xml --- a/quast.xml Fri Mar 25 17:36:59 2022 +0000 +++ b/quast.xml Fri Aug 05 15:21:27 2022 +0000 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="quast" name="Quast" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">\n+<tool id="quast" name="Quast" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n <description>Genome assembly Quality</description>\n <macros>\n <import>macros.xml</import>\n@@ -12,7 +12,7 @@\n \n #if str($in.custom) == \'false\'\n #set $labels = \',\'.join( [re.sub(\'[^\\w\\-_]\', \'_\', str($x.element_identifier)) for $x in $in.inputs])\n- echo $labels &&\n+echo $labels &&\n #else\n #set $labels = []\n #for $x in $in.inputs\n@@ -26,150 +26,176 @@\n #end if\n \n #if $assembly.type == \'metagenome\' and $assembly.ref.origin == \'list\'\n- #set $temp_ref_list_fp = \'temp_ref_list_fp\'\n- #set $temp_ref_list_f = open($temp_ref_list_fp, \'w\')\n- #silent $temp_ref_list_f.write(\'\\n\'.join([x.strip() for x in $assembly.ref.references_list.split(\',\')]))\n- #silent $temp_ref_list_f.close()\n+ #set $temp_ref_list_fp = \'temp_ref_list\'\n+ #for $i in $assembly.ref.references_list.split(\',\')\n+ echo $i >> $temp_ref_list_fp &&\n+ #end for\n+#end if\n+\n+#if $reads.reads_option == \'paired\'\n+ #for $read in $reads.input_1\n+ #set $identifier = re.sub(\'[^\\s\\w\\-\\\\.]\', \'_\', str($read.element_identifier))\n+ln -s \'$read\' \'pe1-${identifier}.${read.ext}\' &&\n+ #end for\n+ #for $read in $reads.input_2\n+ #set $identifier = re.sub(\'[^\\s\\w\\-\\\\.]\', \'_\', str($read.element_identifier))\n+ln -s \'$read\' \'pe2-${identifier}.${read.ext}\' &&\n+ #end for\n+#else if $reads.reads_option == \'paired_collection\'\n+ #set $identifier = re.sub(\'[^\\s\\w\\-\\\\.]\', \'_\', str($reads.input_1.element_identifier))\n+ln -s \'$reads.input_1.forward\' \'pe1-${identifier}.${reads.input_1.forward.ext}\' &&\n+ln -s \'$reads.input_1.reverse\' \'pe2-${identifier}.${reads.input_1.reverse.ext}\' &&\n #end if\n \n #if $assembly.type == \'genome\'\n- quast\n+quast\n #else\n- metaquast\n+metaquast\n #end if\n \n #if $reads.reads_option == \'single\'\n #for $read in $reads.input_1\n- --single \'$read\'\n+ --single \'$read\'\n #end for\n #else if $reads.reads_option == \'paired\'\n #for $read in $reads.input_1\n- --pe1 \'$read\'\n+ #set $identifier = re.sub(\'[^\\s\\w\\-\\\\.]\', \'_\', str($read.element_identifier))\n+ --pe1 \'pe1-${identifier}.${read.ext}\'\n #end for\n #for $read in $reads.input_2\n- --pe2 \'$read\'\n+ #set $identifier = re.sub(\'[^\\s\\w\\-\\\\.]\', \'_\', str($read.element_identifier))\n+ --pe2 \'pe2-${identifier}.${read.ext}\'\n #end for\n+#else if $reads.reads_option == \'paired_collection\'\n+ #set $identifier = re.sub(\'[^\\s\\w\\-\\\\.]\', \'_\', str($reads.input_1.element_identifier))\n+ --pe1 \'pe1-${identifier}.${reads.input_1.forward.ext}\'\n+ --pe2 \'pe2-${identifier}.${reads.input_1.reverse.ext}\'\n #else if $reads.reads_option == \'paired_interlaced\'\n #for $read in $reads.input_1\n- --pe12 \'$read\'\n+ --pe12 \'$read\'\n #end for\n #else if $reads.reads_option == \'mate_paired\'\n #for $read in $reads.input_1\n- --mp1 \'$read\'\n+ --mp1 \'$read\'\n #end for\n #for $read in $reads.input_2\n- --mp2 \'$read\'\n+ --mp2 \'$read\'\n #end for\n #else if $reads.reads_option == \'pacbio\'\n #for $read in $reads.input_1\n- --pacbio \'$read\'\n+ --pacbio \'$read\'\n #end for\n #else if $reads.reads_option == \'nanopore\'\n #for $read in $reads.input_1\n- --nanopore \'$read\'\n+ --nanopore \'$read\'\n #end for\n #end if\n \n---labels \'$labels\'\n--o \'outputdir\'\n+ --labels \'$labels\'\n+ -o \'outputdir\'\n \n #if $assembly.type == \'genome\'\n #if $assembly.ref.use_ref == \'true\'\n -r \'$assembly.ref.r\'\n #if $assembly.ref.features\n- --features \'$assembly.ref.features\'\n+ --features \'$assembly.ref.features\'\n #end if\n #if $assembly.ref.operons\n- --operons \'$assembly.ref.operons\'\n+ --operons \'$assembly.ref.operons\'\n #end if\n $assembly.ref.circos\n $assembly.ref.k_mer.k_mer_stats\n #if str($assembly.ref.k_mer.k'..b' <repeat name="inputs">\n+ <param name="input" value="contigs2.fna"/>\n+ <param name="labels" value="contig2"/>\n+ </repeat>\n+ </conditional>\n+ <section name="alignments">\n+ <param name="local_mis_size" value="210"/>\n+ </section>\n+ <conditional name="assembly">\n+ <param name="type" value="genome"/>\n+ <conditional name="ref">\n+ <param name="use_ref" value="false"/>\n+ </conditional>\n+ </conditional>\n+ <section name="advanced">\n+ <param name="report_all_metrics" value="true"/>\n+ <param name="x_for_Nx" value="80"/>\n+ </section>\n+ <param name="output_files" value="tabular"/>\n+ <output name="report_tabular" file="test10_tabular_report.tab" ftype="tabular"/>\n+ </test>\n+ <!-- Test 11: Test paired fastq.gz inputs -->\n+ <test expect_num_outputs="1">\n+ <conditional name="in">\n+ <param name="custom" value="true"/>\n+ <repeat name="inputs">\n+ <param name="input" value="contigs1.fna"/>\n+ <param name="labels" value="contig1"/>\n+ </repeat>\n+ </conditional>\n+ <conditional name="reads">\n+ <param name="reads_option" value="paired"/>\n+ <param name="input_1" value="reads1.fastq.gz" ftype="fastqsanger.gz"/>\n+ <param name="input_2" value="reads2.fastq.gz" ftype="fastqsanger.gz"/>\n+ </conditional>\n+ <conditional name="assembly">\n+ <param name="type" value="genome"/>\n+ <conditional name="ref">\n+ <param name="use_ref" value="false"/>\n+ </conditional>\n+ </conditional>\n+ <param name="output_files" value="tabular"/>\n+ <output name="report_tabular" ftype="tabular">\n <assert_contents>\n- <has_text text="Vibrio_parahaemolyticus" />\n+ <has_text text="# contigs (>= 0 bp)"/>\n+ <has_text text="contig1"/>\n+ <has_text text="# N\'s per 100 kbp"/>\n+ <has_n_lines n="22"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <!-- Test 12: Test paired-collection fastq.gz inputs -->\n+ <test expect_num_outputs="1">\n+ <conditional name="in">\n+ <param name="custom" value="true"/>\n+ <repeat name="inputs">\n+ <param name="input" value="contigs1.fna"/>\n+ <param name="labels" value="contig1"/>\n+ </repeat>\n+ </conditional>\n+ <conditional name="reads">\n+ <param name="reads_option" value="paired_collection"/>\n+ <param name="input_1">\n+ <collection type="paired">\n+ <element name="forward" value="reads1.fastq.gz" ftype="fastqsanger.gz"/>\n+ <element name="reverse" value="reads2.fastq.gz" ftype="fastqsanger.gz"/>\n+ </collection>\n+ </param>\n+ </conditional>\n+ <conditional name="assembly">\n+ <param name="type" value="genome"/>\n+ <conditional name="ref">\n+ <param name="use_ref" value="false"/>\n+ </conditional>\n+ </conditional>\n+ <param name="output_files" value="tabular"/>\n+ <output name="report_tabular" ftype="tabular">\n+ <assert_contents>\n+ <has_text text="# contigs (>= 0 bp)"/>\n+ <has_text text="contig1"/>\n+ <has_text text="# N\'s per 100 kbp"/>\n+ <has_n_lines n="15"/>\n </assert_contents>\n </output>\n </test>\n' |
| b |
| diff -r 675488238c96 -r 3061c8b029e5 test-data/meta_contigs_1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meta_contigs_1.fasta Fri Aug 05 15:21:27 2022 +0000 |
| b |
| b'@@ -0,0 +1,3173 @@\n+>NODE_0_length_154_cov_0.707071\n+ACAGGTGAGAATCCTGTCCACCGAATGACTAAGGTTTCCTGGGGAAGGCTCGTCCGCCCA\n+GGGTAAGTCGGGACCTAAGGCGAGGCCGAGAGGCGTAGGCGATGGACAACAGGTTGAAAT\n+TCCTGTACTGCACCGAATCGTTATGAGCGATGGA\n+>NODE_1_length_75_cov_29.2\n+CGTCCATTGTGGAAGATTCCCTACTGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGT\n+CCCAATGTGGCCGAT\n+>NODE_2_length_302_cov_1.90688\n+ACTCGCTCACCTTAGGATTCTCTCCTCGACTACCTGTGTCGGTTTGCGGTACGGGTAGTT\n+AAGTACTCACTAGAAGCTTTTCTCGGCAGTGTGACATCAGACGCTTCGCTACTAAATTTC\n+GCTCCCCATCACAGCTTGTCCTTAAAGTGAAAAGCATTTGACTCTTCACAAGACTTACTG\n+CTTGGACATTCTAATCCAACAGAATGCACATCTTAGCCTCCTGCGTCCCTCCATTGCTCA\n+AACGCACTTAACTAGTACAGGAATCTCAACCTGTTATCCATCGTCTATGCTTCTCGGCCT\n+CG\n+>NODE_3_length_311_cov_2.40234\n+CCGTCCTTCATCGGCTCCTAGTGCCAAGGCATTCACCATGCGCCATTGTTAACTTAACCT\n+CATTTACCTAACGGTAAATGCGATTAATGAGTTTAGCGATAATTAAACTTCAATAAAAAA\n+CTCAAAAAACGCGGTGTTCTCGGTTTCATTATGAAAAAATATATTTGATATTATCTAGTT\n+TTCAAAGAACAAGTTTTGAGAGTTAAATCTCTCAAAACTAAACAAAGTTTCGACGTGTGT\n+GTAGGTTTCCGTAATATTCCTTAGAAAGGAGGTGATCCAGCCGCAGGTTCTCCTACGGCT\n+ACCTTGTTACG\n+>NODE_4_length_64_cov_24.3333\n+TTCCTTAGAAAGGAGGTGATCCAGCCGCAGGTTCTCCTACGGCTACCTTGTTACGACTTC\n+ACCC\n+>NODE_5_length_374_cov_1.83072\n+GTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAACGAA\n+CTCTGGTATTGATTGGTGCTTGCATCATGATTTACATTTGAGTGAGTGGCGAACTGGTGA\n+GTAACACGTGGGAAACCTGCCCAGAAGCGGGGGATAACACCTGGAAACAGATGCTAATAC\n+CGCATAACAACTTGGACCGCATGGTCCGAGTTTGAAAGATGGCTTCGGCTATCACTTTTG\n+GATGGTCCCGCGGCGTATTAGCTAGATGGTGGGGTAACGGCTCACCATGGCAATGATACG\n+TAGCCGACCTGAGAGGGTAATCGGCCACATTGGGACTGAGACACGGCCCAAACTCCTACG\n+GGAGGCAGCAGTAG\n+>contigs_not_from_here\n+AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC\n+TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA\n+TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC\n+ATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG\n+CCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA\n+GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC\n+AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTG\n+AAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT\n+GACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTT\n+GCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGC\n+TGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGT\n+TACTGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT\n+GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTCACCG\n+CCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGC\n+TGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGT\n+CAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCG\n+>another_contig_not_from_here\n+ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTGTTTGTGATTG\n+GCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAAAGCTGGCTGAAGAATAAACA\n+TATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAATCTG\n+GAAAACTGGCAGGAAGAACTGGCGCAAGCCAAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGA\n+AAGAATATCATCTGCTGAACCCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGC\n+CGACTTCCTGCGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACACCTCGTCGATGGATTAC\n+TACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAACGTTGGGGCTG\n+GATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAATTGATGAAGTTCTCCGGCAT\n+TCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGACGAAGGCATGAGTTTCTCCGAGGCGACCACG\n+CTGGCGCGGGAAATGGGTTATACCGAACCGGACCCGCGAGATGATCTTTCTGGTATGGATGTGGCGCGTA\n+AACTATTGATTCTCGCTCGTGAAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAACCTGTGCT\n+GCCCGCAGAGTTTAACGCCGAGGGTGATGTTGCCGCTTTTATGGCGAATCTGTCACAACTCGACGATCTC\n+TTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAATATTGATGAAG\n+ATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTGTTCAAAGTGAAAAATGGCGA\n+AAACGCCCTGGCCTTCTATAGCCACTATTATCAGCCGCTGCCGTTGGTACTGCGCGGATATGGTGCGGGC\n+AATGACGTTACAGCTGCCGGTGTCTTTGCTGATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTCTGAC\n+ATGGTTAAAGTTTATGCCCCGGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGG\n+TGACACCTGTTGATGGTGCATTGCTCGG'..b'GATCACCTTAATCGTTTAG\n+TTGATTTAAAGGGTGAATATGTTGGTGTTCGTGAGTTCCGGGGGTTATCGACATACTATA\n+TCAAGGGTATTCCGCGTGCTGCCCGGACTAAAGTAGCGTTAGTCGAGGCAGAAACACTTG\n+ATGAAATGAACGATATTTTTGACCGCTTTGCTGAACAAACTGCAGAACGGGCTGCAAAAA\n+GACAGCAAGCCTAATTACGAGGAGGAGAACTTAAGTGTCACAAGAACTAGATCAAATGCG\n+CGTTCGGCGTGAAAAAATGGAAGAGTTAAAAGAAGCGGGGATTGAACCATTTGGCCGCCG\n+CTTCAAACGAGACCATCTTGCCCAAGACTTGCATGATAAGTTTGATCAATACGATAAAGA\n+AGAATTAAACGAGATGGGCGCCAAAGTAATTATTGCGGGTCGAATGACAAGAAAGCGGAG\n+TAGTGGTAAGGCTGGTTTCGCTGACTTTGTTGATCGGACTGGTAAGATTCAAGTTTACGC\n+TCGTAAGGATATGGTCGGGGATGAACCTTACCATGTTTTCAAACGGTCAGATATTGGTGA\n+CTTCCTTGGAATTGAAGGGGATGTTATCAAAACGGATACAGGTGAATTAACCGTTCGTGC\n+ACATAAAATTACCTTCTTGTCAAAAGCATTGCGTCCGCTTCCTAATAAGTGGGATGGGGT\n+TACTGATCCTGAAACTATCTATCGTCAGCGCTACCTTGATTTAATTTCTAACCCAGAAAG\n+CTTCAAGCGTTTCCACCAACGGACAGCGATTATCAAGGCCGTCCGGAAATACATGGATGA\n+TAATGGCTTTACAGAAGTTGAAACCCCAATTTTGAACACCCAAGCTGGTGGTGCTAATGC\n+GCGACCATTTATCACTCACCACAATGCGCTTGATATTGATATGTACTTGCGGATTGCTAC\n+CGAATTGTACCTTAAGCGGTTAATCGTTGGTGGCTTTGAACGAGTATACGAATTGGGCCG\n+GATTTTCCGGAATGAAGGGATGGACCCTCACCATAACCCTGAATTTACTACAATGGAAAC\n+TTATGCTGCTTACTTTGACTTCCAAGATGTTATGGATGAAACAGAGGGAATCGTTAAGGC\n+AGCAGCTAAAGTTGTTTCAGATGATGGAAAGATTACTTACCAAGGACATGAAATCGACCT\n+TGGAGGGAACTTTAAACGGATCACGATGGTGGATGCCGTTAAGGAAAAGACTGGCATTGA\n+CTTCAGCGATGAATCAATGACGGACGAAGATGCTAAGAAGTTAGCCGATGAACACAAGGT\n+TGAATATAAGCCTTACTGGACAAAGGGGCATATCTTGAACGCATTCTTTGAAGAGTTCGT\n+TGAAGATACACTTATTCAACCAACTTTTGTCTATGAATTCCCTGTCGAAGTTTCACCATT\n+AGCAAAGCGGAATGCTGATAATCCTGCGATGACTGATCGTTTCGAATTGTATGTTGATGG\n+TAGCGAATTGGCAAATGCCTTTAGTGAATTAAACGATCCAATTGACCAGAAGGAACGTTT\n+TGAAATGCAAGCAAAGGAAAAAGCTAACGGTAATGATGAAGCTGAACCAGTCGACTTAGA\n+TTACGTTCAAGCCCTCGAATACGGAATGCCACCTACTGGGGGACTTGGTATCGGAATCGA\n+TCGTCTTGTAATGCTCCTTACTGATGCTAAATCTATTCGGGATGTTATTCTCTTCCCAAC\n+AATGCGTCCAGAAAAGGAAGCTAAGAACGATTCAAAGAAAAAGAAGAACAAGAAGAAGTA\n+AGCTGAATGGTTGATGAAAAATTAGCATAAATAGATAACTCGTATTCCATTTTTATGGGG\n+TGCGAGTTTTTTTGTTTTAGATATGATAGAATAACTATCAATTTAGAGAAGAAATGAGGG\n+GAATTGATGGGAGAATTAGAAAAGTTAAAGCAAGACTGTATAGTAAAACAAAAGCGTGGG\n+TTGCATATAATAATAGCTTCGATCGCAGTATGGGGCGGTATTCTTGCAGTAGAACTACTT\n+AATGTTCCCGTTCTTACTAAAAACTTATTCGTATTTATCTGTACGGCCTTACTTTTACCA\n+GTATCTTATTTCATATCTCGATTGATTAATGTGGATTTTCAAAATAAAACAAATCCGTTG\n+ACTAAATTGGGGATGTTATTTTCGATGAATCAGCTTTTGTATCTTCTAATTGCAATGTGG\n+ATTTATCCGACTATTCCCAATAAAATGCTAATGGTGTTAGCGATAATATTTGGTGCTCAT\n+CTACTGCCATATAGTTGGTTGTATAATTCTAGGGCTTATCTTATTTCATCGATAGTAATT\n+TCAATATTAGCTTTATTGGTGGGAATTAATTTTAAACCGTTTATTTTAGCATCAGTTATG\n+CTTGCCATGGTAGCAGCATTTTGCATTACCTTAATATTAGAAAATCATCAACTTGACTGA\n+AGGGCTCCGATCCGTAAAGAAGATCGAAGCCTTTTTTGCTACATTATTTTAATTCTTGTT\n+AAGCTTACTAATAGTAGAAAAAACAATTGCAAAAAGAGACTAATAGTTATCAAGGGATGT\n+TCCTAACAATCTATCCAAGAAGATATAAAAATTGAATTGGTAAATACATCGAGTTACTAA\n+CCGAGTTTAATATTGATGCTTTCCTCCATACTAATTAGGTGATTTTCGGGATGGAAAAGA\n+AATGCTAATTGGTAAGAATGGTAGAGGAGGCGGGCAAACTTATTAAAGGAATAGTGAGTT\n+TAAGAAGCTAATAGACAGTAATGAAAATAAAATTCAAAAAAGTTAAAAAAAGGTGTTGAC\n+GAAAGAATGAAATCCATGTATAGTAGTTATCGTTGTCAAAACAGCTAAGTGCTGTTGAGA\n+TGGATTAACAAAAAAGTTAAAAATAATTGTTGACATCGACTTGGCAACATGATATATTAA\n+TAAAGCTGCTGATTGAGTTATCGATCAAAAGAAATTCAAAAATAATTAAAATTTCTTCTT\n+GACAAGCTAATCTAATACATGTTATAATAAATATGTTGATTGGCTGCTTAATTAGCCAAC\n+AGGTAGACCTTTGAAAACTGAACAAAGTTTCGACGAATCAAATGTGTAGGGTCTTCGATC\n+ACGATGTGATTTGAAGCAAAACATTTGCGAAGTCAATTCGCTTAATAACAAAGATAATTG\n+AGAGCTATTCAAGTTCTTATATATTTTATATGAGAGTTTGATCCTGGCTCAGGATGAACG\n+CCGGCGGTGTGCCTAATACATGCAAGTCGTACGCACTGGCCCAACTGATTGATGGTGCTT\n+GCACCTGATTGACGATGGATCACCAGTGAGTGGCGGACGGGTGAGTAACACGTAGGTAAC\n+CTGCCCCGGAGCGGGGGATAACATTTGGAAACAGATGCTAATACCGCATAACAACAAAAG\n+CCACATGGCTTTTGTTTGAAAGATGGCTTTGGCTATCACTCTGGGATGGACCTGCGGTGC\n+ATTAGCTAGTTGGTAAGGTAATGGCTTACCAAGGCGATGATGCATAGCCGAGTTGAGAGA\n+CTGATCGGCCACAATGGAACTGAGACACGGTCCATACTCCTACGGGAGGCAGCAGTAGGG\n+AATCTTCCACAATGGGCGCAAGCCTGATGGAGCAACACCGCGTGAGTGAAGAAGGGTTTC\n+GGCTCGTAAAGCTCTGTTGTTGGAGAAGAACGTGCGTGAGAGTAACTGTTCACGCAGTGA\n+CGGTATCCAACCAGAAAGTCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGT\n+GGCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTGCTTAGGTCTGA\n+TGTGAAAGCCTTCGGCTTAACCGAAGAAGTGCATCGGAAACCGGGCGACTTGAGTGCAGA\n+AGAGGACAG\n' |
| b |
| diff -r 675488238c96 -r 3061c8b029e5 test-data/meta_contigs_2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meta_contigs_2.fasta Fri Aug 05 15:21:27 2022 +0000 |
| b |
| b'@@ -0,0 +1,3015 @@\n+>NODE_1_length_55421_cov_26.1146_ID_4744408\n+GTACCAAGCGCCTTCTGGCCGTTCTGGCACTGGTGACGGTTTTTGCCCTTGTTCTGAGCG\n+GCTGCGCCACGCAGACCACCCAGAAGCCAACGCAGATCTCCCATAATTCCAGCAACTGGT\n+GGGATGCCTGGGTAGTTTACTACCTCTCCCAGTTCGTGCTTTGGATTGCCAAAGTCTGCG\n+GGGGCAGCTACGGCTGGGCCATCATCATCTTTACGGTTATCATCCGGGTGATCCTCCTGC\n+CTTTGAACGCGGTGCAGATCAACAGCACCAGAAAGATGCAGGAGATCCAGCCGGAACTGA\n+AGGCCTTGCAGGAGAAGTATTCCAGCAAGGACCTGGAGACCCGGAACAAGCTGAACGAAG\n+AAACGCAGAAGCTTTACAAGGAAGCGGGCGTCAATCCTTACGCCGGCTGCCTGCCGATGG\n+TGATCCAGTTGCCGGTTATGTGGGCCCTGTACCAGGCCATCTGGCGGACGCCAGAGATGC\n+AGAATGGTAAATTCTTGTGGATGGACCTGGGCAAGCCAGACCCATACTACATCCTGCCGA\n+TTTTGGCAACGGTATTTACCTTCCTGTCCTCATACATCGCGACTTTGTCGGTGCCTAAGT\n+CTTCCCAGACCACGATGACTAAGATGATGAGCTATGTCATGGCCATCATGGTCGGGATCT\n+GGGCCATCGTCTTCCAGTCCGCGATCTCCCTTTACTGGGTGATCTCCAACCTCTTCCAGG\n+TTGGCCAGACCCTGGTCCTGCAGAACCCATTCAAGTACCGCAAGGAGCAGGAAGCCAAGG\n+AAGAAGCTGAACGCGAGCGCCAGCGCAAGATTCGGCGGGCTTACAAGCGGATTAAGCGGA\n+AATAATTGAATGTTCATCTAAAGTTTTTTAGATAAAGTAGTGAAAGTGCTTTATCCATCA\n+TTTTTCATGGTGGAAATTGCGCTTTTTTTATTGGAAAAAACGAGGTAACGAGATGGTTCA\n+ACGTTTAACGGAATTTGATACGATCGCGGCGATCTCAACGCCGCTGGGAGAAGGCGGGAT\n+CTCCATCGTCCGCGTCTCCGGGGAAGATGCGGTCGCCATTGTCAACCGCTTGTTTAAGGG\n+CAAGGACCTGGAAAAGGTTCCCAGCCACACGATCAACTACGGCCACATCGTGGACCCGGC\n+AACCGGGCAGGTGATCGACGAGGTCATGGCCTCCGTCATGCTGGCGCCGAAGACTTTTAC\n+CAAGGAAGACATCGTGGAAATCAACTGCCACGGGGGGATCGTGGTCACCAATGACATCCT\n+GCAGCTGCTCTTGGCCAACGGGGCCAGAATGGCTGACCCGGGCGAATTTACCAAGCGGGC\n+CTTCGTCAACGGGCGGATCGACCTAACCCAGGCTGAAAGCGTGATGGACATCATCCGGGC\n+CAAGACTGACAAGGCCCGGCAGGTGGCGGTCAAGCAGCTTTCCGGCGGCCTTTTGACGGA\n+AATCCGGGCCCTGCGCCAGGAAATCCTGGATGTTTTGGCTAATGTCGAAGTCAACATCGA\n+CTACCCGGAATACGATGAAGAAGAAGTGACGGCCCAGAAGCTGCTGGCTTGCGCGGAAGC\n+CGTCAGCGGCAAGATTGACCGCCTGCTGGAGACGGCCCAGGAGGGGCAGATCCTCAGAAA\n+CGGCTTGAAGACAGCCATTGTCGGCCGGCCTAACGTGGGCAAGTCCTCCCTTTTGAACTA\n+CCTGACCCAAAGCGACAAGGCGATCGTAACGGACGTGGCCGGGACCACCCGGGACACCCT\n+GGAAGAGTTCGTGTCTGTCAAGGGGGTGCCCTTGGAGTTGATTGACACGGCTGGGATTCA\n+CCATACCGAGGACCAGGTGGAAAAAATCGGGGTCGAGCGGTCGAAGAAGGCCATTGCCCA\n+GGCGGACTTGATCCTGCTTTTGCTGGACGGCAGCCAGGAATTGACGGAAGAAGACCGGCA\n+GCTTTTGGAACTGACCGCCGGCAAAAAGCGGATCATCGTGCTGAACAAAACGGACCTGGG\n+CCAGAAGCTGACCGCGGCTGAGATTGCTAAAGAAAGCGGCAGTGAAGTGATCAGCACCTC\n+GATCATGATGAAGGAAAACCTGGACGAATTGGAAGCCTTGATCAAGAAGCTCTTCTTCAA\n+GGGGATCGAAAACTCCAACGACCAGGTCCTGGTGACCAACCAGCGGCAGGCGGGCCTTTT\n+GGCCAAGGCCAAGCAGCAATTGGCCGACGTGGCCAGCGGGCTTGAGGCAGGGATGCCGGT\n+TGACCTGGTTCAGATAGACTTTACCGGGGCCTGGGAAAGCCTGGGGGAAATCACTGGTGA\n+CAGCGCCCCGGATGAATTGATCAATGACCTCTTTAGTCAGTTCTGCTTAGGGAAATAGCG\n+AGGAAGGCAAGGAAGACGAAAAAAATGAAGACTTATGTTTCAAACGAATATGACGTGATC\n+GTAGTCGGTGCCGGCCATGCCGGCTGTGAAGCAGCCCTGGCCAGTGCCCGGATGGGGGAG\n+AAGACCCTGCTGCTCACCATCAGCCTGGACATGGTGGCCTTTATGCCCTGCAACCCCTCA\n+GTCGGCGGCCCGGCCAAGGGGACCGTGGTCAGAGAAATCGACGCTTTAGGCGGGGAGATG\n+GGCAAGAACATCGACAAGACCTACATCCAGATGCGGATGCTGAACACGGGCAAGGGGCCG\n+GCTGTCCGGGCATTAAGAGCCCAGGCTGACAAGTGGGACTACCACGAAGAGATGAAGCGG\n+ACCATCGAAAACACCCCTAATCTGACCCTGCGCCAGGCGGTCGTTGACGACTTGATCGTT\n+GAAGACGGGGAATGCCGGGGCGTAGTGACCAACACCGGGGCCCGCTACCGGGCCAAAAGC\n+GTGGTCTTGACGACGGGGACCGCGGCCAGAGGGCGGATTTTTATCGGGGAATTGAACTAC\n+TCATCCGGTCCGAACAACACGATTCCAGCCATTAAGCTGTCTGAAAGCCTGGAGAGACTG\n+GGCTTCAAGCTGCGCCGCTTTAAGACCGGGACGCCGCCCCGCGTCAACCGGCACACCATC\n+GACTATTCCAAGACCGAAGAAGAGCCGGGCGACAAGGAGCCCCGCCACTTCTCCTTTACC\n+AGCAGGGATGAAGACTACCTAACCGACCAGACTTCCTGCTGGATGACCTACACCAACCCG\n+AAGACCCACGAAATCATCAATGAAAACCTGGACCGGTCACCAATGTTCTCCGGTGATATC\n+GTCGGGGTAGGGCCGCGCTACTGCCCGTCAATTGAAACCAAGGTCGTCCGTTTCGCGGAC\n+AAGGACCGGCACCAGATCTTCCTGGAACCGGAAGGGCGGAAGACGGAAGAAATCTATGTC\n+GGGGACTTTTCTACCTCCATGCCGGAAGAAGTGCAGCTGGAAATGCTGCACACGGTCGCT\n+GGCCTGGAAAAGGTTGAAATGATGCGGCCGGGCTACGCCATTGAATACGACGTGGTTGAC\n+CCCTGGCAGTTAACCCACACCCTGGAAACCAAGCGGATCAAGCACCTGTATACGGCAGGG\n+CAGATGAACGGGACTTCCGGCTATGAAGAAGCCGCCGGCCAGGGCCTGATTGCTGGGATC\n+AACGCAGCCTTGAGCGCGGAAGGCAAGCCAGCCTTCACCCTGGGCCGGGACGAAGCTTAT\n+ATCGGGGTTTTGATCGATGACCTGGTAACTAAGGGGACGGAAGAACCTTACCGGCTCTTG\n+ACCAGCCGGGCTGAATACCGCCTGCTTCTCCGCCACGACAATGCCGACCTCCGCTTGACG\n+GAAAAGGGGCATGACCTGGGCTTGATTGACGATGATCGCTATGCTGAATTTTTGGCTAAG\n+AAGGAACTGATCCAGGAAGACCTGGACC'..b'TACTGTAGCTTGATATTGAGTGTTTGTACAGCTTGTACAGGATAGGTAGGAGCCATAGAA\n+ACCGGAACGCTAGTTTCGGTGGAGGCGTTGGTGGGATACTACCCTCGCTGTATGACCACT\n+CTAACCCGCACCACTAATCGTGGTGGGAGACAGTGTCAGGTGGGCAGTTTGACTGGGGCG\n+GTCGCCTCCTAAAAAGTAACGGAGGCGCCCAAAGGTTCCCTCAGAATGGTTGGAAATCAT\n+TCGCAGAGTG\n+>NODE_23_length_247_cov_1.20312_ID_9333398\n+ATTTTAAAGAAAATTTATGGTGATGACTTAAAGATCCTTGAAACAATCCCAGTTCGTTAT\n+GCATGTGATTGCTCGAAAGAACGTTTTGCCCACGCCCATGCAAGTATTTCTAAAGATGAT\n+ATGAAGAAGTTGATTGATGAAGACCACCATGCGGAAGCTGTTTGCCAATTCTGCGGGAAA\n+AAGTACGAATTTAACGAAGACGAATTAAAGAAGATCTACGCGGAAATTACTGCGAATGAT\n+GATAAAA\n+>NODE_24_length_243_cov_1.55851_ID_8972242\n+GAGTTAAGAGAAATAAAGGGGTAGCAGGCATTGACGATATGACAGTCTATGACCTTCTGC\n+CATATCTCAGAGAAAATAAGACGGAAATGATCGCTAGTTTGCGTGAGGGCAAGTATAAAC\n+CAGCACCAGTCAAACGGGTACAAATTCCGAAGCCTAATGGTGGAGTAAGAAAACTCGGAA\n+TACCAACGGTGGTGGACCGAATGGTTCAACAAGCTGTAGCCCAAATTCTTACGCCTATCT\n+TTG\n+>NODE_25_length_235_cov_25.2778_ID_9343528\n+AAGGAGGTGATCCAGCCGCAGGTTCTCCTACGGCTACCTTGTTACGACTTCACCCCAGTC\n+ATCTGCCCTGCCTTAGGCGGCTGACTCCTATAAAGGTTATCCCACCGACTTTGGGCATTG\n+CAGACTTCCATGGTGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGCGGCG\n+TGCTGATCCGCGATTACTAGCGATTCCGACTTCGTGTAGGCGAGTTGCAGCCTAC\n+>NODE_26_length_231_cov_1.71591_ID_8964874\n+CCGCTTAATTAAAGCCCCTGCAATAATTAAGGCGATAGCTAATACGCGGTTTAAAGCGAC\n+GATTGGTGAAGATAATCAGCAACTAGCGATTCGGCTGGTTATTCAACCTAAAATGACTAC\n+TGATGATTGGTTTCACCAGCTACTACAATTTGTAACGGCTTTAGGAAATGTTATGTAAGC\n+CGATGAAAAAGGAGCGGAAAAATGAGATTAGATAAATTTTTAAAAGTATCA\n+>NODE_27_length_231_cov_3.19318_ID_8969130\n+GACACGGCCCAAACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCACAATGGACGAAAGT\n+CTGATGGAGCAACGCCGCGTGAGTGAAGAAGGGTTTCGGCTCGTAAAACTCTGTTGTTAA\n+AGAAGAACATATCTGAGAGTAACTGTTCAGGTATTGACGGTATTTAACCAGAAAGCCACG\n+GCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCC\n+>NODE_28_length_223_cov_33.5179_ID_9335488\n+CACTGGTGTTCTTCCATATATCTACGCATTCCACCGCTACACATGGAATTCCACTCTCCT\n+CTTCTGCACTCAAGAATGACAGTTTCCGATGCAGTTCCACGGTTGAGCCGTGGGCTTTCA\n+CATCAGACTTATCATTCCGCCTGCGCTCGCTTTACGCCCAATAAATCCGGACAACGCTTG\n+CCACCTACGTATTACCGCGGCTGCTGGCACGTAGTTAGCCGTG\n+>NODE_29_length_219_cov_25.5122_ID_8985538\n+CCACCTACGTATTACCGCGGCTGCTGGCACGTAGTTAGCCGTGACTTTCTGGTTGATTAC\n+CGTCAAATAAAGACCAGTTACTGCCTCTATCCTTCTTCACCAACAACAGAGCTTTACGAT\n+CCGAAAACCTTCTTCACTCACGCGGCGTTGCTCCATCAGACTTGCGTCCATTGTGGAAGA\n+TTCCCTACTGCTGCCTCCCGTAGGAGTTTGGGCCGTGTC\n+ATCAAAAAATGGTCTTGCGTCGTGGTGATTTTGCGATTCGTGGATCGATTCTTGATATCT\n+ATGCCTTAAATACTGATAATCCGGTTAGAATTGATCTTTTTGATGCAGAAGTTGATTCAC\n+TTCGGTATTTTGATGCTAGTACCCAACGGAGTATAGATAATGTTGAAGAAGTTCAGATAC\n+TGCCAGCGACAGACTTTATTATCCCAGC\n+AAGGAGGTGATCCAGCCGCAGGTTCTCCTACGGCTACCTTGTTACGACTTCACCCTAATC\n+ATCTGTCCCACCTTAGGCGGCTGGTTCCTAAAAGGTTACCCCACCGACTTTGGGTGTTAC\n+AAACTCTCATGGTGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGCGGCAT\n+GC\n+TCCATCGCTCATAACGATTCGGTGCAGTACAGGAATTTCAACCTGTTGTCCATCGCCTAC\n+GCCTCTCGGCCTCGCCTTAGGTCCCGACTTACCCTGGGCGGACGAGCCTTCCCCAGGAAA\n+CCTTAGTCATTCGGTGGACAGGATTCTCACCTGT\n+>NODE_33_length_81_cov_294.346_ID_9343286\n+CAAAGATAGGCGTAAGAATTTGGGCTACAGCTTGTTGAACCATTCGGTCCACCACTGTTG\n+GTATTCCGAGTTTTCTTACTC\n+>NODE_34_length_59_cov_26.75_ID_2882278\n+AAGTCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCC\n+>NODE_35_specially_unaligned\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n+\n' |
| b |
