Repository 'coverm_genome'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/coverm_genome

Changeset 0:134e4e78e754 (2022-04-26)
Next changeset 1:a671907f96fe (2023-01-24)
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
added:
coverm_genome.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
b
diff -r 000000000000 -r 134e4e78e754 coverm_genome.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/coverm_genome.xml Tue Apr 26 15:27:01 2022 +0000
[
b'@@ -0,0 +1,570 @@\n+<tool id="coverm_genome" name="CoverM-GENOME" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">\n+    <description>read coverage and relative abundance calculator focused on metagenomics applications</description>\n+    <macros>\n+        <import>macros.xml</import>\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_'..b'for_genome2">\n+                            <collection type="paired">\n+                                <element name="forward" value="reads_for_genome2.1.fa"/>\n+                                <element name="reverse" value="reads_for_genome2.2.fa"/>\n+                            </collection>\n+                        </element>\n+                    </collection>\n+                </param>\n+                <conditional name="genome">\n+                <param name="ref_or_genome" value="genomic"/>\n+                    <conditional name="genomic">\n+                        <param name="source" value="history"/>\n+                        <param name="fasta_history" value="genome1.fna,genome2.fna,genome3.fna"/>\n+                    </conditional>\n+                </conditional>\n+            </conditional>\n+            <section name="cov">\n+                <param name="mean" value="true"/>\n+            </section>\n+            <output name="output1" file="test3.tsv" ftype="tsv"/>\n+        </test>\n+        <test expect_num_outputs="1">\n+            <conditional name="reads">\n+                <param name="read_type" value="bam"/>\n+                <param name="bam" value="2seqs.bad_read.1.with_supplementary.bam"/>\n+                <conditional name="genome">\n+                    <param name="ref_or_genome" value="none"/>\n+                    <param name="single_genome" value="true"/>\n+                </conditional>\n+            </conditional>\n+            <section name="cov">\n+                <param name="count" value="true"/>\n+                <param name="min_covered_fraction" value="0"/>\n+            </section>\n+            <output name="output1" file="test5.tsv" ftype="tsv"/>\n+        </test>\n+        </tests>\n+    <help><![CDATA[\n+.. class:: infomark\n+    \n+**Dereplication quality formula**\n+            \n+Scoring function for genome quality:\n+\n+- Parks2020_reduced: A quality formula described in `Parks et. al. 2020 <https://doi.org/10.1038/s41587-020-0501-8>`_ (Supplementary Table 19) but only including those scoring criteria that can be calculated from the sequence without homology searching: *completeness-5*contamination-5*num_contigs/100-5*num_ambiguous_bases/100000*.\n+- completeness-4contamination: *completeness-4*contamination*\n+- completeness-5contamination: *completeness-5*contamination*\n+- dRep: *completeness-5*contamination+contamination*(strain_heterogeneity/100)+0.5*log10(N50)*\n+\n+-----\n+\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'
b
diff -r 000000000000 -r 134e4e78e754 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Tue Apr 26 15:27:01 2022 +0000
b
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'
b
diff -r 000000000000 -r 134e4e78e754 test-data/1mbp.fna
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1mbp.fna Tue Apr 26 15:27:01 2022 +0000
b
