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Project: hmftools (GitHub Link)
  • hmftools-master
    • knowledgebase-importer
      • src
        • main
          • resources
            • knowledgebase_disease_doids.csv
            • log4j2.xml
          • kotlin
            • com
              • hartwig
                • hmftools
                  • knowledgebaseimporter
                    • cgi
                      • CgiActionableRecord.kt
                      • CgiKnownKbRecord.kt
                      • Cgi.kt
                      • CgiDrugConstants.kt
                      • CgiDrug.kt
                      • CgiDrugReader.kt
                      • readers
                        • CgiActionableGeneMutationsReader.kt
                        • CgiActionableCDnaAnnotationReader.kt
                        • CgiActionableCodonMutationsReader.kt
                        • CgiActionableCnvReader.kt
                        • CgiActionableProteinAnnotationReader.kt
                        • CgiKnownInputReader.kt
                        • CgiActionableCodonRangeMutationsReader.kt
                        • CgiActionableMutationListReader.kt
                        • CgiActionableVariantReader.kt
                        • CgiGDnaReader.kt
                        • CgiActionableFusionReader.kt
                      • input
                        • CgiKnownInput.kt
                        • CgiActionableInput.kt
                        • CgiInput.kt
                      • CgiMetadata.kt
                    • output
                      • CsvOutput.kt
                      • HmfDrug.kt
                      • KnownVariantOutput.kt
                      • HmfLevel.kt
                      • CancerTypeDoidOutput.kt
                      • Actionability.kt
                      • ActionableEvent.kt
                      • HmfResponse.kt
                    • diseaseOntology
                      • DiseaseOntology.kt
                      • Doid.kt
                    • CgiTreatmentExtractorApp.kt
                    • transvar
                      • TransvarCdnaAnalyzer.kt
                      • matchers
                        • TransvarProteinMatcher.kt
                        • TransvarCDnaMatcher.kt
                        • Matcher.kt
                        • TransvarMatcher.kt
                        • AminoAcidSymbols.kt
                        • DnaMutations.kt
                        • TransvarGDnaMatcher.kt
                        • CodonMatcher.kt
                      • TransvarOutput.kt
                      • TransvarAnalyzer.kt
                      • TransvarProteinAnalyzer.kt
                      • GDNAVariantExtractor.kt
                    • FusionsAnalysis.kt
                    • oncoKb
                      • OncoKb.kt
                      • OncoKnownRecord.kt
                      • readers
                        • OncoAnyActionableEventReader.kt
                        • OncoExonMutationReader.kt
                        • OncoGeneMutationReader.kt
                        • OncoAnyKnownEventReader.kt
                        • OncoCnvReader.kt
                        • OncoFusionReader.kt
                      • input
                        • OncoKnownInput.kt
                        • OncoKbInput.kt
                        • OncoActionableInput.kt
                      • OncoMetadata.kt
                      • OncoActionableRecord.kt
                    • Constants.kt
                    • CSVFunctions.kt
                    • gene
                      • GeneModel.kt
                    • Knowledgebase.kt
                    • civic
                      • Civic.kt
                      • CivicRecord.kt
                      • CivicMetadata.kt
                      • readers
                        • CivicRangeMutationReader.kt
                        • CivicVariantReader.kt
                        • CivicCDnaAnnotationReader.kt
                        • CivicCnvReader.kt
                        • CivicMultipleEventsReader.kt
                        • CivicFusionReader.kt
                        • CivicKnowledgebaseVariantReader.kt
                      • input
                        • CivicEvidenceInput.kt
                        • CivicVariantInput.kt
                      • CivicEvidence.kt
                    • cosmic
                      • Cosmic.kt
                    • iclusion
                      • IclusionMetadata.kt
                      • Iclusion.kt
                      • IclusionEvent.kt
                      • IclusionRecord.kt
                      • readers
                        • IclusionCnvReader.kt
                        • IclusionExonMutationReader.kt
                        • IclusionTransvarReader.kt
                        • IclusionCodonReader.kt
                        • IclusionGeneMutationReader.kt
                        • IclusionFusionReader.kt
                    • KnowledgebaseImporterApplication.kt
                    • knowledgebases
                      • ActionableItem.kt
                      • ActionableRecord.kt
                      • RecordMetadata.kt
                      • CorrectedInput.kt
                      • KnowledgebaseRecord.kt
                      • SomaticEvent.kt
                      • KnownRecord.kt
                      • KnowledgebaseSource.kt
                      • RecordAnalyzer.kt
                      • readers
                        • CDnaAnnotationReader.kt
                        • ProteinAnnotationReader.kt
                        • SomaticEventReader.kt
                        • KnowledgebaseAnyEventReader.kt
                        • KnowledgebaseEventReader.kt
                      • events
                        • KnowledgebaseEvent.kt
                        • HgvsVariantType.kt
                    • FusionReader.kt
        • test
          • kotlin
            • com
              • hartwig
                • hmftools
                  • knowledgebaseimporter
                    • cgi
                      • readers
                        • CgiActionableCDnaAnnotationReaderTest.kt
                        • CgiGDnaReaderTest.kt
                        • CgiActionableMutationListReaderTest.kt
                        • CgiActionableCodonMutationsReaderTest.kt
                        • CgiActionableGeneMutationsReaderTest.kt
                        • CgiActionableVariantReaderTest.kt
                        • CgiActionableProteinAnnotationReaderTest.kt
                        • CgiActionableCodonRangeMutationsReaderTest.kt
                    • FusionReaderTest.kt
                    • transvar
                      • matchers
                        • CodonMatcherTest.kt
                        • TransvarCDnaMatcherTest.kt
                        • TransvarGDnaMatcherTest.kt
                        • TransvarProteinMatcherTest.kt
                    • oncoKb
                      • OncoKnownRecordTest.kt
                      • readers
                        • OncoAnyActionableEventReaderTest.kt
                        • OncoExonMutationReaderTest.kt
                        • OncoFusionReaderTest.kt
                        • OncoCnvReaderTest.kt
                    • civic
                      • readers
                        • CivicCDnaAnnotationReaderTest.kt
                        • CivicRangeMutationReaderTest.kt
                        • CivicKnowledgebaseVariantReaderTest.kt
                        • CivicMultipleEventsReaderTest.kt
                        • CivicFusionReaderTest.kt
                      • CivicEvidenceTest.kt
                    • iclusion
                      • readers
                        • IclusionCnvReaderTest.kt
                        • IclusionExonMutationReaderTest.kt
                        • IclusionFusionReaderTest.kt
                        • IclusionCodonReaderTest.kt
                        • IclusionGeneMutationReaderTest.kt
      • pom.xml
      • README.md
    • health-checker
      • src
        • main
          • resources
            • log4j2.xml
          • java
            • com
              • hartwig
                • hmftools
                  • healthchecker
                    • result
                      • QCValue.java
                      • QCValueType.java
                    • runners
                      • MetricsChecker.java
                      • AmberChecker.java
                      • PurpleChecker.java
                      • HealthChecker.java
                    • HealthCheckEvaluation.java
                    • HealthChecksApplication.java
        • test
          • resources
            • amber
              • malformed.amber.qc
              • tumor.amber.qc
            • purple
              • malformed.purple.qc
              • tumor.purple.qc
            • metrics
              • tumor.wgsmetrics
              • reference.wgsmetrics
              • malformed.wgsmetrics
          • java
            • com
              • hartwig
                • hmftools
                  • healthchecker
                    • runners
                      • AmberCheckerTest.java
                      • MetricsCheckerTest.java
                      • PurpleCheckerTest.java
                    • HealthCheckEvaluationTest.java
                    • HealthChecksApplicationTest.java
      • pom.xml
    • gripss
      • src
        • main
          • resources
            • gripss.version
            • log4j2.xml
          • kotlin
            • com
              • hartwig
                • hmftools
                  • extensions
                    • VariantContextExtensions.kt
                    • GenotypeExtensions.kt
                  • gripss
                    • link
                      • Link.kt
                      • TransitiveLink.kt
                      • DsbLink.kt
                      • AlternatePath.kt
                      • AssemblyLink.kt
                      • LinkRescue.kt
                    • StructuralVariantContext.kt
                    • store
                      • VariantStore.kt
                      • SoftFilterStore.kt
                      • LocationSeek.kt
                      • LinkStore.kt
                      • LocationStore.kt
                    • GripssConfig.kt
                    • dedup
                      • DedupSingle.kt
                      • DedupPair.kt
                    • GripssApplication.kt
                    • ContigComparator.kt
                    • GripssVCF.kt
                    • VariantType.kt
                  • bedpe
                    • Location.kt
        • test
          • kotlin
            • com
              • hartwig
                • hmftools
                  • gripss
                    • StructuralVariantContextTest.kt
                    • VariantTypeTest.kt
                    • link
                      • AssemblyLinkTest.kt
                      • TransitiveLinkTest.kt
                      • LinkRescueTest.kt
                      • DsbLinkTest.kt
                    • VariantContextTestFactory.kt
                    • RealignmentTest.kt
                    • dedup
                      • DedupSingleTest.kt
                  • bedpe
                    • LocationTest.kt
                  • store
                    • LocationStoreTest.kt
                    • LocationTest.kt
                    • SoftFilterStoreTest.kt
      • pom.xml
      • README.md
    • hmf-gene-panel-builder
      • src
        • main
          • resources
            • ensembl_query.sql
            • log4j2.xml
            • readme
          • java
            • com
              • hartwig
                • hmftools
                  • genepanel
                    • HmfGenePanelBuilder.java
      • pom.xml
    • patient-db
      • src
        • main
          • resources
            • tumor_location_mapping.csv
            • log4j2.xml
            • setup_database.sh
            • treatment_mapping.csv
            • readme
            • biopsy_site_mapping.csv
            • patches
              • patientdb3.2_to_3.3_migration.sql
              • patientdb3.11_to_3.12_migration.sql
              • variant_annotator2.12_to_2.13_migration.sql
              • linx_1.3.sql
              • patientdb2.5_to_2.6_migration.sql
              • patientdb3.29_to_3.30_migration.sql
              • patientdb2.1_to_2.2_migration.sql
              • variant_annotator2.11_to_2.12_migration.sql
              • variant_annotator1.6_to_2.1_migration.sql
              • variant_annotator1.0_to_1.1_migration.sql
              • purple2.29_to_2.30_migration.sql
              • purple2.16_to_2.17_migration.sql
              • patientdb3.41_to_3.42_migration.sql
              • purple2.6_to_2.7_migration.sql
              • variant_annotator1.1_to_1.2_migration.sql
              • patientdb2.6_to_3.0_migration.sql
              • patientdb3.6_to_3.7_migration.sql
              • bachelor1.8_to_1.9_migration.sql
              • patientdb3.22_to_3.23_migration.sql
              • patientdb3.40_to_3.41_migration.sql
              • linx_1.0.sql
              • purple2.24_to_2.25_migration.sql
              • purple2.4_to_2.5_migration.sql
              • purple2.15_to_2.16_migration.sql
              • linx_1.5.sql
              • purple2.30_to_2.31_migration.sql
              • patientdb3.32_to_3.33_migration.sql
