| Next changeset 1:688a777e1b19 (2023-01-24) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94" |
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added:
coverm_contig.xml macros.xml test-data/1mbp.fna test-data/1read.actually_fasta.fq test-data/2seqs.bad_read.1.with_supplementary.bam test-data/2seqs.fasta test-data/500kb.fna test-data/7seqs.fna test-data/7seqs.reads_for_seq1_and_seq2.bam test-data/all_fasta.loc test-data/bad_reads.all.interleaved.fa test-data/bad_reads.interleaved.fq test-data/contig_test1.tsv test-data/contig_test2.tsv test-data/contig_test3.tsv test-data/contig_test4.tsv test-data/contig_test5.tsv test-data/genome1.fna test-data/genome2.fna test-data/genome3.fna test-data/genomeInfo.csv test-data/reads_for_genome2.1.fa test-data/reads_for_genome2.2.fa test-data/reads_for_seq1_and_seq2.1.fq.gz test-data/reads_for_seq1_and_seq2.2.fq.gz test-data/reads_for_seq1_and_seq2.fna test-data/test1.tsv test-data/test2.tsv test-data/test3.tsv test-data/test4.tsv test-data/test5.tsv test-data/tpm_test.bam tool-data/all_fasta.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r 6941d0d453ba coverm_contig.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/coverm_contig.xml Tue Apr 26 15:27:37 2022 +0000 |
| [ |
| b'@@ -0,0 +1,379 @@\n+<tool id="coverm_contig" name="CoverM-CONTIG" version="@TOOL_VERSION@" python_template_version="3.5">\n+ <macros>\n+ <import>macros.xml</import>\n+ <token name="@INPUT_FORMATS@">fasta,fastq,fastq.gz,fasta.gz</token>\n+ <token name="@TOOL_VERSION@">0.2.1</token>\n+ </macros>\n+ <expand macro="requirements"/>\n+ <command><![CDATA[\n+ #if $reads.read_type == "single" or $reads.read_type == "interleaved"\n+ mkdir -p reads1 &&\n+ #set file_paths1 = []\n+ #for $input_file in $reads.single\n+ \n+ #set $fname = $input_file.element_identifier.replace(" ","_")\n+ #set $file_path = \'reads1/\' + $fname\n+ ln -s \'$input_file\' \'$file_path\' &&\n+ $file_paths1.append($file_path)\n+ #end for\n+ #else if $reads.read_type == "bam"\n+ mkdir -p bam &&\n+ #set bam_files = []\n+ #for $input_file in $reads.bam\n+ \n+ #set $fname = $input_file.element_identifier.replace(" ","_")\n+ #set $file_path = \'bam/\' + $fname\n+ ln -s \'$input_file\' \'$file_path\' &&\n+ $bam_files.append($file_path)\n+ #end for\n+ #else if $reads.read_type == "paired"\n+ mkdir -p paired_reads1 &&\n+ #set fw_reads1 = []\n+ #for $input_file in $reads.read1\n+ \n+ #set $fname = $input_file.element_identifier.replace(" ","_")\n+ #set $file_path = \'paired_reads1/\' + str($fname)\n+ ln -s \'$input_file\' \'$file_path\' &&\n+ $fw_reads1.append($file_path)\n+ #end for\n+ #set rv_reads1 = []\n+ #for $input_file in $reads.read2\n+ \n+ #set $fname = $input_file.element_identifier.replace(" ","_")\n+ #set $file_path = \'paired_reads1/\' + str($fname)\n+ ln -s \'$input_file\' \'$file_path\' &&\n+ $rv_reads1.append($file_path)\n+ #end for\n+ #silent $fw_reads1.sort()\n+ #silent $rv_reads1.sort()\n+ #else\n+ mkdir -p paired_reads &&\n+ #set paired_reads1 = []\n+ #for $i, $input_file in enumerate($reads.paired_reads)\n+ #set $file_path = \'paired_reads/fw\' + str($i)\n+ ln -s \'$input_file.forward\' \'$file_path\' &&\n+ $paired_reads1.append($file_path)\n+ #set $file_path = \'paired_reads/rv\' + str($i)\n+ ln -s \'$input_file.reverse\' \'$file_path\' &&\n+ $paired_reads1.append($file_path)\n+ #end for\n+ #end if \n+ #if $add_reads.extra_read.read_type == "single" or $add_reads.extra_read.read_type == "interleaved"\n+ mkdir -p add_reads1 &&\n+ #set add_file_paths1 = []\n+ #for $input_file in $add_reads.extra_read.single\n+ #set $fname = $input_file.element_identifier.replace(" ","_")\n+ #set $file_path = \'add_reads1/\' + $fname\n+ ln -s \'$input_file\' \'$file_path\' &&\n+ $add_file_paths1.append($file_path)\n+ #end for\n+ #else if $add_reads.extra_read.read_type == "bam"\n+ mkdir -p add_bam &&\n+ #set add_bam_files = []\n+ #for $input_file in $reads.bam\n+ #set $fname = $input_file.element_identifier.replace(" ","_")\n+ #set $file_path = \'add_bam/\' + $fname\n+ ln -s \'$input_file\' \'$file_path\' &&\n+ $add_bam_files.append($file_path)\n+ #end for\n+ #else if $add_reads.extra_read.read_type == "paired"\n+ mkdir -p add_paired_reads1 &&\n+ #set add_fw_reads1 = []\n+ #for $input_file in $add_reads.extra_read.read1\n+ #set $fname = $input_file.element_identifier.replace(" ","_")\n+ #set $file_path = \'add_paired_reads1/\' + '..b'rs_only" value="true"/>\n+ </section>\n+ <section name="out">\n+ <param name="output_format" value="sparse"/>\n+ </section> \n+ <output name="output1" file="contig_test3.tsv" ftype="tsv"/>\n+ </test> \n+ <test>\n+ <conditional name="reads">\n+ <param name="read_type" value="paired"/>\n+ <param name="read1" value="reads_for_seq1_and_seq2.1.fq.gz"/>\n+ <param name="read2" value="reads_for_seq1_and_seq2.2.fq.gz"/>\n+ <param name="ref_fasta_history" value="2seqs.fasta"/>\n+ </conditional>\n+ <section name="add_reads">\n+ <conditional name="extra_read">\n+ <param name="read_type" value="paired_collection"/>\n+ <param name="paired_reads">\n+ <collection type="list:paired">\n+ <element name="reads_for_seq1_and_seq2..fq">\n+ <collection type="paired">\n+ <element name="forward" value="reads_for_seq1_and_seq2.1.fq.gz"/>\n+ <element name="reverse" value="reads_for_seq1_and_seq2.2.fq.gz"/>\n+ </collection>\n+ </element>\n+ </collection>\n+ </param>\n+ </conditional>\n+ </section>\n+ <section name="cov">\n+ <param name="contig_end_exclusion" value="0"/>\n+ </section>\n+ <section name="mapping">\n+ <param name="--min-read-percent-identity" value="0.95"/>\n+ </section>\n+ <output name="output1" file="contig_test4.tsv" ftype="tsv"/>\n+ </test> \n+ <test>\n+ <conditional name="reads">\n+ <param name="read_type" value="bam"/>\n+ <param name="bam" value="tpm_test.bam"/>\n+ </conditional>\n+ <section name="cov">\n+ <param name="mean" value="true"/>\n+ <param name="tpm" value="true"/>\n+ </section>\n+ <section name="out">\n+ <param name="output_format" value="sparse"/>\n+ </section> \n+ <output name="output1" file="contig_test5.tsv" ftype="tsv"/>\n+ </test> \n+ </tests>\n+ <help><![CDATA[\n+.. class:: infomark\n+ \n+**Method for calculating coverage**\n+\n+Calculation of genome-wise coverage (genome mode) is similar to calculating contig-wise (contig mode) coverage, except that the unit of reporting is per-genome rather than per-contig. For calculation methods which exclude base positions based on their coverage, all positions from all contigs are considered together. \n+\n+- Relative abundance: Percentage relative abundance of each genome, and the unmapped read percentage\n+- Mean: Average number of aligned reads overlapping each position on the genome\n+- Trimmed mean: Average number of aligned reads overlapping each position after removing the most deeply and shallowly covered positions.\n+- Covered fraction: Fraction of genome covered by 1 or more reads\n+- Covered bases: Number of bases covered by 1 or more reads\n+- Variance: Variance of coverage depths\n+- Length: Length of each genome in base pairs\n+- Count: Number of reads aligned toq each genome. Note that a single read may be aligned to multiple genomes with supplementary alignments\n+- Reads per base: Number of reads aligned divided by the length of the genome\n+- MetaBAT: Reproduction of the `MetaBAT <https://bitbucket.org/berkeleylab/metabat>`_ tool output\n+- Coverage histogram: Histogram of coverage depths\n+- RPKM: Reads mapped per kilobase of genome, per million mapped reads\n+- TPM: Transcripts Per Million as described in `Li et al 2010 <https://doi.org/10.1093/bioinformatics/btp692>`_\n+\n+ ]]></help>\n+ <expand macro="citation"/>\n+</tool>\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r 6941d0d453ba macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Apr 26 15:27:37 2022 +0000 |
