fastqc: Fix install and plist

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: fastqc: Fix install and plist
From: Jason Bacon <bacon4000%gmail.com@localhost>
Date: Fri, 17 Nov 2017 14:37:10 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Fri Nov 17 08:37:10 2017 -0600
Changeset:	1e2a28588070828c4657a00e4dfb4824f8b95137

Modified Files:
	fastqc/Makefile
	fastqc/PLIST

Log Message:
fastqc: Fix install and plist

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=1e2a28588070828c4657a00e4dfb4824f8b95137

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 fastqc/Makefile |  14 +--
 fastqc/PLIST    | 260 ++++++++++++++++++++++++++++++++++++--------------------
 2 files changed, 179 insertions(+), 95 deletions(-)

diffs:
diff --git a/fastqc/Makefile b/fastqc/Makefile
index 1c456d74fd..e7662f00e1 100644
--- a/fastqc/Makefile
+++ b/fastqc/Makefile
@@ -19,8 +19,8 @@ LICENSE=	gnu-gpl-v3
 
 SUBST_CLASSES+=		javapath
 SUBST_STAGE.javapath=	post-patch
-SUBST_SED.javapath+=	-e 's|$$RealBin$$delimiter|${JAVAJARDIR}$$delimiter|g'
-SUBST_SED.javapath+=	-e 's|$$RealBin/|${JAVAJARDIR}/|g'
+SUBST_SED.javapath+=	-e 's|$$RealBin$$delimiter|${DATADIR}$$delimiter${JAVAJARDIR}/fastqc$$delimiter|g'
+SUBST_SED.javapath+=	-e 's|$$RealBin/|${JAVAJARDIR}/fastqc/|g'
 SUBST_FILES.javapath+=	${WRKSRC}/fastqc
 
 USE_TOOLS+=	perl:run pax
@@ -35,18 +35,22 @@ DOCSDIR=	${PREFIX}/share/doc/fastqc
 USE_JAVA=	yes
 JAVAJARDIR=	${PREFIX}/share/java/classes
 
-INSTALLATION_DIRS=	bin ${DATADIR} ${DOCSDIR} ${JAVAJARDIR}
+INSTALLATION_DIRS=	bin ${DATADIR} ${DOCSDIR} ${JAVAJARDIR}/fastqc
 
 do-install:
-	${INSTALL_DATA} ${WRKSRC}/*.jar ${DESTDIR}${JAVAJARDIR}
+	${INSTALL_DATA} ${WRKSRC}/*.jar ${DESTDIR}${JAVAJARDIR}/fastqc
 	${INSTALL_SCRIPT} ${WRKSRC}/fastqc \
 		${DESTDIR}${PREFIX}/bin
 	cd ${WRKSRC} && pax -rw Configuration \
 		${DESTDIR}${DATADIR}
 	cd ${WRKSRC} && pax -rw Templates \
 		${DESTDIR}${DATADIR}
+	cd ${WRKSRC} && pax -rw net \
+		${DESTDIR}${JAVAJARDIR}/fastqc
+	cd ${WRKSRC} && pax -rw org \
+		${DESTDIR}${JAVAJARDIR}/fastqc
 	cd ${WRKSRC} && pax -rw uk \
-		${DESTDIR}${JAVAJARDIR}
+		${DESTDIR}${JAVAJARDIR}/fastqc
 	cd ${WRKSRC} && pax -rw 'Help' \
 		${DESTDIR}${DOCSDIR}
 