              • purple2.5_to_2.6_migration.sql
              • bachelor1.7_to_1.8_migration.sql
              • protect_1.0.sql
              • patientdb1.8_to_2.0_migration.sql
              • bachelor1.6_to_1.7_migration.sql
              • patientdb3.36_to_3.37_migration.sql
              • patientdb3.18_to_3.19_migration.sql
              • linx_1.2.sql
              • variant_annotator1.3_to_1.4_migration.sql
              • purple2.17_to_2.18_migration.sql
              • purple2.14_to_2.15_migration.sql
              • patientdb3.43_to_3.44_migration.sql
              • variant_annotator2.13_to_2.14_migration.sql
              • purple2.37_to_2.38_migration.sql
              • patientdb1.7_to_1.8_migration.sql
              • purple1.4_to_2.0_migration.sql
              • variant_annotator2.6_to_2.7_migration.sql
              • patientdb3.23_to_3.24_migration.sql
              • patientdb3.12_to_3.13_migration.sql
              • purple2.3_to_2.4_migration.sql
              • linx_1.10.sql
              • linx_1.4.sql
              • patientdb2.3_to_2.4_migration.sql
              • variant_annotator1.5_to_1.6_migration.sql
              • patientdb3.13_to_3.14_migration.sql
              • patientdb3.37_to_3.38_migration.sql
              • purple2.0_to_2.3_migration.sql
              • patientdb3.38_to_3.39_migration.sql
              • purple2.43_to_2.44_migration.sql
              • variant_annotator2.2_to_2.3_migration.sql
              • patientdb1.4_to_1.5_migration.sql
              • patientdb1.5_to_1.6_migration.sql
              • purple2.8_to_2.9_migration.sql
            • generate_database.sql
          • java
            • com
              • hartwig
                • hmftools
                  • patientdb
                    • matchers
                      • TreatmentMatcher.java
                      • BiopsyMatcher.java
                      • MatchResult.java
                      • TreatmentResponseMatcher.java
                    • dao
                      • PurityDAO.java
                      • ClinicalDAO.java
                      • CopyNumberDAO.java
                      • GeneCopyNumberDAO.java
                      • StructuralVariantDAO.java
                      • EcrfDAO.java
                      • StructuralVariantFusionDAO.java
                      • RNADAO.java
                      • SomaticVariantDAO.java
                      • DatabaseUtil.java
                      • StructuralVariantClusterDAO.java
                      • ChordDAO.java
                      • AmberDAO.java
                      • MetricDAO.java
                      • SomaticVariantStreamWriter.java
                      • DriverCatalogDAO.java
                      • ClinicalEvidenceDAO.java
                      • DatabaseAccess.java
                      • CanonicalTranscriptDAO.java
                      • PgxDAO.java
                      • ValidationFindingDAO.java
                    • LoadClinicalData.java
                    • CreateShallowSeqDB.java
                    • LoadRNAMetaData.java
                    • Utils.java
                    • DumpTumorLocationData.java
                    • LoadPurpleSomaticVariants.java
                    • validators
                      • PatientValidator.java
                      • CurationValidator.java
                    • EcrfModels.java
                    • context
                      • MetaDataResolver.java
                      • RunContextImpl.java
                      • ProductionRunContextFactory.java
                      • RunContext.java
                    • LoadPurpleData.java
                    • LoadAmberData.java
                    • DeleteSampleFromDatabase.java
                    • LoadMetricsData.java
                    • LoadCanonicalTranscripts.java
                    • LoadChordData.java
                    • Config.java
                    • LoadEvidenceData.java
                    • LoadStructuralVariants.java
                    • data
                      • DrugData.java
                      • BiopsyTreatmentResponseData.java
                      • TumorTypeLims.java
                      • SampleData.java
                      • BiopsyData.java
                      • RanoMeasurementData.java
                      • TreatmentData.java
                      • CuratedDrug.java
                      • PreTreatmentData.java
                      • BiopsyTreatmentData.java
                      • BaselineData.java
                      • Patient.java
                      • CuratedBiopsyType.java
                      • CuratedTumorLocation.java
                      • TumorMarkerData.java
                    • LoadSomaticVariants.java
                    • LoadDriverCatalog.java
                    • curators
                      • CleanableCurator.java
                      • TreatmentCurator.java
                      • SpellCheckerTokenFilter.java
                      • SearchToken.java
                      • TumorLocationCurator.java
                      • BiopsySiteCurator.java
                      • DrugEntry.java
                      • ConcatenatingFilter.java
                    • readers
                      • LimsSampleReader.java
                      • RunsFolderReader.java
                      • EcrfPatientReader.java
                      • WidePatientReader.java
                      • ColoPatientReader.java
                      • cpct
                        • PreTreatmentReader.java
                        • CpctUtil.java
                        • CpctPatientReader.java
                        • BiopsyTreatmentResponseReader.java
                        • TumorMarkerReader.java
                        • BiopsyTreatmentReader.java
                        • RanoMeasurementReader.java
                        • BiopsyReader.java
                        • BaselineReader.java
                      • wide
                        • WideResponseData.java
                        • WideFiveDays.java
                        • WideFileInputInterpreter.java
                        • WideAvlTreatmentData.java
                        • WideEcrfFileReader.java
                        • WideClinicalData.java
                        • WideEcrfModel.java
                        • WideBiopsyData.java
                        • WidePreAvlTreatmentData.java
                      • CorePatientReader.java
                      • drup
                        • DrupPatientReader.java
                        • BiopsyReader.java
                        • BaselineReader.java
                    • LoadPgxData.java
        • test
          • resources
            • context
              • RunDirSomatic
                • metadata
              • RunDirP5
                • metadata.json
              • RunDirNoMetaData
                • .gitkeep
              • RunDirNoRefSample
                • metadata
              • RunDirNoSetName
                • metadata
            • test_biopsy_site_mapping.csv
            • test_tumor_location_mapping.csv
            • wide
              • wide_pre_avl_treatments.csv
              • wide_avl_treatments.csv
              • wide_five_days.csv
              • wide_responses.csv
              • wide_biopsies.csv
            • test_treatment_mapping.csv
          • java
            • com
              • hartwig
                • hmftools
                  • patientdb
                    • matchers
                      • TreatmentMatcherTest.java
                      • TreatmentResponseMatcherTest.java
                      • BiopsyMatcherTest.java
                    • LoadClinicalDataTest.java
                    • validators
                      • PatientValidatorTest.java
                    • context
                      • ProductionRunContextFactoryTest.java
                      • MetaDataResolverTest.java
                    • data
                      • TestDatamodelFactory.java
                      • BiopsyTreatmentResponseDataTest.java
                      • TreatmentDataTest.java
                    • curators
                      • TreatmentCuratorTest.java
                      • TestCuratorFactory.java
                      • BiopsySiteCuratorTest.java
                      • TumorLocationCuratorTest.java
                    • readers
                      • cpct
                        • CpctPatientReaderTest.java
                        • BaselineReaderTest.java
                        • BiopsyReaderTest.java
                        • BiopsyTreatmentResponseReaderTest.java
                      • WidePatientReaderTest.java
                      • wide
                        • WideFileInputInterpreterTest.java
                        • WideEcrfFileReaderTest.java
                      • drup
                        • DrupPatientReaderTest.java
      • pom.xml
    • hmf-extensions
      • pom.xml
      • hmf-extensions-csv
        • src
          • main
            • kotlin
              • com
                • hartwig
                  • hmftools
                    • extensions
                      • csv
                        • CsvData.kt
                        • CsvWriter.kt
                        • CsvReader.kt
                        • Defaults.kt
          • test
            • resources
              • test.csv
            • kotlin
              • com
                • hartwig
                  • hmftools
                    • extensions
                      • csv
                        • CsvExtensionsTest.kt
        • pom.xml
      • hmf-extensions-cli
        • src
          • main
            • kotlin
              • com
                • hartwig
                  • hmftools
                    • extensions
                      • cli
                        • options
                          • filesystem
                            • InputDirOption.kt
                            • InputFileOption.kt
                            • RequiredInputDirOption.kt
                            • RequiredInputFileOption.kt
                          • enums
                            • RequiredEnumOption.kt
                            • EnumOption.kt
                          • HmfOption.kt
                          • validators
                            • primitives
                              • EnumValidator.kt
                              • IsDirectoryValidator.kt
                              • FileSystemExistsValidator.kt
                              • IsFileValidator.kt
                              • CommandValidator.kt
                            • InputFileValidator.kt
                            • OptionValidator.kt
                            • InputDirValidator.kt
                          • commands
                            • CommandOption.kt
                            • RequiredCommandOption.kt
                          • HmfOptions.kt
                          • strings
                            • OutputOption.kt
                            • RequiredInputOption.kt
                            • InputOption.kt
                            • RequiredOutputOption.kt
                          • flags
                            • RequiredFlagOption.kt
                            • FlagOption.kt
                        • OptionsExtensions.kt
          • test
            • resources
              • testFile.txt
            • kotlin
              • com
                • hartwig
                  • hmftools
                    • extensions
                      • cli
                        • options
                          • filesystem
                            • InputFileOptionTest.kt
                            • RequiredInputFileOptionTest.kt
                            • InputDirOptionTest.kt
                          • enums
                            • RequiredEnumOptionTest.kt
                            • EnumOptionTest.kt
                          • commands
                            • CommandOptionTest.kt
        • pom.xml
      • hmf-extensions-samtools
        • src
          • main
            • kotlin
              • com
                • hartwig
                  • hmftools
                    • extensions
                      • samtools
                        • VariantContextExtensions.kt
        • pom.xml
    • sage
      • src
        • main
          • resources
            • sage.version
            • log4j2.xml
            • readme
            • r
              • loadvcf.R
              • baseQualityRecalibrationPlot.R
          • java
            • com
              • hartwig
                • hmftools
                  • sage
                    • rearrange
                      • Rearrangement.java
                    • ref
                      • RefSequence.java
                    • vcf
                      • SageVCF.java
                    • pon
                      • PonApplication.java
                      • PonBuilder.java
                      • PonVCF.java
                      • RunnableTaskCompletion.java
                    • variant
                      • SageVariantTier.java
                      • SageVariantFactory.java
                      • SageVariantContextFactory.java
                      • SageVariant.java
                    • candidate
                      • Candidates.java
                      • Candidate.java