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| b'@@ -0,0 +1,293 @@\n+<macros>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package">coverm</requirement>\n+ </requirements>\n+ </xml>\n+ <token name="@INPUT_FORMATS@">fasta,fastq,fastq.gz,fasta.gz</token>\n+ <token name="@TOOL_VERSION@">0.2.1</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ <xml name="citation">\n+ <citations>\n+ <citation type="bibtex">\n+ @misc{githubCoverm,\n+ author = {B J. Woodcroft},\n+ year = {2021},\n+ title = {CoverM},\n+ publisher = {GitHub},\n+ journal = {GitHub repository},\n+ url = {https://github.com/wwood/CoverM}\n+ }\n+ </citation>\n+ </citations>\n+ </xml>\n+ <xml name="genome_opt">\n+ <conditional name="genome">\n+ <param name="ref_or_genome" type="select" label="Select if you want to specify additional genome files.">\n+ <option value="genomic">yes</option>\n+ <option value="none" selected="true">No (Only when BAM files are provided)</option>\n+ </param>\n+ <when value="none">\n+ <param argument="--single-genome" type="boolean" truevalue="--single-genome" falsevalue="" checked="false" label="All contigs are from the same genome."/>\n+ <param type="text" name="separator" optional="true" label="Character, that separates genome names from contig names in the reference file." >\n+ <sanitizer>\n+ <valid initial="string.punctuation">\n+ </valid>\n+ </sanitizer>\n+ </param>\n+ </when>\n+ <when value="genomic">\n+ <conditional name="genomic">\n+ <param type="select" label="Reference genome source" name="source">\n+ <option value="history" selected="true">History</option>\n+ <option value="builtin">Built-in</option>\n+ </param>\n+ <when value="history">\n+ <param type="data" name="fasta_history" multiple="true" label="FASTA files of each genome" format="fasta" />\n+ </when>\n+ <when value="builtin">\n+ <param type="select" name="fasta_builtin" multiple="true" label="Reference genome(s)">\n+ <options from_data_table="all_fasta" />\n+ </param>\n+ </when>\n+ </conditional>\n+ </when>\n+ </conditional>\n+ </xml>\n+ <xml name="genome">\n+ <conditional name="genome">\n+ <param name="ref_or_genome" type="select" label="Reference sequence mode" help="Select if you want to specify genome file(s) or a FASTA reference file or both. NOTE: If genomic FASTA files are specified, then reference is not needed as a reference FASTA file can be derived by concatenating input genomes. However, while not necessary, reference can be specified if an alternate reference sequence set is desired.">\n+ <option value="genomic" selected="true">Reference genome</option>\n+ <option value="reference">Contigs (e.g. concatenated genomes or metagenome assembly)</option>\n+ </param>\n+ <when value="genomic">\n+ <conditional name="genomic">\n+ <param type="select" label="Reference genome source" name="source">\n+ <option value="history" selected="true">History</option>\n+ <option value="builtin">Built-in</option>\n+ </param>\n+ <when value="history">\n+ <param type="data" name="fasta_history" multiple="true" label="FASTA files of each genome" format="fasta" />\n+ </when>\n+ <when value="builtin">\n+ <param type="select" na'..b't"/>\n+ <param argument="--exclude-supplementary" type="boolean" truevalue="--exclude-supplementary" falsevalue="" \n+ label="Exclude supplementary alignments" help="Default: not set"/>\n+ </section>\n+ </xml>\n+ <xml name="coverage">\n+ <section name="cov" title="Coverage calculation options" expanded="false">\n+ <param name="relative_abundance" type="boolean" falsevalue="" truevalue="relative_abundance" label="Relative abundance (default)"/>\n+ <param name="mean" type="boolean" falsevalue="" truevalue="mean" label="Mean"/>\n+ <conditional name="cond_methods">\n+ <param name="trimmed_mean" type="boolean" falsevalue="" truevalue="trimmed_mean" label="Trimmed mean"/>\n+ <when value="trimmed_mean">\n+ <param name="trim_min" type="integer" min="0" value="5" label="Trim min" help="Remove this smallest fraction of positions when calculating trimmed_mean default: 5"/>\n+ <param name="trim_max" type="integer" min="0" value="95" label="Trim max" help="Maximum fraction for trimmed_mean calculations default: 95"/>\n+ </when>\n+ <when value=""/>\n+ </conditional>\n+ <param name="covered_bases" type="boolean" falsevalue="" truevalue="covered_bases" label="Covered bases"/>\n+ <param name="covered_fraction" type="boolean" falsevalue="" truevalue="covered_fraction" label="Covered fraction"/>\n+ <param name="variance" type="boolean" falsevalue="" truevalue="variance" label="Variance"/>\n+ <param name="length" type="boolean" falsevalue="" truevalue="length" label="Length"/>\n+ <param name="count" type="boolean" falsevalue="" truevalue="count" label="Count"/>\n+ <param name="metabat" type="boolean" falsevalue="" truevalue="metabat" label="MetaBAT"/>\n+ <param name="coverage_histogram" type="boolean" falsevalue="" truevalue="coverage_histogram" label="Coverage histogram"/>\n+ <param name="reads_per_base" type="boolean" falsevalue="" truevalue="reads_per_base" label="Reads per base"/>\n+ <param name="rpkm" type="boolean" falsevalue="" truevalue="rpkm" label="RPKM"/>\n+ <param name="tpm" type="boolean" falsevalue="" truevalue="tpm" label="TPKM"/>\n+ <param name="min_covered_fraction" type="integer" min="0" optional="true"\n+ label="Min covered fraction" help="Genomes with less coverage than this reported as having zero coverage. Default: 10"/>\n+ <param name="contig_end_exclusion" type="integer" min="0" optional="true"\n+ label="Contig end exclusion" help="Exclude bases at the ends of reference sequences from calculation. Default: 75"/>\n+ </section>\n+ </xml>\n+ <xml name="out">\n+ <section name="out" title="Output options" expanded="false">\n+ <param name="output_format" type="select" label="Shape of output" help="\'Sparse\' for long format, \'dense\' for species-by-site. Default: dense]">\n+ <option value="dense" selected="true">Dense</option>\n+ <option value="sparse">Sparse</option>\n+ </param>\n+ <param name="no_zeros" type="boolean" truevalue="--no-zeros" falsevalue="" optional="true" label="Omit printing of genomes that have zero coverage" />\n+ <param argument="--dereplication-output-cluster-definition" type="boolean" truevalue="--dereplication-output-cluster-definition" falsevalue="" label="Output a file of representative TAB member lines." />\n+ <param argument="--dereplication-output-representative-fasta-directory-copy" type="boolean" truevalue="--dereplication-output-representative-fasta-directory-copy" falsevalue="" label="Output representative genomes" />\n+ </section>\n+ </xml>\n+ <xml name="citations">\n+ <citations>\n+ <yield />\n+ </citations>\n+ </xml>\n+</macros>\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r 6941d0d453ba test-data/1mbp.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1mbp.fna Tue Apr 26 15:27:37 2022 +0000 |
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| b'@@ -0,0 +1,2 @@\n+>random_sequence_length_1000000_1\n+GTCACCGTGAACTTAGACGGGTCCGGTGGTTCCTGTCTGCCACAGACAATAACGCAGAGGCGTCAAGACGCGTTGTCGGGGGTGAATCGCGCGTGTATTTATGCTCCGTAGCAATGATGGTACTGTACAAAGCTCAGCCGGGGCGCGTTGAAGTATCAAATCTCTTACTGAGCGTTAGGATAGTTCCGTTGAGATATGTAGGCGTATTAACGCGTGCGCCCGGGCTGCTAACCAGTGAATACCGGGAGCTCCAGAGTGTCATGTCTAGTCAATGGTTGAATAATGGTATGTTTATCAGGCCTAAGAAGCATGCGGAGCAATGGTGCTTCTGTAGCAACCCGCCATGCGCAGGGAGTGACTGCCGGATTTTTGGCGCTACCTAAAGAATTGATAGGCGGGCGGAAACCGCGCGCATAAAGCTTTCGGAGGTCGTGATTAGTGGTGGAATCCTGTATGGAACAAGGCTTGCTCTCGTGCAGCCAAGAATTGCTGCGGGTTTTCCTAATTTCTTAGCGTTACCAGTCCCGTGAATAGATGTAGAGCTAGTATACTCACTCCGACCCATGAGGCTGACCAGAGTGACGCGCACCTGCCAGAGGGGAGCTAACATAGGTATGTGGGCATCAGGGTCGGTGCCCTCTCGTTTCAGTTGGCGTGGAGCCAGCGATAATATACTTTACCCTTGCTCATCGGTGTCGCAACAGTCAATGGTACACTTTTCTCCATTTTTAAAACATACAATTCATTCTCATCGTTCTCTCTGACGCACCGTCTACGGCCCGCTGCAACGTAATGCTAAGCTTAGCGCTTTCGCCGGTCTTCCGTACCTTTTAGTAAGTATGGCGTACACTCTCTAGAAGGTGCCGGACGGGGTCAGTATCGCGTTTTGCGCCAAGGTCGAGGGCGTATCGGGGCGCATATTTGCGCGAGCTCGGGAGGACCACAGGCGTGAGGTCGGCGTATGGTCGATTTGAAAACTACGGCGTCGGTTTGTGATCATACTTAGACTCTGATCTCAAATCCTGAGCAACGGTGAGATCAGTGAATATACAGAGAGTAAAGAGTGGCATTCACCAAAGATGAGGAAGTCGAGCGATGTTCAATTGGAGAACGGTGTCGCTCCCAAGGGAGTGGGATACTCAGTCTTACTCGTACCTCCAGATACGACTGCCGCTTACCATAGGCTATCTACAGCTTCTGCTCCCACGCTATACGCGATATTTGCACGCTTCGTCTCCGTTGCACGTTTGAGCCAGTGAGTGTCCCCAGCGCGGCAGCCGCTCTCCAAGGAAGATACTTCACTCGCCACACTTCATAACCTTAATAGGCGTTCGCTACAGCTACCCCGAGTTCCGGAATAGACGAACACTTATTCAAATGGAGATAATCTTACTTTGCTGGATCACAGGGAACAATTCTTGGGGGGGGTCGCCAGCTCTTGTTCTACAGTCGCCTCTGGAATGCGCGAGCACAGCACTCTAAGCGGTGGCCTGTCGTCTCCAACAAGAAAGGTTCTGGTGGGTGCTAGCTTTGGCATCCATGGTAGGATGTCGGTATATTGCGTCAGACTTTCCAGAGCACAGCGTTTCTTGTCTGTTCTGTCAGGTGTCCTCGTCTCTCGAGAGCCCACGGAAAAGCAAACACACGGTTTGGCCTCCGGACTAGTGTAAAGTACGCTAGATGATCCCGATAGACCCGTTATCTATGGTGGCGGCACTGGCTCCGAGCACTAACGGTTGATATGCTCCGTTGGTTGCTTATGAGCTCTAGAACCCATGCTAACGCCCTATAATCTCTAGTAGTTCGTGCTGGAATCCGCCCATCACACAACGACAATACACGGGGGTTAGAATCCGTCCACCTAACTGGTGCCTCAGATCTTGTTGGTTCATCGAGTAGATCACGATCCATGTTTCTACAGTGGGAATCGTGGGGTGAAAAGTACATCTCTTAGGAGCTCAAAATTATCGAATACATTAAAGGTATCGCAAAAGGCGCATGCATCCTAGAAAGGAGACCGCGGACAATGTCAACTTTACTTAAGACTAAAATCCTTGTCATTAATTGACGGAGGGGGCACGGTTATCTCATATGGGCAGGATCAGTCCAAAAAGTGGGTCTCGATCAGTTAACTAGCTATTCTGAGGACGCGGATAGCGCACCCAACGCCACATAGTCCGGCGTTACCTCATAAGACAAGCAGATATGGGACTCGGGATGTCGGCTACCCAATCTACTCGGGTATGACAATGTCATCTCTTCCAAGATGGCAATTGTATAGGCGTATGGGTGATTCGCATAATTCTATGTGGGTCCGGTTAGCTACCACTGTCGGCCTCCAGCGGCTACCGGTCTCAGTACCCCAGCCGATTACATTGACTATGACTGCGCGAGCAAAGTCGCGAGGCCCGAGCTGTGTCCTAGCTAGCACTGGAAGTTCCAAGCAGAGTAATTTTCTACCCACCCTCTGGCCGGATATATCCGCACTTTCCCATAGGAAGTAGGAACTATAAAGACGCTATATTCACCCAAATGTTGCCCCTAGTCCACCTTTAGCCCATCTTTCAGGCCAATTACTCACTTTCTCATGTTTCCGATTCCCGTAGTGGAATGCTGTAAGCCATACTACGCAAGAGCCGAAATACCATCGAGCCGGCTTGGCATTGCAGAAACTAGATTAACCCCTAGTGTGACCTTGTCGATATGAGAAGACGACACTAAGCAACGTGTGGGAAAGTGTACATATTTCCGTAACGTGTGTGGCCTTCTCGAAGTAACACCTTCATTGCTAACTGTTGCTTCAGCGCAGAGCAAAGAACGTAAGCGGAAGGTATTTACAGCAACCATAACGTAATCAAGGTTCAGTCCCCGTAGCCCATTGCACACAGTCAGAGGTCTAAGCCGTACGATAGCGTGGGAAAGCTCTCGGATACTGGAGCTTAGTGTACCCCGAGGATCCAGGCCACGTAGAGTGAGGGATATGGAATTTATTGGAGCTAATCCCCGAAGTAATGGTAGAACGGAGCACTAGCGACAGTTCTGTGACTACTCACGTGTATACCCGGGAGACAATACTCTGGCCGAGAGGTACTCCTAGTTCAATCTCCTACAGGCATTGTTTACGCCTAACAAGCCTGACGACGAGGTTCCATGATTGAGGGTTCCCCAGTACTCACAGGCCGCGTATGTCAATCGAACTGGTGGAGTTCTGGCCTAAACATACACAGGATCTTTGGGAGGCTCAGCAGCAGCGATTTATACACATTGGCGGCCTTGATTGAATCTCTGTGGCGTGATACGAGATAATTAAAGGCCAACAGTGATAGTACTGCATACCGAAGCGTGCACCCCATTGATGGTTCTGTCTTCGTAAATTAGCTCCAGCGACTGCCGCGAGGTCATGATACGACTACCTATTGGAGTTTAGTTCTGTTGCTTGAGGATATTGACCCGCTCCAGTTTGAGCGGAGCATAGTGCGGCCGATGACCAGGTCCGCTAATATCCACGGATCCGTCAACCCTTCATCGTCCTGAGCTGGTGGTGCGCAGCAAACATAATGAATTCTCCCAGGCGCCTGAAACGTACCTAAGTGCGTACCTAGATTTCTGATCGTGAAGGAACATCCGTCGGGCAAGGAGGTTGTTAATTAACTCCTTGGGTGGATAGCCAGCCCGGTCGGTCACCGAGATTTCTAGTGGTACCGTCAGCGGATCTATAAGTTCCCCTAAACGATCTTACAATCCAGTACTCGCTTCGTGGTACTCGGGTATGTCTTGCTTACCTAGTAAGGGACTTGACCTAATATTCCGAACAACGGTGAACCTTAAGATAACTCAGTAGTTAGAGTCCGGTGGGAGGAGGTACCCGTCGCTTCCGCAAGCACATGACAGTACAAAAAGTTGTGTCGACGCCCGAGTTGCGCCCAACCCTACGCACTTGATTGCCT'..b'ACTTTTGCTAGCCATGTAAGCGCGATCTTGCGGAGGCCGCATATATCTCGTGATTCGCGTTCTAACTGAGTGACTGCTACGCTTCAACTGCTCAGTAGATGGTACCGTCTCCGTATCCTCTTCCAGCGTATTGTGCTGCGGTATCATGAGCATCGGATTATACTCCGCGGCCACTGCGTTTAAAATATGAGTCATTACTATCTTGGCATTGAATGGATTTGCGTCTGTAGAACGGGGGTATAAATGGGCTGCGGTCCGATCATCGAAGAACCTGGGTTATCCTATGCGATGGGGATTAGTTAGGCTGAATGTGCTTTAACGTCTAATCTAGAAGGGCAATGTACCTGCGCCCGGCTGGCGTGGAACTGTTTGTCCGCCTCTGTCCAATTCAGGGACTCGACGCACCCATAGTGCTCAATCGGGTCTTATTGCTCTTCGACGACGTTGGAGACTCTCCGAGATAGGCGTCGGATAGAAATCCTAAATCGCTCCACCAACCGCATGCTTACCGAATCAGTTCGGAACGGCCAAGCGTCGACTTTAGTGCATGGAAGTGTCGATTAAATGTGGCGAACTCAGCATGGAATGCACCGTAACGACCGGCTAACGGCGAGCACTCTAAAACTACCACTGATCTTGTCTGTGTGGATCGAAAGTTCCGTCCAGGACAGTTGGTGTATGTAATTCTGCTACCAGCATTTCCGGAAACACCTGGAATGAGTACCACGGTTCAGGACAACCCACGTGAACGAAGCAGTGTCGTTCGATTATTGTGGCTTGCGCTGAGGGACCCATACGTGATCTTGTCCGGATGCTAAAGGCTTCTTGATCGTTCTGAATACCTACACATAACTCATTCATAGTCATAGCCCTGTAAAGAAGCGTCGGATTATTTCTCACTCGGCACGGGAGCGTTCGAGGCCATGCTACCGACCGTCGGTGATGTGCATACGCCAGGCGTTTCACGTAGGCGAGAGACAGTCAACGTGCGAGCACGCGAACTTCCGAGGCAAAGGCCGTTACCCTGGCAATTATATATTTTAGGTCCAGGGCTACTCCGCGGTCCCCGATTGCACTTATGTTGGGAGTACCACCAATCGCGTTGCAGTGACCTACTTATAAGTGATTCTGGCACATTGACCTAGGCGCGCCAAGTCTTCAGATGACTGTAAACTAACCCCGTAAGCTGTGCTGACTTGCACGTTCGCGGATTTCATTCACGTAAGTTGTCACCTCCAGAATTTTCTGTGTGTACTCACTCCCGTGTGCATACTACTACAGCAGTCGCCATGCGTTGTTTAGGGAAAAACCAAATAGTAGCGCGCGCAATCTCTTGCATTATCAACCCTCTGGACGCGCAGGGCTGCGATCCTGCAAGCCCGGACAGGAGGCTCCAGGGCGTATGTGTTATGCGGGTGACTCACCGATTGATACATCCATGGCGGCTCCTCTAGACAGTCCAAAGCGGCGGTGCGCAGTTCGATTAGCAGCCTTATCGCTTATCCATTCGTATTTTCGACGGCTTAGTGTTACGGGAATTCATCATTTTTTGGGGGCCAAGATGGCTCTGTGCTCGCACCAAGGAGAAGATCCAGCTGCGGTTCTTGGAGCATGCCTCCATAGTGAAAGTCTTTCAGTTGCCCTCGATTCCAGAGGCATAACACGAGGACTCCCTATGTACATTTCGCCGCTAGCAAGATATAAAACCGAGTCGCGCGCAACTAGAACTTAAACATATATGGCCAGAAGAATAATGACCCCATCAATGAGGAGTCTTCTATGAGCATGACGACAACAGGGTCACGCGCTACGAACAGTACCGAGACAGCCGCCTTCCTTGGGCCTGTGAAGAGTTCCATTGTAGTGATGACATTTGAATTACACGAGAAGCACCACTGTGTCGGTCAACCGGCCCTACTCAGGATAGTATCTGGGCCTCCTAAAGACGATGTGGTCCAGGAAACGACTTGTTCTATATAAAAATAGGGACGCTACCGGCGTTGACACTGGATCGTGAACAATGAGTAAAAGCCTGAACTCGGTCTTCGTGAGCCCTCTCTCACGAAACAGGGCACTGCATAACTGCGTGCCGCCGCGGGATACGTCACTTCATGAGAAACCCACACTACTACACAGATTGTGTATGTCGCATTGGATAACGTTCTGGTCAACCTCTACTTATATACCCCTATAGTTACTGAGAGCTAGGTGGAATCACTCCTGGTTGAGACCGAAAGGGAATGGGTGCCCGCGGGTCATAACTGAATACTAACTCACAGAACGTATGCTCCGAGGATCCACTATTTATTAGTAGTGGTGGACCGGTGCGTAAGGAACCATACGGACGTTCAATGGGGCGGGTTGTAACTGTAGCCCCCCGATCACAAAGCAAAAGTTAATACATGGTGGGAAAGTTATGCTTGAGTTGTCCATCGAAATAGTGAGTACGTCTTCGAGCGAGCGCGTTTTCCATAGGCTTCAGGTCTAGCTCCAGAGTAAATACCTTACAGTGAAGATTGATGGTATGGCACGATTACCAGCGACATAAATCAAAGGTATTGGTTTCCATGTCGCCGCACACATGAGGAGAGTCAAGTAACCACGAGCCCCAAGAGTGATTGCGAGGCATGTGTACTGATCACGAACCTACACAGAGCGAAACGATGACGTATGTAATAGATGTGACCCGCCATGACATATCGCTTTTTTGCTCGTCCAAGCACATATGACCTTTGTAGATTTCGTACATTCCTGTGACGTATTATCAAGGGTGACGATAGCCCCCACCTAATTGATGAGGAGCAGGACCTAAACTACTGGTAACAGGATTCAACGAGAAGAGCTTGTGCGTGGCATAGTCCGGCTCAGTTCTGTATGTAAAATCAGGGTATCGAGCTGAAAACGATCTATAATTCTCGGATTCGGAGGACATACGGTGGCACTCTGGTCAGGAAGGGGCGGACATCTGTACTACCATTTCTCGTAGCCAGAACCATACGACTCCTCTTTTGCTAATCGGTCGAACTGTTATCTTCAACACACCGTGGAGCATTTCTCTCTCACCGTGGACCTCGTGTATCGGAGTAGTGGCGGCGCAAGGGCCACACGCTGAGACTATAGACTCCCGCCAACGAAGCGATCGAGCACAGTGTAAGGCCGTCACGAGCGCAATGCATGCGCAGACGAGAACCCGATCAAATCGATATGTTAATATCTACTCGTCGGTGGGGTGAAGTGTCCGCACCGGCGGGGCTGCTGCAGGCGATGCAGGGACGACCTCTCGAGGAGCCCGGAACCAGTCCTGAGTATATATGGTTGTTTACCTCAGGAAGGCTGAGGTGACAGCGCCCGAGAATATGCATATAAAATTTAGCTACGATCTGGCTCCTGATCAAATGCGCGGGGCGCGTGCGTATGGCGCCATTCCGACCTGACTTCTACATTTGTCCAGGTGTGTTGGCGACCCCGCCCGGTAGACTGGACGCATAACACAATTCCGCTGTCTGGTGCTGATAGGCCGTTAAGCCAAACAATACCAGCGCCAATCTTTGTGGGACACTAATATAGTGGGGCCGTTACCTACGTACTGGTCTTAAGAGCATCATATCTTAGGTGTGTCCCTAGGCCCTATGCGTAATATTGTCGTGGAGATGGCACCCTCACACTCTACATACTGCGAACGCTGTTCTCCCGTGGCTTGGTACTATTACAGATCCCAGCTTGGGTGATGCCTGCAAAGTCACACGCCTGACGCGGCAGGGGGAGCCCCGCACGGTTTACGGGGTGAGACCACAGTCCCATGTGTGTAGTGGTAGGGTATCACGTTGCATGGGACATGACAATAACTCCCCGCCCACAGTCGACAGATGGTCAGTGGCTACTTGAGCCCCCTCGTATGTTGGCCGCTAGGTTTTCAGGCTGACCCTCACTGCCTCGATTATCGCAGACCCGTGAGTCCTGATCGCGAGTGGGAACAATTATCTGACTCGGACATGCTA\n' |
| b |
| diff -r 000000000000 -r 6941d0d453ba test-data/1read.actually_fasta.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1read.actually_fasta.fq Tue Apr 26 15:27:37 2022 +0000 |
| b |
| @@ -0,0 +1,30 @@ +>random_sequence_length_1000000_1_chopped_1-500000 +GTCACCGTGAACTTAGACGGGTCCGGTGGTTCCTGTCTGCCACAGACAATAACGCAGAGGCGTCAAGACGCGTTGTCGGG +GGTGAATCGCGCGTGTATTTATGCTCCGTAGCAATGATGGTACTGTACAAAGCTCAGCCGGGGCGCGTTGAAGTATCAAA +TCTCTTACTGAGCGTTAGGATAGTTCCGTTGAGATATGTAGGCGTATTAACGCGTGCGCCCGGGCTGCTAACCAGTGAAT +ACCGGGAGCTCCAGAGTGTCATGTCTAGTCAATGGTTGAATAATGGTATGTTTATCAGGCCTAAGAAGCATGCGGAGCAA +TGGTGCTTCTGTAGCAACCCGCCATGCGCAGGGAGTGACTGCCGGATTTTTGGCGCTACCTAAAGAATTGATAGGCGGGC +GGAAACCGCGCGCATAAAGCTTTCGGAGGTCGTGATTAGTGGTGGAATCCTGTATGGAACAAGGCTTGCTCTCGTGCAGC +CAAGAATTGCTGCGGGTTTTCCTAATTTCTTAGCGTTACCAGTCCCGTGAATAGATGTAGAGCTAGTATACTCACTCCGA +CCCATGAGGCTGACCAGAGTGACGCGCACCTGCCAGAGGGGAGCTAACATAGGTATGTGGGCATCAGGGTCGGTGCCCTC +TCGTTTCAGTTGGCGTGGAGCCAGCGATAATATACTTTACCCTTGCTCATCGGTGTCGCAACAGTCAATGGTACACTTTT +CTCCATTTTTAAAACATACAATTCATTCTCATCGTTCTCTCTGACGCACCGTCTACGGCCCGCTGCAACGTAATGCTAAG +CTTAGCGCTTTCGCCGGTCTTCCGTACCTTTTAGTAAGTATGGCGTACACTCTCTAGAAGGTGCCGGACGGGGTCAGTAT +CGCGTTTTGCGCCAAGGTCGAGGGCGTATCGGGGCGCATATTTGCGCGAGCTCGGGAGGACCACAGGCGTGAGGTCGGCG +TATGGTCGATTTGAAAACTACGGCGTCGGTTTGTGATCATACTTAGACTCTGATCTCAAATCCTGAGCAACGGTGAGATC +AGTGAATATACAGAGAGTAAAGAGTGGCATTCACCAAAGATGAGGAAGTCGAGCGATGTTCAATTGGAGAACGGTGTCGC +TCCCAAGGGAGTGGGATACTCAGTCTTACTCGTACCTCCAGATACGACTGCCGCTTACCATAGGCTATCTACAGCTTCTG +CTCCCACGCTATACGCGATATTTGCACGCTTCGTCTCCGTTGCACGTTTGAGCCAGTGAGTGTCCCCAGCGCGGCAGCCG +CTCTCCAAGGAAGATACTTCACTCGCCACACTTCATAACCTTAATAGGCGTTCGCTACAGCTACCCCGAGTTCCGGAATA +GACGAACACTTATTCAAATGGAGATAATCTTACTTTGCTGGATCACAGGGAACAATTCTTGGGGGGGGTCGCCAGCTCTT +GTTCTACAGTCGCCTCTGGAATGCGCGAGCACAGCACTCTAAGCGGTGGCCTGTCGTCTCCAACAAGAAAGGTTCTGGTG +GGTGCTAGCTTTGGCATCCATGGTAGGATGTCGGTATATTGCGTCAGACTTTCCAGAGCACAGCGTTTCTTGTCTGTTCT +GTCAGGTGTCCTCGTCTCTCGAGAGCCCACGGAAAAGCAAACACACGGTTTGGCCTCCGGACTAGTGTAAAGTACGCTAG +ATGATCCCGATAGACCCGTTATCTATGGTGGCGGCACTGGCTCCGAGCACTAACGGTTGATATGCTCCGTTGGTTGCTTA +TGAGCTCTAGAACCCATGCTAACGCCCTATAATCTCTAGTAGTTCGTGCTGGAATCCGCCCATCACACAACGACAATACA +CGGGGGTTAGAATCCGTCCACCTAACTGGTGCCTCAGATCTTGTTGGTTCATCGAGTAGATCACGATCCATGTTTCTACA +GTGGGAATCGTGGGGTGAAAAGTACATCTCTTAGGAGCTCAAAATTATCGAATACATTAAAGGTATCGCAAAAGGCGCAT +GCATCCTAGAAAGGAGACCGCGGACAATGTCAACTTTACTTAAGACTAAAATCCTTGTCATTAATTGACGGAGGGGGCAC +GGTTATCTCATATGGGCAGGATCAGTCCAAAAAGTGGGTCTCGATCAGTTAACTAGCTATTCTGAGGACGCGGATAGCGC +ACCCAACGCCACATAGTCCGGCGTTACCTCATAAGACAAGCAGATATGGGACTCGGGATGTCGGCTACCCAATCTACTCG +GGTATGACAATGTCATCTCTTCCAAGATGGCAATTGTATAGGCGTATGGGTGATTCGCATAATTCTATGTGGGTCCGGTT |
| b |
| diff -r 000000000000 -r 6941d0d453ba test-data/2seqs.bad_read.1.with_supplementary.bam |
| b |
| Binary file test-data/2seqs.bad_read.1.with_supplementary.bam has changed |
| b |
