| Next changeset 1:adfe9fda2c5f (2019-10-29) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2" |
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added:
qualimap_macros.xml qualimap_multi_bamqc.xml test-data/coverage_across_reference.txt test-data/coverage_histogram.txt test-data/duplication_rate_histogram.txt test-data/features.gtf test-data/genome_fraction_coverage.txt test-data/genome_results_default.txt test-data/genome_results_inside_features.txt test-data/genome_results_outside_features.txt test-data/mapped_reads_clipping_profile.txt test-data/mapped_reads_gc-content_distribution.txt test-data/mapped_reads_nucleotide_content.txt test-data/mapping_quality_across_reference.txt test-data/mapping_quality_histogram.txt test-data/mouse_counts_ensemble_1000_6.tsv test-data/per_base_coverage_default.txt test-data/per_base_coverage_inside_features.txt test-data/per_base_coverage_outside_features.txt test-data/rnaseq_qc_counts_custom.txt test-data/rnaseq_qc_results_custom.txt test-data/rnaseq_qc_results_default.txt test-data/test_mapped_reads.bam |
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| diff -r 000000000000 -r 16beb83e370c qualimap_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qualimap_macros.xml Thu Oct 10 17:40:15 2019 -0400 |
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| @@ -0,0 +1,40 @@ +<macros> + <token name="@VERSION@">2.2.2c</token> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">qualimap</requirement> + <yield /> + </requirements> + </xml> + + <xml name="version_command"> + <version_command>qualimap --help | grep 'QualiMap v.' | cut -d '.' -f 2-</version_command> + </xml> + + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/btv566</citation> + <citation type="doi">10.1093/bioinformatics/bts503</citation> + <yield /> + </citations> + </xml> + + <token name="@SET_JAVA_OPTS@"> + export JAVA_OPTS="-Djava.awt.headless=true -Xmx\${GALAXY_MEMORY_MB:-1024}m" + </token> + + <token name="@MASSAGE_OUTPUT@"><![CDATA[ + sed 's|images_${report_name}/||g;s|css/||g' results/${report_name}.html > '$output_html' && + mkdir '${output_html.extra_files_path}' && + mv results/css/*.css '${output_html.extra_files_path}' && + mv results/css/*.png '${output_html.extra_files_path}' && + if [ -d results/images_${report_name} ]; then + mv results/images_${report_name}/* '${output_html.extra_files_path}' && + for file in \$(ls -A results/raw_data_${report_name}); do mv "results/raw_data_${report_name}/\$file" `echo "results/\$file" | sed 's/(//;s/)//'`; done + fi + #if $summary_report: + && mv results/$summary_report results/summary_report.txt + #end if + ]]></token> +</macros> |
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| diff -r 000000000000 -r 16beb83e370c qualimap_multi_bamqc.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qualimap_multi_bamqc.xml Thu Oct 10 17:40:15 2019 -0400 |
| [ |
| b'@@ -0,0 +1,199 @@\n+<tool id="qualimap_multi_bamqc" name="QualiMap Multi-Sample BamQC" version="@VERSION@">\n+ <macros>\n+ <import>qualimap_macros.xml</import>\n+ <xml name="test_collection">\n+ <collection type="list">\n+ <element name="genome_results" value="genome_results_inside_features.txt" />\n+ <element name="coverage_across_reference" value="coverage_across_reference.txt" />\n+ <element name="coverage_histogram" value="coverage_histogram.txt" />\n+ <element name="genome_fraction_coverage" value="genome_fraction_coverage.txt" />\n+ <element name="duplication_rate_histogram" value="duplication_rate_histogram.txt" />\n+ <element name="mapped_reads_clipping_profile" value="mapped_reads_clipping_profile.txt" />\n+ <element name="mapped_reads_gc-content_distribution" value="mapped_reads_gc-content_distribution.txt" />\n+ <element name="mapped_reads_nucleotide_content" value="mapped_reads_nucleotide_content.txt" />\n+ <element name="mapping_quality_across_reference" value="mapping_quality_across_reference.txt" />\n+ <element name="mapping_quality_histogram" value="mapping_quality_histogram.txt" />\n+ </collection>\n+ </xml>\n+ </macros>\n+ <expand macro="requirements" />\n+ <expand macro="version_command" />\n+ <command detect_errors="exit_code"><![CDATA[\n+ #if str($input.mode) == \'grouped\':\n+ #set $n = 0\n+ #for group in $input.groups:\n+ #set $n = $n + 1\n+ #for $n, $data in enumerate($group.bam_qc_data, $n):\n+ #set $coll = $data.bam_qc_input\n+ #set $sample_name = str($coll.name).replace(\' \', \'_\')\n+ printf \'%s\\tbam_qc_data%d\\t%s\\n\' \'${sample_name}\' ${n} \'${group.name}\' >> data_spec.txt &&\n+ mkdir -p bam_qc_data$n/raw_data_qualimapReport &&\n+ #for $dataset in $coll:\n+ #if str($dataset.element_identifier) == \'genome_results\':\n+ ln -s \'$dataset\' \'bam_qc_data$n/${dataset.element_identifier}.txt\' &&\n+ #else:\n+ ln -s \'$dataset\' \'bam_qc_data$n/raw_data_qualimapReport/${dataset.element_identifier}.txt\' &&\n+ #end if\n+ #end for\n+ #end for\n+ #end for\n+ #if all(len($group.bam_qc_data) == 1 for group in $input.groups):\n+ ## Warn about an inconsistency in the behavior of the current\n+ ## version of Qualimap.\n+ ## When each group consists of exactly one BAM QC input,\n+ ## Qualimap will ignore the group names and use the sample names\n+ ## in the plot legends instead.\n+ printf "Warning: Only a single sample was assigned to each sample group!\\nQualimap will use sample names, not group names in plot legends.\\nYou may want to report samples individually to be able to specify custom sample names.\\n\\n" &&\n+ #end if\n+ #else:\n+ #for $n, $data in enumerate($input.bam_qc_data):\n+ #set $coll = $data.bam_qc_input\n+ #set $sample_name = (str($data.sample_name).strip() or str($coll.name)).replace(\' \', \'_\')\n+ printf \'%s\\tbam_qc_data%d\\t%d\\n\' \'${sample_name}\' \'${n}\' \'${n}\' >> data_spec.txt &&\n+ mkdir -p bam_qc_data$n/raw_data_qualimapReport &&\n+ #for $dataset in $coll:\n+ #if str($dataset.element_identifier) == \'genome_results\':\n+ ln -s \'$dataset\' \'bam_qc_data$n/${dataset.element_identifier}.txt\' &&\n+ #else:\n+ ln -s \'$dataset\' \'bam_qc_data$n/raw_data_qualimapReport/${dataset.element_identifier}.txt\' &&\n+ #end if\n+ #end for\n+ #end for\n+ #end if\n+\n+ @SET_JAVA_OPTS@ &&\n+ qualimap multi-bamqc\n+ --data data_spec.txt\n+ -outdir results -outformat html &&\n+\n+ #set $report_'..b' </repeat>\n+ </when>\n+ <when value="grouped">\n+ <repeat name="groups" default="1" min="1" title="Groups">\n+ <param name="name" type="text" label="Name of the group">\n+ <validator type="expression" message="A name is required for every group">value.strip()</validator>\n+ </param>\n+ <repeat name="bam_qc_data" default="1" min="1"\n+ title="Data associated with this group">\n+ <param name="bam_qc_input" type="data_collection" collection_type="list" format="txt" multiple="true"\n+ label="Single-sample BAM QC data"\n+ help="" />\n+ </repeat>\n+ </repeat>\n+ </when>\n+ </conditional>\n+ </inputs>\n+\n+ <outputs>\n+ <data name="output_html" format="html" />\n+ </outputs>\n+ <tests>\n+ <test>\n+ <conditional name="input">\n+ <param name="mode" value="individual" />\n+ <repeat name="bam_qc_data">\n+ <param name="bam_qc_input">\n+ <expand macro="test_collection" />\n+ </param>\n+ </repeat>\n+ <repeat name="bam_qc_data">\n+ <param name="bam_qc_input">\n+ <expand macro="test_collection" />\n+ </param>\n+ </repeat>\n+ </conditional>\n+ <output name="output_html" ftype="html">\n+ <assert_contents>\n+ <has_text text="Qualimap report: Multi-sample BAM QC" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+**What it does**\n+\n+This tool lets you combine the summary statistics, obtained through multiple\n+runs of the *Qualimap BamQC* tool, of several aligned reads datasets into a\n+single report.