                    • count
                      • EvictingArray.java
                    • SageHotspotBedBuilder.java
                    • context
                      • AltContext.java
                      • RefContextConsumer.java
                      • RefContext.java
                      • RefContextFactory.java
                      • AltRead.java
                    • select
                      • HotspotSelector.java
                      • SamRecordSelector.java
                      • RegionSelector.java
                      • PositionSelector.java
                      • TierSelector.java
                      • PanelSelector.java
                    • SageHotspotApplication.java
                    • config
                      • SageConfig.java
                      • SoftFilter.java
                      • QualityConfig.java
                      • FilterConfig.java
                      • BaseQualityRecalibrationConfig.java
                      • SoftFilterConfig.java
                    • SageHotspotAnnotation.java
                    • quality
                      • QualityRecalibrationRecord.java
                      • QualityRecalibration.java
                      • QualityRecalibrationKey.java
                      • QualityCounterCigarHandler.java
                      • QualityCounter.java
                      • QualityRecalibrationMap.java
                      • QualityCounterKey.java
                      • QualityCounterFactory.java
                      • QualityRecalibrationFactory.java
                      • QualityRecalibrationFile.java
                    • evidence
                      • CandidateEvidence.java
                      • ReadContextEvidence.java
                    • SagePostProcessApplication.java
                    • realign
                      • RealignedContext.java
                      • Realigned.java
                      • RealignedType.java
                    • samtools
                      • NumberEvents.java
                    • pipeline
                      • SomaticPipeline.java
                      • ChromosomePipeline.java
                      • SageVariantPipeline.java
                    • sam
                      • SamSlicerFactory.java
                      • CigarTraversal.java
                      • SamSlicer.java
                      • CigarHandler.java
                    • snpeff
                      • SagePostProcess.java
                    • phase
                      • LocalPhaseSet.java
                      • MixedSomaticGermlineDedup.java
                      • MixedSomaticGermlineIdentifier.java
                      • DedupMnv.java
                      • RightAlignMicrohomology.java
                      • Phase.java
                      • BufferedPostProcessor.java
                      • DedupRealign.java
                      • DedupIndel.java
                      • LocalRealignSet.java
                      • PhasedInframeIndel.java
                    • read
                      • IndexedBases.java
                      • RawContext.java
                      • ReadContextMatch.java
                      • ReadContextCounter.java
                      • RawContextCigarHandler.java
                      • RawContextFactory.java
                      • ReadContextCounterFactory.java
                      • ReadContext.java
                      • ReadContextFactory.java
                      • ReadContextCounters.java
                    • SageApplication.java
                    • SageHotspotApplicationConfig.java
        • test
          • resources
            • refsequence
              • refsequence.fasta
              • refsequence.fasta.fai
          • java
            • com
              • hartwig
                • hmftools
                  • sage
                    • SageHotspotBedBuilderTest.java
                    • rearrange
                      • RearrangementTest.java
                    • ref
                      • RefSequenceTest.java
                    • SageHotspotAnnotationTest.java
                    • count
                      • EvictingArrayTest.java
                    • context
                      • AltContextTest.java
                      • RefContextConsumerTest.java
                    • select
                      • PanelSelectorTest.java
                    • config
                      • SageConfigTest.java
                      • SoftFilterTest.java
                    • quality
                      • QualityRecalibrationFactoryTest.java
                    • realign
                      • RealignedTest.java
                    • phase
                      • RightAlignMicrohomologyTest.java
                      • MixedGermlineTest.java
                      • MixedSomaticGermlineDedupTest.java
                      • BufferedPostProcessorTest.java
                      • LocalPhaseSetTest.java
                    • read
                      • IndexedBasesTest.java
                      • ReadContextCounterTest.java
                      • ReadContextFactoryTest.java
                      • ReadContextTest.java
      • pom.xml
      • README_2.md
      • README.md
    • vicc-knowledgebase-importer
      • src
        • main
          • resources
            • database
              • create_vicc_database.sql
              • readme
              • regenerate_local_vicc_db
            • log4j2.xml
          • java
            • com
              • hartwig
                • hmftools
                  • vicc
                    • dao
                      • ViccDAO.java
                      • CgiDAOFunctions.java
                      • BRCADAOFunctions.java
                      • PmkbDAOFunctions.java
                      • JaxTrialsDAOFunctions.java
                      • JaxDAOFunctions.java
                      • MolecularMatchDAOFunctions.java
                      • CivicDAOFunctions.java
                      • MolecularMatchTrialsDAOFunctions.java
                      • SageDAOFunctions.java
                      • OncokbDAOFunctions.java
                    • selection
                      • ViccQuerySelection.java
                    • util
                      • TranscriptExtractor.java
                      • ProteinAnnotationExtractor.java
                    • ViccReaderTestApplication.java
                    • reader
                      • OncokbObjectFactory.java
                      • PmkbObjectFactory.java
                      • BRCAObjectFactory.java
                      • ViccJsonReader.java
                      • ViccDatamodelChecker.java
                      • CivicObjectFactory.java
                      • JaxObjectFactory.java
                      • MolecularMatchObjectFactory.java
                      • JaxTrialsObjectFactory.java
                      • JsonFunctions.java
                      • ViccDatamodelCheckerFactory.java
                      • SageObjectFactory.java
                      • MolecularMatchTrialsObjectFactory.java
                      • CgiObjectFactory.java
                    • datamodel
                      • Taxonomy.java
                      • EvidenceInfo.java
                      • cgi
                        • Cgi.java
                      • ViccSource.java
                      • pmkb
                        • PmkbVariant.java
                        • PmkbGene.java
                        • PmkbTissue.java
                        • PmkbTumor.java
                        • Pmkb.java
                      • brca
                        • Brca.java
                        • BrcaAnnotationESP.java
                        • BrcaAnnotationLOVD.java
                        • BrcaAnnotationExAC.java
                        • BrcaAnnotationENIGMA.java
                        • BrcaAnnotationClinVar.java
                        • BrcaAnnotationExLOVD.java
                        • BrcaAnnotation1000Genomes.java
                        • BrcaAnnotationBIC.java
                      • KbSpecificObject.java
                      • FeatureInfo.java
                      • Phenotype.java
                      • Evidence.java
                      • sage
                        • Sage.java
                      • molecularmatch
                        • MolecularMatchGRCh37Location.java
                        • MolecularMatchAstRight.java
                        • MolecularMatchAstLeftRight.java
                        • MolecularMatchAstLeftLeft.java
                        • MolecularMatchAstRightRight.java
                        • MolecularMatchWGSALocation.java
                        • MolecularMatchExonBoundaries.java
                        • MolecularMatchFusionGenomicRegion.java
                        • MolecularMatchPosition.java
                        • MolecularMatchFusion.java
                        • MolecularMatchGRCh37TranscriptConsequence.java
                        • MolecularMatchClassification.java
                        • MolecularMatchParent.java
                        • MolecularMatchCriteriaUnmet.java
                        • MolecularMatchExonsInfo.java
                        • MolecularMatchTierExplanation.java
                        • MolecularMatchTherapeuticContext.java
                        • MolecularMatchAst.java
                        • MolecularMatchMutation.java
                        • MolecularMatch.java
                        • MolecularMatchLocation.java
                        • MolecularMatchTag.java
                        • MolecularMatchSource.java
                        • MolecularMatchWGSAMap.java
                        • MolecularMatchFusionData.java
                        • MolecularMatchAstLeft.java
                        • MolecularMatchTranscriptConsequence.java
                        • MolecularMatchVariantInfo.java
                        • MolecularMatchAstRightLeft.java
                        • MolecularMatchPrevalence.java
                      • jaxtrials
                        • JaxTrialsIndication.java
                        • JaxTrials.java
                        • JaxTrialsVariantRequirementDetails.java
                        • JaxTrialsTherapy.java
                        • JaxTrialsMolecularProfile.java
                      • jax
                        • JaxTherapy.java
                        • JaxIndication.java
                        • Jax.java
                        • JaxReference.java
                        • JaxMolecularProfile.java
                      • FeatureAttribute.java
                      • EvidenceType.java
                      • ViccEntry.java
                      • molecularmatchtrials
                        • MolecularMatchTrialsOverallContact.java
                        • MolecularMatchTrialsTag.java
                        • MolecularMatchTrialsSubLocation.java
                        • MolecularMatchTrialsContact.java
                        • MolecularMatchTrials.java
                        • MolecularMatchTrialsLocation.java
                        • MolecularMatchTrialsGeo.java
                        • MolecularMatchTrialsIntervention.java
                      • Association.java
                      • EnvironmentalContext.java
                      • Feature.java
                      • oncokb
                        • OncoKbClinical.java
                        • OncoKb.java
                        • OncoKbBiological.java
                        • OncoKbDrugAbstract.java
                        • OncoKbGene.java
                        • OncoKbVariant.java
                        • OncoKbConsequence.java
                      • civic
                        • CivicOrganization.java
                        • CivicEvidenceItem.java
                        • CivicDrug.java
                        • CivicUser.java
                        • CivicLastModified.java
                        • CivicVariantType.java
                        • CivicLastCommentedOn.java
                        • CivicSource.java
                        • CivicPublicationDate.java
                        • CivicClinicalTrial.java
                        • CivicCoordinates.java
                        • Civic.java
                        • CivicAvatars.java
                        • CivicLifecycleActions.java
                        • CivicDisease.java
                        • CivicVariant.java
                        • CivicVariantGroup.java
                        • CivicProfileImage.java
                        • CivicProvisionalValue.java
                        • CivicLastReviewed.java
                      • PhenotypeType.java
                      • GeneIdentifier.java
                      • SequenceOntology.java
                    • ViccJsonSQLImporter.java
        • test
          • java
            • com
              • hartwig
                • hmftools
                  • vicc
                    • util
                      • ProteinAnnotationExtractorTest.java
                    • ViccJsonSQLImporterTest.java
                    • reader
                      • ViccDatamodelCheckerTest.java
                    • datamodel
                      • ViccSourceTest.java
                      • FeatureTest.java
      • pom.xml
    • pom.xml
    • LICENSE
    • hmf-common
      • src
        • main
