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Changeset 5:f89e3c318453 (2023-06-07)

Previous changeset 4:f9f2ad782d8f (2022-01-20) Next changeset 6:8e66f695d859 (2024-01-10)

Commit message:
planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46

modified:
rna_quast.xml

removed:
test-data/Saccharomyces_cerevisiae.R64-1-1.75.dna.toplevel.fa
test-data/Saccharomyces_cerevisiae.R64-1-1.75.gtf
test-data/Trinity.fasta
test-data/idba.fasta

diff -r f9f2ad782d8f -r f89e3c318453 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Wed Jun 07 12:02:03 2023 +0000

@@ -0,0 +1,17 @@
+
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">rnaquast</requirement>
+            
+        </requirements>
+    </xml>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">rnaQUAST</xref>
+        </xrefs>
+    </xml>
+    <token name="@TOOL_VERSION@">2.2.3</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">20.05</token>
+ </macros>
\ No newline at end of file

diff -r f9f2ad782d8f -r f89e3c318453 rna_quast.xml
--- a/rna_quast.xml Thu Jan 20 21:09:47 2022 +0000
+++ b/rna_quast.xml Wed Jun 07 12:02:03 2023 +0000

[

b'@@ -1,125 +1,54 @@\n-<tool id="rna_quast" name="rnaQUAST" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">\n+<tool id="rna_quast" name="rnaQUAST" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n <description>A quality assessment tool for De Novo transcriptome assemblies</description>\n- <xrefs>\n- <xref type="bio.tools">rnaQUAST</xref>\n- </xrefs>\n <macros>\n- <token name="@TOOL_VERSION@">2.2.1</token>\n- <token name="@VERSION_SUFFIX@">1</token>\n- <xml name="element_matching_line" token_name="" token_expression="">\n- <element name="@NAME@">\n- <assert_contents>\n- <has_line_matching expression="@EXPRESSION@" />\n- </assert_contents>\n- </element>\n- </xml>\n- <xml name="element_has_text" token_name="" token_text="">\n- <element name="@NAME@">\n- <assert_contents>\n- <has_text text="@TEXT@" />\n- </assert_contents>\n- </element>\n- </xml>\n- <xml name="details_output_test" token_assembler="">\n- <element name="@ASSEMBLER@">\n- <element name="5000%-assembled.list">\n- <assert_contents>\n- <has_n_lines n="0" />\n- </assert_contents>\n- </element>\n- <element name="9500%-assembled.list">\n- <assert_contents>\n- <has_n_lines n="0" />\n- </assert_contents>\n- </element>\n- <expand macro="element_matching_line" name="alignment_metrics" expression="\\s*== ALIGNMENT METRICS \$calculated with reference genome but without gene database\$ ==\\s*" />\n- <expand macro="element_matching_line" name="alignment_multiplicity" expression="unaligned=\\d+ aligned=\\d+ alignments=\\d+\\s*" />\n- <expand macro="element_matching_line" name="alignments_per_isoform" expression="avg=[\\d.]+\\s*" />\n- <expand macro="element_matching_line" name="basic_metrics" expression="\\s*== BASIC TRANSCRIPTS METRICS \$calculated without reference genome and gene database\$ ==\\s*" />\n- <expand macro="element_matching_line" name="block_length" expression="avg=[\\d.]+\\s*" />\n- <expand macro="element_matching_line" name="blocks_per_alignment" expression="avg=[\\d.]+\\s+tot=\\d+\\s*" />\n- <expand macro="element_matching_line" name="database_metrics" expression="\\s*== GENE DATABASE METRICS ==\\s*" />\n- <expand macro="element_matching_line" name="misassemblies" expression="\\s*== ALIGNMENT METRICS FOR MISASSEMBLED \$CHIMERIC\$ TRANSCRIPTS \$calculated with reference genome or with gene database\$ ==\\s*" />\n- <expand macro="element_matching_line" name="mismatch_rate" expression="avg=[\\d.]+\\s+tot=\\d+\\s*" />\n- <expand macro="element_matching_line" name="sensitivity" expression="\\s*== ASSEMBLY COMPLETENESS \$SENSITIVITY\$ ==\\s*" />\n- <expand macro="element_matching_line" name="specificity" expression="\\s*== ASSEMBLY SPECIFICITY ==\\s*" />\n- <expand macro="element_matching_line" name="transcript_length" expression="avg=[\\d.]+\\s*" />\n- <expand macro="element_matching_line" name="x-aligned" expression="avg=[\\d.]+\\s*" />\n- <expand macro="element_matching_line" name="x-assembled" expression="avg=[\\d.]+\\s*" />\n- <expand macro="element_matching_line" name="x-assembled_exons" expression="avg=[\\d.]+\\s*" />\n- <expand macro="element_matching_line" name="x-covered" expression="avg=[\\d.]+\\s*" />\n- <expand macro="element_matching_line" name="x-covered_exons" expression="avg=[\\d.]+\\s*" />\n- <expand macro="element_matching_line" name="x-matched" expression="avg=[\\d.]+\\s*" />\n- <expand macro="element_matching_line" name="x-matched_blocks" expressi'..b'lignement/Basic Metrics\n-- Misassemblies/ Specificity/ Sensitivity\n-- Alignment multiplicity\n-- Block/ Transcript Lentgh\n-- Blocks per alignment\n-- Mismatch rate\n-- x-aligned\n-- Nx\n-- Blocks per alignment\n-- gmap build logs\n+**rnaQUAST pipeline**\n+\n+To evaluate quality of the assembled transcripts, rnaQUAST takes a reference genome in FASTA format and optionally its gene database in \n+GFF/GTF format. A user can provide either a FASTA file with transcripts, which will be aligned to the given reference genome using GMAP \n+or BLAT. The alignments are analyzed to calculate simple metrics and then are matched against the isoforms from the gene database in order \n+to obtain statistics that represent completeness and correctness levels of the assembly. In addition, rnaQUAST is capable of estimating \n+gene database coverage by raw reads using STAR or TopHat2. For de novo quality assessment when reference genome and gene database are \n+unavailable, the transcripts are analyzed using BUSCO.\n+\n+.. class:: infomark\n \n-**Using rnaQuast without gene coordinates** you wont get:\n-- x-assembled (Exons)\n-- Alignments per Isoform\n-- x-covered (Exons)\n-- x-matched (Blocks)\n-- gmap build logs\n-- Database Metrics\n-- Alignment multiplicity\n-- Mismatch rate\n-- NAx\n-- x-aligned\n-**Using rnaQuast with gene coordinates** you will get:\n-- Reports\n-- Logs\n-- Alignement/Basic Metrics\n-- Misassemblies/Specificity/Sensitivity\n-- Alignment multiplicity\n-- Block/Transcript length\n-- Blocks per alignment\n-- Mismatch rate\n-- x-aligned\n-- Nx/NAx\n-- gmap build logs\n-- Database Metrics\n-- Alignment multiplicity\n-More informations, see citations.\n+**Metrics and alignment analysis**\n+\n+rnaQUAST calculates various metrics without using alignment information, e.g. length distribution and N50 of the assembled transcripts. \n+Additionally, rnaQUAST computes the following statistics for the gene database: the total number of genes and isoforms, isoform and exon \n+length distribution, average number of exons per gene, etc.\n+\n+To analyze transcripts\' alignments, rnaQUAST firstly filters out short partial alignments (shorter than a user-defined threshold, default \n+value is 50 bp). Such short alignments are typically caused by genomic repeats and thus are ignored. Afterwards, rnaQUAST selects the \n+best-scored spliced alignment for each transcript. If a transcript has more than one alignment with the highest score, it is reported \n+as multiply aligned. Otherwise, it is considered to be uniquely aligned. If the best-scored alignment is discordant (e.g. the transcript \n+has partial alignments that are either mapped to different strands or to different chromosomes) the transcript is classified as misassembled. \n+Transcripts without misassemblies are analyzed to calculate such metrics as average transcript alignment fraction and mismatch rate.\n+\n+For the simplicity of explanation, transcript is further referred to as a sequence generated by the assembler and isoform denotes a sequence \n+from the gene database. rnaQUAST matches best-scored alignments of non-misassembled transcripts to the isoforms\' coordinates and analyzes \n+them to estimate how well the isoforms are covered by the assembly. rnaQUAST computes such metrics as database coverage (the total number \n+of covered bases of all isoforms divided by the total length of all isoforms) and the number of 50%/95%-assembled isoforms. An isoform is \n+considered to be x%-assembled if it has at least x% covered by a single transcript. Vice versa, to evaluate how well the assembled \n+transcripts are covered by the isoforms, rnaQUAST estimates the number of unannotated transcripts (that align to the genome, but do not \n+match to any isoform) and the number of 50%/95%-matched transcripts (that have corresponding fraction mapped to an isoform). Indeed, the \n+thresholds described above (50% and 95%) can be varied by the user.\n+\n+\n ]]> </help>\n <citations>\n <citation type="doi">10.1093/bioinformatics/btw218 </citation>\n'

diff -r f9f2ad782d8f -r f89e3c318453 test-data/Saccharomyces_cerevisiae.R64-1-1.75.dna.toplevel.fa
--- a/test-data/Saccharomyces_cerevisiae.R64-1-1.75.dna.toplevel.fa Thu Jan 20 21:09:47 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,10000 +0,0 @@\n->IV dna:chromosome chromosome:R64-1-1:IV:1:1531933:1 REF\r\n-ACACCACACCCACACCACACCCACACACACCACACCCACACACCACACCCACACCCACAC\r\n-ACCCACACCCACACACCACACACCACACCACACCACACCCACACCCACACCACACCCACA\r\n-CCCACACACCACACCCACACCCACACACCACACACTACCCCTAACACTACCCTATTCTAA\r\n-CCCTGATTTTACCTGTCTCCAAACCTACCCTCACATTACCCTACCTCCCCACTCGTTACC\r\n-CTGCCCCACTCAACCATCCACTCCCAACCACCATCCATCTCTCTACTTACCACTAACCAC\r\n-CGTCCACCATAACCGTTACCCTCCAATTACCCATATCCAACTCCACTACCACTTACCCTA\r\n-CTATTACCCTACCATCCACCATGTCCTACTCACTGTACTGTTGTTCTACCCTCCATATTG\r\n-AAACGTTAACAAATGATCGTAAATAATACATACATACTTACCCTACCACTCTATACCACC\r\n-ACTACCACCACCGCCACTTGCCACACTCACCTTCACTTCTACTGATATGTCATACGCACA\r\n-CGGATGCTACAGTATATACCATCTCAAACTTACCCTACTTTCATATTCCACACCATGGCC\r\n-CCATTCTCACTAAATCAGTACCAAATGCACTCACATCATTATTCACGGCACTTGCCTCAG\r\n-CGGTCTATACCCTGTGCCATTTACGCATAACTCCCACGATTATCCACATTTTATTACCTA\r\n-TATCTCATTCGGCGGCCCCAAATATTGTATAACTGCTCTTAATACATACGTTATACCACT\r\n-TTTACACCGTATACTAACCACTCAATTTATATACACTTATGCCAATATTACAAAAAAATC\r\n-ACCACTAAAATCACCTAAACATAAAAATATTCTATTCTTCAACCATAATACATAAACACA\r\n-CTTAATTGCGTCTTAATACTATCATGGTATCATTAACTTAAAGTTCCTTAATATCGTCAT\r\n-ACCACTATGCTCTATTCCATATATTGTAATATAACTGTACTCTATAGTCATACAGACGCT\r\n-TTTACTTCACCCCATCTTCTCATACTATTGTCATAGAATCTCACACTGACGCATGATTAA\r\n-AACGAATAATTTTTACTGTAAGGGCTGCCATCCGCGCTCTATCCTTTTGTTTGCAATATT\r\n-TATATACAGAATCTCAAAACAAGCGGGAGAAGTGCTAATTACCCAGAGGTCATGCATGAT\r\n-CTGAGTACCACCGTACCTCTAGGTTTTGCTTTGATCCGTTTTACAGTGACACCGAACATA\r\n-AGGGGAAGCTATTGACATGGTATCGAAAGGTTGTCCACATTGGGAAGTAACTTGGTTCTA\r\n-TGAATCTTCATGTCAGATACGTAGGACAGACTCTTTCCTGTGTAAATATTTGTGACAGCT\r\n-ACGTCTATTTTCTACTAGATGTTTACACAGTTTTGTCACAGGAAATCTACGCTTAAAATA\r\n-TGTATTTCATTCAAGCGGTAACCGCTGTACGAGCAGTGACATTGCTGGTCGCACCTTAAA\r\n-TGTAAACCAACGTTACGGCACACCGTGATGTACCCGCATTAAAGTTTTGTAAATTCGTTA\r\n-TTACGATTATTGAATTGGCTAGATAGAAAACAGGAAATGAAATGGATACCCTTTTCGAAT\r\n-AGCTGAGTTTCTTTGCCTAAAATAGCCCAACATTGTTGCCCTTTTTCTATCACGAGGTTA\r\n-CTGAGCCATTGCATGAACGCGCGCGCCTCGGCGGCTTTTTTTTCCTGCTGTATAAAAGCG\r\n-AAAAGCCAGAAGTTACTATCTCGAATAAAAAACCCCTCGAACTGCCATCTCACTACCGAA\r\n-AATGAAAGAGAATGAAGTCAAAGATGAGAAAAGCGTAGATGTGTTATCCTTCAAACAGCT\r\n-CGAATCCCAAAAGATTGTTCTACCTCAAGATCTTTTCAGAAGCAGCTTTACCTGGTTTTG\r\n-TTATGAAATTTACAAGTCCTTAGCGTTTCGCATCTGGATGCTATTATGGCTACCACTTAG\r\n-CGTCTGGTGGAAACTTTCCAACAATTGTATTTACCCACTTATAGTTTCACTTCTGGTCCT\r\n-GTTTCTGGGACCAATATTTGTCCTTGTTATTTGTGGACTTTCTCGTAAGCGTTCCTTATC\r\n-GAAACAACTCATTCAGTTTTGCAAAGAGATTACTGAAAACACACCAAGTTCTGATCCTCA\r\n-TGATTGGGAAGTCGTTGTAGCAAATCTAAATTCGTACTTATATGAAAATAAGGCTTGGAA\r\n-TACTAAGAATTTCTTTTTCAATGCTACGGATTGTGAGAAAATGTTCAGAACAACTGTTCT\r\n-TGAACCATTTTCTTTGAAAAAAGATAAAGCTGCCAAGGTTAAGTCATTTAAGGATTCTGT\r\n-CCCTTATATCGAAGAGGCTTTGCAAGTGTATGCTACAGGATTTGACAAACAGTGGAAGTT\r\n-GTTTATTACTGAAAAATCATGGAGCCCTGTTGGCCTGGAAGACGTTCAGCTTCCCAAGGA\r\n-TATTCATCGGTCCAAGCTTACTTGGTTTTTAAAGCGGATTTTCACTATTTACTCTCTACC\r\n-ATTATGGCTTGCTTTTTTGAACTGTATCTGCGTGTCACAGCATTTTTGCCTTGCATTTCG\r\n-TATCTTGTGTCCTGGATTGTTTTTCCTCATGATGGTGTGGCTTTTCCAAAATATGAGGAC\r\n-GACTGCTTTACTCGTGAAAATGGAACACAAGATGCAATTCTTGTTGACTATTATAAATGA\r\n-GCAAGAAAGTGGTGCGAATGGATGGGACGAAATTGCAAGGAAAATGAATAGGTACTTGTT\r\n-TGAGAAAAAAGCCTGGAAGAATGAAGAGTTTTTCTTCGACGGGATTGACTGTGAATGGTT\r\n-TTTTAGCCACTTCTTCTACCGCCTTCTATCTGCAAAGAAATCTATGTGGCTTTTACCATT\r\n-GAATGTGGAACTATGGCCATATATTAAAGAAGCGCAATTGTCCCGCAATGAAGAGTCTTT\r\n-AATGAAGAAATGAGAACGCCCTTCTGGACTTAAAAATTCATACTTTTGCATTCTGTTAGA\r\n-TATGAATACTACACTCTATTGAGTGACTTTAAAAGGCGAGTGGACACTTTTATCAAGCGA\r\n-TTTATCATGCAGTAATACTAATATTACTAATTAATCACTACTACCTCTCTTAAACAGGAA\r\n-ATATGCTATTCATCAGTAAGAAGCTGCACAAATGTTATATATCATACCAGGAATACACAT\r\n-AAGAGCAAAAATGCTATTCTACAATATCCTCATCTTACCAGCTCACTCACAAAATATTCT\r\n-TACTCCGAGTACGACCATAAAGCAATGCTAACGAATAGTCATACTAAAGTACTATAAAAT\r\n-CTTTCCGTGCGCTCAAACGGAGGCCATGCCATAAAGTTAAATGTGATAACTTAAAAGCAT\r\n-CATAAGAGTGATTTTCCAGTATTGTTTCAGTAATGTAAGGCCTAAAGAAGAACGCATATT\r\n-GGTAAACCTCCAACCTACTAGTAATTAAAAAGCTTTAGTTTAACCCGTAGTTCGGGATAC\r\n-ACTTCGGGCATAACGTACGTTTATTATAAATTTTTATATCTCTTGCGTACCATGTATATT\r\n-CCAGAACAGTGAATACACTTTTCTAGTTCATTTATGCTACTTTCATATCCTCCATTAAAG\r\n-CGGGAGCTACCGTTGAAAAGGCATAATAATTGAAGTTTCGAGTGGGTTAGTTACACTAGG\r\n-TGAAGGATCGTTTGCCTCCATATGGTCAAGCCATTCACGGACATTGATAATAGCTGGGAC\r\n-AATTCTGGTTTCA'..b'ACTAGTCTGGCATCAACATGGCAAACCA\r\n-CAGGACATGTTGAAGGGAATCAGTGAAAAACTACCTAAGGATGAAATGCCTGATTTTGTA\r\n-TTATGTTTGGGTGATGACTTCACTGACGAAGACATGTTTAGACAGTTGAATACCATTGAA\r\n-ACTTGTTGGAAAGAAAAATATCCTGACCAAAAAAATCAATGGGGCAACTACGGATTCTAT\r\n-CCTGTCACTGTGGGATCTGCATCCAAGAAAACTGTCGCAAAGGCTCATTTAACCGATCCT\r\n-CAGCAAGTCCTGGAGACTTTAGGTTTACTTGTTGGTGATGTCTCTCTCTTCCAAAGTGCT\r\n-GGTACGGTCGACCTGGATTCCAGAGGTCATGTCAAGAATAGTGAGAGCAGTTTGAAATCA\r\n-AAGCTAGCATCTAAAGCTTATGTTATGAAAAGATCGGCTTCTTACACCGGCGCAAAGGTT\r\n-TGAAACACCCTTTTTAACGAAATGGTTATGACTAGACAGACATCTTACGTCTTACTCCTT\r\n-CATGCTTTATTTTTTTCTTTGTATTGTATTTGAACAGTCAATATGTGGTGTTGCGACGAA\r\n-GGCATATATATAATAGTCTCAACCCACCATTTTCGAAGATTTACATACACATTATATTTT\r\n-TATAAACTTCCAATATGTAATAACTTTATATGATATGTAACTTCTCACTATTATCCTTAC\r\n-TATTAAACGGTTTTTAATAAATATCATTGTTCTTTGTTTTATTAATGAGAAAAAGAAATT\r\n-TAATACAATGTCCGGCGGGAAGAAAAAAAATCGATGAATTAATTGAAAAAAAGTATCTTT\r\n-ATCATGTGAACTGAGGAGAAGAACGGCATCTCGAAAAGAGCACGTCGAAACAGCGGTAGG\r\n-TAAAAGAGGGTACTACCAGAGGTCTTTTCTCTTTATACGTTAACCTCTCAGCTTTTTCTT\r\n-TTGCAATTCAGGACACTTTAACTTGTAGTCACACGCTAGTCCACGTAGCAAAGTAAAACA\r\n-GCACGAAAAAAGTGATTACAAATTTCAAGGGAGATATGATGGACTTAGATAAGATTATAG\r\n-CATCACTGAGAGACGGAAAACATATTCCTGAAGAAACCGTTTTTAGGCTATGTTTAAATT\r\n-CACAGGAACTATTAATGAATGAAGGCAATGTAACACAAGTCGATACACCGGTTACAATAT\r\n-GCGGTGATATACATGGCCAATTACACGATCTACTAACGCTCTTCGAAAAGAGTGGTGGTG\r\n-TAGAGAAAACAAGGTATATTTTCTTGGGCGATTTTGTGGATAGGGGATTTTACTCATTGG\r\n-AGAGTTTTTTACTTTTACTATGTTACAAATTAAGATATCCTGATAGGATTACTTTAATTA\r\n-GAGGCAATCACGAAACCCGGCAAATTACTAAAGTATACGGATTTTACGATGAAGTAGTAA\r\n-GAAAATATGGTAATAGTAACGTATGGAGGTACTGCTGTGAAGTTTTTGATTATTTATCAT\r\n-TGGGGGCAATAATAAACAATAGCATATTCTGTGTTCATGGTGGATTATCTCCGGATATGA\r\n-CCACGGTTGATGAAATACGAACAATAGACAGGAAACAAGAAGTTCCACATGAAGGTGCTA\r\n-TGTGTGACTTATTATGGAGCGACCCCGAAGACGTTGACACATGGTCATTATCACCAAGAG\r\n-GTGCTGGATTTCTTTTCGGTAAAAGAGAAGTTGATCAATTCTTAGAGAAAAACAACGTTG\r\n-AGTTAATTGCTAGAGCTCATCAGTTAGTGATGGAAGGTTACAAAGAAATGTTCGACGGTG\r\n-GATTAGTGACAGTCTGGTCGGCACCGAATTACTGTTATCGTTGTGGTAATGTAGCAGCTG\r\n-TATTGAAGATAGACGACGATTTGAATCGTGAATATACAATTTTTGAAGCTGTTCAGGCAC\r\n-AAAATGAAGTCGGAAATGCTATAATTCCAACCAAAAAATCTCAAATGGACTATTTCTTAT\r\n-AAATTTTTAACAGGCACTCTAATTGTCAAGTGCATTTTTCTTTTTTTCTTCATAATGCAA\r\n-TAAAGGAAAAAAAATTGTAATATTACATACTTCTTTTCACATCTTAGCTAATTAACAATA\r\n-TGGCTTTTGAATACTAATATATACCCAGCTACCGTTTCTTCTTTTATTTTTTATTCCTTT\r\n-TTTTCTTCAGTAGAATATGTTATAGATGCGGAGGTCCCCTAAGTTCTTCACGTGTTCTCT\r\n-TCTCATCGCGTTTGATATGAAAAATAGAAAAAAATACATAGTAGCATGACTAACTAATAA\r\n-TAAGCTCCGCTATCAAAGATGTCAAGTACATTAAGGAAAGCTTTTAGATAAGGAAAAGAA\r\n-CTTATTAATAATATATAATATGAAAATATGTCGCTTGGTATACCACTTTCCCAATTAATA\r\n-GTAGAAAGTCCAAAGCCATTAAGTAGCGGCATCACAGGATTAGATGAGATATTAAACCTG\r\n-GGATTCCAGGCAAGGTCGATCTACGAAATATTTGGGCCTCCGGGCATTGGCAAGACTAAT\r\n-TTTGGCATTCAATTGGTGTGTAATTCGTTAGAAGGCATACAACAATCGGAAATAAACGAC\r\n-GATAAAATTCTATGGATAGAAACATTTCAAGAAATGCCCATAAACATACTAAGAGAACGC\r\n-TTTCAAAAATTTAAAATCGTGGAAGAAAATGTGAAGCGGGTCCGAATAACGAAATTTGGA\r\n-CAGCTATTATATTTCTTCCAGAATTTGTTCAAATTATCTCAAAGTGTGCGATATAAACTA\r\n-GTTATAATTGATGGATTTTCTCAATTAGTCTGCGATCATCTGTGTACACTAAGTAAAAGA\r\n-GGCGGCGGAATGATAGATAAAACTATACACGAGTTAAAATGTCGACATTTGATATTAATT\r\n-TTTACGGTAATGACCAAATACACACATTCCACGGGTTCGACAATAATAGTTTTAAATGAC\r\n-TGTATGAACACCGCCTTCCAATCAAACGAATTCGAATCCTTGGAAGAATACTACGAAATT\r\n-TTAGACGACGGATCTAACTTCTTTGTCAACTCTAACAACGAAAGGCGTAAGAACAATGTA\r\n-CATATATTGAAAAGCGCGCTCGTTGCCAATATCGCTATGGGAAGCAAGGATTCCACTTGG\r\n-GAAGTATTTCTAAGAGACAGGATCGGCCTTTTTAGGGATTGGAATGAACAAGTGGACGAA\r\n-ACCGTTTTCGTGAAAAGCAAAAGAGTGAAGGCGTCATCCTCGCAGAGTAACGAGGGATGT\r\n-ACTACCATCAAAGAAATGAGAATAAACAAACGAAACTTTGAAAACTTGAGAATAGCTATT\r\n-GTTTTTAATTTACACGGCGAAGATAGAAAAAGAGAAGGACGAAATTTAAAGCGGTCAAGA\r\n-AGCAGCGACGATCGTAACTATATTGTCAAATTTGATTTTGATAAAGCAACAGGTCAACTC\r\n-CGCGATATAATTGATCTGAAACCTGATACTGCTAATATTGCCTCATTTCCAACATTATCA\r\n-ACAAGCAGCAGCAGTTGCTCACAAGTGTTTAACAATATTGACTCCAATGATAATCCATTA\r\n-CCAAATGCGGAGGGAAAGGAGGAGATAATTTATGATAGTGAAGGTTAATAGTAAAATAAA\r\n-AAAACCGAAAACCGAAAACAATAAAAAATGGAAAAACGACAACATTCCACCCAACAACTA\r\n-CAAAGAAAAGTTAAGGGTAATTTTACCTATTTAGGATTTTAATCTGTTGGAGTTAAGGTG\r\n-AATACGTTTTTCCATATTGGGGTATGCAGCTCGAACCTAAAGTGGTATGTACACATCCCC\r\n-TCAAGCACACCCATTACCCTTATAGGATTAATGTAAGCAACAGCTTACACGGAATTGGAA\r\n'

