# HG changeset patch # User iuc # Date 1570743646 14400 # Node ID e020be4f281b9bdd3935ce68fa90439ed258b6ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2" diff -r 000000000000 -r e020be4f281b qualimap_counts.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qualimap_counts.xml Thu Oct 10 17:40:46 2019 -0400 @@ -0,0 +1,442 @@ + + + qualimap_macros.xml + + + + + + + + + + + + + + + + + + + + + + + > data_spec.txt && + #end for + + ln -s '$input' counts_data && + + qualimap counts + --data data_spec.txt + #if str($analysis.mode) == 'comparison': + --compare + #end if + #if str($analysis.mode) != 'multi_sample': + #if str($analysis.gene_info.source) == 'builtin': + --species ${analysis.gene_info.species} + #elif str($analysis.gene_info.source) == 'custom': + --info ${analysis.info} + #end if + #end if + --threshold $threshold + -outdir results -outformat html && + + #if str($analysis.mode) == 'comparison': + #set $report_name = 'ComparisonReport' + #elif str($analysis.mode) == 'multi_sample': + #set $report_name = 'GlobalReport' + #else: + #set $sample = $sample_names[int($analysis.sample_number) - 1] + ## Qualimap replaces '-' in sample names with '_' for + ## determining file names + #set $report_name = str($sample).replace('-', '_') + 'Report' + #end if + #set $summary_report = None + @MASSAGE_OUTPUT@ + ]]> + + + + + + + + + + + + + + + + + + + + all(v.strip() for v in value.split(',')) + len(set(v.strip() for v in value.split(','))) == 2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + `__). + + **Make sure to use the same feature IDs in the annotation and in the counts dataset!** + + To generate a Qualimap-compatible info file based on an arbitrary GTF annotation and a genome FASTA file, the developers of Qualimap offer a `Python script for the command line `__. + +*Counts threshold* + +In order to remove the influence of spurious reads, a feature is considered as +detected if its corresponding number of counts is greater than this threshold. + +By default, the threshold value is set to 5 counts, meaning that features having +less than 5 counts will not be taken into account. + + +Output +====== + +Many of the plots that this tool can produce are created using the NOISeq package. The `NOISeq vignette `__ contains a lot of useful information about the plots and how to interpret them. Here we provide a short explanation: + + +Plots of overview stats for all samples +--------------------------------------- + +*Counts Density* + +This plot shows density of counts computed from the histogram of log-transformed counts. In order to avoid infinite values in case of zero counts the transformation `log2(expr + 0.5)` is applied, where `expr` is the number of read counts for a given feature. Only log-transformed counts having value greater than 1 are plotted. + +*Scatterplot Matrix* + +The panel shows a scatterplot along with smoothed line (lower panel) and Pearson correlation coefficients (upper panel) for each pair of samples. Plots are generated using log-transformed counts. + +*Saturation* + +This plot provides information about the level of saturation in the samples, so it helps the user to decide if more sequencing is needed and more features could be detected when increasing the number of reads. + +Sequencing depth of each sample (on the x-axis) is plotted against the number of detected features (on the y-axis). Here, “detected features” refers to features with more than k counts, where k is the *Counts threshold* selected by the user. + +The highlighted value is the real sequencing depth of the sample(s). The +expected results at other sequencing depths are simulated based on random +sampling of the original data. + +*Counts Distribution* + +This box plot shows the overall counts distribution of each sample. + +*Features With Low Counts* + +This plot shows the proportion of features with low counts in each sample. Such features are usually less reliable and could be filtered out. In this plot, the bars show the percentage of features within each sample having more than 0 counts per million (CPM), or more than 1, 2, 5 and 10 CPM. + + +Plots of single-sample count statistics +--------------------------------------- + +.. class:: infomark + + Note that most single-sample plots require built-in or custom *additional + information about genes* to be generated. The *Saturation* plot is the only + exception. + +*Saturation* + +Similar to the same plot in the overview of all samples. +The single-sample plot, however, has an additional y-axis (on the right) +showing the number of features expected to be newly detected when increasing +the sequencing depth by one million reads from each indicated sequencing depth +value. + +*Bio Detection* + +This barplot allows the user to know which **kind** of features are being +detected in the chosen sample. The x-axis shows all feature categories listed +in the annotations file. The gray bars are the percentage of features of each group within the reference genome (or transcriptome, etc.). The striped color bars are the percentages of features of each group detected in the sample with regard to the genome. The solid color bars are the percentages that each group represents in the total detected features in the sample. + +*Counts Per Biotype* + +This boxplot shows the distribution of counts of features from each detected +feature clas. + +*Length Bias* + +The plot describes the relationship between the length of the features and +their expression values. + +Feature lengths are divided into bins, and mean expression of features falling into a particular length interval is computed and plotted. A cubic spline regression model is fitted to explain the relation between length and expression. Coefficient of determination (`R^2`) and p-value are shown together with the regression curve. + +*GC Bias* + +The plot describes the relantionship between the GC-content of the features and the expression values. The data for the