          • resources
            • genepanel
            • cna
              • DeletionTargets.tsv
              • AmplificationTargets.tsv
            • refgenome
              • hg19_len.tsv
              • hg19_centromere.tsv
              • hg38_len.tsv
              • hg38_centromere.tsv
            • dnds
              • DndsDriverLikelihoodTsg.tsv
              • DndsDriverLikelihoodTsgBiallelic.tsv
              • DndsDriverLikelihoodOnco.tsv
              • DndsDriverLikelihoodTsgNonBiallelic.tsv
            • actionability
              • primary_tumor_locations_mapping.csv
          • java
            • com
              • hartwig
                • hmftools
                  • common
                    • sigs
                      • SigMatrix.java
                      • DataUtils.java
                    • utils
                      • version
                        • VersionInfo.java
                      • PerformanceCounter.java
                      • kde
                        • Statistics.java
                        • KernelEstimator.java
                      • ArrayDeck.java
                      • zipper
                        • RegionZipperHandler.java
                        • RegionZipper.java
                      • collection
                        • Downsample.java
                        • Multimaps.java
                      • sv
                        • SvCommonUtils.java
                        • StartEndIterator.java
                      • GenericDataLoader.java
                      • io
                        • FileWriterUtils.java
                        • path
                          • PathPrefixSuffixFinder.java
                          • PathRegexFinder.java
                          • PathsExtensionFinder.java
                        • exception
                          • EmptyFileException.java
                          • EmptyFolderException.java
                          • FolderDoesNotExistException.java
                          • NotFolderException.java
                          • MalformedFileException.java
                        • FolderChecker.java
                        • reader
                          • LineReader.java
                          • FileReader.java
                      • r
                        • RExecutor.java
                      • Integers.java
                      • sam
                        • SAMRecords.java
                      • Doubles.java
                      • Strings.java
                      • GenericDataCollection.java
                      • pcf
                        • PCFFile.java
                        • PCFRegion.java
                        • PCFPosition.java
                        • PCFSource.java
                        • PCFMerge.java
                    • gripss
                      • GripssFilters.java
                    • sage
                      • SageMetaData.java
                      • SagePostProcessVCF.java
                    • cobalt
                      • CobaltCount.java
                      • CobaltRatioFactory.java
                      • ReadCount.java
                      • CobaltRatio.java
                      • CobaltCountFactory.java
                      • ReadRatio.java
                      • ReferenceRatioStatistics.java
                      • ReferenceRatioStatisticsFactory.java
                      • CobaltRatioFile.java
                    • drivercatalog
                      • TsgDrivers.java
                      • OncoDrivers.java
                      • DriverCatalogFactory.java
                      • DriverCatalog.java
                      • CNADrivers.java
                      • TsgImpactComparator.java
                      • DriverCategory.java
                      • SomaticVariantDrivers.java
                      • DriverCatalogFile.java
                      • dnds
                        • DndsDriverGeneLikelihoodSupplier.java
                        • DndsDriverGeneLikelihood.java
                        • DndsDriverGeneLikelihoodFile.java
                        • DndsDriverImpactLikelihood.java
                      • DriverImpact.java
                      • DriverType.java
                      • LikelihoodMethod.java
                    • variant
                      • VariantTier.java
                      • Variant.java
                      • VariantType.java
                      • VariantConsequence.java
                      • CanonicalAnnotation.java
                      • PurityAdjustedSomaticVariantImpl.java
                      • strelka
                        • StrelkaAllelicDepth.java
                      • kataegis
                        • KataegisWindow.java
                        • KataegisQueue.java
                      • hotspot
                        • HotspotEvidence.java
                        • HotspotEvidenceVCF.java
                        • HotspotEvidenceType.java
                        • VariantHotspotComparator.java
                        • VariantHotspotEvidence.java
                        • VariantHotspot.java
                        • SAMSlicer.java
                        • InframeIndelHotspots.java
                        • VariantHotspotImpl.java
                        • VariantHotspotFile.java
                        • VariantHotspotEvidenceFactory.java
                      • AllelicDepthImpl.java
                      • repeat
                        • RepeatContextFactory.java
                        • RepeatContext.java
                      • recovery
                        • RecoverStructuralVariants.java
                        • RecoveredVariant.java
                        • RecoveredVariantFactory.java
                      • PurityAdjustedSomaticVariant.java
                      • PurityAdjustedSomaticVariantBuilder.java
                      • Microhomology.java
                      • enrich
                        • SubclonalLikelihoodEnrichment.java
                        • VariantHotspotEnrichment.java
                        • SomaticRefContextEnrichment.java
                        • VariantContextEnrichment.java
                        • SomaticEnrichment.java
                        • HotspotEnrichment.java
                        • KataegisEnrichment.java
                        • CompoundEnrichment.java
                        • NoSomaticEnrichment.java
                        • VariantContextEnrichmentPurple.java
                        • NeoEpitopeEnrichment.java
                        • VariantContextEnrichmentFactory.java
                        • PurityEnrichment.java
                        • StructuralRefContextEnrichment.java
                      • SomaticVariantImpl.java
                      • PurityAdjustedSomaticVariantFactory.java
                      • structural
                        • StructuralVariantFile.java
                        • StructuralVariantLegImpl.java
                        • StructuralVariantFactory.java
                        • EnrichedStructuralVariant.java
                        • StructuralVariantFileLoader.java
                        • StructuralVariant.java
                        • StructuralVariantType.java
                        • EnrichedStructuralVariantFactory.java
                        • StructuralVariantData.java
                        • linx
                          • LinxSvDataFile.java
                          • LinxFusion.java
                          • LinxBreakendFile.java
                          • LinxClusterFile.java
                          • LinxBreakend.java
                          • LinxViralInsertFile.java
                          • LinxLinkFile.java
                          • LinxLink.java
                          • LinxFusionFile.java
                          • LinxSvData.java
                          • LinxDriver.java
                          • LinxDriverFile.java
                          • LinxCluster.java
                        • StructuralVariantImpl.java
                        • CopyNumberEnrichedStructuralVariantFactory.java
                        • StructuralVariantHeader.java
                        • EnrichedStructuralVariantLeg.java
                        • StructuralVariantLeg.java
                      • clonality
                        • PeakModelFile.java
                        • PeakModelFactory.java
                        • PeakModel.java
                        • WeightedPloidyHistogram.java
                        • SubclonalLikelihood.java
                        • WeightedPloidy.java
                      • msi
                        • MicrosatelliteIndels.java
                        • MicrosatelliteStatus.java
                      • AllelicDepth.java
                      • TranscriptAnnotation.java
                      • tml
                        • TumorMutationalStatus.java
                        • TumorMutationalLoad.java
                      • snpeff
                        • SnpEffSummary.java
                        • SnpEffSummaryFactory.java
                        • SnpEffAnnotation.java
                        • SnpEffAnnotationFactory.java
                        • SnpEffSummarySerialiser.java
                        • SnpEffHgvsFormatter.java
                      • SomaticVariantHeader.java
                      • filter
                        • ChromosomeFilter.java
                        • HotspotFilter.java
                        • NTFilter.java
                        • AlwaysPassFilter.java
                        • SGTFilter.java
                        • SomaticFilter.java
                        • ExcludeCNVFilter.java
                      • CodingEffect.java
                      • cosmic
                        • CosmicAnnotation.java
                        • CosmicAnnotationFactory.java
                      • SomaticVariant.java
                      • SomaticVariantFactory.java
                      • Hotspot.java
                      • MicrohomologyContext.java
                    • cli
                      • Configs.java
                    • genome
                      • position
                        • GenomePositionImpl.java
                        • GenomePositionSelectorIteratorImpl.java
                        • GenomePositionSelector.java
                        • GenomeInterval.java
                        • GenomeIntervalImpl.java
                        • GenomePosition.java
                        • GenomePositionSelectorListImpl.java
                        • GenomePositionSelectorFactory.java
                        • GenomePositions.java
                      • window
                        • Window.java
                      • genepanel
                        • HmfExonPanelBed.java
                        • HmfGenePanelSupplier.java
                        • HmfGenomeFileLoader.java
                      • refgenome
                        • RefGenomeSource.java
                        • RefGenome.java
                        • RefGenomeVersion.java
                        • RefGenomeInterface.java
                        • MockRefGenome.java
                      • gc
                        • GCProfileFactory.java
                        • GCMedianReadCountBuilder.java
                        • GCMedianReadCountFile.java
                        • GCProfile.java
                        • GCMedianReadCount.java
                        • ReadCountMedian.java
                        • GCMedianReadCountImpl.java
                        • GCBucket.java
                      • chromosome
                        • ChromosomeLengthFile.java
                        • ChromosomeLength.java
                        • MitochondrialChromosome.java
                        • Chromosome.java
                        • ChromosomeLengthFactory.java
                        • ContigComparator.java
                        • HumanChromosome.java
                        • ChromosomeLengths.java
                      • region
                        • GenomeRegionSelectorImpl.java
                        • GenomeRegionSelector.java
                        • GenomeRegionImpl.java
                        • TranscriptRegion.java
                        • CanonicalTranscript.java
                        • Strand.java
                        • CanonicalTranscriptFactory.java
                        • BEDFileLoader.java
                        • GenomeRegion.java
                        • HmfExonRegion.java
                        • GenomeRegionBuilder.java
                        • ReplicationOriginRegion.java
                        • GenomeRegionSelectorFactory.java
                        • GenomeRegions.java
                        • HmfTranscriptRegion.java
                      • slicing
                        • SlicerFactory.java
                        • BidirectionalSlicer.java
                        • Slicer.java
                    • amber
                      • TumorBAF.java
                      • BaseDepth.java
                      • TumorContaminationEvidence.java
                      • TumorContaminationFile.java
                      • BaseDepthFactory.java
                      • AmberSite.java
                      • qc
                        • AmberQCStatus.java
                        • AmberQCFile.java
