# HG changeset patch # User iuc # Date 1570743615 14400 # Node ID 16beb83e370cf1b3575edf51645b5369087545da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2" diff -r 000000000000 -r 16beb83e370c qualimap_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qualimap_macros.xml Thu Oct 10 17:40:15 2019 -0400 @@ -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 16beb83e370c qualimap_multi_bamqc.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qualimap_multi_bamqc.xml Thu Oct 10 17:40:15 2019 -0400 @@ -0,0 +1,199 @@ + + + qualimap_macros.xml + + + + + + + + + + + + + + + + + + > data_spec.txt && + mkdir -p bam_qc_data$n/raw_data_qualimapReport && + #for $dataset in $coll: + #if str($dataset.element_identifier) == 'genome_results': + ln -s '$dataset' 'bam_qc_data$n/${dataset.element_identifier}.txt' && + #else: + ln -s '$dataset' 'bam_qc_data$n/raw_data_qualimapReport/${dataset.element_identifier}.txt' && + #end if + #end for + #end for + #end for + #if all(len($group.bam_qc_data) == 1 for group in $input.groups): + ## Warn about an inconsistency in the behavior of the current + ## version of Qualimap. + ## When each group consists of exactly one BAM QC input, + ## Qualimap will ignore the group names and use the sample names + ## in the plot legends instead. + printf "Warning: Only a single sample was assigned to each sample group!\nQualimap will use sample names, not group names in plot legends.\nYou may want to report samples individually to be able to specify custom sample names.\n\n" && + #end if + #else: + #for $n, $data in enumerate($input.bam_qc_data): + #set $coll = $data.bam_qc_input + #set $sample_name = (str($data.sample_name).strip() or str($coll.name)).replace(' ', '_') + printf '%s\tbam_qc_data%d\t%d\n' '${sample_name}' '${n}' '${n}' >> data_spec.txt && + mkdir -p bam_qc_data$n/raw_data_qualimapReport && + #for $dataset in $coll: + #if str($dataset.element_identifier) == 'genome_results': + ln -s '$dataset' 'bam_qc_data$n/${dataset.element_identifier}.txt' && + #else: + ln -s '$dataset' 'bam_qc_data$n/raw_data_qualimapReport/${dataset.element_identifier}.txt' && + #end if + #end for + #end for + #end if + + @SET_JAVA_OPTS@ && + qualimap multi-bamqc + --data data_spec.txt + -outdir results -outformat html && + + #set $report_name = 'multisampleBamQcReport' + #set $summary_report = None + @MASSAGE_OUTPUT@ + ]]> + + + + + + + + + + + + + + + + + value.strip() + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ``Individually`` / ``In groups`` + +You may decide to group the input data for reporting, in which case you will +need to provide a name for each group that will be used in the plot legends. + +Output +====== + +The single HTML report generated by this tool contains the following: + +*Input data and parameters* + +This section lists the names of the BamQC Raw Data collections that served as +input along with the names of the groups (if any) each input got assigned to. + +*Summary* + +The summary table contains comparison of selected critical alignment metrics for all samples. The metrics include mean and standard deviation of coverage, mean GC content, mean insert size and mean mapping qualities. If the sample groups are provided, they are also shown for each sample. + +*PCA plot* + +The alignment features presented in the Summary section undergo Principal Component Analysis. Afterwards the biplot presenting first and second principal component is constructed. It allows to detect if any samples group together and if there are any outliers among the analyzed samples. + +*Other plots* + +Here you will find plots of: + +- Coverage Across Reference, +- Coverage Histogram, +- Genome Fraction Coverage, +- Duplication Rate Histogram, +- Mapped Reads GC Content, +- Mapped Reads GC Content Distribution, +- Mapped Reads Clipping Profile, +- Mapping Quality Across Reference, +- Mapping Quality Histogram + +and, if applicable, + +- Insert Size Across Reference, +- Insert Size Histogram + +Essentially, these are overlays of the plots of the individual inputs (or of +the groups they have been assigned to) and that are explained in the help of +the *Qualimap BamQC* tool. + ]]> + + diff -r 000000000000 -r 16beb83e370c test-data/coverage_across_reference.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coverage_across_reference.txt Thu Oct 10 17:40:15 2019 -0400 @@ -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 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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 16beb83e370c test-data/coverage_histogram.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coverage_histogram.txt Thu Oct 10 17:40:15 2019 -0400 @@ -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 16beb83e370c test-data/duplication_rate_histogram.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/duplication_rate_histogram.txt Thu Oct 10 17:40:15 2019 -0400 @@ -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 16beb83e370c test-data/features.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/features.gtf Thu Oct 10 17:40:15 2019 -0400 @@ -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 16beb83e370c test-data/genome_fraction_coverage.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_fraction_coverage.txt Thu Oct 10 17:40:15 2019 -0400 @@ -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 16beb83e370c test-data/genome_results_default.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_results_default.txt Thu Oct 10 17:40:15 2019 -0400 @@ -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 16beb83e370c test-data/genome_results_inside_features.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_results_inside_features.txt Thu Oct 10 17:40:15 2019 -0400 @@ -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 16beb83e370c test-data/genome_results_outside_features.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_results_outside_features.txt Thu Oct 10 17:40:15 2019 -0400 @@ -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 16beb83e370c test-data/mapped_reads_clipping_profile.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mapped_reads_clipping_profile.txt Thu Oct 10 17:40:15 2019 -0400 @@ -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 16beb83e370c test-data/mapped_reads_gc-content_distribution.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mapped_reads_gc-content_distribution.txt Thu Oct 10 17:40:15 2019 -0400 @@ -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 16beb83e370c test-data/mapped_reads_nucleotide_content.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mapped_reads_nucleotide_content.txt Thu Oct 10 17:40:15 2019 -0400 @@ -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 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-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 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16beb83e370c test-data/rnaseq_qc_results_custom.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnaseq_qc_results_custom.txt Thu Oct 10 17:40:15 2019 -0400 @@ -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 16beb83e370c test-data/rnaseq_qc_results_default.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnaseq_qc_results_default.txt Thu Oct 10 17:40:15 2019 -0400 @@ -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 16beb83e370c test-data/test_mapped_reads.bam Binary file test-data/test_mapped_reads.bam has changed