From 942b5080ff412d088c9559b05b55e4d1e03109c4 Mon Sep 17 00:00:00 2001 From: Charles Shale Date: Mon, 21 Jun 2021 10:05:19 +1000 Subject: [PATCH] Linx: renamed from sv-linx --- README.md | 2 +- isofox/README.md | 2 +- {sv-linx => linx}/README.md | 8 ++++---- {sv-linx => linx}/README_VIS.md | 0 {sv-linx => linx}/pom.xml | 4 ++-- .../com/hartwig/hmftools/linx/LinxApplication.java | 0 .../java/com/hartwig/hmftools/linx/LinxConfig.java | 0 .../java/com/hartwig/hmftools/linx/LinxOutput.java | 0 .../com/hartwig/hmftools/linx/SvFileLoader.java | 0 .../hartwig/hmftools/linx/analysis/BfbFinder.java | 0 .../hmftools/linx/analysis/ClusterAnalyser.java | 0 .../hmftools/linx/analysis/ClusterAnnotations.java | 0 .../linx/analysis/ClusterClassification.java | 0 .../hmftools/linx/analysis/ClusterMetrics.java | 0 .../hmftools/linx/analysis/ClusteringPrep.java | 0 .../hmftools/linx/analysis/ClusteringReason.java | 0 .../hmftools/linx/analysis/ClusteringState.java | 0 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.../hmftools/linx/visualiser/data/Connector.java | 0 .../hmftools/linx/visualiser/data/Connectors.java | 0 .../linx/visualiser/data/CopyNumberAlteration.java | 0 .../linx/visualiser/data/DisruptedExons.java | 0 .../hartwig/hmftools/linx/visualiser/data/Exon.java | 0 .../hmftools/linx/visualiser/data/FusedExon.java | 0 .../hmftools/linx/visualiser/data/FusedExons.java | 0 .../linx/visualiser/data/FusedProteinDomains.java | 0 .../hmftools/linx/visualiser/data/Fusion.java | 0 .../hartwig/hmftools/linx/visualiser/data/Gene.java | 0 .../hmftools/linx/visualiser/data/Genes.java | 0 .../linx/visualiser/data/ProteinDomain.java | 0 .../hmftools/linx/visualiser/data/Segment.java | 0 .../linx/visualiser/data/VisCopyNumbers.java | 0 .../hmftools/linx/visualiser/data/VisExons.java | 0 .../hmftools/linx/visualiser/data/VisFusions.java | 0 .../hmftools/linx/visualiser/data/VisLinks.java | 0 .../linx/visualiser/data/VisProteinDomains.java | 0 .../hmftools/linx/visualiser/data/VisSegments.java | 0 .../hmftools/linx/visualiser/data/VisSvData.java | 0 .../linx/visualiser/file/VisCopyNumberFile.java | 0 .../linx/visualiser/file/VisDataWriter.java | 0 .../linx/visualiser/file/VisFusionFile.java | 0 .../linx/visualiser/file/VisGeneAnnotationType.java | 0 .../hmftools/linx/visualiser/file/VisGeneData.java | 0 .../linx/visualiser/file/VisGeneExonFile.java | 0 .../linx/visualiser/file/VisProteinDomainFile.java | 0 .../linx/visualiser/file/VisSegmentFile.java | 0 .../linx/visualiser/file/VisSvDataFile.java | 0 {sv-linx => linx}/src/main/resources/linx.version | 0 {sv-linx => linx}/src/main/resources/log4j2.xml | 0 .../src/main/resources/r/chromosomeRangePlot.R | 0 {sv-linx => linx}/src/main/resources/r/cytoBand.txt | 0 {sv-linx => linx}/src/main/resources/r/fusionPlot.R | 0 {sv-linx => linx}/src/main/resources/readme/bfb.gif | Bin .../src/main/resources/readme/chr7.png | Bin .../src/main/resources/readme/default.png | Bin .../src/main/resources/readme/del_dup_ti_event.png | Bin 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.../main/resources/visualisation/line_elements.csv | 0 .../hmftools/linx/analyser/AnnotationTest.java | 0 .../hmftools/linx/analyser/CopyNumberTest.java | 0 .../hmftools/linx/analyser/DoubleMinuteTest.java | 0 .../hmftools/linx/analyser/FilteringTest.java | 0 .../hmftools/linx/analyser/FoldbackTest.java | 0 .../hmftools/linx/analyser/InversionPairTest.java | 0 .../hartwig/hmftools/linx/analyser/LineTest.java | 0 .../linx/analyser/ReplicationRepairTest.java | 0 .../hmftools/linx/analyser/SyntheticTest.java | 0 .../linx/analyser/TranslocationPairTest.java | 0 .../hmftools/linx/chaining/ChainRoutinesTest.java | 0 .../hmftools/linx/chaining/ChainingActualTest.java | 0 .../hmftools/linx/chaining/ChainingComplexTest.java | 0 .../hmftools/linx/chaining/ChainingSimpleTest.java | 0 .../hartwig/hmftools/linx/chaining/LinkingTest.java | 0 .../linx/clustering/ComplexMergeRuleTest.java | 0 .../linx/clustering/SimpleMergeRuleTest.java | 0 .../hmftools/linx/drivers/AmpDriversTest.java | 0 .../hmftools/linx/drivers/HomDisruptionsTest.java | 0 .../hmftools/linx/fusion/DisruptionTest.java | 0 .../hmftools/linx/fusion/FusionRulesTest.java | 0 .../hartwig/hmftools/linx/fusion/FusionTest.java | 0 .../hartwig/hmftools/linx/fusion/RnaFusionTest.java | 0 .../hmftools/linx/fusion/SpecialFusionsTest.java | 0 .../hmftools/linx/gene/GeneCollectionTest.java | 0 .../hartwig/hmftools/linx/misc/JcnCalcsTest.java | 0 .../com/hartwig/hmftools/linx/misc/MiscTest.java | 0 .../hartwig/hmftools/linx/utils/GeneTestUtils.java | 0 .../com/hartwig/hmftools/linx/utils/LinxTester.java | 0 .../hmftools/linx/utils/SampleDataLoader.java | 0 .../hartwig/hmftools/linx/utils/SvTestUtils.java | 0 .../visualiser/circos/CircosConfigWriterTest.java | 0 .../visualiser/circos/CircosDataWriterTest.java | 0 .../linx/visualiser/circos/ColorPickerTest.java | 0 .../visualiser/circos/ProteinDomainColorsTest.java | 0 .../linx/visualiser/circos/ScaleContigTest.java | 0 .../linx/visualiser/circos/ScaleIntronsTest.java | 0 .../linx/visualiser/data/DisruptedExonsTest.java | 0 .../linx/visualiser/data/FusedExonsTest.java | 0 .../hmftools/linx/visualiser/data/SegmentsTest.java | 0 .../src/test/resources/sample_data/COLO829T | 0 .../src/test/resources/sample_data/CT_SAMPLE1 | 0 .../src/test/resources/sample_data/DM_SAMPLE1 | 0 .../src/test/resources/sample_data/DM_SAMPLE2 | 0 .../src/test/resources/sample_data/FB_SAMPLE1 | 0 pom.xml | 8 ++++---- protect/README.md | 4 ++-- purple/DriverCatalog.md | 2 +- sv-tools/pom.xml | 2 +- 253 files changed, 16 insertions(+), 16 deletions(-) rename {sv-linx => linx}/README.md (99%) rename {sv-linx => linx}/README_VIS.md (100%) rename {sv-linx => linx}/pom.xml (97%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/LinxApplication.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/LinxConfig.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/LinxOutput.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/SvFileLoader.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/analysis/BfbFinder.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/analysis/ClusterAnalyser.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/analysis/ClusterAnnotations.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/analysis/ClusterClassification.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/analysis/ClusterMetrics.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/analysis/ClusteringPrep.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/analysis/ClusteringReason.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/analysis/ClusteringState.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/analysis/CohortDataWriter.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/analysis/ComplexClustering.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/analysis/DoubleMinuteData.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/analysis/DoubleMinuteFinder.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/analysis/FoldbackFinder.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/analysis/PairResolution.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/analysis/SampleAnalyser.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/analysis/SimpleClustering.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/analysis/SvFiltering.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/analysis/SvUtilities.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/annotators/FragileSiteAnnotator.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/annotators/IndelAnnotator.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/annotators/IndelData.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/annotators/KataegisAnnotator.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/annotators/KataegisData.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/annotators/LineClusterState.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/annotators/LineElementAnnotator.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/annotators/LineElementType.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/annotators/LineSuspectReason.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/annotators/PseudoGeneFinder.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/annotators/PseudoGeneMatch.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/annotators/ReplicationOriginAnnotator.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/annotators/ViralInsertAnnotator.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/chaining/BreakendJcn.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/chaining/ChainDiagnostics.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/chaining/ChainFinder.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/chaining/ChainJcnLimits.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/chaining/ChainLinkAllocator.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/chaining/ChainMetrics.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/chaining/ChainRuleSelector.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/chaining/ChainState.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/chaining/ChainUtils.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/chaining/ChainingRule.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/chaining/FoldbackBreakendPair.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/chaining/LineChainer.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/chaining/LinkFinder.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/chaining/LinkSkipType.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/chaining/ProposedLinks.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/chaining/SegmentJcn.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/chaining/SvChain.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/chaining/SvChainConnections.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/cn/CnArmStats.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/cn/CnDataLoader.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/cn/CnJcnCalcs.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/cn/CnSegmentBuilder.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/cn/CopyNumberAnalyser.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/cn/HomLossEvent.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/cn/JcnCalcData.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/cn/LohEvent.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/cn/SvCNData.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/cn/TelomereCentromereCnData.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/drivers/AmplificationDrivers.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/drivers/DeletionDrivers.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/drivers/DriverAmpData.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/drivers/DriverDataCache.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/drivers/DriverEventType.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/drivers/DriverGeneAnnotator.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/drivers/DriverGeneData.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/drivers/DriverGeneEvent.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/drivers/GeneCopyNumberRegion.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/drivers/OpposingSegment.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/ext_compare/AmpliconClusterMatch.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/ext_compare/AmpliconCompare.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/ext_compare/AmpliconData.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfBreakendData.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfChain.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfChainClusterOverlap.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfDbMatchType.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfLink.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfSampleData.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfSummaryData.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfSvData.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/ext_compare/ChainFinderCompare.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/ext_compare/ExternalToolCompare.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/fusion/DisruptionFinder.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/fusion/FusionAnnotations.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/fusion/FusionChainInfo.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/fusion/FusionConstants.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/fusion/FusionDisruptionAnalyser.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/fusion/FusionFinder.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/fusion/FusionParameters.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/fusion/FusionReportability.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/fusion/FusionWriter.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/fusion/GeneFusion.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/fusion/NeoEpitopeWriter.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/fusion/ReportableReason.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/fusion/ValidTraversalData.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/fusion/rna/DnaRnaMatchType.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaDataLoader.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaExonMatchData.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaFusionAnnotator.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaFusionData.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaFusionMapper.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaJunctionType.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaMatchWriter.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/gene/EnsemblDAO.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/gene/GenerateEnsemblDataCache.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/types/ArmCluster.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/types/ArmGroup.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/types/DbPair.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/types/GermlineFilter.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/types/LinkedPair.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/types/LinxConstants.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/types/ResolvedType.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/types/SglMapping.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/types/SvBreakend.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/types/SvCluster.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/types/SvVarData.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/CircosConfig.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/SampleData.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/SvVisualiser.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/SvVisualiserConfig.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/ChromosomeRangeExecution.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/CircosConfigWriter.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/CircosData.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/CircosDataWriter.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/ColorPicker.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/FusionDataWriter.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/FusionExecution.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/Highlights.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/ProteinDomainColors.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/ScaleContig.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/ScaleIntrons.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/ScalePosition.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/SegmentTerminal.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/Span.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/Thickness.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/data/AdjustedPosition.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/data/AdjustedPositions.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Connector.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Connectors.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/data/CopyNumberAlteration.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/data/DisruptedExons.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Exon.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/data/FusedExon.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/data/FusedExons.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/data/FusedProteinDomains.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Fusion.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Gene.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Genes.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/data/ProteinDomain.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Segment.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisCopyNumbers.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisExons.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisFusions.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisLinks.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisProteinDomains.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisSegments.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisSvData.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisCopyNumberFile.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisDataWriter.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisFusionFile.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisGeneAnnotationType.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisGeneData.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisGeneExonFile.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisProteinDomainFile.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisSegmentFile.java (100%) rename {sv-linx => linx}/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisSvDataFile.java (100%) rename {sv-linx => linx}/src/main/resources/linx.version (100%) rename {sv-linx => linx}/src/main/resources/log4j2.xml (100%) rename {sv-linx => linx}/src/main/resources/r/chromosomeRangePlot.R (100%) rename {sv-linx => linx}/src/main/resources/r/cytoBand.txt (100%) rename {sv-linx => linx}/src/main/resources/r/fusionPlot.R (100%) rename {sv-linx => linx}/src/main/resources/readme/bfb.gif (100%) rename {sv-linx => linx}/src/main/resources/readme/chr7.png (100%) rename {sv-linx => linx}/src/main/resources/readme/default.png (100%) rename {sv-linx => linx}/src/main/resources/readme/del_dup_ti_event.png (100%) rename {sv-linx => linx}/src/main/resources/readme/fusion1.png (100%) rename {sv-linx => linx}/src/main/resources/readme/fusion2.png (100%) rename {sv-linx => linx}/src/main/resources/readme/fusion3.png (100%) rename {sv-linx => linx}/src/main/resources/readme/fusion4.png (100%) rename {sv-linx => linx}/src/main/resources/readme/fusion_configurations.png (100%) rename {sv-linx => linx}/src/main/resources/readme/gridss_cis_trans.png (100%) rename {sv-linx => linx}/src/main/resources/readme/legend.png (100%) rename {sv-linx => linx}/src/main/resources/readme/line1.png (100%) rename {sv-linx => linx}/src/main/resources/readme/line2.png (100%) rename {sv-linx => linx}/src/main/resources/readme/linx_routine_steps.png (100%) rename {sv-linx => linx}/src/main/resources/readme/one_break_events.png (100%) rename {sv-linx => linx}/src/main/resources/readme/small1.png (100%) rename {sv-linx => linx}/src/main/resources/readme/small2.png (100%) rename {sv-linx => linx}/src/main/resources/readme/small3.png (100%) rename {sv-linx => linx}/src/main/resources/readme/small4.png (100%) rename {sv-linx => linx}/src/main/resources/readme/tmpress2erg.png (100%) rename {sv-linx => linx}/src/main/resources/readme/two_break_events.png (100%) rename {sv-linx => linx}/src/main/resources/visualisation/cluster.template (100%) rename {sv-linx => linx}/src/main/resources/visualisation/fragile_sites.csv (100%) rename {sv-linx => linx}/src/main/resources/visualisation/line_elements.csv (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/analyser/AnnotationTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/analyser/CopyNumberTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/analyser/DoubleMinuteTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/analyser/FilteringTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/analyser/FoldbackTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/analyser/InversionPairTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/analyser/LineTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/analyser/ReplicationRepairTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/analyser/SyntheticTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/analyser/TranslocationPairTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/chaining/ChainRoutinesTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/chaining/ChainingActualTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/chaining/ChainingComplexTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/chaining/ChainingSimpleTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/chaining/LinkingTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/clustering/ComplexMergeRuleTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/clustering/SimpleMergeRuleTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/drivers/AmpDriversTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/drivers/HomDisruptionsTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/fusion/DisruptionTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/fusion/FusionRulesTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/fusion/FusionTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/fusion/RnaFusionTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/fusion/SpecialFusionsTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/gene/GeneCollectionTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/misc/JcnCalcsTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/misc/MiscTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/utils/GeneTestUtils.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/utils/LinxTester.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/utils/SampleDataLoader.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/utils/SvTestUtils.