├── .classpath ├── .devcontainer ├── devcontainer.json └── postCreateCommand.sh ├── .github ├── dependabot.yml └── workflows │ └── pr.yml ├── .gitignore ├── .project ├── .settings └── org.eclipse.jdt.core.prefs ├── Configuration ├── adapter_list.txt ├── contaminant_list.txt └── limits.txt ├── Help ├── 1 Introduction │ ├── .svn │ │ ├── entries │ │ └── text-base │ │ │ └── 1.1 What is FastQC.html.svn-base │ └── 1.1 What is FastQC.html ├── 2 Basic Operations │ ├── .svn │ │ ├── entries │ │ └── text-base │ │ │ ├── 2.1 Opening a sequence file.html.svn-base │ │ │ ├── 2.2 Evaluating Results.html.svn-base │ │ │ └── 2.3 Saving a Report.html.svn-base │ ├── 2.1 Opening a sequence file.html │ ├── 2.2 Evaluating Results.html │ └── 2.3 Saving a Report.html ├── 3 Analysis Modules │ ├── .svn │ │ ├── entries │ │ ├── prop-base │ │ │ ├── duplication_levels.png.svn-base │ │ │ ├── kmer_profiles.png.svn-base │ │ │ ├── per_base_gc_content.png.svn-base │ │ │ ├── per_base_n_content.png.svn-base │ │ │ ├── per_base_quality.png.svn-base │ │ │ ├── per_base_sequence_content.png.svn-base │ │ │ ├── per_sequence_gc_content.png.svn-base │ │ │ ├── per_sequence_quality.png.svn-base │ │ │ ├── per_tile_quality.png.svn-base │ │ │ └── sequence_length_distribution.png.svn-base │ │ └── text-base │ │ │ ├── 1 Basic Statistics.html.svn-base │ │ │ ├── 10 Adapter Content.html.svn-base │ │ │ ├── 11 Kmer Content.html.svn-base │ │ │ ├── 12 Per Tile Sequence Quality.html.svn-base │ │ │ ├── 2 Per Base Sequence Quality.html.svn-base │ │ │ ├── 3 Per Sequence Quality Scores.html.svn-base │ │ │ ├── 4 Per Base Sequence Content.html.svn-base │ │ │ ├── 5 Per Sequence GC Content.html.svn-base │ │ │ ├── 6 Per Base N Content.html.svn-base │ │ │ ├── 7 Sequence Length Distribution.html.svn-base │ │ │ ├── 8 Duplicate Sequences.html.svn-base │ │ │ ├── 9 Overrepresented Sequences.html.svn-base │ │ │ ├── duplication_levels.png.svn-base │ │ │ ├── kmer_profiles.png.svn-base │ │ │ ├── per_base_gc_content.png.svn-base │ │ │ ├── per_base_n_content.png.svn-base │ │ │ ├── per_base_quality.png.svn-base │ │ │ ├── per_base_sequence_content.png.svn-base │ │ │ ├── per_sequence_gc_content.png.svn-base │ │ │ ├── per_sequence_quality.png.svn-base │ │ │ ├── per_tile_quality.png.svn-base │ │ │ └── sequence_length_distribution.png.svn-base │ ├── 1 Basic Statistics.html │ ├── 10 Adapter Content.html │ ├── 11 Kmer Content.html │ ├── 12 Per Tile Sequence Quality.html │ ├── 2 Per Base Sequence Quality.html │ ├── 3 Per Sequence Quality Scores.html │ ├── 4 Per Base Sequence Content.html │ ├── 5 Per Sequence GC Content.html │ ├── 6 Per Base N Content.html │ ├── 7 Sequence Length Distribution.html │ ├── 8 Duplicate Sequences.html │ ├── 9 Overrepresented Sequences.html │ ├── duplication_levels.png │ ├── kmer_profiles.png │ ├── per_base_gc_content.png │ ├── per_base_n_content.png │ ├── per_base_quality.png │ ├── per_base_sequence_content.png │ ├── per_sequence_gc_content.png │ ├── per_sequence_quality.png │ ├── per_tile_quality.png │ └── sequence_length_distribution.png └── fastqc.png ├── INSTALL.md ├── LICENSE ├── LICENSE_JHDF5.txt ├── README.md ├── RELEASE_NOTES.txt ├── Templates ├── Icons │ ├── error.png │ ├── fastqc_icon.png │ ├── tick.png │ └── warning.png ├── fastqc2fo.xsl └── header_template.html ├── cisd-jhdf5.jar ├── fastqc ├── fastqc_icon.ico ├── htsjdk.jar ├── jbzip2-0.9.jar ├── lib ├── apiguardian-api-1.1.2.jar ├── approvaltests-25.4.3.jar ├── approvaltests-util-25.4.3.jar ├── download.sh ├── jsoup-1.18.1.jar ├── junit-jupiter-api-5.10.0.jar ├── junit-jupiter-engine-5.10.0.jar ├── junit-jupiter-params-5.10.0.jar ├── junit-platform-commons-1.10.0.jar ├── junit-platform-engine-1.10.0.jar ├── junit-platform-launcher-1.10.0.jar └── opentest4j-1.3.0.jar ├── net └── sourceforge │ └── iharder │ └── base64 │ └── Base64.java ├── org └── apache │ └── commons │ └── math3 │ ├── analysis │ ├── UnivariateFunction.java │ └── solvers │ │ ├── AbstractUnivariateSolver.java │ │ ├── AllowedSolution.java │ │ ├── BaseAbstractUnivariateSolver.java │ │ ├── BaseUnivariateSolver.java │ │ ├── BracketedUnivariateSolver.java │ │ ├── BrentSolver.java │ │ ├── UnivariateSolver.java │ │ └── UnivariateSolverUtils.java │ ├── distribution │ ├── AbstractIntegerDistribution.java │ ├── AbstractRealDistribution.java │ ├── BetaDistribution.java │ ├── BinomialDistribution.java │ ├── CauchyDistribution.java │ ├── ChiSquaredDistribution.java │ ├── FDistribution.java │ ├── GammaDistribution.java │ ├── HypergeometricDistribution.java │ ├── IntegerDistribution.java │ ├── NormalDistribution.java │ ├── PascalDistribution.java │ ├── PoissonDistribution.java │ ├── RealDistribution.java │ ├── SaddlePointExpansion.java │ ├── TDistribution.java │ ├── WeibullDistribution.java │ └── ZipfDistribution.java │ ├── exception │ ├── ConvergenceException.java │ ├── DimensionMismatchException.java │ ├── MathArithmeticException.java │ ├── MathIllegalArgumentException.java │ ├── MathIllegalNumberException.java │ ├── MathIllegalStateException.java │ ├── MathInternalError.java │ ├── MaxCountExceededException.java │ ├── NoBracketingException.java │ ├── NotFiniteNumberException.java │ ├── NotPositiveException.java │ ├── NotStrictlyPositiveException.java │ ├── NullArgumentException.java │ ├── NumberIsTooLargeException.java │ ├── NumberIsTooSmallException.java │ ├── OutOfRangeException.java │ ├── TooManyEvaluationsException.java │ └── util │ │ ├── ArgUtils.java │ │ ├── ExceptionContext.java │ │ ├── ExceptionContextProvider.java │ │ ├── Localizable.java │ │ └── LocalizedFormats.java │ ├── random │ ├── AbstractWell.java │ ├── BitsStreamGenerator.java │ ├── RandomData.java │ ├── RandomDataImpl.java │ ├── RandomGenerator.java │ └── Well19937c.java │ ├── special │ ├── Beta.java │ ├── Erf.java │ └── Gamma.java │ └── util │ ├── ArithmeticUtils.java │ ├── ContinuedFraction.java │ ├── DoubleArray.java │ ├── FastMath.java │ ├── FastMathCalc.java │ ├── FastMathLiteralArrays.java │ ├── Incrementor.java │ ├── MathUtils.java │ ├── Precision.java │ └── ResizableDoubleArray.java ├── run_fastqc.bat ├── test ├── data │ ├── TestCases.java │ ├── complex.fastq │ └── minimal.fastq ├── integration │ ├── FileContentsTest.java │ ├── FileContentsTest_complex_fastqc_data.approved.txt │ ├── FileContentsTest_complex_fastqc_report.approved.html │ ├── FileContentsTest_minimal_fastqc_data.approved.txt │ ├── FileContentsTest_minimal_fastqc_report.approved.html │ ├── FolderStructureTest.java │ ├── HtmlContentHelpers.java │ ├── HtmlContentHelpersTest.java │ ├── OutDirTest.java │ ├── OutputTest.java │ ├── TestHelpers.java │ ├── ThreadsTest.java │ ├── VersionTest.java │ └── cli │ │ ├── Cli.java │ │ ├── CliResult.java │ │ └── CliScenario.java ├── readme.md ├── ui │ └── Modules │ │ ├── BasicStatsTest.java │ │ ├── BasicStatsTest.testRendering.complex.Linux.approved.png │ │ └── BasicStatsTest.testRendering.minimal.Linux.approved.png └── unit │ ├── FileFilters │ └── SequenceFileFilterTest.java │ ├── FontTests.java │ └── Modules │ └── BasicStatsTest.java └── uk └── ac └── babraham └── FastQC ├── Analysis ├── AnalysisListener.java ├── AnalysisQueue.java ├── AnalysisRunner.java └── OfflineRunner.java ├── Dialogs ├── AboutDialog.java ├── FastQCTitlePanel.java └── WelcomePanel.java ├── FastQCApplication.java ├── FastQCConfig.java ├── FastQCMenuBar.java ├── FileFilters ├── BAMFileFilter.java ├── CasavaFastQFileFilter.java ├── FastQFileFilter.java ├── GobyFileFilter.java ├── MappedBAMFileFilter.java └── SequenceFileFilter.java ├── Graphs ├── BaseGroup.java ├── LineGraph.java ├── QualityBoxPlot.java └── TileGraph.java ├── Help ├── HelpDialog.java ├── HelpIndexRoot.java ├── HelpPage.java ├── HelpPageDisplay.java └── HelpSearchPanel.java ├── Modules ├── AbstractQCModule.java ├── AdapterContent.java ├── BasicStats.java ├── DuplicationLevel.java ├── GCModel │ ├── GCModel.java │ └── GCModelValue.java ├── KmerContent.java ├── ModuleConfig.java ├── ModuleFactory.java ├── NContent.java ├── OverRepresentedSeqs.java ├── PerBaseQualityScores.java ├── PerBaseSequenceContent.java ├── PerSequenceGCContent.java ├── PerSequenceQualityScores.java ├── PerTileQualityScores.java ├── QCModule.java └── SequenceLengthDistribution.java ├── Report ├── HTMLReportArchive.java └── stylesheet.txt ├── Resources ├── error.png ├── fastqc_icon.png ├── fastqc_icon.svg ├── fastqc_icon_100.png ├── tick.png └── warning.png ├── Results └── ResultsPanel.java ├── Sequence ├── BAMFile.java ├── Contaminant │ ├── Contaminant.java │ ├── ContaminantHit.java │ └── ContaminentFinder.java ├── Fast5File.java ├── FastQFile.java ├── QualityEncoding │ └── PhredEncoding.java ├── Sequence.java ├── SequenceFactory.java ├── SequenceFile.java ├── SequenceFileGroup.java └── SequenceFormatException.java ├── Statistics ├── NormalDistribution.java └── PearsonCorrelation.java └── Utilities ├── CasavaBasename.java ├── HotColdColourGradient.java ├── ImageSaver ├── SVGGenerator.java └── SVGImageSaver.java ├── 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