| diff -r 675488238c96 -r 3061c8b029e5 test-data/meta_ref_1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meta_ref_1.fasta Fri Aug 05 15:21:27 2022 +0000 |
| b |
| b'@@ -0,0 +1,918 @@\n+>Lactobacillus_plantarum/22_55k.fa\n+TCGCATGGCAACGTCCTACCCTCGCAGGGAGCGATCCCCCAACTACTCTCGGCGCTAAGA\n+AGCTTAACTTCTGTGTTCGACATGGGAACAGGTGTATCCTTCTCGCCATCATCACCACAC\n+TATGTGAAACTAAATATTAAATTGAATAATATCCATTTAACCTTGCGGTTAAATGAGCCG\n+TGACAGTCTCGAACTGTCGACCCTCTGATTAAAAGTCAGATGCTCTACCAACTGAGCTAA\n+CGGCTCATGATGGAGGATACAGGGCTCGAACCTGTGACCCTCTGCTTGTAAGGCAGACGC\n+TCTCCCAACTGAGCTAATCCTCCAATTTCGCATGGCAACGTCCTACCCTCGCAGGGAGCG\n+ATCCCCCAACTACTCTCGGCGCTAAGAAGCTTAACTTCTGTGTTCGACATGGGAACAGGT\n+GTATCCTTCTCGCCATCGTCACCACACTATTGAGAAACTTGTGCTCTCAAAACTAGCTAA\n+TATCAAATATCTTCATATAAACCGGAACACCAATTACTTGGTTAAGTCCTCGACCGATTA\n+GTATTAGTCCGCTTCATGCGTCACCGCACTGCCACTTCTAACCTATCTACCTGATCATCT\n+TTCAGGGGTCTTACTTCCATAAAGGAATGGGAAATCTCATCTCGAGGTGTGTTTCACACT\n+TAGATGCTTTCAGCGTTTATCACATCCATACGTAGCTACCCAGCGATGCGCCTGGCGGCA\n+CAACTGGTACACCAGAGGTATGTCCATCCCGGTCCTCTCGTACTAAGGACAGGTCCTCTC\n+AAATTTCCTACGCCCGCGACGGATAGGGACCGAACTGTCTCACGACGTTCTGAACCCAGC\n+TCGCGTACCGCTTTAATGGGCGAACAGCCCAACCCTTGGGACCGACTACAGCCCCAGGAT\n+GCGATGAGCCGACATCGAGGTGCCAAACCTCCCCGTCGATGTGGACTCTTGGGGGAGATA\n+AGCCTGTTATCCCCAGGGTAGCTTTTATCCGTTGAGCGATGGCCCTTCCATACGGTACCA\n+CCGGATCACTAAGCCCGACTTTCGTCCCTGCTCGACCTGTCTGTCTCGCAGTCAAGCTCC\n+CTTGTGCCTTTACACTCTGCGAATGATTTCCAACCATTCTGAGGGAACCTTTGGGCGCCT\n+CCGTTACTTTTTAGGAGGCGACCGCCCCAGTCAAACTGCCCACCTGACACTGTCTCCCAC\n+CACGATTAGTGGTGCGGGTTAGAGTGGTCATACAGCGAGGGTAGTATCCCACCAACGCCT\n+CCACCGAAACTAGCGTTCCGGTTTCTATGGCTCCTACCTATCCTGTACAAGCTGTACAAA\n+CACTCAATATCAAGCTACAGTAAAGCTCCATGGGGTCTTTCCGTCCTGTCGCGGGTAGTC\n+CGCATCTTCACGGACAATATAATTTCACCGAGTCTCTCGTTGAGACAGTGCCCAGATCGT\n+TACGCCTTTCGTGCGGGTCGGAACTTACCCGACAAGGAATTTCGCTACCTTAGGACCGTT\n+ATAGTTACGGCCGCCGTTTACTGGGGCTTCAATTCTGAGCTTCGCCGAAGCTAACCCATC\n+CTTTTAACCTTCCAGCACCGGGCAGGCGTCAGCCCCTATACGTCATCTTACGATTTTGCA\n+GAGACCTGTGTTTTTGATAAACAGTCGCCTGGGCCTATTCACTGCGGCTGATCTTGCGAT\n+CAGCACCCCTTCTCCCGAAGTTACGGGGTCATTTTGCCGAGTTCCTTAACGAGAGTTCAC\n+TCGCTCACCTTAGGATTCTCTCCTCGACTACCTGTGTCGGTTTGCGGTACGGGTAGTTAA\n+GTACTCACTAGAAGCTTTTCTCGGCAGTGTGACATCAGACGCTTCGCTACTAAATTTCGC\n+TCCCCATCACAGCTTGTCCTTAAAGTGAAAAGCATTTGACTCTTCACAAGACTTACTGCT\n+TGGACATTCTAATCCAACAGAATGCACATCTTAGCCTCCTGCGTCCCTCCATTGCTCAAA\n+CGCACTTAACTAGTACAGGAATCTCAACCTGTTATCCATCGTCTACGCTTCTCGGCCTCG\n+ACTTAGGTCCCGACTAACCCTGGGAGGACGAGCCTTCCCCAGGAAACCTTAGTCATTCGG\n+TGGATAGGATTCTCACCTATCTTTCGCTACTCATACCGGCATTCTCACTTCTAAGCGCTC\n+CACAAGTCCTCACGATCTTGCTTCACCGCCCTTAGAACGCTCTCCTATCACGCGACCTAA\n+TGGTCGCATCCATGGTTTCGGTAGTATGCTTAGCCCCGGTACATTTTCGGCGCAGGATCA\n+CTCGACTAGTGAGCTATTACGCACTCTTTAAATGGTGGCTGCTTCTGAGCCAACATCCTA\n+GTTGTCTATGCAACTCCACATCCTTTTCCACTTAGCATACATTTAGGGACCTTAACTGAT\n+GGTCTGGGCTGTTCCCCTTTCGACGGTGGATCTTATCACTCATCGTCTGACTCCCGGATA\n+TGAATCAATGGCATTCGGAGTTTATCTGAATTCAGTAACCCAAGACGGGCCCCTAGTCCA\n+AATAGTGCTCTACCTCCATGATCCTAATTCCGAGGCTAGCCCTAAAGCTATTTCGGAGAG\n+AACCAGCTATCTCCAAGTTCGTTTGGAATTTCACCGCTATCCACACCTCATCCCAGCAAT\n+TTTCAACTTACACGGGTTCGGTCCTCCAGTGCGTTTTACCGCACCTTCAACCTGGACATG\n+GATAGGTCACCTGGTTTCGGGTCTATAACCTCGTACTCAAAACGCCCATTTCAGACTCGC\n+TTTCGCTACGGCTCCGACTTTTTAGTCTTAACCTTGCACGGGATCATAACTCGCCGGTTC\n+ATTCTACAAAAGGCACGCCATCACGCATTAACGCGCTCTGACTTATTGTAGGCACATGGT\n+TTCAGGAACTATTTCACTCCCCTCCCGGGGTGCTTTTCACCTTTCCCTCACGGTACTGGT\n+TCACTATCGGTCACTAGGTAGTATTTAGCCTTGGGAGATGGTCCTCCCGGATTCCGACGG\n+AATTTCACGTGTTCCGCCGTACTCAGGATCCTGAACTGAGAGAATTTGATTTAATCTACT\n+GGGCTATCACCATCTATGGCGGATTTTCCCAAATCCTTCGACTATCAAGTTCTTTGGTAA\n+CTCAAATGTTCAGTCCTACAACCCCAAAGTGCAAGCACTTTGGTTTGGGCTGTTCCCCGT\n+TCGCTCGCCGCTACTTAGGGAATCGAAATTTCTTTATATTCCTGCTGCTAATGAGATGTT\n+TCAGTTCACAGCGTTTACCTCCAACTAGACTATGAATTCATCTAGTGGTAACAGTTGATT\n+AAAACTGCTGGGTTGCCCCATTCGGAAATCTCCGGATCATAGCTTACGTACAGCTCCCCG\n+AAGCATATCGGTGTTAGTCCCGTCCTTCATCGGCTCCTAGTGCCAAGGCATTCACCATGC\n+GCCCTTGTTAACTTAACCTCATTTACCTAACGGTAAATGCGATTAATGAGTTTAGCGATA\n+ATTAAACTTCAATAAAAAACTCAAAAAACGCGGTGTTCTCGGTTTCATTATGAAAAAATA\n+TATTTGATATTATCTAGTTTTCAAAGAACAAGTTTTGAGAGTTAAATCTCTCAAAACTAA\n+ACAAAGTTTCGACGTGTGTGTAGGTTTCCGTAATATTCCTTAGAAAGGAGGTGATCCAGC\n+CGCAGGTTCTCCTACGGCTACCTTGTTACGACTTCACCCTAATCATCTGTCCCACCTTAG\n+GCGGCTGGTTCCTAAAAGGTTACCCCACCGACTTTGGGTGTTACAAACTCTCATGGTGTG\n+ACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCG'..b'ATAGGCTTCTTAGGAATCAAAGTTAATTCCTAAGAAGCCTATTTTAATACC\n+GATTTACTCAATTAAGATTGTCTGACACGTTTGTGAAGCCCCCACCAGCAGGCAATCAGT\n+ATGCTAATCACACCACCAATAATACTCGACCATATGCCGATTTTTAGTCCTGGTGTGTGA\n+TACGTCAATCGAATCTGGTGCCGGCCGGCTGTCAACTTGGCCCCCACAAACCCTTTGTTG\n+ACAACTTGGGTCCTAACGGTTTGACCGTCAACTCGTAGCTGCCAACCAGTCGAATACGGA\n+ATTGACGTTGTTAACACGGTTGCTGTCTTAGTCAGCGTGGTTCCCGTAATCTGGTTGTTC\n+GTCACTTGTTGATGCTTCAACCCACTCGTCTGTAGTTGCCGCGTCCGTTGACGATAAGTC\n+TTCCCAAGCGGTACAGCGATCAGTTTAGCGGACTTAAAATGCAAACTACGAATGCTCGTA\n+AAGTTCAGCGTAATCAGCTTACGCGCGTACTTGCTATACCCTAAGTTGATTACTGCTGAT\n+GTCCGGGGCTCATAGTCTGACATATTCGTGGTACCCAACTGACTAAAACTCGTCAAGTTA\n+TCCGTTGTCTGAGCAGTTAAAGAATACCCACTAGCGCTCAAATTGCCCTTCAGACCATCG\n+CGAACATCATCTAGATAATCGACTTTGGTATACGGACGGGCCGTGAACACGTTGATATTT\n+TGACTCGTTGTCAAGGCGTGCTTGATTGAGGAACGCCGATAACTGATGCCATCTAGCACA\n+AGATAGAGTTCCGTATTTCGATACTTCTTAGGGTGTTGAATGGTCAATTGGTACGGTATC\n+TGGTGCCCCTGCACATCACTGACCATGCTCGTTAACTCGTCGGCATTGTTTTCCTGATTT\n+TTCTGGACTAACTTTTGATTAGCTGCAATCAAGTTCAACACGCGGTTTGACGGTGTCGTC\n+AGGCCAGTTGCCGGCGTCAAACTTTCTCGTTGTTCCGGCGTTAATGTGATCGTATCTGCC\n+GGTAACTTAGTCAACGCGTTGTTCGACGCTCCCGTTGCATGTTGATTGCGGTAAATAATC\n+ACCTTGTCCAACGTATCCAAAACATTCGTCGTATCCGCTTGAACCGTATAAGCGACGTTT\n+TTTCCGGTAACGGTTGGCTTGACAGTCTTAACACCACTAACCTGCTGCGTAGTGACTGCA\n+CCTTGTAACAAGGCTTGCTCGCGGTCAACTGCGTTCAAGCGATTAAATTGGCGTTGACTA\n+ATCTGATGCTGCTGTGTATAAACTAACGGCAACGCATTCTTGGATTTTAACAAGATCGTG\n+CCGGTATGATTACTCATGCCATAAATAAACTTGTCCGCAAAAATCTTCGGTTCGCCAGTT\n+TTCATCTTAACAACCTCATATCCGGCTGGTAAGGCTTGTTTCTTCAACTGGTCCTCACGT\n+GCAAATAAATATTTAACACCTAATAAGTTATACATCGTCGTCCGACCGTCCAACGAACCG\n+AGTGGCGAGTTCATCGCATACTCTGAGTTGCCTAAGGCCTGACTAAATGCCCCCACGTAA\n+CCATTTTGAACTGAAAAATACGATCCAACCGTGTGAGTTCCTAACACCATCGGCACATCA\n+CTCTCAGCCGAACGCATCGTATAGTAGTTGGGTGCCAAAGCCGTTCGATAAAATTGGCTA\n+GTCGTGGTTAAACTTTTTTGCGCGCCATCAAAATAATTTTTGACCCATTTCATTGCCGCG\n+CCCTGCCGCAACTGCTCAGTACTATTAGAATTAGTATTGATACTCAACCAGCCCAGTCCG\n+TTATTCGCCAGGTTCAGCGTGACAATTCCCAGTAATAACACATAAAATTGCCGATTGGTC\n+AATTTTAAGGATTGTTTGACCAGCAGGACCCCAATTAACGCTAACAAGATGAGATATGTC\n+GCAATATCATGTTTGCGGATATTGAGATAGAATCCATTGATCAGCCAAATAATGACAAGC\n+AGACCGCCACTAATACCAGCCAACCATTTTAAATCAGCCGCTGTCAGAGCAGTGACTTGG\n+TCCATAAATGCCATCGTCGCATAAGCAAACACGAGGGTTGCCATCAACAACCATCGATTA\n+GAAGGTGTTGAAAAAACGTTGAATACGGCCGCAAATTGAGGCAACAAAATACCCAACATC\n+ATCACGACCAGTACCCAATTAAGCACCCAATAGCGTCTGAAATGACGTAGTGTATAAATA\n+ATTGCAATAAAGCTAATGCTACTCAGCCCGAGGGTCACCCAGTATTGGACACTGCCACCA\n+TTGGTCAACAGTCGATTGGGTAAATTAACGTAATAATTGATGGGATAACTTGTCAAGCCA\n+TTCGCAAAGTTAAAACTCGCACGCGTTGCCGTCAACATCGCGAGCAGCGTGGGCACTAGT\n+AAGATGCCTGCCATCGTGACACCAAGACCAACCGCCACTAGTAACCGCCAAAATAACTGT\n+CCAAACGACCGCATCGTTAAATGATCACGACGACGTGACCAGAAACGCACCAAAGCATAG\n+ACTAAGCCGCCCAATGCGAGTAAGTAAGCAAAATAGAAGTTACTCAAAATTACAACGGCG\n+GTAATCAGACTGAGTGGTAACCAATGTCGGCCTCGTAAGACCCGTTCAATCGCCCAACAC\n+AGTAGCGGAAACCAAATCATTGGTAACAAGAAAAACGGGTGGTGCATCCCAACATAGAAC\n+GTATACGCGGTAAACGTATACGTCAAAGCTCCAATCAATTGACTGACACGTTTGAACTTG\n+AACTGCCGACTGAAACCTAGAAAAGCAAGTCCAACGAAGTACAATCGCAGCAAGATCAAC\n+GCTTGGTAGGCCCATTCCAAATGAGCGCGCGAAACAAACGCCACTAAATAATTAAACGGA\n+TCACCGACCACGTAGTAGGAAAAAGTCGTCAGTTGATCGGCCCCCAAGCCGAGATTCCAT\n+GACCAACTGAATAATTGTTGTGGGTGGTGCTGTAAGATCCGCTGAAATTCCAATAAAATC\n+GGGAAGTGTTGGGCGATGCCATCCACTTCCCAAATCAATGTCCGGCCGGCTAAGAAAAGC\n+CCACTGTAAGTAATCGTCGCAATAACCACAAACATCGCCGTATACCAGACGACTAGTGGT\n+ATCTTCCGTACTGTCTTCAAATCAGGTGCCCCTATCTTGTAATTACGTCGACAACGCAAT\n+CCCCATATTTTGCCATCTCAAACAATGTTTCTATTTTACCATGAACAATTTCGTCTCGTG\n+ATGTTCAGTTTGAATCTTAATAAATTCGTGATTCACAACTGTCCCATCAACAACTAACGC\n+CAATCCCAGTTATCTAAAGTTTCAATCTTAGTAGTCGCCGGATAACTCCCAAACAACTGT\n+ACTAAAGGTTGTAAGCCACTCACAGCATTATCACGTTGTAAGTTGATCGTAGCGATTGCC\n+GCTTGATCATGACGGTTAGGATCGAGCTCAAAAGCAGCAACTTGCTCATATAAATTCAGC\n+GTAATCAATTTGGCGTCCCGCGCACTTGGATGCGCATTTAATTCCCACAGCGTCTTGCGC\n+CCGGCCACGAACGCGGGCGTGGCCTCTGGTAAATCTGCCAAAAAACAATATGCCGAATAA\n+ACCTGGCGATAATAAAGTTTGGTCATATCCAAAACAATCAACTCCCAATCATGTTGAGTG\n+GTCCAAGCACCCGATACGCGCTCACCACTCATTTTAATCAATGATAGCTAACTATTTAAA\n+CCAATTCAATCTGAAATTTTACAACTCAAATTAGTGTCACAAACGCCACTTCCCCAATCT\n+TAAAGTTGTTTTTTAGACCGCAATACTGGCGACAATAAAAGTGTCCCTAGGTTTTTTAAC\n+CCAGGGACTACTCAACATTGCTATTTTTATTCGATAACA\n' |
| b |
| diff -r 675488238c96 -r 3061c8b029e5 test-data/meta_ref_2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meta_ref_2.fasta Fri Aug 05 15:21:27 2022 +0000 |
| b |
| b'@@ -0,0 +1,1001 @@\n+>Lactobacillus_delbrueckii_bulgaricus_ATCC_BAA-365/32_60k.fa\n+ACTCCGCCTGTCAGACTCGAACTGACGACATCCTGATTAACAGTCAAGCGCTCTACCAAC\n+TGAGCTAAGGCGGAATGTTGAGCGCGGCAGCTTCCTATCCTCGCAGGCAGTTTCCCACCA\n+ACTACTTTCGGCGTTAAGAAGCTTAACTACTGTGTTCGGCATGGGAACAGGTGTATCCTT\n+CTTGCCATTGCCACCGCACTCTTGCTTGAGCTTGCACGCTCAAAACTGAATATCTTTTAC\n+CAAGTCAAAACCTCATTGCTTCGCTCTTTTGGTCAAGTCCTCGACTGATTAGTACCGGTC\n+CGCTCCAAGCCTCACGGCTCTTCCACTCCCGGCCTATCTACCTCATCGTCTCTGAGGTGT\n+CTTACTTTCTTGAAGAAATGGGAAATCTCATCTTGAGGGGGGCTTCGCACTTAGATGCTT\n+TCAGCGCTTATCCCGTCCGCACATAGCTACCCAGCGATGCCTTTGGCAAGACAACTGGTA\n+CACCAGCGGTGCGTCCATCCCGGTCCTCTCGTACTAAGGACAGCTCCTCTCAAATTTCCT\n+GCGCCCACGACGGATAGGGACCGAACTGTCTCACGACGTTCTGAACCCAGCTCGCGTGCC\n+GCTTTAATGGGCGAACAGCCCAACCCTTGGGACCGACTTCAGCCCCAGGATGCGACGAGC\n+CGACATCGAGGTGCCAAACCTCCCCGTCGATGTGAACTCTTGGGGGAGATAAGCCTGTTA\n+TCCCCAGGGTAGCTTTTATCCGTTGAGTGATGGCCCTTCCATGCGGTACCACCAGATCAC\n+TAAGCCCTACTTTCGTACCTGCTCGAGTTGTCTCTCTCGCAGTCAAGCTCCCTTTTACCT\n+TTACACTCTGCGAATGATTTCCAACCATTCTGAGGGAACCTTTGGGCGCCTCCGTTACAC\n+TTTAGGAGGCGACCGCCCCAGTCAAACTGCCCGTCAAACACTGTCCTCGGCCTGGATCAC\n+AGGCCTAAGTTAGAGCATCCGTCAAGCAAGGGTAGTATCCCAACAGCGCCTCAGATAAGA\n+CTGGCGTCCTATCTTCTCCGGCTCCTACCTATCCTGTACATGCTTGACAGATACCCAATA\n+TTAAACTGCAGTAAAGCTCCATGGGGTCTTTCCGTCCTGTCGCGGGTAACCCGCATCTTC\n+ACGGGTATTATAATTTCACCGAGTCTCTCGTTGAGACAGTGCCCAAATCATTACACCTTT\n+CGTGCAGGTCGGAACTTACCCGACAAGGAATTTCGCTACCTTAGGACCGTTATAGTTACG\n+GCCGCCGTTTACTGGGGCTTCAATTCAAACCTTCGCTTGCGCTAAGCTCTCCTCTTAACC\n+TTCCAGCACCGGGCAGGTGTCAGCACCTATACTTCATCTTACGATTTTGCAGATGCCTGT\n+GTTTTTGATAAACAGTTGCTTGGGCCTTTTCACTGCGGCTGATCTTGCGACCAGCGCCCC\n+TTCTCCCGAAGTTACGGGGCCATTTTGCCGAGTTCCTTAACGAGAGTTCTCTCGCTCACC\n+TGAGGATACTCTCCTCGACTACCTGTGTCGGTTTGCGGTACGGGTGCACCGTCTCTGGCT\n+AGAAGCTTTTCTCGGCAGTGTGACGTCGCAGCCTTCGCTACTTTAATTTCGCTCCTCATC\n+ACGCCTTGTCCTTATGAGAGCAAGCATTTGACTCGCTCTCAGACTTGACGCTTGAACGTG\n+GTATCCAGCACCACGCGCTGCTAGCCTCCTGCGTCCCTCCATCGCTCATAACGATTCGGT\n+GCAGTACAGGAATTTCAACCTGTTGTCCATCGACTACGCCTCTCGGCCTCGCCTTAGGTC\n+CCGACTTACCCTGGGCGGACGAGCCTGCCCCAGGAAACCTTAGTCTTGCGGCGGACAGGA\n+TTCTCACCTGTCTTTCGTTACTCATACCGGCATTCTCACTTCTAGAAGCTCCACATGTCC\n+TCTCGGTCATGCTTCACCGCCGCTAGAACGCTCTCCTACCACGTGCATAAACGCACATCC\n+ACAGTTTCGGTATCATGCTTAGCCCCGGTAAATTTTCGGCGCGGCGTCACTCGACTAGTG\n+AGCTATTACGCACTCTTTGAATGATGGCTGCTTCTGAGCCAACGTCCTAGTTGTCTGCGC\n+AACTCCACATCCTTTTCCACTTAGCATGAATTTTGGGACCTTAACTGGTGATCTGGGCTG\n+TTTCCCTTTCGACTACGGATCTTATCACTCGCAGTCTGACTCCCGCACATAAATGTCTGG\n+AATTCGCAGTTTATCTGAATTCAGTAACCCTTGACGGGCCCCTAGTCCAAACAGAGCTCT\n+ACCTCCAGCATCCTCTTTGCGAGGCTAGCCCTAAAGCTATTTCGGAGAGAACCAGCTATC\n+TCCAAGTTCGTTTGGAATTTCACCGCTACCCACAACTCATCCCCGCAATTTTCAACTTAC\n+GTGGGTTCGGTCCTCCAGCGCGTTTTACCGCGCCTTCAACCTGGTCATGGGTAGGTCACT\n+TGGTTTCGGGTCTGCGTCAGCCAACTGCTCGCCCTCTTCAGACTCGCTTTCGCTACGGCT\n+CCGTCTTTTCTGACTTAACCTTGCTGACTAACGCAACTCGCCGGTTCATTCTACAAAAGG\n+CACGCCATTACCCGTTAACGGGCTCTGACTACTTGTAGGCACACGGTTTCAGGTTCTCTT\n+TCACTCCCCTCCCGGGGTTCTTTTCACCTTTCCCTCACGGTACTGGTTCACTATCGGTCA\n+CTGGTTAGTATTTAGCCTTGCGAGATGGTCCTCGCGGATTCAAACGGGATTTCACGTGTC\n+CCGCCCTACTCAGGATACTGATAGGCCTCCTTTGGATTTCGCTTACGGGGCTCTCACCCT\n+CTCTGGCGCGCTTTCCCAAACGCTTCTGCTATCCTCTGAAGTGCCATGTCTCAGTCCTAC\n+AACCCCGGCAGATAAATCTGCCGGTTTGGGCTCTTTCCTGTTCGCTCGCCGCTACTTGGG\n+AAATCGATATTTCTTTCTCTTCCTGCAGCTACTTAGATGTTTCAGTTCACTGCGTGTTCC\n+CTCCTTAAGCTATGTATTCACTTAAGGATAGCATGTCTGCACATGCTGGGTTCCCCCATT\n+CGGAGACCTCCGGATCAAAGCCTACTTACGGCTCCCCGAAGACTTTCGCGGTTAGTCGCG\n+TCCTTCATCGGCTTCCAGTGCCAAGGCATTCACCGTGCGCCCTTCTTCACTTGACCTTGC\n+AAGTTTGTTCTTTCGAACTCTCTCGGTCGCTTTGCAATGTTTTCATTGATCTCAATGATT\n+CTCGGTTTTTTCTTGGAATTAAGATATTCAGTTTTCAACGTACAAGTGAGAGCTGATACT\n+CTCAAAACTGAACAAAGTTTCTTTTGCAGTGTGCTTCCGTAACTGATGGATTTCTCTTAG\n+CATTTCTGCTCTCCATCCATCCGTTTTCCTTAGAAAGGAGGTGATCCAGCCGCAGGTTCT\n+CCTACGGCTACCTTGTTACGACTTCACCCCAGTCATCTGCCCTGCCTTAGGCGGCTGACT\n+CCTATAAAGGTTATCCCACCGACTTTGGGCATTGCAGACTTCCATGGTGTGACGGGCGGT\n+GTGTACAAGGCCCGGGAACGTATTCACCGCGGCGTGCTGATCCGCGATTACTAGCGATTC\n+CAGCTTCGTGCAGGCGAGTTGCAGCCTGCAGTCCGAACTGAGAACAGCTTTAAGAGATCC\n+GCTTACCCTCGCGGGTTCGCTTCTCGTTGTACTGCCCATTGTAGCACGTGTGTAGCCCAG\n+GTCATAAGGGGCATGATGACTTGACGTCATCCCCACCTTCCTCCGGTTTGTCACCGGCAG\n+TCTCTTTAGAG'..b'CCTAAACCTGCCAGGTATTCGTTGACGGCAA\n+TGGTCGGATGAACGGTGATTTCGCCCAGCCGGTCCAGGTCTTCCTGGATCAGTTCCTTCT\n+TAGCCAAAAATTCAGCATAGCGATCATCGTCAATCAAGCCCAGGTCATGCCCCTTTTCCG\n+TCAAGCGGAGGTCGGCATTGTCGTGGCGGAGAAGCAGGCGGTATTCAGCCCGGCTGGTCA\n+AGAGCCGGTAAGGTTCTTCCGTCCCCTTAGTTACCAGGTCATCGATCAAAACCCCGATAT\n+AAGCTTCGTCCCGGCCCAGGGTGAAGGCTGGCTTGCCTTCCGCGCTCAAGGCTGCGTTGA\n+TCCCAGCAATCAGGCCCTGGCCGGCGGCTTCTTCATAGCCGGAAGTCCCGTTCATCTGCC\n+CTGCCGTATACAGGTGCTTGATCCGCTTGGTTTCCAGGGTGTGGGTTAACTGCCAGGGGT\n+CAACCACGTCGTATTCAATGGCGTAGCCCGGCCGCATCATTTCAACCTTTTCCAGGCCAG\n+CGACCGTGTGCAGCATTTCCAGCTGCACTTCTTCCGGCATGGAGGTAGAAAAGTCCCCGA\n+CATAGATTTCTTCCGTCTTCCGCCCTTCCGGTTCCAGGAAGATCTGGTGCCGGTCCTTGT\n+CCGCGAAACGGACGACCTTGGTTTCAATTGACGGGCAGTAGCGCGGCCCTACCCCGACGA\n+TATCACCGGAGAACATTGGTGACCGGTCCAGGTTTTCATTGATGATTTCGTGGGTCTTCG\n+GGTTGGTGTAGGTCATCCAGCAGGAAGTCTGGTCGGTTAGGTAGTCTTCATCCCTGCTGG\n+TAAAGGAGAAGTGGCGGGGCTCCTTGTCGCCCGGCTCTTCTTCGGTCTTGGAATAGTCGA\n+TGGTGTGCCGGTTGACGCGGGGCGGCGTCCCGGTCTTAAAGCGGCGCAGCTTGAAGCCCA\n+GTCTCTCCAGGCTTTCAGACAGCTTAATGGCTGGAATCGTGTTGTTCGGACCGGATGAGT\n+AGTTCAATTCCCCGATAAAAATCCGCCCTCTGGCCGCGGTCCCCGTCGTCAAGACCACGC\n+TTTTGGCCCGGTAGCGGGCCCCGGTGTTGGTCACTACGCCCCGGCATTCCCCGTCTTCAA\n+CGATCAAGTCGTCAACGACCGCCTGGCGCAGGGTCAGATTAGGGGTGTTTTCGATGGTCC\n+GCTTCATCTCTTCGTGGTAGTCCCACTTGTCAGCCTGGGCTCTTAATGCCCGGACAGCCG\n+GCCCCTTGCCCGTGTTCAGCATCCGCATCTGGATGTAGGTCTTGTCGATGTTCTTGCCCA\n+TCTCCCCGCCTAAAGCGTCGATTTCTCTGACCACGGTCCCCTTGGCCGGGCCGCCGACTG\n+AGGGGTTGCAGGGCATAAAGGCCACCATGTCCAGGCTGATGGTGAGCAGCAGGGTCTTCT\n+CCCCCATCCGGGCACTGGCCAGGGCTGCTTCACAGCCGGCATGGCCGGCACCGACTACGA\n+TCACGTCATATTCGTTTGAAACATAAGTCTTCATTTTTTTCGTCTTCCTTGCCTTCCTCG\n+CTATTTCCCTAAGCAGAACTGACTAAAGAGGTCATTGATCAATTCATCCGGGGCGCTGTC\n+ACCAGTGATTTCCCCCAGGCTTTCCCAGGCCCCGGTAAAGTCTATCTGAACCAGGTCAAC\n+CGGCATCCCTGCCTCAAGCCCGCTGGCCACGTCGGCCAATTGCTGCTTGGCCTTGGCCAA\n+AAGGCCCGCCTGCCGCTGGTTGGTCACCAGGACCTGGTCGTTGGAGTTTTCGATCCCCTT\n+GAAGAAGAGCTTCTTGATCAAGGCTTCCAATTCGTCCAGGTTTTCCTTCATCATGATCGA\n+GGTGCTGATCACTTCACTGCCGCTTTCTTTAGCAATCTCAGCCGCGGTCAGCTTCTGGCC\n+CAGGTCCGTTTTGTTCAGCACGATGATCCGCTTTTTGCCGGCGGTCAGTTCCAAAAGCTG\n+CCGGTCTTCTTCCGTCAATTCCTGGCTGCCGTCCAGCAAAAGCAGGATCAAGTCCGCCTG\n+GGCAATGGCCTTCTTCGACCGCTCGACCCCGATTTTTTCCACCTGGTCCTCGGTATGGTG\n+AATCCCAGCCGTGTCAATCAACTCCAAGGGCACCCCCTTGACAGACACGAACTCTTCCAG\n+GGTGTCCCGGGTGGTCCCGGCCACGTCCGTTACGATCGCCTTGTCGCTTTGGGTCAGGTA\n+GTTCAAAAGGGAGGACTTGCCCACGTTAGGCCGGCCGACAATGGCTGTCTTCAAGCCGTT\n+TCTGAGGATCTGCCCCTCCTGGGCCGTCTCCAGCAGGCGGTCAATCTTGCCGCTGACGGC\n+TTCCGCGCAAGCCAGCAGCTTCTGGGCCGTCACTTCTTCTTCATCGTATTCCGGGTAGTC\n+GATGTTGACTTCGACATTAGCCAAAACATCCAGGATTTCCTGGCGCAGGGCCCGGATTTC\n+CGTCAAAAGGCCGCCGGAAAGCTGCTTGACCGCCACCTGCCGGGCCTTGTCAGTCTTGGC\n+CCGGATGATGTCCATCACGCTTTCAGCCTGGGTTAGGTCGATCCGCCCGTTGACGAAGGC\n+CCGCTTGGTAAATTCGCCCGGGTCAGCCATTCTGGCCCCGTTGGCCAAGAGCAGCTGCAG\n+GATGTCATTGGTGACCACGATCCCCCCGTGGCAGTTGATTTCCACGATGTCTTCCTTGGT\n+AAAAGTCTTCGGCGCCAGCATGACGGAGGCCATGACCTCGTCGATCACCTGCCCGGTTGC\n+CGGGTCCACGATGTGGCCGTAGTTGATCGTGTGGCTGGGAACCTTTTCCAGGTCCTTGCC\n+CTTAAACAAGCGGTTGACAATGGCGACCGCATCTTCCCCGGAGACGCGGACGATGGAGAT\n+CCCGCCTTCTCCCAGCGGCGTTGAGATCGCCGCGATCGTATCAAATTCCGTTAAACGTTG\n+AACCATCTCGTTACCTCGTTTTTTCCAATAAAAAAAGCGCAATTTCCACCATGAAAAATG\n+ATGGATAAAGCACTTTCACTACTTTATCTAAAAAACTTTAGATGAACATTCAATTATTTC\n+CGCTTAATCCGCTTGTAAGCCCGCCGAATCTTGCGCTGGCGCTCGCGTTCAGCTTCTTCC\n+TTGGCTTCCTGCTCCTTGCGGTACTTGAATGGGTTCTGCAGGACCAGGGTCTGGCCAACC\n+TGGAAGAGGTTGGAGATCACCCAGTAAAGGGAGATCGCGGACTGGAAGACGATGGCCCAG\n+ATCCCGACCATGATGGCCATGACATAGCTCATCATCTTAGTCATCGTGGTCTGGGAAGAC\n+TTAGGCACCGACAAAGTCGCGATGTATGAGGACAGGAAGGTAAATACCGTTGCCAAAATC\n+GGCAGGATGTAGTATGGGTCTGGCTTGCCCAGGTCCATCCACAAGAATTTACCATTCTGC\n+ATCTCTGGCGTCCGCCAGATGGCCTGGTACAGGGCCCACATAACCGGCAACTGGATCACC\n+ATCGGCAGGCAGCCGGCGTAAGGATTGACGCCCGCTTCCTTGTAAAGCTTCTGCGTTTCT\n+TCGTTCAGCTTGTTCCGGGTCTCCAGGTCCTTGCTGGAATACTTCTCCTGCAAGGCCTTC\n+AGTTCCGGCTGGATCTCCTGCATCTTTCTGGTGCTGTTGATCTGCACCGCGTTCAAAGGC\n+AGGAGGATCACCCGGATGATAACCGTAAAGATGATGATGGCCCAGCCGTAGCTGCCCCCG\n+CAGACTTTGGCAATCCAAAGCACGAACTGGGAGAGGTAGTAAACTACCCAGGCATCCCAC\n+CAGTTGCTGGAATTATGGGAGATCTGCGTTGGCTTCTGGGTGGTCTGCGTGGCGCAGCCG\n+CTCAGAACAAGGGCAAAAACCGTCACCAGTGCCAGAACGGCCAGAAGGCGCTTGGTACT\n' |
| b |
| diff -r 675488238c96 -r 3061c8b029e5 test-data/meta_ref_3.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meta_ref_3.fasta Fri Aug 05 15:21:27 2022 +0000 |
| b |
| b'@@ -0,0 +1,1085 @@\n+>Lactobacillus_reuteri_F275_Kitasato/55_65k.fa\n+ACTCCGGCAGTCAGACTCGAACTGACGACAACCTGATTAACAGTCAGGTGCTCTACCAAC\n+TGAGCTATGCCGGAATAACTCAACGGATATAATTATATATTATCTCCTTATACCCGTCAA\n+GCTAATTTAAAATTTGTCTAGAAATATTTTCAAGTAGGAGTTTATTCATTTTCTACTCTA\n+CTTAATCATAAGAGAATAACATAAAAGGTAGGTGCTGATTTTTTAACTGAAATTAAGTTT\n+CAATGAATCGCATGCGCTTTTAGCTCGATCCGCTTAGCAACTCTACTATATAATCATATA\n+ATTTTATTTCTCGCCTTGAGCGTGGTGGTTCAAATGATGTTAATTCAACTACCCTTTTAA\n+GATTGGCAACTGCTCTTGGTACATCTATTCTAAAACAGAGTATTTGAGTAAAATAATATT\n+AAAGCTTCTTGAAACCAAATAGCAAATCATCTTTTTGTTTTTTACTTGATAATGCTTATT\n+ATTAGACTGATTGTTTTTCACTCTCTTTTTCTTATTTTTGTAATTAAATTCGCTGTTTTT\n+GTTGTACTTCCTAACTTGATCGCGTAATTATCGTCTTAGCATCTTTACGTGGGCTGGCTT\n+CATTAACGGAATTAGATCATTTTCCCTGTTCGATATACAAAAAAGTGACTTGTTAGTACG\n+GTTTTATCATTTGTTTTTACTGCATTAATCAATATCAGTAAATGAACATGGAGTTTTCCA\n+CTATCACACAATTTAAAACCAAAATGTTGATATATCAATGGTCAGAACCTTCTCTAAAGT\n+AAGCAGTCAGTAACATTACGGATTGAAAAAATTGGGATCATGAGCTACCGAAAATGGTAA\n+TTCATGACCCCGTTTTATTTATGGCATTCTGCTTGAATTTCTTTTGACCATGGCAAATAA\n+GCCTCAAGTCCTGCGTCCTTGCGGTTTGGTAAGTAATCAAAAAGATACTTAAAGTATTTG\n+TAGATATTTAAATGGTTCTGGTTTGCAGTTGCCACCAAAGTATAGAAAATGGCATTTGCC\n+TGAGCTCCAGCAGAGCTTTTCGCAAATAAGCTATTCTTTCGAATAAGAGTTGATGGACGA\n+ATCGCTTGTTCAACCGGATTATTCGTTAACGGCACTCGACCATCTTCAAATATTTGATAT\n+ACTCGCTTTCTTAGTTTCAAAGCATTATTAATGGCAGCTTTCAACCGTCCTTGAGGAAAA\n+CTGATATTTTCTAAATAAGTATATAACTTATCCATCAAAGGCTTCACGTGCAACCGACGT\n+TGCACTAGTTTTTCCTTATGATTGGAATATGTTAATTGTTTCTCTTCATGAAAGATCGGT\n+CGCATTAGCTGTAAAACTCGGTATGCTTTGGAGTTCTTCAATTGCTCCTTATTCAATAAA\n+CATGTAATGTGATAAAATTCACGTCGAATATGAACTAAACATGACCCAAATTTTGCCTGG\n+GGATATAATCGATCACTATATCCACCATAACCGTCACACATAATAATTCCACGATATTGA\n+TGACCGATAATTTGACCAATGGTTTTACCCGCGCGGGTATTATAGTAATGAAACATGATA\n+ATTTGATGCTTACTGAATTCTTTTGTTGATCGCGTTACCCAAAAGTAGCCAGTTTCATTA\n+GGCTCATCAATTACCTTGAATGGAGTTTCATCCATATGAATTACCGATTCTTTTCTGATT\n+AATTCCTGTAAATAATCATACAACGGTTCAAGGTAGGTTTGACTAACCTTAATAATGTTA\n+GTCGCCAATAATCGAGCATCAACTCGTAAGCCGACGGCTTGCCAAAACTTAATTTGACGA\n+TGAAACGGTAAAGCAAGATTAAACTTCAACTCTGCTACTTTAGCTAAAATAGTACTCGAA\n+AAGTAACTATGGGGTAAAAGACTCTGTGGCATCTTACTACTGACAAGTACATCGCTACCA\n+TTAGAATTAATACACTCATTACATTTATAAGTTTCTTGAATCAAATTCACACAATATAAT\n+TCAGCTGGTTTTAACCGTGCTTCTCTACTATATACATGTTGACCCACTTTTTTCATTAGT\n+TGATGACAGTGTGGGCAGTTAGTATCTTTTAATGGAATAACTTCTTCAACCTGTGGTAAA\n+CCATCTAAAAAAGTGGTCCGCTGACCAGATTGTTTTGCTTTCCGGTGACGCACCACTTGC\n+TTTATTTTCTTTTCAGTCACTTCCGTGACTGAAATATCAGGATCTTGAAGTTGATCCATT\n+TCTTGCTCACTAAATAAGGATTGTTGTCCATCAACGACGGGCTCCATTACTTCAGTTTTT\n+TTCCCAAATATTTGGTTCTTTTGAAGTTTGATAATAGCTGTTAATTGAGCAATCTTTTCA\n+TTGGCCATAGCTAATTGCTGTTTAAGTTCTTTGATTTGTTCTTCCGCTGTTTGCTTCATG\n+GTACGTCACCTCCTTTGAATTATTCTTTGGTAATTATATCAAAGAATTCTTCTTTTAAAT\n+AGAGGTAACTCAATAAAAACTTCCCAGTCGAACAGCTTGAATTTTACGAATTGGTAATGG\n+GTTCAGTCCTTGCAATAACCAGTCGAGCTGTTGAGCAGATAATTCTTTGGCTTCATTACT\n+GTTTCTCGGCCAACTAAGGTGGCCATTTTCAAACCGTTTATAGAGCATAATAAAGCCCTC\n+GCCATCCCAAAACAATCCTTTAAACCGATCATTACGTCCGCCGCAAAATAAGAAAAGCGA\n+ATTATTATATAATTCTAATCCATAGTTCTCAGCGATTACCATTGCGAGCCCATCAACACC\n+TTTTCGCATGTCTGTTTTTCCACAGACTAAATAGATATGATCTGGGTCATGCCAATTAAC\n+GAGCATAACGAATAACCACTTTAACGATATCCGAAGCTAAAACAGAATTAGTCCCCTTGA\n+AAATCGTTAATTCGACTTCATTCACATTAATTTTTACGGCAGGGCGTGCCGTAAAAGAAC\n+GCTTTTGTAAATTACTTGGCTTGTTTTTGAAAACTGGGGTAATAATTTCATTTTGTTCTG\n+TCATACATAAAAATCTCCTTACTGATGATAGTCTCAGTATAGGAGATCCAGGGTAGCTAG\n+TGCTAGACGTACTGTTATTGACTGCTTACTCTCTAAATGTGTATTATTTTTGTGTGGTTA\n+AAATTGTGTTTAGAATAATAATTCATAAAACTTCGGAACAATTCACTTAACTTCTTAAGC\n+ATACAAAAAAGCCCACATAATAAGCTTTATCGGCTTAATCTGTAGACTTCTAATTGGTTA\n+TAAACTCTTTATAATGCCAACTAGAGGAGTCGAACCTCCGACCTTCTCTTTACGAGGGAG\n+ATGCTCTACCAGCTGAGCTAAGTTGGCAAAAAAAAGATGTTAACTAACCGAAGGTAGTCA\n+ACATCTTCATCGACTCCGGCAGTCAGACTCGAACTGACGACAACCTGATTAACAGTCAGG\n+TGCTCTACCAACTGAGCTATGCCGGAATAACGCATGGCAACGTCCTATCCTCGCAGGGAG\n+CGATCCCCCAACTACTTTCGGCGTGTTGAAGCTTAACTTCTGTGTTCGGCATGGGAACAG\n+GTGTATCCTTCAAGCCATCATCACCACACTCTTTGTCCCTTCGGACGAGAGCTTGTGCTC\n+TCAAAACTAAATCCTATCTATTCTCTTCCAATAAACCTTACCGCTCCTTGGTTAAGTCCT\n+CGACCGATTAGTAATGGTCCGCTCCATGCCTCACGGCACTTCCACTTCCATCCTATCTAC\n+CTCATCATCTCTGAGGGGTCTTACTTTCCCGAAGGAAATGGGAAATCTCATCTCGAGGCG\n+AGTTTCACACTTAGATGCTTTCAGC'..b'ACCCCTCAT\n+ATGCTGATGCCATTTTTTAATGGTAAGTTCACCCTGGATGACTATTTGGCGCTTGACGAT\n+GGTGTCTTAACTACTTATTTTATTCATTGGACCCATTCTCGTGATGATATTTTAAGCGAT\n+CTTGCGAGTCGTTTTCTTAACCGCCGACCATTTAAATCAGTCATTTATGATCAAAATACA\n+CAAAAGCTTTTGCCAACTTTACGAAAGCTAATTCAAACTGCTGGATTTAATAGCCAGTAC\n+TACACCGCAGTTAACGATAGCTTTAAACTCCCATACGATACTTATCATCCACAAGATTCT\n+AATACCCAAACGCAGATCGAGCTTCTCCAACCTAATGGCGATTTTATTGAGTTATCCCAA\n+GTTAGTACCTTGGTCGCCAGCGTGTCGGGACGAGAAGCCGGAGATCAACGGTTCTTTTTT\n+CCAAAAGAGATGCTTGAAACGCGAAACAATATTGAAATTTTTGAACCAATCTATGAAGAA\n+TTTCAAGGCTATATCAAAAATAATCATATTATCAACCCAAAGGAGCAAAAATAATGGCAA\n+TTAAATTAGTCGCAATCGATATCGATGGAACATTAATCAATGACCAACGCCAAATTACAC\n+CACAAACTGTTGCCGCAATAAAAAAAGCCAGCGCGCAGGGAGTAAAGATCGTCTTATGCA\n+CTGGACGTCCCATGACAGGCGTAAAGGCATACCTTGACCAACTGGACTTAAATGATTCAG\n+ATAATGAATTTGTTATTAGCTTTAACGGTGCGTTGGCCCAATCAACTAGTGGGAATGTCT\n+TGGTAAACTACACTATGCCTTTCAATGACTATGCAGACTGGCAAACTTATTGTATTAAAG\n+AGGGTGTCAAGTCCCAGATTGAAACCCGGGATTACATCTATACAATTAACCGAGATTTAA\n+GTCCCTATACAGTCTACGAGTCAGACCTTGTAAGTATGCCAATCCGTTACCGCACCTTTG\n+AAGAACTTTCTAAAATGCAAGATCAATACGTAATCGCTAAGGCAATGATGGTTGATACTA\n+AAGAACAAATTGACAAAGCATGGGCAGAACTGCCGGCAGAAATGCGTGATCGCTTTTCCA\n+TTGTCCGCAGCGAAGACTTTTATTTGGAATTCATGAATAAACAAGCAAGTAAAGGAAATG\n+CTCTTCAATTACTTAGTGAAGAACTCGGAATTAAAAAAGATGAAGTAATGGCTCTTGGCA\n+ACGCGCAAAACGATGATTCAATGATTGAATATGCCGGCTTAGGGGTAGCAATGGGAAATT\n+CAATTCCCGGTACATTAAAGATCGCTGACGTAACAACTGCTGATAATAATCATGATGGTG\n+TTGGAAAAGCAATTGAAGAATATGTTCTTAAGTAAAGACAGAAATAAAAAGCAAGAAGCG\n+TACTTTCGAAAAAGTTACACCTCTTGCTTTTATTTTTTGTCATCTTTTATATATTAAGCG\n+ATCTTTGTTACCGCTCCAGTTTGACTGTTATATTGGTAAATACCAATCAAGCTTGCAACA\n+GTGTTATCACTATTGTTTTGCCGAACTTCAAACTTGTAAACATTGCCATCCTTGCCTGTT\n+GGCATAATTTGGTAACCTTGGGAGCCACTAAAGCCCATCTTGTTAGCAAATTGTTGGACT\n+ACATTATCACTAGTTGCATCAGATGCAGCTTGGTTAGCAGCAGAGGATGATTGTTGCGTT\n+GCTGAGCTTGTAGAACTGGATTGCTTATTTGTTTGCTTGCTATTGGTAGATGATGAAGTT\n+TGAGAACTCGTGGAACCTTGTGCAGAACTTACCTTGCTTTGTAAGTCAGCATATGCATTG\n+CGCATTGCCGTACTAGTCGACTTTTGTGATTTTAAATTGTTCTTAGCACCATCATAATCG\n+CCATTTTCATATGCTTTTTGAGCATTCATATAGCTCTGTAAATCATCAGCAAGTGCTTCC\n+GTTTGAGCATTATGATCGTTTAATTGGCTTAATTGTTCATATGCTCCTTCATAGTCATGA\n+TTTTGGATAAGCTTATTAGCTGTACGATAAGCCTTTGAAGCTTTACTTTCGGAAGAACGG\n+ACAGACGATGTGCTGGAAGAACTTGTATCACTACTTGACGCAGATTGTTTACCACAACCA\n+GCGAGGGCAAAGATAGTAGCGACTGCAGCTGTTCCAACCATTGCTTTTTTGAAAAACTTA\n+ATTGTTGTCATTTTTCTCCTCCTTATTTCACATCGTATTATAACATGAATTGATAATGAC\n+TGTTTGCCTTTCCTAAATCTTTATCTTCTTTTAAAACAGAAACGGAAAATAAGAAAGGCC\n+GAAAGAAACTAAAAATATTTTTTCCTTCCGACCTACTTTATTTATTAATTTCAGTTTGCT\n+TAAGCATTACTTCTTTTCCAACTGTGCACTTTGGAAAACCTGTTTAAAGAGTGGACTAAC\n+AGGACGATTTTCGTTAATCCGTTTGATTGCATCCCCAATTAGTGGAGCAACCGATACCTG\n+CTTGATTTTATCGATTTGTTTTTCCTTTGGTAATTGAATCGAATCTGTCACAACCACTTC\n+TTTAAGCGGTGCATTCCGTAAACGTTCAATTGCTGGGCCAGATAATACCGCATGGGTACA\n+TGATGCGTAGACTTCTTCTGCGCCGGCATCTATTAATGCTTGCGAACCTAAACTAATAGT\n+TCCCGCAGTATCAATCATGTCATCAATCATAATACACTTCTTACCCTTAACGTCTCCAAT\n+AATATTCATGATTTGAGCAACGTTCGCCCGTGGACGCCGCTTGTCAATAATCGCAATTGG\n+AGATTTTAAAAACTCGGCAAGTGCTCGTGCCCGTGTTACTCCACCATGATCAGGAGAAAT\n+AACAACTGCATTTTCAGCAACACCCTGGTTGATAAAATACTCTGCTAAAAGCGGAGCACC\n+CATCAAATGATCGACAGGGATATCAAAGAACCCTTGAATTTGTGCGGCATGAAGATCAAG\n+TGCAATAATCCGATCAACACCGGAATTTTGCAACATATTAGCAACCAACTTAGCAGTGAT\n+TGGTTCACGGCTCCGTGCTTTTCGGTCTTGACGGGCATAACCATAGTATGGCATCACCAC\n+GTTAATCGTCTTGGCACTAGCACGACGAAGCGCATCCACCATAATTAATAACTCCATTAA\n+GTTGTCATTAACTGGGGCGGAAGTCGACTGGATGACATAAACATTGTCTCCCCGCACACT\n+TTCCTCAATATTAATTTGGATCTCACCATCACTAAAACGATTAACAGATAATTTTCCTAA\n+ATCAACCCCGACATGCTTAGCAATCTTTTCTGCTAAGGGACGATTTGAATTTAACGCAAA\n+GATTTTTAAATTTTGATCAAAATATTGCTGTGTCATTAGGTCCTCCGCTGATTAATAAAT\n+GTTATACTACTACCACTTACATAATATAAATTAGTGAGGCAAAAAGCAAGTTACCATGGT\n+AGCTTCTTAGCATAATTTTCTTTATTAACCTGCCGTGCCCGCGCAATTGCCATGTCATAT\n+TGTTCCGTACTATCTGTGATGGTCGAACCAGCAGCAACAAATGAATCTTTTGCAATATTA\n+ACAGGAGCTACTAAGTTACTGTTACTACCGATAAAGGCATGGTCGCCAACATTGGTATGG\n+TGCTTATTTGTCCCATCGTAGTTAACAAAGACTACTCCACAGCCAACATTAATATCCTTA\n+CCTAACGTAGCGTTACCGATATAAGTCAGGTGACCGACCTTTGTTCCTTCACCAATATAA\n+GCCTTCTTAACCTCACAGAAGTTACCAATATGAACATTTTCGCCAATTTCTGCTTCTGGA\n+CGCAAGTGGCTATTAGGACCAATATCACTGCCATTGTGCATTTCCGCTTCCTGGAGGGTA\n+GACGAAATAATTTTAACCC\n' |
| b |
| diff -r 675488238c96 -r 3061c8b029e5 test-data/reads1.fastq.gz |
| b |
| Binary file test-data/reads1.fastq.gz has changed |
| b |
| diff -r 675488238c96 -r 3061c8b029e5 test-data/reads2.fastq.gz |
| b |
| Binary file test-data/reads2.fastq.gz has changed |
| b |
| diff -r 675488238c96 -r 3061c8b029e5 test-data/test10_missasembly.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test10_missasembly.tab Fri Aug 05 15:21:27 2022 +0000 |
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| @@ -0,0 +1,25 @@ +All statistics are based on contigs of size >= 500 bp, unless otherwise noted (e.g., "# contigs (>= 0 bp)" and "Total length (>= 0 bp)" include all contigs). + +Assembly contig1 contig2 +# misassemblies 0 0 + # contig misassemblies 0 0 + # c. relocations 0 0 + # c. translocations 0 0 + # c. inversions 0 0 + # scaffold misassemblies 0 0 + # s. relocations 0 0 + # s. translocations 0 0 + # s. inversions 0 0 +# misassembled contigs 0 0 +Misassembled contigs length 0 0 +# local misassemblies 0 0 +# scaffold gap ext. mis. 0 0 +# scaffold gap loc. mis. 0 0 +# structural variations - - +# possible TEs - - +# unaligned mis. contigs 0 0 +# mismatches 0 0 +# indels 0 0 + # indels (<= 5 bp) 0 0 + # indels (> 5 bp) 0 0 +Indels length 0 0 |
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| diff -r 675488238c96 -r 3061c8b029e5 test-data/test10_tabular_report.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test10_tabular_report.tab Fri Aug 05 15:21:27 2022 +0000 |
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| @@ -0,0 +1,77 @@ +Assembly contig1 contig2 +# contigs (>= 0 bp) 3 1 +# contigs (>= 1000 bp) 3 1 +Total length (>= 0 bp) 6710 6650 +Total length (>= 1000 bp) 6710 6650 +# contigs 3 1 +Largest contig 3980 6650 +Total length 6710 6650 +Reference length - - +Estimated reference length - - +GC (%) 51.28 52.00 +Reference GC (%) - - +N50 3980 6650 +NG50 - - +N80 1610 6650 +NG80 - - +auN 2934.0 6650.0 +auNG - - +L50 1 1 +LG50 - - +L80 2 1 +LG80 - - +# total reads - - +# left - - +# right - - +Mapped (%) - - +Reference mapped (%) - - +Properly paired (%) - - +Reference properly paired (%) - - +Avg. coverage depth - - +Reference avg. coverage depth - - +Coverage >= 1x (%) - - +Reference coverage >= 1x (%) - - +# large blocks misassemblies - - +# misassemblies - - +# misassembled contigs - - +Misassembled contigs length - - +# local misassemblies - - +# scaffold gap ext. mis. - - +# scaffold gap loc. mis. - - +# structural variations - - +# possible TEs - - +# unaligned mis. contigs - - +# unaligned contigs - - +Unaligned length - - +Genome fraction (%) - - +Duplication ratio - - +Avg contig read support - - +# N's per 100 kbp 0.00 0.00 +# mismatches per 100 kbp - - +# indels per 100 kbp - - +# genomic features - - +# operons - - +Complete BUSCO (%) - - +Partial BUSCO (%) - - +# predicted genes (unique) - - +# predicted genes (>= 0 bp) - - +# predicted genes (>= 300 bp) - - +# predicted genes (>= 1500 bp) - - +# predicted genes (>= 3000 bp) - - +# predicted rRNA genes - - +Largest alignment - - +Total aligned length - - +NA50 - - +NGA50 - - +NA80 - - +NGA80 - - +auNA - - +auNGA - - +LA50 - - +LGA50 - - +LA80 - - +LGA80 - - +K-mer-based compl. (%) - - +K-mer-based cor. length (%) - - +K-mer-based mis. length (%) - - +# k-mer-based misjoins - - |
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| diff -r 675488238c96 -r 3061c8b029e5 test-data/test10_unalign.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test10_unalign.tab Fri Aug 05 15:21:27 2022 +0000 |
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| @@ -0,0 +1,6 @@ +Assembly contig1 contig2 +# fully unaligned contigs 0 0 +Fully unaligned length 0 0 +# partially unaligned contigs 1 0 +Partially unaligned length 1950 0 +# N's 0 0 |
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| diff -r 675488238c96 -r 3061c8b029e5 test-data/test1_report.html --- a/test-data/test1_report.html Fri Mar 25 17:36:59 2022 +0000 +++ b/test-data/test1_report.html Fri Aug 05 15:21:27 2022 +0000 |
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| b'@@ -4639,7 +4639,7 @@\n \n <div class=\'json-code\'>\n <div id=\'total-report-json\'>\n- {"date":"06 February 2022, Sunday, 19:53:54","assembliesNames":["contig1","contig2"],"referenceName":"dataset_066b3cb5_c2ca_4ed5_b245_29eeab002f94","order":[0,1],"report":[["Genome statistics",[{"metricName":"Genome fraction (%)","quality":"More is better","values":["71.579","100.000"],"isMain":true},{"metricName":"Duplication ratio","quality":"Less is better","values":["1.000","1.000"],"isMain":true},{"metricName":"# genomic features","quality":"More is better","values":["7 + 7 part","13 + 1 part"],"isMain":true},{"metricName":"Largest alignment","quality":"More is better","values":[2030,6650],"isMain":true},{"metricName":"Total aligned length","quality":"More is better","values":[4760,6650],"isMain":true},{"metricName":"NG50","quality":"More is better","values":[3980,6650],"isMain":false},{"metricName":"NG75","quality":"More is better","values":[1610,6650],"isMain":false},{"metricName":"NA50","quality":"More is better","values":[1610,6650],"isMain":false},{"metricName":"NA75","quality":"More is better","values":[null,6650],"isMain":false},{"metricName":"NGA50","quality":"More is better","values":[1610,6650],"isMain":true},{"metricName":"NGA75","quality":"More is better","values":[null,6650],"isMain":false},{"metricName":"LG50","quality":"Less is better","values":[1,1],"isMain":false},{"metricName":"LG75","quality":"Less is better","values":[2,1],"isMain":false},{"metricName":"LA50","quality":"Less is better","values":[2,1],"isMain":false},{"metricName":"LA75","quality":"Less is better","values":[null,1],"isMain":false},{"metricName":"LGA50","quality":"Less is better","values":[2,1],"isMain":true},{"metricName":"LGA75","quality":"Less is better","values":[null,1],"isMain":false}]],["Reads mapping",[]],["Misassemblies",[{"metricName":"# misassemblies","quality":"Less is better","values":[0,0],"isMain":true},{"metricName":" # relocations","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":" # translocations","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":" # inversions","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# misassembled contigs","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"Misassembled contigs length","quality":"Less is better","values":[0,0],"isMain":true},{"metricName":"# local misassemblies","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# scaffold gap ext. mis.","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# scaffold gap loc. mis.","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# unaligned mis. contigs","quality":"Less is better","values":[0,0],"isMain":false}]],["Unaligned",[{"metricName":"# fully unaligned contigs","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"Fully unaligned length","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# partially unaligned contigs","quality":"Less is better","values":[1,0],"isMain":false},{"metricName":"Partially unaligned length","quality":"Less is better","values":[1950,0],"isMain":false}]],["Mismatches",[{"metricName":"# mismatches","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# indels","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"Indels length","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# mismatches per 100 kbp","quality":"Less is better","values":["0.00","0.00"],"isMain":true},{"metricName":"# indels per 100 kbp","quality":"Less is better","values":["0.00","0.00"],"isMain":true},{"metricName":" # indels (<= 5 bp)","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":" # indels (> 5 bp)","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# N\'s","quality":"Less is better","values":[0,0],"isMain":f'..b'e number of total bases contained in all indels.</span>",\n \n "# genomic features" : "<span>is the number of genomic features (genes, transcripts, CDS) in the assembly (complete and partial), based on a user-provided annotated list of gene positions in the reference genome. A feature counts as \'partially covered\' if the assembly contains at least 100 bp of this feature but not the whole feature.</span>",\n "# operons" : "<span>is the number of operons in the assembly (complete and partial), based on a user-provided annotated list of operon positions in the reference genome. An operon counts as \'partially covered\' if the assembly contains at least 100 bp of this operon but not the whole operon.</span>",\n@@ -4799,13 +4796,13 @@\n "NGAx" : "<span>plot shows the NGAx metric value as x varies from 0 to 100.</span><span>NGAx is computed similarly to NGx, but based on lengths of aligned blocks instead of contig lengths. Contigs are broken at misassembly breakpoints. NGAx is the minimum block length <b>y</b> such that using blocks of length at least <b>y</b> accounts for at least x% of the bases of the reference genome. This metric is computed only if a reference genome is provided.</span>",\n "GC content" : "<span>plot shows the distribution of GC percentage among the contigs, i.e., the total number of bases in contigs with such GC content. Typically, the distribution is approximately Gaussian. However, for some genomes it is not Gaussian. For assembly projects with contaminants, the GC distribution of the contaminants often differs from the reference genome and may give a superposition of multiple curves with different peaks.