plot is generated similar to the +*Length Bias* plot. The GC content is divided into bins and the mean expression +of features falling into any given GC interval is computed. The relation between GC-content and expression is investigated using a cubic spline regression model. + + +Plots for comparing two groups of samples +----------------------------------------- + +This mode can generate side-by-side plots of + +- *Counts Distribution*, +- *Features With Low Counts* +- *Bio Detection*, +- *Length Bias* and +- *GC Bias* + +for two groups of samples. + +.. class:: infomark + + Note that the *Bio Detection*, *Length Bias* and *GC Bias* plots can only be + generated when built-in or custom *additional information about genes* is + available. + + ]]> + + diff -r 000000000000 -r e020be4f281b qualimap_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qualimap_macros.xml Thu Oct 10 17:40:46 2019 -0400 @@ -0,0 +1,40 @@ + + 2.2.2c + + + + qualimap + + + + + + qualimap --help | grep 'QualiMap v.' | cut -d '.' -f 2- + + + + + 10.1093/bioinformatics/btv566 + 10.1093/bioinformatics/bts503 + + + + + + export JAVA_OPTS="-Djava.awt.headless=true -Xmx\${GALAXY_MEMORY_MB:-1024}m" + + + '$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 + ]]> + diff -r 000000000000 -r e020be4f281b 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 17:40:46 2019 -0400 @@ -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 diff -r 000000000000 -r e020be4f281b test-data/coverage_histogram.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coverage_histogram.txt Thu Oct 10 17:40:46 2019 -0400 @@ -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 diff -r 000000000000 -r e020be4f281b 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 17:40:46 2019 -0400 @@ -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 diff -r 000000000000 -r e020be4f281b test-data/features.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/features.gtf Thu Oct 10 17:40:46 2019 -0400 @@ -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"; diff -r 000000000000 -r e020be4f281b 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 17:40:46 2019 -0400 @@ -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 diff -r 000000000000 -r e020be4f281b 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 17:40:46 2019 -0400 @@ -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 + + diff -r 000000000000 -r e020be4f281b 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 17:40:46 2019 -0400 @@ -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 + + diff -r 000000000000 -r e020be4f281b 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 17:40:46 2019 -0400 @@ -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 + + diff -r 000000000000 -r e020be4f281b 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 17:40:46 2019 -0400 @@ -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 diff -r 000000000000 -r e020be4f281b 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 17:40:46 2019 -0400 @@ -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 diff -r 000000000000 -r e020be4f281b 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 17:40:46 2019 -0400 @@ -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 diff -r 000000000000 -r e020be4f281b 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 17:40:46 2019 -0400 @@ -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 diff -r 000000000000 -r e020be4f281b 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 17:40:46 2019 -0400 @@ -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 diff -r 000000000000 -r e020be4f281b 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 17:40:46 2019 -0400 @@ -0,0 +1,1000 @@ +#gene -GlcN01 -GlcN02 -GlcN03 +GlcN01 +GlcN02 +GlcN03 +ENSMUSG00000085214 641 542 776 491 791 368 +ENSMUSG00000096956 73 17 47 32 29 63 +ENSMUSG00000021252 2359 1563 2497 2126 2149 1296 +ENSMUSG00000046840 39 165 124 83 144 31 +ENSMUSG00000044062 1 0 3 6 1 0 +ENSMUSG00000007777 292 184 220 228 237 270 +ENSMUSG00000037361 421 300 380 316 393 310 +ENSMUSG00000043644 16 5 7 6 6 8 +ENSMUSG00000024442 812 566 727 569 784 692 +ENSMUSG00000042208 445 273 375 305 410 399 +ENSMUSG00000020831 5 4 5 6 6 3 +ENSMUSG00000025731 1259 942 1113 888 1585 1076 +ENSMUSG00000096232 394 309 396 261 417 306 +ENSMUSG00000055312 53 53 59 43 63 35 +ENSMUSG00000058706 948 581 835 716 927 622 +ENSMUSG00000001418 1440 813 1052 1092 1044 1168 +ENSMUSG00000028608 305 208 262 229 273 225 +ENSMUSG00000089900 3 3 2 7 4 5 +ENSMUSG00000058812 51 30 45 41 32 35 +ENSMUSG00000089889 15 5 21 12 22 9 +ENSMUSG00000087341 82 84 69 145 96 93 +ENSMUSG00000060512 621 495 565 399 691 591 +ENSMUSG00000087361 26 13 20 18 26 10 +ENSMUSG00000051748 5290 4503 5667 8817 5797 1277 +ENSMUSG00000062691 135 92 121 113 141 105 +ENSMUSG00000019689 341 270 361 194 400 200 +ENSMUSG00000071456 38 19 25 22 29 43 +ENSMUSG00000022972 221 148 167 172 215 203 +ENSMUSG00000030663 1070 597 798 671 862 776 +ENSMUSG00000037960 194 88 114 106 114 119 +ENSMUSG00000027637 779 632 672 570 820 868 +ENSMUSG00000029600 6 3 1 6 1 5 +ENSMUSG00000021023 249 234 221 184 237 194 +ENSMUSG00000039195 163 90 166 216 145 199 +ENSMUSG00000045237 267 222 288 198 217 183 +ENSMUSG00000028441 0 0 0 0 0 0 +ENSMUSG00000097616 41 27 32 33 33 48 +ENSMUSG00000097047 12 15 23 9 12 13 +ENSMUSG00000085972 24 7 25 19 25 104 +ENSMUSG00000037971 480 419 491 343 577 361 +ENSMUSG00000046999 0 0 1 1 0 0 +ENSMUSG00000044991 176 58 126 103 123 256 +ENSMUSG00000086191 5 3 4 2 6 2 +ENSMUSG00000097036 0 0 0 0 0 0 +ENSMUSG00000040720 807 491 596 568 621 542 +ENSMUSG00000092203 75 46 59 28 40 65 +ENSMUSG00000063236 196 91 125 110 129 127 +ENSMUSG00000085457 10 5 8 9 4 4 +ENSMUSG00000040591 52 34 59 39 39 24 +ENSMUSG00000097867 125 152 200 139 205 82 +ENSMUSG00000037669 63 43 39 35 45 45 +ENSMUSG00000026154 298 233 285 231 296 211 +ENSMUSG00000035171 488 227 316 257 378 300 +ENSMUSG00000032551 328 126 195 153 278 192 +ENSMUSG00000037086 