diff --git a/fastqc/PLIST b/fastqc/PLIST
index 0da02df4a7..fe1c64c234 100644
--- a/fastqc/PLIST
+++ b/fastqc/PLIST
@@ -35,93 +35,173 @@ share/fastqc/Templates/Icons/tick.png
 share/fastqc/Templates/Icons/warning.png
 share/fastqc/Templates/fastqc2fo.xsl
 share/fastqc/Templates/header_template.html
-share/java/classes/cisd-jhdf5.jar
-share/java/classes/jbzip2-0.9.jar
-share/java/classes/sam-1.103.jar
-share/java/classes/uk/ac/babraham/FastQC/Analysis/AnalysisListener.class
-share/java/classes/uk/ac/babraham/FastQC/Analysis/AnalysisQueue.class
-share/java/classes/uk/ac/babraham/FastQC/Analysis/AnalysisRunner.class
-share/java/classes/uk/ac/babraham/FastQC/Analysis/OfflineRunner.class
-share/java/classes/uk/ac/babraham/FastQC/Dialogs/AboutDialog$1.class
-share/java/classes/uk/ac/babraham/FastQC/Dialogs/AboutDialog.class
-share/java/classes/uk/ac/babraham/FastQC/Dialogs/FastQCTitlePanel$SmoothJLabel.class
-share/java/classes/uk/ac/babraham/FastQC/Dialogs/FastQCTitlePanel.class
-share/java/classes/uk/ac/babraham/FastQC/Dialogs/WelcomePanel.class
-share/java/classes/uk/ac/babraham/FastQC/FastQCApplication$1.class
-share/java/classes/uk/ac/babraham/FastQC/FastQCApplication.class
-share/java/classes/uk/ac/babraham/FastQC/FastQCConfig.class
-share/java/classes/uk/ac/babraham/FastQC/FastQCMenuBar.class
-share/java/classes/uk/ac/babraham/FastQC/FileFilters/BAMFileFilter.class
-share/java/classes/uk/ac/babraham/FastQC/FileFilters/CasavaFastQFileFilter.class
-share/java/classes/uk/ac/babraham/FastQC/FileFilters/FastQFileFilter.class
-share/java/classes/uk/ac/babraham/FastQC/FileFilters/GobyFileFilter.class
-share/java/classes/uk/ac/babraham/FastQC/FileFilters/MappedBAMFileFilter.class
-share/java/classes/uk/ac/babraham/FastQC/FileFilters/SequenceFileFilter.class
-share/java/classes/uk/ac/babraham/FastQC/Graphs/BaseGroup.class
-share/java/classes/uk/ac/babraham/FastQC/Graphs/LineGraph.class
-share/java/classes/uk/ac/babraham/FastQC/Graphs/QualityBoxPlot.class
-share/java/classes/uk/ac/babraham/FastQC/Graphs/TileGraph.class
-share/java/classes/uk/ac/babraham/FastQC/Help/HelpDialog.class
-share/java/classes/uk/ac/babraham/FastQC/Help/HelpIndexRoot$FileSorter.class
-share/java/classes/uk/ac/babraham/FastQC/Help/HelpIndexRoot.class
-share/java/classes/uk/ac/babraham/FastQC/Help/HelpPage.class
-share/java/classes/uk/ac/babraham/FastQC/Help/HelpPageDisplay$HelpEditor.class
-share/java/classes/uk/ac/babraham/FastQC/Help/HelpPageDisplay.class
-share/java/classes/uk/ac/babraham/FastQC/Help/HelpSearchPanel.class
-share/java/classes/uk/ac/babraham/FastQC/Modules/AbstractQCModule.class
-share/java/classes/uk/ac/babraham/FastQC/Modules/AdapterContent$Adapter.class
-share/java/classes/uk/ac/babraham/FastQC/Modules/AdapterContent$ResultsTable.class
-share/java/classes/uk/ac/babraham/FastQC/Modules/AdapterContent.class
-share/java/classes/uk/ac/babraham/FastQC/Modules/BasicStats$ResultsTable.class
-share/java/classes/uk/ac/babraham/FastQC/Modules/BasicStats.class
-share/java/classes/uk/ac/babraham/FastQC/Modules/DuplicationLevel.class
-share/java/classes/uk/ac/babraham/FastQC/Modules/GCModel/GCModel.class
-share/java/classes/uk/ac/babraham/FastQC/Modules/GCModel/GCModelValue.class
-share/java/classes/uk/ac/babraham/FastQC/Modules/KmerContent$Kmer.class
-share/java/classes/uk/ac/babraham/FastQC/Modules/KmerContent$ResultsTable.class
-share/java/classes/uk/ac/babraham/FastQC/Modules/KmerContent.class
-share/java/classes/uk/ac/babraham/FastQC/Modules/ModuleConfig.class
-share/java/classes/uk/ac/babraham/FastQC/Modules/ModuleFactory.class
-share/java/classes/uk/ac/babraham/FastQC/Modules/NContent.class
-share/java/classes/uk/ac/babraham/FastQC/Modules/OverRepresentedSeqs$OverrepresentedSeq.class
-share/java/classes/uk/ac/babraham/FastQC/Modules/OverRepresentedSeqs$ResultsTable.class
-share/java/classes/uk/ac/babraham/FastQC/Modules/OverRepresentedSeqs.class
-share/java/classes/uk/ac/babraham/FastQC/Modules/PerBaseQualityScores.class
-share/java/classes/uk/ac/babraham/FastQC/Modules/PerBaseSequenceContent.class
-share/java/classes/uk/ac/babraham/FastQC/Modules/PerSequenceGCContent.class