| diff -r 000000000000 -r 6941d0d453ba test-data/2seqs.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2seqs.fasta Tue Apr 26 15:27:37 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>seq1 +GAGTCCCTAGAAGCAGGACCTGCATCTCCGAGAAGGGTCCCAGGGGCGGTGCTAGATCTCAGCAAGGAGGCAATGTGGTTGGGTTTTATAGTCACCCTTTCGAATACTCGAAGAAGGCGCCTGCCCGTTCTAGAGGGAGACATAAGCCTCTGCATCTGCAACGCGGATGGCTAATCAATAATGACCTGCGGTGGATCAGATACCGCATCGCAAGGACCACGTAGGTTGGCTGTCCAACGCGCAAGCGCGCACATCCGCCGATGAAATGTATGTTGATATTATGGGGGGTACACTTGGGACAGATGCGAAGAACCTTCACATGCATGTCCCTATAAGGTGTCATCAAATTCATAAACTATCAGGCCGGCGGAGTATGGTGGAGTAGAGGCGGGCATTAAGTTTATTGCTCTAAGAAGAAAGGCAACTACATGGAGAGTAGAGCCCCAGAATGGCCAGTGAAATCGTTAAATTGGAATTGTAAATCAGCAGTTGTACTTTGCCGCTGGTATGACATGACTCCCAGGATGAAATATAACCGCCAAGTATGCGCAAATAGAGTTTTAACCCTGCATTAGACTGTTATCACGGTTGAGCCTTACCCGTTGAAGCCAGGGCCTGGGCAAATGAGGCATCCAAGTACCGGATACTCGCTCTGGCTGCAGCCAGGAAAGAGATGGCACTCTCATGTAAAGTTGTCATTCTAGCCCGTGAGCTCGGATGCTAGTTGTCCTTCAGGCAAGGCTAGAGTTGACTTTCTGTACATTGCCGTGGTTTCTGAACACATGGCCACCCATCTTGAGTAGCGGGATCAAGTATGGTAATCTCCACGGTTCAGCGCATAGTAGGGCGCACACTAGTATCCCGCAGGCAACGTGCCGCCTGCGCAATTCTCATTAGTGACATTCCCCGTGTTATGCAAGAAATCTGTCTCTTCCTTTAAGAAACAGGGGCTCACACCTATCGCTGTTGAGACTAGAGCGCTGGCCAATCTTTCCCCGTG +>seq2 +GCCCATATGTTTAGAGTGAACCCGGACGGGCAAGGTGCGGTACAGGACTCAGCGCACGCCTTCAAGGTAGAGCCTCTCTCCTGCGCCGAATTTGTCCCGCGGGCTCATAGTTGATTGGTCGTCGCCGTCCATGGTTGGAGTATGAATTCGAATGCGCGTATCCAGCTCAGTCCACCCCACGTCATAGCCCACTGGTTCTATTAGGCACTACCTTACGACTAGTCAAAAAAATTCAACAGCTGGGATTTCTAGGCGGAGTGCATAGGACGCGATTAACCGAGAGACAAAGTCATGTGGGAAGCGGGCCAAATTGCTTTGAGGCAGGTCTGTAGTGTTAGCTACGACACCATTGGTAGATGTATCCTAAAATTGGCAACCAAGACTATACAATAGCCGACACAAATGAAACTACTCTGTGAGCCACTTAGACTCTAACAAAAGCGGAGGCCCTGAGCCTGCACGCCAAAACCACTTGTACGTCTGTCTGCGCCGCGATAATTGCGAACGGGTCGCCGGTCAGAAGGGTCGTCTACACCTTCTGCGTCGTGCTACTTTAGTGGGTTAGAAGATTCTAGTGAGTAAAAGGTCTGATCCCTACCCATTTTCATCTTCGCAATATAAATATAATTATTCGTCATGTGGACTCCGCAGCACACCCACCAATAGCAAGTTGGTTACTGACGCCGTGAGCCCGTCAACACCCCTTATCCACTTTCGCACTTAGGCATATAGGCTCGGATTAACCAACTTCCCAGCACCACATGTGTATCCTTGTATAGCCGTCCGCCCTCATGACTAGGGTGGCGAGTATGGGGTAGGACCATTTGTTTCCAAAAAGGTGTGTAAGGCATCGAGCCCACAATAAACAGATGACCGCGGAGTTGGGTCCCCTTGTCCGGAATTGCTGGAGCAACTATGTGGTCTCTCTAGGCTTCCATCACAGCACCACGTGTAATTCATATTTCATTGAAAAGCTTCGCTACGATTGTAATCTTTGTGC |
| b |
| diff -r 000000000000 -r 6941d0d453ba test-data/500kb.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/500kb.fna Tue Apr 26 15:27:37 2022 +0000 |
| b |
| b'@@ -0,0 +1,2 @@\n+>random_sequence_length_1000000_1_chopped_1-500000\n+GTCACCGTGAACTTAGACGGGTCCGGTGGTTCCTGTCTGCCACAGACAATAACGCAGAGGCGTCAAGACGCGTTGTCGGGGGTGAATCGCGCGTGTATTTATGCTCCGTAGCAATGATGGTACTGTACAAAGCTCAGCCGGGGCGCGTTGAAGTATCAAATCTCTTACTGAGCGTTAGGATAGTTCCGTTGAGATATGTAGGCGTATTAACGCGTGCGCCCGGGCTGCTAACCAGTGAATACCGGGAGCTCCAGAGTGTCATGTCTAGTCAATGGTTGAATAATGGTATGTTTATCAGGCCTAAGAAGCATGCGGAGCAATGGTGCTTCTGTAGCAACCCGCCATGCGCAGGGAGTGACTGCCGGATTTTTGGCGCTACCTAAAGAATTGATAGGCGGGCGGAAACCGCGCGCATAAAGCTTTCGGAGGTCGTGATTAGTGGTGGAATCCTGTATGGAACAAGGCTTGCTCTCGTGCAGCCAAGAATTGCTGCGGGTTTTCCTAATTTCTTAGCGTTACCAGTCCCGTGAATAGATGTAGAGCTAGTATACTCACTCCGACCCATGAGGCTGACCAGAGTGACGCGCACCTGCCAGAGGGGAGCTAACATAGGTATGTGGGCATCAGGGTCGGTGCCCTCTCGTTTCAGTTGGCGTGGAGCCAGCGATAATATACTTTACCCTTGCTCATCGGTGTCGCAACAGTCAATGGTACACTTTTCTCCATTTTTAAAACATACAATTCATTCTCATCGTTCTCTCTGACGCACCGTCTACGGCCCGCTGCAACGTAATGCTAAGCTTAGCGCTTTCGCCGGTCTTCCGTACCTTTTAGTAAGTATGGCGTACACTCTCTAGAAGGTGCCGGACGGGGTCAGTATCGCGTTTTGCGCCAAGGTCGAGGGCGTATCGGGGCGCATATTTGCGCGAGCTCGGGAGGACCACAGGCGTGAGGTCGGCGTATGGTCGATTTGAAAACTACGGCGTCGGTTTGTGATCATACTTAGACTCTGATCTCAAATCCTGAGCAACGGTGAGATCAGTGAATATACAGAGAGTAAAGAGTGGCATTCACCAAAGATGAGGAAGTCGAGCGATGTTCAATTGGAGAACGGTGTCGCTCCCAAGGGAGTGGGATACTCAGTCTTACTCGTACCTCCAGATACGACTGCCGCTTACCATAGGCTATCTACAGCTTCTGCTCCCACGCTATACGCGATATTTGCACGCTTCGTCTCCGTTGCACGTTTGAGCCAGTGAGTGTCCCCAGCGCGGCAGCCGCTCTCCAAGGAAGATACTTCACTCGCCACACTTCATAACCTTAATAGGCGTTCGCTACAGCTACCCCGAGTTCCGGAATAGACGAACACTTATTCAAATGGAGATAATCTTACTTTGCTGGATCACAGGGAACAATTCTTGGGGGGGGTCGCCAGCTCTTGTTCTACAGTCGCCTCTGGAATGCGCGAGCACAGCACTCTAAGCGGTGGCCTGTCGTCTCCAACAAGAAAGGTTCTGGTGGGTGCTAGCTTTGGCATCCATGGTAGGATGTCGGTATATTGCGTCAGACTTTCCAGAGCACAGCGTTTCTTGTCTGTTCTGTCAGGTGTCCTCGTCTCTCGAGAGCCCACGGAAAAGCAAACACACGGTTTGGCCTCCGGACTAGTGTAAAGTACGCTAGATGATCCCGATAGACCCGTTATCTATGGTGGCGGCACTGGCTCCGAGCACTAACGGTTGATATGCTCCGTTGGTTGCTTATGAGCTCTAGAACCCATGCTAACGCCCTATAATCTCTAGTAGTTCGTGCTGGAATCCGCCCATCACACAACGACAATACACGGGGGTTAGAATCCGTCCACCTAACTGGTGCCTCAGATCTTGTTGGTTCATCGAGTAGATCACGATCCATGTTTCTACAGTGGGAATCGTGGGGTGAAAAGTACATCTCTTAGGAGCTCAAAATTATCGAATACATTAAAGGTATCGCAAAAGGCGCATGCATCCTAGAAAGGAGACCGCGGACAATGTCAACTTTACTTAAGACTAAAATCCTTGTCATTAATTGACGGAGGGGGCACGGTTATCTCATATGGGCAGGATCAGTCCAAAAAGTGGGTCTCGATCAGTTAACTAGCTATTCTGAGGACGCGGATAGCGCACCCAACGCCACATAGTCCGGCGTTACCTCATAAGACAAGCAGATATGGGACTCGGGATGTCGGCTACCCAATCTACTCGGGTATGACAATGTCATCTCTTCCAAGATGGCAATTGTATAGGCGTATGGGTGATTCGCATAATTCTATGTGGGTCCGGTTAGCTACCACTGTCGGCCTCCAGCGGCTACCGGTCTCAGTACCCCAGCCGATTACATTGACTATGACTGCGCGAGCAAAGTCGCGAGGCCCGAGCTGTGTCCTAGCTAGCACTGGAAGTTCCAAGCAGAGTAATTTTCTACCCACCCTCTGGCCGGATATATCCGCACTTTCCCATAGGAAGTAGGAACTATAAAGACGCTATATTCACCCAAATGTTGCCCCTAGTCCACCTTTAGCCCATCTTTCAGGCCAATTACTCACTTTCTCATGTTTCCGATTCCCGTAGTGGAATGCTGTAAGCCATACTACGCAAGAGCCGAAATACCATCGAGCCGGCTTGGCATTGCAGAAACTAGATTAACCCCTAGTGTGACCTTGTCGATATGAGAAGACGACACTAAGCAACGTGTGGGAAAGTGTACATATTTCCGTAACGTGTGTGGCCTTCTCGAAGTAACACCTTCATTGCTAACTGTTGCTTCAGCGCAGAGCAAAGAACGTAAGCGGAAGGTATTTACAGCAACCATAACGTAATCAAGGTTCAGTCCCCGTAGCCCATTGCACACAGTCAGAGGTCTAAGCCGTACGATAGCGTGGGAAAGCTCTCGGATACTGGAGCTTAGTGTACCCCGAGGATCCAGGCCACGTAGAGTGAGGGATATGGAATTTATTGGAGCTAATCCCCGAAGTAATGGTAGAACGGAGCACTAGCGACAGTTCTGTGACTACTCACGTGTATACCCGGGAGACAATACTCTGGCCGAGAGGTACTCCTAGTTCAATCTCCTACAGGCATTGTTTACGCCTAACAAGCCTGACGACGAGGTTCCATGATTGAGGGTTCCCCAGTACTCACAGGCCGCGTATGTCAATCGAACTGGTGGAGTTCTGGCCTAAACATACACAGGATCTTTGGGAGGCTCAGCAGCAGCGATTTATACACATTGGCGGCCTTGATTGAATCTCTGTGGCGTGATACGAGATAATTAAAGGCCAACAGTGATAGTACTGCATACCGAAGCGTGCACCCCATTGATGGTTCTGTCTTCGTAAATTAGCTCCAGCGACTGCCGCGAGGTCATGATACGACTACCTATTGGAGTTTAGTTCTGTTGCTTGAGGATATTGACCCGCTCCAGTTTGAGCGGAGCATAGTGCGGCCGATGACCAGGTCCGCTAATATCCACGGATCCGTCAACCCTTCATCGTCCTGAGCTGGTGGTGCGCAGCAAACATAATGAATTCTCCCAGGCGCCTGAAACGTACCTAAGTGCGTACCTAGATTTCTGATCGTGAAGGAACATCCGTCGGGCAAGGAGGTTGTTAATTAACTCCTTGGGTGGATAGCCAGCCCGGTCGGTCACCGAGATTTCTAGTGGTACCGTCAGCGGATCTATAAGTTCCCCTAAACGATCTTACAATCCAGTACTCGCTTCGTGGTACTCGGGTATGTCTTGCTTACCTAGTAAGGGACTTGACCTAATATTCCGAACAACGGTGAACCTTAAGATAACTCAGTAGTTAGAGTCCGGTGGGAGGAGGTACCCGTCGCTTCCGCAAGCACATGACAGTACAAAAAGTTGTGTCGACGCCCGAGTTGCGCCCAACCC'..b'TTCTCATCACACTACAAGAGATGTCTGCACCGCTGTCACGGTTCGCCGCATCGTGCTAAGGACCCAAAAGCGCAGCTAACCAGTTAGACCAGAAACTCGTGTAGGACATCGTTGCCTGCCGCAAGGACCAACCGTTGCGCGACAGGAAGCCACGAGCCATTCAACTCAGAGGATATGCCATGCTAGCCCCTGGCTACGCATACTAAAGGCGGTTTAGGGAAGTGACAATTGATGAGCAGGGTAATTGCCTACGGAGCGTGTTCGCGCGCTTCTTCCTCCAAGATAGCTCATAGGCACAATGGACGGTAAAGTTTCAGCCACGGACAGGCGAACATCGAAGTGTAGCTGGGATTAATGGGAGCGGCTAGAGGACTGTGCAGCTTGCAGTTTCTTAAGTCCCATGGCTGAGTCGACACTACCCTCGGCTAGATTAGAGACTTCGATAGTAAGCAATTTGCTCAAGGGTATTGAGAAGTAACGCCTAGGAAGACCTTTACTCGTGATACACTCTAGACGCACGTTCGGCGCCTGGTACGTCTAATCGACAGGAGTTAAGTGGCACAAGAAGCTTCATAACATAATGAAGGTTCCGTATCAGTCTAGATCACAGAGCCCGGTCGGTGAGATCCCTCGCGTTAATATAACCAGTAAGTTCTACTCTAGATCACGAGCAGGAGAAACATTACGGGCACCAGAGGTCCACCAAAAAAATTCAGTCACCGCCTCCTATTTCGGTATACCCATTACCCGTGCGCTTCGATTAATTGTTCAACCCTCTATGAAACTGAACGTGCATTTCACCACGGACCCATCAGTATGTAGTGTCGAAGAGCAAACAGATACGGCCTGAATAAGTAGGAACCACGCGTTTCGCACCCCGTTTTACTACCCCTCATATAGCGGACGCCCAATTTCTTAGTCCAAGCTCGTTAGGGGTAGTCGAGCGAGGCGTGCTTAACCCTTGCCTTGAGCAGCGTACAGTGGTTTCTGCACTTGCAAACTCAAACAGATATGGGGGCATGTACTTAGCGCGCACGACTCATACAGACCTGCATGCGCCACGAGCTCACAAATCTGATCCCGCTCTAGTTGGTGTTGGGTTGCATTGGAGTGCTGCGTTTTAGAACGACTAATCCTCGTACGTAGCATCACCGGTTTACATTTCTGGTCGGGGAGATGACCGGGCACGGAGGACCTCTTCTTCGTCCGATGATCGTAGTATGTCATTGCTACTCCCACCGCACCTCACATTAACTGAACCTACACCTAGTATCGGAGTTGAGTTTGCCGGTACTGAATCTGATTTCCGGTTGCTATGTCTACATTATGGGAAAGTTAACATTCAGCCGTAGTCCGTCCTTGATACTGGCTGCACCGTGCTGGAGGAACATCTGGCTTGCACAGGCACACTCTTGTCGGCGCGTTCTTTACTTTCATGGCGTTCATAATTATGAGCTAAAGCACTCGCGTTCCTAATTCAAGAGTCGCAACCTATCTGGCCGGCGTTCCCTGGGCATAATCGAGCCCCTGCCGGTACATTCGTCTGGTCTGTTGTAGTTTATGACATCAAAACTAGCCATGCCGCCCCGCATTTATAGTATATCCTCGGTTCGCGATGGTTCTTCCATTCCCTTAGTTGCGAAAACGTATAGAGCGGCGGTCCCCCGCAGCGCTTTTGCACCCGCGCCATAAACGTGCCCACGCCGTATGGAGACTAATTAGTCCCGGAGAAAGGCTCATGACGAGTACTGAATACAGCCAGAATAGTACATCTGTTGATGCGCCTGCGGTCGAACGTATCTAAATTGCTGAGTCGTCTCCGTTGTATTGTGTTTGTCAGCCACAAAGCGCGCCCTGCAAGAATAGGCAGCGGCTGGAAGACCCCCATCATAGATAAATAACGTAAGTCCACGGATCCAAAAAGGACCTCGGTCCTCTTCACGCGGGGTCTCCACAGAGTAGTAAACCGGTATTGGATCCCCCCACGTGGACTGGCGCAGGCACACAATAAAGCTAAACTCCGGGGCGTGCCGTACTAGATAGGCGAACCCGATAAGGGGACTCAGCGCAGTTACATTGAGCTTAATTGACGGCAAGTCCCTTGCGTTCCCTTTTTAAACAGTTACGATGGCCTAGTCTACTCTCAGTGCGGGAAGTAACCCAAAGTTGGTGTTTTTGTCAGGGATCAGTTGCAGGCGCAGCGCTGCGCTCCTACAATGGGAAATCTACTCGGAGGACATCGTGAGTCCGAAACGGTTGCGCGCATTCTTTGCGGGCTACGACCGCAATGGGAAGGCGTGCTATTGAGCACGGTCTGTAGGTGCGGTCTTTGGAGGTTCTACATGATGCGGGTAAGCTATCATATTCGACAAGAGAATAGATAGTGTCGAAAAAAAGGCCCCGTGGCACGTCACATGCGCTGCGAAGGAATATACTCTTACTGCACAACCGCGACACCCCAAAGGCTCTACCACTGTCCCATAGAGAATACGTAGTCCGTGAGAATTTCCTCACGGTTGTCGTTAAACGCTGATAGACCGAGCTCTGCCCACCATTAGCTAATGATAAACGGGGTTAACGATCTACACGCGTTCGCCGAGTCCTTGCCACACATTAGTATGAAGACAGACCGAAGAGATGCCCCGTATGAAATCAATGAGCCCCTAGCACGCGACCGCTACGAGCAAGCTCACCATCCCAATCCAAGAGGTTAACCACTTTCAAAGATGAAACGATTGAGCGCACAAAGGCATCCAGGAGTACAGGCCTGTGGACATCCCCAAATGTGCTTGCAGGATTATAGGGACTAAGAACAGGGCCACGCTCCGGGCACGAGCGTAGTGCGGCAAGGCGCGCCTAGAGTTGATAAAATATGCCCCTCCCGAGAGACTAACGAACTGGGTAATTGGAGGGATTACTACCTGTACCTGAAAGCAGACTATTGAGTATAATCTTTTATAGCATTCACTGTTCACGCGTAGGTCTTCGTAGTCTTGCCTCCCTAATTGATATGGTCCAGATCTACGTCCTTGATCTTATTCGTCGGTCCCGTGATAGTCAAGCTGCTATTCTTACTCGAAAGTATGCGGACAATTTAAGGTTGTGCCGCGGCTTGGTAGAGTCGACGCCTAGCCCCGTGATCTGCATGAGAGAGTTCCAATGTCTTGATGAGCCAGTAAGCTCCATCCGTCTACGCCCTACCACATATTGTGACTCAGACGCGTTCATGAGGAGCCCCCGCATAGAGTCAAGCACCTAGAACAATCTTTCTTTTTTGCAAAACCCATAATTTTACATAACTGCAATGGATAGATCTTATGTGAACTGTCCTATGGTCTCCACAACCCTAGCTGCGGGTGGCGTAATAAGAGTTGTGTACTAGACGAGCTCCCCAATGCATTAATTTCGCCAAGTCAGATACCGCGGGCGTACTTTAATTCCGTTCAAAGACATACAGGCCCTCTCGACCCCAGACTCTGGCTCGCCTTGAGCATAGGACTACTCCGGTCGTATTGTGTAGTACAGTTCCGTACTACTTCATCGGCACCGTTTTGTTAACTTTAACAGCGGTTGTCCACCACGGTTATGCTGGAGCGACGACGGGCATTACAGATGAGTAATTGTTTGCTCTCGCGGTACAAACACAGCGCCAACAGACATGGTCGGTTACATTCACGTCGCCTAGTGGGTTAATCTCAAGTGACCTCACTATGTTTGCTGAATGATGCGGGACGCATCTTCATTATCATAAGCTGCATCCTTTTATCTCGTAGTAACTGATCTAAAAATCCTACTCATGGCATTTTGTAAGAGAGGTTCGATTCTCAGCTCGCTTTACTTAGCCTCTTAAGCACGGATAGATATTTTAACTCGGTGCTCGGCCACGACTGGTGGAGTATGGTTCCGCACTATATCCTTACTATCCGTTCGCGTCAGCCGAACCAGCGTAGAGGAACTCCGACTTTTAGGGAACGCGGATAACATCTGGCTATGGGGTT\n' |
| b |
| diff -r 000000000000 -r 6941d0d453ba test-data/7seqs.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/7seqs.fna Tue Apr 26 15:27:37 2022 +0000 |
| b |
| b'@@ -0,0 +1,14 @@\n+>genome1~random_sequence_length_11000\n+ACCGCGGGGCACGCTATTAACTGTTGGAGAGAAAACCGTGTGTCACACTCTATAACTCGTGCAGTCGGATTGGATACCACTTTTGCGGCGCGGAGGTCCTGGTGAGCGATTATAAAATAACGGACTGGTGGGTGACCGAACTATGCAATTCGAGCACTGTAGTAGGACCATGTAGTTGCAGTCTCTTGGTAGTGACCGCCCCGTTGTGCAACGCGCTAGGGCGCCGGAGCCGGCTTAGCCTTTAGAATCCCTAATTTGAGACACCTTAGTTGCCCATTCAAAGTAGTTATTACCCGTGATATCCCGCTCAAAACTTAACTTGACTCCTGACTGGAACAAGTCGCAGCGTGGGTTAAACAAGAAACTCCCCGCGCTTGCCTATAAGTAAGCCCGCGATTGTGGGTTACCGTCCATCAATGGTAACAGGTGAACTCCGTAGTTATACGTACTAAACGACAGATATCCAAACCGTGGGCAGCATTCTTGAAATCCTAGGTTAGCCTTCGTACATACCGGATTCCGCTCCAGGCCAAACTTGTGGGTTATCGATTGGAAGGAATGAGCGGCCCATTCGTTGAGGAAGTCACAAACGAACAGCTTATTGGTCTATTAATACGCCCAAAATTTCACGGACCGCACGATCTATGCGAGGAATCCCTGAGGAAAAGAAACACAAGTTCACTACCTGCTTCAAACCGCTGTACGGTGATTCCTCCAAATCAGACGCGGGACGACAACAAGATGATAGCGCGTCAATGGATTGCCGCCGCCCCAATGTCCCATGTTAACTTCGCCCGCGGTATATTGGGGTGAGCAGGAAATTCTCAACGCTGAAACACCATTTCACAAGCCCAAGTTAAAAGCCGCATGGGCTCATGTAAGTGGAGTAGCGGGATAGAGACACAGGACAATCATTTAGCTTCTGGAAATGGTTCGTCAACACGCTGTGGGTTGTATTATAAAAAGAACGCGCCCTAGCAGCGAATAGACGTCACGATGATCTTATACCCTCGAGCTCAGTACCAGCAATCGTGTCGCAAACGTAGACCTCTTTGATGTGCCCGGTCCTCGCTACATTTCTCGCGCGCAAAGACGACGTTATTAATGCCACGCGAAAATAATACTGTGTCCCCCTGTACGACTTCCTTGTTATGAGTATCAACAGTCCTTGACGAGGACTGGAGTTGAATATACCGCTTCAAGTAAGTCCCCGCAGACATACACTTCCTCAATAGACAGCTTTTAACCGTGTACCTCAACTCCTAACCTGGATTCACGGCTTGTTTGACGCAAGAAGAGGGCGTTTGTTGCGTCATAAGGCCGCGCGTGACAAATGTGGGGTAGATTATTCATTATACGGCTTTACGAAGGATATTGTAGCACCTCTTGGTCTGCCAGTGGTCGTCGTTGAACGCTCTGAACCAGAGTGATTATTACGCGCGCGTCTTTACTTATTAGGATTGCAGAACTTTTTCTCAAACATCGGAACTTCGACCAGGAAGTGAGGTCCTCTAAATTCCCAGCTGTTATCGCTGCCACTACGTGTATGATGTGGGCAAATCAAGGAAATACTGATACAGTAGTCCTATAATTAATGATCATTCATGCGATCGCTCTCCGGTATATGTTTCGATTAGCCAGGCTCCGTGACATTAGAGCCCGACAGACCCTTGTCTCCGAGCGATTCCTCGAGTTCAACATAAGGTACGAGGAACGAAGCATTATATTGTAGTAAGTGAACGGATTAGCAAGGCAATGTTCTTTGCGGCAGATGAGCGTCCGAACGGGGGAAAGGAGAACAACCTTTCCCCCAATCCCATTGTGCTTGCGACGGAGGTCTAAATGACCCTGTCTTTCACTGTCGCCCGCTAGGGGAGCAATCTAATATGCGGAGCCTCTACGTTTCTTCAAGTAAAACTCGCAGCGGTTCGCTACATGTTGGTGCTACAACGCTGCGCGGATAAACCCGTTAGCTGATAACCCTTTCATATTAAGCGAACATAGTAGAGTTCTGTATCCAGGCACAGGGCCTGTTGAGTATATTATCATCTAAGTACCCGCCAGCTACCGCACAACGTACGTCTACTACTCACCCATCGATTGTCCGTGATCAACTTCCCTGTCGAGTATCCTCAGACCGCAATGGTTGTAGCGAGCTTCTCTTTGTGGGCGAGTTTGATTTGTTACGCCATAAAATTCTATACGATCACGATGTGGAAGTGAAAGCGTGGTGGACAGCTACAGTGACAGATTTCGAGTATATCCCTTGTGTTGAACCATCTGAACGTTTGACGGCTCATTACGCCGCACTATGGGGACGATATACCACTTGGCAGTAACCAATCGGCGCCTAGACCGCGATCACTTTGCCAAGATTCGCTCGTGTATCGACCCAGTAGTCCAGACCAATACAGAGGCAAGTGCCAAAGGTAGGGTCGTCGGCGAGCGAACCCCGCACTAACCATTCAAACCACCCGGGACTAGATCACTCCAATATAGGACTTGCACCATAAAGGTAGATGGACCTCAGGGCGATTTCCGTCATAGAGTCACGCCGTTTGTCTGATTTCGGTCGTAGGTCGGATAAATGACGCCATATGCCTTGACGAAGACAGTTACGAAGGAGCCCTCCTTTATTTGACACCACTCAACTTTATGTAGGTAGATGGGGATGCCCCAGTCCGACAGGGTCGCATGAGCCGCCTCTACCTCCCGTGGTTCCCGCGTTCTATTTAGATAGCAGAGGTTTACCAAAAAGTGATGAACTCCCAATGGTGGTCATAGCGTTGGTGGACTATCGATGCGCAAGAGCAGGTACCTGGCACATCCAGGTGTGCCGGATCATCTTCCTATGTCGGATACACCTACGATTAGAACTGTAATACTAGTAGTGACGAACGTGGTGCTCTCCCGACTACATTCAGCTCGAGGGGCAGACGACATTGAGCCTCTGTTACGCAAGCGCAAAAGGCAGCCCAATATGCCGTGCCTAGAAGAGACCGAGCTGCTCATAGGATTGTGAGACTACAGTAACCAGCGAGCCATTTTAGCGGGCCATCCGCTTGATCAAATCTAATCGTCGGTCCTTCGGGGGTTGGTCGCGTAGGAGCTTAACTGTCCCGGCGTAGGGAAGCCTAAGCGAGGAGGGCCTTGTATGCTAGAAATTGCGCCGCGTTTTCCAATAGGGCAGAGGACTGTGCCCCTATGCAAAGTACCTCGGGATTGTGAACAAAGGCACTTCATAGTGAGCACTCGATTGCAGTGCGGGTTCCGGGGGTACACGAATGCGAACGCCGCACTGACCTGGTTGGCCCAGACTTCAATGCACGCATCATCTGTCTTCGTATTGGGTTACGGCCGCCAATTTGAAGACATGATTAAACGCTACGCTGTACAAGTCGATCAAGCGATTGAGGCTCTCCCAGAGACTTCAACAAGAACCACGCAGCTGAGTTTCGATTTTACGTATAGCCCGTTCAGGCGCAATAACACGCGATTGCAGAGCTGAACGCGGTCCTCAGTACCGCGCCCTCGCGGGCACCTATGCTCTGGGCAGTGGAGATGAAGTAGAATGTTTAACAAGTTTGTCGGATGAAACAGAGCCCAGTCACGAGTGAAACAGGTTGTTAAAGAGAGCAGATGTAATAGAGGAGGATCAATTGCTTCGCTGAAACTATTCGACTCTCGTATAGCTTTTGAAGACGTTTCCGGTCATCTCGGAATTGAAAGGCCTATTAAGCGGATGTCGTGCGGTCTGTTACCCCGAGACCTAGAAGGCGTCCGGATGTTTCCTGAGTAAGTTGACGGCAGTCACGACCGACTTGCTTCTGGACCGTCCTGATGAACCCACCGACAACCCAACTGGACTGTACTTATTGAACCGCGATCTTGACTGCAGATCAGCACGGGTATAGATACTCTTTTATAACACAGCGCAATGTC'..b'CGACTTACACGGGACCCACGGGTAGGAGGTGACGTACCGCCTACGCCAGGTGCGTCCGCCATGCCGTGCAATACCCGCGACCAGTTCGACTGTGCGCCTCATTGTTGTAGGATAGTTAATCGAGCGGCTTGGGCGGTGAGACGCGTAGGCGATAGTTTTCGATTATCAGTTACACCTCGTTAAGTGACTGGCTGCAAGTCGCATTAAGCAACAAGGGGATGCAGTGGTCCGGACGGCAGTTAGAAACAGTGATTGAGATTATGGCAACCTGTGGCGCGGGGTACCAAGCATATCACCGAAGACACAAAAGCGATGCCAAGCGTTAGCAATTCGATCTTGGGCCTGCTAAGGCAAGCTCTCCTATAAGGGAACCAGGCTATCCCAGCCGCCCGAACACGACCCCTCGCACCCACTACCTCCCGGGGAAAGACCGGGCACTCTCAGAATGCTTATTCAAAGCTCTACGAATTTGGAACCCAGGTAACGGACCGCCCGGCTCGCTAACCCACATCGCAGGGCCTCAGAAAAACACTGTGTCCGCGCTCTCAGACAACAGGCACGGCAGATTCGTGCTTACCGGTAAAATTTCTTCCGCCAATACAGTCCGACCGGGAAAATTATCGTGTTTCCGGTTAGGGGGACTTCAAGAGCCCCTAAGATAGGCGGTATAGCGCGATGGGCGAGGGCGGAACACATCACCGTACTTGGTACTAACAACCAGAGAAACGAATGTTTGGAGAACATCACGGTATTTGTCGGCAGACACATTAACTATCATGACGCTTCACCCGAAGTTGCTCAGCAGTATTTATCGGTCGAGATGAGGCCTTAGTCAATTCATAGGCGCTATTTATTACGAATCTGCGATTGACGTATACGCGTCAGCACGGTCTGGATTCGGTCTATCCATTCAGATAGCATAATAAAATCCGAAGCGTTGTACGACGCTATGCCTGTGTTACTCCGGTGCCTCCCGTCGGATTTATTGGGGGAGTCCTAAATAGGCGAGGCCCGCGACAAGATTGTTGGTGTTCGCGGACATCAGCCGGAGTTACGTCTATAAACTGCATTGATATATCCGAGCGCCTTAGTCTCTGCAGCGACCACCGAACCACAAGCAAAACTGCCGTAACGACCGCCCCAACAGCTACGAGGTCGGGAAGCGCACAATGGTTCGGCGTGGTCGCCACCAGATACCGTCTAAGATGGAGACATTTCTTCTCTACGATGCAGGCTCCCGGAGGACGTCCAATGAGTCCGCTGTGAATGTACTATCCTAATACGATGACTTTGGACCTTTCCGTGACGTCAGTACACGGGTATGTATAAATCAAGATTTACCATTGCGCTTAGTAGACGTCTAATCGACAGTTAGGGATCGTCATTGACAGTCGACCATTGAGATGCTAAAATAACCGCTAGCTTCTCTTATTTTGGTGGGGTTTAGCAGGTCTCAGAGTAAGGATACCGAGGGACTCAGACCAAAGGCTACCAGACGCCGCTGACCACATGCATAGGTACGCAAAGGACTGGGGTGGTCGTACCCATCTCTTCCTCATAATGATAGCAAGAAGCACTTGCTCCCTATGCGTTGGGACGTTGGATGACCTCAGAAACTGAAACCAAAAAGTCACAAGATCTGCAAGGTCATTTCCTGTGTGTTTTCTAGGCCTGACTGATATTGGAGTTTCGCCCAAGACCGGGCCAGAATTCGTCGCACCGCCTAACGGCTGATACTTTTTAGGACGAACCGGGGCTTCCGTCGAGCATGCCTAGGAAGACTCAAGTAAACTTACTTATCCCGTGGGGTGATGATCATCCCAATACCTCGTAACGCCGTACACAATCGTGGATTCCATTTCGTCCTGGGTTCCACACGTTTGATCACTTCGAGGCCCAGGACCGTCGCACCGAGCGTTGGCTCGCTATGCGATAAGGCTATTTCGCCTAGAGACTGATTTAGCGGAGCGGTGGGAGTGAGTCACACGAGAGAGGGTCGTGTCGTGATCAAGACCCCTGCTTCCGCTTGCGCGTGTGCTTCATGGTTCGCTATTTGATGTTGGTCCTTTTTGTCCCTCATTATTTCGGGGATAGAAGTTAATCTCCGCCCGCCGTCCAGATCTGTGTATTACACCGTGCACTAAGTCGATCCTGCACCCTTTTCCTCGCGGCAAGCAATTTAGCTGCTAAAAGTGAATGAGGGTTCGTAGTTAGGAGCACACTTTGCGTTAAAATATCGTGCCATTGGTATGTACTGGGCCCTACATACCATAGCCGATAAGTATCTGATTGGGTATTGTGTCTCTGTCGCTATCACTCGCTGTGCTCAGCTGGCTTTTGTGGTTATTCCATAAGGATGGTGTCCTCTTTTGGTCGCGATACAAGAACCTTTATGATATGAGATTCTTGGCACGCATCAGCCTCAGCATGTATTTGTACATCAATGGGCCATCCGTAGGGATTGCGTTAACCGTGTACTGACAGGGTGTCGTAGACATTCACCATAGTCGATCTCCACCGGGACAGTTATGAGCAGGAGGAGATAAGTTGTCCGCGGCATTACCAAATACAGCTTTGCACGGTCGTATGTGAAATCGGCTGGGCCTATATCAGCTAGAACTAAGTATCGTGAGGTGCTCACGCAGCAACGTGTTTATATGCATGGCAACCTCCAGTAGCGTGGATATAAAAGGCACTTGTTACAGATCCGAGTCCACGTACGCAAATGTAAACACGCTGCCTCTGTCTACCGCCTCGGGGACCTCCTTCTGTATTAAACAGTCCCTCGCCACTCGTAGGGGTGCCTTGGCACGGGGTCGAAAGCCTCCCGGATTGTCGGCGTAAGGTCGTCCTCCGGGTCTAGAAGGCTTAGGCCGCTTTGTGACCATGTACGCGTTGCCATGTGCCCGGGGTCGTAAGATATCCCAAAAGATACAAGACTTTAGCACTATATTAACTCCTAAGTTCTGGATCAAGTCGGTTGCAGCCATGGGAACCTGCAAATAGGCCTCGGGAATGGTTGGACGGTATTAGTTCATCTTCTGTCTATAGGAAGCCTGCTCCCATCTGGAGCTGATGCTTATCGGTCCCATGCGTTTGCGCCCGAATTTTAAGATAGCCCCCTCTAGTGCCGTTGACGATGCTAGCAATAGCTTAACCATCGTCCGACGCCGAGGGTGAGTCTATTTGTTGTTTGAATACGGCCCCCTAAACCTTCCGGACTCTACCTCAGAATGGCAATGATCGACACCTGATTTGGTTAGACACCCTCTACCTAGACCTGTTTATCATTGGTACACCTGGTTGTTAGTCTTCTCATTCTTAGTGATGGTAAGCCGGCACCCGCATCAAGCTTGATGTCGGAATGTTTCGTCTAAATTTGCTAAGGTCTGAATCCGATTAGAATAGCACGGGAGTCCCTCCACCGCTTTTTAGATGTGGTTCCAACGCATCTAGCGCTACTCCTTATAAATCGTCTCAGTCCAGTAGAGGTTCTTCTGCTTTTCTGAGACCTACGCACGGTTTCACTAAGTTGACCTTCGCAGCTTGCTATAATACTCTATGCTAGAGCTTAACATACCGCGCTACAACAGACTGTCCTCCTTTGCGGATGTCATGGTCGCGGCTCCAACCTTGTCAGATTAACTCCTTCATATATTTAATAGGGCGCTCACACACTGGGCGTTGGCAACAAGTTGGGAAGGTTGCATTCCGGCTGTCTACATTATACTGAAGAGCTGTAACCATCAAGCGAGGGATGAGTTCTGTCTCTGATGTGTTGCGCTAAAATACCAAACCGCGAGTTGGTAGGCGGCCACCGTGCGGTTAGAAAATTTAACGGTAACTAGGTTTGTCAAGATCCGCAATTTTAAGCCTCACTAAGGGTCTGACTTTAATTAGCAGAAGCTGGCCCTCATCTTTGGCACCGCAAATTGGCTGTGTGGTCTGATCTAAGGTTCTTTCTTCGGCGGGTTCTCTAAACAAGGATATTGGGTCGG\n' |