\n+\n+This makes it easy to visualize the degree of similarities between the\n+different inputs and to spot differences between them.\n+\n+Input\n+=====\n+\n+Several *Raw Data* collections obtained from previous runs of *Qualimap BamQC*.\n+\n+Options\n+-------\n+\n+*Report samples* -> ``Individually`` / ``In groups``\n+\n+You may decide to group the input data for reporting, in which case you will\n+need to provide a name for each group that will be used in the plot legends.\n+\n+Output\n+======\n+\n+The single HTML report generated by this tool contains the following:\n+\n+*Input data and parameters*\n+\n+This section lists the names of the BamQC Raw Data collections that served as\n+input along with the names of the groups (if any) each input got assigned to.\n+\n+*Summary*\n+\n+The summary table contains comparison of selected critical alignment metrics for all samples. The metrics include mean and standard deviation of coverage, mean GC content, mean insert size and mean mapping qualities. If the sample groups are provided, they are also shown for each sample.\n+\n+*PCA plot*\n+\n+The alignment features presented in the Summary section undergo Principal Component Analysis. Afterwards the biplot presenting first and second principal component is constructed. It allows to detect if any samples group together and if there are any outliers among the analyzed samples.\n+\n+*Other plots*\n+\n+Here you will find plots of:\n+\n+- Coverage Across Reference,\n+- Coverage Histogram,\n+- Genome Fraction Coverage,\n+- Duplication Rate Histogram,\n+- Mapped Reads GC Content,\n+- Mapped Reads GC Content Distribution,\n+- Mapped Reads Clipping Profile,\n+- Mapping Quality Across Reference,\n+- Mapping Quality Histogram\n+\n+and, if applicable,\n+\n+- Insert Size Across Reference,\n+- Insert Size Histogram\n+\n+Essentially, these are overlays of the plots of the individual inputs (or of\n+the groups they have been assigned to) and that are explained in the help of\n+the *Qualimap BamQC* tool.\n+ ]]></help>\n+ <expand macro="citations"/>\n+</tool>\n' |
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| diff -r 000000000000 -r 16beb83e370c test-data/coverage_across_reference.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coverage_across_reference.txt Thu Oct 10 17:40:15 2019 -0400 |
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| @@ -0,0 +1,326 @@ +#Position (bp) Coverage Std +1.5 0.0 0.0 +3.5 0.0 0.0 +5.5 0.0 0.0 +7.5 0.0 0.0 +9.5 0.0 0.0 +11.5 0.0 0.0 +13.5 0.0 0.0 +15.5 0.0 0.0 +17.5 0.0 0.0 +19.5 0.0 0.0 +21.5 0.0 0.0 +23.5 0.0 0.0 +25.5 0.0 0.0 +27.5 0.0 0.0 +29.5 0.0 0.0 +31.5 0.0 0.0 +33.5 0.0 0.0 +35.5 0.0 0.0 +37.5 0.0 0.0 +39.5 0.0 0.0 +41.5 0.0 0.0 +43.5 0.0 0.0 +45.5 0.0 0.0 +47.5 0.0 0.0 +49.5 0.0 0.0 +51.5 0.0 0.0 +53.5 1.0 0.0 +55.5 2.5 1.5811388300841898 +57.5 3.5 1.8708286933869707 +59.5 4.0 0.0 +61.5 5.0 0.0 +63.5 5.0 0.0 +65.5 5.0 0.0 +67.5 5.0 0.0 +69.5 5.0 0.0 +71.5 5.5 2.345207879911715 +73.5 6.0 0.0 +75.5 6.0 0.0 +77.5 7.0 1.0 +79.5 8.0 0.0 +81.5 8.0 0.0 +83.5 9.0 0.0 +85.5 9.5 3.082207001484488 +87.5 10.5 3.24037034920393 +89.5 12.0 0.0 +91.5 13.5 3.6742346141747673 +93.5 15.0 1.0 +95.5 16.5 4.06201920231798 +97.5 17.5 4.183300132670378 +99.5 18.0 0.0 +101.5 21.5 4.636809247747852 +103.5 23.0 0.0 +105.5 23.5 4.847679857416329 +107.5 25.0 0.0 +109.5 25.0 0.0 +111.5 25.0 0.0 +113.5 25.0 0.0 +115.5 26.0 0.0 +117.5 26.0 0.0 +119.5 26.0 0.0 +121.5 26.5 5.1478150704935 +123.5 29.0 0.0 +125.5 32.0 0.0 +127.5 33.0 0.0 +129.5 32.5 5.70087712549569 +131.5 32.5 5.70087712549569 +133.5 32.0 0.0 +135.5 33.5 5.787918451395113 +137.5 33.0 0.0 +139.5 34.0 0.0 +141.5 36.0 1.0 +143.5 37.5 6.123724356957945 +145.5 38.0 0.0 +147.5 38.0 0.0 +149.5 38.0 0.0 +151.5 38.0 0.0 +153.5 36.0 0.0 +155.5 37.0 0.0 +157.5 36.5 6.041522986797286 +159.5 36.5 6.041522986797286 +161.5 36.5 6.041522986797286 +163.5 35.5 5.958187643906492 +165.5 36.5 6.041522986797286 +167.5 36.0 0.0 +169.5 35.0 1.0 +171.5 36.0 0.0 +173.5 35.0 0.0 +175.5 34.5 6.041522986797286 +177.5 32.0 0.0 +179.5 32.0 0.0 +181.5 31.5 5.612486080160912 +183.5 31.5 5.612486080160912 +185.5 32.0 0.0 +187.5 32.0 0.0 +189.5 31.5 5.612486080160912 +191.5 31.0 0.0 +193.5 31.5 5.612486080160912 +195.5 32.0 0.0 +197.5 31.0 1.0 +199.5 28.5 5.338539126015656 +201.5 30.5 5.522680508593631 +203.5 29.5 5.431390245600108 +205.5 31.0 0.0 +207.5 31.5 5.612486080160912 +209.5 31.0 0.0 +211.5 31.0 0.0 +213.5 31.0 0.0 +215.5 30.5 5.522680508593631 +217.5 28.0 0.0 +219.5 27.0 0.0 +221.5 28.0 0.0 +223.5 28.0 0.0 +225.5 29.0 0.0 +227.5 30.0 0.0 +229.5 30.5 5.522680508593631 +231.5 31.5 5.612486080160912 +233.5 33.5 5.787918451395113 +235.5 33.0 0.0 +237.5 32.0 0.0 +239.5 31.0 1.0 +241.5 29.5 5.431390245600108 +243.5 31.5 5.612486080160912 +245.5 29.5 5.431390245600108 +247.5 29.0 0.0 +249.5 28.5 5.338539126015656 +251.5 27.0 0.0 +253.5 27.0 0.0 +255.5 27.0 0.0 +257.5 27.0 0.0 +259.5 27.0 0.0 +261.5 27.0 0.0 +263.5 27.0 0.0 +265.5 27.0 0.0 +267.5 27.0 0.0 +269.5 27.0 0.0 +271.5 27.0 0.0 +273.5 27.0 0.0 +275.5 27.0 0.0 +277.5 27.0 0.0 +279.5 27.0 0.0 +281.5 27.0 0.0 +283.5 27.0 0.0 +285.5 27.0 0.0 +287.5 27.0 0.0 +289.5 27.0 0.0 +291.5 27.0 0.0 +293.5 27.0 0.0 +295.5 27.0 0.0 +297.5 27.0 0.0 +299.5 27.0 0.0 +301.5 0.0 0.0 +303.5 0.0 0.0 +305.5 0.0 0.0 +307.5 0.0 0.0 +309.5 0.0 0.0 +311.5 0.0 0.0 +313.5 0.0 0.0 +315.5 0.0 0.0 +317.5 0.0 0.0 +319.5 0.0 0.0 +321.5 0.0 0.0 +323.5 0.0 0.0 +325.5 0.0 0.0 +327.5 0.0 0.0 +329.5 0.0 0.0 +331.5 0.0 0.0 +333.5 0.0 0.0 +335.5 0.0 0.0 +337.5 0.0 0.0 +339.5 0.0 0.0 +341.5 0.0 0.0 +343.5 0.0 0.0 +345.5 0.0 0.0 +347.5 0.0 0.0 +349.5 0.0 0.0 +351.5 0.0 0.0 +353.5 0.0 0.0 +355.5 0.0 0.0 +357.5 0.0 0.0 +359.5 0.0 0.0 +361.5 0.0 0.0 +363.5 0.0 0.0 +365.5 0.0 0.0 +367.5 0.0 0.0 +369.5 0.0 0.0 +371.5 0.0 0.0 +373.5 0.0 0.0 +375.5 0.0 0.0 +377.5 0.0 0.0 +379.5 0.0 0.0 +381.5 0.0 0.0 +383.5 0.0 0.0 +385.5 0.0 0.0 +387.5 0.0 0.0 +389.5 0.0 0.0 +391.5 0.0 0.0 +393.5 0.0 0.0 +395.5 0.0 0.0 +397.5 0.0 0.0 +399.5 0.0 0.0 +401.5 0.0 0.0 +403.5 0.0 0.0 +405.5 0.0 0.0 +407.5 0.0 0.0 +409.5 0.0 0.0 +411.5 0.0 0.0 +413.5 0.0 0.0 +415.5 0.0 0.0 +417.5 0.0 0.0 +419.5 0.0 0.0 +421.5 0.0 0.0 +423.5 0.0 0.0 +425.5 0.0 0.0 +427.5 0.0 0.0 +429.5 0.0 0.0 +431.5 0.0 0.0 +433.5 0.0 0.0 +435.5 0.0 0.0 +437.5 0.0 0.0 +439.5 0.0 0.0 +441.5 0.0 0.0 +443.5 0.0 0.0 +445.5 0.0 0.0 +447.5 0.0 0.0 +449.5 0.0 0.0 +451.5 0.0 0.0 +453.5 0.0 0.0 +455.5 0.0 0.0 +457.5 0.0 0.0 +459.5 0.0 0.0 +461.5 0.0 0.0 +463.5 0.0 0.0 +465.5 0.0 0.0 +467.5 0.0 0.0 +469.5 0.0 0.0 +471.5 0.0 0.0 +473.5 0.0 0.0 +475.5 0.0 0.0 +477.5 0.0 0.0 +479.5 0.0 0.0 +481.5 0.0 0.0 +483.5 0.0 0.0 +485.5 0.0 0.0 +487.5 0.0 0.0 +489.5 0.0 0.0 +491.5 0.0 0.0 +493.5 0.0 0.0 +495.5 0.0 0.0 +497.5 0.0 0.0 +499.5 0.0 0.0 +501.5 0.0 0.0 +503.5 0.0 0.0 +505.5 0.0 0.0 +507.5 0.0 0.0 +509.5 0.0 0.0 +511.5 0.0 0.0 +513.5 0.0 0.0 +515.5 0.0 0.0 +517.5 0.0 0.0 +519.5 0.0 0.0 +521.5 0.0 0.0 +523.5 0.0 0.0 +525.5 0.0 0.0 +527.5 0.0 0.0 +529.5 0.0 0.0 +531.5 0.0 0.0 +533.5 0.0 0.0 +535.5 0.0 0.0 +537.5 0.0 0.0 +539.5 0.0 0.0 +541.5 0.0 0.0 +543.5 0.0 0.0 +545.5 0.0 0.0 +547.5 0.0 0.0 +549.5 0.0 0.0 +551.5 0.0 0.0 +553.5 0.0 0.0 +555.5 0.0 0.0 +557.5 0.0 0.0 +559.5 0.0 0.0 +561.5 0.0 0.0 +563.5 0.0 0.0 +565.5 0.0 0.0 +567.5 0.0 0.0 +569.5 0.0 0.0 +571.5 0.0 0.0 +573.5 0.0 0.0 +575.5 0.0 0.0 +577.5 0.0 0.0 +579.5 0.0 0.0 +581.5 0.0 0.0 +583.5 0.0 0.0 +585.5 0.0 0.0 +587.5 0.0 0.0 +589.5 0.0 0.0 +591.5 0.0 0.0 +593.5 0.0 0.0 +595.5 0.0 0.0 +597.5 0.0 0.0 +599.5 0.0 0.0 +601.5 0.0 0.0 +603.5 0.0 0.0 +605.5 0.0 0.0 +607.5 0.0 0.0 +609.5 0.0 0.0 +611.5 0.0 0.0 +613.5 0.0 0.0 +615.5 0.0 0.0 +617.5 0.0 0.0 +619.5 0.0 0.0 +621.5 0.0 0.0 +623.5 0.0 0.0 +625.5 0.0 0.0 +627.5 0.0 0.0 +629.5 0.0 0.0 +631.5 0.0 0.0 +633.5 0.0 0.0 +635.5 0.0 0.0 +637.5 0.0 0.0 +639.5 0.0 0.0 +641.5 0.0 0.0 +643.5 0.0 0.0 +645.5 0.0 0.0 +647.5 0.0 0.0 +649.5 0.0 0.0 |