-share/java/classes/uk/ac/babraham/FastQC/Modules/PerSequenceQualityScores.class
-share/java/classes/uk/ac/babraham/FastQC/Modules/PerTileQualityScores.class
-share/java/classes/uk/ac/babraham/FastQC/Modules/QCModule.class
-share/java/classes/uk/ac/babraham/FastQC/Modules/SequenceLengthDistribution.class
-share/java/classes/uk/ac/babraham/FastQC/Report/HTMLReportArchive.class
-share/java/classes/uk/ac/babraham/FastQC/Report/stylesheet.txt
-share/java/classes/uk/ac/babraham/FastQC/Resources/error.png
-share/java/classes/uk/ac/babraham/FastQC/Resources/fastqc_icon.png
-share/java/classes/uk/ac/babraham/FastQC/Resources/fastqc_icon.svg
-share/java/classes/uk/ac/babraham/FastQC/Resources/fastqc_icon_100.png
-share/java/classes/uk/ac/babraham/FastQC/Resources/tick.png
-share/java/classes/uk/ac/babraham/FastQC/Resources/warning.png
-share/java/classes/uk/ac/babraham/FastQC/Results/ResultsPanel$ModuleRenderer.class
-share/java/classes/uk/ac/babraham/FastQC/Results/ResultsPanel.class
-share/java/classes/uk/ac/babraham/FastQC/Sequence/BAMFile.class
-share/java/classes/uk/ac/babraham/FastQC/Sequence/Contaminant/Contaminant.class
-share/java/classes/uk/ac/babraham/FastQC/Sequence/Contaminant/ContaminantHit.class
-share/java/classes/uk/ac/babraham/FastQC/Sequence/Contaminant/ContaminentFinder.class
-share/java/classes/uk/ac/babraham/FastQC/Sequence/Fast5File.class
-share/java/classes/uk/ac/babraham/FastQC/Sequence/FastQFile.class
-share/java/classes/uk/ac/babraham/FastQC/Sequence/QualityEncoding/PhredEncoding.class
-share/java/classes/uk/ac/babraham/FastQC/Sequence/Sequence.class
-share/java/classes/uk/ac/babraham/FastQC/Sequence/SequenceFactory.class
-share/java/classes/uk/ac/babraham/FastQC/Sequence/SequenceFile.class
-share/java/classes/uk/ac/babraham/FastQC/Sequence/SequenceFileGroup.class
-share/java/classes/uk/ac/babraham/FastQC/Sequence/SequenceFormatException.class
-share/java/classes/uk/ac/babraham/FastQC/Statistics/NormalDistribution.class
-share/java/classes/uk/ac/babraham/FastQC/Statistics/PearsonCorrelation.class
-share/java/classes/uk/ac/babraham/FastQC/Utilities/CasavaBasename.class
-share/java/classes/uk/ac/babraham/FastQC/Utilities/HotColdColourGradient.class
-share/java/classes/uk/ac/babraham/FastQC/Utilities/ImageToBase64.class
-share/java/classes/uk/ac/babraham/FastQC/Utilities/MultiMemberGZIPInputStream.class
-share/java/classes/uk/ac/babraham/FastQC/Utilities/NameFormatException.class
-share/java/classes/uk/ac/babraham/FastQC/Utilities/NanoporeBasename.class
-share/java/classes/uk/ac/babraham/FastQC/Utilities/QualityCount.class
-share/java/classes/uk/ac/babraham/FastQC/Utilities/RGB.class
+share/java/classes/fastqc/cisd-jhdf5.jar
+share/java/classes/fastqc/jbzip2-0.9.jar
+share/java/classes/fastqc/net/sourceforge/iharder/base64/Base64$1.class
+share/java/classes/fastqc/net/sourceforge/iharder/base64/Base64$InputStream.class
+share/java/classes/fastqc/net/sourceforge/iharder/base64/Base64$OutputStream.class
+share/java/classes/fastqc/net/sourceforge/iharder/base64/Base64.class
+share/java/classes/fastqc/org/apache/commons/math3/analysis/UnivariateFunction.class
+share/java/classes/fastqc/org/apache/commons/math3/analysis/solvers/AbstractUnivariateSolver.class
+share/java/classes/fastqc/org/apache/commons/math3/analysis/solvers/AllowedSolution.class
+share/java/classes/fastqc/org/apache/commons/math3/analysis/solvers/BaseAbstractUnivariateSolver.class
+share/java/classes/fastqc/org/apache/commons/math3/analysis/solvers/BaseUnivariateSolver.class
+share/java/classes/fastqc/org/apache/commons/math3/analysis/solvers/BracketedUnivariateSolver.class
+share/java/classes/fastqc/org/apache/commons/math3/analysis/solvers/BrentSolver.class
+share/java/classes/fastqc/org/apache/commons/math3/analysis/solvers/UnivariateSolver.class
+share/java/classes/fastqc/org/apache/commons/math3/analysis/solvers/UnivariateSolverUtils.class
+share/java/classes/fastqc/org/apache/commons/math3/distribution/AbstractIntegerDistribution.class
+share/java/classes/fastqc/org/apache/commons/math3/distribution/AbstractRealDistribution$1.class
+share/java/classes/fastqc/org/apache/commons/math3/distribution/AbstractRealDistribution.class
