├── ChangeLog ├── LICENSE ├── README.md ├── data ├── CMakeLists.txt ├── GcCoverageFitTables │ └── Homo_sapiens.example1.tsv ├── Genomes │ ├── E_coli.fa │ ├── acgt.fa │ ├── acgt.fa.fai │ └── acgt │ │ ├── chr1.fa │ │ ├── chr1.fa.fai │ │ ├── chr2.fa │ │ ├── chr2.fa.fai │ │ ├── chr3.fa │ │ ├── chr3.fa.fai │ │ ├── chr4.fa │ │ ├── chr4.fa.fai │ │ └── genome_size.xml ├── HomopolymerQualityDropTables │ ├── DefaultHomopolymerQualityDropTable.tsv │ ├── HomopolymerQualityDropTableRelaxed33pc.tsv │ ├── HomopolymerQualityDropTableRelaxed50pc.tsv │ └── ZeroHomopolymerQualityDropTable.tsv ├── MismatchTables │ ├── DefaultHomopolymerIndelTable.tsv │ ├── DefaultMismatchTable.tsv │ ├── DefaultMismatchTableWithoutIndels.tsv │ ├── ZeroHomopolymerIndelTable.tsv │ └── ZeroMismatchTable.tsv ├── MotifQualityDropTables │ ├── DefaultMotifQualityDropTable.tsv │ └── ZeroMotifQualityDropTable.tsv ├── QualityTables │ ├── DefaultQQTable.tsv │ ├── DefaultQualityTable.barcode.length7.qval │ ├── DefaultQualityTable.notPF.qval │ ├── DefaultQualityTable.read1.length101.qval │ ├── DefaultQualityTable.read1.length251.qval │ ├── DefaultQualityTable.read2.length101.qval │ ├── DefaultQualityTable.read2.length251.qval │ ├── NewQualityTable.read1.length251.qtable2 │ ├── NewQualityTable.read2.length251.qtable2 │ ├── Q10QualityTable.length101.qval │ ├── Q14QualityTable.length101.qval │ ├── Q20QualityTable.length101.qval │ ├── Q30QualityTable.length101.qval │ ├── Q40QualityTable.length101.qval │ └── Q50QualityTable.length101.qval ├── RunInfo │ ├── RunInfo_PairedReads1x1Tiles.xml │ ├── RunInfo_PairedReads2x151Cycles1x1Tiles.xml │ ├── RunInfo_PairedReads2x251Cycles1x1Tiles.xml │ ├── RunInfo_PairedReads2x251Cycles2x2Tiles.xml │ ├── RunInfo_PairedReads2x251Cycles2x64Tiles.xml │ ├── RunInfo_PairedReads4x4Tiles.xml │ ├── RunInfo_PairedReadsBarcode1x1Tiles.xml │ ├── RunInfo_PairedReadsBarcode1x32Tiles.xml │ ├── RunInfo_PairedReadsBarcode8x32Tiles.xml │ ├── RunInfo_SingleRead1x1Tiles.xml │ └── RunInfo_SingleRead2x2Tiles.xml ├── TemplateLengthTables │ ├── DefaultTemplateLengthTable.tsv │ └── TemplateLengthTableFrom2x250Run.tsv ├── Variants │ ├── None.vcf │ ├── OneAtTelomere.vcf │ ├── OneOfEachType.vcf │ └── Stephens2009.vcf └── tests │ ├── Diploid.txt │ ├── Haploid.txt │ ├── Stress.txt │ ├── WholeDir.txt │ ├── applyVariants.txt │ ├── expectedOutputs │ ├── deletion.fa │ ├── diploid_conflict_deletion_translocation.fa │ ├── diploid_deletion.fa │ ├── diploid_duplication.fa │ ├── diploid_full_deletion.fa │ ├── diploid_indel.fa │ ├── diploid_insertion.fa │ ├── diploid_large_deletion.fa │ ├── diploid_reversed_events.fa │ ├── diploid_transloc_left.fa │ ├── diploid_transloc_right.fa │ ├── diploid_zygosity.fa │ ├── duplication.fa │ ├── full_deletion.fa │ ├── indel.fa │ ├── insertion.fa │ ├── inversion.fa │ ├── large_deletion.fa │ ├── reversed_events.fa │ ├── snp.fa │ ├── transloc_left.fa │ └── transloc_right.fa │ └── givenInputs │ ├── conflict_deletion_translocation.vcf │ ├── deletion.vcf │ ├── duplication.vcf │ ├── full_deletion.vcf │ ├── indel.vcf │ ├── insertion.vcf │ ├── inversion.vcf │ ├── large_deletion.vcf │ ├── reversed_events.vcf │ ├── snp.pl │ ├── transloc_left.vcf │ ├── transloc_right.vcf │ └── zygosity.vcf ├── doc └── html │ ├── Detailed+description+of+EAGLE+tools.html │ ├── EAGLE+-+Developers+portal.html │ ├── EAGLE+-+Enhanced+Artificial+Genome+Engine.html │ ├── EAGLE+-+FAQ.html │ ├── EAGLE+-+Installation+and+configuration+instructions.html │ ├── EAGLE+-+On+simulating+2x250+long+reads.html │ ├── EAGLE+-+Performance+and+resources+recommendations.html │ ├── EAGLE+-+Phase+2.html │ ├── EAGLE+-+Possible+conflicts+between+variants.html │ ├── EAGLE+-+Simulating+Reality+-+Metrics.html │ ├── EAGLE+-+Simulating+Reality+-+Strategy+-+observations-metrics-simulation.html │ ├── EAGLE+-+Simulating+Reality+-+from+reference+to+sample+genome.html │ ├── EAGLE+Data+Files.html │ ├── EAGLE+Features.html │ ├── EAGLE+Genome+Mutator+-+Architecture+and+Design.html │ ├── EAGLE+Phase+2+-+Analysis+Framework+-+Fragment+files.html │ ├── EAGLE+Phase+2+-+Analysis+Framework+-+Requirements.html │ ├── EAGLE+Phase+2+-+Analysis+Framework+-+Specifications.html │ ├── EAGLE+Phase+2+-+Analysis+Framework+-+Variants+Subtraction.html │ ├── EAGLE+Phase+2+-+Analysis+Framework.html │ ├── EAGLE+Phase+2+-+BaseSpace.html │ ├── EAGLE+Phase+2+-+Dissemination.html │ ├── EAGLE+Phase+2+-+Features+development.html │ ├── EAGLE+Phase+2+-+Simulating+Reality.html │ ├── EAGLE+Sequencer+Simulator+-+Architecture.html │ ├── EAGLE+Sequencer+Simulator+-+Design.html │ ├── EAGLE+Sequencer+Simulator+-+Specifications.html │ ├── EAGLE+System+Testing+Framework.html │ ├── EAGLE+Use+Case+-+2x250+realistic+Human+sequencing+simulation.html │ ├── EAGLE+Use+Case+-+Coverage+affected+by+GC+content.html │ ├── EAGLE+Use+Case+-+Gamma+distribution.html │ ├── EAGLE+Use+Case+-+Generating+BAM+files+for+visualisation+with+IGV.html │ ├── EAGLE+Use+Case+-+Interfacing+EAGLE+with+CASAVA.html │ ├── EAGLE+Use+Case+-+Long+reads+simulation.html │ ├── EAGLE+Use+Case+-+Refining+our+Human+sequencing+simulation+%28diploid+version%29.html │ ├── EAGLE+Use+Case+-+Simple+Metagenomics.html │ ├── EAGLE+Use+Case+-+Simulating+Copy+Number+Variations.html │ ├── EAGLE+Use+Case+-+Simulating+a+small+Run+Folder+from+PhiX.html │ ├── EAGLE+Use+Case+-+Simulating+a+typical+HiSeq+run+from+a+Human+sample+%28haploid+version%29.html │ ├── EAGLE+Use+Case+-+Simulating+a+uniform+reads+distribution+in+our+PhiX+simulation.html │ ├── EAGLE+Use+Case+-+Simulating+purity+in+tumour+samples+%28chr21+example%29.html │ ├── EAGLE+Use+Case+-+Simulating+purity.html │ ├── EAGLE+Use+Case+-+Simulating+tumour%2Bnormal+pairs.html │ ├── EAGLE+Use+Case+-+Using+a+different+template+length+distribution.html │ ├── attachments │ ├── 1708520 │ │ ├── 1638714.png │ │ ├── 1638715.png │ │ ├── 1638793.jpg │ │ ├── 1638795.jpg │ │ ├── 1638796.jpg │ │ ├── 1638797.jpg │ │ ├── 1638798.jpg │ │ └── 1638799.jpg │ ├── 1708522 │ │ └── 1638685.png │ ├── 1709470 │ │ ├── 1638716.dot │ │ ├── 1638717.png │ │ ├── 1638718.dot │ │ ├── 1638719.png │ │ └── 1638720.jpg │ ├── 1709472 │ │ ├── 1638721.jpg │ │ ├── 1638722.jpg │ │ ├── 1638724.jpg │ │ └── 1638727.png │ ├── 1709653 │ │ └── 1638728.jpg │ ├── 1709886 │ │ ├── 1638730.jpg │ │ ├── 1638734.png │ │ ├── 1638735.png │ │ ├── 1638742.png │ │ ├── 1638743.png │ │ ├── 1638744.png │ │ ├── 1638747.png │ │ ├── 1638748.png │ │ └── 1638749.pptx │ ├── 1711055 │ │ └── 1638829.jpg │ ├── 1711266 │ │ └── 1638821.jpg │ ├── 1711448 │ │ └── 1638811.jpg │ ├── 1711471 │ │ └── 1638813.jpg │ ├── 1712127 │ │ └── 1638861.jpg │ ├── 1712208 │ │ ├── 1638877.jpg │ │ ├── 1638886.jpg │ │ ├── 1638887.jpg │ │ └── 1638896.jpg │ ├── 1712626 │ │ └── 1638898.jpg │ ├── 3834889 │ │ └── 4128824.jpg │ ├── 3834925 │ │ ├── 4128825.jpg │ │ └── 4128826.jpg │ └── 3834936 │ │ └── 4128827.jpg │ ├── images │ └── icons │ │ ├── bullet_blue.gif │ │ └── grey_arrow_down.gif │ ├── index.html │ ├── index2.html │ └── styles │ └── site.css ├── redist └── beetl-1.0.tar.bz2 ├── src ├── CMakeLists.txt ├── CTestConfig.cmake ├── analysis │ ├── cpp │ │ └── add_translocations │ │ │ ├── AddTranslocations.cpp │ │ │ ├── AddTranslocations.h │ │ │ ├── HumanNCBI37_UCSCgaps.bed │ │ │ ├── Makefile │ │ │ ├── VcfVariant.cpp │ │ │ └── VcfVariant.h │ ├── makefiles │ │ └── tumour_normal.mk │ └── perl │ │ └── vcfGenerator.pl ├── bash │ ├── CMakeLists.txt │ ├── libexec │ │ ├── CMakeLists.txt │ │ ├── getBclBases.sh │ │ └── getFragmentInfo.sh │ └── test │ │ ├── common.sh │ │ ├── testDiploid.sh.in │ │ ├── testHaploid.sh.in │ │ ├── testStress.sh.in │ │ └── testWholeDir.sh.in ├── c++ │ ├── CMakeLists.txt │ ├── Doxyfile.in │ ├── bin │ │ ├── CMakeLists.txt │ │ ├── allocateFragments.cpp │ │ ├── applyVariants.cpp │ │ ├── compareVcf.cpp │ │ ├── createRunFolder.cpp │ │ ├── eagleAnalysis_bclAnalyser.cpp │ │ ├── eagleAnalysis_bclReaderTest.cpp │ │ └── eagleAnalysis_bigTableAnalyser.cpp │ ├── include │ │ ├── common │ │ │ ├── Exceptions.hh │ │ │ ├── FileSystem.hh │ │ │ ├── Logger.hh │ │ │ ├── Program.hh │ │ │ └── Semaphore.hh │ │ ├── genome │ │ │ ├── BamAdapters.hh │ │ │ ├── BamMetadata.hh │ │ │ ├── EnrichedFragment.hh │ │ │ ├── ErrorModelPlugin.hh │ │ │ ├── Event.hh │ │ │ ├── GcContent.hh │ │ │ ├── QualityModel.hh │ │ │ ├── ReadCluster.hh │ │ │ ├── Reference.hh │ │ │ ├── ReferenceToSample.hh │ │ │ ├── SharedFastaReference.hh │ │ │ ├── TmpFastaReader.hh │ │ │ └── VariantList.hh │ │ ├── io │ │ │ ├── Bam.hh │ │ │ ├── BamIndexer.hh │ │ │ ├── BamParserFilter.hh │ │ │ ├── Bcl.hh │ │ │ ├── BgzfCompressor.hh │ │ │ ├── Fasta.hh │ │ │ ├── Fastq.hh │ │ │ ├── RunInfo.hh │ │ │ ├── StorableBamAlignment.hh │ │ │ ├── Text.hh │ │ │ └── Vcf.hh │ │ ├── main │ │ │ ├── FragmentsAllocator.hh │ │ │ ├── FragmentsAllocatorOptions.hh │ │ │ ├── GenomeMutator.hh │ │ │ ├── GenomeMutatorOptions.hh │ │ │ ├── RunFolderGenerator.hh │ │ │ ├── RunFolderGeneratorOptions.hh │ │ │ ├── VcfComparator.hh │ │ │ └── VcfComparatorOptions.hh │ │ └── model │ │ │ ├── Contig.hh │ │ │ ├── Fragment.hh │ │ │ ├── FragmentLengthDist.hh │ │ │ ├── FragmentPosResolver.hh │ │ │ ├── Genotype.hh │ │ │ ├── IntervalGenerator.hh │ │ │ ├── Nucleotides.hh │ │ │ ├── PassFilter.hh │ │ │ ├── Phred.hh │ │ │ ├── SplitString.hh │ │ │ ├── Struct.hh │ │ │ ├── StructuralVariant.hh │ │ │ └── StructuralVariantType.hh │ ├── lib │ │ ├── CMakeLists.txt │ │ ├── common │ │ │ ├── CMakeLists.txt │ │ │ ├── Exceptions.cpp │ │ │ ├── FileSystem.cpp │ │ │ ├── Logger.cpp │ │ │ ├── Program.cpp │ │ │ ├── Semaphore.cpp │ │ │ ├── config.h.in │ │ │ └── cppunit │ │ │ │ ├── CMakeLists.txt │ │ │ │ ├── RegistryNames.txt │ │ │ │ ├── testExceptions.cpp │ │ │ │ ├── testExceptions.hh │ │ │ │ ├── testLogger.cpp │ │ │ │ └── testLogger.hh │ │ ├── genome │ │ │ ├── BamMetadata.cpp │ │ │ ├── CMakeLists.txt │ │ │ ├── EnrichedFragment.cpp │ │ │ ├── ErrorModelPlugin.cpp │ │ │ ├── Event.cpp │ │ │ ├── GcContent.cpp │ │ │ ├── QualityModel.cpp │ │ │ ├── ReadCluster.cpp │ │ │ ├── Reference.cpp │ │ │ ├── SharedFastaReference.cpp │ │ │ ├── TmpFastaReader.cpp │ │ │ ├── VariantList.cpp │ │ │ └── cppunit │ │ │ │ ├── CMakeLists.txt │ │ │ │ ├── RegistryNames.txt │ │ │ │ ├── testEnrichedFragment.cpp │ │ │ │ ├── testEnrichedFragment.hh │ │ │ │ ├── testVariantList.cpp │ │ │ │ └── testVariantList.hh │ │ ├── io │ │ │ ├── Bam.cpp │ │ │ ├── BamParserFilter.cpp │ │ │ ├── Bcl.cpp │ │ │ ├── BgzfCompressor.cpp │ │ │ ├── CMakeLists.txt │ │ │ ├── Fasta.cpp │ │ │ ├── Fastq.cpp │ │ │ ├── RunInfo.cpp │ │ │ ├── Text.cpp │ │ │ ├── Vcf.cpp │ │ │ └── cppunit │ │ │ │ ├── CMakeLists.txt │ │ │ │ ├── RegistryNames.txt │ │ │ │ ├── testBcl.cpp │ │ │ │ ├── testBcl.hh │ │ │ │ ├── testVcf.cpp │ │ │ │ └── testVcf.hh │ │ ├── main │ │ │ ├── CMakeLists.txt │ │ │ ├── FragmentsAllocator.cpp │ │ │ ├── FragmentsAllocatorOptions.cpp │ │ │ ├── GenomeMutator.cpp │ │ │ ├── GenomeMutatorOptions.cpp │ │ │ ├── RunFolderGenerator.cpp │ │ │ ├── RunFolderGeneratorOptions.cpp │ │ │ ├── VcfComparator.cpp │ │ │ └── VcfComparatorOptions.cpp │ │ └── model │ │ │ ├── CMakeLists.txt │ │ │ ├── Contig.cpp │ │ │ ├── Fragment.cpp │ │ │ ├── FragmentLengthDist.cpp │ │ │ ├── Genotype.cpp │ │ │ ├── IntervalGenerator.cpp │ │ │ ├── Nucleotides.cpp │ │ │ ├── Phred.cpp │ │ │ ├── Struct.cpp │ │ │ ├── StructuralVariant.cpp │ │ │ ├── StructuralVariantType.cpp │ │ │ └── cppunit │ │ │ ├── CMakeLists.txt │ │ │ ├── RegistryNames.txt │ │ │ ├── testContig.cpp │ │ │ ├── testContig.hh │ │ │ ├── testFragment.cpp │ │ │ ├── testFragment.hh │ │ │ ├── testGenotype.cpp │ │ │ ├── testGenotype.hh │ │ │ ├── testIntervalGenerator.cpp │ │ │ ├── testIntervalGenerator.hh │ │ │ ├── testPhred.cpp │ │ │ ├── testPhred.hh │ │ │ ├── testStructuralVariant.cpp │ │ │ └── testStructuralVariant.hh │ ├── libexec │ │ ├── CMakeLists.txt │ │ ├── analyseBam │ │ │ ├── BamAnalyser.cpp │ │ │ ├── BamAnalyser.hh │ │ │ ├── BamAnalyserOptions.cpp │ │ │ ├── BamAnalyserOptions.hh │ │ │ ├── CMakeLists.txt │ │ │ └── analyseBam.cpp │ │ ├── analyseFastq │ │ │ ├── CMakeLists.txt │ │ │ ├── FastqAnalyser.cpp │ │ │ ├── FastqAnalyser.hh │ │ │ ├── FastqAnalyserOptions.cpp │ │ │ ├── FastqAnalyserOptions.hh │ │ │ └── analyseFastq.cpp │ │ ├── canonical2segments │ │ │ ├── CMakeLists.txt │ │ │ ├── CanonicalToSegmentsConverter.cpp │ │ │ ├── CanonicalToSegmentsConverter.hh │ │ │ ├── CanonicalToSegmentsConverterOptions.cpp │ │ │ ├── CanonicalToSegmentsConverterOptions.hh │ │ │ └── canonical2segments.cpp │ │ ├── diffBam │ │ │ ├── BamDiff.cpp │ │ │ ├── BamDiff.hh │ │ │ ├── BamDiffOptions.cpp │ │ │ ├── BamDiffOptions.hh │ │ │ ├── CMakeLists.txt │ │ │ └── diffBam.cpp │ │ ├── fastaDump │ │ │ ├── CMakeLists.txt │ │ │ ├── FastaDumper.cpp │ │ │ ├── FastaDumper.hh │ │ │ ├── FastaDumperOptions.cpp │ │ │ ├── FastaDumperOptions.hh │ │ │ └── fastaDump.cpp │ │ ├── generateHomopolymerIndelVcf │ │ │ ├── CMakeLists.txt │ │ │ ├── HomopolymerIndelVcfGenerator.cpp │ │ │ ├── HomopolymerIndelVcfGenerator.hh │ │ │ ├── HomopolymerIndelVcfGeneratorOptions.cpp │ │ │ ├── HomopolymerIndelVcfGeneratorOptions.hh │ │ │ └── generateHomopolymerIndelVcf.cpp │ │ └── simulateSequencer │ │ │ ├── CMakeLists.txt │ │ │ ├── SequencerSimulator.cpp │ │ │ ├── SequencerSimulator.hh │ │ │ ├── SequencerSimulatorOptions.cpp │ │ │ ├── SequencerSimulatorOptions.hh │ │ │ └── simulateSequencer.cpp │ └── unittest │ │ ├── CMakeLists.txt │ │ ├── Helpers.hh │ │ ├── RegistryName.cpp │ │ ├── RegistryName.hh │ │ ├── check-source.sh │ │ └── cppunitTest.cpp ├── cmake │ ├── CTestCustom.cmake │ ├── boost.cmake │ ├── bootstrap │ │ ├── common.sh │ │ ├── installBoost.sh │ │ ├── installCmake.sh │ │ └── installLibzoo.sh │ ├── cppunit.cmake │ ├── cxxConfigure.cmake │ ├── cxxExecutable.cmake │ ├── cxxLibExec.cmake │ ├── cxxLibrary.cmake │ ├── globals.cmake │ ├── libzoo.cmake │ ├── macros.cmake │ ├── postInstall │ │ └── CMakeLists.txt │ ├── preInstall │ │ ├── CMakeLists.txt │ │ ├── checkTargetPathsWritable │ │ │ ├── CMakeLists.txt │ │ │ └── checkTargetPathWritable.cmake │ │ └── copyrightAndChanges │ │ │ └── CMakeLists.txt │ └── validation.cmake ├── configure ├── makefiles │ ├── CMakeLists.txt │ ├── assign.mk │ ├── common.mk │ ├── default.mk │ ├── defaultLane.mk │ └── default_forDistributedGenomeMutator.mk └── perl │ ├── CMakeLists.txt │ ├── bin │ ├── configureEAGLE.pl │ └── configureEAGLE_Normal+Tumour.pl │ ├── doxygen_dot_concat.pl │ ├── lib │ ├── CMakeLists.txt │ └── RunFolder │ │ ├── Config.pm │ │ └── RunInfo.pm │ └── libexec │ ├── CMakeLists.txt │ ├── analyseQualities.pl │ ├── applyCopyNumber.pl │ ├── combineSmallFasta.pl │ ├── convertVcfToGoodOldVcfFormat.pl │ ├── dbSnpGenotype2vcf.pl │ ├── decodeBamIndex.pl │ ├── generateHomopolymerQualityDropTable.pl │ ├── generateMismatchTable.pl │ ├── generateQualityTable.pl │ ├── mergeFragments.pl │ ├── mergeSampleGenomes.pl │ ├── scaleQualityTable.pl │ └── scaleQualityTable.qtable2.pl └── validation ├── CMakeLists.txt ├── Makefile.in ├── MakefileForTests.in └── TestConfig ├── test1.mk ├── test2.mk ├── test3.mk ├── test4.mk ├── test5.mk ├── test6.mk ├── test7.mk ├── 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