diff -r f9f2ad782d8f -r f89e3c318453 test-data/Saccharomyces_cerevisiae.R64-1-1.75.gtf
--- a/test-data/Saccharomyces_cerevisiae.R64-1-1.75.gtf Thu Jan 20 21:09:47 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,1000 +0,0 @@\n-#!genome-build R64-1-1\r\n-#!genome-version R64-1-1\r\n-#!genome-date 2011-09\r\n-#!genome-build-accession :GCA_000146045.2\r\n-#!genebuild-last-updated 2011-12\r\n-IV\tprotein_coding\tgene\t1802\t2953\t.\t+\t.\tgene_id "YDL248W"; gene_name "COS7"; gene_source "ensembl"; gene_biotype "protein_coding";\r\n-IV\tprotein_coding\ttranscript\t1802\t2953\t.\t+\t.\tgene_id "YDL248W"; transcript_id "YDL248W"; gene_name "COS7"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "COS7"; transcript_source "ensembl";\r\n-IV\tprotein_coding\texon\t1802\t2953\t.\t+\t.\tgene_id "YDL248W"; transcript_id "YDL248W"; exon_number "1"; gene_name "COS7"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "COS7"; transcript_source "ensembl"; exon_id "YDL248W.1";\r\n-IV\tprotein_coding\tCDS\t1802\t2950\t.\t+\t0\tgene_id "YDL248W"; transcript_id "YDL248W"; exon_number "1"; gene_name "COS7"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "COS7"; transcript_source "ensembl"; protein_id "YDL248W";\r\n-IV\tprotein_coding\tstart_codon\t1802\t1804\t.\t+\t0\tgene_id "YDL248W"; transcript_id "YDL248W"; exon_number "1"; gene_name "COS7"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "COS7"; transcript_source "ensembl";\r\n-IV\tprotein_coding\tstop_codon\t2951\t2953\t.\t+\t0\tgene_id "YDL248W"; transcript_id "YDL248W"; exon_number "1"; gene_name "COS7"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "COS7"; transcript_source "ensembl";\r\n-IV\tprotein_coding\tgene\t3762\t3836\t.\t+\t.\tgene_id "YDL247W-A"; gene_source "ensembl"; gene_biotype "protein_coding";\r\n-IV\tprotein_coding\ttranscript\t3762\t3836\t.\t+\t.\tgene_id "YDL247W-A"; transcript_id "YDL247W-A"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "YDL247W-A"; transcript_source "ensembl";\r\n-IV\tprotein_coding\texon\t3762\t3836\t.\t+\t.\tgene_id "YDL247W-A"; transcript_id "YDL247W-A"; exon_number "1"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "YDL247W-A"; transcript_source "ensembl"; exon_id "YDL247W-A.1";\r\n-IV\tprotein_coding\tCDS\t3762\t3833\t.\t+\t0\tgene_id "YDL247W-A"; transcript_id "YDL247W-A"; exon_number "1"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "YDL247W-A"; transcript_source "ensembl"; protein_id "YDL247W-A";\r\n-IV\tprotein_coding\tstart_codon\t3762\t3764\t.\t+\t0\tgene_id "YDL247W-A"; transcript_id "YDL247W-A"; exon_number "1"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "YDL247W-A"; transcript_source "ensembl";\r\n-IV\tprotein_coding\tstop_codon\t3834\t3836\t.\t+\t0\tgene_id "YDL247W-A"; transcript_id "YDL247W-A"; exon_number "1"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "YDL247W-A"; transcript_source "ensembl";\r\n-IV\tprotein_coding\tgene\t5985\t7814\t.\t+\t.\tgene_id "YDL247W"; gene_name "MPH2"; gene_source "ensembl"; gene_biotype "protein_coding";\r\n-IV\tprotein_coding\ttranscript\t5985\t7814\t.\t+\t.\tgene_id "YDL247W"; transcript_id "YDL247W"; gene_name "MPH2"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "MPH2"; transcript_source "ensembl";\r\n-IV\tprotein_coding\texon\t5985\t7814\t.\t+\t.\tgene_id "YDL247W"; transcript_id "YDL247W"; exon_number "1"; gene_name "MPH2"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "MPH2"; transcript_source "ensembl"; exon_id "YDL247W.1";\r\n-IV\tprotein_coding\tCDS\t5985\t7811\t.\t+\t0\tgene_id "YDL247W"; transcript_id "YDL247W"; exon_number "1"; gene_name "MPH2"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "MPH2"; transcript_source "ensembl"; protein_id "YDL247W";\r\n-IV\tprotein_coding\tstart_codon\t5985\t5987\t.\t+\t0\tgene_id "YDL247W"; transcript_id "YDL247W"; exon_number "1"; gene_name "MPH2"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "MPH2"; transcript_source "ensembl";\r\n-IV\tprotein_coding\tstop_codon\t7812\t7814\t.\t+\t0\tgene_id "YDL247W"; transcript_id "YDL247W"; exon_number "1"; gene_name "MPH2"; gene_source "ensembl"; gene_biotype "protein_coding"; tra'..b'otein_coding\tgene\t285391\t286695\t.\t-\t.\tgene_id "YDL097C"; gene_name "RPN6"; gene_source "ensembl"; gene_biotype "protein_coding";\r\n-IV\tprotein_coding\ttranscript\t285391\t286695\t.\t-\t.\tgene_id "YDL097C"; transcript_id "YDL097C"; gene_name "RPN6"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "RPN6"; transcript_source "ensembl";\r\n-IV\tprotein_coding\texon\t285391\t286695\t.\t-\t.\tgene_id "YDL097C"; transcript_id "YDL097C"; exon_number "1"; gene_name "RPN6"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "RPN6"; transcript_source "ensembl"; exon_id "YDL097C.1";\r\n-IV\tprotein_coding\tCDS\t285394\t286695\t.\t-\t0\tgene_id "YDL097C"; transcript_id "YDL097C"; exon_number "1"; gene_name "RPN6"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "RPN6"; transcript_source "ensembl"; protein_id "YDL097C";\r\n-IV\tprotein_coding\tstart_codon\t286693\t286695\t.\t-\t0\tgene_id "YDL097C"; transcript_id "YDL097C"; exon_number "1"; gene_name "RPN6"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "RPN6"; transcript_source "ensembl";\r\n-IV\tprotein_coding\tstop_codon\t285391\t285393\t.\t-\t0\tgene_id "YDL097C"; transcript_id "YDL097C"; exon_number "1"; gene_name "RPN6"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "RPN6"; transcript_source "ensembl";\r\n-IV\tprotein_coding\tgene\t286998\t287324\t.\t-\t.\tgene_id "YDL096C"; gene_name "OPI6"; gene_source "ensembl"; gene_biotype "protein_coding";\r\n-IV\tprotein_coding\ttranscript\t286998\t287324\t.\t-\t.\tgene_id "YDL096C"; transcript_id "YDL096C"; gene_name "OPI6"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "OPI6"; transcript_source "ensembl";\r\n-IV\tprotein_coding\texon\t286998\t287324\t.\t-\t.\tgene_id "YDL096C"; transcript_id "YDL096C"; exon_number "1"; gene_name "OPI6"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "OPI6"; transcript_source "ensembl"; exon_id "YDL096C.1";\r\n-IV\tprotein_coding\tCDS\t287001\t287324\t.\t-\t0\tgene_id "YDL096C"; transcript_id "YDL096C"; exon_number "1"; gene_name "OPI6"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "OPI6"; transcript_source "ensembl"; protein_id "YDL096C";\r\n-IV\tprotein_coding\tstart_codon\t287322\t287324\t.\t-\t0\tgene_id "YDL096C"; transcript_id "YDL096C"; exon_number "1"; gene_name "OPI6"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "OPI6"; transcript_source "ensembl";\r\n-IV\tprotein_coding\tstop_codon\t286998\t287000\t.\t-\t0\tgene_id "YDL096C"; transcript_id "YDL096C"; exon_number "1"; gene_name "OPI6"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "OPI6"; transcript_source "ensembl";\r\n-IV\tprotein_coding\tgene\t287059\t289512\t.\t+\t.\tgene_id "YDL095W"; gene_name "PMT1"; gene_source "ensembl"; gene_biotype "protein_coding";\r\n-IV\tprotein_coding\ttranscript\t287059\t289512\t.\t+\t.\tgene_id "YDL095W"; transcript_id "YDL095W"; gene_name "PMT1"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "PMT1"; transcript_source "ensembl";\r\n-IV\tprotein_coding\texon\t287059\t289512\t.\t+\t.\tgene_id "YDL095W"; transcript_id "YDL095W"; exon_number "1"; gene_name "PMT1"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "PMT1"; transcript_source "ensembl"; exon_id "YDL095W.1";\r\n-IV\tprotein_coding\tCDS\t287059\t289509\t.\t+\t0\tgene_id "YDL095W"; transcript_id "YDL095W"; exon_number "1"; gene_name "PMT1"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "PMT1"; transcript_source "ensembl"; protein_id "YDL095W";\r\n-IV\tprotein_coding\tstart_codon\t287059\t287061\t.\t+\t0\tgene_id "YDL095W"; transcript_id "YDL095W"; exon_number "1"; gene_name "PMT1"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "PMT1"; transcript_source "ensembl";\r\n-IV\tprotein_coding\tstop_codon\t289510\t289512\t.\t+\t0\tgene_id "YDL095W"; transcript_id "YDL095W"; exon_number "1"; gene_name "PMT1"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "PMT1"; transcript_source "ensembl";\r\n'

diff -r f9f2ad782d8f -r f89e3c318453 test-data/Trinity.fasta
--- a/test-data/Trinity.fasta Thu Jan 20 21:09:47 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,7000 +0,0 @@\n->c0_g1_i1 len=344 path=[1:0-295 654:296-343]\n-ATTTATTGGACAGTACAAGTGGCTTCAATGGAACAATTTTAGTACAGGTTCACTGCCCAT\n-TGTTTTAAGCTTAGTACATTTTTACAAAGAATACACCCCTCAGATTTACGAATGGAATAT\n-AAGATTACTAGGACCTCGAGGAGGAGCATCAAGTCACAATGATAACAAGCGAGAAGACAA\n-GAGCGCCGTAGAGTGGAAAATCAACGATCAGTTTCTTTTAAATGGGTTAATTCTCCTGCT\n-TATATTAAATCAGGGGTTTGCAGGAATACTATGCGGATTCATAAGCTGGATGTGTGGTAT\n-TTTCATCGATAAGGGCCTGTTACCGGGATTAGACCATTGGAGAA\n->c2_g1_i1 len=284 path=[309:0-283]\n-GCCAGCCAGACAATTCGGTTACGTCATCTTGACCACCTCTGCTGGTATCATGGACCATGA\n-AGAAGCCAGAAGAAAGCACGTTTCTGGTAAGATTTTGGGTTTCGTTTACTAAGCTACTTG\n-TTACAACAACCTTTTCGGTAGCTTTATATACTATAATAAACACAAGATAGCCTCATAACT\n-TTACTCATTTCTTATTATACATTTTTTTAGTTTTCCTGTTAAATACTAATATATTTGTAC\n-TTTAAAACTGTTCAAAAGATTAGAAAAAAAAAAAAAAAAAAAAA\n->c3_g1_i1 len=356 path=[334:0-355]\n-CACGATAATAATACAGCAAAAATGTCAGGTAACGGTGCTCAAGGTACAAAATTCAGAATT\n-TCTTTAGGTTTACCAGTTGGTGCTATCATGAACTGTGCTGACAACAGTGGTGCCAGAAAC\n-TTGTACATCATTGCCGTCAAAGGTTCTGGTTCTAGATTGAACAGATTACCAGCCGCCTCT\n-TTAGGTGACATGGTTATGGCCACTGTTAAAAAGGGTAAGCCAGAATTGAGAAAGAAGGTT\n-ATGCCAGCTATTGTTGTCCGTCAAGCTAAGTCTTGGAGAAGAAGAGACGGTGTCTTTTTG\n-TACTTCGAGGACAATGCTGGTGTCATCGCTAATCCTAAGGGTGAAATGAAGGGGGG\n->c4_g1_i1 len=368 path=[396:0-367]\n-CAGCAACCTACAAAACAACTCAGATTCAGAATCAGATTCAGACTCGGAAACGAACCACAA\n-AAGCAAAGACAACAATAACGGTGACGACGACGATGAGGATGACGACGAGATTGTGATGCC\n-CGTGCCCAATGTTCGGTCTTCCGTTTTGCAGAAGGTTATCGAATGGGCCGAGCACCACAG\n-AGACTCTAACTTCCCTGACGAAGATGACGACGATTCCAGAAAGAGTGCTCCCGTGGACTC\n-ATGGGACAGAGAATTCCTGAAAGTGGACCAAGAGATGCTATACGAAATTATTCTGGCGGC\n-AAACTACCTCAACATCAAGCCCTTGCTTGACGCTGGCTGCAAGGTGGTTGCTGAAATGAT\n-CAGGGGGG\n->c5_g1_i1 len=298 path=[161:0-2 160:3-297]\n-CCCCCCTTTCGCGTCTTTTATCTAATCTTTCCTTTTTGTCTTGAATAAACTCTAACTCAG\n-TTGAAAGATTGTTCCATGGTCTTGTGTCGCCTGTACCCGACATGATCAAAATCATAGTAC\n-CTGGTGTAGCATTCTCGTATAATTGTGTTAGATGTTGCCCTATATCATGAAGAACCATGG\n-ACGCATCCAACGAAGGAGTTTCCTTCCGTGGCTTTTTATTATAGTTGCGTGACCTCTCTA\n-AGTTCTTGATTCTCCCCACAATAAGTTTGACATCTTTATTCAGATTCTCGTGAATATG\n->c6_g1_i1 len=357 path=[53:0-356]\n-ACTGGACAACATCTTACTTGTCCTGGAGTTGATTGATGAATGTATAGACTTTGGTATCGT\n-ACAAGTGACGGATCCAAGTATCATCAAGGACTACATTCGTGTGAAGGTCAACGTACCAAG\n-AGTTACAGTAGACAATGAGGAGTGGAGCCCTGGTGAAGAGAGCAGTAGTAGTAGCGGTAG\n-CGATAGCGATAGCGAGTACAGCAATACTAATAAGAGGAAGGATAAGAAGAAGAAAAGGAA\n-GAAGAAAAAGGGCACTAAAGGGAAAAGCGTGGGCAAAAGTAAATTAAAAAGTATAATGGT\n-AAACAATAAAGAAAATAGGGGCATAAACGTGGTGGAAACTGTCAAGGAGACACTAAG\n->c12_g1_i1 len=442 path=[362:0-441]\n-CATATTTATATAACTAAGATAGTAACGCACTCAAAAAGATGTTTAGATCTGTTGCTACTA\n-GATTATCTGCCTGCCGTGGGTTAGCATCTAACGCTGCTCGCAAATCACTCACTATTGGTC\n-TTATCCCCGGTGACGGTATCGGTAAGGAAGTCATTCCTGCTGGTAAGCAAGTTTTGGAAA\n-ACCTTAACTCCAAGCACGGCCTAAGCTTCAACTTTATTGATCTCTACGCCGGTTTCCAAA\n-CATTCCAAGAAACAGGAAAGGCGTTGCCTGATGAGACTGTTAAAGTGTTGAAGGAACAAT\n-GTCAAGGTGCTCTTTTCGGTGCAGTTCAGTCTCCAACTACTAAGGTGGAAGGTTACTCCT\n-CACCAATTGTTGCTCTAAGGAGGGAAATGGGCCTTTTCGCTAATGTTCGTCCTGTTAAGT\n-CTGTAGAGGGAGAAAAGGGGGG\n->c13_g1_i1 len=323 path=[107:0-124 231:125-128 106:129-322]\n-CAACAATTATCAGTAAAAATGGTTAACGTTCCAAAGACCAGAAAGACCTACTGTAAGGGT\n-AAGACCTGTCGTAAGCACACTCAACACAAGGTTACTCAATACAAAGCTGGTAAGGCTTCC\n-TTGTTCGCTCAAGGTAAGAGACGTTATGACCGTAAACAATCTGGTTTCGGTGGTCAAACC\n-AAGCCTGTTTTCCACAAGAAAGCTAAGACTACCAAGAAGGTTGTTTTGAGATTGGAATGT\n-GTCAAATGTAAGACTAGAGCCCAATTAACCTTGAAGAGATGTAAGCACTTCGAATTGGGT\n-GGTGAAAAGAAGCAAAAGGGGGG\n->c15_g1_i1 len=336 path=[1:0-215 217:216-335]\n-AGCGCTATATACATAAGTAGCTATAGATTATTTATTTCAAGACGGCAACCAACTTTTCGC\n-CAGAATTCCTCCCGTGCTTAATATCATCAAGTAACTGTGGGATATCATCTAACCCGTTCT\n-TGTAAACTTTCACTGGGATGTGGTGGATTTCACCATCATTGATTTTTGGATTGATGAACT\n-TAATAAATTTTATGGCGGCTTCCTTGTATTCAGGGGCTGCTGGCAAAGTAAACGTGCCAA\n-ATGGGACGTCGTTACCTCCTATCAAATATAGAAGGGTTCCTTCAATACTGACGTTTTGCC\n-TCCTGTCTTCCTCCTTGATATCTTTTTCGGTTAAAA\n->c16_g1_i1 len=356 path=[613:0-161 774:162-355]\n-TTTTTTTTTTTTTTTTTTTTTGAACAAAAAGAAAGTACTGTCTTATTGTATTAAAAGCGA\n-CTATATAGAAAAATTATAAAAAATTTTAAATGTTAGAATATGCAATTTCTTCTAAACAGT\n-GCGGCACTTCTAATCAAATAAACCGAAACCCATGTCGTCATCAGATTCTTCTTCTTCTTC\n-AGCAGCAGCTTCTTCAGCTGGAGCAGCGTCACCGGAAGCAGCGGAGGTAGCAGCTGGAGC\n-AGCAGCAGCGTACTTTTCTGGGTTTTCAATTCTGTCAACCAAATCTTCAATTTCAGGGTA\n-GTGGTAGGAAGCAGCAATGGCAAC'..b'AGTAAGGAATCATGGAGGTATGATTGGTACCAAC\n-CATCTAAGGTGAGCTCCAATGTGCAGCAACCACAACAACAGCTAGGGGACATGGAGAATA\n-ACTTGGAGAAATATCCATTCAGGTATAAAACATGGTTGAGGAACCAGGAAGATGAGAAAA\n-ATCTACAGAGGGAGAGCTGTGAGGATATATTAGATTTGGAAGAATTTGATAGAAGAATAC\n-TGAAAAAGTCGTTGATGACATCGCACACTAAGGGGGG\n->c1104_g1_i1 len=342 path=[320:0-341]\n-GGCCGATTTGATTAACGTTGGTGGTACCCAATCTGTGATTAAGTATCTATATGAAAACAA\n-CATGTTGCACGGTAACACAATGACTGTTACCGGTGACACTTTGGCAGAACGTGCAAAGAA\n-AGCACCAAGCCTACCTGAAGGACAAGAGATTATTAAGCCACTCTCCCACCCAATCAAGGC\n-CAACGGTCACTTGCAAATTCTGTACGGTTCATTGGCACCAGGTGGAGCTGTGGGTAAAAT\n-TACCGGTAAGGAAGGTACTTACTTCAAGGGTAGAGCACGTGTGTTCGAAGAGGAAGGTGC\n-CTTTATTGAAGCCTTGGAAAGAGGTGAAATCAAGAAGGGGGG\n->c1105_g1_i1 len=293 path=[1:0-292]\n-GATCCAGAGACCAAAAAACGCAAGAGGAGAGTTGCCACCACAGCCGTTTCACCAAGCACT\n-ATCAGCACGGCAACTGCCGTCAATAATGGCAGGATAGGTACATCTACAGCGTCCAGGGGA\n-GTTAGCAGCGTCGGAAACAGCAACAACAGCAGGATATCAAGACCAAAAACCAACGACTAC\n-GGCGAACCGCTCTACTGCTACTGTAACCAAGTGGCATACGGGGAAATGGTGGGGTGTGAT\n-GGCGCAGACTGTGAGCTAGAATGGTTCCATTTGCCATGTATTGGACTCGAAAC\n->c1106_g1_i1 len=312 path=[290:0-311]\n-TTATCATGGATGCCCTTTCCGTGATTGGAGTCACGAGAGACTATCTGCAGAATTGCGCTC\n-TATGAAGTTGACCCAAGCGCAGATCATCAGTGTTCTGGATTCCTGCCAGAAAGGTGAATA\n-CACAATTGCTTGCACTAAAGTGTTTGAAATGACACACAACTCTGCATCAGCGGATTTGGA\n-AATTGGCGAGCAAACGCATATCGCGCATCCTAACCTATACTTCGAAAGATCAAGGCAACT\n-GCAAAAGAAACAGCAGAAGCTGGAAAAGGAAAAACTATTCAATAATGGTAATCATTAGTG\n-CAGAAAGGGGGG\n->c1107_g1_i1 len=298 path=[1:0-297]\n-TGCAAAGACAAGGTAAATTAGAAGTCCCAGGTTACGTTGACATTGTCAAGACCTCTTCTG\n-GTAATGAAATGCCACCACAAGACGCTGAAGGTTGGTTCTACAAGCGTGCTGCCTCCGTTG\n-CTAGACACATTTACATGAGAAAGCAAGTCGGTGTTGGTAAGTTGAACAAATTGTACGGTG\n-GTGCCAAGAGCAGAGGTGTCAGACCATACAAGCACATTGATGCTTCCGGTTCTATCAACA\n-GAAAGGTCTTGCAAGCTTTGGAAAAAATCGGTATTGTCGAAATCTCTCCAAAGGGGGG\n->c1108_g1_i1 len=487 path=[465:0-486]\n-GCTACGCATCGTACCCAGAGCACACCATTATTGGTATGCCGGCACTGTCTCCTACGATGA\n-CGCAAGGTAATCTTGCTGCTTGGACTAAGAAGGAAGGTGACCAATTGTCTCCCGGTGAAG\n-TTATTGCCGAAATAGAAACAGACAAGGCTCAAATGGACTTTGAGTTCCAAGAAGATGGTT\n-ACTTAGCCAAGATTCTAGTTCCTGAAGGTACAAAGGACATTCCTGTCAACAAGCCTATTG\n-CCGTCTATGTGGAGGACAAAGCTGATGTGCCAGCTTTTAAGGACTTTAAGCTGGAGGATT\n-CAGGTTCTGATTCAAAGACCAGTACGAAGGCTCAGCCTGCCGAACCACAGGCAGAAAAGA\n-AACAAGAAGCGCCAGCTGAAGAGACCAAGACTTCTGCACCTGAAGCTAAGAAATCTGACG\n-TTGCTGCTCCTCAAGGTAGGATTTTTGCCTCTCCACTTGCCAAGACTATCGCCTTGGAAA\n-AGGGGGG\n->c1109_g1_i1 len=278 path=[1:0-277]\n-TTTTGCCTTTAAAAATTGAGTTTCTAGTTAATTAGTAAATAGCGCTAAACACAATTAAAT\n-AATACCGAATTGGCAGTGGTAGAGGAAAGAATGTACGTTACATATATCATTAAAAAAACA\n-TCTATTTCTTGTTAACTTCTCTTCTTTGTCTGACAGCAGCAGCCAATTTCCTCAAGACGT\n-CTTCAGTAGTTTCCCAACCTATACAAGCATCAGTGATGGAAACACCATATTTCAAGCCGG\n-CTTTACCTTCGGCTGGGATGCCTTGGTTACCTTCGTTG\n->c1110_g1_i1 len=292 path=[270:0-291]\n-ACTCCTTTTTGAATCTGTATGTACCACCGTATGACCCGCCTGTATTGTCGTGCTTGTCCC\n-AGGTCCCTGAAGTGTGCCAAGCAAGACGGACTAATACGGGCCCATAGCCTATATAGTTGT\n-CATATTCGTCATCTTCCCTCAGCTTGAGTGCAATCGCATTGTACACCTTTTGGAAGTCCT\n-CGTATGCCCTCCCTTTTTCGACAGAGGCGACATGAACGAGCGGTGTAGTGGAAGCCAAAG\n-CAGCTGCCTTCCCCCAGTTGTTCCATCCGTGGTTACTACCACCCCCGGGAGA\n->c1111_g1_i1 len=284 path=[1:0-283]\n-GTCTGAACAGTATGTTACACCATACCTTCCGAAATCTTTGCAACCTATTGCAAAAATTAG\n-TGCAGAGGAACAAAGGCGTATACAAAGTGAACAGGAAGAAGCCGAATTGAAGCAATCTTT\n-AGAGGGAGAGGCCATTAGAAATGCCACCGTGAATGCCATTAAGGAAAAGATCAAATCTTA\n-TGGTGGTAATGAAACGACGCTAGGGTTCATGGTGCCATCGTATATCAATCATAGAGGATC\n-ACCACCAAAGGCGTGCTTTGTCTCACTAATTACTGAAAGGGGGG\n->c1112_g1_i1 len=353 path=[331:0-352]\n-CAGCATTTCAGAAGTGCATTGGGTGAAACCCAAAAAGATACATATCAAGTTCTTCTGAGA\n-AGAAATAAGCTTCCCATGTCATTGTTGGAAGAAAAGGACGCAGATGAATCCCCAAAAGCC\n-AGAATTTTGGATACCGAAAGTTATGCTGATGCGTTTGGGCCCAAAGCCCAAAGAAAGAGA\n-CCACGTCTTGCTGCATCCAATCTAGAGGACTTGGTCAAGGCTACAAATGAAGACATTACC\n-AAGTATGAGGAAAAGCAAGTCTTAGATGCCACATTAGGACTAATGGGGAACCAGGAAGAC\n-AAAGAAAATGGGTGGACCTCCGCAGCAAAAGAAGCTATTTTCAGTAAGGGGGG\n->c1113_g1_i1 len=265 path=[243:0-264]\n-GGCTACACAGGCCTTCTCTGAGATAGAACCTTGAACAGGCTTGTTATCTGGAGTATAAGG\n-GATTTGACCAGACACGTACACAAAATTGTTGGCCTTCATAGCTTGGGAGTAAGAGGCGGC\n-AGCGGGTGGGGCCAACTTGGTGCTGACCGGGGTCAATGTTGTTATACCCCTCCTCAAGAC\n-TGGAGCTGTTCTCAAAACGGAATTTCTTAAAAACATTATTGGTAATATATTTGTGTGTAT\n-GTGTTGTCCTTTTTACCTGTAAATC\n->c1114_g1_i1 len=269 path=[247:0-268]\n'