0 0 0 0 0 1 +ENSMUSG00000078570 129 50 72 44 86 109 +ENSMUSG00000045414 1179 854 813 640 1108 894 +ENSMUSG00000096537 0 0 0 0 0 0 +ENSMUSG00000043687 72 59 69 42 80 64 +ENSMUSG00000063320 47 29 43 25 43 29 +ENSMUSG00000020783 491 222 312 300 407 381 +ENSMUSG00000097290 253 122 210 126 150 160 +ENSMUSG00000028327 2650 1496 2279 2932 2340 1618 +ENSMUSG00000087382 433 112 307 114 140 121 +ENSMUSG00000033688 11175 8162 11448 9133 11522 6616 +ENSMUSG00000087264 1 0 0 0 0 0 +ENSMUSG00000068099 0 0 0 0 0 0 +ENSMUSG00000087651 1 1 0 0 0 0 +ENSMUSG00000072694 58 13 20 26 15 17 +ENSMUSG00000051319 186 177 170 164 149 229 +ENSMUSG00000074578 356 143 234 122 179 142 +ENSMUSG00000097247 0 0 0 0 0 0 +ENSMUSG00000094732 0 2 1 0 2 0 +ENSMUSG00000026051 1 0 0 1 1 1 +ENSMUSG00000087211 0 0 0 0 0 0 +ENSMUSG00000087579 62 81 134 28 343 91 +ENSMUSG00000086899 1 0 0 0 0 0 +ENSMUSG00000024118 1225 363 383 459 2160 664 +ENSMUSG00000035595 61 46 59 59 54 39 +ENSMUSG00000050088 51 20 29 24 37 42 +ENSMUSG00000054676 321 178 294 187 249 260 +ENSMUSG00000094690 0 0 0 0 0 0 +ENSMUSG00000035491 0 1 1 0 0 0 +ENSMUSG00000029813 0 0 0 0 0 0 +ENSMUSG00000025500 54 15 39 44 28 36 +ENSMUSG00000097048 22 17 11 12 23 23 +ENSMUSG00000085114 0 0 0 0 0 0 +ENSMUSG00000032068 95 33 60 58 83 32 +ENSMUSG00000046242 1 0 1 1 1 0 +ENSMUSG00000057818 0 0 1 0 1 1 +ENSMUSG00000029182 0 0 0 0 0 0 +ENSMUSG00000047150 71 57 82 58 79 34 +ENSMUSG00000095384 0 0 0 0 0 0 +ENSMUSG00000085984 1 0 0 0 0 0 +ENSMUSG00000044744 1 1 1 1 1 4 +ENSMUSG00000095040 1 0 0 0 0 0 +ENSMUSG00000056508 2 0 1 1 2 0 +ENSMUSG00000075511 369 208 462 271 474 273 +ENSMUSG00000021534 2 0 1 0 1 0 +ENSMUSG00000044320 2 0 0 0 1 0 +ENSMUSG00000018543 0 0 0 0 0 1 +ENSMUSG00000085944 8 3 5 2 2 2 +ENSMUSG00000030030 19 21 24 19 30 10 +ENSMUSG00000038523 14 1 1 1 2 9 +ENSMUSG00000086327 30 17 16 15 12 20 +ENSMUSG00000085831 0 0 0 0 0 0 +ENSMUSG00000087621 0 0 0 0 0 0 +ENSMUSG00000039174 0 0 0 0 0 0 +ENSMUSG00000028294 0 0 0 0 0 0 +ENSMUSG00000085389 0 0 0 0 0 0 +ENSMUSG00000027973 0 0 0 0 0 0 +ENSMUSG00000010841 0 0 0 0 0 0 +ENSMUSG00000031620 0 0 0 0 0 0 +ENSMUSG00000057816 0 1 0 1 0 0 +ENSMUSG00000086330 15 7 7 11 9 4 +ENSMUSG00000030858 0 0 0 0 0 0 +ENSMUSG00000026831 1 0 0 1 0 6 +ENSMUSG00000097318 20 12 21 23 19 24 +ENSMUSG00000089730 1 0 0 1 2 1 +ENSMUSG00000020270 0 0 0 0 0 0 +ENSMUSG00000056018 0 0 0 0 0 0 +ENSMUSG00000058252 2 0 0 0 1 1 +ENSMUSG00000008028 0 0 2 1 0 1 +ENSMUSG00000069118 0 0 0 0 0 0 +ENSMUSG00000096573 4 0 0 0 1 1 +ENSMUSG00000028287 0 0 0 0 0 0 +ENSMUSG00000026649 36 31 30 35 25 28 +ENSMUSG00000057047 0 0 0 0 0 0 +ENSMUSG00000071721 0 0 0 0 0 0 +ENSMUSG00000023873 14 3 6 10 8 3 +ENSMUSG00000092599 0 0 0 0 0 0 +ENSMUSG00000063971 1 0 0 0 0 0 +ENSMUSG00000036557 0 0 0 0 0 0 +ENSMUSG00000021850 40 10 11 12 27 12 +ENSMUSG00000058925 2 0 0 0 0 0 +ENSMUSG00000063714 44 23 38 22 36 14 +ENSMUSG00000031682 0 0 3 1 0 0 +ENSMUSG00000079476 0 0 0 0 0 0 +ENSMUSG00000029766 0 0 0 0 0 0 +ENSMUSG00000020617 0 0 0 0 0 0 +ENSMUSG00000031927 0 0 0 0 0 0 +ENSMUSG00000079179 204 146 187 126 179 122 +ENSMUSG00000096571 0 0 0 0 0 0 +ENSMUSG00000028589 0 0 0 0 0 0 +ENSMUSG00000079346 0 0 0 0 0 0 +ENSMUSG00000027886 0 0 1 0 0 0 +ENSMUSG00000085260 0 0 2 1 0 0 +ENSMUSG00000041399 0 0 0 0 0 0 +ENSMUSG00000054727 0 0 0 0 0 0 +ENSMUSG00000042800 4 2 2 1 1 0 +ENSMUSG00000079666 0 0 0 0 0 0 +ENSMUSG00000094445 0 0 0 0 0 0 +ENSMUSG00000015962 1 0 0 0 0 1 +ENSMUSG00000031509 0 0 0 0 1 1 +ENSMUSG00000029320 0 0 0 0 0 0 +ENSMUSG00000053783 0 0 0 0 1 1 +ENSMUSG00000032300 349 112 164 162 195 312 +ENSMUSG00000024729 0 0 0 0 0 0 +ENSMUSG00000037884 0 0 0 0 0 0 +ENSMUSG00000086348 0 0 0 0 0 0 +ENSMUSG00000056912 0 0 0 0 0 0 +ENSMUSG00000038408 0 0 0 0 0 0 +ENSMUSG00000033993 0 0 0 0 0 0 +ENSMUSG00000031809 0 0 0 0 0 0 +ENSMUSG00000037910 0 0 0 0 0 0 +ENSMUSG00000058935 0 0 0 0 0 0 +ENSMUSG00000029620 0 0 0 0 0 0 +ENSMUSG00000060715 0 0 0 0 2 0 +ENSMUSG00000040340 0 1 0 0 2 0 +ENSMUSG00000085757 0 0 0 0 0 0 +ENSMUSG00000043629 2 0 2 0 0 1 +ENSMUSG00000086202 0 0 0 0 0 0 +ENSMUSG00000068299 128 87 144 82 113 100 +ENSMUSG00000085416 0 0 0 0 0 0 +ENSMUSG00000038987 9 3 4 6 1 4 +ENSMUSG00000059695 0 0 0 0 0 0 +ENSMUSG00000026931 0 0 0 0 0 0 +ENSMUSG00000036574 0 0 0 0 0 0 +ENSMUSG00000027409 0 0 0 0 0 0 +ENSMUSG00000085438 59 35 30 32 50 51 +ENSMUSG00000035085 2 0 1 4 2 4 +ENSMUSG00000050844 0 1 1 1 0 0 +ENSMUSG00000059690 0 0 0 0 0 0 +ENSMUSG00000019797 298 227 276 202 324 239 +ENSMUSG00000027518 0 0 0 0 0 0 +ENSMUSG00000035629 5 2 5 3 5 4 +ENSMUSG00000087343 0 0 0 0 0 0 +ENSMUSG00000038165 0 0 0 0 0 0 +ENSMUSG00000028451 0 0 0 0 0 0 +ENSMUSG00000057072 1 0 1 1 4 0 +ENSMUSG00000087393 0 0 0 0 0 0 +ENSMUSG00000029248 0 0 0 0 0 0 +ENSMUSG00000020940 0 0 0 0 0 0 +ENSMUSG00000045709 0 0 0 0 0 0 +ENSMUSG00000072473 0 0 0 0 0 0 +ENSMUSG00000086186 0 0 0 0 0 0 +ENSMUSG00000045022 0 0 1 0 0 0 +ENSMUSG00000078612 413 62 147 176 130 239 +ENSMUSG00000078935 0 0 0 0 0 0 +ENSMUSG00000024728 0 0 0 0 0 0 +ENSMUSG00000032666 184 94 118 121 123 81 +ENSMUSG00000011154 0 0 0 0 0 0 +ENSMUSG00000086379 0 0 0 0 0 0 +ENSMUSG00000026809 7 1 3 3 0 1 +ENSMUSG00000097321 20 12 24 11 16 45 +ENSMUSG00000056821 1 1 0 0 0 1 +ENSMUSG00000038782 2 1 4 4 2 3 +ENSMUSG00000089798 9 4 8 1 5 3 +ENSMUSG00000033053 0 0 0 0 0 0 +ENSMUSG00000086823 0 0 0 0 0 0 +ENSMUSG00000052075 0 0 0 0 0 0 +ENSMUSG00000031452 0 0 1 0 0 0 +ENSMUSG00000044916 1 1 2 2 6 3 +ENSMUSG00000071103 34 22 30 16 34 29 +ENSMUSG00000086788 0 0 0 0 0 0 +ENSMUSG00000098144 1 0 0 0 0 0 +ENSMUSG00000061633 0 0 0 0 0 0 +ENSMUSG00000085333 0 0 0 1 0 0 +ENSMUSG00000091071 43 15 26 9 19 33 +ENSMUSG00000031847 9 4 5 2 9 5 +ENSMUSG00000052794 97 59 63 62 76 83 +ENSMUSG00000097424 0 0 0 0 0 0 +ENSMUSG00000092239 0 0 0 0 0 0 +ENSMUSG00000032894 0 0 0 0 0 0 +ENSMUSG00000024532 0 0 0 0 0 0 +ENSMUSG00000097962 0 0 0 0 0 0 +ENSMUSG00000055833 8 7 14 9 7 11 +ENSMUSG00000074619 1 0 1 0 0 0 +ENSMUSG00000040163 0 0 0 0 0 0 +ENSMUSG00000029867 0 