</span>",\n \n- "Duplication ratio" : "<span>is the total number of aligned bases in the assembly (i.e. <i>Total length</i> - <i>Fully unaligned length</i> - <i>Partially unaligned length</i>), divided by the total number of aligned bases in the reference (see the <b>Genome fraction (%)</b> metric). If the assembly contains many contigs that cover the same regions of the reference, its <i>Duplication ratio</i> may be much larger than 1. This may occur due to overestimating repeat multiplicities and due to small overlaps between contigs, among other reasons.</span>",\n+ "Duplication ratio" : "<span>is the total number of aligned bases in the assembly, divided by the total number of aligned bases in the reference (see the <b>Genome fraction (%)</b> metric). If the assembly contains many contigs that cover the same regions of the reference, its <i>Duplication ratio</i> may be much larger than 1. This may occur due to overestimating repeat multiplicities and due to small overlaps between contigs, among other reasons.</span>",\n "Largest alignment" : "<span>is the length of the largest continuous alignment in the assembly. This metric is always equal to the <i>Largest contig</i> metric but it can be smaller if the largest contig of the assembly contains a misassembly event.</span>",\n "Total aligned length" : "<span>is the total number of aligned bases in the assembly.</span>",\n "Avg contig read support" : "<span>is the average coverage of contigs that have large unique alignments to the reference. Read coverage is extracted from contig names (SPAdes/Velvet naming scheme only).</span>",\n \n "# N\'s" : "<span>is the total number of uncalled bases (N\'s) in the assembly.</span>",\n- "# N\'s per 100 kbp" : "<span>is the average number of uncalled bases (N\'s) per 100000 assembly bases.</span>",\n+ "# N\'s per 100 kbp" : "<span>is the average number of uncalled bases (N\'s) per 100,000 assembly bases.</span>",\n \n "# mapped" : "<span>is the number of reads that mapped to the assembly.</span>",\n "Mapped (%)" : "<span>is the percent of reads that mapped to the assembly.</span>",\n' |
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| diff -r 675488238c96 -r 3061c8b029e5 test-data/test2.log --- a/test-data/test2.log Fri Mar 25 17:36:59 2022 +0000 +++ b/test-data/test2.log Fri Aug 05 15:21:27 2022 +0000 |
| b |
| b"@@ -1,199 +1,199 @@\n-/home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/bin/quast --labels contig1,contig2 -o outputdir -r /tmp/tmpmqu3v_ze/files/f/2/0/dataset_f20bc8a3-6ab5-43f7-a0a3-42dcc6408039.dat --features /tmp/tmpmqu3v_ze/files/2/a/f/dataset_2afd5bcc-2ff5-46bc-83cd-0690bcbd9c67.dat --operons /tmp/tmpmqu3v_ze/files/f/f/a/dataset_ffa07559-8af9-4a08-8719-807dc3575dc8.dat --circos --k-mer-stats --k-mer-size 101 --min-contig 500 --min-alignment 65 --min-identity 95.0 --ambiguity-usage one --ambiguity-score 0.99 --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 /tmp/tmpmqu3v_ze/files/a/e/3/dataset_ae3fd171-9eb4-40d1-a8c8-d896fef3f293.dat /tmp/tmpmqu3v_ze/files/f/c/b/dataset_fcbec1fc-e7c4-42db-b9e4-7c32ac9882dd.dat --threads 1\n+/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/quast --labels contig1,contig2 -o outputdir -r /tmp/tmphjbhe4x0/files/a/d/a/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat --features /tmp/tmphjbhe4x0/files/3/1/a/dataset_31a7a886-1c84-4423-8fc9-cdfda1537f40.dat --operons /tmp/tmphjbhe4x0/files/2/9/8/dataset_29831cd9-b20d-4b69-af42-19aa1c84bbbb.dat --circos --k-mer-stats --k-mer-size 101 --min-identity 95.0 --min-contig 500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --x-for-Nx 90 /tmp/tmphjbhe4x0/files/d/f/0/dataset_df0f2e39-68eb-4a15-949f-d6678854d50e.dat /tmp/tmphjbhe4x0/files/3/4/7/dataset_34703c25-26f5-4dc0-9211-fc1217c11724.dat --threads 1\n \n-Version: 5.0.2\n+Version: 5.2.0\n \n System information:\n- OS: Linux-5.13.0-28-generic-x86_64-with-debian-bullseye-sid (linux_64)\n- Python version: 3.7.12\n+ OS: Linux-5.13.0-51-generic-x86_64-with-glibc2.31 (linux_64)\n+ Python version: 3.9.13\n CPUs number: 8\n \n-Started: 2022-02-06 19:54:35\n+Started: 2022-07-07 16:53:46\n \n-Logging to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/quast.log\n-NOTICE: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified\n+Logging to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/quast.log\n+WARNING: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified\n \n-CWD: /tmp/tmpmqu3v_ze/job_working_directory/000/12/working\n+CWD: /tmp/tmphjbhe4x0/job_working_directory/000/12/working\n Main parameters: \n- MODE: default, threads: 1, minimum contig length: 500, minimum alignment length: 65, \\\n- ambiguity: all, threshold for extensive misassembly size: 1000\n+ MODE: default, threads: 1, min contig length: 500, min alignment length: 65, min alignment IDY: 95.0, \\\n+ ambiguity: all, min local misassembly length: 200, min extensive misassembly length: 1000\n \n Reference:\n- /tmp/tmpmqu3v_ze/files/f/2/0/dataset_f20bc8a3-6ab5-43f7-a0a3-42dcc6408039.dat ==> dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039\n+ /tmp/tmphjbhe4x0/files/a/d/a/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat ==> dataset_adad470c-d758-46ef-afd5-390f178fb362\n \n Contigs:\n Pre-processing...\n- 1 /tmp/tmpmqu3v_ze/files/a/e/3/dataset_ae3fd171-9eb4-40d1-a8c8-d896fef3f293.dat ==> contig1\n- 2 /tmp/tmpmqu3v_ze/files/f/c/b/dataset_fcbec1fc-e7c4-42db-b9e4-7c32ac9882dd.dat ==> contig2\n+ 1 /tmp/tmphjbhe4x0/files/d/f/0/dataset_df0f2e39-68eb-4a15-949f-d6678854d50e.dat ==> contig1\n+ 2 /tmp/tmphjbhe4x0/files/3/4/7/dataset_34703c25-26f5-4dc0-9211-fc1217c11724.dat ==> contig2\n \n-2022-02-06 19:54:39\n+2022-07-07 16:53:55\n Running Basic statistics processor...\n Reference genome:\n- dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039.dat, length = 6650, num fragments = 1, GC % = 52.00\n+ dataset_adad470c-d758-46ef-afd5-390f178fb362.dat, length = 6650, num fragments = 1, GC % = 52.00\n Contig files: \n 1 contig1\n 2 contig2\n Calculating N50 and L50...\n- 1 contig1, N"..b'ir/genome_stats/features_cumulative_plot.pdf\n Drawing genomic features FRCurve plot...\n- saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/genome_stats/features_frcurve_plot.pdf\n+ saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/genome_stats/features_frcurve_plot.pdf\n Drawing # complete genomic features histogram...\n- saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/genome_stats/complete_features_histogram.pdf\n+ saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/genome_stats/complete_features_histogram.pdf\n Drawing Genome fraction, % histogram...\n- saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/genome_stats/genome_fraction_histogram.pdf\n+ saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/genome_stats/genome_fraction_histogram.pdf\n Done.\n \n NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.\n \n-2022-02-06 19:54:42\n+2022-07-07 16:54:04\n Creating large visual summaries...\n This may take a while: press Ctrl-C to skip this step..\n- 1 of 3: Creating Icarus viewers...\n- 2 of 3: Creating Circos plot...\n-/home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/bin/circos \\\n+ 1 of 3: Creating PDF with all tables and plots...\n+ 2 of 3: Creating Icarus viewers...\n+ 3 of 3: Creating Circos plot...\n+/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/circos \\\n -conf outputdir/circos/circos.conf > outputdir/circos/circos.log 2> outputdir/circos/circos.err\n- 3 of 3: Creating PDF with all tables and plots...\n Done\n \n-2022-02-06 19:54:46\n+2022-07-07 16:54:16\n RESULTS:\n- Text versions of total report are saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/report.txt, report.tsv, and report.tex\n- Text versions of transposed total report are saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex\n- HTML version (interactive tables and plots) is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/report.html\n- PDF version (tables and plots) is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/report.pdf\n- Circos plot is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/circos/circos.png (legend is in legend.txt, configuration file is in circos.conf)\n- Icarus (contig browser) is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/icarus.html\n- Log is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/quast.log\n+ Text versions of total report are saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/report.txt, report.tsv, and report.tex\n+ Text versions of transposed total report are saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex\n+ HTML version (interactive tables and plots) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/report.html\n+ PDF version (tables and plots) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/report.pdf\n+ Circos plot is saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/circos/circos.png (legend is in legend.txt, configuration file is in circos.conf)\n+ Icarus (contig browser) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/icarus.html\n+ Log is saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/quast.log\n \n-Finished: 2022-02-06 19:54:46\n-Elapsed time: 0:00:11.313989\n-NOTICEs: 3; WARNINGs: 3; non-fatal ERRORs: 0\n+Finished: 2022-07-07 16:54:16\n+Elapsed time: 0:00:30.044753\n+NOTICEs: 2; WARNINGs: 4; non-fatal ERRORs: 0\n \n Thank you for using QUAST!\n' |
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| diff -r 675488238c96 -r 3061c8b029e5 test-data/test2_report.html --- a/test-data/test2_report.html Fri Mar 25 17:36:59 2022 +0000 +++ b/test-data/test2_report.html Fri Aug 05 15:21:27 2022 +0000 |