diff -r f9f2ad782d8f -r f89e3c318453 test-data/alignment.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alignment.sam Wed Jun 07 12:02:03 2023 +0000

b'@@ -0,0 +1,1024 @@\n+@HD\tVN:1.0\tSO:coordinate\n+@SQ\tSN:phiX174\tLN:5386\n+@PG\tID:hisat2\tPN:hisat2\tVN:2.2.1\tCL:"/usr/local/bin/hisat2-align-s --wrapper basic-0 -p 1 -x genome --read-lengths 70 -1 input_f.fastq -2 input_r.fastq"\n+@PG\tID:samtools\tPN:samtools\tPP:hisat2\tVN:1.13\tCL:samtools view -o /tmp/tmp3qb6tqs4/job_working_directory/000/101/outputs/galaxy_dataset_cfd7fc65-f21d-4c8d-8f65-ebf43813cae0.dat -h /tmp/tmp3qb6tqs4/files/e/d/3/dataset_ed38f53c-9b1a-4db6-8b01-573f991ac775.dat\n+phiX174_17_543_2:0:0_2:0:0_1e\t163\tphiX174\t17\t60\t70M\t=\t474\t527\tATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAACTTATCTTGAAAAAGCAGGAATTA\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-6\tXN:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tNM:i:2\tMD:Z:46A9T13\tYS:i:-6\tYT:Z:CP\tNH:i:1\n+phiX174_21_568_3:0:0_0:0:0_79\t163\tphiX174\t21\t60\t70M\t=\t499\t548\tCGCAGAAGTTAACACTTTCGGATATTTGTGATGAGTCGAAAAATTATCTTGATAAAGGAGGCATTACTAC\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-9\tXN:i:0\tXM:i:3\tXO:i:0\tXG:i:0\tNM:i:3\tMD:Z:27C29C3A8\tYS:i:0\tYT:Z:CP\tNH:i:1\n+phiX174_22_543_0:0:0_1:0:0_188\t99\tphiX174\t22\t60\t70M\t=\t474\t522\tGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACT\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:70\tYS:i:-3\tYT:Z:CP\tNH:i:1\n+phiX174_30_492_1:0:0_2:0:0_3a\t163\tphiX174\t30\t60\t70M\t=\t423\t463\tTAACACTTTCGGAAATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTT\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-3\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:13T56\tYS:i:-6\tYT:Z:CP\tNH:i:1\n+phiX174_36_572_1:0:0_0:0:0_8\t163\tphiX174\t36\t60\t70M\t=\t503\t537\tTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGTAATTACTACTGCTTGTTTACGAAT\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-3\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:45G24\tYS:i:0\tYT:Z:CP\tNH:i:1\n+phiX174_79_485_2:0:0_2:0:0_10\t163\tphiX174\t79\t60\t70M\t=\t416\t407\tAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCAGGCGGACAATGAGAAAATTCGACC\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-6\tXN:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tNM:i:2\tMD:Z:45T6A17\tYS:i:-6\tYT:Z:CP\tNH:i:1\n+phiX174_99_645_0:0:0_2:0:0_1d\t163\tphiX174\t99\t60\t70M\t=\t576\t547\tTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGA\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:70\tYS:i:-6\tYT:Z:CP\tNH:i:1\n+phiX174_122_530_3:0:0_2:0:0_191\t163\tphiX174\t122\t60\t70M\t=\t461\t409\tGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGCGAAGCTCTAACTTTGCGACCTTACG\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-9\tZS:i:-9\tXN:i:0\tXM:i:3\tXO:i:0\tXG:i:0\tNM:i:3\tMD:Z:44A8T13T2\tYS:i:-6\tYT:Z:CP\tNH:i:1\n+phiX174_150_647_3:0:0_0:0:0_d5\t99\tphiX174\t150\t60\t70M\t=\t578\t498\tATCCTTGCGCAGCTCGAGAAGCACATACTTTGCGACCTTTCGCCATCAAGTAACGATTCTGTCAAAAACT\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-9\tXN:i:0\tXM:i:3\tXO:i:0\tXG:i:0\tNM:i:3\tMD:Z:22T1T24C20\tYS:i:0\tYT:Z:CP\tNH:i:1\n+phiX174_163_597_2:0:0_2:0:0_fc\t163\tphiX174\t163\t60\t70M\t=\t528\t435\tTCGAGAAGCTCTTACTTTGCGAGCTTTCGCCATCCACTAACGATTCTGTCAAAAACTGACGCGTTGGATG\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-6\tXN:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tNM:i:2\tMD:Z:22C11A35\tYS:i:-6\tYT:Z:CP\tNH:i:1\n+phiX174_172_742_2:0:0_1:0:0_e8\t163\tphiX174\t172\t60\t70M\t=\t673\t571\tTCTTACTTTGCGACCTTTCGCCATCAACTCCCGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGT\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-6\tXN:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tNM:i:2\tMD:Z:29A0A39\tYS:i:-3\tYT:Z:CP\tNH:i:1\n+phiX174_177_628_1:0:0_0:0:0_1c8\t99\tphiX174\t177\t60\t70M\t=\t559\t452\tCTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAACCTGACGCGTTGGATGAGGAGAAGTGGCTT\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-3\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:40A29\tYS:i:0\tYT:Z:CP\tNH:i:1\n+phiX174_182_623_0:0:0_1:0:0_16\t163\tphiX174\t182\t60\t70M\t=\t554\t442\tCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGAC'..b'2222222222222222222222222222222222222222222222222\tAS:i:-6\tXN:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tNM:i:2\tMD:Z:37G0C31\tYS:i:-6\tYT:Z:CP\tNH:i:1\n+phiX174_4761_5246_1:0:0_2:0:0_16c\t147\tphiX174\t5177\t60\t70M\t=\t4761\t-486\tTCTGTCCACGGAGTGCTTATTCCATCTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTG\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-6\tXN:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tNM:i:2\tMD:Z:19A4A45\tYS:i:-3\tYT:Z:CP\tNH:i:1\n+phiX174_4743_5249_3:0:0_1:0:0_cd\t83\tphiX174\t5180\t60\t70M\t=\t4743\t-507\tGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTTCGACGCGACGCCGTTCAACCAGATATTGAAG\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-3\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:38A31\tYS:i:-9\tYT:Z:CP\tNH:i:1\n+phiX174_4733_5272_1:0:0_1:0:0_1c2\t83\tphiX174\t5203\t60\t70M\t=\t4733\t-540\tTTACCAAGCTGGGTTACCACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAG\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-3\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:17G52\tYS:i:-3\tYT:Z:CP\tNH:i:1\n+phiX174_4824_5276_2:0:0_1:0:0_ab\t147\tphiX174\t5207\t60\t70M\t=\t4824\t-453\tCAAGCTGGGTTAAGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTG\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-3\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:12C57\tYS:i:-6\tYT:Z:CP\tNH:i:1\n+phiX174_4831_5285_3:0:0_1:0:0_108\t147\tphiX174\t5216\t60\t70M\t=\t4831\t-455\tTTACGACGCGACGCCGTTCTACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGA\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-3\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:19A50\tYS:i:-9\tYT:Z:CP\tNH:i:1\n+phiX174_4783_5286_3:0:0_0:0:0_167\t147\tphiX174\t5217\t60\t70M\t=\t4783\t-504\tTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAA\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:70\tYS:i:-9\tYT:Z:CP\tNH:i:1\n+phiX174_4736_5291_1:0:0_1:0:0_177\t83\tphiX174\t5222\t60\t70M\t=\t4736\t-556\tCGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAATAGAGAGATGAGATTGAGGCTGGGAAAAGTT\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-3\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:39A30\tYS:i:-3\tYT:Z:CP\tNH:i:1\n+phiX174_4780_5302_3:0:0_0:0:0_157\t147\tphiX174\t5233\t60\t70M\t=\t4780\t-523\tTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGA\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:70\tYS:i:-9\tYT:Z:CP\tNH:i:1\n+phiX174_4844_5303_1:0:0_1:0:0_12b\t83\tphiX174\t5234\t60\t70M\t=\t4844\t-460\tCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACGGTAGCCGAC\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-3\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:60T9\tYS:i:-3\tYT:Z:CP\tNH:i:1\n+phiX174_4843_5331_1:0:0_1:0:0_77\t83\tphiX174\t5262\t60\t70M\t=\t4843\t-489\tAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTTGCCGACGTTTTGGCGGCGCAACCTGTGACGACAA\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-3\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:35A34\tYS:i:-3\tYT:Z:CP\tNH:i:1\n+phiX174_4839_5348_0:0:0_1:0:1_63\t83\tphiX174\t5278\t60\t64M6S\t=\t4839\t-509\tGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAAGCTGCTCAATTTATG\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-9\tZS:i:-11\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:55T8\tYS:i:0\tYT:Z:CP\tNH:i:1\n+phiX174_4874_5385_0:0:0_0:0:0_96\t83\tphiX174\t5316\t60\t70M\t=\t4874\t-512\tCAACCTGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGC\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:70\tYS:i:0\tYT:Z:CP\tNH:i:1\n+phiX174_1484_2067_3:0:0_4:0:0_10d\t77\t*\t0\t0\t*\t*\t0\t0\tCGTTGCTTCCATCACAAAAACATTAGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGA\t2222222222222222222222222222222222222222222222222222222222222222222222\tYT:Z:UP\n+phiX174_1484_2067_3:0:0_4:0:0_10d\t141\t*\t0\t0\t*\t*\t0\t0\tGTCGCATAACGATACCACTTACCCTCAGCAATCTTAAACTTCTTATACGAAACACCAGAACGGAAAACAT\t2222222222222222222222222222222222222222222222222222222222222222222222\tYT:Z:UP\n'

diff -r f9f2ad782d8f -r f89e3c318453 test-data/busco_database.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/busco_database.loc Wed Jun 07 12:02:03 2023 +0000

@@ -0,0 +1,6 @@
+# Tab separated with 4 columns:
+# - value
+# - name
+# - version
+# - /path/to/data
+busco-demo-db-20230328 BUSCO-DEMO-DB-20230328 5.4.6 ${__HERE__}/test-db/busco_downloads