+share/java/classes/fastqc/org/apache/commons/math3/distribution/BetaDistribution.class
+share/java/classes/fastqc/org/apache/commons/math3/distribution/BinomialDistribution.class
+share/java/classes/fastqc/org/apache/commons/math3/distribution/CauchyDistribution.class
+share/java/classes/fastqc/org/apache/commons/math3/distribution/ChiSquaredDistribution.class
+share/java/classes/fastqc/org/apache/commons/math3/distribution/FDistribution.class
+share/java/classes/fastqc/org/apache/commons/math3/distribution/GammaDistribution.class
+share/java/classes/fastqc/org/apache/commons/math3/distribution/HypergeometricDistribution.class
+share/java/classes/fastqc/org/apache/commons/math3/distribution/IntegerDistribution.class
+share/java/classes/fastqc/org/apache/commons/math3/distribution/NormalDistribution.class
+share/java/classes/fastqc/org/apache/commons/math3/distribution/PascalDistribution.class
+share/java/classes/fastqc/org/apache/commons/math3/distribution/PoissonDistribution.class
+share/java/classes/fastqc/org/apache/commons/math3/distribution/RealDistribution.class
+share/java/classes/fastqc/org/apache/commons/math3/distribution/SaddlePointExpansion.class
+share/java/classes/fastqc/org/apache/commons/math3/distribution/TDistribution.class
+share/java/classes/fastqc/org/apache/commons/math3/distribution/WeibullDistribution.class
+share/java/classes/fastqc/org/apache/commons/math3/distribution/ZipfDistribution.class
+share/java/classes/fastqc/org/apache/commons/math3/exception/ConvergenceException.class
+share/java/classes/fastqc/org/apache/commons/math3/exception/DimensionMismatchException.class
+share/java/classes/fastqc/org/apache/commons/math3/exception/MathArithmeticException.class
+share/java/classes/fastqc/org/apache/commons/math3/exception/MathIllegalArgumentException.class
+share/java/classes/fastqc/org/apache/commons/math3/exception/MathIllegalNumberException.class
+share/java/classes/fastqc/org/apache/commons/math3/exception/MathIllegalStateException.class
+share/java/classes/fastqc/org/apache/commons/math3/exception/MathInternalError.class
+share/java/classes/fastqc/org/apache/commons/math3/exception/MaxCountExceededException.class
+share/java/classes/fastqc/org/apache/commons/math3/exception/NoBracketingException.class
+share/java/classes/fastqc/org/apache/commons/math3/exception/NotFiniteNumberException.class
+share/java/classes/fastqc/org/apache/commons/math3/exception/NotPositiveException.class
+share/java/classes/fastqc/org/apache/commons/math3/exception/NotStrictlyPositiveException.class
+share/java/classes/fastqc/org/apache/commons/math3/exception/NullArgumentException.class
+share/java/classes/fastqc/org/apache/commons/math3/exception/NumberIsTooLargeException.class
+share/java/classes/fastqc/org/apache/commons/math3/exception/NumberIsTooSmallException.class
+share/java/classes/fastqc/org/apache/commons/math3/exception/OutOfRangeException.class
+share/java/classes/fastqc/org/apache/commons/math3/exception/TooManyEvaluationsException.class
+share/java/classes/fastqc/org/apache/commons/math3/exception/util/ArgUtils.class
+share/java/classes/fastqc/org/apache/commons/math3/exception/util/ExceptionContext.class
+share/java/classes/fastqc/org/apache/commons/math3/exception/util/ExceptionContextProvider.class
+share/java/classes/fastqc/org/apache/commons/math3/exception/util/Localizable.class
+share/java/classes/fastqc/org/apache/commons/math3/exception/util/LocalizedFormats.class
+share/java/classes/fastqc/org/apache/commons/math3/random/AbstractWell.class
+share/java/classes/fastqc/org/apache/commons/math3/random/BitsStreamGenerator.class
+share/java/classes/fastqc/org/apache/commons/math3/random/RandomData.class
+share/java/classes/fastqc/org/apache/commons/math3/random/RandomDataImpl.class
+share/java/classes/fastqc/org/apache/commons/math3/random/RandomGenerator.class
+share/java/classes/fastqc/org/apache/commons/math3/random/Well19937c.class
+share/java/classes/fastqc/org/apache/commons/math3/special/Beta$1.class
+share/java/classes/fastqc/org/apache/commons/math3/special/Beta.class