0 0 0 0 0 +ENSMUSG00000097893 26 18 13 19 23 22 +ENSMUSG00000005983 16 5 14 11 9 11 +ENSMUSG00000027327 123 86 100 81 110 118 +ENSMUSG00000070568 2 0 0 0 0 0 +ENSMUSG00000092369 0 0 0 0 0 0 +ENSMUSG00000019945 71 67 80 43 84 29 +ENSMUSG00000086999 0 0 0 0 0 0 +ENSMUSG00000057402 0 0 0 0 0 0 +ENSMUSG00000078593 0 0 0 0 0 0 +ENSMUSG00000087044 0 0 0 0 0 0 +ENSMUSG00000086391 2 0 0 0 0 0 +ENSMUSG00000078492 8 3 3 3 7 1 +ENSMUSG00000085561 0 0 0 0 0 0 +ENSMUSG00000094103 0 0 0 0 0 0 +ENSMUSG00000043773 17 20 20 12 30 11 +ENSMUSG00000085077 0 0 0 0 0 1 +ENSMUSG00000070709 84 45 76 64 60 46 +ENSMUSG00000043859 0 0 0 0 0 0 +ENSMUSG00000086951 3 0 0 4 0 0 +ENSMUSG00000061759 293 185 174 245 326 310 +ENSMUSG00000085889 4 0 0 0 0 1 +ENSMUSG00000040456 1 1 0 1 0 0 +ENSMUSG00000093616 0 0 0 0 0 0 +ENSMUSG00000037263 11 58 149 123 3 3 +ENSMUSG00000044854 19 8 13 14 7 7 +ENSMUSG00000074139 0 0 0 0 0 0 +ENSMUSG00000084757 0 0 0 0 0 0 +ENSMUSG00000020164 0 0 1 0 0 0 +ENSMUSG00000086887 0 0 0 2 0 0 +ENSMUSG00000078957 0 0 1 0 0 0 +ENSMUSG00000085580 0 0 0 0 0 0 +ENSMUSG00000024209 4 2 0 1 0 1 +ENSMUSG00000028009 3 13 5 4 9 5 +ENSMUSG00000096655 2 0 2 1 2 1 +ENSMUSG00000032900 0 0 0 0 0 0 +ENSMUSG00000073598 5 0 0 4 0 1 +ENSMUSG00000036162 51 23 28 28 22 20 +ENSMUSG00000038323 442 255 299 303 514 403 +ENSMUSG00000085800 0 0 0 0 0 0 +ENSMUSG00000046408 4 6 1 4 6 4 +ENSMUSG00000021545 0 0 0 0 1 0 +ENSMUSG00000042184 0 0 0 0 0 0 +ENSMUSG00000080980 0 0 0 0 0 0 +ENSMUSG00000090307 25 8 17 20 7 7 +ENSMUSG00000087204 0 0 0 0 0 0 +ENSMUSG00000029883 0 0 0 0 0 0 +ENSMUSG00000032566 0 0 0 0 0 0 +ENSMUSG00000084859 0 0 0 0 0 0 +ENSMUSG00000031118 0 0 0 0 0 0 +ENSMUSG00000085265 0 0 0 0 0 0 +ENSMUSG00000070532 9 0 2 0 3 8 +ENSMUSG00000052222 5 1 5 1 2 3 +ENSMUSG00000058101 0 0 0 0 0 0 +ENSMUSG00000087104 0 0 0 0 0 0 +ENSMUSG00000071265 0 0 0 0 0 0 +ENSMUSG00000097080 31 22 26 14 18 12 +ENSMUSG00000033029 45 29 34 23 46 41 +ENSMUSG00000086128 2 1 0 0 4 1 +ENSMUSG00000086781 0 0 0 0 0 0 +ENSMUSG00000092499 11 15 10 4 18 5 +ENSMUSG00000084811 0 0 0 0 0 0 +ENSMUSG00000078600 0 0 0 0 0 0 +ENSMUSG00000090840 0 1 0 1 1 0 +ENSMUSG00000020286 0 0 0 0 0 0 +ENSMUSG00000078667 97 61 73 57 80 70 +ENSMUSG00000086046 0 0 0 0 0 0 +ENSMUSG00000098230 0 0 0 0 0 0 +ENSMUSG00000074346 0 0 0 0 0 0 +ENSMUSG00000079502 4 2 8 5 3 2 +ENSMUSG00000097675 18 19 26 10 24 19 +ENSMUSG00000032611 2 5 0 0 14 8 +ENSMUSG00000074343 0 0 0 0 0 0 +ENSMUSG00000034031 0 0 0 0 0 0 +ENSMUSG00000052371 0 0 0 0 0 0 +ENSMUSG00000085044 0 0 0 0 0 0 +ENSMUSG00000008307 19 5 11 8 8 12 +ENSMUSG00000079407 0 0 0 0 0 0 +ENSMUSG00000087047 4 1 1 4 2 1 +ENSMUSG00000042888 0 0 0 0 0 0 +ENSMUSG00000063458 43 22 35 49 15 61 +ENSMUSG00000096935 93 62 95 66 96 89 +ENSMUSG00000047129 1 0 1 0 1 0 +ENSMUSG00000086333 0 0 0 0 0 0 +ENSMUSG00000092066 0 0 0 0 0 0 +ENSMUSG00000094928 0 0 0 0 0 0 +ENSMUSG00000024786 1 0 1 1 0 1 +ENSMUSG00000029526 0 0 0 0 0 0 +ENSMUSG00000072878 0 0 0 1 0 0 +ENSMUSG00000085614 7 1 0 1 2 0 +ENSMUSG00000086080 0 0 0 0 0 0 +ENSMUSG00000040822 438 271 352 333 370 310 +ENSMUSG00000085263 0 0 0 0 0 0 +ENSMUSG00000097584 0 0 0 0 0 0 +ENSMUSG00000085197 1 0 0 0 0 0 +ENSMUSG00000018479 0 1 0 0 0 0 +ENSMUSG00000031998 2 0 2 0 0 0 +ENSMUSG00000021977 0 0 0 0 0 0 +ENSMUSG00000086550 0 0 0 0 0 0 +ENSMUSG00000071653 271 169 239 209 201 215 +ENSMUSG00000094808 0 0 0 0 0 0 +ENSMUSG00000078607 114 38 110 62 83 37 +ENSMUSG00000041707 109 23 40 56 25 27 +ENSMUSG00000056313 655 508 337 514 846 280 +ENSMUSG00000022507 827 430 671 669 618 973 +ENSMUSG00000097412 46 35 50 31 52 37 +ENSMUSG00000086390 46 34 40 48 30 20 +ENSMUSG00000037600 3 1 0 1 1 1 +ENSMUSG00000089997 2 1 1 0 2 1 +ENSMUSG00000087331 28 18 24 23 32 9 +ENSMUSG00000078784 425 242 310 287 371 370 +ENSMUSG00000044145 13 5 6 6 14 6 +ENSMUSG00000048429 873 650 688 675 927 832 +ENSMUSG00000044148 369 143 245 176 196 215 +ENSMUSG00000020812 34 16 15 13 20 15 +ENSMUSG00000013974 17 4 12 22 1 4 +ENSMUSG00000097101 143 98 147 103 89 121 +ENSMUSG00000086818 6 0 2 1 3 1 +ENSMUSG00000054091 431 230 301 261 267 319 +ENSMUSG00000062760 6 3 4 25 8 0 +ENSMUSG00000020284 176 72 143 104 114 107 +ENSMUSG00000078572 193 156 225 177 193 152 +ENSMUSG00000036027 52 81 157 68 118 6 +ENSMUSG00000035372 1324 371 687 303 750 758 +ENSMUSG00000073155 357 389 396 267 438 536 +ENSMUSG00000027713 24 8 14 10 12 13 +ENSMUSG00000084925 9 2 6 4 6 5 +ENSMUSG00000090925 505 48 197 144 177 155 +ENSMUSG00000013653 0 0 0 0 0 0 +ENSMUSG00000039339 4 3 0 1 3 4 +ENSMUSG00000085042 16 14 6 7 12 7 +ENSMUSG00000067297 9 1 4 3 2 3 +ENSMUSG00000042041 517 118 212 369 153 971 +ENSMUSG00000028407 79 88 100 71 116 57 +ENSMUSG00000095620 0 0 1 0 1 1 +ENSMUSG00000062376 249 147 199 225 221 206 +ENSMUSG00000042233 19 14 27 10 17 12 +ENSMUSG00000091575 25 10 14 3 4 12 +ENSMUSG00000025528 0 0 0 0 0 0 +ENSMUSG00000021290 1313 863 1206 805 1319 945 +ENSMUSG00000029847 6 0 0 0 0 0 +ENSMUSG00000020083 47 20 53 42 27 54 +ENSMUSG00000029384 1 2 2 1 2 2 +ENSMUSG00000063522 11 2 6 8 7 1 +ENSMUSG00000021458 211 118 147 166 197 228 +ENSMUSG00000063018 2 1 2 0 1 3 +ENSMUSG00000026090 17 6 8 4 4 0 +ENSMUSG00000074829 18 16 12 12 11 7 +ENSMUSG00000030587 249 59 120 215 192 344 +ENSMUSG00000013083 0 0 0 0 3 1 +ENSMUSG00000029882 0 0 0 0 0 0 +ENSMUSG00000086316 98 24 49 37 27 50 +ENSMUSG00000083844 153 128 140 93 121 129 +ENSMUSG00000021550 638 374 512 454 536 459 +ENSMUSG00000029559 277 160 229 180 211 194 +ENSMUSG00000035401 315 176 204 178 273 197 +ENSMUSG00000092570 0 0 0 0 0 0 +ENSMUSG00000078439 39 13 31 22 22 48 +ENSMUSG00000078546 48 22 31 32 31 18 +ENSMUSG00000037145 5 0 1 0 2 1 +ENSMUSG00000087380 13 11 12 13 10 19 +ENSMUSG00000071252 58 12 24 32 43 33 +ENSMUSG00000081766 0 0 0 0 0 0 +ENSMUSG00000085394 1 0 0 1 0 0 +ENSMUSG00000086494 24 22 17 32 35 29 +ENSMUSG00000085347 1 1 0 1 0 0 +ENSMUSG00000039269 0 0 0 0 0 0 +ENSMUSG00000078257 0 0 0 0 0 0 +ENSMUSG00000075605 0 0 0 0 0 0 +ENSMUSG00000032403 121 77 121 73 119 101 +ENSMUSG00000097354 