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/visualiser/circos/CircosConfigWriterTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/visualiser/circos/CircosDataWriterTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/visualiser/circos/ColorPickerTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/visualiser/circos/ProteinDomainColorsTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/visualiser/circos/ScaleContigTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/visualiser/circos/ScaleIntronsTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/visualiser/data/DisruptedExonsTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/visualiser/data/FusedExonsTest.java (100%) rename {sv-linx => linx}/src/test/java/com/hartwig/hmftools/linx/visualiser/data/SegmentsTest.java (100%) rename {sv-linx => linx}/src/test/resources/sample_data/COLO829T (100%) rename {sv-linx => linx}/src/test/resources/sample_data/CT_SAMPLE1 (100%) rename {sv-linx => linx}/src/test/resources/sample_data/DM_SAMPLE1 (100%) rename {sv-linx => linx}/src/test/resources/sample_data/DM_SAMPLE2 (100%) rename {sv-linx => linx}/src/test/resources/sample_data/FB_SAMPLE1 (100%) diff --git a/README.md b/README.md index 9818e0f068..28fd481cc5 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ More detailed descriptions of the following algorithms are available from the li - [COBALT](./cobalt/README.md) - [GRIPSS](./gripss/README.md) - [PURPLE](./purple/README.md) - - [Linx](./sv-linx/README.md) + - [Linx](./linx/README.md) - [Isofox](./isofox/README.md) - [SERVE](./serve/README.md) - [PROTECT](./protect/README.md) diff --git a/isofox/README.md b/isofox/README.md index 8e4cd33cb2..879e3db4b7 100644 --- a/isofox/README.md +++ b/isofox/README.md @@ -195,7 +195,7 @@ The output file is approximately 120MB. To annotate SVs with gene information and to support fusion detection, ISOFOX uses gene, transcript, exon and protein domain information from the Ensembl database. To improve performance, this data is first extracted into 4 CSV data files and then loaded into memory each time ISOFOX runs. -These files can be downloaded from the Hartwig resources page, or generated using the Hartwig LINX application (see https://github.com/hartwigmedical/hmftools/blob/master/sv-linx/README.md for instructions). +These files can be downloaded from the Hartwig resources page, or generated using the Hartwig LINX application (see https://github.com/hartwigmedical/hmftools/blob/master/linx/README.md for instructions). Note that the ensembl gene cache currently generates for standard autosomes and sex chromosomes only (alt contigs and MT chromosomes are excluded). diff --git a/sv-linx/README.md b/linx/README.md similarity index 99% rename from sv-linx/README.md rename to linx/README.md index acf91a4a06..41c6364ba9 100644 --- a/sv-linx/README.md +++ b/linx/README.md @@ -100,7 +100,7 @@ log_debug | logs in debug mode Single sample - Load SVs and purple data from file, upload Linx results to database: ``` -java -jar sv-linx.jar +java -jar linx.jar -sample SAMPLE_ID -ref_genome_version 37 -sv_vcf /path_to_purple_vcf/ @@ -121,7 +121,7 @@ java -jar sv-linx.jar Single sample - query SVs and purple data from database, upload Linx results to database: ``` -java -jar sv-linx.jar +java -jar linx.jar -sample SAMPLE_ID -db_url [db_url] -db_user [username] -db_pass [password] -output_dir /path_to_sample_data/ @@ -141,7 +141,7 @@ Cohort analysis - run all samples by sampleId in provided file, query SVs and pu Write Linx results to cohort files, no upload to database: ``` -java -jar sv-linx.jar +java -jar linx.jar -sample cohort_sample_ids.csv -db_url [db_url] -db_user [username] -db_pass [password] -output_dir /path_to_sample_data/ @@ -162,7 +162,7 @@ To improve performance, this data is first extracted into 4 CSV data files and t To generate these 4 data files, first run Linx with these command line options: ``` -java -cp sv-linx.jar com.hartwig.hmftools.linx.gene.GenerateEnsemblDataCache +java -cp linx.jar com.hartwig.hmftools.linx.gene.GenerateEnsemblDataCache -ensembl_db [see below] -ensembl_user "anonymous" -ensembl_pass "" -output_dir /path_to_write_data_files/ -ref_genome_version [37 or 38] ``` diff --git a/sv-linx/README_VIS.md b/linx/README_VIS.md similarity index 100% rename from sv-linx/README_VIS.md rename to linx/README_VIS.md diff --git a/sv-linx/pom.xml b/linx/pom.xml similarity index 97% rename from sv-linx/pom.xml rename to linx/pom.xml index a01305235c..cd7f5e5d10 100644 --- a/sv-linx/pom.xml +++ b/linx/pom.xml @@ -8,9 +8,9 @@ local-SNAPSHOT - sv-linx + linx jar - ${sv-linx.version} + ${linx.version} HMF Tools - Linx diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/LinxApplication.java b/linx/src/main/java/com/hartwig/hmftools/linx/LinxApplication.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/LinxApplication.java rename to linx/src/main/java/com/hartwig/hmftools/linx/LinxApplication.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/LinxConfig.java b/linx/src/main/java/com/hartwig/hmftools/linx/LinxConfig.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/LinxConfig.java rename to linx/src/main/java/com/hartwig/hmftools/linx/LinxConfig.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/LinxOutput.java b/linx/src/main/java/com/hartwig/hmftools/linx/LinxOutput.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/LinxOutput.java rename to linx/src/main/java/com/hartwig/hmftools/linx/LinxOutput.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/SvFileLoader.java b/linx/src/main/java/com/hartwig/hmftools/linx/SvFileLoader.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/SvFileLoader.java rename to linx/src/main/java/com/hartwig/hmftools/linx/SvFileLoader.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/BfbFinder.java b/linx/src/main/java/com/hartwig/hmftools/linx/analysis/BfbFinder.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/BfbFinder.java rename to linx/src/main/java/com/hartwig/hmftools/linx/analysis/BfbFinder.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/ClusterAnalyser.java b/linx/src/main/java/com/hartwig/hmftools/linx/analysis/ClusterAnalyser.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/ClusterAnalyser.java rename to linx/src/main/java/com/hartwig/hmftools/linx/analysis/ClusterAnalyser.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/ClusterAnnotations.java b/linx/src/main/java/com/hartwig/hmftools/linx/analysis/ClusterAnnotations.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/ClusterAnnotations.java rename to linx/src/main/java/com/hartwig/hmftools/linx/analysis/ClusterAnnotations.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/ClusterClassification.java b/linx/src/main/java/com/hartwig/hmftools/linx/analysis/ClusterClassification.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/ClusterClassification.java rename to linx/src/main/java/com/hartwig/hmftools/linx/analysis/ClusterClassification.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/ClusterMetrics.java b/linx/src/main/java/com/hartwig/hmftools/linx/analysis/ClusterMetrics.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/ClusterMetrics.java rename to linx/src/main/java/com/hartwig/hmftools/linx/analysis/ClusterMetrics.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/ClusteringPrep.java b/linx/src/main/java/com/hartwig/hmftools/linx/analysis/ClusteringPrep.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/ClusteringPrep.java rename to linx/src/main/java/com/hartwig/hmftools/linx/analysis/ClusteringPrep.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/ClusteringReason.java b/linx/src/main/java/com/hartwig/hmftools/linx/analysis/ClusteringReason.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/ClusteringReason.java rename to linx/src/main/java/com/hartwig/hmftools/linx/analysis/ClusteringReason.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/ClusteringState.java b/linx/src/main/java/com/hartwig/hmftools/linx/analysis/ClusteringState.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/ClusteringState.java rename to linx/src/main/java/com/hartwig/hmftools/linx/analysis/ClusteringState.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/CohortDataWriter.java b/linx/src/main/java/com/hartwig/hmftools/linx/analysis/CohortDataWriter.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/CohortDataWriter.java rename to linx/src/main/java/com/hartwig/hmftools/linx/analysis/CohortDataWriter.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/ComplexClustering.java b/linx/src/main/java/com/hartwig/hmftools/linx/analysis/ComplexClustering.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/ComplexClustering.java rename to linx/src/main/java/com/hartwig/hmftools/linx/analysis/ComplexClustering.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/DoubleMinuteData.java b/linx/src/main/java/com/hartwig/hmftools/linx/analysis/DoubleMinuteData.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/DoubleMinuteData.java rename to linx/src/main/java/com/hartwig/hmftools/linx/analysis/DoubleMinuteData.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/DoubleMinuteFinder.java b/linx/src/main/java/com/hartwig/hmftools/linx/analysis/DoubleMinuteFinder.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/DoubleMinuteFinder.java rename to linx/src/main/java/com/hartwig/hmftools/linx/analysis/DoubleMinuteFinder.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/FoldbackFinder.java b/linx/src/main/java/com/hartwig/hmftools/linx/analysis/FoldbackFinder.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/FoldbackFinder.java rename to linx/src/main/java/com/hartwig/hmftools/linx/analysis/FoldbackFinder.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/PairResolution.java b/linx/src/main/java/com/hartwig/hmftools/linx/analysis/PairResolution.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/PairResolution.java rename to linx/src/main/java/com/hartwig/hmftools/linx/analysis/PairResolution.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/SampleAnalyser.java b/linx/src/main/java/com/hartwig/hmftools/linx/analysis/SampleAnalyser.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/SampleAnalyser.java rename to linx/src/main/java/com/hartwig/hmftools/linx/analysis/SampleAnalyser.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/SimpleClustering.java b/linx/src/main/java/com/hartwig/hmftools/linx/analysis/SimpleClustering.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/SimpleClustering.java rename to linx/src/main/java/com/hartwig/hmftools/linx/analysis/SimpleClustering.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/SvFiltering.java b/linx/src/main/java/com/hartwig/hmftools/linx/analysis/SvFiltering.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/SvFiltering.java rename to linx/src/main/java/com/hartwig/hmftools/linx/analysis/SvFiltering.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/SvUtilities.java b/linx/src/main/java/com/hartwig/hmftools/linx/analysis/SvUtilities.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/analysis/SvUtilities.java rename to linx/src/main/java/com/hartwig/hmftools/linx/analysis/SvUtilities.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/annotators/FragileSiteAnnotator.java b/linx/src/main/java/com/hartwig/hmftools/linx/annotators/FragileSiteAnnotator.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/annotators/FragileSiteAnnotator.java rename to linx/src/main/java/com/hartwig/hmftools/linx/annotators/FragileSiteAnnotator.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/annotators/IndelAnnotator.java b/linx/src/main/java/com/hartwig/hmftools/linx/annotators/IndelAnnotator.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/annotators/IndelAnnotator.java rename to linx/src/main/java/com/hartwig/hmftools/linx/annotators/IndelAnnotator.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/annotators/IndelData.java b/linx/src/main/java/com/hartwig/hmftools/linx/annotators/IndelData.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/annotators/IndelData.java rename to linx/src/main/java/com/hartwig/hmftools/linx/annotators/IndelData.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/annotators/KataegisAnnotator.java b/linx/src/main/java/com/hartwig/hmftools/linx/annotators/KataegisAnnotator.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/annotators/KataegisAnnotator.java rename to linx/src/main/java/com/hartwig/hmftools/linx/annotators/KataegisAnnotator.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/annotators/KataegisData.java b/linx/src/main/java/com/hartwig/hmftools/linx/annotators/KataegisData.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/annotators/KataegisData.java rename to linx/src/main/java/com/hartwig/hmftools/linx/annotators/KataegisData.