                        • AmberQC.java
                        • AmberQCFactory.java
                      • AmberSiteFactory.java
                      • TumorContamination.java
                      • TumorBAFEvidence.java
                      • TumorContaminationModel.java
                      • AmberBAFFile.java
                      • AmberBAF.java
                      • BaseDepthIntersectFilter.java
                      • BaseDepthEvidence.java
                      • TumorBAFFactory.java
                      • NormalHetrozygousFilter.java
                      • NormalHomozygousFilter.java
                      • BaseDepthFilter.java
                    • chord
                      • ChordStatus.java
                      • ChordFileReader.java
                      • ChordAnalysis.java
                    • lims
                      • LimsJsonSubmissionData.java
                      • LimsCoreCohort.java
                      • hospital
                        • HospitalAddress.java
                        • HospitalContactData.java
                        • HospitalPersons.java
                        • HospitalModel.java
                        • HospitalModelFactory.java
                      • LimsGermlineReportingLevel.java
                      • LimsConstants.java
                      • Lims.java
                      • LimsJsonSampleData.java
                      • LimsFactory.java
                      • LimsStudy.java
                      • LimsGsonAdapter.java
                      • LimsShallowSeqData.java
                    • circos
                      • CircosINDELWriter.java
                      • CircosLinkWriter.java
                      • CircosFileWriter.java
                      • CircosSNPWriter.java
                      • CircosExecution.java
                    • purple
                      • copynumber
                        • ExtendDiploid.java
                        • ExtendStructuralVariant.java
                        • PurpleCopyNumber.java
                        • ExtendRegion.java
                        • PurpleCopyNumberFile.java
                        • PopulateUnknown.java
                        • ExtractGermlineDeletions.java
                        • sv
                          • CopyNumberChange.java
                          • StructuralVariantLegPloidyFactory.java
                          • StructuralVariantLegCopyNumberImpl.java
                          • StructuralVariantLegsFactory.java
                          • StructuralVariantLegCopyNumberChangeFactory.java
                          • StructuralVariantLegCopyNumber.java
                          • StructuralVariantLegCopyNumberFactory.java
                          • StructuralVariantLegs.java
                          • StructuralVariantLegPloidy.java
                        • PurpleCopyNumberFactory.java
                        • Extend.java
                        • ExtendLongArm.java
                        • StructuralVariantImplied.java
                        • ExtendNonDiploid.java
                        • CopyNumberInterpretation.java
                        • tolerance
                          • CopyNumberTolerance.java
                          • AlleleTolerance.java
                        • CombinedRegion.java
                        • ExtendDiploidBAF.java
                        • ExtractChildren.java
                        • CombinedRegionImpl.java
                        • CopyNumberMethod.java
                      • CheckPurpleQuality.java
                      • qc
                        • PurpleQCFile.java
                        • PurpleQCFactory.java
                        • PurpleQCStatus.java
                        • PurpleQC.java
                      • purity
                        • BestFitFactory.java
                        • FittedPurityScore.java
                        • FittedPurity.java
                        • BestFit.java
                        • SomaticFitFactory.java
                        • SomaticDeviation.java
                        • WholeGenomeDuplication.java
                        • SomaticPeakFactory.java
                        • SomaticPeak.java
                        • FittedPurityFile.java
                        • FittedPurityStatus.java
                        • PurityContext.java
                        • FittedPurityFactory.java
                        • SomaticPenaltyFactory.java
                        • FittedPurityRangeFile.java
                        • FittedPurityScoreFactory.java
                      • PurityAdjuster.java
                      • gender
                        • Gender.java
                      • region
                        • ObservedRegion.java
                        • ObservedRegionFactory.java
                        • GCAccumulator.java
                        • GermlineStatusFactory.java
                        • EventPenalty.java
                        • GermlineStatus.java
                        • FittedRegionFactoryV2.java
                        • EnrichedRegion.java
                        • SegmentFile.java
                        • PloidyDeviation.java
                        • FittedRegionFactory.java
                        • FittedRegion.java
                      • gene
                        • GeneCopyNumberFile.java
                        • GeneCopyNumberFactory.java
                        • GeneCopyNumberBuilder.java
                        • GeneCopyNumber.java
                      • segment
                        • SVSegmentFactory.java
                        • PurpleSegment.java
                        • ClusterFactory.java
                        • Cluster.java
                        • SVSegment.java
                        • SegmentSupport.java
                        • PurpleSegmentFactory.java
                      • baf
                        • ExpectedBAF.java
                    • pharmacogenetics
                      • PGXGenotypeFile.java
                      • PGXGenotype.java
                      • PGXCalls.java
                      • PGXCallsFile.java
                    • ecrf
                      • formstatus
                        • FormStatus.java
                        • FormStatusModel.java
                        • FormStatusKey.java
                        • FormStatusState.java
                        • FormStatusReader.java
                      • EcrfModel.java
                      • projections
                        • PatientTumorLocationFunctions.java
                        • PatientTumorLocation.java
                      • reader
                        • CodeListFactory.java
                        • Item.java
                        • StudyEvent.java
                        • XMLEcrfDatamodelToEcrfFields.java
                        • XMLEcrfDatamodel.java
                        • Form.java
                        • XMLEcrfDatamodelReader.java
                        • OIDFunctions.java
                        • XMLPatientReader.java
                        • EcrfReader.java
                        • OIDObject.java
                        • ItemGroup.java
                        • CodeList.java
                      • datamodel
                        • EcrfDataField.java
                        • EcrfStudyEvent.java
                        • EcrfPatient.java
                        • ValidationFinding.java
                        • EcrfFieldFunctions.java
                        • EcrfResolveException.java
                        • EcrfDatamodelField.java
                        • EcrfField.java
                        • EcrfForm.java
                        • EcrfItemGroup.java
                    • stats
                      • FisherExactTest.java
                    • metrics
                      • WGSMetrics.java
                      • WGSMetricWithQC.java
                      • WGSMetricsLines.java
                      • WGSMetricQC.java
                      • WGSMetricsFile.java
                    • ensemblcache
                      • TranscriptProteinData.java
                      • EnsemblDataCache.java
                      • EnsemblDataLoader.java
                      • GeneTestUtils.java
                      • ExonData.java
                      • TranscriptData.java
                      • EnsemblGeneData.java
                    • actionability
                      • Actionable.java
                      • EvidenceItem.java
                      • ClinicalTrial.java
                      • EvidenceScope.java
                      • variant
                        • ActionableVariant.java
                        • ActionableRange.java
                        • VariantEvidenceAnalyzerFactory.java
                        • VariantEvidenceAnalyzer.java
                      • ActionabilityAnalyzer.java
                      • util
                        • MultiDrugCurator.java
                      • EvidenceLevel.java
                      • panel
                        • ActionablePanelFile.java
                        • ActionablePanelBuilder.java
                        • ActionablePanel.java
                      • cancertype
                        • CancerTypeAnalyzer.java
                        • PrimaryTumorToDOIDMapper.java
                        • CancerTypeToDOIDMappingEntry.java
                        • CancerTypeToDOIDMapper.java
                      • cnv
                        • CopyNumberEvidenceAnalyzer.java
                        • ActionableCopyNumber.java
                        • CopyNumberType.java
                        • SignificantGeneCopyNumberFilter.java
                        • CopyNumberEvidenceAnalyzerFactory.java
                      • ActionabilitySource.java
                      • fusion
                        • FusionEvidenceAnalyzer.java
                        • ActionableFusion.java
                        • ActionablePromiscuous.java
                        • FusionEvidenceAnalyzerFactory.java
                      • drup
                        • DrupActionabilityModelFactory.java
                        • DrupActionabilityModel.java
                    • fusion
                      • ReportableGeneFusionFile.java
                      • KnownFusionType.java
                      • ReportableDisruptionFile.java
                      • GeneAnnotation.java
                      • ReportableDisruption.java
                      • KnownFusionData.java
                      • TranscriptCodingType.java
                      • FusionCommon.java
                      • ReportableGeneFusion.java
                      • TranscriptRegionType.java
                      • Transcript.java
                      • KnownFusionCache.java
        • test
          • resources
            • copynumber
              • ratio
                • sample.bam_normal_ratio.txt
                • sample.bam_ratio.txt
              • sample.bam_CNVs
            • empty
              • .gitkeep
            • cobalt
              • hg19.cobalt.tsv
              • hg38.cobalt.tsv
            • drivercatalog
              • sample.drivers.catalog.tsv
            • variant
              • somatics.vcf
              • structural
                • linx
                  • sample.linx.viral_inserts.tsv
            • log4j2.xml
            • amber
              • contamination.none
              • contamination.high
              • contamination.low
              • old.amber.baf
              • hg38.amber.baf.tsv
              • new.amber.baf.tsv
            • gc
              • EXAMPLE.purple.gc.median
              • GC_profile.1000bp.cnp
            • chord
              • sample_chord_prediction.txt
            • gene
              • KRAS.tsv
              • WASH7P.tsv
              • PTEN.tsv
              • test_gene_panel.tsv
            • io
              • FolderChecker
                • somefile
              • FolderCheckerEmpty
                • .gitkeep
              • PathFinderRegex
                • base_file
                • directory
                  • file_in_dir
              • NotAFolder
              • empty.file
            • clonality
            • lims
              • sample_hospital_mapping.tsv
              • hospital_wide.tsv
              • samples_without_sampling_date.tsv
              • lims.json
              • shallow_seq_purity.tsv
              • hospital_cpct.tsv
              • hospital_address.tsv
              • patient_blacklist.tsv
              • pre_lims_arrival_dates.tsv
              • hospital_drup.tsv
            • r
              • dummyR.R
            • purple
              • v2-24.purple.cnv
              • v2-25.purple.cnv
              • v2-14.purple.purity
            • pharmacogenetics
              • sample_calls.txt
              • sample_genotype.txt
            • bed
              • valid.bed
              • invalid.bed
              • unsorted.bed
            • ecrf
              • formstatus
                • formstatus.csv
              • example
              • tests
                • datamodel.xml
                • patients.xml
            • metrics
              • sample1_pv4.wgsmetrics
              • sample2_pv4.wgsmetrics
              • sample1_pv5.wgsmetrics
              • sample2_pv5.wgsmetrics
              • sample4.wgsmetrics