59 35 53 46 98 31 +ENSMUSG00000053353 1 2 2 1 5 4 +ENSMUSG00000036731 0 0 0 0 0 0 +ENSMUSG00000028396 0 0 0 0 0 0 +ENSMUSG00000025384 212 110 181 126 133 144 +ENSMUSG00000087254 10 7 13 4 7 1 +ENSMUSG00000046748 0 0 3 0 4 0 +ENSMUSG00000034159 0 0 0 0 0 1 +ENSMUSG00000009210 0 0 1 0 0 2 +ENSMUSG00000079283 57 29 42 27 29 48 +ENSMUSG00000097162 7 7 21 7 13 11 +ENSMUSG00000020133 331 177 299 229 298 275 +ENSMUSG00000033967 23 30 71 52 28 34 +ENSMUSG00000097729 192 66 148 83 91 82 +ENSMUSG00000019933 0 0 0 1 0 0 +ENSMUSG00000049643 51 22 30 24 36 38 +ENSMUSG00000031983 419 258 311 283 440 383 +ENSMUSG00000032062 320 181 253 203 211 244 +ENSMUSG00000020441 210 113 126 122 101 126 +ENSMUSG00000068078 0 0 0 0 0 0 +ENSMUSG00000026319 4 6 8 4 12 2 +ENSMUSG00000041203 650 340 447 440 471 418 +ENSMUSG00000062619 527 328 535 349 564 343 +ENSMUSG00000078486 13 5 9 4 5 3 +ENSMUSG00000090356 0 1 1 4 0 1 +ENSMUSG00000034157 18 33 18 27 45 37 +ENSMUSG00000002345 226 165 194 188 189 168 +ENSMUSG00000045176 204 90 148 201 122 165 +ENSMUSG00000085779 0 0 0 0 0 0 +ENSMUSG00000090314 0 0 0 0 0 0 +ENSMUSG00000015519 0 0 0 0 0 0 +ENSMUSG00000040177 67 36 62 47 47 84 +ENSMUSG00000048830 0 0 0 0 0 0 +ENSMUSG00000050705 424 281 369 228 439 355 +ENSMUSG00000050704 0 0 0 0 0 0 +ENSMUSG00000087410 0 0 0 0 0 0 +ENSMUSG00000020747 1002 828 978 786 914 651 +ENSMUSG00000097102 1 1 5 0 1 0 +ENSMUSG00000045331 0 0 0 0 0 0 +ENSMUSG00000045411 323 147 229 155 216 188 +ENSMUSG00000085860 0 0 0 0 0 0 +ENSMUSG00000036873 78 49 77 80 86 93 +ENSMUSG00000085338 2 0 0 0 0 0 +ENSMUSG00000087590 44 37 52 23 42 20 +ENSMUSG00000071398 0 0 1 0 0 0 +ENSMUSG00000086841 372 154 269 136 161 167 +ENSMUSG00000090470 0 0 0 0 0 0 +ENSMUSG00000049760 1227 796 1071 873 1185 1141 +ENSMUSG00000046791 119 90 89 118 121 96 +ENSMUSG00000038311 0 1 0 2 1 4 +ENSMUSG00000073164 5 2 1 3 7 3 +ENSMUSG00000034173 68 18 76 20 61 33 +ENSMUSG00000086745 0 1 0 1 0 0 +ENSMUSG00000038065 41 18 14 13 21 25 +ENSMUSG00000074269 41 21 7 6 10 23 +ENSMUSG00000097398 0 0 0 0 0 0 +ENSMUSG00000039801 357 113 165 138 231 242 +ENSMUSG00000085824 0 1 3 0 1 0 +ENSMUSG00000051297 0 0 0 1 0 0 +ENSMUSG00000024726 467 277 328 275 401 294 +ENSMUSG00000032840 224 199 197 179 221 195 +ENSMUSG00000086219 28 12 22 17 14 13 +ENSMUSG00000064308 1 0 0 0 0 0 +ENSMUSG00000074832 0 0 0 0 0 0 +ENSMUSG00000073236 32 23 40 36 34 43 +ENSMUSG00000071632 345 190 266 177 480 328 +ENSMUSG00000086438 0 0 0 0 0 0 +ENSMUSG00000036955 340 249 322 253 365 325 +ENSMUSG00000043391 351 183 272 339 185 212 +ENSMUSG00000044496 717 410 523 491 610 485 +ENSMUSG00000068011 468 273 341 465 278 496 +ENSMUSG00000052419 459 227 320 286 313 322 +ENSMUSG00000073684 50 17 42 33 30 24 +ENSMUSG00000031242 617 339 398 370 465 405 +ENSMUSG00000071793 454 265 377 174 375 268 +ENSMUSG00000060301 285 193 270 172 220 161 +ENSMUSG00000022701 160 81 121 87 114 103 +ENSMUSG00000060424 0 0 0 0 0 0 +ENSMUSG00000031112 42 11 14 15 9 13 +ENSMUSG00000093565 19 13 19 17 18 13 +ENSMUSG00000097537 10 1 0 2 2 3 +ENSMUSG00000030924 36 18 14 14 32 13 +ENSMUSG00000085562 1 0 0 0 0 1 +ENSMUSG00000009114 2 0 3 3 0 0 +ENSMUSG00000039043 248 142 181 161 174 186 +ENSMUSG00000024227 0 0 1 0 0 0 +ENSMUSG00000087259 28 5 22 12 12 7 +ENSMUSG00000085555 0 0 0 0 0 0 +ENSMUSG00000097536 1 0 4 1 0 0 +ENSMUSG00000074415 27 7 15 12 15 23 +ENSMUSG00000079671 34 7 14 8 7 15 +ENSMUSG00000054514 4 2 8 3 6 2 +ENSMUSG00000085236 0 1 0 0 0 0 +ENSMUSG00000059482 123 59 77 92 128 65 +ENSMUSG00000066000 62 2 5 0 80 49 +ENSMUSG00000085936 2 0 1 0 1 4 +ENSMUSG00000097040 0 0 0 0 0 2 +ENSMUSG00000049916 3 0 3 4 0 0 +ENSMUSG00000010277 4799 3039 3572 3011 4929 3796 +ENSMUSG00000085882 531 358 503 423 505 366 +ENSMUSG00000092486 33 5 11 11 4 10 +ENSMUSG00000096001 0 0 2 0 1 1 +ENSMUSG00000028536 153 85 155 98 152 71 +ENSMUSG00000038005 217 93 109 108 155 117 +ENSMUSG00000097180 0 0 0 0 2 0 +ENSMUSG00000041789 2 2 1 2 0 1 +ENSMUSG00000097787 23 18 22 10 23 16 +ENSMUSG00000034601 7 1 8 6 3 4 +ENSMUSG00000039990 593 425 498 419 663 447 +ENSMUSG00000021807 1589 887 1142 1047 1420 1258 +ENSMUSG00000024273 123 70 103 90 133 102 +ENSMUSG00000086224 3 3 2 4 0 1 +ENSMUSG00000085763 0 0 0 0 0 0 +ENSMUSG00000053080 128 94 106 79 110 80 +ENSMUSG00000085696 0 0 0 0 0 0 +ENSMUSG00000072704 1763 1391 1589 1094 1824 1464 +ENSMUSG00000076437 17 5 8 13 12 19 +ENSMUSG00000062198 8 6 9 2 4 6 +ENSMUSG00000098090 32 6 4 4 4 13 +ENSMUSG00000087497 45 26 43 31 42 28 +ENSMUSG00000045464 41 16 31 30 36 36 +ENSMUSG00000031984 530 349 435 440 461 402 +ENSMUSG00000047635 139 83 137 112 155 91 +ENSMUSG00000030378 330 202 179 37 995 169 +ENSMUSG00000086859 132 66 84 52 88 69 +ENSMUSG00000097929 0 0 0 0 1 0 +ENSMUSG00000020491 81 56 51 61 61 56 +ENSMUSG00000049881 136 90 62 89 109 102 +ENSMUSG00000096995 8 3 3 4 3 1 +ENSMUSG00000037735 3 0 2 2 1 1 +ENSMUSG00000092574 51 24 29 28 28 36 +ENSMUSG00000090386 8 10 8 7 10 10 +ENSMUSG00000028060 1119 640 780 555 986 960 +ENSMUSG00000086629 10 6 21 13 15 6 +ENSMUSG00000018570 3 3 4 3 2 0 +ENSMUSG00000087213 45 3 6 7 19 27 +ENSMUSG00000039725 110 75 57 84 73 82 +ENSMUSG00000075389 24 32 45 28 34 39 +ENSMUSG00000040204 79 2 22 60 8 33 +ENSMUSG00000058833 426 300 392 280 375 344 +ENSMUSG00000097709 0 0 0 0 0 0 +ENSMUSG00000086283 0 0 0 0 0 1 +ENSMUSG00000087060 3 0 1 5 0 1 +ENSMUSG00000090260 1 1 1 3 1 1 +ENSMUSG00000026227 8 7 8 7 12 11 +ENSMUSG00000091475 10 1 2 0 4 0 +ENSMUSG00000084966 0 0 0 0 0 0 +ENSMUSG00000032712 1019 516 523 383 717 716 +ENSMUSG00000055188 2 1 4 0 0 2 +ENSMUSG00000043833 100 35 101 46 50 46 +ENSMUSG00000087271 7 12 21 13 10 6 +ENSMUSG00000044117 4 3 7 4 15 8 +ENSMUSG00000051339 2367 1258 2398 2502 1759 1790 +ENSMUSG00000054418 2 0 0 2 0 0 +ENSMUSG00000071860 0 0 0 0 0 0 +ENSMUSG00000087403 3 2 3 3 1 2 +ENSMUSG00000073596 0 1 0 0 0 1 +ENSMUSG00000097277 44 16 23 18 28 23 +ENSMUSG00000087038 0 0 0 0 0 0 +ENSMUSG00000030385 0 0 0 0 0 0 +ENSMUSG00000086284 0 0 0 0 0 0 +ENSMUSG00000067833 3770 2005 