b'@@ -0,0 +1,2 @@\n+>random_sequence_length_1000000_1\n+GTCACCGTGAACTTAGACGGGTCCGGTGGTTCCTGTCTGCCACAGACAATAACGCAGAGGCGTCAAGACGCGTTGTCGGGGGTGAATCGCGCGTGTATTTATGCTCCGTAGCAATGATGGTACTGTACAAAGCTCAGCCGGGGCGCGTTGAAGTATCAAATCTCTTACTGAGCGTTAGGATAGTTCCGTTGAGATATGTAGGCGTATTAACGCGTGCGCCCGGGCTGCTAACCAGTGAATACCGGGAGCTCCAGAGTGTCATGTCTAGTCAATGGTTGAATAATGGTATGTTTATCAGGCCTAAGAAGCATGCGGAGCAATGGTGCTTCTGTAGCAACCCGCCATGCGCAGGGAGTGACTGCCGGATTTTTGGCGCTACCTAAAGAATTGATAGGCGGGCGGAAACCGCGCGCATAAAGCTTTCGGAGGTCGTGATTAGTGGTGGAATCCTGTATGGAACAAGGCTTGCTCTCGTGCAGCCAAGAATTGCTGCGGGTTTTCCTAATTTCTTAGCGTTACCAGTCCCGTGAATAGATGTAGAGCTAGTATACTCACTCCGACCCATGAGGCTGACCAGAGTGACGCGCACCTGCCAGAGGGGAGCTAACATAGGTATGTGGGCATCAGGGTCGGTGCCCTCTCGTTTCAGTTGGCGTGGAGCCAGCGATAATATACTTTACCCTTGCTCATCGGTGTCGCAACAGTCAATGGTACACTTTTCTCCATTTTTAAAACATACAATTCATTCTCATCGTTCTCTCTGACGCACCGTCTACGGCCCGCTGCAACGTAATGCTAAGCTTAGCGCTTTCGCCGGTCTTCCGTACCTTTTAGTAAGTATGGCGTACACTCTCTAGAAGGTGCCGGACGGGGTCAGTATCGCGTTTTGCGCCAAGGTCGAGGGCGTATCGGGGCGCATATTTGCGCGAGCTCGGGAGGACCACAGGCGTGAGGTCGGCGTATGGTCGATTTGAAAACTACGGCGTCGGTTTGTGATCATACTTAGACTCTGATCTCAAATCCTGAGCAACGGTGAGATCAGTGAATATACAGAGAGTAAAGAGTGGCATTCACCAAAGATGAGGAAGTCGAGCGATGTTCAATTGGAGAACGGTGTCGCTCCCAAGGGAGTGGGATACTCAGTCTTACTCGTACCTCCAGATACGACTGCCGCTTACCATAGGCTATCTACAGCTTCTGCTCCCACGCTATACGCGATATTTGCACGCTTCGTCTCCGTTGCACGTTTGAGCCAGTGAGTGTCCCCAGCGCGGCAGCCGCTCTCCAAGGAAGATACTTCACTCGCCACACTTCATAACCTTAATAGGCGTTCGCTACAGCTACCCCGAGTTCCGGAATAGACGAACACTTATTCAAATGGAGATAATCTTACTTTGCTGGATCACAGGGAACAATTCTTGGGGGGGGTCGCCAGCTCTTGTTCTACAGTCGCCTCTGGAATGCGCGAGCACAGCACTCTAAGCGGTGGCCTGTCGTCTCCAACAAGAAAGGTTCTGGTGGGTGCTAGCTTTGGCATCCATGGTAGGATGTCGGTATATTGCGTCAGACTTTCCAGAGCACAGCGTTTCTTGTCTGTTCTGTCAGGTGTCCTCGTCTCTCGAGAGCCCACGGAAAAGCAAACACACGGTTTGGCCTCCGGACTAGTGTAAAGTACGCTAGATGATCCCGATAGACCCGTTATCTATGGTGGCGGCACTGGCTCCGAGCACTAACGGTTGATATGCTCCGTTGGTTGCTTATGAGCTCTAGAACCCATGCTAACGCCCTATAATCTCTAGTAGTTCGTGCTGGAATCCGCCCATCACACAACGACAATACACGGGGGTTAGAATCCGTCCACCTAACTGGTGCCTCAGATCTTGTTGGTTCATCGAGTAGATCACGATCCATGTTTCTACAGTGGGAATCGTGGGGTGAAAAGTACATCTCTTAGGAGCTCAAAATTATCGAATACATTAAAGGTATCGCAAAAGGCGCATGCATCCTAGAAAGGAGACCGCGGACAATGTCAACTTTACTTAAGACTAAAATCCTTGTCATTAATTGACGGAGGGGGCACGGTTATCTCATATGGGCAGGATCAGTCCAAAAAGTGGGTCTCGATCAGTTAACTAGCTATTCTGAGGACGCGGATAGCGCACCCAACGCCACATAGTCCGGCGTTACCTCATAAGACAAGCAGATATGGGACTCGGGATGTCGGCTACCCAATCTACTCGGGTATGACAATGTCATCTCTTCCAAGATGGCAATTGTATAGGCGTATGGGTGATTCGCATAATTCTATGTGGGTCCGGTTAGCTACCACTGTCGGCCTCCAGCGGCTACCGGTCTCAGTACCCCAGCCGATTACATTGACTATGACTGCGCGAGCAAAGTCGCGAGGCCCGAGCTGTGTCCTAGCTAGCACTGGAAGTTCCAAGCAGAGTAATTTTCTACCCACCCTCTGGCCGGATATATCCGCACTTTCCCATAGGAAGTAGGAACTATAAAGACGCTATATTCACCCAAATGTTGCCCCTAGTCCACCTTTAGCCCATCTTTCAGGCCAATTACTCACTTTCTCATGTTTCCGATTCCCGTAGTGGAATGCTGTAAGCCATACTACGCAAGAGCCGAAATACCATCGAGCCGGCTTGGCATTGCAGAAACTAGATTAACCCCTAGTGTGACCTTGTCGATATGAGAAGACGACACTAAGCAACGTGTGGGAAAGTGTACATATTTCCGTAACGTGTGTGGCCTTCTCGAAGTAACACCTTCATTGCTAACTGTTGCTTCAGCGCAGAGCAAAGAACGTAAGCGGAAGGTATTTACAGCAACCATAACGTAATCAAGGTTCAGTCCCCGTAGCCCATTGCACACAGTCAGAGGTCTAAGCCGTACGATAGCGTGGGAAAGCTCTCGGATACTGGAGCTTAGTGTACCCCGAGGATCCAGGCCACGTAGAGTGAGGGATATGGAATTTATTGGAGCTAATCCCCGAAGTAATGGTAGAACGGAGCACTAGCGACAGTTCTGTGACTACTCACGTGTATACCCGGGAGACAATACTCTGGCCGAGAGGTACTCCTAGTTCAATCTCCTACAGGCATTGTTTACGCCTAACAAGCCTGACGACGAGGTTCCATGATTGAGGGTTCCCCAGTACTCACAGGCCGCGTATGTCAATCGAACTGGTGGAGTTCTGGCCTAAACATACACAGGATCTTTGGGAGGCTCAGCAGCAGCGATTTATACACATTGGCGGCCTTGATTGAATCTCTGTGGCGTGATACGAGATAATTAAAGGCCAACAGTGATAGTACTGCATACCGAAGCGTGCACCCCATTGATGGTTCTGTCTTCGTAAATTAGCTCCAGCGACTGCCGCGAGGTCATGATACGACTACCTATTGGAGTTTAGTTCTGTTGCTTGAGGATATTGACCCGCTCCAGTTTGAGCGGAGCATAGTGCGGCCGATGACCAGGTCCGCTAATATCCACGGATCCGTCAACCCTTCATCGTCCTGAGCTGGTGGTGCGCAGCAAACATAATGAATTCTCCCAGGCGCCTGAAACGTACCTAAGTGCGTACCTAGATTTCTGATCGTGAAGGAACATCCGTCGGGCAAGGAGGTTGTTAATTAACTCCTTGGGTGGATAGCCAGCCCGGTCGGTCACCGAGATTTCTAGTGGTACCGTCAGCGGATCTATAAGTTCCCCTAAACGATCTTACAATCCAGTACTCGCTTCGTGGTACTCGGGTATGTCTTGCTTACCTAGTAAGGGACTTGACCTAATATTCCGAACAACGGTGAACCTTAAGATAACTCAGTAGTTAGAGTCCGGTGGGAGGAGGTACCCGTCGCTTCCGCAAGCACATGACAGTACAAAAAGTTGTGTCGACGCCCGAGTTGCGCCCAACCCTACGCACTTGATTGCCT'..b'ACTTTTGCTAGCCATGTAAGCGCGATCTTGCGGAGGCCGCATATATCTCGTGATTCGCGTTCTAACTGAGTGACTGCTACGCTTCAACTGCTCAGTAGATGGTACCGTCTCCGTATCCTCTTCCAGCGTATTGTGCTGCGGTATCATGAGCATCGGATTATACTCCGCGGCCACTGCGTTTAAAATATGAGTCATTACTATCTTGGCATTGAATGGATTTGCGTCTGTAGAACGGGGGTATAAATGGGCTGCGGTCCGATCATCGAAGAACCTGGGTTATCCTATGCGATGGGGATTAGTTAGGCTGAATGTGCTTTAACGTCTAATCTAGAAGGGCAATGTACCTGCGCCCGGCTGGCGTGGAACTGTTTGTCCGCCTCTGTCCAATTCAGGGACTCGACGCACCCATAGTGCTCAATCGGGTCTTATTGCTCTTCGACGACGTTGGAGACTCTCCGAGATAGGCGTCGGATAGAAATCCTAAATCGCTCCACCAACCGCATGCTTACCGAATCAGTTCGGAACGGCCAAGCGTCGACTTTAGTGCATGGAAGTGTCGATTAAATGTGGCGAACTCAGCATGGAATGCACCGTAACGACCGGCTAACGGCGAGCACTCTAAAACTACCACTGATCTTGTCTGTGTGGATCGAAAGTTCCGTCCAGGACAGTTGGTGTATGTAATTCTGCTACCAGCATTTCCGGAAACACCTGGAATGAGTACCACGGTTCAGGACAACCCACGTGAACGAAGCAGTGTCGTTCGATTATTGTGGCTTGCGCTGAGGGACCCATACGTGATCTTGTCCGGATGCTAAAGGCTTCTTGATCGTTCTGAATACCTACACATAACTCATTCATAGTCATAGCCCTGTAAAGAAGCGTCGGATTATTTCTCACTCGGCACGGGAGCGTTCGAGGCCATGCTACCGACCGTCGGTGATGTGCATACGCCAGGCGTTTCACGTAGGCGAGAGACAGTCAACGTGCGAGCACGCGAACTTCCGAGGCAAAGGCCGTTACCCTGGCAATTATATATTTTAGGTCCAGGGCTACTCCGCGGTCCCCGATTGCACTTATGTTGGGAGTACCACCAATCGCGTTGCAGTGACCTACTTATAAGTGATTCTGGCACATTGACCTAGGCGCGCCAAGTCTTCAGATGACTGTAAACTAACCCCGTAAGCTGTGCTGACTTGCACGTTCGCGGATTTCATTCACGTAAGTTGTCACCTCCAGAATTTTCTGTGTGTACTCACTCCCGTGTGCATACTACTACAGCAGTCGCCATGCGTTGTTTAGGGAAAAACCAAATAGTAGCGCGCGCAATCTCTTGCATTATCAACCCTCTGGACGCGCAGGGCTGCGATCCTGCAAGCCCGGACAGGAGGCTCCAGGGCGTATGTGTTATGCGGGTGACTCACCGATTGATACATCCATGGCGGCTCCTCTAGACAGTCCAAAGCGGCGGTGCGCAGTTCGATTAGCAGCCTTATCGCTTATCCATTCGTATTTTCGACGGCTTAGTGTTACGGGAATTCATCATTTTTTGGGGGCCAAGATGGCTCTGTGCTCGCACCAAGGAGAAGATCCAGCTGCGGTTCTTGGAGCATGCCTCCATAGTGAAAGTCTTTCAGTTGCCCTCGATTCCAGAGGCATAACACGAGGACTCCCTATGTACATTTCGCCGCTAGCAAGATATAAAACCGAGTCGCGCGCAACTAGAACTTAAACATATATGGCCAGAAGAATAATGACCCCATCAATGAGGAGTCTTCTATGAGCATGACGACAACAGGGTCACGCGCTACGAACAGTACCGAGACAGCCGCCTTCCTTGGGCCTGTGAAGAGTTCCATTGTAGTGATGACATTTGAATTACACGAGAAGCACCACTGTGTCGGTCAACCGGCCCTACTCAGGATAGTATCTGGGCCTCCTAAAGACGATGTGGTCCAGGAAACGACTTGTTCTATATAAAAATAGGGACGCTACCGGCGTTGACACTGGATCGTGAACAATGAGTAAAAGCCTGAACTCGGTCTTCGTGAGCCCTCTCTCACGAAACAGGGCACTGCATAACTGCGTGCCGCCGCGGGATACGTCACTTCATGAGAAACCCACACTACTACACAGATTGTGTATGTCGCATTGGATAACGTTCTGGTCAACCTCTACTTATATACCCCTATAGTTACTGAGAGCTAGGTGGAATCACTCCTGGTTGAGACCGAAAGGGAATGGGTGCCCGCGGGTCATAACTGAATACTAACTCACAGAACGTATGCTCCGAGGATCCACTATTTATTAGTAGTGGTGGACCGGTGCGTAAGGAACCATACGGACGTTCAATGGGGCGGGTTGTAACTGTAGCCCCCCGATCACAAAGCAAAAGTTAATACATGGTGGGAAAGTTATGCTTGAGTTGTCCATCGAAATAGTGAGTACGTCTTCGAGCGAGCGCGTTTTCCATAGGCTTCAGGTCTAGCTCCAGAGTAAATACCTTACAGTGAAGATTGATGGTATGGCACGATTACCAGCGACATAAATCAAAGGTATTGGTTTCCATGTCGCCGCACACATGAGGAGAGTCAAGTAACCACGAGCCCCAAGAGTGATTGCGAGGCATGTGTACTGATCACGAACCTACACAGAGCGAAACGATGACGTATGTAATAGATGTGACCCGCCATGACATATCGCTTTTTTGCTCGTCCAAGCACATATGACCTTTGTAGATTTCGTACATTCCTGTGACGTATTATCAAGGGTGACGATAGCCCCCACCTAATTGATGAGGAGCAGGACCTAAACTACTGGTAACAGGATTCAACGAGAAGAGCTTGTGCGTGGCATAGTCCGGCTCAGTTCTGTATGTAAAATCAGGGTATCGAGCTGAAAACGATCTATAATTCTCGGATTCGGAGGACATACGGTGGCACTCTGGTCAGGAAGGGGCGGACATCTGTACTACCATTTCTCGTAGCCAGAACCATACGACTCCTCTTTTGCTAATCGGTCGAACTGTTATCTTCAACACACCGTGGAGCATTTCTCTCTCACCGTGGACCTCGTGTATCGGAGTAGTGGCGGCGCAAGGGCCACACGCTGAGACTATAGACTCCCGCCAACGAAGCGATCGAGCACAGTGTAAGGCCGTCACGAGCGCAATGCATGCGCAGACGAGAACCCGATCAAATCGATATGTTAATATCTACTCGTCGGTGGGGTGAAGTGTCCGCACCGGCGGGGCTGCTGCAGGCGATGCAGGGACGACCTCTCGAGGAGCCCGGAACCAGTCCTGAGTATATATGGTTGTTTACCTCAGGAAGGCTGAGGTGACAGCGCCCGAGAATATGCATATAAAATTTAGCTACGATCTGGCTCCTGATCAAATGCGCGGGGCGCGTGCGTATGGCGCCATTCCGACCTGACTTCTACATTTGTCCAGGTGTGTTGGCGACCCCGCCCGGTAGACTGGACGCATAACACAATTCCGCTGTCTGGTGCTGATAGGCCGTTAAGCCAAACAATACCAGCGCCAATCTTTGTGGGACACTAATATAGTGGGGCCGTTACCTACGTACTGGTCTTAAGAGCATCATATCTTAGGTGTGTCCCTAGGCCCTATGCGTAATATTGTCGTGGAGATGGCACCCTCACACTCTACATACTGCGAACGCTGTTCTCCCGTGGCTTGGTACTATTACAGATCCCAGCTTGGGTGATGCCTGCAAAGTCACACGCCTGACGCGGCAGGGGGAGCCCCGCACGGTTTACGGGGTGAGACCACAGTCCCATGTGTGTAGTGGTAGGGTATCACGTTGCATGGGACATGACAATAACTCCCCGCCCACAGTCGACAGATGGTCAGTGGCTACTTGAGCCCCCTCGTATGTTGGCCGCTAGGTTTTCAGGCTGACCCTCACTGCCTCGATTATCGCAGACCCGTGAGTCCTGATCGCGAGTGGGAACAATTATCTGACTCGGACATGCTA\n'