              • sample3.wgsmetrics
            • actionability
              • actionablePromiscuousThree.tsv
              • actionablePromiscuousFive.tsv
              • actionableVariants.tsv
              • knowledgebaseCancerTypes.tsv
              • drup_genes.csv
              • actionableFusionPairs.tsv
              • actionableRanges.tsv
              • actionableCNVs.tsv
            • pcf
              • baf.pcf
              • ratio.pcf
          • java
            • com
              • hartwig
                • hmftools
                  • common
                    • utils
                      • IntegersTest.java
                      • ArrayDeckTest.java
                      • zipper
                        • RegionZipperTest.java
                      • io
                        • FolderCheckerTest.java
                        • path
                          • PathRegexFinderTest.java
                          • PathsExtensionFinderTest.java
                      • r
                        • RExecutorTest.java
                      • sam
                        • SAMRecordsTest.java
                      • pcf
                        • PCFFileTest.java
                    • cobalt
                      • ReferenceRatioStatisticsTest.java
                      • CobaltRatioFileTest.java
                    • drivercatalog
                      • DriverCatalogFileTest.java
                      • TsgImpactComparatorTest.java
                      • OncoDriversTest.java
                      • dnds
                        • DndsDriverGeneLikelihoodSupplierTest.java
                      • CNADriversTest.java
                      • DriverCatalogFactoryTest.java
                      • TsgDriversTest.java
                    • variant
                      • VariantConsequenceTest.java
                      • CodingEffectTest.java
                      • AllelicDepthTest.java
                      • MicrohomologyTest.java
                      • strelka
                        • StrelkaAllelicDepthTest.java
                      • kataegis
                        • KataegisWindowTest.java
                        • KataegisQueueTest.java
                      • hotspot
                        • HotspotEvidenceVCFTest.java
                        • HotspotEvidenceTest.java
                        • VariantHotspotEvidenceFactoryTest.java
                        • InframeIndelHotspotsTest.java
                      • repeat
                        • RepeatContextFactoryTest.java
                        • RepeatContextTest.java
                      • recovery
                        • RecoveredVariantFactoryTest.java
                        • RecoverStructuralVariantsTest.java
                      • VariantContextFromString.java
                      • CanonicalAnnotationTest.java
                      • enrich
                        • HotspotEnrichmentTest.java
                      • SomaticVariantTestBuilderFactory.java
                      • structural
                        • StructuralVariantFactoryTest.java
                        • linx
                          • LinxViralInsertFileTest.java
                      • clonality
                        • SubclonalLikelihoodFactoryTest.java
                        • PealModelFactoryTest.java
                        • WeightedPloidyHistogramTest.java
                      • msi
                        • MicrosatelliteIndelsTest.java
                      • SomaticVariantFactoryTest.java
                      • snpeff
                        • SnpEffSummarySerialiserTest.java
                        • SnpEffAnnotationTestFactory.java
                        • SnpEffAnnotationFactoryTest.java
                        • SnpEffAnnotationTest.java
                        • SnpEffHgvsFormatterTest.java
                      • cosmic
                        • CosmicAnnotationFactoryTest.java
                    • genome
                      • position
                        • GenomePositionSelectorTest.java
                      • window
                        • WindowTest.java
                      • genepanel
                        • HmfGenePanelSupplierTest.java
                        • HmfExonPanelBedTest.java
                      • gc
                        • GCMedianReadCountFileTest.java
                        • GCProfileFactoryTest.java
                        • ReadCountMedianTest.java
                      • chromosome
                        • HumanChromosomeTest.java
                        • MitochondrialChromosomeTest.java
                        • ContigComparatorTest.java
                      • region
                        • GenomeRegionSelectorTest.java
                        • BEDFileLoaderTest.java
                        • GenomeRegionTest.java
                        • GenomeRegionsTest.java
                        • HmfTranscriptRegionTest.java
                        • CanonicalTranscriptFactoryTest.java
                      • slicing
                        • BidirectionalSlicerTest.java
                        • SlicerFactoryTest.java
                    • amber
                      • TumorBAFFactoryTest.java
                      • TumorContaminationFileTest.java
                      • BaseDepthIntersectFilterTest.java
                      • qc
                        • AmberQCTest.java
                      • AmberBAFFileTest.java
                      • TumorContaminationModelTest.java
                    • chord
                      • ChordFileReaderTest.java
                      • ChordStatusTest.java
                    • lims
                      • LimsFactoryTest.java
                      • hospital
                        • HospitalModelFactoryTest.java
                        • HospitalModelTest.java
                      • LimsGermlineReportingChoiceTest.java
                      • LimsTest.java
                      • LimsJsonSampleDataTest.java
                      • LimsTestUtil.java
                      • LimsCoreCohortTest.java
                      • LimsStudyTest.java
                    • purple
                      • copynumber
                        • ExtendLongArmTest.java
                        • PopulateUnknownTest.java
                        • ExtendStructuralVariantTest.java
                        • ExtendNonDiploidTest.java
                        • sv
                          • StructuralVariantLegsFactoryTest.java
                          • StructuralVariantPloidyTest.java
                          • StructuralVariantPloidyFactoryTest.java
                          • CopyNumberChangeTest.java
                        • ExtendDiploidBAFTest.java
                        • PurpleCopyNumberFileTest.java
                        • CombinedRegionTest.java
                        • StructuralVariantImpliedTest.java
                        • tolerance
                          • AlleleToleranceTest.java
                        • ExtendDiploidTest.java
                      • qc
                        • PurpleQCFileTest.java
                        • PurpleQCTest.java
                      • purity
                        • FittedPurityScoreFactoryTest.java
                        • SomaticDeviationTest.java
                        • SomaticPeakFactoryTest.java
                        • WholeGenomeDuplicationTest.java
                        • FittedPurityRangeFileTest.java
                        • FittedPurityFileTest.java
                      • PurpleDatamodelTest.java
                      • gender
                        • GenderTest.java
                      • region
                        • ExtendMinSupportTest.java
                        • CobaltAccumulatorTest.java
                        • EventPenaltyTest.java
                        • GermlineStatusFactoryTest.java
                        • FittedRegionFactoryTest.java
                        • PloidyDeviationTest.java
                        • GCAccumulatorTest.java
                      • gene
                        • GeneCopyNumberBuilderTest.java
                        • GeneCopyNumberFileTest.java
                      • segment
                        • StructuralVariantPositionFactoryTest.java
                        • PurpleSegmentFactoryTest.java
                        • ClusterFactoryTest.java
                      • PurityAdjusterTest.java
                      • baf
                        • ExpectedBAFTest.java
                    • pharmacogenetics
                      • PGXGenotypeFileTest.java
                      • PGXCallsFileTest.java
                    • ecrf
                      • EcrfModelTest.java
                      • formstatus
                        • FormStatusReaderTest.java
                        • FormStatusTest.java
                      • reader
                        • XMLEcrfDatamodelToEcrfFieldsTest.java
                        • XMLPatientReaderTest.java
                        • XMLEcrfDatamodelReaderTest.java
                        • CodeListFactoryTest.java
                        • OIDFunctionsTest.java
                      • datamodel
                        • EcrfFieldFunctionsTest.java
                    • metrics
                      • WGSMetricsFileTest.java
                    • actionability
                      • ActionabilityAnalyzerTest.java
                      • variant
                        • VariantEvidenceAnalyzerTest.java
                      • util
                        • MultiDrugCuratorTest.java
                      • cancertype
                        • CancerTypeAnalyzerTestFactory.java
                        • PrimaryTumorToDOIDMapperTest.java
                        • CancerTypeAnalyzerTest.java
                      • cnv
                        • CopyNumberEvidenceAnalyzerTest.java
                        • SignificantGeneCopyNumberFilterTest.java
                      • fusion
                        • FusionEvidenceAnalyzerTest.java
                      • drup
                        • DrupActionabilityModelFactoryTest.java
      • pom.xml
    • strelka-post-process
      • src
        • main
          • resources
            • log4j2.xml
          • java
            • com
              • hartwig
                • hmftools
                  • strelka
                    • MNVDetectorApplication.java
                    • mnv
                      • MNVDetector.java
                      • scores
                        • SamRecordScoring.java
                        • VariantScore.java
                        • ReadType.java
                        • VariantScoreAggregate.java
                      • MNVRegionValidator.java
                      • MNVValidator.java
                      • GapReads.java
                      • MNVScore.java
                      • PotentialMNV.java
                      • MNVMerger.java
                      • PotentialMNVRegion.java
                    • StrelkaPostProcess.java
                    • StrelkaPostProcessApplication.java
                    • MNVValidatorApplication.java
        • test
          • resources
            • mnvs.vcf
            • variants.vcf
            • high_conf.bed
          • java
            • com
              • hartwig
                • hmftools
                  • strelka
                    • StrelkaPostProcessTest.java
                    • mnv
                      • MNVDetectorTest.java
                      • scores
                        • ScoringSNVTest.java
                        • ScoringInsertionsTest.java
                        • ScoringDeletionsTest.java
                      • GapReadsTest.java
                      • TestUtils.java
                      • MNVMergerTest.java
                      • MNVValidatorTest.java
                      • PotentialMNVRegionTest.java
                      • ScoringMNVTest.java
      • pom.xml
    • stat-calcs
      • src
        • main
          • resources
            • log4j2.xml
          • java
            • com
              • hartwig
                • hmftools
                  • stat_calcs
                    • TwoCategoryData.java
                    • TwoVarCoOccurence.java
                    • SampleGeneData.java
                    • SampleCategoryData.java
                    • CoOccurenceCalcs.java
                    • SampleCountsCoOccurence.java
                    • ThreeVarCoOccurence.java
        • test
          • java
            • com
              • hartwig
                • hmftools
                  • stat_calcs
                    • FisherTest.java
      • pom.xml
    • amber
      • src
        • main
          • resources
            • log4j2.xml
            • r
              • bafSegmentation.R
            • amber.version
          • java
            • com
              • hartwig
                • hmftools
                  • amber
                    • AmberVCF.java
                    • AmberPersistence.java
                    • SnpCheckFilter.java
                    • AmberConfig.java
                    • AmberApplication.java
                    • AmberHetNormalEvidence.java
                    • AmberTaskCompletion.java
                    • BAFSegmentation.java
      • pom.xml
      • README_2.md
      • README.md
    • .gitattributes
    • sv-tools
      • src
        • main
          • resources