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| diff -r 000000000000 -r 16beb83e370c test-data/coverage_histogram.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coverage_histogram.txt Thu Oct 10 17:40:15 2019 -0400 |
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| @@ -0,0 +1,36 @@ +#Coverage Number of genomic locations +0.0 102.0 +1.0 2.0 +2.0 1.0 +3.0 2.0 +4.0 3.0 +5.0 11.0 +6.0 6.0 +8.0 5.0 +9.0 3.0 +10.0 2.0 +11.0 1.0 +12.0 2.0 +13.0 1.0 +14.0 2.0 +16.0 2.0 +17.0 2.0 +18.0 3.0 +21.0 1.0 +22.0 1.0 +23.0 3.0 +24.0 1.0 +25.0 8.0 +26.0 7.0 +27.0 3.0 +28.0 8.0 +29.0 11.0 +30.0 10.0 +31.0 20.0 +32.0 27.0 +33.0 11.0 +34.0 5.0 +35.0 4.0 +36.0 13.0 +37.0 8.0 +38.0 9.0 |
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| diff -r 000000000000 -r 16beb83e370c test-data/duplication_rate_histogram.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/duplication_rate_histogram.txt Thu Oct 10 17:40:15 2019 -0400 |
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| @@ -0,0 +1,51 @@ +#Duplication rate Coverage +1.0 57.0 +2.0 8.0 +3.0 3.0 +4.0 0.0 +5.0 0.0 +6.0 0.0 +7.0 0.0 +8.0 0.0 +9.0 0.0 +10.0 0.0 +11.0 0.0 +12.0 0.0 +13.0 0.0 +14.0 0.0 +15.0 0.0 +16.0 0.0 +17.0 0.0 +18.0 0.0 +19.0 0.0 +20.0 0.0 +21.0 0.0 +22.0 0.0 +23.0 0.0 +24.0 0.0 +25.0 0.0 +26.0 0.0 +27.0 0.0 +28.0 0.0 +29.0 0.0 +30.0 0.0 +31.0 0.0 +32.0 0.0 +33.0 0.0 +34.0 0.0 +35.0 0.0 +36.0 0.0 +37.0 0.0 +38.0 0.0 +39.0 0.0 +40.0 0.0 +41.0 0.0 +42.0 0.0 +43.0 0.0 +44.0 0.0 +45.0 0.0 +46.0 0.0 +47.0 0.0 +48.0 0.0 +49.0 0.0 +50.0 0.0 |
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| diff -r 000000000000 -r 16beb83e370c test-data/features.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/features.gtf Thu Oct 10 17:40:15 2019 -0400 |
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| @@ -0,0 +1,4 @@ +test_chromosome test gene 1 300 . + . gene_id "GENE1"; gene_name "GENE1"; transcript_id "GENE1_t1"; +test_chromosome test transcript 1 300 . + . gene_id "GENE1"; gene_name "GENE1"; transcript_id "GENE1_t1"; +test_chromosome test exon 1 300 . + . gene_id "GENE1"; transcript_id "GENE1_t1"; exon_number "1"; gene_name "GENE1"; +test_chromosome test CDS 100 250 . + . gene_id "GENE1"; transcript_id "GENE1_t1"; exon_number "1"; gene_name "GENE1"; |
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| diff -r 000000000000 -r 16beb83e370c test-data/genome_fraction_coverage.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_fraction_coverage.txt Thu Oct 10 17:40:15 2019 -0400 |
| b |
| @@ -0,0 +1,52 @@ +#Coverage (X) Coverage +1.0 66.0 +2.0 65.33333333333334 +3.0 65.0 +4.0 64.33333333333334 +5.0 63.333333333333336 +6.0 59.66666666666667 +7.0 57.66666666666667 +8.0 57.66666666666667 +9.0 56.00000000000001 +10.0 55.00000000000001 +11.0 54.33333333333334 +12.0 54.00000000000001 +13.0 53.33333333333334 +14.0 53.00000000000001 +15.0 52.33333333333334 +16.0 52.33333333333334 +17.0 51.66666666666668 +18.0 51.000000000000014 +19.0 50.000000000000014 +20.0 50.000000000000014 +21.0 50.000000000000014 +22.0 49.66666666666668 +23.0 49.33333333333334 +24.0 48.33333333333334 +25.0 48.00000000000001 +26.0 45.33333333333334 +27.0 43.00000000000001 +28.0 42.00000000000001 +29.0 39.33333333333334 +30.0 35.66666666666667 +31.0 32.33333333333334 +32.0 25.66666666666667 +33.0 16.66666666666667 +34.0 13.0 +35.0 11.333333333333329 +36.0 10.0 +37.0 5.666666666666671 +38.0 3.0 +39.0 0.0 +40.0 0.0 +41.0 0.0 +42.0 0.0 +43.0 0.0 +44.0 0.0 +45.0 0.0 +46.0 0.0 +47.0 0.0 +48.0 0.0 +49.0 0.0 +50.0 0.0 +51.0 0.0 |
| b |
| diff -r 000000000000 -r 16beb83e370c test-data/genome_results_default.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_results_default.txt Thu Oct 10 17:40:15 2019 -0400 |
| b |
| @@ -0,0 +1,122 @@ +BamQC report +----------------------------------- + +>>>>>>> Input + + bam file = /tmp/tmprT4oZK/files/b/1/f/dataset_b1fbaad4-1b5a-4769-8a15-b4cec4de5731.dat + outfile = results/genome_results.txt + + +>>>>>>> Reference + + number of bases = 650 bp + number of contigs = 1 + + +>>>>>>> Globals + + number of windows = 325 + + number of reads = 100 + number of mapped reads = 100 (100%) + number of secondary alignments = 1 + + number of mapped bases = 12,665 bp + number of sequenced bases = 7,465 bp + number of aligned bases = 0 bp + number of duplicated reads (estimated) = 18 + duplication rate = 15.85% + + +>>>>>>> Insert size + + mean insert size = 0 + std insert size = 0 + median insert size = 0 + + +>>>>>>> Mapping quality + + mean mapping quality = 115.8402 + + +>>>>>>> ACTG content + + number of A's = 1,910 bp (25.59%) + number of C's = 1,902 bp (25.48%) + number of T's = 1,497 bp (20.05%) + number of G's = 2,156 bp (28.88%) + number of N's = 0 bp (0%) + + GC percentage = 54.36% + + +>>>>>>> Mismatches and indels + + general error rate = 0.0118 + number of mismatches = 149 + + +>>>>>>> Coverage + + mean coverageData = 19.4846X + std coverageData = 16.5813X + + There is a 45.85% of reference with a coverageData >= 1X + There is a 45.38% of reference with a coverageData >= 2X + There is a 44.92% of reference with a coverageData >= 3X + There is a 44.62% of reference with a coverageData >= 4X + There is a 43.85% of reference with a coverageData >= 5X + There is a 41.85% of reference with a coverageData >= 6X + There is a 40.46% of reference with a coverageData >= 7X + There is a 39.85% of reference with a coverageData >= 8X + There is a 38.77% of reference with a coverageData >= 9X + There is a 38% of reference with a coverageData >= 10X + There is a 37.23% of reference with a coverageData >= 11X + There is a 36.92% of reference with a coverageData >= 12X + There is a 36.46% of reference with a coverageData >= 13X + There is a 36.15% of reference with a coverageData >= 14X + There is a 35.54% of reference with a coverageData >= 15X + There is a 35.23% of reference with a coverageData >= 16X + There is a 34.77% of reference with a coverageData >= 17X + There is a 34% of reference with a coverageData >= 18X + There is a 33.38% of reference with a coverageData >= 19X + There is a 33.38% of reference with a coverageData >= 20X + There is a 33.23% of reference with a coverageData >= 21X + There is a 31.85% of reference with a coverageData >= 22X + There is a 31.54% of reference with a coverageData >= 23X + There is a 30.92% of reference with a coverageData >= 24X + There is a 30.62% of reference with a coverageData >= 25X + There is a 28.62% of reference with a coverageData >= 26X + There is a 27.54% of reference with a coverageData >= 27X + There is a 26.92% of reference with a coverageData >= 28X + There is a 25.23% of reference with a coverageData >= 29X + There is a 23.38% of reference with a coverageData >= 30X + There is a 20.77% of reference with a coverageData >= 31X + There is a 16.77% of reference with a coverageData >= 32X + There is a 12.15% of reference with a coverageData >= 33X + There is a 10.15% of reference with a coverageData >= 34X + There is a 8.62% of reference with a coverageData >= 35X + There is a 7.38% of reference with a coverageData >= 36X + There is a 4% of reference with a coverageData >= 37X + There is a 1.85% of reference with a coverageData >= 38X + There is a 0.31% of reference with a coverageData >= 39X + There is a 0% of reference with a coverageData >= 40X + There is a 0% of reference with a coverageData >= 41X + There is a 0% of reference with a coverageData >= 42X + There is a 0% of reference with a coverageData >= 43X + There is a 0% of reference with a coverageData >= 44X + There is a 0% of reference with a coverageData >= 45X + There is a 0% of reference with a coverageData >= 46X + There is a 0% of reference with a coverageData >= 47X + There is a 0% of reference with a coverageData >= 48X + There is a 0% of reference with a coverageData >= 49X + There is a 0% of reference with a coverageData >= 50X + There is a 0% of reference with a coverageData >= 51X + + +>>>>>>> Coverage per contig + + test_chromosome 650 12665 19.484615384615385 16.581284452141826 + + |
| b |
| diff -r 000000000000 -r 16beb83e370c test-data/genome_results_inside_features.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_results_inside_features.txt Thu Oct 10 17:40:15 2019 -0400 |
| b |
| @@ -0,0 +1,128 @@ +BamQC report +----------------------------------- + +>>>>>>> Input + + bam file = /tmp/tmpB4Sf0A/files/e/d/7/dataset_ed7510d4-c8f3-41fc-8cc1-3b854d9bdf14.dat + outfile = results/genome_results.txt + + +>>>>>>> Reference + + number of bases = 650 bp + number of contigs = 1 + + +>>>>>>> Globals + + number of windows = 325 + + number of reads = 100 + number of mapped reads = 100 (100%) + number of secondary alignments = 1 + + number of mapped bases = 6,451 bp + number of sequenced bases = 5,101 bp + number of aligned bases = 0 bp + number of duplicated reads (estimated) = 14 + duplication rate = 16.18% + + +>>>>>>> Globals inside + + regions size = 300 (46.15%) + number of mapped reads = 82 (82%) + + +>>>>>>> Insert size + + mean insert size = 0 + std insert size = 0 + median insert size = 0 + + +>>>>>>> Mapping quality + + mean mapping quality = 251.3687 + + +>>>>>>> ACTG content + + number of A's = 1,243 bp (24.37%) + number of C's = 1,257 bp (24.64%) + number of T's = 985 bp (19.31%) + number of G's = 1,616 bp (31.68%) + number of N's = 0 bp (0%) + + GC percentage = 56.32% + + +>>>>>>> Mismatches and indels + + general error rate = 0.0211 + number of mismatches = 136 + + +>>>>>>> Coverage + + mean coverageData = 21.5033X + std coverageData = 15.658X + + There is a 66% of reference with a coverageData >= 1X + There is a 65.33% of reference with a coverageData >= 2X + There is a 65% of reference with a coverageData >= 3X + There is a 64.33% of reference with a coverageData >= 4X + There is a 63.33% of reference with a coverageData >= 5X + There is a 59.67% of reference with a coverageData >= 6X + There is a 57.67% of reference with a coverageData >= 7X + There is a 57.67% of reference with a coverageData >= 8X + There is a 56% of reference with a coverageData >= 9X + There is a 55% of reference with a coverageData >= 10X + There is a 54.33% of reference with a coverageData >= 11X + There is a 54% of reference with a coverageData >= 12X + There is a 53.33% of reference with a coverageData >= 13X + There is a 53% of reference with a coverageData >= 14X + There is a 52.33% of reference with a coverageData >= 15X + There is a 52.33% of reference with a coverageData >= 16X + There is a 51.67% of reference with a coverageData >= 17X + There is a 51% of reference with a coverageData >= 18X + There is a 50% of reference with a coverageData >= 19X + There is a 50% of reference with a coverageData >= 20X + There is a 50% of reference with a coverageData >= 21X + There is a 49.67% of reference with a coverageData >= 22X + There is a 49.33% of reference with a coverageData >= 23X + There is a 48.33% of reference with a coverageData >= 24X + There is a 48% of reference with a coverageData >= 25X + There is a 45.33% of reference with a coverageData >= 26X + There is a 43% of reference with a coverageData >= 27X + There is a 42% of reference with a coverageData >= 28X + There is a 39.33% of reference with a coverageData >= 29X + There is a 35.67% of reference with a coverageData >= 30X + There is a 32.33% of reference with a coverageData >= 31X + There is a 25.67% of reference with a coverageData >= 32X + There is a 16.67% of reference with a coverageData >= 33X + There is a 13% of reference with a coverageData >= 34X + There is a 11.33% of reference with a coverageData >= 35X + There is a 10% of reference with a coverageData >= 36X + There is a 5.67% of reference with a coverageData >= 37X + There is a 3% of reference with a coverageData >= 38X + There is a 0% of reference with a coverageData >= 39X + There is a 0% of reference with a coverageData >= 40X + There is a 0% of reference with a coverageData >= 41X + There is a 0% of reference with a coverageData >= 42X + There is a 0% of reference with a coverageData >= 43X + There is a 0% of reference with a coverageData >= 44X + There is a 0% of reference with a coverageData >= 45X + There is a 0% of reference with a coverageData >= 46X + There is a 0% of reference with a coverageData >= 47X + There is a 0% of reference with a coverageData >= 48X + There is a 0% of reference with a coverageData >= 49X + There is a 0% of reference with a coverageData >= 50X + There is a 0% of reference with a coverageData >= 51X + + +>>>>>>> Coverage per contig + + test_chromosome 300 6451 21.503333333333334 15.658011438947867 + + |
| b |
| diff -r 000000000000 -r 16beb83e370c test-data/genome_results_outside_features.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_results_outside_features.txt Thu Oct 10 17:40:15 2019 -0400 |
| b |
| @@ -0,0 +1,128 @@ +BamQC report +----------------------------------- + +>>>>>>> Input + + bam file = /tmp/tmprT4oZK/files/6/4/1/dataset_6416c0ca-3ecd-4273-ae01-22f2ac60965d.dat + outfile = results/outside_results.txt + + +>>>>>>> Reference + + number of bases = 650 bp + number of contigs = 1 + + +>>>>>>> Globals + + number of windows = 325 + + number of reads = 100 + number of mapped reads = 100 (100%) + number of secondary alignments = 1 + + number of mapped bases = 6,214 bp + number of sequenced bases = 2,364 bp + number of aligned bases = 0 bp + number of duplicated reads (estimated) = 4 + duplication rate = 14.29% + + +>>>>>>> Globals outside + + regions size = 350 (53.85%) + number of mapped reads = 18 (18%) + + +>>>>>>> Insert size + + mean insert size = 0 + std insert size = 0 + median insert size = 0 + + +>>>>>>> Mapping quality + + mean mapping quality = 255 + + +>>>>>>> ACTG content + + number of A's = 667 bp (28.21%) + number of C's = 645 bp (27.28%) + number of T's = 512 bp (21.66%) + number of G's = 540 bp (22.84%) + number of N's = 0 bp (0%) + + GC percentage = 50.13% + + +>>>>>>> Mismatches and indels + + general error rate = 0.0021 + number of mismatches = 13 + + +>>>>>>> Coverage + + mean coverageData = 17.7543X + std coverageData = 16.4764X + + There is a 10.58% of reference with a coverageData >= 1X + There is a 10.58% of reference with a coverageData >= 2X + There is a 10.58% of reference with a coverageData >= 3X + There is a 10.58% of reference with a coverageData >= 4X + There is a 10.58% of reference with a coverageData >= 5X + There is a 10.58% of reference with a coverageData >= 6X + There is a 10.58% of reference with a coverageData >= 7X + There is a 10.58% of reference with a coverageData >= 8X + There is a 10.58% of reference with a coverageData >= 9X + There is a 10.58% of reference with a coverageData >= 10X + There is a 10.58% of reference with a coverageData >= 11X + There is a 10.58% of reference with a coverageData >= 12X + There is a 10.58% of reference with a coverageData >= 13X + There is a 10.58% of reference with a coverageData >= 14X + There is a 10.58% of reference with a coverageData >= 15X + There is a 10.58% of reference with a coverageData >= 16X + There is a 10.58% of reference with a coverageData >= 17X + There is a 10.58% of reference with a coverageData >= 18X + There is a 10.58% of reference with a coverageData >= 19X + There is a 10.58% of reference with a coverageData >= 20X + There is a 10.58% of reference with a coverageData >= 21X + There is a 