+share/java/classes/fastqc/org/apache/commons/math3/special/Erf.class
+share/java/classes/fastqc/org/apache/commons/math3/special/Gamma$1.class
+share/java/classes/fastqc/org/apache/commons/math3/special/Gamma.class
+share/java/classes/fastqc/org/apache/commons/math3/util/ArithmeticUtils.class
+share/java/classes/fastqc/org/apache/commons/math3/util/ContinuedFraction.class
+share/java/classes/fastqc/org/apache/commons/math3/util/DoubleArray.class
+share/java/classes/fastqc/org/apache/commons/math3/util/FastMath$ExpFracTable.class
+share/java/classes/fastqc/org/apache/commons/math3/util/FastMath$ExpIntTable.class
+share/java/classes/fastqc/org/apache/commons/math3/util/FastMath$lnMant.class
+share/java/classes/fastqc/org/apache/commons/math3/util/FastMath.class
+share/java/classes/fastqc/org/apache/commons/math3/util/FastMathCalc.class
+share/java/classes/fastqc/org/apache/commons/math3/util/FastMathLiteralArrays.class
+share/java/classes/fastqc/org/apache/commons/math3/util/Incrementor$1.class
+share/java/classes/fastqc/org/apache/commons/math3/util/Incrementor$MaxCountExceededCallback.class
+share/java/classes/fastqc/org/apache/commons/math3/util/Incrementor.class
+share/java/classes/fastqc/org/apache/commons/math3/util/MathUtils.class
+share/java/classes/fastqc/org/apache/commons/math3/util/Precision.class
+share/java/classes/fastqc/org/apache/commons/math3/util/ResizableDoubleArray.class
+share/java/classes/fastqc/sam-1.103.jar
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Analysis/AnalysisListener.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Analysis/AnalysisQueue.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Analysis/AnalysisRunner.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Analysis/OfflineRunner.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Dialogs/AboutDialog$1.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Dialogs/AboutDialog.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Dialogs/FastQCTitlePanel$SmoothJLabel.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Dialogs/FastQCTitlePanel.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Dialogs/WelcomePanel.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/FastQCApplication$1.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/FastQCApplication.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/FastQCConfig.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/FastQCMenuBar.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/FileFilters/BAMFileFilter.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/FileFilters/CasavaFastQFileFilter.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/FileFilters/FastQFileFilter.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/FileFilters/GobyFileFilter.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/FileFilters/MappedBAMFileFilter.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/FileFilters/SequenceFileFilter.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Graphs/BaseGroup.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Graphs/LineGraph.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Graphs/QualityBoxPlot.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Graphs/TileGraph.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Help/HelpDialog.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Help/HelpIndexRoot$FileSorter.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Help/HelpIndexRoot.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Help/HelpPage.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Help/HelpPageDisplay$HelpEditor.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Help/HelpPageDisplay.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Help/HelpSearchPanel.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/AbstractQCModule.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/AdapterContent$Adapter.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/AdapterContent$ResultsTable.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/AdapterContent.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/BasicStats$ResultsTable.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/BasicStats.