            • log4j2.xml
          • java
            • com
              • hartwig
                • hmftools
                  • svtools
                    • germline
                      • GermlineFilters.java
                      • GeneImpact.java
                      • GermlineSV.java
                      • GermlineVcfReader.java
                      • GermlineVcfConfig.java
                      • AssemblyData.java
                    • mult_biopsy
                      • MultiBiopsyData.java
                      • MultipleBiopsyAnalyser.java
                    • simulation
                      • ShatteringResult.java
                      • ShatteringSim.java
                      • Segment.java
                      • SvSimulator.java
                      • ShatteringConfig.java
                    • common
                      • ConfigUtils.java
                    • fusion_likelihood
                      • FusionLikelihood.java
                      • RegionAllocator.java
                      • LikelihoodCalc.java
                      • PhaseRegionUtils.java
                      • CohortExpFusions.java
                      • GeneRangeData.java
                      • GenePhaseType.java
                      • GenePhaseRegion.java
                    • sequence
                      • KmerGenerator.java
                      • InsertSeqData.java
                      • InsertSequenceAnalyser.java
        • test
          • java
            • com
              • hartwig
                • hmftools
                  • svtools
                    • simulation
                      • SimulationTest.java
                    • fusion_likelihood
                      • FusionLikelihoodTest.java
                    • sequence
                      • InsertSequenceTest.java
      • pom.xml
    • fastq-stats
      • src
        • main
          • resources
            • log4j2.xml
          • java
            • com
              • hartwig
                • hmftools
                  • fastqstats
                    • FastqStats.java
                    • FastqStatsRunner.java
                    • FastqTrackerWrapper.java
                    • FastqReader.java
                    • FastqTracker.java
                    • FastqData.java
        • test
          • resources
            • UndeterminedBaseCalls0Q30
              • UndeterminedF1_H7YRLADXX_S1_L002_R1_001.fastq
              • UndeterminedF3_H7YRLADXX_S1_L002_R1_001.fastq
              • HMFregCPCT
                • TESTZ
                  • TESTZ_H7YRLADXX_S1_L001_R1_001.fastq
                • TESTY
                  • TESTY_H7YRLADXX_S1_L001_R1_001.fastq
                • TESTX
                  • TESTX_H7YRLADXX_S1_L001_R1_001.fastq
              • UndeterminedF2_H7YRLADXX_S1_L002_R1_001.fastq
            • DeterminedBaseCalls-100&50
              • HMFregCPCT
                • TESTZ
                  • TESTZ_H7YRLADXX_S1_L001_R1_001.fastq
                • TESTY
                  • TESTY_H7YRLADXX_S1_L001_R1_001.fastq
                • TESTX
                  • TESTX_H7YRLADXX_S1_L001_R1_001.fastq
            • 170101_TEST_000_TESTFLOWCELL
              • RunInfo.xml
              • Data
                • Intensities
                  • BaseCalls
                    • HMFregCPCT
                      • TESTZ
                      • TESTY
                      • TESTX
            • CorruptSampleXFile
              • HMFregCPCT
                • TESTZ
                  • TESTZ_H7YRLADXX_S1_L001_R1_001.fastq
                • TESTY
                  • TESTY_H7YRLADXX_S1_L001_R1_001.fastq
                • TESTX
                  • TESTX_H7YRLADXX_S1_L001_R1_001.fastq.gz
            • CorruptUndeterminedSampleFile
              • UndeterminedF3_H7YRLADXX_S1_L002_R1_001.fastq
              • UndeterminedF1_H7YRLADXX_S1_L002_R1_001.fastq.gz
              • UndeterminedF2_H7YRLADXX_S1_L002_R1_001.fastq
            • 50UndeterminedBaseCalls
              • HMFregCPCT
                • TESTZ
                  • TESTZ_H7YRLADXX_S1_L001_R1_001.fastq
                • TESTY
                  • TESTY_H7YRLADXX_S1_L001_R1_001.fastq
                • TESTX
                  • TESTX_H7YRLADXX_S1_L001_R1_001.fastq
              • UndeterminedF1_H7YRLADXX_S1_L001_R1_001.fastq
              • UndeterminedF3_H7YRLADXX_S1_L001_R1_001.fastq
              • UndeterminedF2_H7YRLADXX_S1_L001_R1_001.fastq
            • fastq
              • q30-0.fastq
              • q30-100.fastq
              • q30-10_Flowcell_S1_L001_R1_001.fastq.gz
              • q30-10.err
              • q30-10.fastq
            • DeterminedBaseCallsMultiLane-100&50
              • HMFregCPCT
                • TESTX
                  • TESTX_H7YRLADXX_S1_L001_R1_001.fastq
                  • TESTX_H7YRLADXX_S1_L002_R1_001.fastq
                  • TESTX_H7YRLADXX_S1_L003_R1_001.fastq
            • DeterminedBaseCalls-100
              • HMFregCPCT
                • TESTZ
                  • TESTZ_H7YRLADXX_S1_L001_R1_001.fastq
                • TESTY
                  • TESTY_H7YRLADXX_S1_L001_R1_001.fastq
                • TESTX
                  • TESTX_H7YRLADXX_S1_L001_R1_001.fastq
            • 100UndeterminedBaseCalls
              • UndeterminedF1_H7YRLADXX_S1_L002_R1_001.fastq
              • UndeterminedF3_H7YRLADXX_S1_L002_R1_001.fastq
              • UndeterminedF2_H7YRLADXX_S1_L002_R1_001.fastq
          • java
            • com
              • hartwig
                • hmftools
                  • fastqstats
                    • FastqTrackerTest.java
                    • FastqStatsTest.java
                    • FastqStatsRunnerTest.java
      • pom.xml
    • ensembl-db
      • src
        • main
          • java
            • org
              • ensembl
                • database
                  • homo_sapiens_core
                    • Keys.java
                    • enums
                      • UnmappedObjectType.java
                      • ObjectXrefEnsemblObjectType.java
                      • DensityTypeValueType.java
                      • MarkerType.java
                      • GeneStatus.java
                      • TranscriptStatus.java
                      • DataFileFileType.java
                      • TranscriptSupportingFeatureFeatureType.java
                      • ExternalDbStatus.java
                      • AssemblyExceptionExcType.java
                      • ExternalDbType.java
                      • SupportingFeatureFeatureType.java
                      • IntronSupportingEvidenceScoreType.java
                      • UnmappedObjectEnsemblObjectType.java
                      • DitagFeatureDitagSide.java
                      • XrefInfoType.java
                      • StableIdEventType.java
                      • AltAlleleAttribAttrib.java
                    • tables
                      • RepeatConsensus.java
                      • DependentXref.java
                      • MappingSet.java
                      • Operon.java
                      • DnaAlignFeatureAttrib.java
                      • PredictionExon.java
                      • TranscriptSupportingFeature.java
                      • StableIdEvent.java
                      • UnmappedReason.java
                      • ExternalDb.java
                      • ExternalSynonym.java
                      • MiscFeature.java
                      • TranscriptAttrib.java
                      • MappingSession.java
                      • MarkerMapLocation.java
                      • Analysis.java
                      • MiscFeatureMiscSet.java
                      • AnalysisDescription.java
                      • ExonTranscript.java
                      • IntronSupportingEvidence.java
                      • AssemblyException.java
                      • UnmappedObject.java
                      • AltAllele.java
                      • MiscSet.java
                      • SeqRegionSynonym.java
                      • Map.java
                      • Translation.java
                      • RepeatFeature.java
                      • DitagFeature.java
                      • Karyotype.java
                      • OntologyXref.java
                      • DensityType.java
                      • SupportingFeature.java
                      • Ditag.java
                      • ProteinFeature.java
                      • SeqRegionMapping.java
                      • Marker.java
                      • OperonTranscript.java
                      • AttribType.java
                      • TranscriptIntronSupportingEvidence.java
                      • GenomeStatistics.java
                      • ProteinAlignFeature.java
                      • SeqRegionAttrib.java
                      • OperonTranscriptGene.java
                      • DataFile.java
                      • MarkerSynonym.java
                      • DensityFeature.java
                      • AssociatedGroup.java
                      • MarkerFeature.java
                      • ObjectXref.java
                      • AltAlleleGroup.java
                      • Xref.java
                      • SimpleFeature.java
                      • PeptideArchive.java
                      • GeneAttrib.java
                      • Interpro.java
                      • AltAlleleAttrib.java
                      • TranslationAttrib.java
                      • SeqRegion.java
                      • Transcript.java
                      • Meta.java
                      • DnaAlignFeature.java
                      • AssociatedXref.java
                      • IdentityXref.java
                      • Exon.java
                      • Gene.java
                      • records
                        • SeqRegionRecord.java
                        • AnalysisRecord.java
                        • TranscriptIntronSupportingEvidenceRecord.java
                        • IdentityXrefRecord.java
                        • StableIdEventRecord.java
                        • KaryotypeRecord.java
                        • AltAlleleAttribRecord.java
                        • CoordSystemRecord.java
                        • TranslationRecord.java
                        • DnaRecord.java
                        • DitagFeatureRecord.java
                        • OperonTranscriptGeneRecord.java
                        • DnaAlignFeatureRecord.java
                        • TranscriptSupportingFeatureRecord.java
                        • InterproRecord.java
                        • DataFileRecord.java
                        • GeneRecord.java
                        • XrefRecord.java
                        • MapRecord.java
                        • SeqRegionSynonymRecord.java
                        • OperonRecord.java
                        • OperonTranscriptRecord.java
                        • MiscFeatureMiscSetRecord.java
                        • TranscriptRecord.java
                        • GeneAttribRecord.java
                        • DnaAlignFeatureAttribRecord.java
                        • SimpleFeatureRecord.java
                        • ExternalSynonymRecord.java
                        • AnalysisDescriptionRecord.java
                        • DitagRecord.java
                        • ObjectXrefRecord.java
                        • OntologyXrefRecord.java
                        • ProteinAlignFeatureRecord.java
                        • UnmappedReasonRecord.java
                        • MarkerRecord.java
                        • MappingSessionRecord.java
                        • MarkerSynonymRecord.java
                        • PeptideArchiveRecord.java
                        • ExonTranscriptRecord.java
                        • AssemblyRecord.java
                        • ExternalDbRecord.java
                        • GenomeStatisticsRecord.java
                        • GeneArchiveRecord.java
                        • MarkerFeatureRecord.java
                        • SeqRegionMappingRecord.java
                        • AssociatedXrefRecord.java
                        • UnmappedObjectRecord.java
                        • AttribTypeRecord.java
                        • DensityTypeRecord.java
                        • MiscSetRecord.java
                        • ProteinFeatureRecord.java
                        • MappingSetRecord.java
                        • PredictionExonRecord.java
                        • AssemblyExceptionRecord.java
                        • TranslationAttribRecord.java
                        • AssociatedGroupRecord.java
                        • MetaRecord.java
                        • ExonRecord.java
                        • RepeatFeatureRecord.java
                        • AltAlleleRecord.java
                        • SupportingFeatureRecord.java
                        • SeqRegionAttribRecord.java
                        • MarkerMapLocationRecord.java
                        • PredictionTranscriptRecord.java
                        • MetaCoordRecord.java
                        • IntronSupportingEvidenceRecord.java
                        • MiscAttribRecord.java
                        • DensityFeatureRecord.java
                        • MiscFeatureRecord.java
                        • RepeatConsensusRecord.java
                        • DependentXrefRecord.java
                        • AltAlleleGroupRecord.java