b
diff -r 000000000000 -r 134e4e78e754 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 15:27:01 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 134e4e78e754 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 134e4e78e754 test-data/2seqs.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2seqs.fasta Tue Apr 26 15:27:01 2022 +0000
b
@@ -0,0 +1,4 @@
+>seq1
+GAGTCCCTAGAAGCAGGACCTGCATCTCCGAGAAGGGTCCCAGGGGCGGTGCTAGATCTCAGCAAGGAGGCAATGTGGTTGGGTTTTATAGTCACCCTTTCGAATACTCGAAGAAGGCGCCTGCCCGTTCTAGAGGGAGACATAAGCCTCTGCATCTGCAACGCGGATGGCTAATCAATAATGACCTGCGGTGGATCAGATACCGCATCGCAAGGACCACGTAGGTTGGCTGTCCAACGCGCAAGCGCGCACATCCGCCGATGAAATGTATGTTGATATTATGGGGGGTACACTTGGGACAGATGCGAAGAACCTTCACATGCATGTCCCTATAAGGTGTCATCAAATTCATAAACTATCAGGCCGGCGGAGTATGGTGGAGTAGAGGCGGGCATTAAGTTTATTGCTCTAAGAAGAAAGGCAACTACATGGAGAGTAGAGCCCCAGAATGGCCAGTGAAATCGTTAAATTGGAATTGTAAATCAGCAGTTGTACTTTGCCGCTGGTATGACATGACTCCCAGGATGAAATATAACCGCCAAGTATGCGCAAATAGAGTTTTAACCCTGCATTAGACTGTTATCACGGTTGAGCCTTACCCGTTGAAGCCAGGGCCTGGGCAAATGAGGCATCCAAGTACCGGATACTCGCTCTGGCTGCAGCCAGGAAAGAGATGGCACTCTCATGTAAAGTTGTCATTCTAGCCCGTGAGCTCGGATGCTAGTTGTCCTTCAGGCAAGGCTAGAGTTGACTTTCTGTACATTGCCGTGGTTTCTGAACACATGGCCACCCATCTTGAGTAGCGGGATCAAGTATGGTAATCTCCACGGTTCAGCGCATAGTAGGGCGCACACTAGTATCCCGCAGGCAACGTGCCGCCTGCGCAATTCTCATTAGTGACATTCCCCGTGTTATGCAAGAAATCTGTCTCTTCCTTTAAGAAACAGGGGCTCACACCTATCGCTGTTGAGACTAGAGCGCTGGCCAATCTTTCCCCGTG
+>seq2
+GCCCATATGTTTAGAGTGAACCCGGACGGGCAAGGTGCGGTACAGGACTCAGCGCACGCCTTCAAGGTAGAGCCTCTCTCCTGCGCCGAATTTGTCCCGCGGGCTCATAGTTGATTGGTCGTCGCCGTCCATGGTTGGAGTATGAATTCGAATGCGCGTATCCAGCTCAGTCCACCCCACGTCATAGCCCACTGGTTCTATTAGGCACTACCTTACGACTAGTCAAAAAAATTCAACAGCTGGGATTTCTAGGCGGAGTGCATAGGACGCGATTAACCGAGAGACAAAGTCATGTGGGAAGCGGGCCAAATTGCTTTGAGGCAGGTCTGTAGTGTTAGCTACGACACCATTGGTAGATGTATCCTAAAATTGGCAACCAAGACTATACAATAGCCGACACAAATGAAACTACTCTGTGAGCCACTTAGACTCTAACAAAAGCGGAGGCCCTGAGCCTGCACGCCAAAACCACTTGTACGTCTGTCTGCGCCGCGATAATTGCGAACGGGTCGCCGGTCAGAAGGGTCGTCTACACCTTCTGCGTCGTGCTACTTTAGTGGGTTAGAAGATTCTAGTGAGTAAAAGGTCTGATCCCTACCCATTTTCATCTTCGCAATATAAATATAATTATTCGTCATGTGGACTCCGCAGCACACCCACCAATAGCAAGTTGGTTACTGACGCCGTGAGCCCGTCAACACCCCTTATCCACTTTCGCACTTAGGCATATAGGCTCGGATTAACCAACTTCCCAGCACCACATGTGTATCCTTGTATAGCCGTCCGCCCTCATGACTAGGGTGGCGAGTATGGGGTAGGACCATTTGTTTCCAAAAAGGTGTGTAAGGCATCGAGCCCACAATAAACAGATGACCGCGGAGTTGGGTCCCCTTGTCCGGAATTGCTGGAGCAACTATGTGGTCTCTCTAGGCTTCCATCACAGCACCACGTGTAATTCATATTTCATTGAAAAGCTTCGCTACGATTGTAATCTTTGTGC
b
diff -r 000000000000 -r 134e4e78e754 test-data/500kb.fna
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/500kb.fna Tue Apr 26 15:27:01 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 134e4e78e754 test-data/7seqs.fna
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/7seqs.fna Tue Apr 26 15:27:01 2022 +0000
b