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/annotators/LineClusterState.java b/linx/src/main/java/com/hartwig/hmftools/linx/annotators/LineClusterState.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/annotators/LineClusterState.java rename to linx/src/main/java/com/hartwig/hmftools/linx/annotators/LineClusterState.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/annotators/LineElementAnnotator.java b/linx/src/main/java/com/hartwig/hmftools/linx/annotators/LineElementAnnotator.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/annotators/LineElementAnnotator.java rename to linx/src/main/java/com/hartwig/hmftools/linx/annotators/LineElementAnnotator.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/annotators/LineElementType.java b/linx/src/main/java/com/hartwig/hmftools/linx/annotators/LineElementType.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/annotators/LineElementType.java rename to linx/src/main/java/com/hartwig/hmftools/linx/annotators/LineElementType.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/annotators/LineSuspectReason.java b/linx/src/main/java/com/hartwig/hmftools/linx/annotators/LineSuspectReason.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/annotators/LineSuspectReason.java rename to linx/src/main/java/com/hartwig/hmftools/linx/annotators/LineSuspectReason.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/annotators/PseudoGeneFinder.java b/linx/src/main/java/com/hartwig/hmftools/linx/annotators/PseudoGeneFinder.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/annotators/PseudoGeneFinder.java rename to linx/src/main/java/com/hartwig/hmftools/linx/annotators/PseudoGeneFinder.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/annotators/PseudoGeneMatch.java b/linx/src/main/java/com/hartwig/hmftools/linx/annotators/PseudoGeneMatch.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/annotators/PseudoGeneMatch.java rename to linx/src/main/java/com/hartwig/hmftools/linx/annotators/PseudoGeneMatch.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/annotators/ReplicationOriginAnnotator.java b/linx/src/main/java/com/hartwig/hmftools/linx/annotators/ReplicationOriginAnnotator.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/annotators/ReplicationOriginAnnotator.java rename to linx/src/main/java/com/hartwig/hmftools/linx/annotators/ReplicationOriginAnnotator.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/annotators/ViralInsertAnnotator.java b/linx/src/main/java/com/hartwig/hmftools/linx/annotators/ViralInsertAnnotator.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/annotators/ViralInsertAnnotator.java rename to linx/src/main/java/com/hartwig/hmftools/linx/annotators/ViralInsertAnnotator.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/BreakendJcn.java b/linx/src/main/java/com/hartwig/hmftools/linx/chaining/BreakendJcn.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/BreakendJcn.java rename to linx/src/main/java/com/hartwig/hmftools/linx/chaining/BreakendJcn.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainDiagnostics.java b/linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainDiagnostics.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainDiagnostics.java rename to linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainDiagnostics.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainFinder.java b/linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainFinder.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainFinder.java rename to linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainFinder.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainJcnLimits.java b/linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainJcnLimits.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainJcnLimits.java rename to linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainJcnLimits.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainLinkAllocator.java b/linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainLinkAllocator.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainLinkAllocator.java rename to linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainLinkAllocator.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainMetrics.java b/linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainMetrics.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainMetrics.java rename to linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainMetrics.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainRuleSelector.java b/linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainRuleSelector.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainRuleSelector.java rename to linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainRuleSelector.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainState.java b/linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainState.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainState.java rename to linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainState.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainUtils.java b/linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainUtils.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainUtils.java rename to linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainUtils.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainingRule.java b/linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainingRule.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainingRule.java rename to linx/src/main/java/com/hartwig/hmftools/linx/chaining/ChainingRule.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/FoldbackBreakendPair.java b/linx/src/main/java/com/hartwig/hmftools/linx/chaining/FoldbackBreakendPair.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/FoldbackBreakendPair.java rename to linx/src/main/java/com/hartwig/hmftools/linx/chaining/FoldbackBreakendPair.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/LineChainer.java b/linx/src/main/java/com/hartwig/hmftools/linx/chaining/LineChainer.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/LineChainer.java rename to linx/src/main/java/com/hartwig/hmftools/linx/chaining/LineChainer.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/LinkFinder.java b/linx/src/main/java/com/hartwig/hmftools/linx/chaining/LinkFinder.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/LinkFinder.java rename to linx/src/main/java/com/hartwig/hmftools/linx/chaining/LinkFinder.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/LinkSkipType.java b/linx/src/main/java/com/hartwig/hmftools/linx/chaining/LinkSkipType.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/LinkSkipType.java rename to linx/src/main/java/com/hartwig/hmftools/linx/chaining/LinkSkipType.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/ProposedLinks.java b/linx/src/main/java/com/hartwig/hmftools/linx/chaining/ProposedLinks.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/ProposedLinks.java rename to linx/src/main/java/com/hartwig/hmftools/linx/chaining/ProposedLinks.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/SegmentJcn.java b/linx/src/main/java/com/hartwig/hmftools/linx/chaining/SegmentJcn.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/SegmentJcn.java rename to linx/src/main/java/com/hartwig/hmftools/linx/chaining/SegmentJcn.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/SvChain.java b/linx/src/main/java/com/hartwig/hmftools/linx/chaining/SvChain.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/SvChain.java rename to linx/src/main/java/com/hartwig/hmftools/linx/chaining/SvChain.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/SvChainConnections.java b/linx/src/main/java/com/hartwig/hmftools/linx/chaining/SvChainConnections.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/chaining/SvChainConnections.java rename to linx/src/main/java/com/hartwig/hmftools/linx/chaining/SvChainConnections.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/cn/CnArmStats.java b/linx/src/main/java/com/hartwig/hmftools/linx/cn/CnArmStats.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/cn/CnArmStats.java rename to linx/src/main/java/com/hartwig/hmftools/linx/cn/CnArmStats.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/cn/CnDataLoader.java b/linx/src/main/java/com/hartwig/hmftools/linx/cn/CnDataLoader.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/cn/CnDataLoader.java rename to linx/src/main/java/com/hartwig/hmftools/linx/cn/CnDataLoader.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/cn/CnJcnCalcs.java b/linx/src/main/java/com/hartwig/hmftools/linx/cn/CnJcnCalcs.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/cn/CnJcnCalcs.java rename to linx/src/main/java/com/hartwig/hmftools/linx/cn/CnJcnCalcs.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/cn/CnSegmentBuilder.java b/linx/src/main/java/com/hartwig/hmftools/linx/cn/CnSegmentBuilder.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/cn/CnSegmentBuilder.java rename to linx/src/main/java/com/hartwig/hmftools/linx/cn/CnSegmentBuilder.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/cn/CopyNumberAnalyser.java b/linx/src/main/java/com/hartwig/hmftools/linx/cn/CopyNumberAnalyser.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/cn/CopyNumberAnalyser.java rename to linx/src/main/java/com/hartwig/hmftools/linx/cn/CopyNumberAnalyser.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/cn/HomLossEvent.java b/linx/src/main/java/com/hartwig/hmftools/linx/cn/HomLossEvent.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/cn/HomLossEvent.java rename to linx/src/main/java/com/hartwig/hmftools/linx/cn/HomLossEvent.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/cn/JcnCalcData.java b/linx/src/main/java/com/hartwig/hmftools/linx/cn/JcnCalcData.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/cn/JcnCalcData.java rename to linx/src/main/java/com/hartwig/hmftools/linx/cn/JcnCalcData.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/cn/LohEvent.java b/linx/src/main/java/com/hartwig/hmftools/linx/cn/LohEvent.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/cn/LohEvent.java rename to linx/src/main/java/com/hartwig/hmftools/linx/cn/LohEvent.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/cn/SvCNData.java b/linx/src/main/java/com/hartwig/hmftools/linx/cn/SvCNData.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/cn/SvCNData.java rename to linx/src/main/java/com/hartwig/hmftools/linx/cn/SvCNData.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/cn/TelomereCentromereCnData.java b/linx/src/main/java/com/hartwig/hmftools/linx/cn/TelomereCentromereCnData.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/cn/TelomereCentromereCnData.java rename to linx/src/main/java/com/hartwig/hmftools/linx/cn/TelomereCentromereCnData.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/drivers/AmplificationDrivers.java b/linx/src/main/java/com/hartwig/hmftools/linx/drivers/AmplificationDrivers.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/drivers/AmplificationDrivers.java rename to linx/src/main/java/com/hartwig/hmftools/linx/drivers/AmplificationDrivers.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/drivers/DeletionDrivers.java b/linx/src/main/java/com/hartwig/hmftools/linx/drivers/DeletionDrivers.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/drivers/DeletionDrivers.java rename to linx/src/main/java/com/hartwig/hmftools/linx/drivers/DeletionDrivers.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/drivers/DriverAmpData.java b/linx/src/main/java/com/hartwig/hmftools/linx/drivers/DriverAmpData.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/drivers/DriverAmpData.java rename to linx/src/main/java/com/hartwig/hmftools/linx/drivers/DriverAmpData.