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/DuplicationLevel.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/GCModel/GCModel.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/GCModel/GCModelValue.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/KmerContent$Kmer.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/KmerContent$ResultsTable.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/KmerContent.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/ModuleConfig.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/ModuleFactory.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/NContent.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/OverRepresentedSeqs$OverrepresentedSeq.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/OverRepresentedSeqs$ResultsTable.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/OverRepresentedSeqs.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/PerBaseQualityScores.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/PerBaseSequenceContent.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/PerSequenceGCContent.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/PerSequenceQualityScores.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/PerTileQualityScores.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/QCModule.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/SequenceLengthDistribution.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Report/HTMLReportArchive.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Report/stylesheet.txt
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Resources/error.png
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Resources/fastqc_icon.png
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Resources/fastqc_icon.svg
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Resources/fastqc_icon_100.png
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Resources/tick.png
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Resources/warning.png
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Results/ResultsPanel$ModuleRenderer.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Results/ResultsPanel.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/BAMFile.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/Contaminant/Contaminant.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/Contaminant/ContaminantHit.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/Contaminant/ContaminentFinder.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/Fast5File.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/FastQFile.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/QualityEncoding/PhredEncoding.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/Sequence.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/SequenceFactory.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/SequenceFile.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/SequenceFileGroup.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/SequenceFormatException.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Statistics/NormalDistribution.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Statistics/PearsonCorrelation.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Utilities/CasavaBasename.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Utilities/HotColdColourGradient.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Utilities/ImageToBase64.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Utilities/MultiMemberGZIPInputStream.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Utilities/NameFormatException.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Utilities/NanoporeBasename.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Utilities/QualityCount.class
+share/java/classes/fastqc/uk/ac/babraham/FastQC/Utilities/RGB.class
Prev by Date: google-benchmark: Add NetBSD bits
Next by Date: swftools: Add reference to recent CVEs
Previous by Thread: google-benchmark: Add NetBSD bits
Next by Thread: swftools: Add reference to recent CVEs
Indexes:
Home | Main Index | Thread Index | Old Index