b'@@ -0,0 +1,14 @@\n+>genome1~random_sequence_length_11000\n+ACCGCGGGGCACGCTATTAACTGTTGGAGAGAAAACCGTGTGTCACACTCTATAACTCGTGCAGTCGGATTGGATACCACTTTTGCGGCGCGGAGGTCCTGGTGAGCGATTATAAAATAACGGACTGGTGGGTGACCGAACTATGCAATTCGAGCACTGTAGTAGGACCATGTAGTTGCAGTCTCTTGGTAGTGACCGCCCCGTTGTGCAACGCGCTAGGGCGCCGGAGCCGGCTTAGCCTTTAGAATCCCTAATTTGAGACACCTTAGTTGCCCATTCAAAGTAGTTATTACCCGTGATATCCCGCTCAAAACTTAACTTGACTCCTGACTGGAACAAGTCGCAGCGTGGGTTAAACAAGAAACTCCCCGCGCTTGCCTATAAGTAAGCCCGCGATTGTGGGTTACCGTCCATCAATGGTAACAGGTGAACTCCGTAGTTATACGTACTAAACGACAGATATCCAAACCGTGGGCAGCATTCTTGAAATCCTAGGTTAGCCTTCGTACATACCGGATTCCGCTCCAGGCCAAACTTGTGGGTTATCGATTGGAAGGAATGAGCGGCCCATTCGTTGAGGAAGTCACAAACGAACAGCTTATTGGTCTATTAATACGCCCAAAATTTCACGGACCGCACGATCTATGCGAGGAATCCCTGAGGAAAAGAAACACAAGTTCACTACCTGCTTCAAACCGCTGTACGGTGATTCCTCCAAATCAGACGCGGGACGACAACAAGATGATAGCGCGTCAATGGATTGCCGCCGCCCCAATGTCCCATGTTAACTTCGCCCGCGGTATATTGGGGTGAGCAGGAAATTCTCAACGCTGAAACACCATTTCACAAGCCCAAGTTAAAAGCCGCATGGGCTCATGTAAGTGGAGTAGCGGGATAGAGACACAGGACAATCATTTAGCTTCTGGAAATGGTTCGTCAACACGCTGTGGGTTGTATTATAAAAAGAACGCGCCCTAGCAGCGAATAGACGTCACGATGATCTTATACCCTCGAGCTCAGTACCAGCAATCGTGTCGCAAACGTAGACCTCTTTGATGTGCCCGGTCCTCGCTACATTTCTCGCGCGCAAAGACGACGTTATTAATGCCACGCGAAAATAATACTGTGTCCCCCTGTACGACTTCCTTGTTATGAGTATCAACAGTCCTTGACGAGGACTGGAGTTGAATATACCGCTTCAAGTAAGTCCCCGCAGACATACACTTCCTCAATAGACAGCTTTTAACCGTGTACCTCAACTCCTAACCTGGATTCACGGCTTGTTTGACGCAAGAAGAGGGCGTTTGTTGCGTCATAAGGCCGCGCGTGACAAATGTGGGGTAGATTATTCATTATACGGCTTTACGAAGGATATTGTAGCACCTCTTGGTCTGCCAGTGGTCGTCGTTGAACGCTCTGAACCAGAGTGATTATTACGCGCGCGTCTTTACTTATTAGGATTGCAGAACTTTTTCTCAAACATCGGAACTTCGACCAGGAAGTGAGGTCCTCTAAATTCCCAGCTGTTATCGCTGCCACTACGTGTATGATGTGGGCAAATCAAGGAAATACTGATACAGTAGTCCTATAATTAATGATCATTCATGCGATCGCTCTCCGGTATATGTTTCGATTAGCCAGGCTCCGTGACATTAGAGCCCGACAGACCCTTGTCTCCGAGCGATTCCTCGAGTTCAACATAAGGTACGAGGAACGAAGCATTATATTGTAGTAAGTGAACGGATTAGCAAGGCAATGTTCTTTGCGGCAGATGAGCGTCCGAACGGGGGAAAGGAGAACAACCTTTCCCCCAATCCCATTGTGCTTGCGACGGAGGTCTAAATGACCCTGTCTTTCACTGTCGCCCGCTAGGGGAGCAATCTAATATGCGGAGCCTCTACGTTTCTTCAAGTAAAACTCGCAGCGGTTCGCTACATGTTGGTGCTACAACGCTGCGCGGATAAACCCGTTAGCTGATAACCCTTTCATATTAAGCGAACATAGTAGAGTTCTGTATCCAGGCACAGGGCCTGTTGAGTATATTATCATCTAAGTACCCGCCAGCTACCGCACAACGTACGTCTACTACTCACCCATCGATTGTCCGTGATCAACTTCCCTGTCGAGTATCCTCAGACCGCAATGGTTGTAGCGAGCTTCTCTTTGTGGGCGAGTTTGATTTGTTACGCCATAAAATTCTATACGATCACGATGTGGAAGTGAAAGCGTGGTGGACAGCTACAGTGACAGATTTCGAGTATATCCCTTGTGTTGAACCATCTGAACGTTTGACGGCTCATTACGCCGCACTATGGGGACGATATACCACTTGGCAGTAACCAATCGGCGCCTAGACCGCGATCACTTTGCCAAGATTCGCTCGTGTATCGACCCAGTAGTCCAGACCAATACAGAGGCAAGTGCCAAAGGTAGGGTCGTCGGCGAGCGAACCCCGCACTAACCATTCAAACCACCCGGGACTAGATCACTCCAATATAGGACTTGCACCATAAAGGTAGATGGACCTCAGGGCGATTTCCGTCATAGAGTCACGCCGTTTGTCTGATTTCGGTCGTAGGTCGGATAAATGACGCCATATGCCTTGACGAAGACAGTTACGAAGGAGCCCTCCTTTATTTGACACCACTCAACTTTATGTAGGTAGATGGGGATGCCCCAGTCCGACAGGGTCGCATGAGCCGCCTCTACCTCCCGTGGTTCCCGCGTTCTATTTAGATAGCAGAGGTTTACCAAAAAGTGATGAACTCCCAATGGTGGTCATAGCGTTGGTGGACTATCGATGCGCAAGAGCAGGTACCTGGCACATCCAGGTGTGCCGGATCATCTTCCTATGTCGGATACACCTACGATTAGAACTGTAATACTAGTAGTGACGAACGTGGTGCTCTCCCGACTACATTCAGCTCGAGGGGCAGACGACATTGAGCCTCTGTTACGCAAGCGCAAAAGGCAGCCCAATATGCCGTGCCTAGAAGAGACCGAGCTGCTCATAGGATTGTGAGACTACAGTAACCAGCGAGCCATTTTAGCGGGCCATCCGCTTGATCAAATCTAATCGTCGGTCCTTCGGGGGTTGGTCGCGTAGGAGCTTAACTGTCCCGGCGTAGGGAAGCCTAAGCGAGGAGGGCCTTGTATGCTAGAAATTGCGCCGCGTTTTCCAATAGGGCAGAGGACTGTGCCCCTATGCAAAGTACCTCGGGATTGTGAACAAAGGCACTTCATAGTGAGCACTCGATTGCAGTGCGGGTTCCGGGGGTACACGAATGCGAACGCCGCACTGACCTGGTTGGCCCAGACTTCAATGCACGCATCATCTGTCTTCGTATTGGGTTACGGCCGCCAATTTGAAGACATGATTAAACGCTACGCTGTACAAGTCGATCAAGCGATTGAGGCTCTCCCAGAGACTTCAACAAGAACCACGCAGCTGAGTTTCGATTTTACGTATAGCCCGTTCAGGCGCAATAACACGCGATTGCAGAGCTGAACGCGGTCCTCAGTACCGCGCCCTCGCGGGCACCTATGCTCTGGGCAGTGGAGATGAAGTAGAATGTTTAACAAGTTTGTCGGATGAAACAGAGCCCAGTCACGAGTGAAACAGGTTGTTAAAGAGAGCAGATGTAATAGAGGAGGATCAATTGCTTCGCTGAAACTATTCGACTCTCGTATAGCTTTTGAAGACGTTTCCGGTCATCTCGGAATTGAAAGGCCTATTAAGCGGATGTCGTGCGGTCTGTTACCCCGAGACCTAGAAGGCGTCCGGATGTTTCCTGAGTAAGTTGACGGCAGTCACGACCGACTTGCTTCTGGACCGTCCTGATGAACCCACCGACAACCCAACTGGACTGTACTTATTGAACCGCGATCTTGACTGCAGATCAGCACGGGTATAGATACTCTTTTATAACACAGCGCAATGTC'..b'CGACTTACACGGGACCCACGGGTAGGAGGTGACGTACCGCCTACGCCAGGTGCGTCCGCCATGCCGTGCAATACCCGCGACCAGTTCGACTGTGCGCCTCATTGTTGTAGGATAGTTAATCGAGCGGCTTGGGCGGTGAGACGCGTAGGCGATAGTTTTCGATTATCAGTTACACCTCGTTAAGTGACTGGCTGCAAGTCGCATTAAGCAACAAGGGGATGCAGTGGTCCGGACGGCAGTTAGAAACAGTGATTGAGATTATGGCAACCTGTGGCGCGGGGTACCAAGCATATCACCGAAGACACAAAAGCGATGCCAAGCGTTAGCAATTCGATCTTGGGCCTGCTAAGGCAAGCTCTCCTATAAGGGAACCAGGCTATCCCAGCCGCCCGAACACGACCCCTCGCACCCACTACCTCCCGGGGAAAGACCGGGCACTCTCAGAATGCTTATTCAAAGCTCTACGAATTTGGAACCCAGGTAACGGACCGCCCGGCTCGCTAACCCACATCGCAGGGCCTCAGAAAAACACTGTGTCCGCGCTCTCAGACAACAGGCACGGCAGATTCGTGCTTACCGGTAAAATTTCTTCCGCCAATACAGTCCGACCGGGAAAATTATCGTGTTTCCGGTTAGGGGGACTTCAAGAGCCCCTAAGATAGGCGGTATAGCGCGATGGGCGAGGGCGGAACACATCACCGTACTTGGTACTAACAACCAGAGAAACGAATGTTTGGAGAACATCACGGTATTTGTCGGCAGACACATTAACTATCATGACGCTTCACCCGAAGTTGCTCAGCAGTATTTATCGGTCGAGATGAGGCCTTAGTCAATTCATAGGCGCTATTTATTACGAATCTGCGATTGACGTATACGCGTCAGCACGGTCTGGATTCGGTCTATCCATTCAGATAGCATAATAAAATCCGAAGCGTTGTACGACGCTATGCCTGTGTTACTCCGGTGCCTCCCGTCGGATTTATTGGGGGAGTCCTAAATAGGCGAGGCCCGCGACAAGATTGTTGGTGTTCGCGGACATCAGCCGGAGTTACGTCTATAAACTGCATTGATATATCCGAGCGCCTTAGTCTCTGCAGCGACCACCGAACCACAAGCAAAACTGCCGTAACGACCGCCCCAACAGCTACGAGGTCGGGAAGCGCACAATGGTTCGGCGTGGTCGCCACCAGATACCGTCTAAGATGGAGACATTTCTTCTCTACGATGCAGGCTCCCGGAGGACGTCCAATGAGTCCGCTGTGAATGTACTATCCTAATACGATGACTTTGGACCTTTCCGTGACGTCAGTACACGGGTATGTATAAATCAAGATTTACCATTGCGCTTAGTAGACGTCTAATCGACAGTTAGGGATCGTCATTGACAGTCGACCATTGAGATGCTAAAATAACCGCTAGCTTCTCTTATTTTGGTGGGGTTTAGCAGGTCTCAGAGTAAGGATACCGAGGGACTCAGACCAAAGGCTACCAGACGCCGCTGACCACATGCATAGGTACGCAAAGGACTGGGGTGGTCGTACCCATCTCTTCCTCATAATGATAGCAAGAAGCACTTGCTCCCTATGCGTTGGGACGTTGGATGACCTCAGAAACTGAAACCAAAAAGTCACAAGATCTGCAAGGTCATTTCCTGTGTGTTTTCTAGGCCTGACTGATATTGGAGTTTCGCCCAAGACCGGGCCAGAATTCGTCGCACCGCCTAACGGCTGATACTTTTTAGGACGAACCGGGGCTTCCGTCGAGCATGCCTAGGAAGACTCAAGTAAACTTACTTATCCCGTGGGGTGATGATCATCCCAATACCTCGTAACGCCGTACACAATCGTGGATTCCATTTCGTCCTGGGTTCCACACGTTTGATCACTTCGAGGCCCAGGACCGTCGCACCGAGCGTTGGCTCGCTATGCGATAAGGCTATTTCGCCTAGAGACTGATTTAGCGGAGCGGTGGGAGTGAGTCACACGAGAGAGGGTCGTGTCGTGATCAAGACCCCTGCTTCCGCTTGCGCGTGTGCTTCATGGTTCGCTATTTGATGTTGGTCCTTTTTGTCCCTCATTATTTCGGGGATAGAAGTTAATCTCCGCCCGCCGTCCAGATCTGTGTATTACACCGTGCACTAAGTCGATCCTGCACCCTTTTCCTCGCGGCAAGCAATTTAGCTGCTAAAAGTGAATGAGGGTTCGTAGTTAGGAGCACACTTTGCGTTAAAATATCGTGCCATTGGTATGTACTGGGCCCTACATACCATAGCCGATAAGTATCTGATTGGGTATTGTGTCTCTGTCGCTATCACTCGCTGTGCTCAGCTGGCTTTTGTGGTTATTCCATAAGGATGGTGTCCTCTTTTGGTCGCGATACAAGAACCTTTATGATATGAGATTCTTGGCACGCATCAGCCTCAGCATGTATTTGTACATCAATGGGCCATCCGTAGGGATTGCGTTAACCGTGTACTGACAGGGTGTCGTAGACATTCACCATAGTCGATCTCCACCGGGACAGTTATGAGCAGGAGGAGATAAGTTGTCCGCGGCATTACCAAATACAGCTTTGCACGGTCGTATGTGAAATCGGCTGGGCCTATATCAGCTAGAACTAAGTATCGTGAGGTGCTCACGCAGCAACGTGTTTATATGCATGGCAACCTCCAGTAGCGTGGATATAAAAGGCACTTGTTACAGATCCGAGTCCACGTACGCAAATGTAAACACGCTGCCTCTGTCTACCGCCTCGGGGACCTCCTTCTGTATTAAACAGTCCCTCGCCACTCGTAGGGGTGCCTTGGCACGGGGTCGAAAGCCTCCCGGATTGTCGGCGTAAGGTCGTCCTCCGGGTCTAGAAGGCTTAGGCCGCTTTGTGACCATGTACGCGTTGCCATGTGCCCGGGGTCGTAAGATATCCCAAAAGATACAAGACTTTAGCACTATATTAACTCCTAAGTTCTGGATCAAGTCGGTTGCAGCCATGGGAACCTGCAAATAGGCCTCGGGAATGGTTGGACGGTATTAGTTCATCTTCTGTCTATAGGAAGCCTGCTCCCATCTGGAGCTGATGCTTATCGGTCCCATGCGTTTGCGCCCGAATTTTAAGATAGCCCCCTCTAGTGCCGTTGACGATGCTAGCAATAGCTTAACCATCGTCCGACGCCGAGGGTGAGTCTATTTGTTGTTTGAATACGGCCCCCTAAACCTTCCGGACTCTACCTCAGAATGGCAATGATCGACACCTGATTTGGTTAGACACCCTCTACCTAGACCTGTTTATCATTGGTACACCTGGTTGTTAGTCTTCTCATTCTTAGTGATGGTAAGCCGGCACCCGCATCAAGCTTGATGTCGGAATGTTTCGTCTAAATTTGCTAAGGTCTGAATCCGATTAGAATAGCACGGGAGTCCCTCCACCGCTTTTTAGATGTGGTTCCAACGCATCTAGCGCTACTCCTTATAAATCGTCTCAGTCCAGTAGAGGTTCTTCTGCTTTTCTGAGACCTACGCACGGTTTCACTAAGTTGACCTTCGCAGCTTGCTATAATACTCTATGCTAGAGCTTAACATACCGCGCTACAACAGACTGTCCTCCTTTGCGGATGTCATGGTCGCGGCTCCAACCTTGTCAGATTAACTCCTTCATATATTTAATAGGGCGCTCACACACTGGGCGTTGGCAACAAGTTGGGAAGGTTGCATTCCGGCTGTCTACATTATACTGAAGAGCTGTAACCATCAAGCGAGGGATGAGTTCTGTCTCTGATGTGTTGCGCTAAAATACCAAACCGCGAGTTGGTAGGCGGCCACCGTGCGGTTAGAAAATTTAACGGTAACTAGGTTTGTCAAGATCCGCAATTTTAAGCCTCACTAAGGGTCTGACTTTAATTAGCAGAAGCTGGCCCTCATCTTTGGCACCGCAAATTGGCTGTGTGGTCTGATCTAAGGTTCTTTCTTCGGCGGGTTCTCTAAACAAGGATATTGGGTCGG\n'
b
diff -r 000000000000 -r 134e4e78e754 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 134e4e78e754 test-data/all_fasta.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_fasta.loc Tue Apr 26 15:27:01 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 134e4e78e754 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 15:27:01 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 134e4e78e754 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 15:27:01 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 134e4e78e754 test-data/contig_test1.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contig_test1.tsv Tue Apr 26 15:27:01 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 134e4e78e754 test-data/contig_test2.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contig_test2.tsv Tue Apr 26 15:27:01 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 134e4e78e754 test-data/contig_test3.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contig_test3.tsv Tue Apr 26 15:27:01 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 134e4e78e754 test-data/contig_test4.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contig_test4.tsv Tue Apr 26 15:27:01 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 134e4e78e754 test-data/contig_test5.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contig_test5.tsv Tue Apr 26 15:27:01 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 134e4e78e754 test-data/genome1.fna
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome1.fna Tue Apr 26 15:27:01 2022 +0000
b
@@ -0,0 +1,4 @@
+>random_sequence_length_500_1
+GAACATGGGGGGTTGTACACCGCTGGCAGGATATAAAAGAGCGAATTCTTCGTGGTGGGATGCAGAATGTTCATGCACCGCAAACCTTAGGCCCTACCCAATAACAGTCAGCTCCTCCCCTAGAAATACCGTGTCTACGTGTATGTAATGTCAAAACCGCGCTGGTCCATAACTGACCACGACATACGCTTAAGCGACGCAGGTCCCCGTTTATGGACGCAGTAAGATGATATGACAGTAACAGAACGAACGCCTTGATAGCCACTTGGCCTGGTGCCAACGGGGAACGACCTATAGGGGCCAAATTGATTCCAGCTGGTCGGGTGCGCGTATCATCCAATCCAGCCAGGCAGCAACCTCGTATAAGCATCCACACAGCGAGATTTCCAGGACCTTTGAGACGCATCTAGCAGTTTTCCCCCCTTCCACTGACACGTAGTTGATCAAATATCTCGTGTCCACCGGAATCCTCAGAGATTCTCTTCTGTCAAAAAACACTC
+>random_sequence_length_500_2
+CGCTCATGTGCCAAGCATGGACGCCGGAGACACATTTGCTAGTCGGGATGTACGCGGTCTTGTCCACTCTAAAGGGTAAATACAGGAAGCGGTCTCTAGGGACGGGCACTTAATGTAGTTGCATTTATCGATCGCGGGTCCAGATCTGATAGCCGTGCTATGCACATACGATGCTCATAACGCGCGTGATTCCCTTCATTAAGGTACGGCTACCCTGCACCTCTAGACTTGTTTGTACTATCTAGAGCAGTGAGTCGAGCGTCGACAATAGGGTCAGGGCCGGGTACTATTTTGAGCTTTACGGTAATTGCCTTGGGCTAGTAAAACCGCTTCTATACCGCAGACTCATCGAATAATGATTCCTGCAAAACGAGCACGATACGGGAGTTCCTTATGACCAGTCTAATGGTCTCAAGGGTCTCCCCCGGGGAATTACGGTGCCAAGAATGTCTCTGTAATTGACCTAAGTTGTCTGTCGATCCAGAAAATCTGACCAAGAT
b
diff -r 000000000000 -r 134e4e78e754 test-data/genome2.fna
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome2.fna Tue Apr 26 15:27:01 2022 +0000
b
@@ -0,0 +1,4 @@
+>random_sequence_length_500_1
+TCATGAACGGTAGTCAGTCAAGTTTCGCCAGCAATAGGCACAGCTTGTATGGAGGGGTTTAGTCGCCGGAGTGTTACGAGTTTGACGATCCAAAGTTGGAGTCGCCGTGATAATTAATGATATTGCGTCTTCGGTGGGCACGATGAGCCAATCTGCGTCGCACTAGTTTACGTGTTAACGTAGTGAACCTAGACATGACGGGACTATGGCAGTAAGCCGTCACAGCATGTCGGTTCCGGACCACGAGGGTCCATAAGACTAACGATCCACGCTAATTGGCGGATTTACCAAGGCGTCTTCTCTGCGTGTAAGACCCACACCGTGCCTCTGTACCTATGGACGTGCGCGACCATCTTATGATATGAGCATCACATGTTTAATAGAGCGTCCGGTGTCCCTGTAATGCCACCACTTCTGTTTCAACGGACGCTGAATCTAAGCCGATATTTTTGCCTTGATCAGAACGGGGCAGTGAAGGAGCTGCACTAAACTGGCCCTTA
+>random_sequence_length_500_2