diff -r f9f2ad782d8f -r f89e3c318453 test-data/idba.fasta
--- a/test-data/idba.fasta Thu Jan 20 21:09:47 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,3000 +0,0 @@\n->contig-60_0 length_1811 read_count_3587\n-AACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCGCGCAATTAACCCTCACTAAAGGGAACAAAAGCTGGGTACCGGGCCCCCCCTCGAGATGTGGAAAGGACTTATCCATCAATATAAAGAATTTTTACCTGTAACAGATCAAACACCGGCGCTAACTTTACATGAAGGAAACACACCTCTTATTCACCTGCCGAAGCTGTCTGAGCAGCTCGGAATTGAGCTTCATGTCAAAACGGAAGGCGTCAATCCTACGGGATCATTTAAAGATCGCGGAATGGTTATGGCTGTGGCAAAGGCAAAAGAAGAAGGCAATGACACGATTATGTGCGCGTCAACAGGTAACACTTCCGCTGCTGCGGCAGCATATGCAGCCCGTGCTAACATGAAATGCATTGTCATCATCCCGAACGGAAAAATTGCATTTGGAAAACTCGCTCAAGCTGTCATGTACGGAGCCGAGATTATCGCAATTGACGGAAACTTTGACGATGCGCTTAAAATTGTCCGTTCCATCTGTGAGAAATCACCGATTGCCCTTGTCAACTCAGTCAACCCTTACCGCATTGAAGGCCAAAAAACTGCTGCCTTCGAAGTGTGCGAACAGCTGGGGGAAGCGCCTGATGTTTTAGCGATCCCGGTCGGAAATGCTGGAAACATCACTGCGTACTGGAAGGGCTTCAAGGAATATCATGAGAAAAACGGCACAGGCCTTCCGAAAATGCGCGGCTTTGAAGCTGAGGGTGCGGCGGCAATCGTGCGCAATGAAGTGATTGAAAATCCGGAAACAATAGCGACAGCCATTCGTATCGGAAACCCGGCAAGCTGGGACAAAGCTGTAAAGGCAGCCGAGGAATCCAATGGGAAAATTGACGAAGTCACTGATGATGAAATCCTTCACGCATATCAGCTGATCGCCCGTGTAGAAGGCGTGTTTGCAGAACCAGGTTCTTGCGCGTCTATCGCAGGAGTGCTGAAACAGGTGAAATCCGGAGAAATTCCGAAAGGCAGCAAGGTCGTAGCTGTGTTAACAGGAAACGGACTGAAAGATCCGAACACAGCGGTCGACATTTCAGAAATCAAGCCTGTCACATTGCCGACTGATGAAGACAGCATCCTTGAATATGTAAAAGGAGCGGCCCGTGTATGAACGAAGCCGACATGCTGTTCTCTGTCACTGTTCCCGGAAGCACAGCTAACCTAGGCCCCGGCTTTGATTCAGTCGGAATGGCGCTCAGCAGATATTTGAAGCTGACCGTCTTTGAAAGCGACAAATGGTCTTTTGAGGCTGAAACAGAAACAGTCGCCGGAATTCCGGCGGGTACAGATAACCTGATCTACCAAGTGGCTAAACGGACCGCAGATTTGTACGGAAAAGAAATGCCTCCTGTCCATGTGAAGGTGTGGAGCGACATCCCGCTTGCACGCGGCCTTGGCAGCAGCGCCGCAGCGATTGTAGCGGCCATTGAACTGGCTGATGAATTATGCGGCTTAAAGCTGTCTGAAGCGGACAAGCTGCATTTAGCGAGTCTAGAAGAAGGACACCCGGACAATGCTGGCGCTTCTCTCGTCGGCGGACTTGTGATCGGCCTGCATGAGGATGACGAGACCCAAATGATCCGCGTCCCGAATGCTGACATTGACGTAGTCGTTGTCATTCCTTTTTATGAAGTGCTGACAAGAGACGCGAGAGACGTGCTTCCGAAGGAGTTTCCATATGCCGATGCCGTAAAAGCAAGTGCTGTCAGCAATATCCTCATTGCTGCGATCATGTCCAAGGATTGGCCGCTTGTCGGGAAAA\n->contig-60_1 length_1662 read_count_1507\n-AAACTGCTCACAACATGAAGGTCATGAAATTCTCTGTCTCTCCAGTTGTGCAAGTCGCTGTCGAAGTCAAGAACGCTAACGACTTACCAAAATTGGTCGAAGGTTTGAAGAGATTGTCCAAGTCTGATCCATGTGTCTTGACCTATATGTCTGAATCCGGTGAACATATCGTTGCTGGTACCGGTGAATTGCATTTGGAAATTTGTTTGCAAGATTTGGAACACGACCACGCTGGTGTTCCATTGAAGATCTCCCCACCAGTTGTCGCTTACAGAGAAACTGTTGAAAGTGAATCTTCTCAAACTGCTTTGTCCAAGTCTCCAAACAAGCATAACAGAATCTACTTGAAGGCTGAACCAATTGACGAAGAAGTCTCTTTGGCTATTGAAAACGGTATCATCAACCCAAGAGATGATTTCAAGGCCAGAGCTAGAATCATGGCTGACGACTACGGTTGGGATGTCACCGATGCCAGAAAGATCTGGTGTTTCGGTCCAGACGGTAACGGTCCAAACTTGGTTATTGACCAAACTAAGGCTGTCCAATACTTGCACGAAATCAAGGATTCCGTTGTTGCTGCTTTCCAATGGGCTACCAAGGAAGGTCCAATTTTCGGTGAAGAAATGAGATCTGTCAGAGTTAACATTTTGGATGTTACTTTACATGCCGATGCTATCCACAGAGGTGGTGGTCAAATCATCCCAACCATGAGAAGAGCTACTTACGCTGGTTTCTTGTTGGCTGATCCAAAGATCCAAGAACCAGTTTTCTTGGTCGAAATTCAATGTCCAGAACAAGCCGTCGGTGGTATCTACTCCGTCTTAAACAAGAAGAGAGGTCAAGTCGTTTCTGAAGAACAAAGACCAGGTACTCCATTGTTTACCGTCAAGGCCTACTTGCCAGTTAACGAATCTTTCGGTTTCACTGGTGAATTGAGACAAGCTACCGGTGGTCAAGCTTTCCCACAAATGGTTTTCGACCATTGGTCCACTTTAGGTTCTGACCCATTGGACCCAACCTCTAAGGCTGGTGAAATTGTTCTTGCTGCTCGTAAGAGACACGGTATGAAGGAAGAAGTTCCAGGCTGGCAAGAATATTACGACAAATTGTAAGAAGTCTAAATGAGAAAAGGTGGTTCTGTAAGAGCAAACCTTACCGCCTTATGATCTTTTTCATTTATTCTCTGCTTTAAAATTTTGTCGTAATAAAAATAGTATGGTAATAGACTTATATATTATTTTCTTACACATTTTTGTCATATAGTTATATTCCGAATGTTTACAATCGAACCCATCATAAAAATGGACCTTTTCGTATTACCGCCCCCTTTGTAGAGGGGGAGGAACGGCAACTTCTTGACTATTACGACGTATCACCACCCCGTTAGATATACTATGGAAAAAACTATTAAAAACCATTATAATTCATTAATGACATCGGTCCTGAGGTAGTATTACGTATAACTTACCTGGCTCTTGGTCATAGCTTTTTATCCGTTTACGAAAAAAGGAGAAGAAGATTGGGCTTCCGCGGCTATTGTTTGGTTTATACCCCGCCGTATGTTGGTGCTTCTATAATTAGAGCGAAATAGGAAATACAAAAAATCCTTGGAGGGGAGGACCAGCCTCATCGGGCTAAAACTCCCTCAAAACCGTTGGGGGG\n->contig-60_2 length_1112 read_count_3123\n-TAAAGGGAACAAAAGCTGGGTACCGGGCCCCCCCTCGAGCTGTCCTTTCATCCATAAGCGGAGAAAAAGGGAATGACATTGTTCTTACACGGCACAAGCAGACAAAATCAACATGGTCATTTAGAAATCGGAGGTGTGGATGCTCTCTATTTAGCGGAGAAATATGGTACACCTCTTTACGTATATGATGTGGCTTTAATACGTGAGCGTGCTAAAAGCTTTAAGCAGGCGTTTATTTCTGCAGGGCTGAAAGCACAGGTGGCATATGCGAGCAAAGCATTCTCATCAGTCGCAATGATTCAGCTCGCTGAGGAAGGGGGGCTTTCTTTAGATGTCGTATCCGGAGGAGAGCTATATACGGCTGTTGCAGCAGGCT'..b'CCGGACTTATGTGGCTCCCTTTAGAATATAAGGGTCTTCCCTTTAACGGAACAGTAAGGTTCCACAAGGTGGCAAAAAAGGCAATCCAACCGACACTTCGGCAAATTTCTTTCA\n->contig-60_1488 length_279 read_count_87\n-CCCCCCAAGACTATTCGTTTGGTGGCTATCTTTATAATTCGAATCAGTTCGCAAATTTTTTGGTGAAGAGCTATTCAATTATTAGCTAATTATGGAAACTATTTTGCAGCCAAAGGCTAGACCATTTGAGTCTTTGAAAAGAAAACGTTTTAGAGAATGGTTGAGGCCGTCGACTGCGCATGGATCCCTGTTGCATTCTGATACATTAGATTTGCGTGACTTTGCAAAACCTAATCCCGCTGACACATTTTCTAATCTTGATTCTGGTCATTGTCCTTT\n->contig-60_1489 length_279 read_count_658\n-CGGCAAAGTAAAGCTTCTGAAAGAAGACATGTCAATTTCTCTATTAGGTAGAATTGTTTCACAACAATTCTCCGGCATACGGGCGGCTGAGCCAGGGAGATCTCTATATTTACCGTTTACCTTACTATTGAAACAGCCCGGTGCTTACAAGGTGAGCCTACACAGATATGTACATAGCACCCAAACGAAGAGCCACTTGAGCTTTTTAATGAATAATAACGATATAACACCTTTTCAAAAATTTACAGTTAAAGTTTTCAAAGAGCAGTGCAAATCTTG\n->contig-60_1490 length_279 read_count_99\n-AGGTTTCAAATGAGATGGTAAAACCTTATATCTTTAGTTCTGATCCAGTTTTAGAAGCTTACCTTATTAAAGCTGCGGAAATTCACAAAGAAGCTGAATTTGAGTATTGGAGAAAGCAATACCCAGAGGTTGATTTGCCTTAGGGCCGAATTTTTGGTATTTATCTAGTATATTCTAATATAAAATGTACGAGCATCATTAACTTCAAGAACATTACGAAGCCCGCAATTAAGTGTCAGTCCATCTGGGTGTAAAAGTTATGTACGCTCGAAACAAATT\n->contig-60_1491 length_279 read_count_498\n-CCAAGGTTTGATTCCATGGGCATGGATCGAAGCCTCCACTAAAGGTGCTGTGTTGCTGTTCGTGTCAGCTGAGGCTGAGTATCGTTTCAAAAGTTTGGGGTTGAACAACTTTGCCTCAGGTATATTAGGTGGTGTCACGGGTGGTGTCACTCAAGCCTACTTAACCATGGGGTTCTGTACCTGTATGAAAACGGTGGAAATTACAAGACATAAATCTGCCTCCGCAGGTGGTGTCCCACAATCTTCTTGGAGTGTGTTCAAGAATATTTATAAAAAGGT\n->contig-60_1492 length_279 read_count_1472\n-GGATTACAAACCAGGCATGCCCCATCTCCACGCTCAAGAGGAGAATAATAACTTCAGCATCTTTAGATGGGACCAGGTACAACAACCATTACCAGGCGAAGGTAACATTCTGCCTCCAGGAGTCAGCTTACCAAACGATGGTGGTCGGAAATCGAAAAGCGCCGATGTAGCTGCAGGGCTACACAAGCAAACCGGTGTAGATCCGGATTATATCACTAGAAAGTTGACTATGAAGCCGCTGGTGATGAAAATTGTGTCAAATCAGACTGGGTTGGGGGG\n->contig-60_1493 length_279 read_count_992\n-AGTAGTGGTTATTTGGCTGACTATTATTGGCTCCAGAGTATTGGTTATCATGAGGAGGAAATTTCTTGTAGCCATTGGCTTGCTGCGGGTGTGGGGGCGGTGGACCTCTTTGGTCAGTCATAGTGCCTACAATTGATCTATTGTTCTTTGTAATAAATTCTTTCTTTCAGGAACAGTAAAAACAGCCTAAAAATATGAAGTCGCCGTAGTAAACGTTATCTTCTAGTTACTATCAACACAGACGCCTTTTTAAATTCGAGGGTCAAGGCTGTTAGGCTG\n->contig-60_1494 length_278 read_count_151\n-GTTCACTGTCAGTGATATCAAAGCAGAATGGAGAGGCCGTATGTAGAACTATCTTGATATCCTTGCCGTGCTTTTGGAAAACATGGTCAAATGCGTCCAGCTTAGATATGTCTGGGACAACTTCCATGGAGAATTTTGGGTTGTTACCAAAGGCCTCCGTTAAATTCTCGGCCTTTTCTTGACTTCTGGCAGAACCGATGACCTTATAGTCTTCCTTCAACAGGAGATCGACAATGTGTTGGGCAATGAACCCGTTAGCACCTGAAACGAAAACTGAC\n->contig-60_1495 length_278 read_count_832\n-ATAATAAAAGAAGATACAAAAGTAAAGAAATCGAATTGGTCAAATTACTTCAAATCGTGATTTTAAATGTCGAAATTATGCCTGGCCTGCGTTTCTTCATGGCACTTTCGGAAAAGGCGGAAGAACACAGGTAAATGTTCTTACGACCGAGGTCCTACAGCCTCCCTTTTTTCTTATTTTACATATTAATATACATAAATATACCATAATGCATTCTTTTTCTAATGATTTAGCTCTCCTTTTTTTGACATTTTTGAAAATAAATATATATTGGGGGG\n->contig-60_1496 length_278 read_count_1311\n-ATCGAATCATGCCTGACTCTAAGTACACAATGCAAGGTTATAACCTTGTTAAGCTATTAAAAAGGCTAGAAGAAGCCACTGCAAGATTAGAGGATGTCACCATCTATCAAGAAGGTTATATTCAGAATAAATTGGAGGCATCTAAAAATAACAAGCCTTCCGACTCCGGGGCCGATGCGAATACTACGAATGAACCTTCTGCAGAAAATGCTCCTGAAGTAGAACAAGATCCGAAATGCATAACTGCGTTCCAATCTTACATCGGTGAGAATATTGAT\n->contig-60_1497 length_278 read_count_206\n-TGAAAACCGAAAGGTTATTTTGAGAAATCTAAACAAATTGAAATGGATTAGAGTTCCAATATACATAAAGGCTGTAAATGCGCATGGCGTGATTGTGGCACGTAGAGGAATGGACGAGAATACAGCTGCTACTGGGATTGCTTGTATCGAATTTACGGCCCAATTACTAGCATACTTGATGCACAAGAGTAATTGAGCACTTGATTTACACGAAATAGTATATATTTTTGAATGAACACTCTCATGTGATTAAAATGTATTACTACCACTAATGCTTG\n->contig-60_1498 length_278 read_count_1999\n-GACAACCAAATCTATGCTATTGAAAAGCCAGAAGTCTTCAGATCTGCCGGTGGTAACTACGTTGTCTTCGGTGAAGCTAAGGTTGACAACTTTACCCAAAAGCTAGCCGCTGCTCAACAACAAGCTCAAGCTAGCGGTATTATGCCATCTAACGAAGACGTCGCTACCAAGTCCCCAGAAGACATCCAAGCTGACATGCAAGCCGCCGCAGAAGGCAGTGTCAACGCCGCAGCAGAAGAAGATGACGAAGAAGGTGAAGTTGATGCCGGTGACTTGAA\n->contig-60_1499 length_278 read_count_2179\n-TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCAGCAAATAAATGATAATATTCGTACGACACTAGAGAATATGATATTGTATTAAGTAAATATATATATATAGAGAAGGAGAGAGAAAGACAAGAACAGGGCGGCTATTAAGCGTCGTCTTCGTCATTCATAGAGATAGCTGTCTGTGGCTTTTCTTCTTCTGCAACCTCAGGCTTTGCTTCCGGCTCTTCCGCAAATGAGTTGGATAGGAACTCTTTCATTAGGCCAGCCGAGGTTTCAAAAT\n'

diff -r f9f2ad782d8f -r f89e3c318453 test-data/input_F.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_F.fastqsanger Wed Jun 07 12:02:03 2023 +0000

b'@@ -0,0 +1,2040 @@\n+@phiX174_1980_2501_0:1:0_3:0:0_0/1\n+TTAGGTGTGTGTAAAACAGGTGCCGAAGAAGCTGGATTAACAGAATTGAGAACCAGCTTATCAGAAAAAA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_1542_1965_0:0:0_0:0:0_1/1\n+CTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2950_3377_0:0:0_2:0:0_2/1\n+CTCAAATCCGGCGTCAACCATACCAGCATAGGAAGCATCAGCACCAGCACGCTCCCAAGCATTAATCTCA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2259_2739_1:0:0_1:0:0_3/1\n+CTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAAAT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_1141_1609_1:0:0_1:0:0_4/1\n+TGGCGCTCTCCGTCTTTCTCCATTTCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_185_708_0:0:0_1:0:0_5/1\n+CCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_1363_1914_3:0:0_0:0:0_6/1\n+GCGTTAAGGTACTGAATCTCTTTAGTCGCAGTAGGCGGAAAACGAACAAGCGCAAGAGTAAACATAGTGC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_3199_3732_0:0:0_1:0:0_7/1\n+CTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_36_572_1:0:0_0:0:0_8/1\n+ACCATAAACGCAAGCCTCAACGCAGCGACGAGCACGAGAGCGGTCAGTAGCAATCCAAACTTTGTTACTC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2128_2577_0:0:0_4:0:0_9/1\n+TTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4023_4544_0:0:0_0:0:0_0/1\n+TTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAAT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_927_1458_2:0:0_2:0:0_1/1\n+TTAAGCTCATTAGGGTTAGCCTCGGTACGGTCAGGCATCCACGGCTCATTAAAATAGTTGTTATAGATAT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2195_2674_0:0:0_4:0:0_2/1\n+AGCGAACCAAACAGGCAAAAACTTTAGGGTCGGCATCAAAAGCAATATCAGCACCCACAGAACCAACCAG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4438_4887_3:0:0_0:0:0_3/1\n+ATTACCCCAACCAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCACCACTATGAAATCGCG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4418_4896_1:0:0_1:0:0_4/1\n+GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGAGTTCAAGATTGCTGGAG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_1459_1934_0:0:0_1:0:0_5/1\n+TCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2580_3121_1:0:0_1:0:0_6/1\n+GGATACATCTGTCAACGCCGCTAATCAGGTTGTTACTGTTGGTGCTGATATTGCTTTTGATGCCGACCCT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_268_822_1:0:0_2:0:0_7/1\n+TTTGACGCACGTTTTCTTCTGCGTCAGTCAGAACGTCAGTGTTTCCTGGGCGTACACGCAAGGTAAACGC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4373_4951_0:0:0_2:0:0_8/1\n+GGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTAC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4817_5237_1:0:0_1:0:0_9/1\n+GTTGAACGGCGTCGCGTCGTAACCCAGCTTGGTAAGTTGGATTAATCACTCCGTGGACAGATTTGTCATT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_498_1078_5:0:0_0:0:0_a/1\n+CTGAGGAGTAACAAAGTTTGGATTGCTACTGACCGCTCACGTGCTCGTGGCAGCGTTGAGTCTTGCGTTT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4746_5200_3:0:0_0:0:0_b/1\n+TGGATTAAGCACTCCGTGGACAGATTTGTCATTGTGAGCATTTTCATCCCGAAGTTGCGGCTCATTCTGA\n++\n+2222222222222222222222222222222222'..b'ACCGATAACAATACTGTAGGCAAGGGTGATGCTGGTATTAAATCTG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_3247_3815_1:0:0_2:0:0_1df/1\n+AACCACACCAGAAGCAGCATCAGTGACGACATTAGAAATATCCTTTGCAGAAGCGCCAATAAGAGAAGAG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_3223_3567_2:0:0_3:0:0_1e0/1\n+AGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCAGATAAAGTAAAGGATACTCGTGATTATCT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_1692_2163_3:0:0_1:0:0_1e1/1\n+CTGACAACCGTCCTTTACTTTTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTTATTGAACTGA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2788_3310_1:0:0_5:0:0_1e2/1\n+TCATGAAATGCCTCAGCAAGATAATCACGAGTATCCTTTCCTTTATGAGCGGCAGACATGCCACCAAGTC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_3894_4392_0:0:0_0:0:0_1e3/1\n+TGCGGCAAAACTGCGTAACCGTCTTCTCGTTCTCTAAAAACCATTTTTCGTCCCCTTCGGGGCGGTGGTC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4515_5044_3:0:0_0:0:0_1e4/1\n+TCCATATCTGACTTTTTGTTAACGTATTTAGCCACATAGAAACCAACAGCCATATAACTGGTAGCTTTAA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4404_4767_2:0:0_4:0:0_1e5/1\n+GAATACGGCCATTAGCTGTACCATACTCAGGGACACAAAAATACTGATCGCAGTCTGCGTGTGAATCATT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_225_637_0:0:0_1:0:0_1e6/1\n+GCAATGACGGCAGCAATAAACTCAACAGGAGCAGGAAAGCGAGGGTATCCCAGAAAGTCCAGCGTACCAT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_543_956_2:0:0_3:0:0_1e7/1\n+CGTCGCTGCGTTGAGGCTTTCGATTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_1929_2438_3:0:0_0:0:0_1e8/1\n+CTTATACCTATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTTAAAATTCTATGAAGGA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_492_987_1:0:0_1:0:0_1e9/1\n+GATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACGGCTCTCGTGCTCGTCGCTGCGTTGAGGCTT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_3808_4333_2:0:0_1:0:0_1ea/1\n+GGGCGGTGGTCTATAGTGTTATTAATATCACGTTGGGGGAGCACATTGTAGCATTGTGCCAATTCATCCA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2304_2701_0:0:0_1:0:0_1eb/1\n+TTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2008_2481_4:0:0_1:0:0_1ec/1\n+TTCTGGTGATTCGTCTAAGAAGTTTCAGATTGCTGAGGGTCAGAGGTATCGTTATGCGCCTTGGTATGAT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_3419_3973_2:0:0_0:0:0_1ed/1\n+AGAGATTGCCGAGATTCAAAATGAGAGTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_383_987_3:0:0_1:0:0_1ee/1\n+GTAAGGGGCCGAAGCCCCTGCAATTAAAATTGTTGACCACCTACAAACCAAAGACGAGCGCCTTTACGCT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_1054_1487_0:0:0_2:0:0_1ef/1\n+AACGGAAACGATAACGAGCATCATCTTGATTAAGCTCATTAGGGTTAGCCTCGGTACGTTCAGGCATCCA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4040_4592_2:0:0_0:0:0_1f0/1\n+CGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCAATTCTACTCTTTCTCACTCCCCAATGCTTGGCTTC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2907_3500_0:0:0_0:0:0_1f1/1\n+GTCTTTCGTATTCTGGCGTGAAGTCGCCGACTGAATGCCAGCAATCTCTTTTTGAGTCTCATTTTGCATC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2716_3207_1:0:0_1:0:0_1f2/1\n+AAGTGCCAGCCTGCAACGTACCTTCAAGAAGTCCTTTACCAGCTTTAGCCATAGCACCAGAAACAAAACA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_3328_3788_1:0:0_1:0:0_1f3/1\n+GTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTCA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n'

diff -r f9f2ad782d8f -r f89e3c318453 test-data/input_R.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_R.fastqsanger Wed Jun 07 12:02:03 2023 +0000

b'@@ -0,0 +1,2040 @@\n+@phiX174_1980_2501_0:1:0_3:0:0_0/2\n+GTGAAATTTCTAGGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_1542_1965_0:0:0_0:0:0_1/2\n+CCATACAAAACAGGGTCGCCAGCAATATCGGTATAAGTCAAAGCACCTTTAGCGTTAAGGTACTGAATCT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2950_3377_0:0:0_2:0:0_2/2\n+GCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2259_2739_1:0:0_1:0:0_3/2\n+GCGACCATTCAAAGGATAAACATCATAGGCAGTCGGGAGGGTAGTCGGAACCGACGAAGACTCAAAGCGA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_1141_1609_1:0:0_1:0:0_4/2\n+CAAATTAGCATAAGCAGCTTGCAGACCCATAATGTCAATAGATGTGGTAGAAGTCGTCATTTGGCTAGAA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_185_708_0:0:0_1:0:0_5/2\n+TGTTTTCCGTAAATTCAGCGCCTTCCATGATGCGACAGGCCGTTTGAATGTTGACGGGATGAACATAATA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_1363_1914_3:0:0_0:0:0_6/2\n+TAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTCAAGCGCCGAGGATGCGTGACCGT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_3199_3732_0:0:0_1:0:0_7/2\n+TCTGCGTTTGCTGATGAACTAAGTCAACCTCAGCACTAACCTTGCGAGTCATTTCATTGATTTGGTCATT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_36_572_1:0:0_0:0:0_8/2\n+TTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGTAATTACTACTGCTTGTTTACGAAT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2128_2577_0:0:0_4:0:0_9/2\n+CTGAATGGAATTAAGAAAACCACCAATACCAGCATTAACCTTCAAACTATCAAAATATAACGTTGACGAT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4023_4544_0:0:0_0:0:0_0/2\n+CATTGCATTCATCAAACGCTGAATAGTAAAGCCTCTACGCGATTTCATAGTGGAGGCCTCCAGCAATCTT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_927_1458_2:0:0_2:0:0_1/2\n+GCGCTCGTCTTTGGTATGTATGTGGTCCACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2195_2674_0:0:0_4:0:0_2/2\n+CAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4438_4887_3:0:0_0:0:0_3/2\n+AACCATAAGGCCACGTATTTTGCAAGCTATTTAACTGGCGGCGATTGCGTACCCGACGACCAAAATTAGG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4418_4896_1:0:0_1:0:0_4/2\n+GCATACTGTAACCATCAGGCCACGTATTTTGCAAGCTATTTAACTGGCGGCGATTGCGTACCCGACGACC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_1459_1934_0:0:0_1:0:0_5/2\n+TATAAGTCAAAGCACCTTTAGCGTTAAGGTACTGAATCTCTTTATTCGCAGTAGGCGGAAAACGAACAAG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2580_3121_1:0:0_1:0:0_6/2\n+GGGTTAGGAACATTAGAGCCTTGAATGGCAGATTTAATCCCAGCATCACCCATGCCTACAGTATTGTTAT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_268_822_1:0:0_2:0:0_7/2\n+AAGGACTGGTTTAGATATGAGTCACATTTAGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4373_4951_0:0:0_2:0:0_8/2\n+GGCCACAACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTATCTAACTGCGATGGGCATACTGTAACCAT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4817_5237_1:0:0_1:0:0_9/2\n+CCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCATGCAAAATACGTGGCCTTATGGT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_498_1078_5:0:0_0:0:0_a/2\n+ACCAATCTGACCAGCAAGGAAGCCAAGATGGGAAAGGTCATGCGGCATACGCTCGGCGCCAGTTTGAATA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4746_5200_3:0:0_0:0:0_b/2\n+TGTACAGCTAATGGCCGTCTTCATTTCCATGCGGTGCATTTTATGCGGACAGTTCCTACAGGTAGCGTAG\n++\n+2222222222222222222222222222222222'..b'CTTCTGTTGATAAGCAAGCATCTCATTTTTTGCATATACCTGGTCT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_3247_3815_1:0:0_2:0:0_1df/2\n+GTGGCAAGTGTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_3223_3567_2:0:0_3:0:0_1e0/2\n+TAGACGCAACGCGAGCAGTCGACTCCTTCTGTTGAAAAGCAAGCATCTCATTATGTGCATATACCTGGTC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_1692_2163_3:0:0_1:0:0_1e1/2\n+TGGCGAATAAGTACGCGTTCTTGCAAATCACCAGAAGGCGGTTCCTGAATGAATGGGACGCCTTCAAGAA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2788_3310_1:0:0_5:0:0_1e2/2\n+CTTCCCCGTACGCCGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACATTACCGCTACTAAAT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_3894_4392_0:0:0_0:0:0_1e3/2\n+GGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4515_5044_3:0:0_0:0:0_1e4/2\n+TTTACTATTCAGCGATTGATTCATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4404_4767_2:0:0_4:0:0_1e5/2\n+GAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAACCAGAAAGGTATTAAGGATGAGTGTT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_225_637_0:0:0_1:0:0_1e6/2\n+GTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACAT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_543_956_2:0:0_3:0:0_1e7/2\n+GTTGACCACCTACATACCAAAGACGAGCGCCTTTAGGCTTGCCTTAAGTACGTCGCAACGGCTGCGGACG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_1929_2438_3:0:0_0:0:0_1e8/2\n+GAAAAAAAGTTTGAATTATGGCGAGAAATAAAAGTCTGAAACATGATTAAACTCCTAAGCAGAAAACCTA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_492_987_1:0:0_1:0:0_1e9/2\n+GTAAGGGGCCGAAGCCCCTGCAATTAAAATTGTTGACCACCTACCTACCAAAGACGAGCGCCTTTACGCT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_3808_4333_2:0:0_1:0:0_1ea/2\n+GTGTGGTTGATATTTTTGATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAATACGG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2304_2701_0:0:0_1:0:0_1eb/2\n+GGGTAGTCGGAACCGAAGAAGACTCAAAGCGAACCAAACAGGCAAAAAATTTAGGGTCGGCATGAAAAGC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2008_2481_4:0:0_1:0:0_1ec/2\n+TGCCGAAGAAGCTGGAGTAACAGAAGTGAGAACCAGCTTATCAGAAAAAAAGATTGAATTATGGCGAGAA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_3419_3973_2:0:0_0:0:0_1ed/2\n+CCTCCAAGATTTGGAGGCATGAAAACATACAATTGGGAGGGTGTCAATCCTGACGGTTATTTCCTAGACA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_383_987_3:0:0_1:0:0_1ee/2\n+AGAAATGATGAGTCAAGTTACTGAACAATCCGTACGTATCCAGACCGCTTTGGCCTCTATTAAGCTCAAT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_1054_1487_0:0:0_2:0:0_1ef/2\n+TGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4040_4592_2:0:0_0:0:0_1f0/2\n+CGTGAGAGTGTCAAAAACGATAAACCAACCATCAGCATGAGCCTGTCGCATTGCATTCATCAAACGCTGA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2907_3500_0:0:0_0:0:0_1f1/2\n+CCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2716_3207_1:0:0_1:0:0_1f2/2\n+GATGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACAATTGACG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_3328_3788_1:0:0_1:0:0_1f3/2\n+GACATTAGAAATATGCTTTGCAGTAGCGCCAATATGAGAAGAGCCATACCGCTGATTCTGCGTTTGCTGA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n'

diff -r f9f2ad782d8f -r f89e3c318453 test-data/reference.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reference.fasta Wed Jun 07 12:02:03 2023 +0000