| b |
| diff -r 000000000000 -r 6941d0d453ba test-data/7seqs.reads_for_seq1_and_seq2.bam |
| b |
| Binary file test-data/7seqs.reads_for_seq1_and_seq2.bam has changed |
| b |
| diff -r 000000000000 -r 6941d0d453ba test-data/all_fasta.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc Tue Apr 26 15:27:37 2022 +0000 |
| b |
| @@ -0,0 +1,30 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of sequence data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/, +# +#then the all_fasta.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/hg19canon.fasta +# +#and your /depot/data2/galaxy/hg19/ directory +#would contain hg19canon.fasta files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/hg18canon.fasta +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/hg18full.fasta +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/hg19canon.fasta +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/hg19full.fasta +test1tg01 "TestGenome" ${__HERE__}/reference.fasta \ No newline at end of file |
| b |
| diff -r 000000000000 -r 6941d0d453ba test-data/bad_reads.all.interleaved.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bad_reads.all.interleaved.fa Tue Apr 26 15:27:37 2022 +0000 |
| b |
| @@ -0,0 +1,40 @@ +>1 1 +GAGTCCTAAAAGCATGACCTGCATCTCCGAGAAGGGTCCCAGGGGCGGTGCTAGATCTCAGCAAGGAGGCAATGTGGTTGGGTTTTATAGTCACCCTTTCGAATACTCGAAGAAGGCGCCTGCCCGTTCTAGAGGGAGACATAAGCCTC +>1 2 +GCAAAGTACAACTGCTGATTTACAATTCCAATTTAACGATTTCACTGGCCATTCTGGGGCTCTACTCTCCATGTAGTTGCCTTTCTTCTTAGAGCAATAAACTTAATGCCCGCCTCTACTCCACCATACTCCGCCGGCCTGATAGTTTAT +>2 1 +CGAATACTCGAAGAAGGCGCCTGCCCGTTCTAGAGGGAGACATAAGCCTCTGCATCTGCAACGCGGATGGCTAATCAATAATGACCTGCGGTGGATCAGATACCGCATCGCAAGGACCACGTAGGTTGGCTGTCCAACGCGCAAGCGCGC +>2 2 +GGTAAGGCTCAACCGTGATAACAGTCTAATGCAGGGTTAAAACTCTATTTGCGCATACTTGGCGGTTATATTTCATCCTGGGAGTCATGTCATACCAGCGGCAAAGTACAACTGCTGATTTACAATTCCAATTTAACGATTTCACTGGCC +>3 1 +TACCGCATCGCAAGGACCACGTAGGTTGGCTGTCCAACGCGCAAGCGCGCACATCCGCCGATGAAATGTATGTTGATATTATGGGGGGTACACTTGGGACAGATGCGAAGAACCTTCACATGCATGTCCCTATAAGGTGTCATCAAATTC +>3 2 +AATGACAACTTTACATGAGAGTGCCATCTCTTTCCTGGCTGCAGCCAGAGCGAGTATCCGGTACTTGGATGCCTCATTTGCCCAGGCCCTGGCTTCAACGGGTAAGGCTCAACCGTGATAACAGTCTAATGCAGGGTTAAAACTCTATTT +>4 1 +AGATGCGAAGAACCTTCACATGCATGTCCCTATAAGGTGTCATCAAATTCATAAACTATCAGGCCGGCGGAGTATGGTGGAGTAGAGGCGGGCATTAAGTTTATTGCTCTAAGAAGAAAGGCAACTACATGGAGAGTAGAGCCCCAGAAT +>4 2 +CTCAAGATGGGTGGCCATGTGTTCAGAAACCACGGCAATGTACAGAAAGTCAACTCTAGCCTTGCCTGAAGGACAACTAGCATCCGAGCTCACGGGCTAGAATGACAACTTTACATGAGAGTGCCATCTCTTTCCTGGCTGCAGCCAGAG +>5 1 +TTATTGCTCTAAGAAGAAAGGCAACTACATGGAGAGTAGAGCCCCAGAATGGCCAGTGAAATCGTTAAATTGGAATTGTAAATCAGCAGTTGTACTTTGCCGCTGGTATGACATGACTCCCAGGATGAAATATAACCGCCAAGTATGCGC +>5 2 +TCACTAATGAGAATTGCGCAGGCGGCACGTTGCCTGCGGGATACTAGTGTGCGCCCTACTATGCGCTGAACCGTGGAGATTACCATACTTGATCCCGCTACTCAAGATGGGTGGCCATGTGTTCAGAAACCACGGCAATGTACAGAAAGT +>6 1 +GCCCATATGTTTAGAGTGAACCCGGACGGGCAAGGTGCGGTACAGGACTCAGCGCACGCCTTCAAGGTAGAGCCTCTCTCCTGCGCCGAATTTGTCCCGCGGGCTCATAGTTGATTGGTCGTCGCCGTCCATGGTTGGAGTATGAATTCG +>6 2 +AATTATCGCGGCGCAGACAGACGTACAAGTGGTTTTGGCGTGCAGGCTCAGGGCCTCCGCTTTTGTTAGAGTCTAAGTGGCTCACAGAGTAGTTTCATTTGTGTCGGCTATTGTATAGTCTTGGTTGCCAATTTTAGGATACATCTACCA +>7 1 +GGGCTCATAGTTGATTGGTCGTCGCCGTCCATGGTTGGAGTATGAATTCGAATGCGCGTATCCAGCTCAGTCCACCCCACGTCATAGCCCACTGGTTCTATTAGGCACTACCTTACGACTAGTCAAAAAAATTCAACAGCTGGGATTTCT +>7 2 +GGGTAGGGATCAGACCTTTTACTCACTAGAATCTTCTAACCCACTAAAGTAGCACGACGCAGAAGGTGTAGACGACCCTTCTGACCGGCGACCCGTTCGCAATTATCGCGGCGCAGACAGACGTACAAGTGGTTTTGGCGTGCAGGCTCA +>8 1 +TTAGGCACTACCTTACGACTAGTCAAAAAAATTCAACAGCTGGGATTTCTAGGCGGAGTGCATAGGACGCGATTAACCGAGAGACAAAGTCATGTGGGAAGCGGGCCAAATTGCTTTGAGGCAGGTCTGTAGTGTTAGCTACGACACCAT +>8 2 +TGTTGACGGGCTCACGGCGTCAGTAACCAACTTGCTATTGGTGGGTGTGCTGCGGAGTCCACATGACGAATAATTATATTTATATTGCGAAGATGAAAATGGGTAGGGATCAGACCTTTTACTCACTAGAATCTTCTAACCCACTAAAGT +>9 1 +GCGGGCCAAATTGCTTTGAGGCAGGTCTGTAGTGTTAGCTACGACACCATTGGTAGATGTATCCTAAAATTGGCAACCAAGACTATACAATAGCCGACACAAATGAAACTACTCTGTGAGCCACTTAGACTCTAACAAAAGCGGAGGCCC +>9 2 +CCTAGTCATGAGGGCGGACGGCTATACAAGGATACACATGTGGTGCTGGGAAGTTGGTTAATCCGAGCCTATATGCCTAAGTGCGAAAGTGGATAAGGGGTGTTGACGGGCTCACGGCGTCAGTAACCAACTTGCTATTGGTGGGTGTGC +>10 1 +AAATGAAACTACTCTGTGAGCCACTTAGACTCTAACAAAAGCGGAGGCCCTGAGCCTGCACGCCAAAACCACTTGTACGTCTGTCTGCGCCGCGATAATTGCGAACGGGTCGCCGGTCAGAAGGGTCGTCTACACCTTCTGCGTCGTGCT +>10 2 +TCCGGACAAGGGGACCCAACTCCGCGGTCATCTGTTTATTGTGGGCTCGATGCCTTACACACCTTTTTGGAAACAAATGGTCCTACCCCATACTCGCCACCCTAGTCATGAGGGCGGACGGCTATACAAGGATACACATGTGGTGCTGGG |
| b |
| diff -r 000000000000 -r 6941d0d453ba test-data/bad_reads.interleaved.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bad_reads.interleaved.fq Tue Apr 26 15:27:37 2022 +0000 |
| b |
| @@ -0,0 +1,24 @@ +@1 +GAGTCCTAAAAGCATGACCTGCATCTCCGAGAAGGGTCCCAGGGGCGGTGCTAGATCTCAGCAAGGAGGCAATGTGGTTGGGTTTTATAGTCACCCTTTCGAATACTCGAAGAAGGCGCCTGCCCGTTCTAGAGGGAGACATAAGCCTC ++ +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +@1 +GCAAAGTACAACTGCTGATTTACAATTCCAATTTAACGATTTCACTGGCCATTCTGGGGCTCTACTCTCCATGTAGTTGCCTTTCTTCTTAGAGCAATAAACTTAATGCCCGCCTCTACTCCACCATACTCCGCCGGCCTGATAGTTTAT ++ +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +@2 +CGAATACTCGAAGAAGGCGCCTGCCCGTTCTAGAGGGAGACATAAGCCTCTGCATCTGCAACGCGGATGGCTAATCAATAATGACCTGCGGTGGATCAGATACCGCATCGCAAGGACCACGTAGGTTGGCTGTCCAACGCGCAAGCGCGC ++ +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +@2 +GGTAAGGCTCAACCGTGATAACAGTCTAATGCAGGGTTAAAACTCTATTTGCGCATACTTGGCGGTTATATTTCATCCTGGGAGTCATGTCATACCAGCGGCAAAGTACAACTGCTGATTTACAATTCCAATTTAACGATTTCACTGGCC ++ +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +@3 +TACCGCATCGCAAGGACCACGTAGGTTGGCTGTCCAACGCGCAAGCGCGCACATCCGCCGATGAAATGTATGTTGATATTATGGGGGGTACACTTGGGACAGATGCGAAGAACCTTCACATGCATGTCCCTATAAGGTGTCATCAAATTC ++ +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +@3 +AATGACAACTTTACATGAGAGTGCCATCTCTTTCCTGGCTGCAGCCAGAGCGAGTATCCGGTACTTGGATGCCTCATTTGCCCAGGCCCTGGCTTCAACGGGTAAGGCTCAACCGTGATAACAGTCTAATGCAGGGTTAAAACTCTATTT ++ +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
| b |
| diff -r 000000000000 -r 6941d0d453ba test-data/contig_test1.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contig_test1.tsv Tue Apr 26 15:27:37 2022 +0000 |
| b |
| @@ -0,0 +1,8 @@ +Contig 7seqs.fna/fw0 Mean +genome1~random_sequence_length_11000 0 +genome1~random_sequence_length_11010 0 +genome2~seq1 1.4117647 +genome3~random_sequence_length_11001 0 +genome4~random_sequence_length_11002 0 +genome5~seq2 1.2435294 +genome6~random_sequence_length_11003 0 |
| b |
| diff -r 000000000000 -r 6941d0d453ba test-data/contig_test2.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contig_test2.tsv Tue Apr 26 15:27:37 2022 +0000 |
| b |
| @@ -0,0 +1,3 @@ +Sample Contig Mean +2seqs.fasta/bad_reads.interleaved.fq seq1 0.9705882 +2seqs.fasta/bad_reads.interleaved.fq seq2 0 |
| b |
| diff -r 000000000000 -r 6941d0d453ba test-data/contig_test3.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contig_test3.tsv Tue Apr 26 15:27:37 2022 +0000 |
| b |
| @@ -0,0 +1,3 @@ +Sample Contig Mean +2seqs.fasta/bad_reads.all.interleaved.fa seq1 1.4117647 +2seqs.fasta/bad_reads.all.interleaved.fa seq2 1.6764706 |
| b |
| diff -r 000000000000 -r 6941d0d453ba test-data/contig_test4.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contig_test4.tsv Tue Apr 26 15:27:37 2022 +0000 |
| b |
| @@ -0,0 +1,3 @@ +Contig 2seqs.fasta/reads_for_seq1_and_seq2.1.fq.gz Mean 2seqs.fasta/fw0.fasta.gz Mean +seq1 1.4117647 1.4117647 +seq2 1.2435294 1.2435294 |
| b |
| diff -r 000000000000 -r 6941d0d453ba test-data/contig_test5.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contig_test5.tsv Tue Apr 26 15:27:37 2022 +0000 |