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/drivers/DriverDataCache.java b/linx/src/main/java/com/hartwig/hmftools/linx/drivers/DriverDataCache.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/drivers/DriverDataCache.java rename to linx/src/main/java/com/hartwig/hmftools/linx/drivers/DriverDataCache.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/drivers/DriverEventType.java b/linx/src/main/java/com/hartwig/hmftools/linx/drivers/DriverEventType.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/drivers/DriverEventType.java rename to linx/src/main/java/com/hartwig/hmftools/linx/drivers/DriverEventType.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/drivers/DriverGeneAnnotator.java b/linx/src/main/java/com/hartwig/hmftools/linx/drivers/DriverGeneAnnotator.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/drivers/DriverGeneAnnotator.java rename to linx/src/main/java/com/hartwig/hmftools/linx/drivers/DriverGeneAnnotator.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/drivers/DriverGeneData.java b/linx/src/main/java/com/hartwig/hmftools/linx/drivers/DriverGeneData.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/drivers/DriverGeneData.java rename to linx/src/main/java/com/hartwig/hmftools/linx/drivers/DriverGeneData.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/drivers/DriverGeneEvent.java b/linx/src/main/java/com/hartwig/hmftools/linx/drivers/DriverGeneEvent.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/drivers/DriverGeneEvent.java rename to linx/src/main/java/com/hartwig/hmftools/linx/drivers/DriverGeneEvent.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/drivers/GeneCopyNumberRegion.java b/linx/src/main/java/com/hartwig/hmftools/linx/drivers/GeneCopyNumberRegion.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/drivers/GeneCopyNumberRegion.java rename to linx/src/main/java/com/hartwig/hmftools/linx/drivers/GeneCopyNumberRegion.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/drivers/OpposingSegment.java b/linx/src/main/java/com/hartwig/hmftools/linx/drivers/OpposingSegment.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/drivers/OpposingSegment.java rename to linx/src/main/java/com/hartwig/hmftools/linx/drivers/OpposingSegment.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/AmpliconClusterMatch.java b/linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/AmpliconClusterMatch.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/AmpliconClusterMatch.java rename to linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/AmpliconClusterMatch.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/AmpliconCompare.java b/linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/AmpliconCompare.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/AmpliconCompare.java rename to linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/AmpliconCompare.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/AmpliconData.java b/linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/AmpliconData.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/AmpliconData.java rename to linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/AmpliconData.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfBreakendData.java b/linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfBreakendData.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfBreakendData.java rename to linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfBreakendData.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfChain.java b/linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfChain.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfChain.java rename to linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfChain.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfChainClusterOverlap.java b/linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfChainClusterOverlap.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfChainClusterOverlap.java rename to linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfChainClusterOverlap.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfDbMatchType.java b/linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfDbMatchType.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfDbMatchType.java rename to linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfDbMatchType.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfLink.java b/linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfLink.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfLink.java rename to linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfLink.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfSampleData.java b/linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfSampleData.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfSampleData.java rename to linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfSampleData.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfSummaryData.java b/linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfSummaryData.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfSummaryData.java rename to linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfSummaryData.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfSvData.java b/linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfSvData.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfSvData.java rename to linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/CfSvData.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/ChainFinderCompare.java b/linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/ChainFinderCompare.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/ChainFinderCompare.java rename to linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/ChainFinderCompare.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/ExternalToolCompare.java b/linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/ExternalToolCompare.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/ExternalToolCompare.java rename to linx/src/main/java/com/hartwig/hmftools/linx/ext_compare/ExternalToolCompare.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/DisruptionFinder.java b/linx/src/main/java/com/hartwig/hmftools/linx/fusion/DisruptionFinder.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/DisruptionFinder.java rename to linx/src/main/java/com/hartwig/hmftools/linx/fusion/DisruptionFinder.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/FusionAnnotations.java b/linx/src/main/java/com/hartwig/hmftools/linx/fusion/FusionAnnotations.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/FusionAnnotations.java rename to linx/src/main/java/com/hartwig/hmftools/linx/fusion/FusionAnnotations.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/FusionChainInfo.java b/linx/src/main/java/com/hartwig/hmftools/linx/fusion/FusionChainInfo.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/FusionChainInfo.java rename to linx/src/main/java/com/hartwig/hmftools/linx/fusion/FusionChainInfo.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/FusionConstants.java b/linx/src/main/java/com/hartwig/hmftools/linx/fusion/FusionConstants.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/FusionConstants.java rename to linx/src/main/java/com/hartwig/hmftools/linx/fusion/FusionConstants.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/FusionDisruptionAnalyser.java b/linx/src/main/java/com/hartwig/hmftools/linx/fusion/FusionDisruptionAnalyser.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/FusionDisruptionAnalyser.java rename to linx/src/main/java/com/hartwig/hmftools/linx/fusion/FusionDisruptionAnalyser.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/FusionFinder.java b/linx/src/main/java/com/hartwig/hmftools/linx/fusion/FusionFinder.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/FusionFinder.java rename to linx/src/main/java/com/hartwig/hmftools/linx/fusion/FusionFinder.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/FusionParameters.java b/linx/src/main/java/com/hartwig/hmftools/linx/fusion/FusionParameters.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/FusionParameters.java rename to linx/src/main/java/com/hartwig/hmftools/linx/fusion/FusionParameters.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/FusionReportability.java b/linx/src/main/java/com/hartwig/hmftools/linx/fusion/FusionReportability.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/FusionReportability.java rename to linx/src/main/java/com/hartwig/hmftools/linx/fusion/FusionReportability.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/FusionWriter.java b/linx/src/main/java/com/hartwig/hmftools/linx/fusion/FusionWriter.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/FusionWriter.java rename to linx/src/main/java/com/hartwig/hmftools/linx/fusion/FusionWriter.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/GeneFusion.java b/linx/src/main/java/com/hartwig/hmftools/linx/fusion/GeneFusion.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/GeneFusion.java rename to linx/src/main/java/com/hartwig/hmftools/linx/fusion/GeneFusion.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/NeoEpitopeWriter.java b/linx/src/main/java/com/hartwig/hmftools/linx/fusion/NeoEpitopeWriter.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/NeoEpitopeWriter.java rename to linx/src/main/java/com/hartwig/hmftools/linx/fusion/NeoEpitopeWriter.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/ReportableReason.java b/linx/src/main/java/com/hartwig/hmftools/linx/fusion/ReportableReason.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/ReportableReason.java rename to linx/src/main/java/com/hartwig/hmftools/linx/fusion/ReportableReason.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/ValidTraversalData.java b/linx/src/main/java/com/hartwig/hmftools/linx/fusion/ValidTraversalData.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/ValidTraversalData.java rename to linx/src/main/java/com/hartwig/hmftools/linx/fusion/ValidTraversalData.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/rna/DnaRnaMatchType.java b/linx/src/main/java/com/hartwig/hmftools/linx/fusion/rna/DnaRnaMatchType.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/rna/DnaRnaMatchType.java rename to linx/src/main/java/com/hartwig/hmftools/linx/fusion/rna/DnaRnaMatchType.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaDataLoader.java b/linx/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaDataLoader.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaDataLoader.java rename to linx/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaDataLoader.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaExonMatchData.java b/linx/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaExonMatchData.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaExonMatchData.java rename to linx/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaExonMatchData.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaFusionAnnotator.java b/linx/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaFusionAnnotator.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaFusionAnnotator.java rename to linx/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaFusionAnnotator.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaFusionData.java b/linx/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaFusionData.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaFusionData.java rename to linx/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaFusionData.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaFusionMapper.java b/linx/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaFusionMapper.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaFusionMapper.java rename to linx/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaFusionMapper.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaJunctionType.java b/linx/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaJunctionType.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaJunctionType.java rename to linx/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaJunctionType.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaMatchWriter.java b/linx/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaMatchWriter.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaMatchWriter.java rename to linx/src/main/java/com/hartwig/hmftools/linx/fusion/rna/RnaMatchWriter.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/gene/EnsemblDAO.java b/linx/src/main/java/com/hartwig/hmftools/linx/gene/EnsemblDAO.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/gene/EnsemblDAO.java rename to linx/src/main/java/com/hartwig/hmftools/linx/gene/EnsemblDAO.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/gene/GenerateEnsemblDataCache.java b/linx/src/main/java/com/hartwig/hmftools/linx/gene/GenerateEnsemblDataCache.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/gene/GenerateEnsemblDataCache.java rename to linx/src/main/java/com/hartwig/hmftools/linx/gene/GenerateEnsemblDataCache.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/types/ArmCluster.java b/linx/src/main/java/com/hartwig/hmftools/linx/types/ArmCluster.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/types/ArmCluster.java rename to linx/src/main/java/com/hartwig/hmftools/linx/types/ArmCluster.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/types/ArmGroup.java b/linx/src/main/java/com/hartwig/hmftools/linx/types/ArmGroup.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/types/ArmGroup.java rename to linx/src/main/java/com/hartwig/hmftools/linx/types/ArmGroup.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/types/DbPair.java b/linx/src/main/java/com/hartwig/hmftools/linx/types/DbPair.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/types/DbPair.java rename to linx/src/main/java/com/hartwig/hmftools/linx/types/DbPair.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/types/GermlineFilter.java b/linx/src/main/java/com/hartwig/hmftools/linx/types/GermlineFilter.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/types/GermlineFilter.java rename to linx/src/main/java/com/hartwig/hmftools/linx/types/GermlineFilter.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/types/LinkedPair.java b/linx/src/main/java/com/hartwig/hmftools/linx/types/LinkedPair.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/types/LinkedPair.java rename to linx/src/main/java/com/hartwig/hmftools/linx/types/LinkedPair.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/types/LinxConstants.java b/linx/src/main/java/com/hartwig/hmftools/linx/types/LinxConstants.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/types/LinxConstants.java rename to linx/src/main/java/com/hartwig/hmftools/linx/types/LinxConstants.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/types/ResolvedType.java b/linx/src/main/java/com/hartwig/hmftools/linx/types/ResolvedType.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/types/ResolvedType.java rename to linx/src/main/java/com/hartwig/hmftools/linx/types/ResolvedType.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/types/SglMapping.java b/linx/src/main/java/com/hartwig/hmftools/linx/types/SglMapping.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/types/SglMapping.java rename to linx/src/main/java/com/hartwig/hmftools/linx/types/SglMapping.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/types/SvBreakend.java b/linx/src/main/java/com/hartwig/hmftools/linx/types/SvBreakend.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/types/SvBreakend.java rename to linx/src/main/java/com/hartwig/hmftools/linx/types/SvBreakend.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/types/SvCluster.java b/linx/src/main/java/com/hartwig/hmftools/linx/types/SvCluster.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/types/SvCluster.java rename to linx/src/main/java/com/hartwig/hmftools/linx/types/SvCluster.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/types/SvVarData.java b/linx/src/main/java/com/hartwig/hmftools/linx/types/SvVarData.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/types/SvVarData.java rename to linx/src/main/java/com/hartwig/hmftools/linx/types/SvVarData.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/CircosConfig.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/CircosConfig.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/CircosConfig.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/CircosConfig.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/SampleData.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/SampleData.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/SampleData.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/SampleData.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/SvVisualiser.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/SvVisualiser.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/SvVisualiser.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/SvVisualiser.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/SvVisualiserConfig.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/SvVisualiserConfig.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/SvVisualiserConfig.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/SvVisualiserConfig.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/ChromosomeRangeExecution.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/ChromosomeRangeExecution.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/ChromosomeRangeExecution.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/ChromosomeRangeExecution.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/CircosConfigWriter.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/CircosConfigWriter.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/CircosConfigWriter.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/CircosConfigWriter.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/CircosData.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/CircosData.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/CircosData.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/CircosData.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/CircosDataWriter.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/CircosDataWriter.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/CircosDataWriter.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/CircosDataWriter.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/ColorPicker.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/ColorPicker.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/ColorPicker.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/ColorPicker.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/FusionDataWriter.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/FusionDataWriter.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/FusionDataWriter.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/FusionDataWriter.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/FusionExecution.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/FusionExecution.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/FusionExecution.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/FusionExecution.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/Highlights.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/Highlights.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/Highlights.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/Highlights.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/ProteinDomainColors.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/ProteinDomainColors.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/ProteinDomainColors.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/ProteinDomainColors.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/ScaleContig.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/ScaleContig.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/ScaleContig.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/ScaleContig.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/ScaleIntrons.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/ScaleIntrons.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/ScaleIntrons.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/ScaleIntrons.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/ScalePosition.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/ScalePosition.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/ScalePosition.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/ScalePosition.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/SegmentTerminal.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/SegmentTerminal.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/SegmentTerminal.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/SegmentTerminal.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/Span.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/Span.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/Span.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/Span.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/Thickness.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/Thickness.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/Thickness.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/Thickness.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/AdjustedPosition.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/AdjustedPosition.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/AdjustedPosition.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/AdjustedPosition.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/AdjustedPositions.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/AdjustedPositions.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/AdjustedPositions.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/AdjustedPositions.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Connector.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Connector.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Connector.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Connector.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Connectors.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Connectors.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Connectors.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Connectors.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/CopyNumberAlteration.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/CopyNumberAlteration.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/CopyNumberAlteration.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/CopyNumberAlteration.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/DisruptedExons.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/DisruptedExons.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/DisruptedExons.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/DisruptedExons.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Exon.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Exon.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Exon.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Exon.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/FusedExon.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/FusedExon.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/FusedExon.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/FusedExon.