10.58% of reference with a coverageData >= 22X + There is a 10.58% of reference with a coverageData >= 23X + There is a 10.58% of reference with a coverageData >= 24X + There is a 10.58% of reference with a coverageData >= 25X + There is a 10.58% of reference with a coverageData >= 26X + There is a 10.58% of reference with a coverageData >= 27X + There is a 10.58% of reference with a coverageData >= 28X + There is a 10.58% of reference with a coverageData >= 29X + There is a 10.58% of reference with a coverageData >= 30X + There is a 10.58% of reference with a coverageData >= 31X + There is a 10.1% of reference with a coverageData >= 32X + There is a 9.62% of reference with a coverageData >= 33X + There is a 9.13% of reference with a coverageData >= 34X + There is a 7.21% of reference with a coverageData >= 35X + There is a 5.29% of reference with a coverageData >= 36X + There is a 3.37% of reference with a coverageData >= 37X + There is a 1.44% of reference with a coverageData >= 38X + There is a 0.96% of reference with a coverageData >= 39X + There is a 0% of reference with a coverageData >= 40X + There is a 0% of reference with a coverageData >= 41X + There is a 0% of reference with a coverageData >= 42X + There is a 0% of reference with a coverageData >= 43X + There is a 0% of reference with a coverageData >= 44X + There is a 0% of reference with a coverageData >= 45X + There is a 0% of reference with a coverageData >= 46X + There is a 0% of reference with a coverageData >= 47X + There is a 0% of reference with a coverageData >= 48X + There is a 0% of reference with a coverageData >= 49X + There is a 0% of reference with a coverageData >= 50X + There is a 0% of reference with a coverageData >= 51X + + +>>>>>>> Coverage per contig + + test_chromosome 4424 6214 1.404611211573237 3.9981701358234454 + + |
| b |
| diff -r 000000000000 -r 16beb83e370c test-data/mapped_reads_clipping_profile.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mapped_reads_clipping_profile.txt Thu Oct 10 17:40:15 2019 -0400 |
| b |
| @@ -0,0 +1,76 @@ +#Read position (bp) Clipping profile +0.0 16.666666666666664 +1.0 5.555555555555555 +2.0 0.0 +3.0 0.0 +4.0 0.0 +5.0 0.0 +6.0 0.0 +7.0 0.0 +8.0 0.0 +9.0 0.0 +10.0 0.0 +11.0 0.0 +12.0 0.0 +13.0 0.0 +14.0 0.0 +15.0 0.0 +16.0 0.0 +17.0 0.0 +18.0 0.0 +19.0 0.0 +20.0 0.0 +21.0 0.0 +22.0 0.0 +23.0 0.0 +24.0 0.0 +25.0 0.0 +26.0 0.0 +27.0 0.0 +28.0 0.0 +29.0 0.0 +30.0 0.0 +31.0 0.0 +32.0 0.0 +33.0 0.0 +34.0 0.0 +35.0 0.0 +36.0 0.0 +37.0 0.0 +38.0 0.0 +39.0 0.0 +40.0 0.0 +41.0 0.0 +42.0 0.0 +43.0 0.0 +44.0 0.0 +45.0 0.0 +46.0 0.0 +47.0 0.0 +48.0 0.0 +49.0 0.0 +50.0 0.0 +51.0 0.0 +52.0 0.0 +53.0 0.0 +54.0 0.0 +55.0 0.0 +56.0 0.0 +57.0 0.0 +58.0 0.0 +59.0 0.0 +60.0 0.0 +61.0 0.0 +62.0 0.0 +63.0 0.0 +64.0 0.0 +65.0 0.0 +66.0 0.0 +67.0 0.0 +68.0 0.0 +69.0 0.0 +70.0 0.0 +71.0 5.555555555555555 +72.0 11.11111111111111 +73.0 16.666666666666664 +74.0 44.44444444444444 |
| b |
| diff -r 000000000000 -r 16beb83e370c test-data/mapped_reads_gc-content_distribution.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mapped_reads_gc-content_distribution.txt Thu Oct 10 17:40:15 2019 -0400 |
| b |
| @@ -0,0 +1,101 @@ +#GC Content (%) Sample HUMAN (hg19) +1.0 0.0 0.0 +2.0 0.0 3.0E-6 +3.0 0.0 3.0E-6 +4.0 0.0 1.0E-5 +5.0 0.0 8.0E-6 +6.0 0.0 1.2000000000000002E-5 +7.0 0.0 6.999999999999999E-6 +8.0 0.0 9.999999999999999E-6 +9.0 0.0 1.6E-5 +10.0 0.0 1.5000000000000002E-5 +11.0 0.0 1.9999999999999998E-5 +12.0 0.0 1.6E-5 +13.0 0.0 1.6E-5 +14.0 0.0 2.4999999999999998E-5 +15.0 0.0 2.2000000000000003E-5 +16.0 0.0 2.6999999999999996E-5 +17.0 0.0 3.3E-5 +18.0 0.0 3.7000000000000005E-5 +19.0 0.0 4.7000000000000004E-5 +20.0 0.0 5.4999999999999995E-5 +21.0 0.0 6.400000000000001E-5 +22.0 0.0 9.3E-5 +23.0 0.0 1.66E-4 +24.0 0.0 3.03E-4 +25.0 0.0 7.059999999999999E-4 +26.0 0.0 0.0016020000000000001 +27.0 0.0 0.0033690000000000005 +28.0 0.0 0.006167999999999999 +29.0 0.0 0.010352 +30.0 0.0 0.015647 +31.0 0.0 0.022148 +32.0 0.0 0.028808 +33.0 0.0 0.035106000000000005 +34.0 0.0 0.041161 +35.0 0.0 0.047408 +36.0 0.0 0.052698999999999996 +37.0 0.0 0.057517000000000006 +38.0 0.0 0.061487999999999994 +39.0 0.0 0.063321 +40.0 0.0 0.060248 +41.0 0.0 0.055508 +42.0 0.0 0.051446000000000006 +43.0 0.0 0.048194 +44.0 0.017857142857142856 0.044423 +45.0 0.0 0.040655000000000004 +46.0 0.03571428571428571 0.03652 +47.0 0.0 0.032315 +48.0 0.017857142857142856 0.028137999999999996 +49.0 0.0 0.02458 +50.0 0.017857142857142856 0.020810000000000002 +51.0 0.0 0.017532 +52.0 0.05357142857142857 0.014506999999999997 +53.0 0.017857142857142856 0.012007 +54.0 0.14285714285714285 0.010018 +55.0 0.08928571428571429 0.008414999999999999 +56.0 0.17857142857142855 0.007258 +57.0 0.03571428571428571 0.006174999999999999 +58.0 0.08928571428571429 0.005363000000000001 +59.0 0.03571428571428571 0.0046159999999999994 +60.0 0.14285714285714285 0.003946 +61.0 0.0 0.0034579999999999993 +62.0 0.03571428571428571 0.002915 +63.0 0.017857142857142856 0.0024610000000000005 +64.0 0.05357142857142857 0.0019950000000000002 +65.0 0.0 0.0016779999999999998 +66.0 0.017857142857142856 0.0013500000000000003 +67.0 0.0 0.001069 +68.0 0.0 8.119999999999999E-4 +69.0 0.0 6.4E-4 +70.0 0.0 5.05E-4 +71.0 0.0 4.0299999999999993E-4 +72.0 0.0 3.2E-4 +73.0 0.0 2.79E-4 +74.0 0.0 2.0700000000000002E-4 +75.0 0.0 2.0099999999999998E-4 +76.0 0.0 1.54E-4 +77.0 0.0 1.12E-4 +78.0 0.0 7.699999999999999E-5 +79.0 0.0 6.3E-5 +80.0 0.0 3.7E-5 +81.0 0.0 2.8000000000000003E-5 +82.0 0.0 1.6E-5 +83.0 0.0 9.0E-6 +84.0 0.0 4.0E-6 +85.0 0.0 0.0 +86.0 0.0 1.0E-6 +87.0 0.0 0.0 +88.0 0.0 0.0 +89.0 0.0 0.0 +90.0 0.0 0.0 +91.0 0.0 0.0 +92.0 0.0 0.0 +93.0 0.0 0.0 +94.0 0.0 0.0 +95.0 0.0 0.0 +96.0 0.0 0.0 +97.0 0.0 0.0 +98.0 0.0 0.0 +99.0 0.0 0.0 +100.0 0.0 0.0 |
| b |
| diff -r 000000000000 -r 16beb83e370c test-data/mapped_reads_nucleotide_content.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mapped_reads_nucleotide_content.txt Thu Oct 10 17:40:15 2019 -0400 |
| b |
| @@ -0,0 +1,76 @@ +# Position (bp) A C G T N +0.0 34.177215189873415 21.518987341772153 26.582278481012654 17.72151898734177 0.0 +1.0 23.456790123456788 33.33333333333333 20.98765432098765 22.22222222222222 0.0 +2.0 25.609756097560975 20.73170731707317 35.36585365853659 18.29268292682927 0.0 +3.0 23.170731707317074 28.04878048780488 28.04878048780488 20.73170731707317 0.0 +4.0 31.70731707317073 26.82926829268293 24.390243902439025 17.073170731707318 0.0 +5.0 25.609756097560975 19.51219512195122 34.146341463414636 20.73170731707317 0.0 +6.0 25.609756097560975 23.170731707317074 34.146341463414636 17.073170731707318 0.0 +7.0 28.04878048780488 21.951219512195124 30.48780487804878 19.51219512195122 0.0 +8.0 23.170731707317074 18.29268292682927 39.02439024390244 19.51219512195122 0.0 +9.0 28.04878048780488 29.268292682926827 24.390243902439025 18.29268292682927 0.0 +10.0 24.390243902439025 23.170731707317074 34.146341463414636 18.29268292682927 0.0 +11.0 19.51219512195122 31.70731707317073 28.04878048780488 20.73170731707317 0.0 +12.0 34.146341463414636 23.170731707317074 28.04878048780488 14.634146341463413 0.0 +13.0 26.82926829268293 18.29268292682927 36.58536585365854 18.29268292682927 0.0 +14.0 24.390243902439025 26.82926829268293 29.268292682926827 19.51219512195122 0.0 +15.0 29.268292682926827 21.951219512195124 28.04878048780488 20.73170731707317 0.0 +16.0 31.70731707317073 25.609756097560975 29.268292682926827 13.414634146341465 0.0 +17.0 15.853658536585366 25.609756097560975 35.36585365853659 23.170731707317074 0.0 +18.0 31.70731707317073 17.073170731707318 31.70731707317073 19.51219512195122 0.0 +19.0 24.390243902439025 29.268292682926827 29.268292682926827 17.073170731707318 0.0 +20.0 21.951219512195124 