@@ -0,0 +1,79 @@
+>phiX174
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT
+GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA
+ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG
+TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA
+GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
+TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT
+TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT
+CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT
+TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG
+TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC
+GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
+CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG
+TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT
+AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC
+CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA
+TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC
+TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
+CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA
+GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT
+GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA
+ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC
+TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
+TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC
+ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC
+CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT
+GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
+CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC
+TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG
+TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT
+TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA
+AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT
+TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
+ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC
+GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC
+TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT
+TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA
+TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG
+TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
+CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG
+AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC
+CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT
+TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG
+CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA
+AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT
+GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG
+GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA
+TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT
+CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG
+TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA
+GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC
+CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA
+TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA
+AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC
+TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT
+CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA
+TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG
+TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT
+CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT
+TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC
+ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG
+TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA
+ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG
+GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
+CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT
+GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG
+GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT
+ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG
+CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC
+CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
+GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT
+CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG
+CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA
+TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
+TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG
+TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC
+AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC
+TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
+

diff -r f9f2ad782d8f -r f89e3c318453 test-data/reference.gtf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reference.gtf Wed Jun 07 12:02:03 2023 +0000

@@ -0,0 +1,4 @@
+# stringtie /tmp/tmp3qb6tqs4/files/c/1/f/dataset_c1fd9ae0-5da1-47fe-a836-aebb9f0c8b87.dat -o /tmp/tmp3qb6tqs4/job_working_directory/000/9/outputs/galaxy_dataset_a1b533cb-fdd6-428d-8565-7686254dec8b.dat -p 1 -f 0.01 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0
+# StringTie version 2.2.1
+phiX174 StringTie transcript 17 5385 1000 . . gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "12.758615"; FPKM "186254.437500"; TPM "1000000.062500";
+phiX174 StringTie exon 17 5385 1000 . . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "12.758615";

diff -r f9f2ad782d8f -r f89e3c318453 test-data/single_end.fastq.gz

Binary file test-data/single_end.fastq.gz has changed

diff -r f9f2ad782d8f -r f89e3c318453 test-data/test-db/busco_downloads_odb10/ancestral
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-db/busco_downloads_odb10/ancestral Wed Jun 07 12:02:03 2023 +0000

b'@@ -0,0 +1,994 @@\n+>101957at2157\n+ELKVSKIKNGTVIDHIEAGKALKVLKILGIKESEEVSVAMNVESKKLGKKDIVKVEGREL\n+SEEEVDKIALIAPEATINIIRDYEVVEKKKVELPEEVEGVLKCPNPNCITNKEEPVESKF\n+EVLRCEYCERILEEEEI\n+>102178at2157\n+VLDASAFIAGTTPEVVEELKDESVEKVKEAALSETDIEVLALALEVLVTDDYAVQNVAKK\n+LGIKVESIAQKGIKECKGCGREFDEECPICGSELKRK\n+>10236at2157\n+FEIKEKDAAGRIGKLKTPHGTVETPALLPVINPPKELKEFGAEILITNSYIIYKKEELRE\n+KALEKGLHELLDFDGVIMTDSGSFQLLEYGDVEVTNEEIVEFQEKIGSDIGVILDIPTPP\n+DVSREKAEEELEETLERAKEAEELEMLLNAPVQGSTYPDLREKSARELSELDFDVLPIGA\n+VVPLMESYRYKELVDVVLAAKKGLPPSKPVHLFGAGHPMIFALAVALGCDLFDSASYALY\n+AKDDRYLTEEGTEKLEELEYLPCSCPVCSKYTPKELREMKEERERLLAEHNLYVIFEEIR\n+RIKQAIKEGRLLELVEERARAHPKLLDALRELLKYADQLEKYDPVSKSAFFYTSEESLRR\n+PEVLRHKKRLERLPPFGLIPLELSETYPLSQAEVPEELDELLEKNEKSKKTGKRQTLRAE\n+DGGKSKF\n+>102360at2157\n+MLTFIGLGLYDEKDITLKGLEALRKADKVYAEFYTSRLVGTTVEGKEIEVLDREDVEILE\n+EAKDVAFLTAGDPMIATTHVDLRLEAKKRGIETRVIHGVSILSAASSLTGLQNYRFGKAV\n+TLPFPNVVPESVYDVIKENLERGLHTLVLLDIKERYMTANEALELLLEVEELAVVVARAG\n+SEDPVVKAGKLEELDFGEPLHLLVIPGKLHFVEAEALVELAGAPEEILE\n+>102399at2157\n+MRLFVAVDLEVQEELLKLVEPENLHITLKFLGEVDEEKLPFEVKVKGLGVFPSLEYIRVV\n+WLGVEEGEAVEEELLGFKKEKEFTPHVTLARVKLVQELEEFGEFEVEEIRLKKSTLTPKG\n+PIYETLAEVEL\n+>103467at2157\n+PEKTAKAMLRELKISPKHSVEIAREIKGMKVEEAKEYLEDVIAKKRAVPFKRHNKKVGHR\n+KGAGRYPVKAAKEFLKLLENAEANAEYKGLDTEKLKIVHVAAHKGRATPKNTIELILEE\n+>104254at2157\n+KTNPRLRKLIAELKKASRAPIWKDVAERLEKPRRKRAEVNLSKINRYAKETVVVPGKVLG\n+SGKLVTVAALSFSESAKEKIEEAGGKALSIEELLENPKGSNVRII\n+>104636at2157\n+MGERELIKLVVTTDMLHESTDFPMTPYDIGWKAVAANLSDIAAMGAKPLGFLVSLGLPKD\n+LDEEELEEIVKGIRDACEEYGAEYVGGDLNELTIDGTAIGRVDVTRSGKPGDLVCVTGEL\n+GRAAAALEPRVEEGRALAATAMMDISDGLARSLHELAEASGGIEIEEDKLPIELALYSGE\n+DFELVFTVPEEKLLTVIGEVTEDRGYEH\n+>104702at2157\n+AFVPGHITGFFTGSLGAGIVLEKGVTVEVDLPLGAGFGVSGALALATALALNELVQIAHE\n+AEVEAGTGLGDVVAQGLVIRLKPGVSLGELSTKEVLNEAGEKAEPTLENFMELSREFAEE\n+TGLLSLGKTVFAL\n+>104786at2157\n+IHNIELRTFVHATEDEEKVLEALENLLPIEREEAEGHYGNPILVLSARIEKKREAKEFLK\n+KLLEKLSEEELEERVDELYLRLDKQAAYLGEVKLIKVKIKVEAYPAKKEAVENLRELL\n+>105095at2157\n+QCELCGAEIKVKIEGAELEVCKECAKFGTEVKELVEDYAERIREAREKKGLSQEELAKKL\n+KEKASLIKKIERGELLPEDKVAKKLEKALKIKLIEKVETLGDVVKIK\n+>105165at2157\n+MNPRKLKMKQMGIDEELEVIIRTKDKELVIEDPEVTVMDAQGTYQIVGIPEEDVELVAEQ\n+TGVSEEEARKALGDLAEAILKL\n+>105421at2157\n+MVVAAVAVDGVKDSKKLTPKRREELNLNELEVAKAIEKLVDAVDVKEEREVVAEHKADIV\n+SAASIVAKVERDREIEELKVGSGYPSDPKTREFLEEYLPPIVRRSWKTVKKI\n+>105604at2157\n+MEFEEWEPYEAILKDFGFSREKDERAAELLSSLLGKTVAVVGAGPSLEKELGVVIAADGA\n+TSALLEGIVPDIVVTDLDGNETLLEANEKGSIVVVHAHGDNIEKLRKVVPERVLGTTQAE\n+PVYNFGGFTDGDRAVFLALGAKEIVLVGFDFDDSVTYSKKKRKKLEWAERLLEWLERFEV\n+LDGR\n+>105851at2157\n+MSRKFCPRCGKEELCKDCYLKEFELVELPDRIEVEVCSKCGAVKKGGRWVDVGAEEETEV\n+AEEEVEEALKVHEEVEDVEVEPEQVDENTIRVHVEVKGKVRGEEVEVEVRIKRETCPRCS\n+RIAGGYYEAIVQVRADGRELTEEEREEAEEIVEEVVEELEKGDRLAFISEVEETKEGLDI\n+YLGSKKLARKIARAIKEELGGKVSESPKLVGEDSDGKEVYRVTISVRLPEFRKGDIVEYE\n+DKPYLVRSVSGKKLKGVDLETGERYEISWEELEKAKLLGKREDAEEAVVISEDENAVQVL\n+DPETYETVEVKRPLEEGDEVKVLKIEGGLYILPKEE\n+>106462at2157\n+ERTFVMVKPDAVQRGLVGEIISRLEKKGLKIVALKLLKIDEELAEEHYEEHKPFFEELVE\n+YITSGPVVAMVLEGAISVVRKLVGATDPAEAEPGTIRGDFALDLGNVIHASDSAEREIKL\n+FF\n+>106603at2157\n+KMPKKIRTYCPKCKKHTEHEVEKVKKGKRSELKFSKVPKGGAKPTKKLDLRYRCTECGKA\n+HLRGFRAKKLEL\n+>107015at2157\n+LMSKQPRKQRKAPLHERQKLLSATLSKELREKYGRSLRVRKGDTVKVLRGDKGEEGKVVE\n+VDLKIAVEGVTVEKADGTEVPIHPSNVMITKLDLSDKRREKKLERKKE\n+>107212at2157\n+KSHGPRTRKKLKKKPRERGPLSRALQEFEEGDKVHIKIDPSVHKGMPHPRFHGKTGTVVG\n+KRGRAYVVEVKDGGKEKTLIVRPEHLKPQK\n+>107993at2157\n+QKARIKLASTLDEVCDQIKEIAEKTGVKLSGPIPLPTKRLEVPTRKSPDGEGTATFEKWE\n+LRVHKRLIDIEADERALRQLMRIKVPDDVSIEIEL\n+>108145at2157\n+VRAIGLDVVEPEEECDDEKCPFHGELSVRGQILEGTVVSTKMKKTVVVEREYDVYVPKYD\n+RYEKRRSRIHAHVPPCLEVKVGDKVKIAETRPLSKTKSFVVVEKKEEEE\n+>108717at2157\n+MATGPRYKVPFRRRREGKTDYHKRLKLLKSGKPRLVVRKSNKHVIVQLVGDETLASAHSK\n+ELKKYGWKGNTPAAYLTGLLAGKKALKAGIEEAVLDIGLTKGSRVFAALKGAVDAGLEVP\n+HSEEVLPDEERIRGEHIAEYAEKLDEELYKLDPEDLPEHFEEVKEKIKE\n+>109335at2157\n+DLKAQKRLAADVLKVGENRVWIDPEALEEVAEAITREDIRELIEEGVIKAKPKKGNSRGR\n+ARERAEKRKKGHRKGEGSRKGKKGARQPKKEEWVKKIRALRRELKELRDEGEIDYRKLYR\n+KAKGGEFRSVAHLKAYI\n+>110798at2157\n+VVHLNDLVVVDLDALIVESHLAHLLDRVIVLRCNPEELEERLKERGYSENVEAEALDV'..b'NRFECEWVKLRVENAKTPFTKAY\n+EEGEVIELPIAHAEGRYEEQIVFRYVDEEGNVNPNGSLENIAGVLNEGLMPHPERASDGL\n+KIFKSL\n+>90882at2157\n+SAPGKVILFGEHAVVYGEPAIACAIDLRATVTVEKSDDYVAEAIEIESEIPVGSGLGSSA\n+AVTVATIKALSKELSKEEIAKLAYEVEKEVQGKASPTDTTVSTYGGLVLIELPLVIGSTG\n+ELVAKVRKLKEKILEAIGKIVEEAELGELMNINHGLLEALGVSTRELDELVYAARALGAK\n+ITGAGKGGCIVFKVKIS\n+>91154at2157\n+DPLANALSTIKNAESVGIEPASKLIGEVLKVLQDEGYIGEFEFIDDGKAGKFKVELKGKI\n+NKCGAIKPRYSVLEKWEKRYLPAKDFGILIVSTSKGVMSHKEAREKGIGGQLLAYVY\n+>91297at2157\n+VKLLKKLALKGALKKKVKISSSELAKELGASQQTASRRLKELEEEGLIEREVVKDGQLVK\n+ITEKGEELLKKEYEDYRRIFESELKGTVVSGLGEGRYYISLEGYKEQFKEKLGFEPYPGT\n+LNVKLDEESVRERIEIEGFEDEERTFGDVKCYPAKIEAAIVVPERTHHDEDILEIIAPVK\n+LREKLNLKDGDEVEVEV\n+>91632at2157\n+VTRGLEKGSLVKCADNTGAKEVEIISVKGYKGVKRRLPKAGVGDLVVVSVKKGTPEMRKQ\n+VLEAVVVRQKKEIRRPDGTRVKFEDNAAVIVGEPKGTEIKGPVAREAAERIASLASIIV\n+>91936at2157\n+IFAVKTTAGQEKNVAELLAERIKAILVPDELKGYVLVEAGIRHARGVVKGEIEKFLKPKP\n+EIEEGDIVELIAGPFKGEKAKVVRVDESKEEVTVELLEAAVPIPVTVRGDQVRVLEK\n+>92409at2157\n+MVTVYDVPADELIEKLAEKLKEPEWAEFVKTGVHKERPPEQEDWWYVRAASLLRKVGPVG\n+VERLRTEYGGKKDRGVKPGSGSIIRKALQQLEKAGLVEKAKEGRVVTPEGRSLLDKLAKE\n+VLKELAEDRPELEKYA\n+>92795at2157\n+EDFIVEEIKYLVLRLEKRNWDTVRELSKALGISAGTKDKRAVTTQLISIIKDVELEVLGR\n+AGDLAGNRFEIRVRDGVPNYFGYQRFGSRRPVTHLVGKAILKGDLEEAVRLYLGNPEARK\n+AVRYERAMLALEALPKNLQRLFVHAYQSYLFNRILSERLEAFVTAPLGEIEREVLEEEGL\n+EPEDFRRAILLKLEFSLPKGSYATVVLREIMK\n+>93236at2157\n+DVKPTRIELIRLKRRIKLAERGHKLLKEKRDALIMEFFEILDEAEKVREEVGDVAVKSAA\n+ASVSKNIMGVKVPKIESSERGYGLLGTSAELDEAAEKFEELLEKIIELAEVETTLKKLLE\n+EIEKTKRRVNALEYVIIPRLEETIKYILDEMEREEFVRLKRIKA\n+>93256at2157\n+KKNRKKYETPKHPWQKERIAEEKELLKKYGLKNKKELWKAQSELRKYRREARELLAELLK\n+RLKRLGILLDDVLSLKVEDILERRLQTIVYRKGLAKTIKQARQLIVHGHIAVNGRRVTSP\n+SYLVEEDKIEYSPLAK\n+>94875at2157\n+MNTLLWVLVLLAYWLVVISVSGPILMIRTKRGRKFLDRLAKKRFWRAYANIGIVIAFMFY\n+LLLLSALSLLQPRNVLLIPGVNLPLSAALIALVVALVVHEFSHGILARVEGIRVKSMGLL\n+LAVIPIGAFVEPDEEELKKASRGSRLRIFAAGVTANFVLALIAFALLVLGAIANEAGIEE\n+GDRITAVVENNEDLGAVGTAVPAGVYITGVVELKEGDVITRVTSLEDLSAVLNKTKPGET\n+VTVTVLRDGETYTVTLGEHPEGKGFLGVGVQLYPALLILPFAGFTGSVTNFYEVQGPLEA\n+GFFLLANLLFWTGWINLQLGLFNCLPAFPLDGGHILRELLEAVLSRKLVRAITTSVSLLL\n+LASLL\n+>94889at2157\n+LTFVTSNEGKVREAKEILYPEIQADSLEEIAAKGAKEAPVIVDDSGLFIEALNGFPGPYS\n+AYVEKTLGNEGILKLMEEDRRAEFKSVIAYADLFEGKVEGKIAEEERGEGGFGYDPIFEP\n+EGKTFAEMSTEEKNKISHRGRALEKFAEWL\n+>95578at2157\n+MEERTKKRFREYYRLPEDLEEREFGFMVRHKSFKSEEELKDFLKAPRHVYYSVALYEKPS\n+AMEEKGWLGADLVFDIDADHLPCLEEAKEEALKLLDILEEDFGLEEDIKIVFSGGRGYHV\n+HVRDEELDSEERREIVDYVSGKGLESGWKKRVAEIDEKVTTDIKRLIRLPGSLHGKSGLK\n+VKELKRDELEKFDPDAVPEVFREEEVKVEVVELKGEKLEVPEYVAVFLILRGLAE\n+>96138at2157\n+AAKKSERRVKDKWKEKKWYTVLAPEQFGRKEIGETPADDPEKVIGRVVETTLGDLTGDFS\n+IKLYFKINDVEGDKAYTEFVGHELTRDYLRSLVRRGTSKIDAIVDVTTKDGYKLRVKVVA\n+LTTKRAKSSQKKAIRKIMEEIVEEKAEELTFEELVKEVVEGLSSEIYKEAKKIYPLRRVE\n+IRKSKVLAEPE\n+>97230at2157\n+IEKVVVNIGVGESGERLEKAEKILEELTGQKPVRTKAKKTNKEFGIRKGEPIGVKVTLRG\n+EKAEEFLKKALASQFDETGNVSFGIEEHIDFPGVKYDPEIGIFGLDVTVTLERPGYRVAK\n+RHRVTKEEAIEFLFGVEV\n+>98179at2157\n+RMHTRRRGKSGSKRPSAEEIEELVVELAKEGVSPSQIGLILRDQVPDVKLVTGKKITEIL\n+EENDEIPEDLRNLIKKAVNLRKHLEENKKDLHNKRALQLIESKIRRLVKYYKDWKYKPEK\n+AELLV\n+>98187at2157\n+KTVEVLVEGGKAKPAPQLKQALGVNVKEVVKEINEKTKDFEGMEVPVKVFEIEVGVPPTT\n+ALILKELGIEKGSGEPVGDLSIEQVVKIAEMKLLAKDLKAAVKEVLGTCVSMGVTVEGKD\n+PKEVQKEVDEGKYDEVL\n+>98221at2157\n+KKQVEVRELKEGSYVVIDDEPCKISTSKPGKHGSAKARIEAVGVFDGKKRSLVKPVDAKV\n+EVPIIEKKKGQVISVGDEVQLMDLETYETFELEIPEGEEVEYGKRKI\n+>98657at2157\n+AKRAAAEEAAEVEDGMVVGLGTGSTAAYFIEELGERVLLDVRGVPTSFQSELLAREAGIP\n+LTSLDEDIAIDGADEVLIKGGGAALLREKIVAYAAKEFVVVVDESKLVEKLRPVPVEVLP\n+FAEKLEELGGEPELRAERKDGPVITDNGNLILDCEFGEIEDPLEKELKSIPGVVEHGIFV\n+LVGTEDGGVEVLE\n+>99236at2157\n+EFKYRGKTLEELQEMSLEELAELLPARQRRSLKRGQKKLLEKIKIRTHLRDLIILPEMVG\n+LTIEVYNGKEFVEVEIEPEMIGHYLGEFALTRKKVEHGEAGVGATRSSKFVPL\n+>99734at2157\n+LLKKAGLRLRGQHFLVDDRVLDRIDTVLEIGAGTGILTKVIAIEKDERLVEILREEFADN\n+LELIEGDALKVDFDKVVSNLPYSISSEITFKLLKKAVLMYQKEFAERLVAKPGTKEYGRL\n+SVLVQLYADVEILEKVPKEAFSPKPKVDSAVVRLTPKKLVKALFSQRRKKVRNALKNSAH\n+LEKRVEKLSPEEIAELAELL\n+>99842at2157\n+MEIKLTDEEIRYIALFESVTGADCLVDDRVIFVVKKGDMGLAIGKGGENVKKLEELGKKV\n+ELVEYSDDPEEFVKNLLAPAVTISEKDVAYVEVDKGVAIGKEGRNIEKARELAKRHFDID\n+DVQL\n'

diff -r f9f2ad782d8f -r f89e3c318453 test-data/test-db/busco_downloads_odb10/ancestral_variants
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-db/busco_downloads_odb10/ancestral_variants Wed Jun 07 12:02:03 2023 +0000