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| b'@@ -4639,7 +4639,7 @@\n \n <div class=\'json-code\'>\n <div id=\'total-report-json\'>\n- {"date":"06 February 2022, Sunday, 19:54:46","assembliesNames":["contig1","contig2"],"referenceName":"dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039","order":[0,1],"report":[["Genome statistics",[{"metricName":"Genome fraction (%)","quality":"More is better","values":["71.579","100.000"],"isMain":true},{"metricName":"Duplication ratio","quality":"Less is better","values":["1.000","1.000"],"isMain":true},{"metricName":"# genomic features","quality":"More is better","values":["7 + 7 part","13 + 1 part"],"isMain":true},{"metricName":"Largest alignment","quality":"More is better","values":[2030,6650],"isMain":true},{"metricName":"Total aligned length","quality":"More is better","values":[4760,6650],"isMain":true},{"metricName":"NG50","quality":"More is better","values":[3980,6650],"isMain":false},{"metricName":"NG75","quality":"More is better","values":[1610,6650],"isMain":false},{"metricName":"NA50","quality":"More is better","values":[1610,6650],"isMain":false},{"metricName":"NA75","quality":"More is better","values":[null,6650],"isMain":false},{"metricName":"NGA50","quality":"More is better","values":[1610,6650],"isMain":true},{"metricName":"NGA75","quality":"More is better","values":[null,6650],"isMain":false},{"metricName":"LG50","quality":"Less is better","values":[1,1],"isMain":false},{"metricName":"LG75","quality":"Less is better","values":[2,1],"isMain":false},{"metricName":"LA50","quality":"Less is better","values":[2,1],"isMain":false},{"metricName":"LA75","quality":"Less is better","values":[null,1],"isMain":false},{"metricName":"LGA50","quality":"Less is better","values":[2,1],"isMain":true},{"metricName":"LGA75","quality":"Less is better","values":[null,1],"isMain":false}]],["Reads mapping",[]],["Misassemblies",[{"metricName":"# misassemblies","quality":"Less is better","values":[0,0],"isMain":true},{"metricName":" # relocations","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":" # translocations","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":" # inversions","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# misassembled contigs","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"Misassembled contigs length","quality":"Less is better","values":[0,0],"isMain":true},{"metricName":"# local misassemblies","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# scaffold gap ext. mis.","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# scaffold gap loc. mis.","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# unaligned mis. contigs","quality":"Less is better","values":[0,0],"isMain":false}]],["Unaligned",[{"metricName":"# fully unaligned contigs","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"Fully unaligned length","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# partially unaligned contigs","quality":"Less is better","values":[1,0],"isMain":false},{"metricName":"Partially unaligned length","quality":"Less is better","values":[1950,0],"isMain":false}]],["Mismatches",[{"metricName":"# mismatches","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# indels","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"Indels length","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# mismatches per 100 kbp","quality":"Less is better","values":["0.00","0.00"],"isMain":true},{"metricName":"# indels per 100 kbp","quality":"Less is better","values":["0.00","0.00"],"isMain":true},{"metricName":" # indels (<= 5 bp)","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":" # indels (> 5 bp)","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# N\'s","quality":"Less is better","values":[0,0],"isMain":f'..b'e number of total bases contained in all indels.</span>",\n \n "# genomic features" : "<span>is the number of genomic features (genes, transcripts, CDS) in the assembly (complete and partial), based on a user-provided annotated list of gene positions in the reference genome. A feature counts as \'partially covered\' if the assembly contains at least 100 bp of this feature but not the whole feature.</span>",\n "# operons" : "<span>is the number of operons in the assembly (complete and partial), based on a user-provided annotated list of operon positions in the reference genome. An operon counts as \'partially covered\' if the assembly contains at least 100 bp of this operon but not the whole operon.</span>",\n@@ -4799,13 +4796,13 @@\n "NGAx" : "<span>plot shows the NGAx metric value as x varies from 0 to 100.</span><span>NGAx is computed similarly to NGx, but based on lengths of aligned blocks instead of contig lengths. Contigs are broken at misassembly breakpoints. NGAx is the minimum block length <b>y</b> such that using blocks of length at least <b>y</b> accounts for at least x% of the bases of the reference genome. This metric is computed only if a reference genome is provided.</span>",\n "GC content" : "<span>plot shows the distribution of GC percentage among the contigs, i.e., the total number of bases in contigs with such GC content. Typically, the distribution is approximately Gaussian. However, for some genomes it is not Gaussian. For assembly projects with contaminants, the GC distribution of the contaminants often differs from the reference genome and may give a superposition of multiple curves with different peaks.</span>",\n \n- "Duplication ratio" : "<span>is the total number of aligned bases in the assembly (i.e. <i>Total length</i> - <i>Fully unaligned length</i> - <i>Partially unaligned length</i>), divided by the total number of aligned bases in the reference (see the <b>Genome fraction (%)</b> metric). If the assembly contains many contigs that cover the same regions of the reference, its <i>Duplication ratio</i> may be much larger than 1. This may occur due to overestimating repeat multiplicities and due to small overlaps between contigs, among other reasons.</span>",\n+ "Duplication ratio" : "<span>is the total number of aligned bases in the assembly, divided by the total number of aligned bases in the reference (see the <b>Genome fraction (%)</b> metric). If the assembly contains many contigs that cover the same regions of the reference, its <i>Duplication ratio</i> may be much larger than 1. This may occur due to overestimating repeat multiplicities and due to small overlaps between contigs, among other reasons.</span>",\n "Largest alignment" : "<span>is the length of the largest continuous alignment in the assembly. This metric is always equal to the <i>Largest contig</i> metric but it can be smaller if the largest contig of the assembly contains a misassembly event.</span>",\n "Total aligned length" : "<span>is the total number of aligned bases in the assembly.</span>",\n "Avg contig read support" : "<span>is the average coverage of contigs that have large unique alignments to the reference. Read coverage is extracted from contig names (SPAdes/Velvet naming scheme only).</span>",\n \n "# N\'s" : "<span>is the total number of uncalled bases (N\'s) in the assembly.</span>",\n- "# N\'s per 100 kbp" : "<span>is the average number of uncalled bases (N\'s) per 100000 assembly bases.</span>",\n+ "# N\'s per 100 kbp" : "<span>is the average number of uncalled bases (N\'s) per 100,000 assembly bases.</span>",\n \n "# mapped" : "<span>is the number of reads that mapped to the assembly.</span>",\n "Mapped (%)" : "<span>is the percent of reads that mapped to the assembly.</span>",\n' |
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| @@ -11,12 +11,14 @@ Reference GC (%) 52.00 52.00 N50 3980 6650 NG50 3980 6650 -N75 1610 6650 -NG75 1610 6650 +N90 1120 6650 +NG90 1120 6650 +auN 2934.0 6650.0 +auNG 2960.4 6650.0 L50 1 1 LG50 1 1 -L75 2 1 -LG75 2 1 +L90 3 1 +LG90 3 1 # misassemblies 0 0 # misassembled contigs 0 0 Misassembled contigs length 0 0 @@ -36,12 +38,14 @@ Total aligned length 4760 6650 NA50 1610 6650 NGA50 1610 6650 -NA75 - 6650 -NGA75 - 6650 +NA90 - 6650 +NGA90 - 6650 +auNA 1187.4 6650.0 +auNGA 1198.1 6650.0 LA50 2 1 LGA50 2 1 -LA75 - 1 -LGA75 - 1 +LA90 - 1 +LGA90 - 1 K-mer-based compl. (%) 68.09 100.00 K-mer-based cor. length (%) 100.00 100.00 K-mer-based mis. length (%) 0.00 0.00 |
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| diff -r 675488238c96 -r 3061c8b029e5 test-data/test3.log --- a/test-data/test3.log Fri Mar 25 17:36:59 2022 +0000 +++ b/test-data/test3.log Fri Aug 05 15:21:27 2022 +0000 |
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| @@ -1,67 +1,67 @@ -/home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/bin/quast --labels contigs1_fna,contigs2_fna -o outputdir --eukaryote --min-contig 500 --min-alignment 65 --min-identity 95.0 --ambiguity-usage one --ambiguity-score 0.99 --contig-thresholds 0,1000,500 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --skip-unaligned-mis-contigs /tmp/tmpmqu3v_ze/files/c/a/f/dataset_cafcd90b-16e7-46aa-8617-cdefd1766b23.dat /tmp/tmpmqu3v_ze/files/6/4/e/dataset_64ec6db4-a92f-4ec5-b641-96e96830b6b5.dat --threads 1 +/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/quast --labels contigs1_fna,contigs2_fna -o outputdir --eukaryote --min-identity 95.0 --min-contig 500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000,500 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --skip-unaligned-mis-contigs --x-for-Nx 90 /tmp/tmphjbhe4x0/files/0/2/b/dataset_02bce539-33f0-4693-bfe9-a92ebf1615f8.dat /tmp/tmphjbhe4x0/files/6/0/2/dataset_60253425-26a2-4019-bae6-07285864be68.dat --threads 1 -Version: 5.0.2 +Version: 5.2.0 System information: - OS: Linux-5.13.0-28-generic-x86_64-with-debian-bullseye-sid (linux_64) - Python version: 3.7.12 + OS: Linux-5.13.0-51-generic-x86_64-with-glibc2.31 (linux_64) + Python version: 3.9.13 CPUs number: 8 -Started: 2022-02-06 19:55:07 +Started: 2022-07-07 16:55:02 -Logging to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/quast.log -NOTICE: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified +Logging to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/quast.log +WARNING: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified -CWD: /tmp/tmpmqu3v_ze/job_working_directory/000/15/working +CWD: /tmp/tmphjbhe4x0/job_working_directory/000/15/working Main parameters: - MODE: default, threads: 1, eukaryotic: true, minimum contig length: 500, minimum alignment length: 65, \ - ambiguity: all, threshold for extensive misassembly size: 1000 + MODE: default, threads: 1, eukaryotic: true, min contig length: 500, min alignment length: 65, \ + min alignment IDY: 95.0, ambiguity: all, min local misassembly length: 200, min extensive misassembly length: 1000 Contigs: Pre-processing... - 1 /tmp/tmpmqu3v_ze/files/c/a/f/dataset_cafcd90b-16e7-46aa-8617-cdefd1766b23.dat ==> contigs1_fna - 2 /tmp/tmpmqu3v_ze/files/6/4/e/dataset_64ec6db4-a92f-4ec5-b641-96e96830b6b5.dat ==> contigs2_fna + 1 /tmp/tmphjbhe4x0/files/0/2/b/dataset_02bce539-33f0-4693-bfe9-a92ebf1615f8.dat ==> contigs1_fna + 2 /tmp/tmphjbhe4x0/files/6/0/2/dataset_60253425-26a2-4019-bae6-07285864be68.dat ==> contigs2_fna -2022-02-06 19:55:10 +2022-07-07 16:55:11 Running Basic statistics processor... Contig files: 1 contigs1_fna 2 contigs2_fna Calculating N50 and L50... - 1 contigs1_fna, N50 = 3980, L50 = 1, Total length = 6710, GC % = 51.28, # N's per 100 kbp = 0.00 - 2 contigs2_fna, N50 = 6650, L50 = 1, Total length = 6650, GC % = 52.00, # N's per 100 kbp = 0.00 + 1 contigs1_fna, N50 = 3980, L50 = 1, auN = 2934.0, Total length = 6710, GC % = 51.28, # N's per 100 kbp = 0.00 + 2 contigs2_fna, N50 = 6650, L50 = 1, auN = 6650.0, Total length = 6650, GC % = 52.00, # N's per 100 kbp = 0.00 Drawing Nx plot... - saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/basic_stats/Nx_plot.pdf + saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/Nx_plot.pdf Drawing cumulative plot... - saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/basic_stats/cumulative_plot.pdf + saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/cumulative_plot.pdf Drawing GC content plot... - saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/basic_stats/GC_content_plot.pdf + saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/GC_content_plot.pdf Drawing contigs1_fna GC content plot... - saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/basic_stats/contigs1_fna_GC_content_plot.pdf + saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/contigs1_fna_GC_content_plot.pdf Drawing contigs2_fna GC content plot... - saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/basic_stats/contigs2_fna_GC_content_plot.pdf + saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/contigs2_fna_GC_content_plot.pdf Done. NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it. -2022-02-06 19:55:11 +2022-07-07 16:55:13 Creating large visual summaries... This may take a while: press Ctrl-C to skip this step.. - 1 of 2: Creating Icarus viewers... - 2 of 2: Creating PDF with all tables and plots... + 1 of 2: Creating PDF with all tables and plots... + 2 of 2: Creating Icarus viewers... Done -2022-02-06 19:55:12 +2022-07-07 16:55:14 RESULTS: - Text versions of total report are saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/report.txt, report.tsv, and report.tex - Text versions of transposed total report are saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex - HTML version (interactive tables and plots) is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/report.html - PDF version (tables and plots) is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/report.pdf - Icarus (contig browser) is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/icarus.html - Log is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/quast.log + Text versions of total report are saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/report.txt, report.tsv, and report.tex + Text versions of transposed total report are saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex + HTML version (interactive tables and plots) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/report.html + PDF version (tables and plots) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/report.pdf + Icarus (contig browser) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/icarus.html + Log is saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/quast.log -Finished: 2022-02-06 19:55:12 -Elapsed time: 0:00:04.673393 -NOTICEs: 2; WARNINGs: 0; non-fatal ERRORs: 0 +Finished: 2022-07-07 16:55:14 +Elapsed time: 0:00:11.737584 +NOTICEs: 1; WARNINGs: 1; non-fatal ERRORs: 0 Thank you for using QUAST! |