25.609756097560975 29.268292682926827 23.170731707317074 0.0 +21.0 23.170731707317074 28.04878048780488 36.58536585365854 12.195121951219512 0.0 +22.0 28.04878048780488 30.48780487804878 18.29268292682927 23.170731707317074 0.0 +23.0 23.170731707317074 18.29268292682927 29.268292682926827 29.268292682926827 0.0 +24.0 25.609756097560975 19.51219512195122 35.36585365853659 19.51219512195122 0.0 +25.0 23.170731707317074 26.82926829268293 25.609756097560975 24.390243902439025 0.0 +26.0 21.951219512195124 19.51219512195122 41.46341463414634 17.073170731707318 0.0 +27.0 18.29268292682927 29.268292682926827 35.36585365853659 17.073170731707318 0.0 +28.0 29.268292682926827 30.48780487804878 25.609756097560975 14.634146341463413 0.0 +29.0 17.073170731707318 25.609756097560975 36.58536585365854 20.73170731707317 0.0 +30.0 25.609756097560975 21.951219512195124 32.926829268292686 19.51219512195122 0.0 +31.0 29.268292682926827 23.170731707317074 32.926829268292686 14.634146341463413 0.0 +32.0 29.268292682926827 21.951219512195124 24.390243902439025 24.390243902439025 0.0 +33.0 20.73170731707317 31.70731707317073 26.82926829268293 20.73170731707317 0.0 +34.0 18.29268292682927 20.73170731707317 40.243902439024396 20.73170731707317 0.0 +35.0 37.80487804878049 13.414634146341465 28.04878048780488 20.73170731707317 0.0 +36.0 28.04878048780488 28.04878048780488 28.04878048780488 15.853658536585366 0.0 +37.0 21.951219512195124 20.73170731707317 39.02439024390244 18.29268292682927 0.0 +38.0 34.146341463414636 26.82926829268293 14.634146341463413 24.390243902439025 0.0 +39.0 31.70731707317073 17.073170731707318 26.82926829268293 24.390243902439025 0.0 +40.0 26.82926829268293 24.390243902439025 31.70731707317073 17.073170731707318 0.0 +41.0 30.48780487804878 19.51219512195122 25.609756097560975 24.390243902439025 0.0 +42.0 15.853658536585366 25.609756097560975 34.146341463414636 24.390243902439025 0.0 +43.0 29.268292682926827 24.390243902439025 28.04878048780488 18.29268292682927 0.0 +44.0 26.82926829268293 24.390243902439025 31.70731707317073 17.073170731707318 0.0 +45.0 29.268292682926827 23.170731707317074 29.268292682926827 18.29268292682927 0.0 +46.0 24.390243902439025 23.170731707317074 30.48780487804878 21.951219512195124 0.0 +47.0 25.609756097560975 28.04878048780488 30.48780487804878 15.853658536585366 0.0 +48.0 29.268292682926827 25.609756097560975 29.268292682926827 15.853658536585366 0.0 +49.0 23.170731707317074 23.170731707317074 32.926829268292686 20.73170731707317 0.0 +50.0 24.390243902439025 28.04878048780488 31.70731707317073 15.853658536585366 0.0 +51.0 24.390243902439025 24.390243902439025 31.70731707317073 19.51219512195122 0.0 +52.0 18.29268292682927 26.82926829268293 34.146341463414636 20.73170731707317 0.0 +53.0 26.82926829268293 23.170731707317074 36.58536585365854 13.414634146341465 0.0 +54.0 26.82926829268293 23.170731707317074 31.70731707317073 18.29268292682927 0.0 +55.0 25.609756097560975 26.82926829268293 28.04878048780488 19.51219512195122 0.0 +56.0 10.975609756097562 32.926829268292686 40.243902439024396 15.853658536585366 0.0 +57.0 26.82926829268293 19.51219512195122 29.268292682926827 24.390243902439025 0.0 +58.0 26.82926829268293 30.48780487804878 25.609756097560975 17.073170731707318 0.0 +59.0 21.951219512195124 19.51219512195122 32.926829268292686 25.609756097560975 0.0 +60.0 20.73170731707317 28.04878048780488 32.926829268292686 18.29268292682927 0.0 +61.0 30.48780487804878 19.51219512195122 32.926829268292686 17.073170731707318 0.0 +62.0 24.390243902439025 23.170731707317074 30.48780487804878 21.951219512195124 0.0 +63.0 19.51219512195122 23.170731707317074 29.268292682926827 28.04878048780488 0.0 +64.0 25.609756097560975 31.70731707317073 24.390243902439025 18.29268292682927 0.0 +65.0 18.29268292682927 24.390243902439025 30.48780487804878 26.82926829268293 0.0 +66.0 20.73170731707317 19.51219512195122 36.58536585365854 23.170731707317074 0.0 +67.0 23.170731707317074 31.70731707317073 25.609756097560975 19.51219512195122 0.0 +68.0 15.853658536585366 24.390243902439025 42.68292682926829 17.073170731707318 0.0 +69.0 25.609756097560975 26.82926829268293 29.268292682926827 18.29268292682927 0.0 +70.0 24.390243902439025 34.146341463414636 31.70731707317073 9.75609756097561 0.0 +71.0 19.753086419753085 27.160493827160494 29.629629629629626 23.456790123456788 0.0 +72.0 25.0 37.5 17.5 20.0 0.0 +73.0 24.050632911392405 20.253164556962027 34.177215189873415 21.518987341772153 0.0 +74.0 17.56756756756757 31.08108108108108 28.37837837837838 22.972972972972975 0.0 |
| b |
| diff -r 000000000000 -r 16beb83e370c test-data/mapping_quality_across_reference.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mapping_quality_across_reference.txt Thu Oct 10 17:40:15 2019 -0400 |
| b |
| @@ -0,0 +1,326 @@ +#Position (bp) mapping quality +1.5 0.0 +3.5 0.0 +5.5 0.0 +7.5 0.0 +9.5 0.0 +11.5 0.0 +13.5 0.0 +15.5 0.0 +17.5 0.0 +19.5 0.0 +21.5 0.0 +23.5 0.0 +25.5 0.0 +27.5 0.0 +29.5 0.0 +31.5 0.0 +33.5 0.0 +35.5 0.0 +37.5 0.0 +39.5 0.0 +41.5 0.0 +43.5 0.0 +45.5 0.0 +47.5 0.0 +49.5 0.0 +51.5 0.0 +53.5 255.0 +55.5 255.0 +57.5 255.0 +59.5 255.0 +61.5 255.0 +63.5 255.0 +65.5 255.0 +67.5 255.0 +69.5 255.0 +71.5 255.0 +73.5 255.0 +75.5 255.0 +77.5 255.0 +79.5 255.0 +81.5 255.0 +83.5 255.0 +85.5 255.0 +87.5 255.0 +89.5 255.0 +91.5 236.33333333333334 +93.5 238.2 +95.5 239.72727272727272 +97.5 240.6 +99.5 241.0 +101.5 243.27906976744185 +103.5 244.04347826086956 +105.5 244.27659574468086 +107.5 244.92 +109.5 244.92 +111.5 244.92 +113.5 244.92 +115.5 245.30769230769232 +117.5 245.30769230769232 +119.5 245.30769230769232 +121.5 245.49056603773585 +123.5 246.31034482758622 +125.5 247.125 +127.5 247.36363636363637 +129.5 247.24615384615385 +131.5 247.24615384615385 +133.5 247.125 +135.5 247.47761194029852 +137.5 247.36363636363637 +139.5 247.58823529411765 +141.5 248.0 +143.5 248.28 +145.5 248.3684210526316 +147.5 248.3684210526316 +149.5 248.3684210526316 +151.5 248.3684210526316 +153.5 248.0 +155.5 248.1891891891892 +157.5 248.0958904109589 +159.5 248.0958904109589 +161.5 248.0958904109589 +163.5 247.90140845070422 +165.5 251.54794520547946 +167.5 255.0 +169.5 255.0 +171.5 255.0 +173.5 255.0 +175.5 255.0 +177.5 255.0 +179.5 255.0 +181.5 255.0 +183.5 255.0 +185.5 255.0 +187.5 255.0 +189.5 255.0 +191.5 255.0 +193.5 255.0 +195.5 255.0 +197.5 255.0 +199.5 255.0 +201.5 255.0 +203.5 255.0 +205.5 255.0 +207.5 255.0 +209.5 255.0 +211.5 255.0 +213.5 255.0 +215.5 255.0 +217.5 255.0 +219.5 255.0 +221.5 255.0 +223.5 255.0 +225.5 255.0 +227.5 255.0 +229.5 255.0 +231.5 255.0 +233.5 255.0 +235.5 255.0 +237.5 255.0 +239.5 255.0 +241.5 255.0 +243.5 255.0 +245.5 255.0 +247.5 255.0 +249.5 255.0 +251.5 0.0 +253.5 0.0 +255.5 0.0 +257.5 0.0 +259.5 0.0 +261.5 0.0 +263.5 0.0 +265.5 0.0 +267.5 0.0 +269.5 0.0 +271.5 0.0 +273.5 0.0 +275.5 0.0 +277.5 0.0 +279.5 0.0 +281.5 0.0 +283.5 0.0 +285.5 0.0 +287.5 0.0 +289.5 0.0 +291.5 0.0 +293.5 0.0 +295.5 0.0 +297.5 0.0 +299.5 0.0 +301.5 0.0 +303.5 0.0 +305.5 0.0 +307.5 0.0 +309.5 0.0 +311.5 0.0 +313.5 0.0 +315.5 0.0 +317.5 0.0 +319.5 0.0 +321.5 0.0 +323.5 0.0 +325.5 0.0 +327.5 0.0 +329.5 0.0 +331.5 0.0 +333.5 0.0 +335.5 0.0 +337.5 0.0 +339.5 0.0 +341.5 0.0 +343.5 0.0 +345.5 0.0 +347.5 0.0 +349.5 0.0 +351.5 0.0 +353.5 0.0 +355.5 0.0 +357.5 0.0 +359.5 0.0 +361.5 0.0 +363.5 0.0 +365.5 0.0 +367.5 0.0 +369.5 0.0 +371.5 0.0 +373.5 0.0 +375.5 0.0 +377.5 0.0 +379.5 0.0 +381.5 0.0 +383.5 0.0 +385.5 0.0 +387.5 0.0 +389.5 0.0 +391.5 0.0 +393.5 0.0 +395.5 0.0 +397.5 0.0 +399.5 0.0 +401.5 0.0 +403.5 0.0 +405.5 0.0 +407.5 0.0 +409.5 0.0 +411.5 0.0 +413.5 0.0 +415.5 0.0 +417.5 0.0 +419.5 0.0 +421.5 0.0 +423.5 0.0 +425.5 0.0 +427.5 0.0 +429.5 0.0 +431.5 0.0 +433.5 0.0 +435.5 0.0 +437.5 0.0 +439.5 0.0 +441.5 0.0 +443.5 0.0 +445.5 0.0 +447.5 0.0 +449.5 0.0 +451.5 0.0 +453.5 0.0 +455.5 0.0 +457.5 0.0 +459.5 0.0 +461.5 0.0 +463.5 0.0 +465.5 0.0 +467.5 0.0 +469.5 0.0 +471.5 0.0 +473.5 0.0 +475.5 0.0 +477.5 0.0 +479.5 0.0 +481.5 0.0 +483.5 0.0 +485.5 0.0 +487.5 0.0 +489.5 0.0 +491.5 0.0 +493.5 0.0 +495.5 0.0 +497.5 0.0 +499.5 0.0 +501.5 0.0 +503.5 0.0 +505.5 0.0 +507.5 0.0 +509.5 0.0 +511.5 0.0 +513.5 0.0 +515.5 0.0 +517.5 0.0 +519.5 0.0 +521.5 0.0 +523.5 0.0 +525.5 0.0 +527.5 0.0 +529.5 0.0 +531.5 0.0 +533.5 0.0 +535.5 0.0 +537.5 0.0 +539.5 0.0 +541.5 0.0 +543.5 0.0 +545.5 0.0 +547.5 0.0 +549.5 0.0 +551.5 0.0 +553.5 0.0 +555.5 0.0 +557.5 0.0 +559.5 0.0 +561.5 0.0 +563.5 0.0 +565.5 0.0 +567.5 0.0 +569.5 0.0 +571.5 0.0 +573.5 0.0 +575.5 0.0 +577.5 0.0 +579.5 0.0 +581.5 0.0 +583.5 0.0 +585.5 0.0 +587.5 0.0 +589.5 0.0 +591.5 0.0 +593.5 0.0 +595.5 0.0 +597.5 0.0 +599.5 0.0 +601.5 0.0 +603.5 0.0 +605.5 0.0 +607.5 0.0 +609.5 0.0 +611.5 0.0 +613.5 0.0 +615.5 0.0 +617.5 0.0 +619.5 0.0 +621.5 0.0 +623.5 0.0 +625.5 0.0 +627.5 0.0 +629.5 0.0 +631.5 0.0 +633.5 0.0 +635.5 0.0 +637.5 0.0 +639.5 0.0 +641.5 0.0 +643.5 0.0 +645.5 0.0 +647.5 0.0 +649.5 0.0 |
| b |
| diff -r 000000000000 -r 16beb83e370c test-data/mapping_quality_histogram.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mapping_quality_histogram.txt Thu Oct 10 17:40:15 2019 -0400 |
| b |
| @@ -0,0 +1,13 @@ +#Mapping quality mapping quality +235.0 1.0 +237.0 2.0 +239.0 2.0 +240.0 2.0 +241.0 3.0 +243.0 2.0 +244.0 12.0 +245.0 8.0 +246.0 2.0 +247.0 18.0 +248.0 23.0 +255.0 123.0 |
| b |
| diff -r 000000000000 -r 16beb83e370c test-data/mouse_counts_ensemble_1000_6.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mouse_counts_ensemble_1000_6.tsv Thu Oct 10 17:40:15 2019 -0400 |
| b |
| b'@@ -0,0 +1,1000 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|
| b |
| diff -r 000000000000 -r 16beb83e370c test-data/per_base_coverage_default.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/per_base_coverage_default.txt Thu Oct 10 17:40:15 2019 -0400 |
| b |
| @@ -0,0 +1,299 @@ +#chr pos coverage +test_chromosome 53 1 +test_chromosome 54 1 +test_chromosome 55 2 +test_chromosome 56 3 +test_chromosome 57 3 +test_chromosome 58 4 +test_chromosome 59 4 +test_chromosome 60 4 +test_chromosome 61 5 +test_chromosome 62 5 +test_chromosome 63 5 +test_chromosome 64 5 +test_chromosome 65 5 +test_chromosome 66 5 +test_chromosome 67 5 +test_chromosome 68 5 +test_chromosome 69 5 +test_chromosome 70 5 +test_chromosome 71 5 +test_chromosome 72 6 +test_chromosome 73 6 +test_chromosome 74 6 +test_chromosome 75 6 +test_chromosome 76 6 +test_chromosome 77 6 +test_chromosome 78 8 +test_chromosome 79 8 +test_chromosome 80 8 +test_chromosome 81 8 +test_chromosome 82 8 +test_chromosome 83 9 +test_chromosome 84 9 +test_chromosome 85 9 +test_chromosome 86 10 +test_chromosome 87 10 +test_chromosome 88 11 +test_chromosome 89 12 +test_chromosome 90 12 +test_chromosome 91 13 +test_chromosome 92 14 +test_chromosome 93 14 +test_chromosome 94 16 +test_chromosome 95 16 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33 +test_chromosome 138 33 +test_chromosome 139 34 +test_chromosome 140 34 +test_chromosome 141 35 +test_chromosome 142 37 +test_chromosome 143 37 +test_chromosome 144 38 +test_chromosome 145 38 +test_chromosome 146 38 +test_chromosome 147 38 +test_chromosome 148 38 +test_chromosome 149 38 +test_chromosome 150 38 +test_chromosome 151 38 +test_chromosome 152 38 +test_chromosome 153 36 +test_chromosome 154 36 +test_chromosome 155 37 +test_chromosome 156 37 +test_chromosome 157 37 +test_chromosome 158 36 +test_chromosome 159 36 +test_chromosome 160 37 +test_chromosome 161 36 +test_chromosome 162 37 +test_chromosome 163 36 +test_chromosome 164 35 +test_chromosome 165 37 +test_chromosome 166 36 +test_chromosome 167 36 +test_chromosome 168 36 +test_chromosome 169 34 +test_chromosome 170 36 +test_chromosome 171 36 +test_chromosome 172 36 +test_chromosome 173 35 +test_chromosome 174 35 +test_chromosome 175 36 +test_chromosome 176 33 +test_chromosome 177 32 +test_chromosome 178 32 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503 25 +test_chromosome 504 25 +test_chromosome 505 25 +test_chromosome 506 24 +test_chromosome 507 23 +test_chromosome 508 22 +test_chromosome 509 21 +test_chromosome 510 21 +test_chromosome 511 21 +test_chromosome 512 21 +test_chromosome 513 21 +test_chromosome 514 21 +test_chromosome 515 21 +test_chromosome 516 21 +test_chromosome 517 20 +test_chromosome 518 18 +test_chromosome 519 17 +test_chromosome 520 17 +test_chromosome 521 17 +test_chromosome 522 16 +test_chromosome 523 15 +test_chromosome 524 15 +test_chromosome 525 14 +test_chromosome 526 14 +test_chromosome 527 13 +test_chromosome 528 12 +test_chromosome 529 11 +test_chromosome 530 10 +test_chromosome 531 10 +test_chromosome 532 10 +test_chromosome 533 9 +test_chromosome 534 9 +test_chromosome 535 8 +test_chromosome 536 8 +test_chromosome 537 7 +test_chromosome 538 7 +test_chromosome 539 7 +test_chromosome 540 7 +test_chromosome 541 6 +test_chromosome 542 6 +test_chromosome 543 6 +test_chromosome 544 5 +test_chromosome 545 5 +test_chromosome 546 4 +test_chromosome 547 4 +test_chromosome 548 2 +test_chromosome 549 2 +test_chromosome 550 1 |
| b |
| diff -r 000000000000 -r 16beb83e370c test-data/per_base_coverage_inside_features.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/per_base_coverage_inside_features.txt Thu Oct 10 17:40:15 2019 -0400 |
| b |
| @@ -0,0 +1,199 @@ +#chr pos coverage +test_chromosome 53 1 +test_chromosome 54 1 +test_chromosome 55 2 +test_chromosome 56 3 +test_chromosome 57 3 +test_chromosome 58 4 +test_chromosome 59 4 +test_chromosome 60 4 +test_chromosome 61 5 +test_chromosome 62 5 +test_chromosome 63 5 +test_chromosome 64 5 +test_chromosome 65 5 +test_chromosome 66 5 +test_chromosome 67 5 +test_chromosome 68 5 +test_chromosome 69 5 +test_chromosome 70 5 +test_chromosome 71 5 +test_chromosome 72 6 +test_chromosome 73 6 +test_chromosome 74 6 +test_chromosome 75 6 +test_chromosome 76 6 +test_chromosome 77 6 +test_chromosome 78 8 +test_chromosome 79 8 +test_chromosome 80 8 +test_chromosome 81 8 +test_chromosome 82 8 +test_chromosome 83 9 +test_chromosome 84 9 +test_chromosome 85 9 +test_chromosome 86 10 +test_chromosome 87 10 +test_chromosome 88 11 +test_chromosome 89 12 +test_chromosome 90 12 +test_chromosome 91 13 +test_chromosome 92 14 +test_chromosome 93 14 +test_chromosome 94 16 +test_chromosome 95 16 +test_chromosome 96 17 +test_chromosome 97 17 +test_chromosome 98 18 +test_chromosome 99 18 +test_chromosome 100 18 +test_chromosome 101 21 +test_chromosome 102 22 +test_chromosome 103 23 +test_chromosome 104 23 +test_chromosome 105 23 +test_chromosome 106 24 +test_chromosome 107 25 +test_chromosome 108 25 +test_chromosome 109 25 +test_chromosome 110 25 +test_chromosome 111 25 +test_chromosome 112 25 +test_chromosome 113 25 +test_chromosome 114 25 +test_chromosome 115 26 +test_chromosome 116 26 +test_chromosome 117 26 +test_chromosome 118 26 +test_chromosome 119 26 +test_chromosome 120 26 +test_chromosome 121 26 +test_chromosome 122 27 +test_chromosome 123 29 +test_chromosome 124 29 +test_chromosome 125 32 +test_chromosome 126 32 +test_chromosome 127 33 +test_chromosome 128 33 +test_chromosome 129 33 +test_chromosome 130 32 +test_chromosome 131 32 +test_chromosome 132 33 +test_chromosome 133 32 +test_chromosome 134 32 +test_chromosome 135 34 +test_chromosome 136 33 +test_chromosome 137 33 +test_chromosome 138 33 +test_chromosome 139 34 +test_chromosome 140 34 +test_chromosome 141 35 +test_chromosome 142 37 +test_chromosome 143 37 +test_chromosome 144 38 +test_chromosome 145 38 +test_chromosome 146 38 +test_chromosome 147 38 +test_chromosome 