b'@@ -0,0 +1,10080 @@\n+>101957at2157_0\n+NLVVSIITDGTPIDAANPHQYFNVFAYLDVEKRQPVATVTLNVDAAEVGTHAVVNIMKDF\n+KRKLATTQIAYVGARATINKIKGWNIAPVMMVQTFPADEKTTKPAECACISNSPGIESLV\n+TVLNKKYCERQAETT\n+>101957at2157_1\n+SLIINEFMDFKVIRHIKKKTALNVPIILHSKATLTFTIGIIWKSDQKRVGTAQGRLAQVS\n+NKEVEETKVIVNGAASINRAKDIEVTDIKLAQSISSLLECGAATCIGKQVVILGSKFKVL\n+MLVAYCTDITGKQDQA\n+>101957at2157_2\n+DLLLERINKGTVIDDIKATKKSAQIQQKIEYLLKVNEEVDWSYAYNVSSTNSRSKEIKAA\n+EKQMNESQLNLVASLGPDATVDIHRDYEEIGKQTVENHEQSSEDIFSNNARTSVTYSNGL\n+NTDTRIRIDMKPLQKKYCHTIRIFHAS\n+>101957at2157_3\n+YMIVRNVTAGIVLHQIRAARTLNVVTILASSARISSSILMKINQAAARTKQANLTIMFIV\n+VANSAASEEENTKLALYAPQATVNAATGYPHQKEYETYRPMKMQVISKVVVVHENVESAT\n+VNLTPAQMMKKKLKILFCEYTDKEQK\n+>101957at2157_4\n+EILAEQAKRTEGRVLTDVQAHEARIRKITGSLTLSITSNMLANEHGKKDICGKNGTTAGE\n+NRIHQIAKVAPSASGAIVRKIPMCTKQLGTEPSVVVESKGIAEGPNGPCTGSEATPEPVV\n+IGCKGSLVKVCTKIFGTKSA\n+>101957at2157_5\n+DLDVRAIRTGHSEHHIIRKQAVAVWITMQILETIAVVTGVTMRLSTGKDGLLNSARKVPS\n+QACGISFEIISKPQIAIVLIMNIVVNGRRSLEDHEAVAGITICPNNVCIEQSDEDVLSSM\n+IYFRCHMCILTWTGPKA\n+>101957at2157_6\n+TSIPSTISIPGYVVLSGIAQGDSKEVHESFKILASCVEILIMAVIANQGCASQAQQPIKL\n+VQKTLDSSETEHPAVVAVRAYQLMLKNAKIAEDSYTQIIRCLRTAIKCPERRCITETHME\n+IRSNITVMRCSYVNIIVQGKV\n+>101957at2157_7\n+SLPVNSILKNTVDKHADEPARYPQQSSARAHDVHGPAITRNKATSIMENSDTIDLRERMS\n+DLERVDCWFIISAQTKLGVCVKWNAVKIVAGVRSRLITDAFVCETSECIMNDPAKQTEQF\n+RMIKCQFCEFKLSI\n+>101957at2157_8\n+VLHIEGWLQPTKFDHMDKSQPLFVAPTYRNIQNQGGPIVGGMVARDINMKDFLKAEEIQP\n+VENWSIAEKVRQLAIRAIRTIKVNWVNEPRLVKTLLRCHNYRAITDGHVKKELTIVKCLC\n+KAIWRSSTV\n+>101957at2157_9\n+EVKVKHIIDIVLVDSIDLGREWSIIDILDKNSTSTIETGGDQVTVPGIHGLKKVMVSIES\n+AVFTGKKVVDEGIIAPQTIEQVKVPITIIIEHRCTPPFRTNGDRAMHSLVSCANPVCLSL\n+PNTAVREIEFKVTQCFYCGSAVAQSNM\n+>102178at2157_0\n+VPGTANAANEETPACLQENKTRVYFNVKCAALKETDEYIPSASGPSAVTDTFRVQFVMTP\n+LCIKVGDTRLGGPHQCVTCGKETLTHCCLCKSNVSPR\n+>102178at2157_1\n+VIDHAVFIKDYKALNWNEPLKGDFAKEEVQDCMSSHTCKVQAHKVACPFSDLYTLQNAAP\n+RFVIVVDRLGESQEGIDMVTDCVKWVELKECTVCGNNIKRL\n+>102178at2157_2\n+ILNTFAIILNVAMHVAMAPAHAETNVMNTASLVTLVVNILTGGCNIIDTTKFKVQQSYLR\n+RRIEGVMVEVSMIANMVAVAKAKRMEEECIVCAHQIGRT\n+>102178at2157_3\n+IKDASTFIRLANRLCCREVNDWILKFVEKLNMTKSDFHERMAMCELILQEDYKVPNAYHS\n+CCVEVARAKSEKFATCAGYQAKFGQECTLCNDRLMSK\n+>102178at2157_4\n+MEDDAAIVTAINEASNSTFILQMEDKFTSNVRETIVSATNMRVSTLAIIALILDRFTIVE\n+VFPLLNVRLEVFIKKFVVQCKDGGELVAATCGATGNQSRWK\n+>102178at2157_5\n+VLDTAFFVAATVSLVLDEVEDSRLFEILGIVSDTTMLVMFTDYTWLLELLYAQQPCATSV\n+HVEWRAAQLKKITFLWGSEEYFGQERKICQLDLNSM\n+>102178at2157_6\n+ILDNQAWINQQDHVIDSEVCGIPVIEEARQLAVKTSDISADALLTETSNTDEYRLQNLLR\n+AQQTQTAEALQKQIGECSGKDRYPYAFCNLCSERCFEH\n+>102178at2157_7\n+IVDAFAITGDEIAEYSDAVGGEGLRRVLLNQSCTKGAIEVFALATVRVIVADDYALQLIN\n+ASLKITITPAEQGIINLARVCGAEYQEPCGSAVENL\n+>102178at2157_8\n+VLQTASIFDESVSASVEMDEDTEVEEGTATSIRVTHHNKNKSCMTYVFREDFAIASVGGQ\n+DHFILAAGPQAKRAKSKCPGCGHITEKCTCGAARREH\n+>102178at2157_9\n+VHQDARLLLKETTQKAIRAPQALDRPALVKDAVDEHRKLALAEQEFNAMLGDVQDINTDD\n+YMVTFANIEHMIQYEESTQNSFTKCKPIENVIVNAWAKKGEGIKYA\n+>10236at2157_0\n+FEAKLTEEVQSKLGKFTTQRALLDAPQDFPKAREEDEMRSMGVEFIMNSSLFMYKNKAAG\n+DDMIKPEIASLIVFLGGAFTDSGSYQESVNGDILQEDTVEFAQTINSDQIQSIDQPSRES\n+KVRANAENNLDAQTYDRVNELLRRPQTISGSAQGGNYLKLEELAVARDVQLMKSKVCAAP\n+AMTPMLTAYLYNDALECIAVSSQTGGNHISAHQFGQGHPSALRAAVAMQSAPFDSNVGQR\n+IYKACKAFSDPSEQRTELLNREGLKHSDACSKILRQEFRELSANEMIDNARENLHTLTSE\n+KRTVKDVISHESIVQVGMKQARSHFEMNDGYHLVPQMHMEILGKRPRSKKPYQYYCRTEV\n+ESHLFKEPRNLLTAHKLCSVSTKGLDKAYPLGKMNTENFTRTQRNNDLVQVQGEKVSTVR\n+RQNKRLASFHKFGKS\n+>10236at2157_1\n+QRVSRKDNVGRLAKLVINGGKINAQELAPFINERRVMQALAAEIGIGNFFLLRTVENIDV\n+QVYEPTILAPIGHDGAVTTASGEFQVKVFGEAETSAEHMIAFHSAVQSDGLPVGKRIPTA\n+PRTKELNKLHKKIQTGVNNKMATTLATFEEDNIYEKDNSAFKDLVVKGFGSAGICNFGTH\n+PDGSWVVFFVKYHYNDIQEVTNSKESIHSADHGSQVYGAGLPSMTAEAVCLGARRINPAP\n+ELLSKTHYYSFAFPGANGMLGPRAEMRQRCPASGLNTHQNVGPMIKKNRAPDLALHNLDR\n+CIEEARKVTDEIARAILSQWDESKCEKKPAVLMHFANMKQMMADAFKRYQYLTSFIRKTL\n+KRKEVVILTARGYLIVALGVIRRKMQSVHPCTNSELSSLIDHLMEADNKEDCQLKTDNVW\n+TNIGADKERPRVIESQIATGRDADTLGGVPKTLSLTAGYDDQKGASQLRATRGTCLRLSN\n+RVRRQP\n+>10236at2157_2\n+ILFTRNDLAARISASTINPQMLDTNAMPNEYVEKDKLRIGFMPIVNSYIVKKDPQWENEF\n+LEMGYRQMTDEENPILIDSGTSAYHQRGKIKVKKEQAIQDHTIDSDYRAIKEIAVECHRG\n+YELRSESSVSVYVEEIEVTASTQRHARHPVQ'..b'TWIKHGNTGVVVTRPDVFVDA\n+>99236at2157_8\n+IVKYFTQENECIELHPLEVQQMTSEAKVRQVRNVMSVQQKAVDKVSLKTYLRSMGFAPYV\n+ARKGVGCIQGVKFVTIHAEIEVINKATGAFLEQFEVMHEKKGFEATDNNTLMNL\n+>99236at2157_9\n+EFQYRGNKGHTILELARFPLILMLPSLSKHALAEDQRKLASWIIIKQLRSMVILPEYATP\n+ELESHNGIELLQIEPSMLGHKLSEWDLTMQEVAHGTAGLRASRSRDVVQI\n+>99734at2157_0\n+TTCKCPTGQSFLASDNALKMLKSVIEVLILKKNLARVTAIEKDRKVIGENHTNLPLQEIP\n+CIQGDFRLFSVKVVLTNAPDRTSSPTLTSRYAMMTKAIVLYYQGEFAPYLAKDPVEPEIR\n+KMEVLSGRPLWAKIASTVGTIDNDPNESLRRKILIRAPKGIRLCVFNKTTKPVKDALREI\n+ASLQRNAQFVAILAVVTIANKI\n+>99734at2157_1\n+RNSGNAPQVQTFRVDRSIADRLFQKHEIIIGKLMRLNAALAIEQDRMVARAAKKMFDTKA\n+ELMPIPVLKVTHHTMIECLPYGVKHAEFRKAARFALLMVQDEAAARMWAKDGSSYKRLSC\n+KVSVMAYNVVIADVATKDCFVEWMQPYSSSAAVKIEKDDSTIKIFSNRYKTIRRHILNSQ\n+KHKLRLEDMTAVKALRLDVLS\n+>99734at2157_2\n+MTMKAIVEQYNQRFPISREATKKFTKVERTKQKAGTISDLRGVEIGEQFVRTTGSIIAKT\n+VTNIEKDGIALRPYKFIGNLPFCETRTLYFMLGNNLVILQQREFASKMNSRKGPTDYANL\n+TVPFTCDLVVEAVCPYIQSEAGPKRKVREATWKHKPLETMPTLHSHRSETNKAGLIHYGL\n+LRAKEVTLHKQALVEAEKQL\n+>99734at2157_3\n+TIFEHELILEGQHFLGEHNAITEVDKVAEQAIAKGALNKWTEIYKDALSLNAEVHREYLS\n+TPFFSNVGLLHADTLYVKSAMVVSNTPFSKTRALFFTNMKNEVLAVQSEFGKRMAANVGE\n+FENSKLDVLVKVFLPTEIDLLEPEQPKYAGKGNALYRTFVNITPMHVTKTLVQQYDEDHR\n+YKCTKLYEHKERAHKLMDRDIIKLTNDI\n+>99734at2157_4\n+NATRKNMRQRLQEGIIFQRIMERSEHIAEIAGNIITLERSSAVDDDRRLIRKLKSQLRVL\n+HILAEQASSVGSNKAIGNLPYFNFERIAQEMSQPAILVKQMEVVKRGVMETEDTKRLYAT\n+LFGDATARFTCGVKQEQFDPRPIVYDAGVMAERRQGYMLSASHKTFDARWVAIETAKLKV\n+RMITLMPGRIKTVRSLW\n+>99734at2157_5\n+ESAISGIRASTSNFLMDKHIATSQIMAVVFQASDVGAALPLFDITSVEIEPVISELRASV\n+ENTLKTANQDALSYLFDMLLSSVPYNWSEDIDGKLIKPLVLGRQYEVSERMYASQNAAEY\n+EQMTLSAKAFMEVNFLQTYKKGALQAVPRNNSAWIQLVNFNFIEADMEYKNNKAGSALFE\n+IKGSKRESTLVQHFVFTKAKQI\n+>99734at2157_6\n+NRAKERVVRDQNYKINELIYKVVEDAIEVLSGKIELAKIKAIEQDMSLHTFLSVRFPDML\n+DVDARLTEATAVDFNVSIADVPYRESRTLQLQIGSRLIVCYTEVANRLVKGKTRNMGRTS\n+VFTKYLGDIHVVSRILKAFFWNEQNFDSFLVRMIREEVERVLIFTRQGKLYLKILNDPSS\n+LQMKWRTIEGKECFRTAEML\n+>99734at2157_7\n+MMAELTGEDHLCSVLKIREEDRWLEIAPHPALLTHPNVVDVDSAMSIRVTRLIANEDIFV\n+QQDKLQLDINLAYVRMPYDDSSEIEISMIRLAIMTVQSENVSSQKLLPKYESTEFAKFAL\n+KTHFFVKLSLALKYHAPGYFSLAPPSRKRVLELEPRTILAEAFDGQNKQTDKPLVQAPDF\n+AARVHSADPTTILDVREFM\n+>99734at2157_8\n+SVSGSDSHAQQKQGAFDPLDIIREVQADTGKLVGVFKVDKASKFTKQLEVKITDIVLLIM\n+QLALEVEYDLEVNNLPYQLTEVMTFKTVRLCVVLFQRELAEHIWFSEPGNNSYARYKVDV\n+AKSAQISCVKKGPQEDFVAGHQVANAIVVLLPKRLVVRIKKRSRRLCRTTAIEMPLETKP\n+FPLLPKITMKHLRSG\n+>99734at2157_9\n+LKGCRVANKAEQKILVNRQSANKHTGLTEAGTTAVYLTQVTAIGRNTEERSILQQEITQR\n+QSIISQDMLQIVVDKKVRNPPFGVYSPHVFQVAPRMVMMIQYELALDWAAMAQQRKYGRA\n+LVSTMYKMSVTLLTEVNNGIFVDATKKISYIVAISPASVTQPFVESARDILYTLPDSKNV\n+QKMSTTVVVEMISIIP\n+>99842at2157_0\n+PEDTLAAELLGHINVLRMLALRISHVRNANGIMVEERLVVGTVQKNYEPMQQVRDVGGSI\n+GLIEMSNNTAEGIRHLLCPSYWYSESQVASTKIDRMFILAFLTYNKDADHRKEATKRQSA\n+VDDIEI\n+>99842at2157_1\n+TKVVMMANRLPVLSTRRVETGRHCVNINALVMCGDEGKLTPAINTTEIRIVTLTQSSKQK\n+HKPELVWSQKRVEEDCSVVHHETVHANGAQYAYITVDRKNKAKGADGMNINKERDLNARC\n+GPFAKLNL\n+>99842at2157_2\n+MPAGVTEQGLDYIVSFEDLIGVDIKRRVIILAKEDCMAVLVQRNSVAVAILERSISNVFV\n+VDRSSCTEMIAEILMVLNEFSGANNNQVEKADAYEETLLGDDARDIELAIDLLVRHIEPH\n+GYLI\n+>99842at2157_3\n+MKVTLEAREVRAVKLFETLTTAHCIVLDRLQFVLKQKRSGDMTERMSSRLVLVTMVDRRV\n+TTASHVDNALEAVITAIQKDAVKINESKIAYVTSEKGYAIGTSRQPIKRAKDALKVQANI\n+KNVKY\n+>99842at2157_4\n+VPRALGIEKRRHLHMPENIMGVDCLYNNKVVAQTIDGDATPAPLHTESIVADTRLKPYKV\n+SLIETDENIEALLMTSMKQAVEINEEIDVMLIEEDTDRTIGTKGRTIEGARNLLAKFQTI\n+DVAII\n+>99842at2157_5\n+FTLKLATNDIRDMQLFDDLTSAADCIINEEGTVVVKPQTIALAIGTGLHQIQRVENLDKD\n+VEIAEDAVNLCEPGVPKEVEHNRMTSQNLTEQKYVLIKKRVGYHHNWQNISLYNDLALRQ\n+DNLSAIAI\n+>99842at2157_6\n+LGLTKAEMMYLSYFEKVTGIEMRAEERQIIVVKGRDLGEATGQPAGEHVENLKARRADML\n+LIEDSKTVQDILPSLSYREVSMITKNLQKGRVHRYAAAGRQNSNAEKAAQLYNFYHGIKI\n+IVL\n+>99842at2157_7\n+ESASRRTELSYVAQFSAATADDCFNLKKKMVNVPEGKMGMDVQRDGDCSNGMKEISKILG\n+LVEESKEEGSFLGQSESNICAQFDKLDKYQIVVNIAVAIGFVYGADKTNAERQVPEHHFN\n+IAAMSG\n+>99842at2157_8\n+GTREMRPAAIQLLDVFEISTGVECIVVQNLVVAVKKGWFGAEISKTEKDVQAIQGFKRQM\n+DVKYQNRDNKTLNTKLFSSATTPEITDILVVGISVKRAIKRNQKSLLLLRTLVFRKFGGT\n+AIEV\n+>99842at2157_9\n+VANELTNETLAYIAIREKASMAACIGDKAVELVGESAMGLATQKGGEEITREVQYGARRI\n+PLIKDELAWVLVVMEQLHEAIDVSMKKRSYTEIKRREYIGKLGKTVQLALEVTLRHIKVK\n+DIVL\n'

diff -r f9f2ad782d8f -r f89e3c318453 test-data/test-db/busco_downloads_odb10/dataset.cfg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-db/busco_downloads_odb10/dataset.cfg Wed Jun 07 12:02:03 2023 +0000

@@ -0,0 +1,8 @@
+name=archaea_odb10
+domain=prokaryota
+creation_date=2021-02-23
+number_of_BUSCOs=194
+number_of_species=404
+prodigal_genetic_code=11
+ambiguous_cd_range_lower=0.73
+ambiguous_cd_range_upper=0.8

diff -r f9f2ad782d8f -r f89e3c318453 test-data/test-db/busco_downloads_odb10/hmms/39322at2157.hmm
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-db/busco_downloads_odb10/hmms/39322at2157.hmm Wed Jun 07 12:02:03 2023 +0000

[

b'@@ -0,0 +1,1240 @@\n+HMMER3/f [3.1b1 | May 2013]\n+NAME 39322at2157\n+LENG 406\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Thu Dec 6 15:59:51 2018\n+NSEQ 384\n+EFFN 2.358398\n+CKSUM 1247492646\n+STATS LOCAL MSV -11.4327 0.69916\n+STATS LOCAL VITERBI -12.1946 0.69916\n+STATS LOCAL FORWARD -5.9046 0.69916\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 2.41786 4.46430 3.02322 2.54513 3.52862 3.02262 3.53279 2.86391 2.69723 2.45638 3.48630 3.11298 3.51174 3.07257 2.83553 2.64023 2.73629 2.64638 4.71786 3.54286\n+ 2.68623 4.42276 2.77457 2.73146 3.46387 2.40552 3.72492 3.29405 2.67785 2.69282 4.24386 2.90381 2.73712 3.18190 2.89773 2.37873 2.77493 2.98556 4.58528 3.61550\n+ 0.49689 1.02480 3.42009 1.44212 0.26975 0.00000 *\n+ 1 2.35947 4.84624 2.72457 2.57013 4.05157 3.43058 3.49364 3.44990 2.68492 3.06370 1.85441 3.16629 4.01991 2.87515 3.11656 2.73962 3.00252 3.15957 5.09845 3.02526 7 m - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01340 4.71497 5.43732 0.61958 0.77255 0.49638 0.93837\n+ 2 1.42459 4.44396 3.66937 3.18079 3.53219 3.69136 3.94575 2.62268 3.12546 2.58431 3.36475 3.55907 3.35331 3.22299 3.45392 2.71137 2.91382 2.49449 4.52183 3.45693 8 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01320 4.72965 5.45199 0.61958 0.77255 0.48235 0.96058\n+ 3 3.22668 4.54820 5.06478 4.50557 3.74407 4.53626 4.96115 1.24326 4.36204 2.39516 3.44599 4.63044 4.85165 3.86170 4.47887 3.87486 3.18031 1.08901 5.47408 4.28724 9 v - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01307 4.73942 5.46176 0.61958 0.77255 0.49541 0.93987\n+ 4 2.76589 2.96464 3.52202 2.97146 3.89140 3.38833 2.03638 3.27357 2.92518 2.62713 3.82835 3.40470 4.10229 3.26083 3.27129 1.68146 2.99555 3.00847 5.28553 4.02382 10 s - - -\n+ 2.68618 4.42225 2.77520 2.73123 3.46354 2.40513 3.72495 3.29354 2.67741 2.69355 4.24690 2.90347 2.73736 3.18146 2.89801 2.37887 2.77520 2.98518 4.58477 3.61503\n+ 0.02007 4.15922 5.46176 0.56084 0.84567 0.49541 0.93987\n+ 5 2.68029 4.66343 4.07130 3.89425 4.90491 3.08353 4.92481 4.26068 3.94619 4.01471 4.88479 3.93472 0.55612 4.24355 4.18602 2.94074 3.26847 3.13277 6.27664 5.08709 12 P - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01307 4.73942 5.46176 0.61958 0.77255 0.49541 0.93987\n+ 6 3.47587 4.76147 5.33477 4.76421 2.76677 4.73346 5.03810 1.26459 4.60291 1.02520 3.19364 4.86139 4.95245 4.64276 4.61732 4.08494 3.69681 2.50596 5.31818 4.23710 13 l - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01307 4.73942 5.46176 0.61958 0.77255 0.49541 0.93987\n+ 7 3.06578 5.52597 1.11187 1.71304 3.60473 3.60032 3.96257 4.33136 2.83813 3.84120 4.62717 3.06745 4.10825 3.05234 '..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.08624 4.68438 2.61206 0.61958 0.77255 0.60447 0.79045\n+ 399 2.41536 5.15315 2.73641 1.91611 4.52707 3.28214 3.68011 3.91584 2.09583 3.46039 4.24087 2.68713 3.81884 2.68926 2.58816 2.41738 2.88265 3.43413 5.55114 4.12144 439 e - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.09262 4.61300 2.54415 0.61958 0.77255 0.72300 0.66416\n+ 400 2.49313 5.04927 2.90619 2.15794 4.12936 3.41264 3.50399 3.79823 2.00398 3.26623 4.06381 2.79606 3.79891 2.64220 2.85156 2.45584 2.82442 3.46780 4.94516 2.93406 440 k - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.04037 4.53642 3.54558 0.61958 0.77255 0.82857 0.57389\n+ 401 2.12809 3.39591 4.00404 3.29124 3.21570 3.62587 3.63853 2.45194 3.24696 1.97301 3.31175 3.68653 4.11946 3.57086 3.50316 2.65851 2.77254 2.09461 4.76543 3.36150 441 l - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02172 4.51248 4.55533 0.61958 0.77255 0.85791 0.55173\n+ 402 2.63622 5.13022 2.80732 1.99635 4.49821 3.27667 3.61587 3.99163 1.90693 3.48335 4.21163 2.86830 3.54117 2.68330 2.34531 2.56063 2.78993 3.56744 5.53367 4.06536 442 k - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01925 4.50729 4.82319 0.61958 0.77255 0.86408 0.54721\n+ 403 2.56463 5.13688 2.76372 1.97435 4.50106 3.30231 3.60918 3.95408 2.05992 3.46084 4.17999 2.57115 3.29432 2.70494 2.55229 2.54205 2.90385 3.53107 5.54477 3.81944 443 e - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03518 4.50460 3.75030 0.61958 0.77255 0.86725 0.54491\n+ 404 2.40502 4.28609 3.56245 3.11109 3.21710 3.62353 3.95859 2.61695 2.74278 2.13722 3.21020 3.34030 4.02563 3.16547 3.22103 2.94760 2.56715 2.15214 3.40475 3.59708 444 l - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.07021 4.48629 2.87277 0.61958 0.77255 0.88831 0.52993\n+ 405 2.54124 3.38917 4.08084 3.04228 2.80453 3.72041 4.04556 2.23712 3.18554 1.85274 3.16718 3.62123 4.07186 3.53561 3.43525 2.89805 2.83749 2.27783 4.72308 3.13928 445 l - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.11229 4.43387 2.36080 0.61958 0.77255 0.94432 0.49257\n+ 406 2.57379 5.05954 2.83396 2.14477 4.36035 3.04647 3.60244 3.74191 1.99981 3.15106 4.13153 2.77626 3.79154 2.62842 2.57162 2.38896 2.86342 3.43143 5.38651 4.08129 446 k - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01319 4.33477 * 0.61958 0.77255 0.00000 *\n+//\n'

diff -r f9f2ad782d8f -r f89e3c318453 test-data/test-db/busco_downloads_odb10/info/ogs.id.info
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-db/busco_downloads_odb10/info/ogs.id.info Wed Jun 07 12:02:03 2023 +0000