| b |
| @@ -0,0 +1,8 @@ +Sample Contig Mean TPM +tpm_test genome1~random_sequence_length_11000 0 0 +tpm_test genome1~random_sequence_length_11010 0 0 +tpm_test genome2~seq1 1.5882353 900000.0357627869 +tpm_test genome3~random_sequence_length_11001 0 0 +tpm_test genome4~random_sequence_length_11002 0 0 +tpm_test genome5~seq2 0.14467005 99999.99403953552 +tpm_test genome6~random_sequence_length_11003 0 0 |
| b |
| diff -r 000000000000 -r 6941d0d453ba test-data/genome1.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome1.fna Tue Apr 26 15:27:37 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>random_sequence_length_500_1 +GAACATGGGGGGTTGTACACCGCTGGCAGGATATAAAAGAGCGAATTCTTCGTGGTGGGATGCAGAATGTTCATGCACCGCAAACCTTAGGCCCTACCCAATAACAGTCAGCTCCTCCCCTAGAAATACCGTGTCTACGTGTATGTAATGTCAAAACCGCGCTGGTCCATAACTGACCACGACATACGCTTAAGCGACGCAGGTCCCCGTTTATGGACGCAGTAAGATGATATGACAGTAACAGAACGAACGCCTTGATAGCCACTTGGCCTGGTGCCAACGGGGAACGACCTATAGGGGCCAAATTGATTCCAGCTGGTCGGGTGCGCGTATCATCCAATCCAGCCAGGCAGCAACCTCGTATAAGCATCCACACAGCGAGATTTCCAGGACCTTTGAGACGCATCTAGCAGTTTTCCCCCCTTCCACTGACACGTAGTTGATCAAATATCTCGTGTCCACCGGAATCCTCAGAGATTCTCTTCTGTCAAAAAACACTC +>random_sequence_length_500_2 +CGCTCATGTGCCAAGCATGGACGCCGGAGACACATTTGCTAGTCGGGATGTACGCGGTCTTGTCCACTCTAAAGGGTAAATACAGGAAGCGGTCTCTAGGGACGGGCACTTAATGTAGTTGCATTTATCGATCGCGGGTCCAGATCTGATAGCCGTGCTATGCACATACGATGCTCATAACGCGCGTGATTCCCTTCATTAAGGTACGGCTACCCTGCACCTCTAGACTTGTTTGTACTATCTAGAGCAGTGAGTCGAGCGTCGACAATAGGGTCAGGGCCGGGTACTATTTTGAGCTTTACGGTAATTGCCTTGGGCTAGTAAAACCGCTTCTATACCGCAGACTCATCGAATAATGATTCCTGCAAAACGAGCACGATACGGGAGTTCCTTATGACCAGTCTAATGGTCTCAAGGGTCTCCCCCGGGGAATTACGGTGCCAAGAATGTCTCTGTAATTGACCTAAGTTGTCTGTCGATCCAGAAAATCTGACCAAGAT |
| b |
| diff -r 000000000000 -r 6941d0d453ba test-data/genome2.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome2.fna Tue Apr 26 15:27:37 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>random_sequence_length_500_1 +TCATGAACGGTAGTCAGTCAAGTTTCGCCAGCAATAGGCACAGCTTGTATGGAGGGGTTTAGTCGCCGGAGTGTTACGAGTTTGACGATCCAAAGTTGGAGTCGCCGTGATAATTAATGATATTGCGTCTTCGGTGGGCACGATGAGCCAATCTGCGTCGCACTAGTTTACGTGTTAACGTAGTGAACCTAGACATGACGGGACTATGGCAGTAAGCCGTCACAGCATGTCGGTTCCGGACCACGAGGGTCCATAAGACTAACGATCCACGCTAATTGGCGGATTTACCAAGGCGTCTTCTCTGCGTGTAAGACCCACACCGTGCCTCTGTACCTATGGACGTGCGCGACCATCTTATGATATGAGCATCACATGTTTAATAGAGCGTCCGGTGTCCCTGTAATGCCACCACTTCTGTTTCAACGGACGCTGAATCTAAGCCGATATTTTTGCCTTGATCAGAACGGGGCAGTGAAGGAGCTGCACTAAACTGGCCCTTA +>random_sequence_length_500_2 +GGATCGGATTACTAATGTTTTTCCAGTCGCCTGTTACTCCAGGCGCGGATGCGAGTGGTCTTTGCCAAGTAGCCCCATGCCACCTGTACAAGGCGGACAAACGCGGATGCGTTTGCATAAATTACCACCGTAAGATACGTTGGCGTATTGCCGTACAAAGGCGGACAGTCCAGATATTTCTTCGGATGTAATTATTGTAGGCGTGCACAACCTACTAGGCGAAAGAGCGGCCCGTTAATCGCGGGTCGCGCCGTGCCCAATTGAACACTTTGCCACGCACGTGACTGGCGGACGGCTCACACGCTATCTCCAAAAATCTACACTTCCGGAGCTAGGCTCCATGACAGGGATGTTCTTATTCAACAAGATGGAGTGCTAATATTAACAATCGACGACACAGGTGAAAAACCTCTTGTCATGTAGCTAGCAGTTATGCGGGCGTACACACTAGTGCTAATCTACTAATCATCCACGGGCCCCTGCTAGAGATCCAAAGGGGT |
| b |
| diff -r 000000000000 -r 6941d0d453ba test-data/genome3.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome3.fna Tue Apr 26 15:27:37 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>random_sequence_length_500_1 +AGAGGGAGCCTTGCGTCGGTGCTCCACGTCGTAAAGCCGTTGAGACCGCGATTACTTTGTTTATTTTCAATTCACTTGTCACAATCAGAAGGACACCGGCGACGGCCAGTTTCCATCGCCCGTCCAGGGTATCGGGGTACCTCTCTACTCGAACGTCTGCGGGGGTTTATCGGGTCTTTACAGGGGGACCAAATGGTTGGACACGGTACCTCAACGCGATAATATATGTCCTGAGTGTGATCATCGGCTGCTTGATTGACTAGTAAGTAAATAACTCCGCCCGCCGAAAGTGACCATTCTAGGAAAATACCCTCTAGCCTCTTGCTTTTGTACGGACTCACTTTCAACGTCCAGGGGTTGCGAACTAATACAGTGAAAGCGATGACCGACAGTAGCAGTTGAGTCTCCCAATGCACCGGTCCCTAACCTCAACCCGGCGTCTAGTCTGACCAGCCTATACAGATAGCAAACAACGTGGACGCGACGGACATGACGAAATA +>random_sequence_length_500_2 +GCTACTTTACCGTGCGGAAGTAGGTGGGTAGGCCCACATCCTCGTCCTTCAGTGGGCACCCATCTCTCTAAGTACATCTCAAGTGAGGAGGGCTGAGAAAATTGGACGATCTAGTGGAAGCGCGCCGAAATATGGCCTGAGTGAGATCGACCCCGAGGAGCGAGCTCGTTTTCCGAAGTTCGTTATGAGTATGGCGTTCGTTGCTGGCCGAGTACCCCCTGGTGACGTAAAGTGTTTATTTACACAGCTACTTCTCCGAACCAACGACTTATATGTGGGTCCCTGATTGCCTCCCATAGGTCCGGCATAGTTAAGAAAGTTAACGGAACCAAAGTCCAGTACATGGAGTTCTATGATAGACAGCTGTCTCCATTCCCGTATCTGCCAAAGAGATTAGATCCTAGTTGATCCCAGCAGCTACTCGTAATGACAGGATCCGGCGTGTCACTATACGACGCTTGCGGGAGGATGGTCGCCCTGCCCGTACCGTTACTTAGATC |
| b |
| diff -r 000000000000 -r 6941d0d453ba test-data/genomeInfo.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genomeInfo.csv Tue Apr 26 15:27:37 2022 +0000 |
| b |
| @@ -0,0 +1,3 @@ +genome,completeness,contamination +1mbp,100.0,0.00 +500kb,50.0,1.00 |
| b |
| diff -r 000000000000 -r 6941d0d453ba test-data/reads_for_genome2.1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads_for_genome2.1.fa Tue Apr 26 15:27:37 2022 +0000 |
| b |
| @@ -0,0 +1,60 @@ +>1 +TCATGAACGGTAGTCAGTCAAGTTTCGCCAGCAATAGGCACAGCTTGTATGGAGGGGTTTAGTCGCCGGAGTGTT +>2 +TAGTCAGTCAAGTTTCGCCAGCAATAGGCACAGCTTGTATGGAGGGGTTTAGTCGCCGGAGTGTTACGAGTTTGA +>3 +AGTTTCGCCAGCAATAGGCACAGCTTGTATGGAGGGGTTTAGTCGCCGGAGTGTTACGAGTTTGACGATCCAAAG +>4 +GCAATAGGCACAGCTTGTATGGAGGGGTTTAGTCGCCGGAGTGTTACGAGTTTGACGATCCAAAGTTGGAGTCGC +>5 +CAGCTTGTATGGAGGGGTTTAGTCGCCGGAGTGTTACGAGTTTGACGATCCAAAGTTGGAGTCGCCGTGATAATT +>6 +GGAGGGGTTTAGTCGCCGGAGTGTTACGAGTTTGACGATCCAAAGTTGGAGTCGCCGTGATAATTAATGATATTG +>7 +AGTCGCCGGAGTGTTACGAGTTTGACGATCCAAAGTTGGAGTCGCCGTGATAATTAATGATATTGCGTCTTCGGT +>8 +GTGTTACGAGTTTGACGATCCAAAGTTGGAGTCGCCGTGATAATTAATGATATTGCGTCTTCGGTGGGCACGATG +>9 +TTTGACGATCCAAAGTTGGAGTCGCCGTGATAATTAATGATATTGCGTCTTCGGTGGGCACGATGAGCCAATCTG +>10 +CAAAGTTGGAGTCGCCGTGATAATTAATGATATTGCGTCTTCGGTGGGCACGATGAGCCAATCTGCGTCGCACTA +>11 +GTCGCCGTGATAATTAATGATATTGCGTCTTCGGTGGGCACGATGAGCCAATCTGCGTCGCACTAGTTTACGTGT +>12 +TAATTAATGATATTGCGTCTTCGGTGGGCACGATGAGCCAATCTGCGTCGCACTAGTTTACGTGTTAACGTAGTG +>13 +TATTGCGTCTTCGGTGGGCACGATGAGCCAATCTGCGTCGCACTAGTTTACGTGTTAACGTAGTGAACCTAGACA +>14 +TCGGTGGGCACGATGAGCCAATCTGCGTCGCACTAGTTTACGTGTTAACGTAGTGAACCTAGACATGACGGGACT +>15 +CGATGAGCCAATCTGCGTCGCACTAGTTTACGTGTTAACGTAGTGAACCTAGACATGACGGGACTATGGCAGTAA +>16 +GGATCGGATTACTAATGTTTTTCCAGTCGCCTGTTACTCCAGGCGCGGATGCGAGTGGTCTTTGCCAAGTAGCCC +>17 +ACTAATGTTTTTCCAGTCGCCTGTTACTCCAGGCGCGGATGCGAGTGGTCTTTGCCAAGTAGCCCCATGCCACCT +>18 +TTCCAGTCGCCTGTTACTCCAGGCGCGGATGCGAGTGGTCTTTGCCAAGTAGCCCCATGCCACCTGTACAAGGCG +>19 +CTGTTACTCCAGGCGCGGATGCGAGTGGTCTTTGCCAAGTAGCCCCATGCCACCTGTACAAGGCGGACAAACGCG +>20 +AGGCGCGGATGCGAGTGGTCTTTGCCAAGTAGCCCCATGCCACCTGTACAAGGCGGACAAACGCGGATGCGTTTG +>21 +GCGAGTGGTCTTTGCCAAGTAGCCCCATGCCACCTGTACAAGGCGGACAAACGCGGATGCGTTTGCATAAATTAC +>22 +TTTGCCAAGTAGCCCCATGCCACCTGTACAAGGCGGACAAACGCGGATGCGTTTGCATAAATTACCACCGTAAGA +>23 +AGCCCCATGCCACCTGTACAAGGCGGACAAACGCGGATGCGTTTGCATAAATTACCACCGTAAGATACGTTGGCG +>24 +CACCTGTACAAGGCGGACAAACGCGGATGCGTTTGCATAAATTACCACCGTAAGATACGTTGGCGTATTGCCGTA +>25 +AGGCGGACAAACGCGGATGCGTTTGCATAAATTACCACCGTAAGATACGTTGGCGTATTGCCGTACAAAGGCGGA +>26 +ACGCGGATGCGTTTGCATAAATTACCACCGTAAGATACGTTGGCGTATTGCCGTACAAAGGCGGACAGTCCAGAT +>27 +GTTTGCATAAATTACCACCGTAAGATACGTTGGCGTATTGCCGTACAAAGGCGGACAGTCCAGATATTTCTTCGG +>28 +ATTACCACCGTAAGATACGTTGGCGTATTGCCGTACAAAGGCGGACAGTCCAGATATTTCTTCGGATGTAATTAT +>29 +TAAGATACGTTGGCGTATTGCCGTACAAAGGCGGACAGTCCAGATATTTCTTCGGATGTAATTATTGTAGGCGTG +>30 +TGGCGTATTGCCGTACAAAGGCGGACAGTCCAGATATTTCTTCGGATGTAATTATTGTAGGCGTGCACAACCTAC |
| b |
| diff -r 000000000000 -r 6941d0d453ba test-data/reads_for_genome2.2.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads_for_genome2.2.fa Tue Apr 26 15:27:37 2022 +0000 |
| b |