148 38 +test_chromosome 149 38 +test_chromosome 150 38 +test_chromosome 151 38 +test_chromosome 152 38 +test_chromosome 153 36 +test_chromosome 154 36 +test_chromosome 155 37 +test_chromosome 156 37 +test_chromosome 157 37 +test_chromosome 158 36 +test_chromosome 159 36 +test_chromosome 160 37 +test_chromosome 161 36 +test_chromosome 162 37 +test_chromosome 163 36 +test_chromosome 164 35 +test_chromosome 165 37 +test_chromosome 166 36 +test_chromosome 167 36 +test_chromosome 168 36 +test_chromosome 169 34 +test_chromosome 170 36 +test_chromosome 171 36 +test_chromosome 172 36 +test_chromosome 173 35 +test_chromosome 174 35 +test_chromosome 175 36 +test_chromosome 176 33 +test_chromosome 177 32 +test_chromosome 178 32 +test_chromosome 179 32 +test_chromosome 180 32 +test_chromosome 181 32 +test_chromosome 182 31 +test_chromosome 183 31 +test_chromosome 184 32 +test_chromosome 185 32 +test_chromosome 186 32 +test_chromosome 187 32 +test_chromosome 188 32 +test_chromosome 189 32 +test_chromosome 190 31 +test_chromosome 191 31 +test_chromosome 192 31 +test_chromosome 193 31 +test_chromosome 194 32 +test_chromosome 195 32 +test_chromosome 196 32 +test_chromosome 197 32 +test_chromosome 198 30 +test_chromosome 199 29 +test_chromosome 200 28 +test_chromosome 201 31 +test_chromosome 202 30 +test_chromosome 203 29 +test_chromosome 204 30 +test_chromosome 205 31 +test_chromosome 206 31 +test_chromosome 207 31 +test_chromosome 208 32 +test_chromosome 209 31 +test_chromosome 210 31 +test_chromosome 211 31 +test_chromosome 212 31 +test_chromosome 213 31 +test_chromosome 214 31 +test_chromosome 215 31 +test_chromosome 216 30 +test_chromosome 217 28 +test_chromosome 218 28 +test_chromosome 219 27 +test_chromosome 220 27 +test_chromosome 221 28 +test_chromosome 222 28 +test_chromosome 223 28 +test_chromosome 224 28 +test_chromosome 225 29 +test_chromosome 226 29 +test_chromosome 227 30 +test_chromosome 228 30 +test_chromosome 229 31 +test_chromosome 230 30 +test_chromosome 231 31 +test_chromosome 232 32 +test_chromosome 233 33 +test_chromosome 234 34 +test_chromosome 235 33 +test_chromosome 236 33 +test_chromosome 237 32 +test_chromosome 238 32 +test_chromosome 239 32 +test_chromosome 240 30 +test_chromosome 241 30 +test_chromosome 242 29 +test_chromosome 243 31 +test_chromosome 244 32 +test_chromosome 245 30 +test_chromosome 246 29 +test_chromosome 247 29 +test_chromosome 248 29 +test_chromosome 249 29 +test_chromosome 250 28 |
| b |
| diff -r 000000000000 -r 16beb83e370c test-data/per_base_coverage_outside_features.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/per_base_coverage_outside_features.txt Thu Oct 10 17:40:15 2019 -0400 |
| b |
| @@ -0,0 +1,101 @@ +#chr pos coverage +test_chromosome 351 31 +test_chromosome 352 32 +test_chromosome 353 33 +test_chromosome 354 34 +test_chromosome 355 35 +test_chromosome 356 34 +test_chromosome 357 34 +test_chromosome 358 35 +test_chromosome 359 34 +test_chromosome 360 35 +test_chromosome 361 35 +test_chromosome 362 36 +test_chromosome 363 36 +test_chromosome 364 36 +test_chromosome 365 36 +test_chromosome 366 37 +test_chromosome 367 37 +test_chromosome 368 37 +test_chromosome 369 37 +test_chromosome 370 36 +test_chromosome 371 37 +test_chromosome 372 37 +test_chromosome 373 39 +test_chromosome 374 39 +test_chromosome 375 38 +test_chromosome 376 36 +test_chromosome 377 36 +test_chromosome 378 36 +test_chromosome 379 36 +test_chromosome 380 34 +test_chromosome 381 33 +test_chromosome 382 32 +test_chromosome 383 32 +test_chromosome 384 31 +test_chromosome 385 31 +test_chromosome 386 31 +test_chromosome 387 31 +test_chromosome 388 31 +test_chromosome 389 30 +test_chromosome 390 30 +test_chromosome 391 30 +test_chromosome 392 30 +test_chromosome 393 30 +test_chromosome 394 30 +test_chromosome 395 30 +test_chromosome 396 29 +test_chromosome 397 28 +test_chromosome 398 28 +test_chromosome 399 28 +test_chromosome 400 27 +test_chromosome 501 25 +test_chromosome 502 25 +test_chromosome 503 25 +test_chromosome 504 25 +test_chromosome 505 25 +test_chromosome 506 24 +test_chromosome 507 23 +test_chromosome 508 22 +test_chromosome 509 21 +test_chromosome 510 21 +test_chromosome 511 21 +test_chromosome 512 21 +test_chromosome 513 21 +test_chromosome 514 21 +test_chromosome 515 21 +test_chromosome 516 21 +test_chromosome 517 20 +test_chromosome 518 18 +test_chromosome 519 17 +test_chromosome 520 17 +test_chromosome 521 17 +test_chromosome 522 16 +test_chromosome 523 15 +test_chromosome 524 15 +test_chromosome 525 14 +test_chromosome 526 14 +test_chromosome 527 13 +test_chromosome 528 12 +test_chromosome 529 11 +test_chromosome 530 10 +test_chromosome 531 10 +test_chromosome 532 10 +test_chromosome 533 9 +test_chromosome 534 9 +test_chromosome 535 8 +test_chromosome 536 8 +test_chromosome 537 7 +test_chromosome 538 7 +test_chromosome 539 7 +test_chromosome 540 7 +test_chromosome 541 6 +test_chromosome 542 6 +test_chromosome 543 6 +test_chromosome 544 5 +test_chromosome 545 5 +test_chromosome 546 4 +test_chromosome 547 4 +test_chromosome 548 2 +test_chromosome 549 2 +test_chromosome 550 1 |
| b |
| diff -r 000000000000 -r 16beb83e370c test-data/rnaseq_qc_counts_custom.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnaseq_qc_counts_custom.txt Thu Oct 10 17:40:15 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +#GeneID try_this +GENE1 45 |
| b |
| diff -r 000000000000 -r 16beb83e370c test-data/rnaseq_qc_results_custom.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnaseq_qc_results_custom.txt Thu Oct 10 17:40:15 2019 -0400 |
| b |
| @@ -0,0 +1,48 @@ +RNA-Seq QC report +----------------------------------- + +>>>>>>> Input + + bam file = /tmp/tmp_CFvEQ/files/000/dataset_49.dat + gff file = /tmp/tmp_CFvEQ/files/000/dataset_2.dat + counting algorithm = proportional + protocol = strand-specific-forward + + +>>>>>>> Reads alignment + + reads aligned (left/right) = 0 / 0 + read pairs aligned = 0 + total alignments = 101 + secondary alignments = 1 + non-unique alignments = 0 + aligned to genes = 46 + ambiguous alignments = 0 + no feature assigned = 55 + not aligned = 0 + + +>>>>>>> Reads genomic origin + + exonic = 46 (45.54%) + intronic = 0 (0%) + intergenic = 55 (54.46%) + overlapping exon = 0 (0%) + + +>>>>>>> Transcript coverage profile + + 5' bias = NaN + 3' bias = NaN + 5'-3' bias = NaN + + +>>>>>>> Junction analysis + + reads at junctions = 53 + + CTTT : 47.17% + CCAC : 47.17% + GCAC : 1.89% + CTAC : 1.89% + GAAT : 1.89% |
| b |
| diff -r 000000000000 -r 16beb83e370c test-data/rnaseq_qc_results_default.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnaseq_qc_results_default.txt Thu Oct 10 17:40:15 2019 -0400 |
| b |
| @@ -0,0 +1,47 @@ +RNA-Seq QC report +----------------------------------- + +>>>>>>> Input + + bam file = /tmp/tmp_CFvEQ/files/000/dataset_1.dat + gff file = /tmp/tmp_CFvEQ/files/000/dataset_2.dat + counting algorithm = uniquely-mapped-reads + protocol = non-strand-specific + + +>>>>>>> Reads alignment + + reads aligned = 100 + total alignments = 101 + secondary alignments = 1 + non-unique alignments = 2 + aligned to genes = 54 + ambiguous alignments = 0 + no feature assigned = 45 + not aligned = 0 + SSP estimation (fwd/rev) = 0.59 / 0.41 + + +>>>>>>> Reads genomic origin + + exonic = 54 (54.55%) + intronic = 0 (0%) + intergenic = 45 (45.45%) + overlapping exon = 0 (0%) + + +>>>>>>> Transcript coverage profile + + 5' bias = NaN + 3' bias = NaN + 5'-3' bias = NaN + + +>>>>>>> Junction analysis + + reads at junctions = 52 + + CTTT : 48.08% + CCAC : 48.08% + GCAC : 1.92% + CTAC : 1.92% |
| b |
| diff -r 000000000000 -r 16beb83e370c test-data/test_mapped_reads.bam |
| b |
| Binary file test-data/test_mapped_reads.bam has changed |