+GGATCGGATTACTAATGTTTTTCCAGTCGCCTGTTACTCCAGGCGCGGATGCGAGTGGTCTTTGCCAAGTAGCCCCATGCCACCTGTACAAGGCGGACAAACGCGGATGCGTTTGCATAAATTACCACCGTAAGATACGTTGGCGTATTGCCGTACAAAGGCGGACAGTCCAGATATTTCTTCGGATGTAATTATTGTAGGCGTGCACAACCTACTAGGCGAAAGAGCGGCCCGTTAATCGCGGGTCGCGCCGTGCCCAATTGAACACTTTGCCACGCACGTGACTGGCGGACGGCTCACACGCTATCTCCAAAAATCTACACTTCCGGAGCTAGGCTCCATGACAGGGATGTTCTTATTCAACAAGATGGAGTGCTAATATTAACAATCGACGACACAGGTGAAAAACCTCTTGTCATGTAGCTAGCAGTTATGCGGGCGTACACACTAGTGCTAATCTACTAATCATCCACGGGCCCCTGCTAGAGATCCAAAGGGGT
b
diff -r 000000000000 -r 134e4e78e754 test-data/genome3.fna
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome3.fna Tue Apr 26 15:27:01 2022 +0000
b
@@ -0,0 +1,4 @@
+>random_sequence_length_500_1
+AGAGGGAGCCTTGCGTCGGTGCTCCACGTCGTAAAGCCGTTGAGACCGCGATTACTTTGTTTATTTTCAATTCACTTGTCACAATCAGAAGGACACCGGCGACGGCCAGTTTCCATCGCCCGTCCAGGGTATCGGGGTACCTCTCTACTCGAACGTCTGCGGGGGTTTATCGGGTCTTTACAGGGGGACCAAATGGTTGGACACGGTACCTCAACGCGATAATATATGTCCTGAGTGTGATCATCGGCTGCTTGATTGACTAGTAAGTAAATAACTCCGCCCGCCGAAAGTGACCATTCTAGGAAAATACCCTCTAGCCTCTTGCTTTTGTACGGACTCACTTTCAACGTCCAGGGGTTGCGAACTAATACAGTGAAAGCGATGACCGACAGTAGCAGTTGAGTCTCCCAATGCACCGGTCCCTAACCTCAACCCGGCGTCTAGTCTGACCAGCCTATACAGATAGCAAACAACGTGGACGCGACGGACATGACGAAATA
+>random_sequence_length_500_2
+GCTACTTTACCGTGCGGAAGTAGGTGGGTAGGCCCACATCCTCGTCCTTCAGTGGGCACCCATCTCTCTAAGTACATCTCAAGTGAGGAGGGCTGAGAAAATTGGACGATCTAGTGGAAGCGCGCCGAAATATGGCCTGAGTGAGATCGACCCCGAGGAGCGAGCTCGTTTTCCGAAGTTCGTTATGAGTATGGCGTTCGTTGCTGGCCGAGTACCCCCTGGTGACGTAAAGTGTTTATTTACACAGCTACTTCTCCGAACCAACGACTTATATGTGGGTCCCTGATTGCCTCCCATAGGTCCGGCATAGTTAAGAAAGTTAACGGAACCAAAGTCCAGTACATGGAGTTCTATGATAGACAGCTGTCTCCATTCCCGTATCTGCCAAAGAGATTAGATCCTAGTTGATCCCAGCAGCTACTCGTAATGACAGGATCCGGCGTGTCACTATACGACGCTTGCGGGAGGATGGTCGCCCTGCCCGTACCGTTACTTAGATC
b
diff -r 000000000000 -r 134e4e78e754 test-data/genomeInfo.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genomeInfo.csv Tue Apr 26 15:27:01 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 134e4e78e754 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 15:27:01 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 134e4e78e754 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 15:27:01 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 134e4e78e754 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 134e4e78e754 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 134e4e78e754 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 15:27:01 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
b
diff -r 000000000000 -r 134e4e78e754 test-data/test1.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1.tsv Tue Apr 26 15:27:01 2022 +0000
b
@@ -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
b
diff -r 000000000000 -r 134e4e78e754 test-data/test2.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test2.tsv Tue Apr 26 15:27:01 2022 +0000
b
@@ -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
b
diff -r 000000000000 -r 134e4e78e754 test-data/test3.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test3.tsv Tue Apr 26 15:27:01 2022 +0000
b
@@ -0,0 +1,4 @@
+Genome fw0 Mean
+genome1 0
+genome2 4.8142858
+genome3 0
b
diff -r 000000000000 -r 134e4e78e754 test-data/test4.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test4.tsv Tue Apr 26 15:27:01 2022 +0000
b
@@ -0,0 +1,4 @@
+Genome fw0 Mean
+genome1 0
+genome2 4.8142858
+genome3 0
b
diff -r 000000000000 -r 134e4e78e754 test-data/tpm_test.bam
b
Binary file test-data/tpm_test.bam has changed
b
diff -r 000000000000 -r 134e4e78e754 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 15:27:01 2022 +0000
b
@@ -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
b
diff -r 000000000000 -r 134e4e78e754 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 15:27:01 2022 +0000
b
@@ -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
b
diff -r 000000000000 -r 134e4e78e754 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 15:27:01 2022 +0000
b
@@ -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