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| diff -r 675488238c96 -r 3061c8b029e5 test-data/test3_report.html --- a/test-data/test3_report.html Fri Mar 25 17:36:59 2022 +0000 +++ b/test-data/test3_report.html Fri Aug 05 15:21:27 2022 +0000 |
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| b'@@ -4639,7 +4639,7 @@\n \n <div class=\'json-code\'>\n <div id=\'total-report-json\'>\n- {"date":"06 February 2022, Sunday, 19:55:12","assembliesNames":["contigs1_fna","contigs2_fna"],"referenceName":"","order":[0,1],"report":[["Genome statistics",[]],["Reads mapping",[]],["Misassemblies",[]],["Unaligned",[]],["Mismatches",[{"metricName":"# N\'s","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# N\'s per 100 kbp","quality":"Less is better","values":["0.00","0.00"],"isMain":true}]],["Statistics without reference",[{"metricName":"# contigs","quality":"Equal","values":[3,1],"isMain":true},{"metricName":"# contigs (>= 0 bp)","quality":"Equal","values":[3,1],"isMain":false},{"metricName":"# contigs (>= 1000 bp)","quality":"Equal","values":[3,1],"isMain":false},{"metricName":"# contigs (>= 500 bp)","quality":"Equal","values":[3,1],"isMain":false},{"metricName":"Largest contig","quality":"More is better","values":[3980,6650],"isMain":true},{"metricName":"Total length","quality":"More is better","values":[6710,6650],"isMain":true},{"metricName":"Total length (>= 0 bp)","quality":"More is better","values":[6710,6650],"isMain":false},{"metricName":"Total length (>= 1000 bp)","quality":"More is better","values":[6710,6650],"isMain":true},{"metricName":"Total length (>= 500 bp)","quality":"More is better","values":[6710,6650],"isMain":false},{"metricName":"N50","quality":"More is better","values":[3980,6650],"isMain":false},{"metricName":"N75","quality":"More is better","values":[1610,6650],"isMain":false},{"metricName":"L50","quality":"Less is better","values":[1,1],"isMain":false},{"metricName":"L75","quality":"Less is better","values":[2,1],"isMain":false},{"metricName":"GC (%)","quality":"Equal","values":["51.28","52.00"],"isMain":false}]],["K-mer-based statistics",[]],["Predicted genes",[]],["Similarity statistics",[]],["Reference statistics",[]]],"subreferences":[],"subreports":[],"minContig":500}\n+ {"date":"07 July 2022, Thursday, 16:55:14","assembliesNames":["contigs1_fna","contigs2_fna"],"referenceName":"","order":[0,1],"report":[["Genome statistics",[]],["Reads mapping",[]],["Misassemblies",[]],["Unaligned",[]],["Mismatches",[{"metricName":"# N\'s per 100 kbp","quality":"Less is better","values":["0.00","0.00"],"isMain":true},{"metricName":"# N\'s","quality":"Less is better","values":[0,0],"isMain":false}]],["Statistics without reference",[{"metricName":"# contigs","quality":"Equal","values":[3,1],"isMain":true},{"metricName":"# contigs (>= 0 bp)","quality":"Equal","values":[3,1],"isMain":false},{"metricName":"# contigs (>= 1000 bp)","quality":"Equal","values":[3,1],"isMain":false},{"metricName":"# contigs (>= 500 bp)","quality":"Equal","values":[3,1],"isMain":false},{"metricName":"Largest contig","quality":"More is better","values":[3980,6650],"isMain":true},{"metricName":"Total length","quality":"More is better","values":[6710,6650],"isMain":true},{"metricName":"Total length (>= 0 bp)","quality":"More is better","values":[6710,6650],"isMain":false},{"metricName":"Total length (>= 1000 bp)","quality":"More is better","values":[6710,6650],"isMain":true},{"metricName":"Total length (>= 500 bp)","quality":"More is better","values":[6710,6650],"isMain":false},{"metricName":"N50","quality":"More is better","values":[3980,6650],"isMain":false},{"metricName":"N90","quality":"More is better","values":[1120,6650],"isMain":false},{"metricName":"auN","quality":"More is better","values":["2934.0","6650.0"],"isMain":false},{"metricName":"L50","quality":"Less is better","values":[1,1],"isMain":false},{"metricName":"L90","quality":"Less is better","values":[3,1],"isMain":false},{"metricName":"GC (%)","quality":"Equal","values":["51.28","52.00"],"isMain":false}]],["K-mer-based statistics",[]],["Predicted genes",[]],["Similarity statistics",[]],["Reference statistics",[]]],"subreferences":[],"subreports":[],"minContig":500}\n </div>\n <div id=\'qualities-json\'>'..b'e number of total bases contained in all indels.</span>",\n \n "# genomic features" : "<span>is the number of genomic features (genes, transcripts, CDS) in the assembly (complete and partial), based on a user-provided annotated list of gene positions in the reference genome. A feature counts as \'partially covered\' if the assembly contains at least 100 bp of this feature but not the whole feature.</span>",\n "# operons" : "<span>is the number of operons in the assembly (complete and partial), based on a user-provided annotated list of operon positions in the reference genome. An operon counts as \'partially covered\' if the assembly contains at least 100 bp of this operon but not the whole operon.</span>",\n@@ -4799,13 +4796,13 @@\n "NGAx" : "<span>plot shows the NGAx metric value as x varies from 0 to 100.</span><span>NGAx is computed similarly to NGx, but based on lengths of aligned blocks instead of contig lengths. Contigs are broken at misassembly breakpoints. NGAx is the minimum block length <b>y</b> such that using blocks of length at least <b>y</b> accounts for at least x% of the bases of the reference genome. This metric is computed only if a reference genome is provided.</span>",\n "GC content" : "<span>plot shows the distribution of GC percentage among the contigs, i.e., the total number of bases in contigs with such GC content. Typically, the distribution is approximately Gaussian. However, for some genomes it is not Gaussian. For assembly projects with contaminants, the GC distribution of the contaminants often differs from the reference genome and may give a superposition of multiple curves with different peaks.</span>",\n \n- "Duplication ratio" : "<span>is the total number of aligned bases in the assembly (i.e. <i>Total length</i> - <i>Fully unaligned length</i> - <i>Partially unaligned length</i>), divided by the total number of aligned bases in the reference (see the <b>Genome fraction (%)</b> metric). If the assembly contains many contigs that cover the same regions of the reference, its <i>Duplication ratio</i> may be much larger than 1. This may occur due to overestimating repeat multiplicities and due to small overlaps between contigs, among other reasons.</span>",\n+ "Duplication ratio" : "<span>is the total number of aligned bases in the assembly, divided by the total number of aligned bases in the reference (see the <b>Genome fraction (%)</b> metric). If the assembly contains many contigs that cover the same regions of the reference, its <i>Duplication ratio</i> may be much larger than 1. This may occur due to overestimating repeat multiplicities and due to small overlaps between contigs, among other reasons.</span>",\n "Largest alignment" : "<span>is the length of the largest continuous alignment in the assembly. This metric is always equal to the <i>Largest contig</i> metric but it can be smaller if the largest contig of the assembly contains a misassembly event.</span>",\n "Total aligned length" : "<span>is the total number of aligned bases in the assembly.</span>",\n "Avg contig read support" : "<span>is the average coverage of contigs that have large unique alignments to the reference. Read coverage is extracted from contig names (SPAdes/Velvet naming scheme only).</span>",\n \n "# N\'s" : "<span>is the total number of uncalled bases (N\'s) in the assembly.</span>",\n- "# N\'s per 100 kbp" : "<span>is the average number of uncalled bases (N\'s) per 100000 assembly bases.</span>",\n+ "# N\'s per 100 kbp" : "<span>is the average number of uncalled bases (N\'s) per 100,000 assembly bases.</span>",\n \n "# mapped" : "<span>is the number of reads that mapped to the assembly.</span>",\n "Mapped (%)" : "<span>is the percent of reads that mapped to the assembly.</span>",\n' |
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| diff -r 675488238c96 -r 3061c8b029e5 test-data/test5.tab --- a/test-data/test5.tab Fri Mar 25 17:36:59 2022 +0000 +++ b/test-data/test5.tab Fri Aug 05 15:21:27 2022 +0000 |
| b |
| @@ -11,16 +11,18 @@ Reference GC (%) 52.00 52.00 N50 3980 6650 NG50 3980 6650 -N75 1610 6650 -NG75 1610 6650 +N90 1120 6650 +NG90 1120 6650 +auN 2934.0 6650.0 +auNG 2960.4 6650.0 L50 1 1 LG50 1 1 -L75 2 1 -LG75 2 1 -# total reads 331 331 +L90 3 1 +LG90 3 1 +# total reads 330 330 # left 0 0 # right 0 0 -Mapped (%) 2.72 2.42 +Mapped (%) 2.73 2.42 Reference mapped (%) 2.42 2.42 Properly paired (%) 0.0 0.0 Reference properly paired (%) 0.0 0.0 @@ -46,9 +48,11 @@ Total aligned length 4760 6650 NA50 1610 6650 NGA50 1610 6650 -NA75 - 6650 -NGA75 - 6650 +NA90 - 6650 +NGA90 - 6650 +auNA 1187.4 6650.0 +auNGA 1198.1 6650.0 LA50 2 1 LGA50 2 1 -LA75 - 1 -LGA75 - 1 +LA90 - 1 +LGA90 - 1 |
| b |
| diff -r 675488238c96 -r 3061c8b029e5 test-data/test6.tab --- a/test-data/test6.tab Fri Mar 25 17:36:59 2022 +0000 +++ b/test-data/test6.tab Fri Aug 05 15:21:27 2022 +0000 |
| b |
| @@ -8,9 +8,10 @@ Total length 6710 6650 GC (%) 51.28 52.00 N50 3980 6650 -N75 1610 6650 +N90 1120 6650 +auN 2934.0 6650.0 L50 1 1 -L75 2 1 +L90 3 1 # total reads 167 167 # left 0 0 # right 0 0 |
| b |
| diff -r 675488238c96 -r 3061c8b029e5 test-data/test7.tab --- a/test-data/test7.tab Fri Mar 25 17:36:59 2022 +0000 +++ b/test-data/test7.tab Fri Aug 05 15:21:27 2022 +0000 |
| b |
| @@ -8,9 +8,10 @@ Total length 6710 6650 GC (%) 51.28 52.00 N50 3980 6650 -N75 1610 6650 +N90 1120 6650 +auN 2934.0 6650.0 L50 1 1 -L75 2 1 +L90 3 1 # total reads 167 167 # left 0 0 # right 0 0 |