| @@ -0,0 +1,60 @@ +>1 +TTGGCGGATTTACCAAGGCGTCTTCTCTGCGTGTAAGACCCACACCGTGCCTCTGTACCTATGGACGTGCGCGAC +>2 +TACCAAGGCGTCTTCTCTGCGTGTAAGACCCACACCGTGCCTCTGTACCTATGGACGTGCGCGACCATCTTATGA +>3 +TCTTCTCTGCGTGTAAGACCCACACCGTGCCTCTGTACCTATGGACGTGCGCGACCATCTTATGATATGAGCATC +>4 +GTGTAAGACCCACACCGTGCCTCTGTACCTATGGACGTGCGCGACCATCTTATGATATGAGCATCACATGTTTAA +>5 +CACACCGTGCCTCTGTACCTATGGACGTGCGCGACCATCTTATGATATGAGCATCACATGTTTAATAGAGCGTCC +>6 +CTCTGTACCTATGGACGTGCGCGACCATCTTATGATATGAGCATCACATGTTTAATAGAGCGTCCGGTGTCCCTG +>7 +ATGGACGTGCGCGACCATCTTATGATATGAGCATCACATGTTTAATAGAGCGTCCGGTGTCCCTGTAATGCCACC +>8 +GCGACCATCTTATGATATGAGCATCACATGTTTAATAGAGCGTCCGGTGTCCCTGTAATGCCACCACTTCTGTTT +>9 +TATGATATGAGCATCACATGTTTAATAGAGCGTCCGGTGTCCCTGTAATGCCACCACTTCTGTTTCAACGGACGC +>10 +GCATCACATGTTTAATAGAGCGTCCGGTGTCCCTGTAATGCCACCACTTCTGTTTCAACGGACGCTGAATCTAAG +>11 +TTTAATAGAGCGTCCGGTGTCCCTGTAATGCCACCACTTCTGTTTCAACGGACGCTGAATCTAAGCCGATATTTT +>12 +CGTCCGGTGTCCCTGTAATGCCACCACTTCTGTTTCAACGGACGCTGAATCTAAGCCGATATTTTTGCCTTGATC +>13 +CCCTGTAATGCCACCACTTCTGTTTCAACGGACGCTGAATCTAAGCCGATATTTTTGCCTTGATCAGAACGGGGC +>14 +CCACCACTTCTGTTTCAACGGACGCTGAATCTAAGCCGATATTTTTGCCTTGATCAGAACGGGGCAGTGAAGGAG +>15 +TGTTTCAACGGACGCTGAATCTAAGCCGATATTTTTGCCTTGATCAGAACGGGGCAGTGAAGGAGCTGCACTAAA +>16 +CGCACGTGACTGGCGGACGGCTCACACGCTATCTCCAAAAATCTACACTTCCGGAGCTAGGCTCCATGACAGGGA +>17 +TGGCGGACGGCTCACACGCTATCTCCAAAAATCTACACTTCCGGAGCTAGGCTCCATGACAGGGATGTTCTTATT +>18 +CTCACACGCTATCTCCAAAAATCTACACTTCCGGAGCTAGGCTCCATGACAGGGATGTTCTTATTCAACAAGATG +>19 +ATCTCCAAAAATCTACACTTCCGGAGCTAGGCTCCATGACAGGGATGTTCTTATTCAACAAGATGGAGTGCTAAT +>20 +ATCTACACTTCCGGAGCTAGGCTCCATGACAGGGATGTTCTTATTCAACAAGATGGAGTGCTAATATTAACAATC +>21 +CCGGAGCTAGGCTCCATGACAGGGATGTTCTTATTCAACAAGATGGAGTGCTAATATTAACAATCGACGACACAG +>22 +GCTCCATGACAGGGATGTTCTTATTCAACAAGATGGAGTGCTAATATTAACAATCGACGACACAGGTGAAAAACC +>23 +AGGGATGTTCTTATTCAACAAGATGGAGTGCTAATATTAACAATCGACGACACAGGTGAAAAACCTCTTGTCATG +>24 +TTATTCAACAAGATGGAGTGCTAATATTAACAATCGACGACACAGGTGAAAAACCTCTTGTCATGTAGCTAGCAG +>25 +AGATGGAGTGCTAATATTAACAATCGACGACACAGGTGAAAAACCTCTTGTCATGTAGCTAGCAGTTATGCGGGC +>26 +CTAATATTAACAATCGACGACACAGGTGAAAAACCTCTTGTCATGTAGCTAGCAGTTATGCGGGCGTACACACTA +>27 +CAATCGACGACACAGGTGAAAAACCTCTTGTCATGTAGCTAGCAGTTATGCGGGCGTACACACTAGTGCTAATCT +>28 +CACAGGTGAAAAACCTCTTGTCATGTAGCTAGCAGTTATGCGGGCGTACACACTAGTGCTAATCTACTAATCATC +>29 +AAACCTCTTGTCATGTAGCTAGCAGTTATGCGGGCGTACACACTAGTGCTAATCTACTAATCATCCACGGGCCCC +>30 +TCATGTAGCTAGCAGTTATGCGGGCGTACACACTAGTGCTAATCTACTAATCATCCACGGGCCCCTGCTAGAGAT |
| b |
| diff -r 000000000000 -r 6941d0d453ba test-data/reads_for_seq1_and_seq2.1.fq.gz |
| b |
| Binary file test-data/reads_for_seq1_and_seq2.1.fq.gz has changed |
| b |
| diff -r 000000000000 -r 6941d0d453ba test-data/reads_for_seq1_and_seq2.2.fq.gz |
| b |
| Binary file test-data/reads_for_seq1_and_seq2.2.fq.gz has changed |
| b |
| diff -r 000000000000 -r 6941d0d453ba test-data/reads_for_seq1_and_seq2.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads_for_seq1_and_seq2.fna Tue Apr 26 15:27:37 2022 +0000 |
| b |
| @@ -0,0 +1,48 @@ +>1 1 +GCTGGGATTTCTAGGCGGAGTGCATAGGACGCGATTAACCGAGAGACAAAGTCATGTGGGAAGCGGGCCAAATTGCTTTGAGGCAGGTCTGTAGTGTTAG +>1 2 +TGACGGGCTCACGGCGTCAGTAACCAACTTGCTATTGGTGGGTGTGCTGCGGAGTCCACATGACGAATAATTATATTTATATTGCGAAGATGAAAATGGG +>2 1 +GCTGGGAAGTTGGTTAATCCGAGCCTATATGCCTAAGTGCGAAAGTGGATAAGGGGTGTTGACGGGCTCACGGCGTCAGTAACCAACTTGCTATTGGTGG +>2 2 +TAACCGAGAGACAAAGTCATGTGGGAAGCGGGCCAAATTGCTTTGAGGCAGGTCTGTAGTGTTAGCTACGACACCATTGGTAGATGTATCCTAAAATTGG +>3 1 +AGCCTAGAGAGACCACATAGTTGCTCCAGCAATTCCGGACAAGGGGACCCAACTCCGCGGTCATCTGTTTATTGTGGGCTCGATGCCTTACACACCTTTT +>3 2 +CCCTGAGCCTGCACGCCAAAACCACTTGTACGTCTGTCTGCGCCGCGATAATTGCGAACGGGTCGCCGGTCAGAAGGGTCGTCTACACCTTCTGCGTCGT +>4 1 +TTCGCAATTATCGCGGCGCAGACAGACGTACAAGTGGTTTTGGCGTGCAGGCTCAGGGCCTCCGCTTTTGTTAGAGTCTAAGTGGCTCACAGAGTAGTTT +>4 2 +TAGAGTGAACCCGGACGGGCAAGGTGCGGTACAGGACTCAGCGCACGCCTTCAAGGTAGAGCCTCTCTCCTGCGCCGAATTTGTCCCGCGGGCTCATAGT +>5 1 +AAAGATTACAATCGTAGCGAAGCTTTTCAATGAAATATGAATTACACGTGGTGCTGTGATGGAAGCCTAGAGAGACCACATAGTTGCTCCAGCAATTCCG +>5 2 +TAACAAAAGCGGAGGCCCTGAGCCTGCACGCCAAAACCACTTGTACGTCTGTCTGCGCCGCGATAATTGCGAACGGGTCGCCGGTCAGAAGGGTCGTCTA +>6 1 +GTCGTCGCCGTCCATGGTTGGAGTATGAATTCGAATGCGCGTATCCAGCTCAGTCCACCCCACGTCATAGCCCACTGGTTCTATTAGGCACTACCTTACG +>6 2 +CGAAGATGAAAATGGGTAGGGATCAGACCTTTTACTCACTAGAATCTTCTAACCCACTAAAGTAGCACGACGCAGAAGGTGTAGACGACCCTTCTGACCG +>7 1 +TCAATAATGACCTGCGGTGGATCAGATACCGCATCGCAAGGACCACGTAGGTTGGCTGTCCAACGCGCAAGCGCGCACATCCGCCGATGAAATGTATGTT +>7 2 +CTTGCCTGAAGGACAACTAGCATCCGAGCTCACGGGCTAGAATGACAACTTTACATGAGAGTGCCATCTCTTTCCTGGCTGCAGCCAGAGCGAGTATCCG +>8 1 +AGCCCCAGAATGGCCAGTGAAATCGTTAAATTGGAATTGTAAATCAGCAGTTGTACTTTGCCGCTGGTATGACATGACTCCCAGGATGAAATATAACCGC +>8 2 +AATGTCACTAATGAGAATTGCGCAGGCGGCACGTTGCCTGCGGGATACTAGTGTGCGCCCTACTATGCGCTGAACCGTGGAGATTACCATACTTGATCCC +>9 1 +CGCCGATGAAATGTATGTTGATATTATGGGGGGTACACTTGGGACAGATGCGAAGAACCTTCACATGCATGTCCCTATAAGGTGTCATCAAATTCATAAA +>9 2 +TCCTGGCTGCAGCCAGAGCGAGTATCCGGTACTTGGATGCCTCATTTGCCCAGGCCCTGGCTTCAACGGGTAAGGCTCAACCGTGATAACAGTCTAATGC +>10 1 +TCCGCCGATGAAATGTATGTTGATATTATGGGGGGTACACTTGGGACAGATGCGAAGAACCTTCACATGCATGTCCCTATAAGGTGTCATCAAATTCATA +>10 2 +GCTGAACCGTGGAGATTACCATACTTGATCCCGCTACTCAAGATGGGTGGCCATGTGTTCAGAAACCACGGCAATGTACAGAAAGTCAACTCTAGCCTTG +>11 1 +AAGAACCTTCACATGCATGTCCCTATAAGGTGTCATCAAATTCATAAACTATCAGGCCGGCGGAGTATGGTGGAGTAGAGGCGGGCATTAAGTTTATTGC +>11 2 +ACTCAAGATGGGTGGCCATGTGTTCAGAAACCACGGCAATGTACAGAAAGTCAACTCTAGCCTTGCCTGAAGGACAACTAGCATCCGAGCTCACGGGCTA +>12 1 +CACATCCGCCGATGAAATGTATGTTGATATTATGGGGGGTACACTTGGGACAGATGCGAAGAACCTTCACATGCATGTCCCTATAAGGTGTCATCAAATT +>12 2 +CCGAGCTCACGGGCTAGAATGACAACTTTACATGAGAGTGCCATCTCTTTCCTGGCTGCAGCCAGAGCGAGTATCCGGTACTTGGATGCCTCATTTGCCC |
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| diff -r 000000000000 -r 6941d0d453ba test-data/test1.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1.tsv Tue Apr 26 15:27:37 2022 +0000 |
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| @@ -0,0 +1,15 @@ +Sample Genome Relative Abundance (%) Mean Variance +7seqs.fna/fw0 unmapped 0 NA NA +7seqs.fna/fw0 genome1 0 0 0 +7seqs.fna/fw0 genome2 53.16792 1.4117647 1.3049262 +7seqs.fna/fw0 genome3 0 0 0 +7seqs.fna/fw0 genome4 0 0 0 +7seqs.fna/fw0 genome5 46.832077 1.2435294 0.6862065 +7seqs.fna/fw0 genome6 0 0 0 +7seqs.fna/reads_for_seq1_and_seq2.fna unmapped 0 NA NA +7seqs.fna/reads_for_seq1_and_seq2.fna genome1 0 0 0 +7seqs.fna/reads_for_seq1_and_seq2.fna genome2 53.16792 1.4117647 1.3049262 +7seqs.fna/reads_for_seq1_and_seq2.fna genome3 0 0 0 +7seqs.fna/reads_for_seq1_and_seq2.fna genome4 0 0 0 +7seqs.fna/reads_for_seq1_and_seq2.fna genome5 46.832077 1.2435294 0.6862065 +7seqs.fna/reads_for_seq1_and_seq2.fna genome6 0 0 0 |
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| diff -r 000000000000 -r 6941d0d453ba test-data/test2.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test2.tsv Tue Apr 26 15:27:37 2022 +0000 |
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| @@ -0,0 +1,8 @@ +Sample Genome Relative Abundance (%) Mean +7seqs.reads_for_seq1_and_seq2 unmapped 0 NA +7seqs.reads_for_seq1_and_seq2 genome1 0 0 +7seqs.reads_for_seq1_and_seq2 genome2 53.16792 1.4117647 +7seqs.reads_for_seq1_and_seq2 genome3 0 0 +7seqs.reads_for_seq1_and_seq2 genome4 0 0 +7seqs.reads_for_seq1_and_seq2 genome5 46.832077 1.2435294 +7seqs.reads_for_seq1_and_seq2 genome6 0 0 |
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| diff -r 000000000000 -r 6941d0d453ba test-data/test3.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test3.tsv Tue Apr 26 15:27:37 2022 +0000 |
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| @@ -0,0 +1,4 @@ +Genome fw0 Mean +genome1 0 +genome2 4.8142858 +genome3 0 |
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| diff -r 000000000000 -r 6941d0d453ba test-data/test4.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test4.tsv Tue Apr 26 15:27:37 2022 +0000 |
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| @@ -0,0 +1,4 @@ +Genome fw0 Mean +genome1 0 +genome2 4.8142858 +genome3 0 |
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| diff -r 000000000000 -r 6941d0d453ba test-data/tpm_test.bam |
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| Binary file test-data/tpm_test.bam has changed |
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| diff -r 000000000000 -r 6941d0d453ba tool-data/all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Tue Apr 26 15:27:37 2022 +0000 |
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| @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of sequence data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/, +# +#then the all_fasta.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/hg19canon.fasta +# +#and your /depot/data2/galaxy/hg19/ directory +#would contain hg19canon.fasta files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/hg18canon.fasta +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/hg18full.fasta +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/hg19canon.fasta +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/hg19full.fasta \ No newline at end of file |
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| diff -r 000000000000 -r 6941d0d453ba tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Apr 26 15:27:37 2022 +0000 |
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| @@ -0,0 +1,7 @@ +<?xml version="1.0"?> +<tables> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc"/> + </table> +</tables> \ No newline at end of file |
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| diff -r 000000000000 -r 6941d0d453ba tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Tue Apr 26 15:27:37 2022 +0000 |
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| @@ -0,0 +1,7 @@ +<?xml version="1.0"?> +<tables> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/all_fasta.loc"/> + </table> +</tables> \ No newline at end of file |