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No newline at end of file\n'

diff -r f9f2ad782d8f -r f89e3c318453 test-data/test-db/busco_downloads_odb10/info/species.info
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-db/busco_downloads_odb10/info/species.info Wed Jun 07 12:02:03 2023 +0000

b'@@ -0,0 +1,404 @@\n+1198449\tAeropyrum camini SY1 = JCM 12091\n+588898\tHaloterrigena daqingensis\n+859350\tCandidatus Nitrosopumilus salaria BD31\n+933801\tAcidianus hospitalis W1\n+1932360\tHalorientalis sp. IM1011\n+267377\tMethanococcus maripaludis S2\n+694430\tNatronococcus occultus SP4\n+1227497\tNatronococcus amylolyticus DSM 10524\n+1448860\tHalobellus rufus\n+163003\tThermococcus cleftensis\n+1379702\tMethanobacterium sp. MB1\n+1227487\tHalogeometricum pallidum JCM 14848\n+593117\tThermococcus gammatolerans EJ3\n+593750\tMethanoregula formicica SMSP\n+1873524\tHalodesulfurarchaeum formicicum\n+302484\tHaloferax larsenii\n+410358\tMethanocorpusculum labreanum Z\n+1227493\tNatrialba hulunbeirensis JCM 10989\n+797299\tHalostagnicola larsenii XH-48\n+572546\tArchaeoglobus profundus DSM 5631\n+268739\tNatronomonas moolapensis 8.8.11\n+523845\tMethanothermococcus thermolithotrophicus DSM 2095\n+1353158\tMethanococcoides vulcani\n+1898749\tCandidatus Nitrosomarinus catalina\n+273063\tSulfurisphaera tokodaii str. 7\n+429572\tSulfolobus islandicus L.S.2.15\n+553468\tHaladaptatus litoreus\n+1480675\tHalolamina sediminis\n+553469\tHalogeometricum rufum\n+224325\tArchaeoglobus fulgidus DSM 4304\n+1036679\tMethanosarcina spelaei\n+391623\tThermococcus barophilus MP\n+558529\tNatronoarchaeum philippinense\n+523843\tMethanohalophilus portucalensis FDF-1\n+1194088\tHalorubrum sp. T3\n+937775\tMethanoplanus limicola DSM 2279\n+29284\tHalorubrum trapanicum\n+1495314\tMethanoculleus sp. MH98A\n+1434104\tMethanococcoides methylutens MM1\n+1419722\tHalorubrum sp. SD626R\n+2016361\tThermococcus sp. EXT12c\n+28892\tMethanofollis liminatans DSM 4140\n+2008440\tThermococcus sp. 5-4\n+931277\tHalococcus morrhuae DSM 1307\n+113653\tGeoglobus ahangari\n+118126\tMethanoculleus chikugoensis\n+662477\tHaloarcula vallismortis ATCC 29715\n+1604004\tHalanaeroarchaeum sulfurireducens\n+1765057\tHalobacterium sp. CBA1132\n+1227468\tHalorubrum distributum JCM 10118\n+1853690\tHalolamina sp. CBA1230\n+1927129\tMethanonatronarchaeum thermophilum\n+1544718\tHaloferax sp. SB29\n+582419\tThermococcus paralvinellae\n+640943\tNatronorubrum sediminis\n+1860098\tMethanosarcina sp. A14\n+323259\tMethanospirillum hungatei JF-1\n+1202768\tHalopiger salifodinae\n+1392998\tCandidatus Methanoperedens nitroreducens\n+890420\tHalovenus aranensis\n+392421\tHaloterrigena hispanica\n+1114856\tNatronorubrum tibetense GA33\n+662479\tHaloferax mucosum ATCC BAA-1512\n+1227491\tNatrialba aegyptia DSM 13077\n+634497\tHaloarcula hispanica ATCC 33960\n+1609559\tPyrococcus kukulkanii\n+413816\tHalorubrum halophilum\n+768672\tDesulfurococcus amylolyticus DSM 16532\n+521011\tMethanosphaerula palustris E1-9c\n+1227453\tHaloarcula japonica DSM 6131\n+1869245\tNatrialba sp. SSL1\n+1897478\tHaladaptatus sp. W1\n+483214\tMethanobrevibacter smithii DSM 2375\n+444158\tMethanococcus maripaludis C6\n+1048396\tHalopenitus persicus\n+1932004\tHaloarcula taiwanensis\n+1042877\tThermococcus sp. 4557\n+2209\tMethanosarcina mazei\n+755307\tSalinigranum rubrum\n+589924\tFerroglobus placidus DSM 10642\n+83986\tMethanoculleus bourgensis\n+44930\tNatronobacterium gregoryi\n+1048396\tHalopenitus persicus\n+699433\tHalobellus limi\n+797209\tHaladaptatus paucihalophilus DX253\n+660518\tHalorientalis regularis\n+1227488\tHaloterrigena salina JCM 13891\n+1476858\tHaloferax massiliensis\n+1041930\tMethanocella conradii HZ254\n+384616\tPyrobaculum islandicum DSM 4184\n+1324957\tCandidatus Halobonum tyrrellensis G22\n+1227465\tHalorubrum californiensis DSM 19288\n+1712654\tThermococcus piezophilus\n+339860\tMethanosphaera stadtmanae DSM 3091\n+877455\tMethanobacterium lacus\n+926571\tNitrososphaera viennensis EN76\n+1434103\tMethanosarcina sp. WWM596\n+1434107\tMethanosarcina barkeri 3\n+1236689\tCandidatus Methanomethylophilus alvus Mx1201\n+1434115\tMethanosarcina mazei SarPi\n+1367881\tHalorientalis persicus\n+374847\tCandidatus Korarchaeum cryptofilum OPF8\n+397948\tCaldivirga maquilingensis IC-167\n+859192\tCandidatus Nitrosarchaeum limnium BG20\n+911122\tMethanobrevibacter smithii TS146E\n+1874706\tMethanolobus psychrotolerans\n+1227500\tNatronorubrum bangense JCM 10635\n+644295\tMethanohalobium evestigatum Z-7303\n+'..b'077256\tMethanosphaera cuniculi\n+1227489\tHaloterrigena thermotolerans DSM 11522\n+43687\tMetallosphaera sedula\n+1230457\tHaloterrigena limicola JCM 13563\n+415426\tHyperthermus butylicus DSM 5456\n+1227481\tHalorubrum hochstenium ATCC 700873\n+59277\tMethanobacterium subterraneum\n+604354\tThermococcus sibiricus MM 739\n+1293039\tMethanobrevibacter arboriphilus JCM 9315\n+1608465\tNatrinema sp. CBA1119\n+1008153\tHalalkalicoccus paucihalophilus\n+1230453\tHaloferax elongans ATCC BAA-1513\n+1650354\tCaldivirga sp. MU80\n+195522\tThermococcus nautili\n+186497\tPyrococcus furiosus DSM 3638\n+55758\tMethanobrevibacter filiformis\n+227598\tThermococcus celericrescens\n+1056495\tCaldisphaera lagunensis DSM 15908\n+1227454\tHalobiforma nitratireducens JCM 10879\n+230361\tMethanobrevibacter millerae\n+699431\tHalolamina pelagica\n+2035255\tCandidatus Methanoperedens sp. BLZ2\n+1227485\tHalorubrum tebenquichense DSM 14210\n+1151117\tThermococcus zilligii AN1\n+528314\tMethanoculleus horonobensis\n+572478\tVulcanisaeta distributa DSM 14429\n+1232219\tHalococcus agarilyticus\n+387957\tMethanobrevibacter sp. 87.7\n+1027374\tNitrosopumilus sp. SJ\n+1550241\tThermofilum uzonense\n+188937\tMethanosarcina acetivorans C2A\n+2177\tMethanohalophilus halophilus\n+588319\tPalaeococcus ferrophilus DSM 13482\n+1333523\tSalinarchaeum sp. Harcht-Bsk1\n+277988\tThermococcus thioreducens\n+1457250\tHalapricum salinum\n+1432656\tThermococcus guaymasensis DSM 11113\n+118062\tMethanobacterium congolense\n+1230454\tHalorubrum aidingense JCM 13560\n+1434120\tMethanosarcina siciliae T4/M\n+456320\tMethanococcus voltae A3\n+1544719\tHaloferax sp. SB3\n+1227482\tHalorubrum lipolyticum DSM 21995\n+2226\tMethanococcoides methylutens\n+1416969\tHaloterrigena mahii\n+1401244\tMethanobrevibacter arboriphilus ANOR1\n+1227455\tHalococcus saccharolyticus DSM 5350\n+565033\tGeoglobus acetivorans\n+1577791\tCandidatus Methanoplasma termitum\n+523844\tMethanosarcina thermophila TM-1\n+765177\tDesulfurococcus mucosus DSM 2162\n+1227466\tHalorubrum coriense DSM 10284\n+1227498\tNatronococcus jeotgali DSM 18795\n+355548\tHalobacterium jilantaiense\n+148448\tHalobiforma haloterrestris\n+1230460\tNatronorubrum sulfidifaciens JCM 14089\n+1985678\tHaloferacaceae archaeon SYSU A9-0\n+71998\tThermococcus pacificus\n+1410664\tMethanobrevibacter wolinii SH\n+756883\thalophilic archaeon DL31\n+1175296\tMethanomassiliicoccus luminyensis B10\n+49547\tMethanobrevibacter curvatus\n+1434100\tMethanosarcina sp. MTP4\n+1365176\tThermofilum adornatus\n+399550\tStaphylothermus marinus F1\n+72803\tThermococcus siculi\n+619731\tHalostagnicola kamekurae\n+190974\tMethanobrevibacter gottschalkii\n+301967\tHaloterrigena saccharevitans\n+768679\tThermoproteus tenax Kra 1\n+2200\tMethanoculleus thermophilus\n+990316\tMethanothrix soehngenii GP6\n+573063\tMethanocaldococcus infernus ME\n+63740\tHalorubrum vacuolatum\n+485914\tHalomicrobium mukohataei DSM 12286\n+387631\tArchaeoglobus sulfaticallidus PM70-1\n+866790\tMethanothermobacter sp. CaT2\n+145261\tMethanothermobacter wolfeii\n+1483596\tMethanosarcina sp. 2.H.T.1A.15\n+2045011\tCandidatus Nitrosocaldus islandicus\n+1674923\tThermococcus sp. 2319x1\n+1514971\tHaloprofundus marisrubri\n+553467\tHalopelagius inordinatus\n+348780\tNatronomonas pharaonis DSM 2160\n+867904\tMethanomethylovorans hollandica DSM 15978\n+51203\tMethanohalophilus euhalobius\n+406552\tNatrinema sp. J7-2\n+797210\tHalopiger xanaduensis SH-6\n+1236180\tHalopelagius longus\n+43928\tHalobaculum gomorrense\n+882090\tMethanolinea tarda NOBI-1\n+579137\tMethanocaldococcus vulcanius M7\n+1273541\tPyrodictium delaneyi\n+1293048\tHalopiger goleimassiliensis\n+38026\tMethanolobus vulcani\n+1526048\tHaloferax sp. Q22\n+507754\tAcidiplasma aeolicum\n+1846278\tCandidatus Nitrosotenuis aquarius\n+351160\tMethanocella arvoryzae MRE50\n+70601\tPyrococcus horikoshii OT3\n+1561964\tMethanosphaera sp. WGK6\n+2032630\tHalorubrum sp. WN019\n+1758255\tHalorubrum aethiopicum\n+386456\tMethanobacterium arcticum\n+666510\tAcidilobus saccharovorans 345-15\n+1410606\tCandidatus Nitrosopelagicus brevis\n+679926\tMethanolacinia petrolearia DSM 11571\n+222984\tNatrinema altunense\n+1855873\tHalorubrum sp. SD683\n'

diff -r f9f2ad782d8f -r f89e3c318453 test-data/test-db/busco_downloads_odb10/lengths_cutoff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-db/busco_downloads_odb10/lengths_cutoff Wed Jun 07 12:02:03 2023 +0000

@@ -0,0 +1,194 @@
+60366at2157 0 17.6 176.0
+41305at2157 0 39.2 392.0
+117241at2157 0 14.5 145.0
+84684at2157 0 18.5 185.0
+25871at2157 0 34.6 346.0
+116879at2157 0 13.8 138.0
+97230at2157 0 12.7 127.0
+44076at2157 0 20.8 208.0
+127293at2157 0 3.8 38.0
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+92795at2157 0 21.209015129780635 179
+62508at2157 0 19.0 190.0
+13010at2157 0 50.1 501.0
+98657at2157 0 17.7 177.0
+96138at2157 0 18.5 185.0
+114285at2157 0 12.4 124.0
+55024at2157 0 47.1 471.0
+64860at2157 0 20.8 208.0
+111803at2157 0 21.1 211.0
+117225at2157 0 13.5 135.0
+90096at2157 0 30.2 302.0
+22545at2157 0 30.0 300.0
+106603at2157 0 7.8 78.0
+119723at2157 0 4.8 48.0
+85293at2157 0 12.3 123.0
+37299at2157 0 40.7 407.0
+8922at2157 0 36.6 366.0
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+124429at2157 0 4.7 47.0
+129447at2157 0 5.0 50.0
+22842at2157 0 29.5 295.0
+107993at2157 0 9.4 94.0
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+14889at2157 0 51.7 517.0
+115808at2157 0 28.2 282.0
+75288at2157 0 13.9 139.0
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+70525at2157 0 18.3 183.0
+98187at2157 0 13.2 132.0
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+110798at2157 0 8.402604995150394 66
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+24257at2157 0 32.57467713832944 323
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+80629at2157 0 14.2 142.0
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+115384at2157 0 5.7 57.0
+76134at2157 0 25.8 258.0
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+113971at2157 0 7.5 75.0
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+87520at2157 0 26.2 262.0
+105851at2157 0 32.2 322.0
+115947at2157 0 8.6 86.0
+50844at2157 0 20.5 205.0
+104702at2157 0 18.534659571185585 111
+18705at2157 0 36.3 363.0
+88531at2157 0 10.8 108.0
+29893at2157 0 27.9 279.0
+89321at2157 0 16.2 162.0
+124805at2157 0 9.1 91.0
+25592at2157 0 35.2 352.0
+91297at2157 0 31.314905455218828 176
+121943at2157 0 4.067844733953197 35
+17629at2157 0 34.2 342.0
+109335at2157 0 13.6 136.0
+80498at2157 0 16.3 163.0
+21317at2157 0 31.5 315.0
+35648at2157 0 27.6 276.0
+99734at2157 0 18.4 184.0
+47919at2157 0 34.4 344.0
+115425at2157 0 11.7 117.0
+74812at2157 0 19.7 197.0
+36028at2157 0 24.5 245.0
+116732at2157 0 9.148472525998754 89
+60954at2157 0 18.8 188.0
+98221at2157 0 9.8 98.0
+95578at2157 0 21.989222174276406 218
+103467at2157 0 10.6 106.0
+19750at2157 0 59.6 596.0
+66811at2157 0 30.6 306.0
+99236at2157 0 11.2 112.0
+128227at2157 0 4.7 47.0
+104636at2157 0 18.356482806722777 181
+122290at2157 0 9.30936849179749 46
+59861at2157 0 19.8 198.0
+3905at2157 0 70.2 702.0
+123859at2157 0 5.1 51.0
+61613at2157 0 35.1 351.0
+85279at2157 0 17.59972006309375 100
+116294at2157 0 9.8 98.0
+107015at2157 0 9.9 99.0
+126193at2157 0 4.5 45.0
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+58340at2157 0 15.2 152.0
+59314at2157 0 18.7 187.0
+10236at2157 0 40.8 408.0
+107212at2157 0 8.5 85.0
+61936at2157 0 31.3 313.0
+860at2157 0 53.5 535.0
+130316at2157 0 11.695174826871927 69
+80501at2157 0 17.2 172.0
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+112720at2157 0 8.6 86.0
+82104at2157 0 13.0 130.0
+123853at2157 0 3.7 37.0
+76877at2157 0 20.1 201.0
+48934at2157 0 12.9 129.0
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+14454at2157 0 33.1 331.0
+60670at2157 0 18.2 182.0
+105421at2157 0 19.505798515174902 86
+91936at2157 0 11.6 116.0
+84219at2157 0 11.5 115.0
+7046at2157 0 42.2 422.0
+73593at2157 0 24.4 244.0
+128960at2157 0 10.166161586727076 66
+108717at2157 0 16.5 165.0
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+79065at2157 0 13.1 131.0
+7896at2157 0 43.9 439.0
+94875at2157 0 33.3 333.0
+56027at2157 0 28.5 285.0
+106462at2157 0 12.1 121.0
+98179at2157 0 12.1 121.0
+22747at2157 0 40.0 400.0
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+66209at2157 0 25.2 252.0
+23182at2157 0 27.8 278.0
+13565at2157 0 44.2 442.0
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+51351at2157 0 24.9 249.0
+125788at2157 0 16.601454136449775 93
+70865at2157 0 22.6 226.0
+94889at2157 0 14.9 149.0
+129924at2157 0 2.6 26.0
+23221at2157 0 32.4 324.0
+130364at2157 0 4.2284353073265555 33
+112466at2157 0 9.5 95.0
+58022at2157 0 35.9 359.0
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+69351at2157 0 55.6 556.0
+104786at2157 0 11.2 112.0
+13531at2157 0 33.9 339.0
+124073at2157 0 11.002723345792045 60
+70269at2157 0 18.9 189.0
+46017at2157 0 35.3 353.0
+32191at2157 0 34.8 348.0
+91154at2157 0 11.6 116.0
+32623at2157 0 36.5 365.0
+39322at2157 0 39.9 399.0
+102399at2157 0 11.8 118.0
+105095at2157 0 10.0 100.0
+65833at2157 0 22.3 223.0
+35861at2157 0 54.6 546.0
+93256at2157 0 12.8 128.0
+87367at2157 0 10.3 103.0
+83050at2157 0 14.1 141.0
+99842at2157 0 12.3 123.0
+30130at2157 0 25.0 250.0
+129321at2157 0 8.590937512754035 65
+102178at2157 0 14.68516161106274 103
+58019at2157 0 28.5 285.0
+90882at2157 0 17.6 176.0
+14061at2157 0 45.7 457.0
+31316at2157 0 26.0 260.0
+8899at2157 0 41.2 412.0
+114541at2157 0 10.633454828794354 90
+6590at2157 0 39.2 392.0
+43727at2157 0 26.0 260.0
+93236at2157 0 15.8 158.0
+102360at2157 0 22.3 223.0
+89943at2157 0 18.6 186.0
+124913at2157 0 8.2 82.0
+78046at2157 0 16.5 165.0
+37207at2157 0 184.3175766058845 397
+82755at2157 0 32.7 327.0
+7724at2157 0 35.7 357.0
+72726at2157 0 19.4 194.0

diff -r f9f2ad782d8f -r f89e3c318453 test-data/test-db/busco_downloads_odb10/links_to_ODB10.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-db/busco_downloads_odb10/links_to_ODB10.txt Wed Jun 07 12:02:03 2023 +0000

b'@@ -0,0 +1,194 @@\n+60366at2157\tK Homology domain\thttps://www.orthodb.org/v10?query=60366at2157\n+41305at2157\tBifunctional NAD(P)H-hydrate repair enzyme\thttps://www.orthodb.org/v10?query=41305at2157\n+117241at2157\tDNA-directed RNA polymerase\thttps://www.orthodb.org/v10?query=117241at2157\n+84684at2157\tTranslation initiation factor 2 subunit alpha\thttps://www.orthodb.org/v10?query=84684at2157\n+25871at2157\tsignal recognition particle protein\thttps://www.orthodb.org/v10?query=25871at2157\n+116879at2157\tPeptidyl-prolyl cis-trans isomerase\thttps://www.orthodb.org/v10?query=116879at2157\n+97230at2157\tRibosomal protein L5\thttps://www.orthodb.org/v10?query=97230at2157\n+44076at2157\tserine protein kinase RIO\thttps://www.orthodb.org/v10?query=44076at2157\n+127293at2157\tRibosomal protein L40e\thttps://www.orthodb.org/v10?query=127293at2157\n+52427at2157\tthreonylcarbamoyl-AMP synthase\thttps://www.orthodb.org/v10?query=52427at2157\n+92795at2157\ttRNA pseudouridine(13) synthase TruD\thttps://www.orthodb.org/v10?query=92795at2157\n+62508at2157\tPhosphoribosylformylglycinamidine cyclo-ligase\thttps://www.orthodb.org/v10?query=62508at2157\n+13010at2157\tribosome biogenesis/translation initiation ATPase RLI\thttps://www.orthodb.org/v10?query=13010at2157\n+98657at2157\tRibose-5-phosphate isomerase A\thttps://www.orthodb.org/v10?query=98657at2157\n+96138at2157\t30S ribosomal protein S3Ae\thttps://www.orthodb.org/v10?query=96138at2157\n+114285at2157\t30S ribosomal protein S11\thttps://www.orthodb.org/v10?query=114285at2157\n+55024at2157\tPhenylalanine--tRNA ligase beta subunit\thttps://www.orthodb.org/v10?query=55024at2157\n+64860at2157\ttRNA (adenine-N1)-methyltransferase\thttps://www.orthodb.org/v10?query=64860at2157\n+111803at2157\tRibonuclease Z\thttps://www.orthodb.org/v10?query=111803at2157\n+117225at2157\tOrotate phosphoribosyltransferase\thttps://www.orthodb.org/v10?query=117225at2157\n+90096at2157\tProtein pelota homolog\thttps://www.orthodb.org/v10?query=90096at2157\n+22545at2157\ttRNA-splicing ligase RtcB\thttps://www.orthodb.org/v10?query=22545at2157\n+106603at2157\t50S ribosomal protein L44e\thttps://www.orthodb.org/v10?query=106603at2157\n+119723at2157\tTranscription elongation factor Spt4\thttps://www.orthodb.org/v10?query=119723at2157\n+85293at2157\t30S ribosomal protein S12\thttps://www.orthodb.org/v10?query=85293at2157\n+37299at2157\tAmidophosphoribosyltransferase\thttps://www.orthodb.org/v10?query=37299at2157\n+8922at2157\tGlutamate--tRNA ligase\thttps://www.orthodb.org/v10?query=8922at2157\n+104254at2157\t50S ribosomal protein L18e\thttps://www.orthodb.org/v10?query=104254at2157\n+124429at2157\t50S ribosomal protein L37e\thttps://www.orthodb.org/v10?query=124429at2157\n+129447at2157\t30S ribosomal protein S27e\thttps://www.orthodb.org/v10?query=129447at2157\n+22842at2157\tDNA topoisomerase VI subunit A\thttps://www.orthodb.org/v10?query=22842at2157\n+107993at2157\tRibosomal protein S10\thttps://www.orthodb.org/v10?query=107993at2157\n+124973at2157\tCDP-archaeol synthase\thttps://www.orthodb.org/v10?query=124973at2157\n+14889at2157\tV-type ATP synthase subunit I\thttps://www.orthodb.org/v10?query=14889at2157\n+115808at2157\tGeranylgeranyl reductase\thttps://www.orthodb.org/v10?query=115808at2157\n+75288at2157\ttranscription factor\thttps://www.orthodb.org/v10?query=75288at2157\n+131584at2157\t50S ribosomal protein L39e\thttps://www.orthodb.org/v10?query=131584at2157\n+70525at2157\tTranslation initiation factor 6\thttps://www.orthodb.org/v10?query=70525at2157\n+98187at2157\t50S ribosomal protein L11\thttps://www.orthodb.org/v10?query=98187at2157\n+82853at2157\tMethionine aminopeptidase\thttps://www.orthodb.org/v10?query=82853at2157\n+101957at2157\taspartate carbamoyltransferase regulatory subunit\thttps://www.orthodb.org/v10?query=101957at2157\n+121171at2157\t50S ribosomal protein L15\thttps://www.orthodb.org/v10?query=121171at2157\n+79845at2157\tFAD synthase\thttps://www.orthodb.org/v10?query=79845at2157\n+125162at2157\t50S ribosomal protein L24\thttps://www.orthodb.org/v10?query=125162at2157\n+110798at2157\tadenylate kinase\thttps://www.or'..b"10?query=130364at2157\n+112466at2157\tDUF655 domain-containing protein\thttps://www.orthodb.org/v10?query=112466at2157\n+58022at2157\tPhosphoribosylamine--glycine ligase\thttps://www.orthodb.org/v10?query=58022at2157\n+17053at2157\ttranslation initiation factor IF-2\thttps://www.orthodb.org/v10?query=17053at2157\n+85023at2157\tRibosomal protein L15e\thttps://www.orthodb.org/v10?query=85023at2157\n+90817at2157\tphosphoribosylformylglycinamidine synthase I\thttps://www.orthodb.org/v10?query=90817at2157\n+90641at2157\tSignal recognition particle receptor FtsY\thttps://www.orthodb.org/v10?query=90641at2157\n+69351at2157\tDUF814 domain-containing protein\thttps://www.orthodb.org/v10?query=69351at2157\n+104786at2157\texosome subunit\thttps://www.orthodb.org/v10?query=104786at2157\n+13531at2157\tProtein translocase subunit SecY\thttps://www.orthodb.org/v10?query=13531at2157\n+124073at2157\tElongation factor 1-beta\thttps://www.orthodb.org/v10?query=124073at2157\n+70269at2157\tRibosomal protein L1\thttps://www.orthodb.org/v10?query=70269at2157\n+46017at2157\tPhosphoglycerate kinase\thttps://www.orthodb.org/v10?query=46017at2157\n+32191at2157\tpeptide chain release factor 1\thttps://www.orthodb.org/v10?query=32191at2157\n+91154at2157\t30S ribosomal protein S8\thttps://www.orthodb.org/v10?query=91154at2157\n+32623at2157\tglycine--tRNA ligase\thttps://www.orthodb.org/v10?query=32623at2157\n+39322at2157\tAdenylosuccinate lyase\thttps://www.orthodb.org/v10?query=39322at2157\n+102399at2157\tRNA 2',3'-cyclic phosphodiesterase\thttps://www.orthodb.org/v10?query=102399at2157\n+105095at2157\tTIGR00270 family protein\thttps://www.orthodb.org/v10?query=105095at2157\n+65833at2157\t50S ribosomal protein L4\thttps://www.orthodb.org/v10?query=65833at2157\n+35861at2157\tGlutamyl-tRNA(Gln) amidotransferase subunit E\thttps://www.orthodb.org/v10?query=35861at2157\n+93256at2157\t30S ribosomal protein S4\thttps://www.orthodb.org/v10?query=93256at2157\n+87367at2157\t50S ribosomal protein L13\thttps://www.orthodb.org/v10?query=87367at2157\n+83050at2157\ttRNA (cytidine(56)-2'-O)-methyltransferase\thttps://www.orthodb.org/v10?query=83050at2157\n+99842at2157\tProbable transcription termination protein NusA\thttps://www.orthodb.org/v10?query=99842at2157\n+30130at2157\tDNA repair and recombination protein RadA\thttps://www.orthodb.org/v10?query=30130at2157\n+129321at2157\tDNA-directed RNA polymerase subunit L\thttps://www.orthodb.org/v10?query=129321at2157\n+102178at2157\tDNA-binding protein\thttps://www.orthodb.org/v10?query=102178at2157\n+58019at2157\ttRNA(Ile2) 2-agmatinylcytidine synthetase TiaS\thttps://www.orthodb.org/v10?query=58019at2157\n+90882at2157\tMevalonate kinase\thttps://www.orthodb.org/v10?query=90882at2157\n+14061at2157\tCTP synthase\thttps://www.orthodb.org/v10?query=14061at2157\n+31316at2157\tDihydroorotate dehydrogenase\thttps://www.orthodb.org/v10?query=31316at2157\n+8899at2157\tV-type ATP synthase beta chain\thttps://www.orthodb.org/v10?query=8899at2157\n+114541at2157\t50S ribosomal protein L7Ae\thttps://www.orthodb.org/v10?query=114541at2157\n+6590at2157\tMethionine--tRNA ligase\thttps://www.orthodb.org/v10?query=6590at2157\n+43727at2157\tOrnithine carbamoyltransferase\thttps://www.orthodb.org/v10?query=43727at2157\n+93236at2157\tV-type ATP synthase subunit D\thttps://www.orthodb.org/v10?query=93236at2157\n+102360at2157\tDiphthine synthase\thttps://www.orthodb.org/v10?query=102360at2157\n+89943at2157\tRibosomal protein S4e\thttps://www.orthodb.org/v10?query=89943at2157\n+124913at2157\tribonuclease P\thttps://www.orthodb.org/v10?query=124913at2157\n+78046at2157\tPyridoxal 5'-phosphate synthase subunit PdxT\thttps://www.orthodb.org/v10?query=78046at2157\n+37207at2157\tReplication factor C small subunit\thttps://www.orthodb.org/v10?query=37207at2157\n+82755at2157\tCCA-adding enzyme\thttps://www.orthodb.org/v10?query=82755at2157\n+7724at2157\ttRNA uridine(34) 5-carboxymethylaminomethyl modification radical SAM/GNAT enzyme Elp3\thttps://www.orthodb.org/v10?query=7724at2157\n+72726at2157\tDNA-directed RNA polymerase subunit D\thttps://www.orthodb.org/v10?query=72726at2157\n"

