├── .classpath ├── .dockerignore ├── .gitattributes ├── .github └── workflows │ ├── docker.yml │ ├── docker_publish.yml │ └── maven.yml ├── .gitignore ├── .gitmodules ├── .project ├── .travis.yml ├── COPYING ├── Dockerfile ├── LICENSE ├── QuickStart.md ├── Readme.md ├── VIRUSBreakend_Readme.md ├── docker ├── Readme.md ├── run_cohort_from_csv.sh └── sample.csv ├── example ├── COLO829v003T.purple.sv.vcf ├── COLO829v003T.purple.sv.vcf.gz ├── DO52605T.purple.sv.vcf ├── ENCFF001TDO.bed ├── ENCFF356LFX.bed ├── ERR093636_virusbreakend_minimal_example.bam ├── ERR093636_virusbreakend_minimal_example_slower_fastq_input_R1.fq ├── ERR093636_virusbreakend_minimal_example_slower_fastq_input_R2.fq ├── annotate_most_likely_centromere.R ├── annotate_repeatmasker.sh ├── bedpe-export-example.R ├── chr12.1527326.DEL1024.bam ├── example.R1.fq ├── example.R2.fq ├── example_regions_of_interest.bed ├── hbv_sim.bam ├── simple-event-annotation.R ├── somatic-fusion-gene-candidates.R ├── torque_example.sh ├── virusbreakend-debian9-install-dependencies.sh └── wgEncodeDacMapabilityConsensusExcludable.bed ├── pom.xml ├── repo ├── jaligner │ └── jaligner │ │ ├── 1.0 │ │ ├── jaligner-1.0.jar │ │ ├── jaligner-1.0.jar.md5 │ │ ├── jaligner-1.0.jar.sha1 │ │ ├── jaligner-1.0.pom │ │ ├── jaligner-1.0.pom.md5 │ │ └── jaligner-1.0.pom.sha1 │ │ ├── maven-metadata.xml │ │ ├── maven-metadata.xml.md5 │ │ └── maven-metadata.xml.sha1 └── ssw │ └── ssw │ ├── 1.0 │ ├── ssw-1.0.jar │ ├── ssw-1.0.jar.md5 │ ├── ssw-1.0.jar.sha1 │ ├── ssw-1.0.pom │ ├── ssw-1.0.pom.md5 │ └── ssw-1.0.pom.sha1 │ ├── maven-metadata.xml │ ├── maven-metadata.xml.md5 │ └── maven-metadata.xml.sha1 ├── scripts ├── circos_export │ ├── bedpeToCircos.py │ ├── circos.sh │ └── dictToCircosKaryotype.py ├── cohort_analysis │ ├── 0_README.txt │ ├── 1_setup.sh │ ├── 2_generate_analysis_scripts.py │ ├── 3_run_scripts.sh │ ├── 4_cleanup.py │ ├── somatic_template.sh │ └── test_samples.csv ├── dev │ ├── assembly_timing_analysis.R │ ├── create_release.sh │ ├── debug_validate.sh │ ├── debugassembly.sh │ ├── diff_debugspammingiterator.sh │ ├── gridss_adjust_call_positions.R │ ├── gridsssanitycheck.R │ ├── metrics_approximation.R │ ├── metrics_approximation.sh │ ├── print_repeats.sh │ ├── regression_diff.R │ ├── setup_debug.sh │ └── setup_sanity_failure_debug.sh ├── gridss ├── gridss.config.R ├── gridss2_manuscript │ ├── CentromericSGLs.R │ ├── HG002_roc.R │ ├── anchorSupportSummary.R │ ├── breakendRepeat.R │ ├── calculate_probe_validation_counts.R │ ├── chain_length_fnr_impact.R │ ├── cohort_analysis.R │ ├── colo829.R │ ├── gen_sim.R │ ├── germline.R │ ├── gridss1_somatic_filter.R │ ├── gridss2_manuscript.Rproj │ ├── libbenchmark.R │ ├── patient_probe_single_breakend_repeat.R │ ├── patient_probe_validation.R │ ├── pcawg_direct_comparison.R │ ├── pcawg_svcn_consistency.R │ ├── probes.csv │ ├── sim.sh │ ├── sim_aggregate_results.sh │ ├── smallDupSignature.R │ └── vaf_consistency.R ├── gridss_annotate_vcf_kraken2 ├── gridss_annotate_vcf_repeatmasker ├── gridss_extract_overlapping_fragments ├── gridss_somatic_filter ├── libgridss.R ├── virusbreakend ├── virusbreakend-build └── virusbreakend_manuscript │ ├── Figure2_simulations.ai │ ├── figure1.ai │ ├── figure3.ai │ └── scripts │ ├── LC500247.1.fa │ ├── LC500247.1.fa.fai │ ├── MT783410.1.fa │ ├── MT783410.1.fa.fai │ ├── bwa │ ├── cleanup_gce.sh │ ├── ecoli_1.fq │ ├── ecoli_2.fq │ ├── gce_bucket_stream_virusbreakend.sh │ ├── gridss_annotate.sh │ ├── hartwig.R │ ├── hartwig_aggregate.sh │ ├── hmf_mapping_rate.sh │ ├── sim.R │ ├── sim.sh │ └── summarise_sim.sh └── src ├── main ├── c │ └── gridsstools │ │ ├── .gitattributes │ │ ├── .gitignore │ │ ├── Makefile.in │ │ ├── configure.ac │ │ ├── extractFragmentsToBam.c │ │ ├── extractFragmentsToFastq.c │ │ ├── fastq.c │ │ ├── fastq.h │ │ ├── gridsstools.c │ │ ├── install-sh │ │ ├── m4 │ │ └── ax_with_htslib.m4 │ │ └── unmappedSequencesToFastq.c ├── java │ ├── assfolder │ │ ├── OlcExporter.java │ │ ├── OverlapGraph.java │ │ ├── PositionalConstraints.java │ │ ├── Read.java │ │ ├── ReadOffset.java │ │ ├── ReadOverlapSuccessor.java │ │ └── SeedLookup.java │ ├── au │ │ └── edu │ │ │ └── wehi │ │ │ ├── idsv │ │ │ ├── AdapterHelper.java │ │ │ ├── AggregateEvidenceSource.java │ │ │ ├── AlleleFractionAnnotator.java │ │ │ ├── AssemblyAssociator.java │ │ │ ├── AssemblyAttributes.java │ │ │ ├── AssemblyEvidenceSource.java │ │ │ ├── AssemblyEvidenceSupport.java │ │ │ ├── AssemblyFactory.java │ │ │ ├── AssemblyIdGenerator.java │ │ │ ├── AttributeConverter.java │ │ │ ├── BedMergingCounter.java │ │ │ ├── BedpeMergingCounter.java │ │ │ ├── BreakendDirection.java │ │ │ ├── BreakendMaximalEvidenceCliqueIterator.java │ │ │ ├── BreakendSummary.java │ │ │ ├── BreakendSummaryWindowedSortingIterator.java │ │ │ ├── BreakpointSummary.java │ │ │ ├── CalledBreakpointPositionLookup.java │ │ │ ├── CoverageCalculationMethod.java │ │ │ ├── Defaults.java │ │ │ ├── DirectEvidenceWindowedSortingIterator.java │ │ │ ├── DirectedBreakpoint.java │ │ │ ├── DirectedEvidence.java │ │ │ ├── DirectedEvidenceBoundsAssertionIterator.java │ │ │ ├── DirectedEvidenceChromosomePairFilter.java │ │ │ ├── DirectedEvidenceDensityThrottlingIterator.java │ │ │ ├── DirectedEvidenceErrorCorrectingIterator.java │ │ │ ├── DirectedEvidenceIterator.java │ │ │ ├── DirectedEvidenceOrder.java │ │ │ ├── DirectedEvidenceScoreFilteringIterator.java │ │ │ ├── DiscordantReadPair.java │ │ │ ├── DynamicSAMSequenceDictionary.java │ │ │ ├── EvidenceIdentifierGenerator.java │ │ │ ├── EvidenceSource.java │ │ │ ├── EvidenceToCsv.java │ │ │ ├── FileSystemContext.java │ │ │ ├── FixedSizeReadPairConcordanceCalculator.java │ │ │ ├── FullReadExtractor.java │ │ │ ├── GcBiasAdjuster.java │ │ │ ├── GenomicProcessingContext.java │ │ │ ├── HashedEvidenceIdentifierGenerator.java │ │ │ ├── IdsvVariantContext.java │ │ │ ├── IdsvVariantContextBuilder.java │ │ │ ├── IndelEvidence.java │ │ │ ├── IndexedLookupFullReadExtractor.java │ │ │ ├── IndexedReadExtractor.java │ │ │ ├── IntegerLinearGenomicCoordinate.java │ │ │ ├── IntermediateFileUtil.java │ │ │ ├── IntervalCoverageAccumulator.java │ │ │ ├── IterativeSplitReadRealigner.java │ │ │ ├── LinearGenomicCoordinate.java │ │ │ ├── MaximalEvidenceCliqueIterator.java │ │ │ ├── NonReferenceReadPair.java │ │ │ ├── PaddedLinearGenomicCoordinate.java │ │ │ ├── PerChromosomeAggregateIterator.java │ │ │ ├── PercentageReadPairConcordanceCalculator.java │ │ │ ├── PrecomputedGcBiasAdjuster.java │ │ │ ├── ProcessingContext.java │ │ │ ├── ProgressLoggingDirectedEvidenceIterator.java │ │ │ ├── ProgressLoggingSAMRecordIterator.java │ │ │ ├── QueryIntervalUtil.java │ │ │ ├── ReadExtractor.java │ │ │ ├── ReadGcSummary.java │ │ │ ├── ReadPairConcordanceCalculator.java │ │ │ ├── ReferenceCoverageLookup.java │ │ │ ├── SAMEvidenceSource.java │ │ │ ├── SAMFlagReadPairConcordanceCalculator.java │ │ │ ├── SAMRecordChangeTracker.java │ │ │ ├── SAMRecordCoordinateOnlyComparator.java │ │ │ ├── SAMRecordDensityThrottlingIterator.java │ │ │ ├── SanityCheckFailureException.java │ │ │ ├── SequentialCoverageAnnotator.java │ │ │ ├── SequentialCoverageThreshold.java │ │ │ ├── SequentialEvidenceAllocator.java │ │ │ ├── SequentialEvidenceAnnotator.java │ │ │ ├── SequentialIdGenerator.java │ │ │ ├── SequentialReferenceCoverageLookup.java │ │ │ ├── SequentialSAMRecordFactoryBase.java │ │ │ ├── SingleReadEvidence.java │ │ │ ├── SoftClipEvidence.java │ │ │ ├── SplitReadEvidence.java │ │ │ ├── SplitReadHelper.java │ │ │ ├── SplitReadRealigner.java │ │ │ ├── StreamingSplitReadRealigner.java │ │ │ ├── StringEvidenceIdentifierGenerator.java │ │ │ ├── StructuralVariationCallBuilder.java │ │ │ ├── UnmappedMateReadPair.java │ │ │ ├── VariantCallIterator.java │ │ │ ├── VariantCaller.java │ │ │ ├── VariantContextDirectedBreakpoint.java │ │ │ ├── VariantContextDirectedEvidence.java │ │ │ ├── VariantContextRepeatMaskerAnnotator.java │ │ │ ├── VariantContextWindowedSortingIterator.java │ │ │ ├── VariantIdGenerator.java │ │ │ ├── VcfBreakendSummary.java │ │ │ ├── VcfBreakendToBedpe.java │ │ │ ├── VcfBreakendToReadPair.java │ │ │ ├── alignment │ │ │ │ ├── Aligner.java │ │ │ │ ├── AlignerFactory.java │ │ │ │ ├── Alignment.java │ │ │ │ ├── BreakpointHomology.java │ │ │ │ ├── BwaAligner.java │ │ │ │ ├── BwaStreamingAligner.java │ │ │ │ ├── ExternalProcessFastqAligner.java │ │ │ │ ├── ExternalProcessHelper.java │ │ │ │ ├── ExternalProcessStreamingAligner.java │ │ │ │ ├── FastqAligner.java │ │ │ │ ├── GKLAligner.java │ │ │ │ ├── JAlignerAligner.java │ │ │ │ ├── SequentialExecutionFastqAligner.java │ │ │ │ ├── SmithWatermanFastqAligner.java │ │ │ │ ├── SmithWatermanStreamingAligner.java │ │ │ │ ├── SswJniAligner.java │ │ │ │ ├── StreamingAligner.java │ │ │ │ └── StreamingAlignerIterator.java │ │ │ ├── bed │ │ │ │ ├── BedWriter.java │ │ │ │ ├── BedpeIterator.java │ │ │ │ ├── BedpeRecord.java │ │ │ │ ├── BedpeWriter.java │ │ │ │ └── IntervalBed.java │ │ │ ├── configuration │ │ │ │ ├── AssemblyConfiguration.java │ │ │ │ ├── DownsamplingConfiguration.java │ │ │ │ ├── ErrorCorrectionConfiguration.java │ │ │ │ ├── GridssConfiguration.java │ │ │ │ ├── PositionalAssemblyConfiguration.java │ │ │ │ ├── ScoringConfiguration.java │ │ │ │ ├── SoftClipConfiguration.java │ │ │ │ ├── VariantCallingConfiguration.java │ │ │ │ └── VisualisationConfiguration.java │ │ │ ├── debruijn │ │ │ │ ├── ContigKmerCounter.java │ │ │ │ ├── DeBruijnGraph.java │ │ │ │ ├── DeBruijnGraphBase.java │ │ │ │ ├── DeBruijnGraphUtil.java │ │ │ │ ├── DeBruijnNodeBase.java │ │ │ │ ├── DeBruijnPathGraph.java │ │ │ │ ├── DeBruijnPathNode.java │ │ │ │ ├── DeBruijnPathNodeFactory.java │ │ │ │ ├── DeBruijnSequenceGraphNode.java │ │ │ │ ├── DeBruijnSequenceGraphNodeUtil.java │ │ │ │ ├── HighestWeightSimilarPath.java │ │ │ │ ├── KmerEncodingHelper.java │ │ │ │ ├── KmerSequenceGraphNode.java │ │ │ │ ├── PackedKmerList.java │ │ │ │ ├── PackedSequence.java │ │ │ │ ├── ReadErrorCorrector.java │ │ │ │ ├── ReadKmer.java │ │ │ │ ├── ReadKmerIterable.java │ │ │ │ ├── VariantEvidence.java │ │ │ │ └── positional │ │ │ │ │ ├── AggregateNodeIterator.java │ │ │ │ │ ├── AssemblyThresholdReachedException.java │ │ │ │ │ ├── Contig.java │ │ │ │ │ ├── ContigCaller.java │ │ │ │ │ ├── EvidenceTracker.java │ │ │ │ │ ├── ImmutableKmerNode.java │ │ │ │ │ ├── KmerEvidence.java │ │ │ │ │ ├── KmerNode.java │ │ │ │ │ ├── KmerNodeGraph.java │ │ │ │ │ ├── KmerNodeUtil.java │ │ │ │ │ ├── KmerPathNode.java │ │ │ │ │ ├── KmerPathNodeBasePath.java │ │ │ │ │ ├── KmerPathNodeKmerNode.java │ │ │ │ │ ├── KmerPathNodePath.java │ │ │ │ │ ├── KmerPathSubnode.java │ │ │ │ │ ├── KmerSupportNode.java │ │ │ │ │ ├── MemoizedContigCaller.java │ │ │ │ │ ├── MemoizedTraverse.java │ │ │ │ │ ├── MisassemblyFixer.java │ │ │ │ │ ├── NonReferenceContigAssembler.java │ │ │ │ │ ├── PathNodeIterator.java │ │ │ │ │ ├── PathSimplificationIterator.java │ │ │ │ │ ├── PositionalAssembler.java │ │ │ │ │ ├── SupportNodeIterator.java │ │ │ │ │ ├── TraversalNode.java │ │ │ │ │ └── optimiseddatastructures │ │ │ │ │ ├── IntegerIntervalSet.java │ │ │ │ │ ├── KmerIntervalLookup.java │ │ │ │ │ ├── KmerNodeAggregatorSnapshotByEndPriorityQueue.java │ │ │ │ │ ├── KmerNodeByFirstStartEndKmerReferenceNavigablePartiallyOrderedSet.java │ │ │ │ │ ├── KmerNodeByFirstStartPriorityQueue.java │ │ │ │ │ ├── KmerNodeByLastEndPriorityQueue.java │ │ │ │ │ ├── KmerNodeByLastEndStartKmerReferenceNavigablePartiallyOrderedSet.java │ │ │ │ │ ├── KmerNodeByLastKmerIntervalLookup.java │ │ │ │ │ ├── KmerNodeNonOverlappingLookup.java │ │ │ │ │ ├── SortedByPosition.java │ │ │ │ │ ├── SortedByPositionArrayBackedNavigablePartiallyOrderedSet.java │ │ │ │ │ ├── SortedByPositionCollection.java │ │ │ │ │ ├── SortedByPositionUnorderedWithinPosition.java │ │ │ │ │ ├── TraversalNodeByLastEndKmerSortedSet.java │ │ │ │ │ ├── TraversalNodeByPathFirstStartEndSubnodeSortedSet.java │ │ │ │ │ └── TraversalNodeByScoreDescPathFirstIdentity.java │ │ │ ├── graph │ │ │ │ ├── DirectedAcyclicGraph.java │ │ │ │ ├── DirectedGraph.java │ │ │ │ ├── MaximumCliqueIntervalGraph.java │ │ │ │ ├── PathGraph.java │ │ │ │ ├── PathNode.java │ │ │ │ ├── PathNodeBaseFactory.java │ │ │ │ ├── PathNodeFactory.java │ │ │ │ ├── RectangleGraphMaximalCliqueCalculator.java │ │ │ │ ├── RectangleGraphMaximalCliqueIterator.java │ │ │ │ ├── RectangleGraphNode.java │ │ │ │ ├── RectangleGraphNodeMergingIterator.java │ │ │ │ ├── ScalingHelper.java │ │ │ │ ├── WeightedDirectedGraph.java │ │ │ │ ├── WeightedSequenceGraphNode.java │ │ │ │ └── WeightedSequenceGraphNodeUtil.java │ │ │ ├── kraken │ │ │ │ ├── AnnotateKraken.java │ │ │ │ ├── KrakenClassification.java │ │ │ │ ├── KrakenClassificationChecker.java │ │ │ │ ├── KrakenKmerClassification.java │ │ │ │ ├── KrakenParser.java │ │ │ │ ├── KrakenReportLine.java │ │ │ │ └── SeqIdToTaxIdMap.java │ │ │ ├── metrics │ │ │ │ ├── IdsvSamFileMetrics.java │ │ │ │ └── IdsvSamFileMetricsCollector.java │ │ │ ├── model │ │ │ │ ├── EmpiricalLlrModel.java │ │ │ │ ├── EmpiricalReferenceLikelihoodModel.java │ │ │ │ ├── ExclusionModel.java │ │ │ │ ├── FastEmpiricalReferenceLikelihoodModel.java │ │ │ │ ├── MapqModel.java │ │ │ │ ├── Models.java │ │ │ │ ├── ReadCountModel.java │ │ │ │ ├── ReadNameWeightedModel.java │ │ │ │ └── VariantScoringModel.java │ │ │ ├── ncbi │ │ │ │ ├── MinimalTaxonomyNode.java │ │ │ │ ├── TaxonomyHelper.java │ │ │ │ ├── TaxonomyLevel.java │ │ │ │ └── TaxonomyNode.java │ │ │ ├── picard │ │ │ │ ├── BufferedReferenceSequenceFile.java │ │ │ │ ├── InMemoryReferenceSequenceFile.java │ │ │ │ ├── ReferenceLookup.java │ │ │ │ ├── SynchronousReferenceLookupAdapter.java │ │ │ │ └── TwoBitBufferedReferenceSequenceFile.java │ │ │ ├── repeatmasker │ │ │ │ ├── AnnotateRepeatMasker.java │ │ │ │ ├── RepeatAlignmentInformation.java │ │ │ │ ├── RepeatAlignmentSummaryInformation.java │ │ │ │ ├── RepeatMaskerBEDCodec.java │ │ │ │ ├── RepeatMaskerCodec.java │ │ │ │ └── RepeatMaskerFeature.java │ │ │ ├── sam │ │ │ │ ├── ChimericAlignment.java │ │ │ │ ├── CigarUtil.java │ │ │ │ ├── NmTagIterator.java │ │ │ │ ├── SAMFileHeaderUtil.java │ │ │ │ ├── SAMFileUtil.java │ │ │ │ ├── SAMRecordCigarCleaningIterator.java │ │ │ │ ├── SAMRecordEndCoordinateComparator.java │ │ │ │ ├── SAMRecordMateCoordinateComparator.java │ │ │ │ ├── SAMRecordUtil.java │ │ │ │ └── SamTags.java │ │ │ ├── sim │ │ │ │ ├── Fragment.java │ │ │ │ ├── FragmentedChromosome.java │ │ │ │ ├── GenerateChromothripsis.java │ │ │ │ ├── GenerateSimpleVariants.java │ │ │ │ ├── RandomBaseGenerator.java │ │ │ │ ├── RepeatFragmentedChromosome.java │ │ │ │ ├── RepeatMaskerRepeat.java │ │ │ │ ├── SequentialVariantPlacer.java │ │ │ │ ├── SimpleVariantChromosome.java │ │ │ │ ├── SimulatedChromosome.java │ │ │ │ └── SimulationGenerator.java │ │ │ ├── util │ │ │ │ ├── AlgorithmRuntimeSafetyLimitExceededException.java │ │ │ │ ├── ArrayHelper.java │ │ │ │ ├── AsyncBufferedIterator.java │ │ │ │ ├── AutoClosingIterator.java │ │ │ │ ├── AutoClosingMergedIterator.java │ │ │ │ ├── BatchingIterator.java │ │ │ │ ├── BufferedIterator.java │ │ │ │ ├── CachedEnumeratedIntegerDistribution.java │ │ │ │ ├── CollectionUtil.java │ │ │ │ ├── CountingIterator.java │ │ │ │ ├── DebugSpammingIterator.java │ │ │ │ ├── DensityThrottlingIterator.java │ │ │ │ ├── DeterministicIterators.java │ │ │ │ ├── DuplicatingIterable.java │ │ │ │ ├── FileHelper.java │ │ │ │ ├── FilenameUtil.java │ │ │ │ ├── FlatMapIterator.java │ │ │ │ ├── GroupingIterator.java │ │ │ │ ├── IntervalAccumulator.java │ │ │ │ ├── IntervalUtil.java │ │ │ │ ├── MathUtil.java │ │ │ │ ├── MessageThrottler.java │ │ │ │ ├── ParallelTransformIterator.java │ │ │ │ ├── RangeUtil.java │ │ │ │ ├── SequenceUtil.java │ │ │ │ ├── SlidingWindowIntervalAccumulator.java │ │ │ │ ├── SlidingWindowList.java │ │ │ │ ├── SubsetToMissing.java │ │ │ │ ├── UngroupingIterator.java │ │ │ │ └── WindowedSortingIterator.java │ │ │ ├── validation │ │ │ │ ├── BreakpointFilterTracker.java │ │ │ │ ├── OrderAssertingIterator.java │ │ │ │ ├── PairedEvidenceTracker.java │ │ │ │ └── TruthAnnotator.java │ │ │ ├── vcf │ │ │ │ ├── GridssVcfConstants.java │ │ │ │ ├── InsertedSequenceAnnotator.java │ │ │ │ ├── PassFiltersIterator.java │ │ │ │ ├── SvType.java │ │ │ │ ├── VcfFileUtil.java │ │ │ │ ├── VcfFilter.java │ │ │ │ ├── VcfFormatAttributes.java │ │ │ │ ├── VcfInfoAttributes.java │ │ │ │ ├── VcfStructuralVariantHeaderLines.java │ │ │ │ └── VcfSvConstants.java │ │ │ └── visualisation │ │ │ │ ├── AssemblyTelemetry.java │ │ │ │ ├── BufferTracker.java │ │ │ │ ├── DeBruijnGraphExporter.java │ │ │ │ ├── DeBruijnPathGraphExporter.java │ │ │ │ ├── DynamicDeBruijnPathGraphGexfExporter.java │ │ │ │ ├── GexfHelper.java │ │ │ │ ├── NodeTraversalTracker.java │ │ │ │ ├── NontrackingSubgraphTracker.java │ │ │ │ ├── PositionalDeBruijnGraphTracker.java │ │ │ │ ├── PositionalExporter.java │ │ │ │ ├── StateTracker.java │ │ │ │ ├── StaticDeBruijnPathGraphGexfExporter.java │ │ │ │ ├── SubgraphAssemblyAlgorithmTracker.java │ │ │ │ ├── TimeoutNodeTraversalTracker.java │ │ │ │ ├── TrackedBuffer.java │ │ │ │ └── TrackedState.java │ │ │ └── validation │ │ │ ├── BamToBed.java │ │ │ ├── BedpeDeletion.java │ │ │ ├── LongReadSupportFinder.java │ │ │ ├── LongReadSupportLevel.java │ │ │ └── ValidateDeletions.java │ ├── gridss │ │ ├── AllocateEvidence.java │ │ ├── AnnotateAlleleFraction.java │ │ ├── AnnotateInexactHomology.java │ │ ├── AnnotateInexactHomologyBedpe.java │ │ ├── AnnotateInsertedSequence.java │ │ ├── AnnotateReferenceCoverage.java │ │ ├── AnnotateVariants.java │ │ ├── AssembleBreakends.java │ │ ├── CallVariants.java │ │ ├── CollectGridssMetricsAndExtractSVReads.java │ │ ├── ComputeCoverage.java │ │ ├── ComputeSamTags.java │ │ ├── Defaults.java │ │ ├── DumpReadSupport.java │ │ ├── Echo.java │ │ ├── ExtractFragmentsToFastq.java │ │ ├── ExtractSVReads.java │ │ ├── GeneratePonBedpe.java │ │ ├── IdentifyVariants.java │ │ ├── InsertedSequencesToFasta.java │ │ ├── PrepareReference.java │ │ ├── PreprocessForBreakendAssembly.java │ │ ├── ReadsToBedpe.java │ │ ├── SanityCheckEvidence.java │ │ ├── SoftClipsToSplitReads.java │ │ ├── SyntheticDelDupSimulator.java │ │ ├── VirusBreakendFilter.java │ │ ├── analysis │ │ │ ├── CigarDetailMetrics.java │ │ │ ├── CigarSizeDistribution.java │ │ │ ├── CollectCigarMetrics.java │ │ │ ├── CollectFragmentGCMetrics.java │ │ │ ├── CollectGridssMetrics.java │ │ │ ├── CollectIdsvMetrics.java │ │ │ ├── CollectMapqMetrics.java │ │ │ ├── CollectTagMetrics.java │ │ │ ├── GcMetrics.java │ │ │ ├── GcMetricsCollector.java │ │ │ ├── IdsvMetrics.java │ │ │ ├── InsertSizeDistribution.java │ │ │ ├── MapqMetrics.java │ │ │ ├── MapqMetricsCollector.java │ │ │ ├── ReportThresholdCoverage.java │ │ │ └── TagSummaryMetrics.java │ │ ├── cmdline │ │ │ ├── ByReadNameSinglePassSamProgram.java │ │ │ ├── CommandLineProgramHelper.java │ │ │ ├── FullEvidenceCommandLineProgram.java │ │ │ ├── GcSinglePassSamProgram.java │ │ │ ├── MultipleSamFileCommandLineProgram.java │ │ │ ├── ProcessStructuralVariantReadsCommandLineProgram.java │ │ │ ├── ReferenceCommandLineProgram.java │ │ │ ├── VcfTransformCommandLineProgram.java │ │ │ └── programgroups │ │ │ │ ├── Assembly.java │ │ │ │ ├── Benchmarking.java │ │ │ │ ├── DataCleaning.java │ │ │ │ ├── DataConversion.java │ │ │ │ ├── Metrics.java │ │ │ │ └── VariantCalling.java │ │ ├── filter │ │ │ ├── ClippedReadFilter.java │ │ │ ├── FixedFilter.java │ │ │ ├── IndelReadFilter.java │ │ │ ├── OneEndAnchoredReadFilter.java │ │ │ ├── ReadPairConcordanceFilter.java │ │ │ ├── SplitReadFilter.java │ │ │ └── UnionAggregateFilter.java │ │ ├── kraken │ │ │ ├── AnnotateVariantsKraken.java │ │ │ ├── ExtractBestViralReference.java │ │ │ ├── IdentifyViralTaxa.java │ │ │ └── SubsetToTaxonomy.java │ │ └── repeatmasker │ │ │ └── AnnotateVariantsRepeatMasker.java │ ├── htsjdk │ │ └── samtools │ │ │ ├── BAMFileReader.java │ │ │ ├── BAMRecordCodec.java │ │ │ ├── Defaults.java │ │ │ ├── SAMUtils.java │ │ │ ├── fastq │ │ │ └── BasicFastqWriter.java │ │ │ └── util │ │ │ ├── AsyncBlockCompressedInputStream.java │ │ │ ├── AsyncReadTaskRunner.java │ │ │ ├── BlockCompressedInputStream.java │ │ │ ├── IOUtil.java │ │ │ └── RecyclingSupplier.java │ ├── picard │ │ └── analysis │ │ │ └── SinglePassSamProgram.java │ └── scambler │ │ ├── Overlap.java │ │ ├── OverlapLookup.java │ │ ├── Poc.java │ │ ├── Read.java │ │ ├── SgEdge.java │ │ ├── SgNode.java │ │ ├── StreamingStringGraphIterator.java │ │ └── StringGraphTransitiveCompressor.java ├── r │ ├── filter-hc.R │ ├── filter.R │ ├── germline_plots.R │ └── plots.R └── resources │ ├── gridss.properties │ ├── gridss │ └── analysis │ │ └── mapqHistogram.R │ └── libsswjni.so └── test ├── java ├── assfolder │ ├── OlcExporterTest.java │ ├── OverlapGraphTest.java │ ├── ReadOverlapSuccessorTest.java │ └── SeedLookupTest.java ├── au │ └── edu │ │ └── wehi │ │ ├── BedpeMergingCounterTest.java │ │ ├── VirusbreakenddbTests.java │ │ ├── idsv │ │ ├── AdapterHelperTest.java │ │ ├── AlleleFractionAnnotatorTest.java │ │ ├── AssemblyAttributesTest.java │ │ ├── AssemblyEvidenceSourceTest.java │ │ ├── AssemblyFactoryTest.java │ │ ├── AttributeConverterTest.java │ │ ├── BedMergingCounterTest.java │ │ ├── BreakendMaximalEvidenceCliqueIteratorTest.java │ │ ├── BreakendSummaryTest.java │ │ ├── BreakpointSummaryTest.java │ │ ├── DirectEvidenceWindowedSortingIteratorTest.java │ │ ├── DirectedEvidenceErrorCorrectingIteratorTest.java │ │ ├── DirectedEvidenceIteratorTest.java │ │ ├── DirectedEvidenceOrderTest.java │ │ ├── DiscordantReadPairTest.java │ │ ├── DynamicSAMSequenceDictionaryTest.java │ │ ├── EColiTests.java │ │ ├── EvidenceIdentifierGeneratorTest.java │ │ ├── FileSystemContextTest.java │ │ ├── FullReadExtractorTest.java │ │ ├── HashedEvidenceIdentifierGeneratorTest.java │ │ ├── Hg19Tests.java │ │ ├── Hg38Tests.java │ │ ├── IdsvVariantContextBuilderTest.java │ │ ├── IdsvVariantContextTest.java │ │ ├── IndelEvidenceTest.java │ │ ├── IntermediateFilesTest.java │ │ ├── IterativeSplitReadRealignerTest.java │ │ ├── LinuxTests.java │ │ ├── Manual.java │ │ ├── MaximalEvidenceCliqueIteratorTest.java │ │ ├── MockDirectedBreakpoint.java │ │ ├── MockDirectedEvidence.java │ │ ├── NonReferenceReadPairTest.java │ │ ├── PaddedLinearGenomicCoordinateTest.java │ │ ├── PerChromosomeAggregateIteratorTest.java │ │ ├── PrecomputedGcBiasAdjusterTest.java │ │ ├── ProgressLoggingSAMRecordIteratorTest.java │ │ ├── ReadPairConcordanceCalculatorTest.java │ │ ├── ReferenceTests.java │ │ ├── SAMEvidenceSourceTest.java │ │ ├── SAMFlagReadPairConcordanceCalculatorTest.java │ │ ├── SAMRecordAssemblyEvidenceTest.java │ │ ├── SAMRecordChangeTrackerTest.java │ │ ├── SAMRecordSummaryTest.java │ │ ├── SequentialCoverageAnnotatorTest.java │ │ ├── SequentialCoverageThresholdTest.java │ │ ├── SequentialEvidenceAllocatorTest.java │ │ ├── SequentialEvidenceAnnotatorTest.java │ │ ├── SequentialReferenceCoverageLookupTest.java │ │ ├── SingleReadEvidenceTest.java │ │ ├── SoftClipEvidenceTest.java │ │ ├── SplitReadEvidenceTest.java │ │ ├── SplitReadHelperTest.java │ │ ├── SplitReadRealignerTest.java │ │ ├── StreamingSplitReadRealignerTest.java │ │ ├── StringEvidenceIdentifierGeneratorTest.java │ │ ├── StructuralVariationCallBuilderTest.java │ │ ├── TestHelper.java │ │ ├── TestHelperTest.java │ │ ├── UnmappedMateReadPairTest.java │ │ ├── VariantCallIteratorTest.java │ │ ├── VariantCallerTest.java │ │ ├── VariantContextDirectedBreakpointTest.java │ │ ├── VariantContextDirectedEvidenceTest.java │ │ ├── VariantContextRepeatMaskerAnnotatorTest.java │ │ ├── VcfBreakendSummaryTest.java │ │ ├── VcfBreakendToBedpeTest.java │ │ ├── VcfBreakendToReadPairTest.java │ │ ├── alignment │ │ │ ├── AlignerFactoryTest.java │ │ │ ├── AlignmentHelperTest.java │ │ │ ├── BreakpointHomologyTest.java │ │ │ ├── BwaAlignerTest.java │ │ │ ├── BwaStreamingAlignerTest.java │ │ │ ├── ExternalAlignerTests.java │ │ │ ├── ExternalProcessStreamingAlignerTest.java │ │ │ ├── GKLAlignerTest.java │ │ │ ├── JAlignerAlignerTest.java │ │ │ ├── JniAlignerTests.java │ │ │ ├── SmithWatermanAlignerTest.java │ │ │ ├── SswJniAlignerTest.java │ │ │ └── StubFastqAligner.java │ │ ├── bed │ │ │ ├── BedpeWriterTest.java │ │ │ ├── IntervalBedTest.java │ │ │ └── RepeatMaskerBEDCodecTest.java │ │ ├── configuration │ │ │ └── VariantCallingConfigurationTest.java │ │ ├── debruijn │ │ │ ├── ContigCategorySupportHelperTest.java │ │ │ ├── ContigKmerCounterTest.java │ │ │ ├── DeBruijnNodeBaseTest.java │ │ │ ├── DeBruijnPathGraphTest.java │ │ │ ├── DeBruijnSequenceGraphNodeUtilTest.java │ │ │ ├── KmerEncodingHelperTest.java │ │ │ ├── PackedKmerListTest.java │ │ │ ├── PackedSequenceTest.java │ │ │ ├── ReadErrorCorrectorTest.java │ │ │ ├── ReadKmerIterableTest.java │ │ │ ├── VariantEvidenceTest.java │ │ │ └── positional │ │ │ │ ├── AggregateNodeIteratorTest.java │ │ │ │ ├── ContigCallerTest.java │ │ │ │ ├── EvidenceTrackerTest.java │ │ │ │ ├── KmerEvidenceTest.java │ │ │ │ ├── KmerPathNodePathTest.java │ │ │ │ ├── KmerPathNodeTest.java │ │ │ │ ├── KmerPathSubnodeTest.java │ │ │ │ ├── MemoizedContigCallerTest.java │ │ │ │ ├── MemoizedTraverseTest.java │ │ │ │ ├── NonReferenceContigAssemblerTest.java │ │ │ │ ├── PathNodeIteratorTest.java │ │ │ │ ├── PathSimplificationIteratorTest.java │ │ │ │ ├── PositionalAssemblerTest.java │ │ │ │ ├── PositionalContigCategorySupportHelperTest.java │ │ │ │ ├── SupportNodeIteratorTest.java │ │ │ │ ├── TraversalNodeTest.java │ │ │ │ └── optimiseddatastructures │ │ │ │ ├── IntegerIntervalSetTest.java │ │ │ │ ├── KmerNodeByFirstKmerIntervalLookupTest.java │ │ │ │ ├── KmerNodeByFirstStartEndKmerReferenceNavigablePartiallyOrderedSetTest.java │ │ │ │ ├── KmerNodeByFirstStartPriorityQueueTest.java │ │ │ │ ├── KmerNodeNonOverlappingLookupTest.java │ │ │ │ └── TraversalNodeByScoreDescPathFirstIdentityTest.java │ │ ├── graph │ │ │ ├── MaximumCliqueIntervalGraphTest.java │ │ │ ├── PathGraphTest.java │ │ │ ├── PathNodeTest.java │ │ │ ├── RectangleGraphMaximalCliqueCalculatorTest.java │ │ │ └── WeightedSequenceGraphNodeUtilTest.java │ │ ├── kraken │ │ │ ├── KrakenClassificationCheckerTest.java │ │ │ ├── KrakenClassificationTest.java │ │ │ └── KrakenParserTest.java │ │ ├── metrics │ │ │ ├── IdsvSamFileMetricsCollectorTest.java │ │ │ └── IdsvSamFileMetricsTest.java │ │ ├── model │ │ │ ├── EmpiricalReferenceLikelihoodModelTest.java │ │ │ ├── MapqModelTest.java │ │ │ ├── ModelsTest.java │ │ │ ├── ReadCountModelTest.java │ │ │ ├── ReadNameWeightedModelTest.java │ │ │ └── ScoringComparisonTest.java │ │ ├── ncbi │ │ │ └── TaxonomyHelperTest.java │ │ ├── picard │ │ │ ├── BufferedReferenceSequenceFileTest.java │ │ │ ├── InMemoryReferenceSequenceFileTest.java │ │ │ ├── ReferenceLookupTest.java │ │ │ ├── SynchronousReferenceLookupAdapterTest.java │ │ │ └── TwoBitBufferedReferenceSequenceFileTest.java │ │ ├── repeatmasker │ │ │ └── RepeatMaskerCodecTest.java │ │ ├── sam │ │ │ ├── ChimericAlignmentTest.java │ │ │ ├── CigarUtilTest.java │ │ │ ├── SAMFileUtilTest.java │ │ │ ├── SAMRecordCigarCleaningIteratorTest.java │ │ │ └── SAMRecordUtilTest.java │ │ ├── sim │ │ │ ├── SequentialVariantPlacerTest.java │ │ │ └── SimpleVariantChromosomeTest.java │ │ ├── util │ │ │ ├── ArrayHelperTest.java │ │ │ ├── AsyncBufferedIteratorTest.java │ │ │ ├── AutoClosingIteratorTest.java │ │ │ ├── AutoClosingMergedIteratorTest.java │ │ │ ├── BatchingIteratorTest.java │ │ │ ├── BufferedIteratorTest.java │ │ │ ├── DensityThrottlingIteratorTest.java │ │ │ ├── DuplicatingIterableTest.java │ │ │ ├── ErrorIterator.java │ │ │ ├── FileHelperTest.java │ │ │ ├── FilenameUtilTest.java │ │ │ ├── FlatMapIteratorTest.java │ │ │ ├── GroupingIteratorTest.java │ │ │ ├── IntervalAccumulatorTest.java │ │ │ ├── IntervalUtilTest.java │ │ │ ├── MathUtilTest.java │ │ │ ├── MessageThrottlerTest.java │ │ │ ├── ParallelTransformIteratorTest.java │ │ │ ├── RangeUtilTest.java │ │ │ ├── SequenceUtilTest.java │ │ │ ├── SlidingWindowIntervalAccumulatorTest.java │ │ │ ├── SlidingWindowListTest.java │ │ │ └── ThreadPoolTest.java │ │ ├── validation │ │ │ └── TruthAnnotatorTest.java │ │ ├── vcf │ │ │ ├── InsertedSequenceAnnotatorTest.java │ │ │ └── VcfFileUtilTest.java │ │ └── visualisation │ │ │ ├── PositionalExporterTest.java │ │ │ └── StaticDeBruijnPathGraphGexfExporterTest.java │ │ └── validation │ │ └── LongReadSupportFinderTest.java ├── gridss │ ├── AllocateEvidenceTest.java │ ├── AnnotateInexactHomologyBedpeTest.java │ ├── AnnotateInexactHomologyTest.java │ ├── AssembleBreakendsTest.java │ ├── CallVariantsTest.java │ ├── ComputeCoverageTest.java │ ├── ComputeSamTagsTest.java │ ├── ExtractFragmentsToFastqTest.java │ ├── ExtractSVReadsTest.java │ ├── GeneratePonBedpeTest.java │ ├── InsertedSequencesToFastaTest.java │ ├── PrepareReferenceTest.java │ ├── PreprocessForBreakendAssemblyTest.java │ ├── SanityCheckEvidenceTest.java │ ├── VirusBreakendFilterTest.java │ ├── analysis │ │ ├── CigarSizeDistributionTest.java │ │ ├── CollectGridssMetricsTest.java │ │ ├── CollectIdsvMetricsTest.java │ │ ├── CollectMapqMetricsTest.java │ │ └── ReportThresholdCoverageTest.java │ ├── cmdline │ │ ├── FullEvidenceCommandLineProgramTest.java │ │ └── ReferenceCommandLineProgramTest.java │ ├── filter │ │ ├── ClippedReadFilterTest.java │ │ ├── IndelReadFilterTest.java │ │ ├── SplitReadFilterTest.java │ │ └── UnionAggregateFilterTest.java │ ├── kraken │ │ ├── AnnotateVariantsKrakenTest.java │ │ ├── ExtractBestViralReferenceTest.java │ │ └── IdentifyViralTaxaTest.java │ └── repeatmasker │ │ └── AnnotateVariantsRepeatMaskerTest.java ├── htsjdk │ └── samtools │ │ ├── Colo829BAMFileReaderTest.java │ │ └── fastq │ │ └── BasicFastqWriterTest.java ├── misc │ └── OffTargetReporter.java ├── performancetesting │ └── BamReadTest.java ├── samtools │ └── htsjdk │ │ ├── SAMReaderTest.java │ │ └── fastq │ │ └── MockFastqWriter.java └── scambler │ ├── OverlapLookupTest.java │ ├── PocTest.java │ ├── StreamingStringGraphIteratorTest.java │ ├── StringGraphTestHelper.java │ └── StringGraphTransitiveCompressorTest.java └── resources ├── 203541.bai ├── 203541.bam ├── 203541.bam.idsv.realign.bam ├── 203541.vcf.idsv.realign.bam ├── 2762cb5d343cd0f882d1d93a743c69a4_chr12_867621 ├── breakend.vcf.idsv.working │ ├── breakend.vcf.idsv.breakend.vcf │ ├── breakend.vcf.idsv.realign.bam │ └── breakend.vcf.idsv.realign.fq ├── debug.bai ├── debug.bam └── debug.bam.idsv.working │ ├── debug.bam.idsv.metrics.idsv.txt │ ├── debug.bam.idsv.metrics.insertsize.txt │ ├── debug.bam.idsv.realign.bam │ ├── debug.bam.idsv.realign.fq │ ├── debug.bam.idsv.realignremote.bam │ ├── debug.bam.idsv.rp.bai │ ├── debug.bam.idsv.rp.bam │ ├── debug.bam.idsv.rpmate.bam │ ├── debug.bam.idsv.sc.bai │ ├── debug.bam.idsv.sc.bam │ └── debug.bam.idsv.scremote.bam ├── anchor_misassembly ├── anchor_misassembly.bam ├── anchor_misassembly.bam.bai ├── anchor_misassembly.bam.gridss.working │ ├── anchor_misassembly.bam.cigar_metrics │ ├── anchor_misassembly.bam.computesamtags.changes.tsv │ ├── anchor_misassembly.bam.idsv_metrics │ ├── anchor_misassembly.bam.insert_size_histogram.pdf │ ├── anchor_misassembly.bam.insert_size_metrics │ ├── anchor_misassembly.bam.mapq_metrics │ ├── anchor_misassembly.bam.sv.bam │ ├── anchor_misassembly.bam.sv.bam.bai │ └── anchor_misassembly.bam.tag_metrics ├── anchor_misassembly.sam ├── ref.fa ├── ref.fa.amb ├── ref.fa.ann ├── ref.fa.bwt ├── ref.fa.dict ├── ref.fa.fai ├── ref.fa.pac └── ref.fa.sa ├── assembly_score_mismatch.sam ├── chr12-244000.tagged.bam ├── chr12.1527326.DEL1024.bam ├── chr1_170849600_170849850.dict ├── chr1_170849600_170849850.fa ├── chr1_170849600_170849850.fa.dict ├── chr1_170849600_170849850.fa.fai ├── colo829 └── v2.7.2_regression │ ├── COLO829v003T_dedup.realigned.bam │ ├── COLO829v003T_dedup.realigned.bam.bai │ └── COLO829v003T_dedup.realigned.bam.gridss.working │ ├── COLO829v003T_dedup.realigned.bam.cigar_metrics │ ├── COLO829v003T_dedup.realigned.bam.coverage.blacklist.bed │ ├── COLO829v003T_dedup.realigned.bam.idsv_metrics │ ├── COLO829v003T_dedup.realigned.bam.insert_size_histogram.pdf │ ├── COLO829v003T_dedup.realigned.bam.insert_size_metrics │ ├── COLO829v003T_dedup.realigned.bam.mapq_metrics │ ├── COLO829v003T_dedup.realigned.bam.sv.bam │ ├── COLO829v003T_dedup.realigned.bam.sv.bam.bai │ ├── COLO829v003T_dedup.realigned.bam.sv_metrics │ └── COLO829v003T_dedup.realigned.bam.tag_metrics ├── colo829_1.gridss.somatic.vcf ├── del_of_duplicated_sine.sam ├── empty.bam ├── empty.bam.bai ├── empty.bam.gridss.working ├── empty.bam.sv.bam └── empty.bam.sv.bam.bai ├── extractFragmentsToFastq ├── in.sam ├── in.sam.out.1.fq ├── in.sam.out.2.fq ├── in.sam.out.u.fq ├── in.sam.readnames.txt └── out.sam ├── extractOverlappingFragments ├── extractOverlappingFragments.in.bed ├── extractOverlappingFragments.in.sam └── extractOverlappingFragments.out.sam ├── flag.sam ├── fullymappedsplitread.sam ├── gridss294.colo829.somatic.vcf ├── hg19.rm.bedops.bed ├── hg38_primary_flag_failure.sam ├── homass.sam ├── indel_mismapping_false_positive_assembly.sv.bam ├── issue278 ├── c43_S1.bam ├── c43_S1.bam.bai └── c43_S1.bam.gridss.working │ ├── c43_S1.bam.cigar_metrics │ ├── c43_S1.bam.coverage.blacklist.bed │ ├── c43_S1.bam.idsv_metrics │ ├── c43_S1.bam.insert_size_histogram.pdf │ ├── c43_S1.bam.insert_size_metrics │ ├── c43_S1.bam.mapq_metrics │ ├── c43_S1.bam.sv.bam │ ├── c43_S1.bam.sv_metrics │ └── c43_S1.bam.tag_metrics ├── kraken ├── genus │ ├── hbv.kraken2.report.all.txt │ ├── herpes_should_not_mask_HBV │ │ ├── herpes_HBV.kraken2.report.all.txt │ │ ├── relevant_nodes.dmp │ │ ├── relevant_ref.dict │ │ ├── relevant_ref.fa │ │ ├── relevant_ref.fa.dict │ │ ├── relevant_ref.fa.fai │ │ └── seqid2taxid.map │ ├── relevant_nodes.dmp │ ├── relevant_ref.dict │ ├── relevant_ref.fa │ ├── relevant_ref.fa.dict │ ├── relevant_ref.fa.fai │ └── seqid2taxid.map ├── multiple_dictionaries │ ├── all_subspecies.txt │ ├── kraken.fa │ ├── kraken.fa.dict │ ├── kraken.fa.fai │ ├── matching.nodes.dmp │ ├── seqid2taxid.map │ ├── virushostdb.fa │ ├── virushostdb.fa.dict │ └── virushostdb.fa.fai ├── multistrain │ ├── 26T.virusbreakend.vcf.kraken2.report.all.txt │ ├── 26T.virusbreakend.vcf.viral.fa │ ├── 26T.virusbreakend.vcf.viral.fa.dict │ ├── 26T.virusbreakend.vcf.viral.fa.fai │ ├── relevant_nodes.dmp │ └── seqid2taxid.map ├── regression_should_not_throw_npe.krakenout.txt └── regression_should_not_throw_npe.vcf ├── kraken2_output.tsv ├── malformedsv.sam ├── malformedsv.sam.gridss.working ├── malformedsv.sam.sv.bam └── malformedsv.sam.sv.bam.bai ├── multiple.idsv.metrics.insertsize.txt ├── ncbi ├── homo_sapiens.nodes.dmp └── test.nodes.dmp ├── ont └── 778.namesorted.head.sam ├── pacbiona12989chem1chr1_196132675-196183463.bam ├── pacbiona12989chem1chr1_196132675-196183463.bam.bai ├── repeatmasker ├── ebv │ ├── merged.bwa.bam.gridss.vcf │ ├── merged.bwa.fa.align │ └── merged.bwa.fa.out ├── hmmer_test.fa.out ├── norepeats.fa.out ├── rmtest.fa.cat └── rmtest.fa.out ├── sa.split ├── test.insert_size_metrics ├── test1.sam └── test2.sam ├── sanity_failure_debug ├── bl21_de3_.ASM956v1_S2.bam ├── bl21_de3_.ASM956v1_S2.bam.gridss.working │ ├── bl21_de3_.ASM956v1_S2.bam.cigar_metrics │ ├── bl21_de3_.ASM956v1_S2.bam.coverage.blacklist.bed │ ├── bl21_de3_.ASM956v1_S2.bam.idsv_metrics │ ├── bl21_de3_.ASM956v1_S2.bam.insert_size_metrics │ ├── bl21_de3_.ASM956v1_S2.bam.mapq_metrics │ ├── bl21_de3_.ASM956v1_S2.bam.sv.bam │ ├── bl21_de3_.ASM956v1_S2.bam.sv_metrics │ └── bl21_de3_.ASM956v1_S2.bam.tag_metrics ├── bl21_de3_.ASM956v1_assembly.bam ├── bl21_de3_.ASM956v1_assembly.bam.gridss.working │ ├── bl21_de3_.ASM956v1_assembly.bam.cigar_metrics │ ├── bl21_de3_.ASM956v1_assembly.bam.coverage.blacklist.bed │ ├── bl21_de3_.ASM956v1_assembly.bam.idsv_metrics │ ├── bl21_de3_.ASM956v1_assembly.bam.mapq_metrics │ ├── bl21_de3_.ASM956v1_assembly.bam.quality_distribution_metrics │ ├── bl21_de3_.ASM956v1_assembly.bam.sv.bam │ └── bl21_de3_.ASM956v1_assembly.bam.tag_metrics └── colo829_1 │ ├── COLO829v001R_dedup.realigned.bam │ └── COLO829v001R_dedup.realigned.bam.gridss.working │ ├── COLO829v001R_dedup.realigned.bam.cigar_metrics │ ├── COLO829v001R_dedup.realigned.bam.coverage.blacklist.bed │ ├── COLO829v001R_dedup.realigned.bam.idsv_metrics │ ├── COLO829v001R_dedup.realigned.bam.insert_size_metrics │ ├── COLO829v001R_dedup.realigned.bam.mapq_metrics │ ├── COLO829v001R_dedup.realigned.bam.sv.bam │ ├── COLO829v001R_dedup.realigned.bam.sv_metrics │ └── COLO829v001R_dedup.realigned.bam.tag_metrics ├── simple.bedpe ├── small.fa ├── small.fa.amb ├── small.fa.ann ├── small.fa.bwt ├── small.fa.dict ├── small.fa.fai ├── small.fa.gridsscache ├── small.fa.img ├── small.fa.pac ├── small.fa.sa ├── test_del_of_duplicated_sine.bam ├── test_del_of_duplicated_sine.bam.bai ├── testmetrics.metrics.cigar.txt ├── testmetrics.metrics.idsv.txt ├── testmetrics.metrics.insertsize.txt ├── 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