2385 1886 2500 2574 +ENSMUSG00000070282 16 5 15 8 8 7 +ENSMUSG00000084885 0 1 1 0 0 0 +ENSMUSG00000020381 91 35 64 76 89 77 +ENSMUSG00000086254 0 0 0 0 0 0 +ENSMUSG00000079737 46 36 38 22 44 53 +ENSMUSG00000024410 449 323 399 278 476 448 +ENSMUSG00000079450 10 8 8 4 6 6 +ENSMUSG00000026388 6 3 7 8 4 2 +ENSMUSG00000050604 5 2 1 1 1 4 +ENSMUSG00000094958 27 28 37 21 40 30 +ENSMUSG00000067879 7 2 6 12 4 34 +ENSMUSG00000089922 0 0 0 0 0 0 +ENSMUSG00000025102 216 117 162 125 155 169 +ENSMUSG00000028300 410 129 189 180 247 307 +ENSMUSG00000097503 40 33 47 78 34 32 +ENSMUSG00000090061 9 2 11 3 5 5 +ENSMUSG00000035868 120 153 138 156 144 194 +ENSMUSG00000085622 39 30 32 28 38 35 +ENSMUSG00000037818 290 233 328 160 405 235 +ENSMUSG00000046806 42 11 17 16 21 29 +ENSMUSG00000074635 13 4 8 11 12 3 +ENSMUSG00000026258 0 1 0 0 0 0 +ENSMUSG00000053553 188 25 67 72 115 49 +ENSMUSG00000086815 0 0 0 0 0 0 +ENSMUSG00000085582 0 0 0 0 0 0 +ENSMUSG00000063364 5 4 2 4 4 4 +ENSMUSG00000096965 2 0 0 0 0 0 +ENSMUSG00000071540 0 0 4 1 0 1 +ENSMUSG00000036242 7 0 1 5 5 1 +ENSMUSG00000089759 1 0 3 0 0 0 +ENSMUSG00000031125 0 0 2 0 1 0 +ENSMUSG00000033111 15 19 21 20 22 13 +ENSMUSG00000071181 10 6 10 3 9 3 +ENSMUSG00000031179 0 0 0 0 0 0 +ENSMUSG00000038917 4 4 2 4 2 2 +ENSMUSG00000064202 14 23 12 11 26 10 +ENSMUSG00000048106 318 172 243 183 278 190 +ENSMUSG00000074024 6 5 7 2 3 4 +ENSMUSG00000097184 23 4 17 10 6 13 +ENSMUSG00000020101 10 7 4 7 3 6 +ENSMUSG00000030641 70 8 12 17 13 42 +ENSMUSG00000048699 0 0 0 0 0 0 +ENSMUSG00000053714 17 12 35 10 18 11 +ENSMUSG00000085421 2 0 1 0 0 3 +ENSMUSG00000097350 26 10 18 23 15 15 +ENSMUSG00000097236 70 30 83 23 62 32 +ENSMUSG00000024481 2 0 0 0 0 0 +ENSMUSG00000097697 0 0 0 1 1 0 +ENSMUSG00000086015 8 10 12 10 8 4 +ENSMUSG00000085287 64 36 55 36 41 34 +ENSMUSG00000062822 48 16 29 22 30 32 +ENSMUSG00000074782 59 34 69 28 49 47 +ENSMUSG00000075217 0 0 0 0 0 0 +ENSMUSG00000033342 18 6 15 16 29 7 +ENSMUSG00000092171 2 2 0 3 3 2 +ENSMUSG00000032057 0 0 0 0 0 0 +ENSMUSG00000097074 0 0 0 0 0 0 +ENSMUSG00000025871 54 39 41 31 61 47 +ENSMUSG00000023350 0 0 0 0 0 0 +ENSMUSG00000026734 0 0 0 0 0 0 +ENSMUSG00000027196 11 4 5 3 12 10 +ENSMUSG00000029828 6 4 8 3 4 5 +ENSMUSG00000084980 42 17 31 33 34 27 +ENSMUSG00000027345 0 0 0 0 0 0 +ENSMUSG00000061525 0 0 0 0 0 0 +ENSMUSG00000049815 0 0 0 0 0 0 +ENSMUSG00000040514 0 0 0 0 0 0 +ENSMUSG00000094577 0 0 0 0 0 0 +ENSMUSG00000044544 2 1 0 0 0 0 +ENSMUSG00000098150 1 1 0 0 0 0 +ENSMUSG00000049902 0 0 0 0 0 0 +ENSMUSG00000036934 19 17 15 22 25 32 +ENSMUSG00000039540 0 0 0 0 0 0 +ENSMUSG00000089707 2 0 1 2 1 0 +ENSMUSG00000026940 4 1 4 1 2 3 +ENSMUSG00000086657 19 7 17 11 7 10 +ENSMUSG00000034689 0 0 0 0 0 0 +ENSMUSG00000085704 38 15 28 20 31 20 +ENSMUSG00000020434 1 0 0 0 0 0 +ENSMUSG00000028520 0 0 0 0 0 0 +ENSMUSG00000056919 157 52 60 70 67 110 +ENSMUSG00000042943 0 0 0 0 0 0 +ENSMUSG00000047720 0 0 1 0 0 0 +ENSMUSG00000043429 0 0 0 0 0 0 +ENSMUSG00000085528 0 0 0 0 0 0 +ENSMUSG00000087460 4 0 0 0 0 0 +ENSMUSG00000079421 0 0 0 0 0 0 +ENSMUSG00000027309 820 447 503 459 555 1103 +ENSMUSG00000020332 0 0 1 0 0 0 +ENSMUSG00000087354 14 4 1 4 12 6 +ENSMUSG00000020234 70 29 31 47 38 43 +ENSMUSG00000086638 4 1 5 5 4 6 +ENSMUSG00000085940 0 0 0 0 0 0 +ENSMUSG00000087338 124 90 124 100 87 66 +ENSMUSG00000086923 0 0 0 0 0 0 +ENSMUSG00000075524 0 0 0 0 0 0 +ENSMUSG00000086221 0 0 0 0 0 0 +ENSMUSG00000085558 95 58 81 66 98 46 +ENSMUSG00000025783 0 0 0 0 0 0 +ENSMUSG00000020191 2 0 2 0 0 1 +ENSMUSG00000035387 0 0 0 0 0 0 +ENSMUSG00000022993 0 0 0 1 1 1 +ENSMUSG00000071818 0 0 1 3 1 0 +ENSMUSG00000087625 0 0 0 0 0 0 +ENSMUSG00000051278 100 14 19 16 13 35 +ENSMUSG00000086066 0 0 0 0 0 0 +ENSMUSG00000026736 2 1 0 2 1 3 +ENSMUSG00000037466 53 1 6 21 5 25 +ENSMUSG00000073085 0 0 0 0 0 0 +ENSMUSG00000049507 4 2 3 4 1 2 +ENSMUSG00000086918 7 0 1 1 5 5 +ENSMUSG00000027157 0 0 0 0 0 0 +ENSMUSG00000068046 0 0 0 0 0 0 +ENSMUSG00000046567 77 70 92 78 85 81 +ENSMUSG00000075042 6 4 2 2 3 2 +ENSMUSG00000002240 0 0 0 0 0 0 +ENSMUSG00000008129 0 0 0 0 0 0 +ENSMUSG00000074248 0 0 1 0 0 0 +ENSMUSG00000091692 0 0 0 0 0 0 +ENSMUSG00000042360 4 2 5 1 3 0 +ENSMUSG00000022798 0 0 0 0 0 0 +ENSMUSG00000093472 0 0 0 0 0 0 +ENSMUSG00000085405 0 0 0 0 0 0 +ENSMUSG00000044081 11 8 9 9 10 3 +ENSMUSG00000087609 0 0 0 0 0 0 +ENSMUSG00000087223 3 4 4 4 4 5 +ENSMUSG00000086969 0 0 0 2 0 1 +ENSMUSG00000069712 0 0 1 0 0 0 +ENSMUSG00000097172 0 0 0 0 0 0 +ENSMUSG00000067795 0 0 0 0 0 0 +ENSMUSG00000022288 0 0 0 0 0 0 +ENSMUSG00000021098 0 0 0 0 0 0 +ENSMUSG00000089879 0 0 0 0 0 0 +ENSMUSG00000082843 0 0 0 0 0 0 +ENSMUSG00000022116 0 0 0 0 0 0 +ENSMUSG00000079093 0 0 0 0 0 0 +ENSMUSG00000022759 0 0 0 0 0 0 +ENSMUSG00000045989 0 0 0 0 0 0 +ENSMUSG00000021747 5 1 1 0 2 10 +ENSMUSG00000087358 0 0 0 0 0 0 +ENSMUSG00000059920 412 223 259 311 346 333 +ENSMUSG00000097898 0 0 0 0 0 0 +ENSMUSG00000097553 0 0 0 0 0 0 +ENSMUSG00000080907 48 36 45 20 41 79 +ENSMUSG00000078618 0 0 0 0 0 0 +ENSMUSG00000097651 0 0 0 0 0 1 +ENSMUSG00000087459 0 0 0 0 0 0 +ENSMUSG00000056682 0 0 0 0 0 0 +ENSMUSG00000085641 0 0 0 0 0 0 +ENSMUSG00000097516 0 0 0 0 0 0 +ENSMUSG00000096265 1 0 0 0 1 1 +ENSMUSG00000097370 0 0 0 0 0 0 +ENSMUSG00000079525 0 0 0 0 0 0 +ENSMUSG00000049160 0 0 0 0 0 0 +ENSMUSG00000043583 0 0 0 0 0 0 +ENSMUSG00000091686 0 0 0 0 1 0 +ENSMUSG00000086529 394 342 413 392 410 242 +ENSMUSG00000097693 0 0 0 0 0 0 +ENSMUSG00000060029 3 2 1 0 1 1 +ENSMUSG00000096405 0 0 0 0 0 0 +ENSMUSG00000085238 0 0 1 0 0 2 +ENSMUSG00000035651 0 0 0 0 0 0 +ENSMUSG00000086332 42 25 28 45 56 23 +ENSMUSG00000090160 0 0 0 0 0 0 +ENSMUSG00000086938 39 26 38 32 46 27 +ENSMUSG00000047938 0 0 3 0 0 0 +ENSMUSG00000086241 199 88 193 237 111 135 +ENSMUSG00000085435 0 0 0 0 0 0 +ENSMUSG00000089914 4 1 0 3 0 1 +ENSMUSG00000050345 29 9 7 4 6 6 +ENSMUSG00000092578 0 0 0 0 0 0 +ENSMUSG00000086454 0 0 0 0 0 0 +ENSMUSG00000086799 2 0 0 1 2 0 +ENSMUSG00000055555 41 0 0 0 0 1 +ENSMUSG00000090202 0 0 0 0 0 0 +ENSMUSG00000072595 0 0 0 0 0 0 +ENSMUSG00000082612 0 0 0 0 0 0 +ENSMUSG00000044906 171 60 63 70 82 83 +ENSMUSG00000052642 0 0 0 0 0 0 +ENSMUSG00000040919 0 0 0 0 0 0 +ENSMUSG00000093551 0 0 0 0 0 0 +ENSMUSG00000041362 173 53 87 108 82 91 +ENSMUSG00000097129 7 4 8 5 10 5 +ENSMUSG00000096986 3 2 5 3 4 1 +ENSMUSG00000087137 0 0 0 0 0 0 +ENSMUSG00000097841 0 0 0 0 0 0 +ENSMUSG00000086607 0 0 0 0 0 0 +ENSMUSG00000014529 0 0 0 0 0 0 +ENSMUSG00000020992 22 6 10 5 11 15 +ENSMUSG00000074136 13 4 9 9 8 10 +ENSMUSG00000031270 3 3 2 3 4 4 +ENSMUSG00000087045 0 0 0 0 0 0 +ENSMUSG00000092183 4 2 3 2 2 3 +ENSMUSG00000085157 0 0 0 0 1 0 +ENSMUSG00000085496 1 0 0 0 0 0 +ENSMUSG00000086263 0 0 0 0 0 0 +ENSMUSG00000090126 10 2 4 4 6 2 +ENSMUSG00000031325 0 0 0 0 0 0 +ENSMUSG00000029564 3 2 6 1 3 1 +ENSMUSG00000074039 0 0 1 0 0 1 +ENSMUSG00000060491 0 0 0 0 0 0 +ENSMUSG00000086947 0 0 0 0 0 0 +ENSMUSG00000050883 303 224 348 108 233 138 +ENSMUSG00000020299 0 0 0 1 0 0 +ENSMUSG00000039545 10 1 5 3 3 0 +ENSMUSG00000059663 0 0 0 0 0 0 +ENSMUSG00000097276 8 7 7 3 8 6 +ENSMUSG00000068173 0 0 0 0 0 0 +ENSMUSG00000045794 0 0 0 0 0 1 +ENSMUSG00000097091 3 0 2 0 4 8 +ENSMUSG00000097502 3 2 2 1 1 5 +ENSMUSG00000087309 0 0 0 0 0 0 +ENSMUSG00000086377 0 4 5 0 0 0 +ENSMUSG00000093528 0 0 0 0 0 0 +ENSMUSG00000037143 0 0 0 0 0 0 +ENSMUSG00000084798 0 0 3 1 0 1 +ENSMUSG00000028642 7 3 6 0 6 0 +ENSMUSG00000048905 10 3 10 8 4 11 +ENSMUSG00000097032 15 4 11 5 6 9 +ENSMUSG00000086569 0 0 0 0 0 0 +ENSMUSG00000087279 0 0 0 0 2 0 +ENSMUSG00000036463 0 0 0 0 0 0 +ENSMUSG00000051758 0 0 0 0 0 0 +ENSMUSG00000085247 0 0 0 0 0 0 +ENSMUSG00000024546 0 0 0 0 0 0 +ENSMUSG00000028314 2 1 0 0 0 0 +ENSMUSG00000086687 0 0 0 0 0 0 +ENSMUSG00000051198 0 0 0 0 0 0 +ENSMUSG00000029138 1 0 0 0 0 0 +ENSMUSG00000086257 0 0 0 0 0 0 +ENSMUSG00000036921 0 0 0 0 0 0 +ENSMUSG00000005131 2 0 1 0 1 1 +ENSMUSG00000046180 0 0 0 0 0 0 +ENSMUSG00000070984 0 0 0 0 0 0 +ENSMUSG00000097632 7 3 3 4 2 0 +ENSMUSG00000086396 0 0 0 0 0 0 +ENSMUSG00000096197 0 0 1 0 0 0 +ENSMUSG00000085522 0 0 0 0 0 0 +ENSMUSG00000096971 68 52 61 81 75 76 +ENSMUSG00000048994 1 0 0 0 0 1 +ENSMUSG00000086244 0 0 0 0 0 0 +ENSMUSG00000097519 4 0 1 0 1 1 +ENSMUSG00000086277 0 0 0 0 0 0 +ENSMUSG00000022518 111 35 48 31 53 60 +ENSMUSG00000026729 45 25 43 17 33 24 +ENSMUSG00000051728 1 0 0 2 0 0 +ENSMUSG00000097387 0 1 0 1 1 2 +ENSMUSG00000053574 7 2 7 4 7 4 +ENSMUSG00000022002 0 0 0 0 0 0 +ENSMUSG00000051788 0 0 0 0 0 0 +ENSMUSG00000084764 0 0 0 0 0 0 +ENSMUSG00000086273 2 0 0 2 2 2 +ENSMUSG00000084834 57 35 38 31 48 29 +ENSMUSG00000073141 0 0 0 0 0 0 +ENSMUSG00000026882 0 0 0 0 0 0 +ENSMUSG00000090220 0 1 0 0 0 2 +ENSMUSG00000085084 0 0 1 0 0 0 +ENSMUSG00000090457 0 0 0 0 0 0 +ENSMUSG00000037358 0 1 2 1 0 2 +ENSMUSG00000021961 0 1 6 0 0 0 +ENSMUSG00000097587 0 0 0 0 0 0 +ENSMUSG00000012042 0 0 0 0 0 0 +ENSMUSG00000040840 33 6 23 8 12 7 +ENSMUSG00000027811 39 20 9 18 13 41 +ENSMUSG00000051074 8 0 3 4 1 1 +ENSMUSG00000070315 287 213 330 223 341 143 +ENSMUSG00000055159 2 0 3 0 1 0 +ENSMUSG00000086954 0 0 0 0 0 0 +ENSMUSG00000029044 0 0 0 0 0 0 +ENSMUSG00000034063 0 0 1 0 0 0 +ENSMUSG00000039138 0 0 0 0 0 0 +ENSMUSG00000097725 1 0 1 0 0 0 +ENSMUSG00000086365 0 0 0 0 0 0 +ENSMUSG00000087233 0 0 0 0 0 0 +ENSMUSG00000060673 0 0 0 0 0 0 +ENSMUSG00000041068 0 0 0 0 0 0 +ENSMUSG00000084995 0 0 0 0 0 0 +ENSMUSG00000073144 40 14 21 17 18 18 +ENSMUSG00000093772 15 12 11 3 7 5 +ENSMUSG00000097329 16 5 5 2 6 6 +ENSMUSG00000013353 2 1 1 0 0 2 +ENSMUSG00000031938 92 102 90 72 101 94 +ENSMUSG00000066571 694 343 429 324 515 465 +ENSMUSG00000073722 0 0 0 0 0 0 +ENSMUSG00000038199 0 0 0 0 0 0 +ENSMUSG00000022179 69 46 96 65 62 35 +ENSMUSG00000056197 0 0 0 0 0 0 +ENSMUSG00000026774 0 0 0 0 0 0 +ENSMUSG00000014837 4 3 2 11 9 9 +ENSMUSG00000086727 0 1 0 0 0 1 +ENSMUSG00000032023 0 0 0 0 0 0 +ENSMUSG00000056617 4 0 2 0 3 3 +ENSMUSG00000047324 0 0 0 0 0 0 +ENSMUSG00000055061 57 23 24 38 38 30 +ENSMUSG00000055643 0 0 0 0 0 0 +ENSMUSG00000078157 0 1 0 0 0 0 +ENSMUSG00000097775 5 2 5 8 6 7 +ENSMUSG00000046367 0 0 0 0 0 0 +ENSMUSG00000074580 6 3 4 2 6 1 +ENSMUSG00000047490 0 0 0 0 0 0 +ENSMUSG00000058670 0 0 0 0 0 0 +ENSMUSG00000075070 0 1 0 0 0 0 +ENSMUSG00000078962 1 0 0 0 0 0 +ENSMUSG00000079324 1 0 1 0 0 1 +ENSMUSG00000062036 0 0 0 0 0 0 +ENSMUSG00000069925 0 0 0 0 0 0 +ENSMUSG00000048038 1 0 0 0 0 0 +ENSMUSG00000079513 0 0 0 0 0 0 +ENSMUSG00000062391 0 0 0 0 0 0 +ENSMUSG00000037270 1535 987 1191 921 1235 1363 +ENSMUSG00000039851 0 0 0 0 0 1 +ENSMUSG00000097216 0 0 0 0 0 0 +ENSMUSG00000090336 0 0 0 0 0 0 +ENSMUSG00000086796 61 74 75 49 87 66 +ENSMUSG00000055357 0 0 0 0 0 0 +ENSMUSG00000055700 0 0 0 0 0 0 +ENSMUSG00000087487 0 0 0 0 0 0 +ENSMUSG00000025961 1 0 2 0 3 3 +ENSMUSG00000045330 0 0 0 0 0 0 +ENSMUSG00000069971 0 0 0 0 0 0 +ENSMUSG00000013668 0 0 0 0 0 0 +ENSMUSG00000067848 0 0 0 0 0 0 +ENSMUSG00000044084 0 0 0 0 0 0 +ENSMUSG00000079460 0 0 0 0 0 0 +ENSMUSG00000085122 1 0 2 0 1 0 +ENSMUSG00000097908 74 144 79 100 101 47 +ENSMUSG00000097852 2 1 4 3 3 2 +ENSMUSG00000086209 0 0 0 0 0 0 +ENSMUSG00000013158 0 1 1 1 2 0 +ENSMUSG00000084234 0 0 0 0 0 0 +ENSMUSG00000097494 4 3 10 1 0 6 +ENSMUSG00000085796 0 0 0 0 0 0 +ENSMUSG00000090585 0 0 0 0 0 0 +ENSMUSG00000086025 0 0 0 0 0 0 +ENSMUSG00000087475 9 7 6 3 9 5 +ENSMUSG00000027229 0 0 0 0 0 0 +ENSMUSG00000086690 1 0 0 0 0 0 +ENSMUSG00000085820 0 0 0 0 0 0 +ENSMUSG00000050526 0 0 0 0 0 0 +ENSMUSG00000073759 0 0 0 0 0 0 +ENSMUSG00000087396 46 21 25 26 24 29 +ENSMUSG00000026224 0 0 0 0 0 0 +ENSMUSG00000049357 2 3 7 4 3 8 +ENSMUSG00000097407 6 2 7 5 2 2 +ENSMUSG00000084848 5 2 3 3 3 2 +ENSMUSG00000053896 0 0 0 0 0 0 +ENSMUSG00000062224 0 0 0 0 0 0 +ENSMUSG00000029586 0 0 0 0 0 0 +ENSMUSG00000090369 108 83 112 75 91 37 +ENSMUSG00000031631 435 262 313 297 409 306 +ENSMUSG00000071749 0 0 0 0 0 0 +ENSMUSG00000079304 0 0 0 0 0 0 +ENSMUSG00000021874 7 0 0 1 0 1 +ENSMUSG00000079048 0 0 0 0 0 0 +ENSMUSG00000073730 0 0 0 0 0 0 +ENSMUSG00000074734 