diff -r f9f2ad782d8f -r f89e3c318453 test-data/test-db/busco_downloads_odb10/scores_cutoff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-db/busco_downloads_odb10/scores_cutoff Wed Jun 07 12:02:03 2023 +0000

@@ -0,0 +1,194 @@
+60366at2157 126.91
+41305at2157 67.69
+117241at2157 50.33
+84684at2157 89.94999999999999
+25871at2157 198.72999999999996
+116879at2157 50.26
+97230at2157 85.25999999999999
+44076at2157 123.96999999999998
+127293at2157 29.959999999999997
+52427at2157 63.699999999999996
+92795at2157 41.3
+62508at2157 32.230000000000004
+13010at2157 311.36
+98657at2157 24.709999999999997
+96138at2157 76.44
+114285at2157 84.63
+55024at2157 218.47
+64860at2157 54.04
+111803at2157 80.91999999999999
+117225at2157 37.07
+90096at2157 126.17
+22545at2157 140.14
+106603at2157 32.199999999999996
+119723at2157 18.2
+85293at2157 117.17999999999999
+37299at2157 248.70999999999998
+8922at2157 206.85
+104254at2157 27.929999999999996
+124429at2157 30.799999999999997
+129447at2157 39.129999999999995
+22842at2157 125.16
+107993at2157 69.58
+124973at2157 58.309999999999995
+14889at2157 31.919999999999998
+115808at2157 36.75
+75288at2157 43.12
+131584at2157 16.66
+70525at2157 87.21999999999998
+98187at2157 66.22
+82853at2157 118.64999999999999
+101957at2157 91.56
+121171at2157 50.903630054563365
+79845at2157 68.11
+125162at2157 30.799999999999997
+110798at2157 12.32
+108145at2157 47.53
+32079at2157 18.2
+24257at2157 203.9850527110197
+57545at2157 154.21
+6736at2157 648.2752139468217
+105165at2157 37.79399483597369
+119044at2157 29.749999999999996
+80629at2157 76.58
+121548at2157 49.559999999999995
+92409at2157 77.84
+24288at2157 220.01
+123463at2157 15.329999999999998
+123503at2157 20.02
+115384at2157 26.109999999999996
+76134at2157 61.04
+59062at2157 138.25
+113971at2157 37.87
+63341at2157 143.07999999999998
+87520at2157 60.55
+105851at2157 88.34
+115947at2157 35.42
+50844at2157 92.61
+104702at2157 13.72
+18705at2157 199.64
+88531at2157 37.309999999999995
+29893at2157 44.73
+89321at2157 66.78
+124805at2157 28.77
+25592at2157 180.10999999999999
+91297at2157 35.629999999999995
+121943at2157 12.67
+17629at2157 116.61999999999999
+109335at2157 55.44
+80498at2157 110.53
+21317at2157 146.85999999999999
+35648at2157 178.01
+99734at2157 72.52
+47919at2157 97.16
+115425at2157 58.309999999999995
+74812at2157 128.66
+36028at2157 118.86
+116732at2157 31.359999999999996
+60954at2157 157.78
+98221at2157 67.34
+95578at2157 33.04
+103467at2157 64.05
+19750at2157 24.419999999999998
+66811at2157 187.32
+99236at2157 86.03
+128227at2157 20.929999999999996
+104636at2157 98.17393274503115
+122290at2157 19.46
+59861at2157 108.91999999999999
+3905at2157 540.9599999999999
+123859at2157 45.29
+61613at2157 241.01
+85279at2157 52.910000000000004
+116294at2157 41.37
+107015at2157 46.059999999999995
+126193at2157 24.709999999999997
+31722at2157 75.88
+58340at2157 88.55
+59314at2157 42.91
+10236at2157 227.85
+107212at2157 52.08
+61936at2157 35.98
+860at2157 198.58999999999997
+130316at2157 18.549999999999997
+80501at2157 72.52
+41214at2157 109.33999999999999
+112720at2157 21.56
+82104at2157 75.88
+123853at2157 21.560000000000002
+76877at2157 128.45
+48934at2157 31.849999999999998
+105604at2157 38.709999999999994
+14454at2157 160.23
+60670at2157 29.959999999999997
+105421at2157 21.419999999999998
+91936at2157 55.019999999999996
+84219at2157 34.089999999999996
+7046at2157 91.35
+73593at2157 51.38
+128960at2157 15.54
+108717at2157 86.73
+91632at2157 82.66999999999999
+79065at2157 57.33
+7896at2157 171.22
+94875at2157 47.459999999999994
+56027at2157 63.419999999999995
+106462at2157 58.86999999999999
+98179at2157 68.66999999999999
+22747at2157 175.0
+1642at2157 465.29
+66209at2157 119.35
+23182at2157 176.39999999999998
+13565at2157 36.54
+54988at2157 85.39999999999999
+51351at2157 186.27
+125788at2157 42.000314253135386
+70865at2157 48.3
+94889at2157 57.54
+129924at2157 30.213014428478537
+23221at2157 171.57
+130364at2157 15.26
+112466at2157 39.69
+58022at2157 98.0
+17053at2157 279.09
+85023at2157 105.48999999999998
+90817at2157 67.21000000000001
+90641at2157 176.0
+69351at2157 165.97
+104786at2157 36.19
+13531at2157 128.94
+124073at2157 13.929999999999998
+70269at2157 115.63999999999999
+46017at2157 100.58999999999999
+32191at2157 226.93999999999997
+91154at2157 73.99
+32623at2157 125.22999999999999
+39322at2157 200.68999999999997
+102399at2157 33.67
+105095at2157 35.699999999999996
+65833at2157 110.6
+35861at2157 533.4849414296743
+93256at2157 82.6
+87367at2157 43.82
+83050at2157 79.38
+99842at2157 53.9
+30130at2157 101.01
+129321at2157 23.54
+102178at2157 24.09
+58019at2157 80.64
+90882at2157 43.60999999999999
+14061at2157 330.82
+31316at2157 58.8
+8899at2157 352.52
+114541at2157 63.839999999999996
+6590at2157 122.57
+43727at2157 180.32
+93236at2157 50.54
+102360at2157 79.30999999999999
+89943at2157 81.89999999999999
+124913at2157 41.8
+78046at2157 102.48
+37207at2157 236.95
+82755at2157 148.32999999999998
+7724at2157 67.05999999999999
+72726at2157 102.68999999999998

diff -r f9f2ad782d8f -r f89e3c318453 test-data/test_01_short_report.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_01_short_report.tab Wed Jun 07 12:02:03 2023 +0000

@@ -0,0 +1,4 @@
+METRICS/TRANSCRIPTS transcriptome01
+Transcripts 1
+Transcripts > 500 bp 1
+Transcripts > 1000 bp 1

diff -r f9f2ad782d8f -r f89e3c318453 test-data/test_03_short_report.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_03_short_report.tab Wed Jun 07 12:02:03 2023 +0000

@@ -0,0 +1,6 @@
+METRICS/TRANSCRIPTS transcriptome01
+Genes 1
+Avg. number of exons per isoform 1.0
+Transcripts 1
+Transcripts > 500 bp 1
+Transcripts > 1000 bp 1

diff -r f9f2ad782d8f -r f89e3c318453 test-data/test_07_paralogs.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_07_paralogs.fasta Wed Jun 07 12:02:03 2023 +0000

@@ -0,0 +1,91 @@
+>STRG.1.1
+ATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAA
+GCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGA
+GAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATC
+AACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTG
+GCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTC
+TTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAA
+TAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGC
+CTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTT
+TCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGA
+GGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGA
+GTTTATTGCTGCCGTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCT
+CATCATGGAAGGCGCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAA
+AGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTAC
+TGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAGTGATGTAATGTCTAAA
+GGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGC
+AAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTT
+CGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCG
+CATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCA
+ACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTT
+TCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTTTATGTC
+CCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGCC
+ACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACG
+ATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTAT
+AACAACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTT
+AATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCT
+CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGAC
+ATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTC
+ATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGAC
+AACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGA
+ACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCT
+GTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTT
+CCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACC
+GATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAG
+GATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTAT
+CGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATT
+CAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGAC
+CAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACC
+GTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAG
+TGTGAGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCA
+AGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTC
+GCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTT
+CGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGA
+CGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACG
+CCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTT
+TTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATG
+ATGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGA
+CTATTGACGTCCTTCCCCGTACGCCGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGT
+CTAACTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGA
+TTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTAT
+TGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGC
+CTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGA
+TGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCC
+TAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCA
+GGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTC
+TGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAA
+TGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGA
+GAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCA
+AAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAA
+AGACCAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCG
+CGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTAT
+GCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAA
+AGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCA
+GCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGA
+TGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTG
+GAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATA
+ACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTT
+TTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCG
+TATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCC
+AATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTC
+TTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGC
+TGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGC
+ACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGA
+AGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCT
+GGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGG
+TATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTT
+TACTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGT
+TTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGC
+TTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGC
+TAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAA
+TGGCCGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGA
+CCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTG
+GCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTC
+TGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGC
+TGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAA
+AGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAA
+GAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAA
+TCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAA
+CCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGT
+AGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCGCGCTTC
+GATAAAAATGATTGGCGTATCCAACCTGC

diff -r f9f2ad782d8f -r f89e3c318453 test-data/test_07_short_report.pdf

Binary file test-data/test_07_short_report.pdf has changed

diff -r f9f2ad782d8f -r f89e3c318453 test-data/test_07_short_report.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_07_short_report.tab Wed Jun 07 12:02:03 2023 +0000

@@ -0,0 +1,31 @@
+METRICS/TRANSCRIPTS transcriptome01
+Genes 1
+Avg. number of exons per isoform 1.0
+Transcripts 1
+Transcripts > 500 bp 1
+Transcripts > 1000 bp 1
+Aligned 1
+Uniquely aligned 0
+Multiply aligned 1
+Unaligned 0
+Avg. aligned fraction 1.0
+Avg. alignment length 5369.0
+Avg. mismatches per transcript 0.0
+Misassemblies 0
+Database coverage 1.0
+Duplication ratio 4.0
+Relative database coverage 1.0
+5000%-assembled genes 0
+9500%-assembled genes 0
+5000%-covered genes 0
+9500%-covered genes 0
+5000%-assembled isoforms 0
+9500%-assembled isoforms 0
+5000%-covered isoforms 0
+9500%-covered isoforms 0
+Mean isoform coverage 1.0
+Mean isoform assembly 1.0
+5000%-matched 0
+9500%-matched 0
+Unannotated 0
+Mean fraction of transcript matched 1.0

diff -r f9f2ad782d8f -r f89e3c318453 test-data/test_08_complete_report.tab

Binary file test-data/test_08_complete_report.tab has changed

diff -r f9f2ad782d8f -r f89e3c318453 test-data/test_08_paralogs.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_08_paralogs.fasta Wed Jun 07 12:02:03 2023 +0000

diff -r f9f2ad782d8f -r f89e3c318453 test-data/test_08_short_report.pdf

Binary file test-data/test_08_short_report.pdf has changed

diff -r f9f2ad782d8f -r f89e3c318453 test-data/test_08_short_report.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_08_short_report.tab Wed Jun 07 12:02:03 2023 +0000

@@ -0,0 +1,31 @@
+METRICS/TRANSCRIPTS transcriptome01 transcriptome02
+Genes 1 1
+Avg. number of exons per isoform 1.0 1.0
+Transcripts 1 1
+Transcripts > 500 bp 1 1
+Transcripts > 1000 bp 1 1
+Aligned 1 1
+Uniquely aligned 0 0
+Multiply aligned 1 1
+Unaligned 0 0
+Avg. aligned fraction 1.0 1.0
+Avg. alignment length 5369.0 5369.0
+Avg. mismatches per transcript 0.0 0.0
+Misassemblies 0 0
+Database coverage 1.0 1.0
+Duplication ratio 4.0 8.0
+Relative database coverage 0.0 0.0
+5000%-assembled genes 0 0
+9500%-assembled genes 0 0
+5000%-covered genes 0 0
+9500%-covered genes 0 0
+5000%-assembled isoforms 0 0
+9500%-assembled isoforms 0 0
+5000%-covered isoforms 0 0
+9500%-covered isoforms 0 0
+Mean isoform coverage 1.0 1.0
+Mean isoform assembly 1.0 1.0
+5000%-matched 0 0
+9500%-matched 0 0
+Unannotated 0 0
+Mean fraction of transcript matched 1.0 1.0

diff -r f9f2ad782d8f -r f89e3c318453 test-data/transcriptome01.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/transcriptome01.fasta Wed Jun 07 12:02:03 2023 +0000

b'@@ -0,0 +1,314 @@\n+>STRG.1.1\n+ATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTA\n+CTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTG\n+CGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGT\n+TGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTT\n+TGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTT\n+CAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGC\n+CTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGT\n+AACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGC\n+TGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGT\n+TCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATTATTAAT\n+GGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTG\n+ACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAGTGATGTAATGTCTAAA\n+GGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAG\n+GCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATA\n+AATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCT\n+GGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACG\n+CCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTAC\n+TTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGCC\n+ACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTG\n+ATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCC\n+GTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGT\n+TGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGA\n+CTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACG\n+TGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGAC\n+AACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA\n+CGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCC\n+TGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTAC\n+CTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGC\n+CGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGG\n+TCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATT\n+CAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCC\n+AGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGAC\n+CACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAA\n+TTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCAT\n+GTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACT\n+CCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGA\n+CGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCA\n+GGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCTTT\n+GAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGCCATGATG\n+GTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAATGTTTA\n+TGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTT\n+ATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTAT\n+TGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGC\n+ATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCA\n+TTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGC\n+TGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTG\n+GTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTC\n+CTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGA\n+GAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACT\n+CAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAAA\n+ATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCT\n+TTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTAT\n+TTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAA\n+CGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGA\n+TGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTC\n+TGGAAAGAC'..b'AACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGA\n+CTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACG\n+TGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGAC\n+AACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA\n+CGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCC\n+TGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTAC\n+CTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGC\n+CGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGG\n+TCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATT\n+CAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCC\n+AGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGAC\n+CACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAA\n+TTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCAT\n+GTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACT\n+CCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGA\n+CGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCA\n+GGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCTTT\n+GAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGCCATGATG\n+GTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAATGTTTA\n+TGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTT\n+ATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTAT\n+TGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGC\n+ATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCA\n+TTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGC\n+TGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTG\n+GTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTC\n+CTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGA\n+GAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACT\n+CAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAAA\n+ATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCT\n+TTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTAT\n+TTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAA\n+CGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGA\n+TGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTC\n+TGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCT\n+CCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGA\n+ATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATT\n+TCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAG\n+AGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGC\n+TGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTAC\n+AATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTT\n+TAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCG\n+CGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACT\n+ATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTT\n+GGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGC\n+TTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCA\n+CACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATTTCCATG\n+CGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCG\n+CCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACG\n+CAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCA\n+GTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAA\n+AGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTC\n+AGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAA\n+TCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGA\n+GATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTG\n+CTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGC\n+\n+\n'

diff -r f9f2ad782d8f -r f89e3c318453 test-data/transcriptome02.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/transcriptome02.fasta Wed Jun 07 12:02:03 2023 +0000

b'@@ -0,0 +1,626 @@\n+>STRG.1.1\n+ATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTA\n+CTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTG\n+CGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGT\n+TGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTT\n+TGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTT\n+CAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGC\n+CTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGT\n+AACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGC\n+TGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGT\n+TCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATTATTAAT\n+GGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTG\n+ACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAGTGATGTAATGTCTAAA\n+GGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAG\n+GCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATA\n+AATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCT\n+GGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACG\n+CCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTAC\n+TTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGCC\n+ACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTG\n+ATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCC\n+GTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGT\n+TGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGA\n+CTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACG\n+TGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGAC\n+AACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA\n+CGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCC\n+TGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTAC\n+CTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGC\n+CGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGG\n+TCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATT\n+CAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCC\n+AGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGAC\n+CACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAA\n+TTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCAT\n+GTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACT\n+CCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGA\n+CGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCA\n+GGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCTTT\n+GAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGCCATGATG\n+GTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAATGTTTA\n+TGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTT\n+ATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTAT\n+TGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGC\n+ATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCA\n+TTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGC\n+TGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTG\n+GTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTC\n+CTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGA\n+GAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACT\n+CAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAAA\n+ATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCT\n+TTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTAT\n+TTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAA\n+CGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGA\n+TGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTC\n+TGGAAAGAC'..b'AACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGA\n+CTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACG\n+TGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGAC\n+AACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA\n+CGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCC\n+TGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTAC\n+CTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGC\n+CGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGG\n+TCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATT\n+CAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCC\n+AGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGAC\n+CACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAA\n+TTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCAT\n+GTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACT\n+CCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGA\n+CGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCA\n+GGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCTTT\n+GAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGCCATGATG\n+GTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAATGTTTA\n+TGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTT\n+ATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTAT\n+TGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGC\n+ATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCA\n+TTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGC\n+TGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTG\n+GTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTC\n+CTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGA\n+GAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACT\n+CAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAAA\n+ATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCT\n+TTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTAT\n+TTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAA\n+CGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGA\n+TGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTC\n+TGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCT\n+CCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGA\n+ATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATT\n+TCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAG\n+AGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGC\n+TGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTAC\n+AATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTT\n+TAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCG\n+CGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACT\n+ATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTT\n+GGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGC\n+TTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCA\n+CACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATTTCCATG\n+CGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCG\n+CCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACG\n+CAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCA\n+GTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAA\n+AGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTC\n+AGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAA\n+TCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGA\n+GATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTG\n+CTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGC\n+\n+\n'

diff -r f9f2ad782d8f -r f89e3c318453 tool-data/busco_database.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/busco_database.loc.sample Wed Jun 07 12:02:03 2023 +0000

@@ -0,0 +1,8 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of busco files.
+#file has this format (white space characters are TAB characters)
+# - value
+# - name
+# - version
+# - /path/to/data
+#virus_lineage_1.0 Virus_Lineage_1.0 5.4.6 /path/to/data
\ No newline at end of file

diff -r f9f2ad782d8f -r f89e3c318453 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Wed Jun 07 12:02:03 2023 +0000

@@ -0,0 +1,6 @@
+<tables>
+    <table name="busco_database" comment_char="#">
+        <columns>value, name, version, path</columns>
+        <file path="tool-data/busco_database.loc" />
+    </table>
+</tables>

diff -r f9f2ad782d8f -r f89e3c318453 tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Wed Jun 07 12:02:03 2023 +0000

@@ -0,0 +1,6 @@
+<tables>
+    <table name="busco_database" comment_char="#">
+        <columns>value, name, version, path</columns>
+        <file path="${__HERE__}/test-data/busco_database.loc" />
+    </table>
+</tables>
\ No newline at end of file