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/FusedExons.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/FusedExons.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/FusedExons.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/FusedExons.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/FusedProteinDomains.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/FusedProteinDomains.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/FusedProteinDomains.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/FusedProteinDomains.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Fusion.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Fusion.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Fusion.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Fusion.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Gene.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Gene.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Gene.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Gene.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Genes.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Genes.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Genes.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Genes.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/ProteinDomain.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/ProteinDomain.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/ProteinDomain.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/ProteinDomain.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Segment.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Segment.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Segment.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/Segment.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisCopyNumbers.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisCopyNumbers.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisCopyNumbers.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisCopyNumbers.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisExons.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisExons.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisExons.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisExons.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisFusions.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisFusions.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisFusions.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisFusions.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisLinks.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisLinks.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisLinks.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisLinks.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisProteinDomains.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisProteinDomains.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisProteinDomains.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisProteinDomains.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisSegments.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisSegments.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisSegments.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisSegments.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisSvData.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisSvData.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisSvData.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/data/VisSvData.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisCopyNumberFile.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisCopyNumberFile.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisCopyNumberFile.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisCopyNumberFile.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisDataWriter.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisDataWriter.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisDataWriter.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisDataWriter.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisFusionFile.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisFusionFile.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisFusionFile.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisFusionFile.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisGeneAnnotationType.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisGeneAnnotationType.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisGeneAnnotationType.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisGeneAnnotationType.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisGeneData.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisGeneData.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisGeneData.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisGeneData.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisGeneExonFile.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisGeneExonFile.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisGeneExonFile.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisGeneExonFile.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisProteinDomainFile.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisProteinDomainFile.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisProteinDomainFile.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisProteinDomainFile.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisSegmentFile.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisSegmentFile.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisSegmentFile.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisSegmentFile.java diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisSvDataFile.java b/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisSvDataFile.java similarity index 100% rename from sv-linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisSvDataFile.java rename to linx/src/main/java/com/hartwig/hmftools/linx/visualiser/file/VisSvDataFile.java diff --git a/sv-linx/src/main/resources/linx.version b/linx/src/main/resources/linx.version similarity index 100% rename from sv-linx/src/main/resources/linx.version rename to linx/src/main/resources/linx.version diff --git a/sv-linx/src/main/resources/log4j2.xml b/linx/src/main/resources/log4j2.xml similarity index 100% rename from sv-linx/src/main/resources/log4j2.xml rename to linx/src/main/resources/log4j2.xml diff --git a/sv-linx/src/main/resources/r/chromosomeRangePlot.R b/linx/src/main/resources/r/chromosomeRangePlot.R similarity index 100% rename from sv-linx/src/main/resources/r/chromosomeRangePlot.R rename to linx/src/main/resources/r/chromosomeRangePlot.R diff --git a/sv-linx/src/main/resources/r/cytoBand.txt b/linx/src/main/resources/r/cytoBand.txt similarity index 100% rename from sv-linx/src/main/resources/r/cytoBand.txt rename to linx/src/main/resources/r/cytoBand.txt diff --git a/sv-linx/src/main/resources/r/fusionPlot.R b/linx/src/main/resources/r/fusionPlot.R similarity index 100% rename from sv-linx/src/main/resources/r/fusionPlot.R rename to linx/src/main/resources/r/fusionPlot.R diff --git a/sv-linx/src/main/resources/readme/bfb.gif b/linx/src/main/resources/readme/bfb.gif similarity index 100% rename from sv-linx/src/main/resources/readme/bfb.gif rename to linx/src/main/resources/readme/bfb.gif diff --git a/sv-linx/src/main/resources/readme/chr7.png 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a/sv-linx/src/test/java/com/hartwig/hmftools/linx/analyser/AnnotationTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/analyser/AnnotationTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/analyser/AnnotationTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/analyser/AnnotationTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/analyser/CopyNumberTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/analyser/CopyNumberTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/analyser/CopyNumberTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/analyser/CopyNumberTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/analyser/DoubleMinuteTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/analyser/DoubleMinuteTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/analyser/DoubleMinuteTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/analyser/DoubleMinuteTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/analyser/FilteringTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/analyser/FilteringTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/analyser/FilteringTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/analyser/FilteringTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/analyser/FoldbackTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/analyser/FoldbackTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/analyser/FoldbackTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/analyser/FoldbackTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/analyser/InversionPairTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/analyser/InversionPairTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/analyser/InversionPairTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/analyser/InversionPairTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/analyser/LineTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/analyser/LineTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/analyser/LineTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/analyser/LineTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/analyser/ReplicationRepairTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/analyser/ReplicationRepairTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/analyser/ReplicationRepairTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/analyser/ReplicationRepairTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/analyser/SyntheticTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/analyser/SyntheticTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/analyser/SyntheticTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/analyser/SyntheticTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/analyser/TranslocationPairTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/analyser/TranslocationPairTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/analyser/TranslocationPairTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/analyser/TranslocationPairTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/chaining/ChainRoutinesTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/chaining/ChainRoutinesTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/chaining/ChainRoutinesTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/chaining/ChainRoutinesTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/chaining/ChainingActualTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/chaining/ChainingActualTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/chaining/ChainingActualTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/chaining/ChainingActualTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/chaining/ChainingComplexTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/chaining/ChainingComplexTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/chaining/ChainingComplexTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/chaining/ChainingComplexTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/chaining/ChainingSimpleTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/chaining/ChainingSimpleTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/chaining/ChainingSimpleTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/chaining/ChainingSimpleTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/chaining/LinkingTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/chaining/LinkingTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/chaining/LinkingTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/chaining/LinkingTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/clustering/ComplexMergeRuleTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/clustering/ComplexMergeRuleTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/clustering/ComplexMergeRuleTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/clustering/ComplexMergeRuleTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/clustering/SimpleMergeRuleTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/clustering/SimpleMergeRuleTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/clustering/SimpleMergeRuleTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/clustering/SimpleMergeRuleTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/drivers/AmpDriversTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/drivers/AmpDriversTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/drivers/AmpDriversTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/drivers/AmpDriversTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/drivers/HomDisruptionsTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/drivers/HomDisruptionsTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/drivers/HomDisruptionsTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/drivers/HomDisruptionsTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/fusion/DisruptionTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/fusion/DisruptionTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/fusion/DisruptionTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/fusion/DisruptionTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/fusion/FusionRulesTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/fusion/FusionRulesTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/fusion/FusionRulesTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/fusion/FusionRulesTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/fusion/FusionTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/fusion/FusionTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/fusion/FusionTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/fusion/FusionTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/fusion/RnaFusionTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/fusion/RnaFusionTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/fusion/RnaFusionTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/fusion/RnaFusionTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/fusion/SpecialFusionsTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/fusion/SpecialFusionsTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/fusion/SpecialFusionsTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/fusion/SpecialFusionsTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/gene/GeneCollectionTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/gene/GeneCollectionTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/gene/GeneCollectionTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/gene/GeneCollectionTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/misc/JcnCalcsTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/misc/JcnCalcsTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/misc/JcnCalcsTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/misc/JcnCalcsTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/misc/MiscTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/misc/MiscTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/misc/MiscTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/misc/MiscTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/utils/GeneTestUtils.java b/linx/src/test/java/com/hartwig/hmftools/linx/utils/GeneTestUtils.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/utils/GeneTestUtils.java rename to linx/src/test/java/com/hartwig/hmftools/linx/utils/GeneTestUtils.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/utils/LinxTester.java b/linx/src/test/java/com/hartwig/hmftools/linx/utils/LinxTester.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/utils/LinxTester.java rename to linx/src/test/java/com/hartwig/hmftools/linx/utils/LinxTester.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/utils/SampleDataLoader.java b/linx/src/test/java/com/hartwig/hmftools/linx/utils/SampleDataLoader.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/utils/SampleDataLoader.java rename to linx/src/test/java/com/hartwig/hmftools/linx/utils/SampleDataLoader.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/utils/SvTestUtils.java b/linx/src/test/java/com/hartwig/hmftools/linx/utils/SvTestUtils.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/utils/SvTestUtils.java rename to linx/src/test/java/com/hartwig/hmftools/linx/utils/SvTestUtils.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/visualiser/circos/CircosConfigWriterTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/visualiser/circos/CircosConfigWriterTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/visualiser/circos/CircosConfigWriterTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/visualiser/circos/CircosConfigWriterTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/visualiser/circos/CircosDataWriterTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/visualiser/circos/CircosDataWriterTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/visualiser/circos/CircosDataWriterTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/visualiser/circos/CircosDataWriterTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/visualiser/circos/ColorPickerTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/visualiser/circos/ColorPickerTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/visualiser/circos/ColorPickerTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/visualiser/circos/ColorPickerTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/visualiser/circos/ProteinDomainColorsTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/visualiser/circos/ProteinDomainColorsTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/visualiser/circos/ProteinDomainColorsTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/visualiser/circos/ProteinDomainColorsTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/visualiser/circos/ScaleContigTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/visualiser/circos/ScaleContigTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/visualiser/circos/ScaleContigTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/visualiser/circos/ScaleContigTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/visualiser/circos/ScaleIntronsTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/visualiser/circos/ScaleIntronsTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/visualiser/circos/ScaleIntronsTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/visualiser/circos/ScaleIntronsTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/visualiser/data/DisruptedExonsTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/visualiser/data/DisruptedExonsTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/visualiser/data/DisruptedExonsTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/visualiser/data/DisruptedExonsTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/visualiser/data/FusedExonsTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/visualiser/data/FusedExonsTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/visualiser/data/FusedExonsTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/visualiser/data/FusedExonsTest.java diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/visualiser/data/SegmentsTest.java b/linx/src/test/java/com/hartwig/hmftools/linx/visualiser/data/SegmentsTest.java similarity index 100% rename from sv-linx/src/test/java/com/hartwig/hmftools/linx/visualiser/data/SegmentsTest.java rename to linx/src/test/java/com/hartwig/hmftools/linx/visualiser/data/SegmentsTest.java diff --git a/sv-linx/src/test/resources/sample_data/COLO829T b/linx/src/test/resources/sample_data/COLO829T similarity index 100% rename from sv-linx/src/test/resources/sample_data/COLO829T rename to linx/src/test/resources/sample_data/COLO829T diff --git a/sv-linx/src/test/resources/sample_data/CT_SAMPLE1 b/linx/src/test/resources/sample_data/CT_SAMPLE1 similarity index 100% rename from sv-linx/src/test/resources/sample_data/CT_SAMPLE1 rename to linx/src/test/resources/sample_data/CT_SAMPLE1 diff --git a/sv-linx/src/test/resources/sample_data/DM_SAMPLE1 b/linx/src/test/resources/sample_data/DM_SAMPLE1 similarity index 100% rename from sv-linx/src/test/resources/sample_data/DM_SAMPLE1 rename to linx/src/test/resources/sample_data/DM_SAMPLE1 diff --git a/sv-linx/src/test/resources/sample_data/DM_SAMPLE2 b/linx/src/test/resources/sample_data/DM_SAMPLE2 similarity index 100% rename from sv-linx/src/test/resources/sample_data/DM_SAMPLE2 rename to linx/src/test/resources/sample_data/DM_SAMPLE2 diff --git a/sv-linx/src/test/resources/sample_data/FB_SAMPLE1 b/linx/src/test/resources/sample_data/FB_SAMPLE1 similarity index 100% rename from sv-linx/src/test/resources/sample_data/FB_SAMPLE1 rename to linx/src/test/resources/sample_data/FB_SAMPLE1 diff --git a/pom.xml b/pom.xml index e057d1c53d..9ac7b3d661 100644 --- a/pom.xml +++ b/pom.xml @@ -23,7 +23,7 @@ cobalt purple sage - sv-linx + linx sv-tools virus-interpreter neo @@ -63,7 +63,7 @@ 3.1 1.11 1.0 - 1.16 + 1.16 1.0 1.0 3.2 @@ -196,8 +196,8 @@ com.hartwig - sv-linx - ${sv-linx.version} + linx + ${linx.version} com.hartwig diff --git a/protect/README.md b/protect/README.md index 0f54fb313f..65226db512 100644 --- a/protect/README.md +++ b/protect/README.md @@ -35,12 +35,12 @@ gene inactivation is considered applicable in case of a deletion. #### Homozygous disruptions -When a gene has been homozygously disrupted according to [LINX](../sv-linx/README.md), evidence is applicable when it has been defined +When a gene has been homozygously disrupted according to [LINX](../linx/README.md), evidence is applicable when it has been defined on a gene level with event either inactivation, deletion or any mutation. #### Fusions -For fusions that are deemed reportable according to [LINX](../sv-linx/README.md) the following matching is performed: +For fusions that are deemed reportable according to [LINX](../linx/README.md) the following matching is performed: - Evidence defined on a promiscuous gene level is always considered applicable if a fusion with that gene is reported either in 5' or 3' position. - Evidence that is applicable on an exact fusion pair has to match with the actual fusion pair, and also has to match the (optional) diff --git a/purple/DriverCatalog.md b/purple/DriverCatalog.md index 049223f04d..a96c4fa083 100644 --- a/purple/DriverCatalog.md +++ b/purple/DriverCatalog.md @@ -2,7 +2,7 @@ If a gene panel is configured, PURPLE will compile a catalog of drivers including point mutations and copy number events. To include point mutations in the driver catalog, the somatic VCF must be annotated with SnpEff. -Running [LINX](https://github.com/hartwigmedical/hmftools/tree/master/sv-linx) enriches the PURPLE driver catalog with the addition of both homozygous disruption drivers and fusions +Running [LINX](https://github.com/hartwigmedical/hmftools/tree/master/linx) enriches the PURPLE driver catalog with the addition of both homozygous disruption drivers and fusions ## Gene Panel Configuration diff --git a/sv-tools/pom.xml b/sv-tools/pom.xml index a6b9f9d522..5bb7dbb4e5 100644 --- a/sv-tools/pom.xml +++ b/sv-tools/pom.xml @@ -24,7 +24,7 @@ com.hartwig - sv-linx + linx org.jooq