0 0 0 0 0 0 +ENSMUSG00000085198 0 0 0 0 0 0 +ENSMUSG00000071763 0 0 0 0 0 0 +ENSMUSG00000097262 1 0 0 0 0 0 +ENSMUSG00000021415 0 31 22 22 0 0 +ENSMUSG00000097637 40 28 38 30 50 21 +ENSMUSG00000030463 0 0 0 0 0 0 +ENSMUSG00000085037 119 51 74 59 96 96 +ENSMUSG00000070332 32 49 68 42 42 33 +ENSMUSG00000085785 0 0 0 0 0 0 +ENSMUSG00000021718 0 0 0 0 0 0 +ENSMUSG00000086446 0 0 1 0 0 0 +ENSMUSG00000021133 27 11 17 15 22 18 +ENSMUSG00000055403 0 0 0 0 0 0 +ENSMUSG00000020807 193 75 109 79 79 117 +ENSMUSG00000044276 1 1 2 1 1 1 +ENSMUSG00000033015 0 0 0 0 0 0 +ENSMUSG00000030877 2 1 0 1 0 1 +ENSMUSG00000085928 0 0 0 0 0 0 +ENSMUSG00000086355 0 0 0 0 0 0 +ENSMUSG00000058046 2 4 3 2 3 5 +ENSMUSG00000086892 0 0 0 0 0 0 +ENSMUSG00000086968 102 43 78 96 70 142 +ENSMUSG00000036770 1 0 0 0 0 0 +ENSMUSG00000097044 0 0 0 0 0 0 +ENSMUSG00000097021 4 1 0 2 0 2 +ENSMUSG00000027942 311 193 281 250 336 312 +ENSMUSG00000035057 0 0 0 0 0 0 +ENSMUSG00000031736 2 4 4 3 1 0 +ENSMUSG00000025288 0 0 0 0 0 0 +ENSMUSG00000093617 6 1 0 0 5 7 +ENSMUSG00000072893 73 44 47 40 57 46 +ENSMUSG00000085184 4 3 1 0 2 1 +ENSMUSG00000097082 1 0 4 0 3 4 +ENSMUSG00000045928 0 0 0 0 0 0 +ENSMUSG00000051940 0 0 0 0 0 0 +ENSMUSG00000034959 64 16 36 30 13 18 +ENSMUSG00000073147 217 93 166 118 178 192 +ENSMUSG00000085129 9 4 4 11 6 6 +ENSMUSG00000044574 0 0 0 0 0 0 +ENSMUSG00000097885 6 1 2 2 2 0 +ENSMUSG00000036046 1374 858 1055 838 917 1196 +ENSMUSG00000055137 558 652 687 315 846 515 +ENSMUSG00000087455 8 0 2 3 0 1 +ENSMUSG00000086822 0 0 0 0 0 0 +ENSMUSG00000040412 51 14 52 23 18 16 +ENSMUSG00000022639 41 9 13 19 24 18 +ENSMUSG00000087620 0 0 0 0 0 0 +ENSMUSG00000094113 0 0 0 0 0 0 +ENSMUSG00000044121 0 0 0 0 0 0 +ENSMUSG00000085776 1 0 0 0 1 2 +ENSMUSG00000085741 2 3 2 3 1 1 +ENSMUSG00000097772 73 47 49 27 79 45 +ENSMUSG00000028475 20 6 14 8 7 13 +ENSMUSG00000074918 173 111 115 170 185 175 +ENSMUSG00000006204 0 0 0 0 0 0 +ENSMUSG00000067613 0 0 1 1 0 0 +ENSMUSG00000021566 0 0 0 0 0 0 +ENSMUSG00000085004 0 0 0 0 0 0 +ENSMUSG00000025058 87 10 32 22 18 21 +ENSMUSG00000052688 155 30 54 73 33 63 +ENSMUSG00000055594 0 0 0 0 0 0 +ENSMUSG00000020703 0 0 0 0 0 0 +ENSMUSG00000087174 82 44 68 45 60 46 +ENSMUSG00000087424 10 10 11 9 9 14 +ENSMUSG00000073755 2 0 2 1 1 2 +ENSMUSG00000087553 0 0 0 0 0 0 +ENSMUSG00000081793 0 0 1 0 0 0 +ENSMUSG00000097766 0 0 0 0 0 1 +ENSMUSG00000097191 0 0 0 0 0 1 +ENSMUSG00000091370 2 4 1 3 7 2 +ENSMUSG00000057181 540 306 400 355 504 467 +ENSMUSG00000086126 0 0 0 0 0 0 +ENSMUSG00000062046 0 0 0 2 0 0 +ENSMUSG00000093459 40 16 25 12 28 13 +ENSMUSG00000073197 0 0 0 0 0 0 +ENSMUSG00000050549 110 55 68 54 72 95 +ENSMUSG00000073101 6 2 3 3 6 7 +ENSMUSG00000041605 14 3 2 1 2 13 +ENSMUSG00000062470 17 6 16 9 13 13 +ENSMUSG00000045968 4 3 5 3 5 63 +ENSMUSG00000086259 0 0 0 0 2 0 +ENSMUSG00000054672 2 0 0 0 0 0 diff -r 000000000000 -r e020be4f281b 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 17:40:46 2019 -0400 @@ -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 +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 +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 diff -r 000000000000 -r e020be4f281b 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 17:40:46 2019 -0400 @@ -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 diff -r 000000000000 -r e020be4f281b 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 17:40:46 2019 -0400 @@ -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 diff -r 000000000000 -r e020be4f281b 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 17:40:46 2019 -0400 @@ -0,0 +1,2 @@ +#GeneID try_this +GENE1 45 diff -r 000000000000 -r e020be4f281b 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 17:40:46 2019 -0400 @@ -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% diff -r 000000000000 -r e020be4f281b 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 17:40:46 2019 -0400 @@ -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% diff -r 000000000000 -r e020be4f281b test-data/test_mapped_reads.bam Binary file test-data/test_mapped_reads.bam has changed _[��8 tG}�I��E��u��B@fd<��N��#�?��G��?�wr#�vE?��x$��IG\��Ԉ�?��_��a�^��ѥpW�q��6<��h-5�Q��~c��e,�n@��"�� ٪P%K��=j�+O��)&��W�^�[�X��׊��H}�mEʠ@Fȓ��tԸ-~��U�Ȋ��?%�L1��C��c��r�C*,��3��X��ʗ�� 9��Ҥ8�ch��`�Yw�6��4˔/�m��\�;��(5��X��a�|��~ڰ+W��._ j��+�ġ��g3�eC�9��W�č��3D��kR��t��@( d�Z�c�1�m�Tv�Id��^{U)nZȄ��?m�\0F�Kf�Y:��t��s� DPF�=�q{|}�_t8qd�l��D�Nz��E�'B��>�{$mI�GЯ:��j�^_�4@��pX�[��Rz�� N�XFFW�E�8�,�M ��(��xȘ��f)��{5<3��s��[9�>yd��"��/F['��Q�%a�-/�%��r�@[��g�BR��=��'��Y/G\Q��&䊾K&��ʔ�6�8^�p�m\��餣�%�2*�Sm7]U'�wk! �u��%L�Ycf�l I�PU�� 7�vo�kl ��h�{B�7q�p�P |�̰L)��x0Q��y��"��rdJ"X��*�>�rs�x�~Ž��\�x��S��g��}�h<��4�$� t9��3X@q�W��ؙ�r;;��YSl�͢�a�îǡS�^;��^t3��$�K8z9-�1��U�^*>�Y�o�"�9z��y�( iU��7�<ۯr�背7�¹��۪R�W��^�9价"�g��g��Rd#�]�r�9��Js�2�E��t1��zK��`�r��86(��d��>O7��ǔs�y�u�RfբV��F��-��a�A/Э�X�Cb`Uߧ�N�f��k~[v�,��*9�2��I�?��綵[��u��|S��DV�|�#�ʽ��@P`/�Q�F��JW�:-O>D�Đӟ�pQ�b-��k,\'�/I��ٳ�A��`j��J+�6 ��/�Qn�kI)��;O{]��xz��n�2��%��2�<&�D��J��q��Vr[��.D�mHαڇ��;B��BB��c��Z��k�L�=J��EE ��Ɓu�Cyol�|*�!�ͅ��Ğ�� \9��r��:��-8N�F�ӿG`��@�7E�4<�;��]0J�Fu��*��9-� U�$��8"m4�Kl+��d\��)�.F^�Ur��&��r��$��V��з#��l�Q�Ϥ�m9תqo�@��*��w��r/n9��O��Uh��?��?}N�� ᦍ$ֱn��%�>��O>��+ EqiZ<)F��W��W�J�]�+�D��&�'vO��Sx��t,V�ctS�R�)Lm��e��p$��]�&� ��\�q��sZ[��?�d��Qh�&�P��V�˷&x�*J��9#ˉ��冽Kؗ\��AvQ$^��@�ݴ�7_kL�Vy�^�H9+g$��Yw�J tl�� }nm ��v��2 bm��wE��b�0�� m�b�S�E�<μ��m�e&�Fy�D7��A�߶"��מ��^��$�cR}]��(.�Jo��5�B��Ss��z�7�:��d��x'EK�l�?�v��s��A՛�ORE�� S��Rڟ39\J�l�wڨd�E�[T̥L��9^|� FA��nrm�'�b�w��A&'�� {�l��v\��.��挑$�e�S$%�@n�?�GpK��a�þ��r��>��K��A%{t��s�Ob�⦽�c��ua4R��e��5�'�׾s8�3E��!��Ƨ�w��6�'��W4�{��!��1e� B}*�c��J�L MЦ�4�8j5�Q��/�J��\G+��DU��b��n��Æ��&5ʍA��1F�n��Φq�Q-�6��7��>~�Ό%O.\�XH�ݥ��]�UW��ہ��h��/��~�3s)��%�W��ebp�7�(��+cZ�J�>w�ȃ��9��w�A��Ih��F� L��4��<�ˏz3% �@��Q�C/vF.uР q}Ey-��w�}�ً)�|Y��+m�7;�28�>��A��P{J��ډ��-��F��_��p��dǮ̐#�q�YU!�C�U|��@��2�&��G��"w��}��V�-�.Z�{?��'v)�z�Y0�i5 ��ꫜ2��1s�zj�M��+& �!��.�O=��_��]D� ��^��Q<