                        • TranscriptAttribRecord.java
                      • PredictionTranscript.java
                      • CoordSystem.java
                      • Dna.java
                      • MetaCoord.java
                      • Assembly.java
                      • MiscAttrib.java
                      • GeneArchive.java
                    • Tables.java
                    • DefaultCatalog.java
                    • HomoSapiensCore_89_37.java
      • pom.xml
    • sig-analyser
      • src
        • main
          • resources
            • log4j2.xml
          • java
            • com
              • hartwig
                • hmftools
                  • sig_analyser
                    • SigAnalyser.java
                    • common
                      • SigReporter.java
                      • CosineSim.java
                      • SigUtils.java
                      • LeastSquaresFit.java
                    • SampleFitter.java
                    • sim
                      • SampleSimulator.java
                      • SimConfig.java
                      • SimSigFactors.java
                    • nmf
                      • NmfManager.java
                      • NmfCalculator.java
                      • NmfRun.java
                      • NmfConfig.java
                      • NmfSampleFitter.java
                    • buckets
                      • BucketGroup.java
                      • BaSampleFitter.java
                      • SigOptimiser.java
                      • SampleData.java
                      • BucketAnalyser.java
                      • SigDiscovery.java
                      • BaConfig.java
                      • BaReporter.java
                      • BackgroundSigDiscovery.java
                      • SigContribOptimiser.java
                    • loaders
                      • SigIndelLoader.java
                      • SigMnvLoader.java
                      • SigDataLoader.java
                      • DataLoaderConfig.java
                      • SigSnvLoader.java
        • test
          • java
            • com
              • hartwig
                • hmftools
                  • sig_analyser
                    • SigContribOptimiserTest.java
                    • SampleTest.java
                    • BucketGroupTest.java
                    • SigMatrixTest.java
                    • MiscTest.java
                    • StatisticTest.java
                    • SigSampleTest.java
                    • SigOptimiserTest.java
      • pom.xml
      • README.md
      • docs
        • methods.txt
    • sv-linx
      • src
        • main
          • resources
            • log4j2.xml
            • visualisation
              • fragile_sites.csv
              • line_elements.csv
              • cluster.template
            • readme
            • linx.version
            • r
              • chromosomeRangePlot.R
              • fusionPlot.R
              • cytoBand.txt
          • java
            • com
              • hartwig
                • hmftools
                  • linx
                    • LinxOutput.java
                    • chaining
                      • ChainRuleSelector.java
                      • FoldbackBreakendPair.java
                      • SvChain.java
                      • ProposedLinks.java
                      • ChainFinder.java
                      • SvChainState.java
                      • LinkFinder.java
                      • ChainLinkAllocator.java
                      • SegmentJcn.java
                      • ChainingRule.java
                      • BreakendJcn.java
                      • ChainJcnLimits.java
                      • ChainUtils.java
                      • ChainDiagnostics.java
                      • LinkSkipType.java
                      • ChainMetrics.java
                    • LinxConfig.java
                    • cn
                      • CnJcnCalcs.java
                      • CnDataLoader.java
                      • JcnCalcData.java
                      • CnArmStats.java
                      • SvCNData.java
                      • HomLossEvent.java
                      • LohEvent.java
                      • CnSegmentBuilder.java
                      • CopyNumberAnalyser.java
                      • TelomereCentromereCnData.java
                    • drivers
                      • DeletionDrivers.java
                      • DriverEventType.java
                      • DriverGeneData.java
                      • DriverGeneAnnotator.java
                      • AmplificationDrivers.java
                      • GeneCopyNumberRegion.java
                      • DriverAmpData.java
                      • DriverGeneEvent.java
                      • DriverDataCache.java
                      • OpposingSegment.java
                    • ext_compare
                      • CfSampleData.java
                      • CfChainClusterOverlap.java
                      • CfSummaryData.java
                      • ChainFinderCompare.java
                      • CfLink.java
                      • CfDbMatchType.java
                      • CfBreakendData.java
                      • CfChain.java
                      • CfSvData.java
                    • SvLinxApplication.java
                    • neoepitope
                      • AminoAcidConverter.java
                      • NeoEpitopeFinder.java
                      • NeoEpitopeData.java
                    • annotators
                      • PseudoGeneMatch.java
                      • ViralInsertAnnotator.java
                      • KataegisAnnotator.java
                      • IndelData.java
                      • FragileSiteAnnotator.java
                      • LineElementAnnotator.java
                      • PseudoGeneFinder.java
                      • KataegisData.java
                      • IndelAnnotator.java
                      • ReplicationOriginAnnotator.java
                    • visualiser
                      • SvVisualiserConfig.java
                      • file
                        • VisGeneData.java
                        • VisSvDataFile.java
                        • VisSegmentFile.java
                        • VisCopyNumberFile.java
                        • VisualiserWriter.java
                        • VisGeneExonFile.java
                        • VisProteinDomainFile.java
                        • VisFusionFile.java
                      • SvVisualiser.java
                      • data
                        • Link.java
                        • DisruptedExons.java
                        • Links.java
                        • Fusion.java
                        • FusedExon.java
                        • Fusions.java
                        • CopyNumberAlteration.java
                        • Genes.java
                        • ProteinDomains.java
                        • Connectors.java
                        • Segments.java
                        • Segment.java
                        • Exons.java
                        • AdjustedPositions.java
                        • ProteinDomain.java
                        • AdjustedPosition.java
                        • ExonType.java
                        • Exon.java
                        • Gene.java
                        • Connector.java
                        • FusedProteinDomains.java
                        • CopyNumberAlterations.java
                        • FusedExons.java
                      • SvCircosConfig.java
                      • circos
                        • ScalePosition.java
                        • Span.java
                        • ColorPicker.java
                        • CircosDataWriter.java
                        • FusionDataWriter.java
                        • ScaleContig.java
                        • ScaleIntrons.java
                        • ChromosomeRangeExecution.java
                        • Highlights.java
                        • CircosData.java
                        • CircosConfigWriter.java
                        • ProteinDomainColors.java
                        • Thickness.java
                        • SegmentTerminal.java
                        • FusionExecution.java
                    • types
                      • SvArmCluster.java
                      • ResolvedType.java
                      • SvVarData.java
                      • SglMapping.java
                      • SvCluster.java
                      • SvBreakend.java
                      • SvArmGroup.java
                      • LinkType.java
                      • LinxConstants.java
                      • ChromosomeArm.java
                      • DoubleMinuteData.java
                      • SvLinkedPair.java
                    • analysis
                      • ClusterMetrics.java
                      • DoubleMinuteFinderOld.java
                      • ClusterAnalyser.java
                      • SvSampleAnalyser.java
                      • ClusteringPrep.java
                      • ClusterAnnotations.java
                      • SimpleClustering.java
                      • DoubleMinuteFinder.java
                      • ClusteringState.java
                      • PairResolution.java
                      • SvFilters.java
                      • CohortDataWriter.java
                      • SvClassification.java
                      • SvUtilities.java
                      • FoldbackFinder.java
                      • ComplexClustering.java
                      • ClusteringReason.java
                      • BfbFinder.java
                    • gene
                      • GenerateEnsemblDataCache.java
                      • EnsemblDAO.java
                    • SvDataLoader.java
                    • fusion
                      • DisruptionFinder.java
                      • FusionAnnotations.java
                      • FusionChainInfo.java
                      • FusionParameters.java
                      • FusionReportability.java
                      • rna
                        • RnaFusionAnnotator.java
                        • DnaRnaMatchType.java
                        • RnaFusionMapper.java
                        • RnaDataLoader.java
                        • RnaExonMatchData.java
                        • RnaFusionData.java
                        • RnaMatchWriter.java
                        • RnaJunctionType.java
                      • FusionFinder.java
                      • FusionConstants.java
                      • FusionDisruptionAnalyser.java
                      • FusionWriter.java
                      • GeneFusion.java
        • test
          • resources
            • sample_data
              • DM_SAMPLE2
              • FB_SAMPLE1
              • DM_SAMPLE1
              • COLO829T
              • CT_SAMPLE1
          • java
            • com
              • hartwig
                • hmftools
                  • linx
                    • utils
                      • LinxTester.java
                      • SampleDataLoader.java
                      • SvTestUtils.java
                      • GeneTestUtils.java
                    • chaining
                      • ChainingSimpleTest.java
                      • LinkingTest.java
                      • ChainRoutinesTest.java
                      • ChainingActualTest.java
                      • ChainingComplexTest.java
                    • drivers
                      • HomDisruptionsTest.java
                      • AmpDriversTest.java
                    • misc
                      • MiscTest.java
                    • analyser
                      • DoubleMinuteTest.java
                      • TranslocationPairTest.java
                      • FoldbackTest.java
                      • CopyNumberTest.java
                      • MergeRuleTest.java
                      • LineTest.java
                      • AnnotationTest.java
                      • FilteringTest.java
                      • SyntheticTest.java
                      • InversionPairTest.java
                      • ReplicationRepairTest.java
                    • visualiser
                      • data
                        • SegmentsTest.java
                        • FusedExonsTest.java
                        • DisruptedExonsTest.java
                      • circos
                        • CircosConfigWriterTest.java
                        • ScaleContigTest.java
                        • ProteinDomainColorsTest.java
                        • ScaleIntronsTest.java
                        • ColorPickerTest.java
                        • CircosDataWriterTest.java
                    • gene
                      • GeneCollectionTest.java
                    • fusion
                      • SpecialFusionsTest.java
                      • NeoEpitopeTest.java
                      • RnaFusionTest.java
                      • FusionRulesTest.java
                      • FusionTest.java
                      • DisruptionTest.java
      • pom.xml
      • README_VIS.md
      • README.md
    • hmf-id-generator
      • src
        • main
          • resources
            • log4j2.xml
          • kotlin
            • com
              • hartwig
                • hmftools
                  • idgenerator
                    • IdGenerator.kt
                    • HmfIdApplication.kt
                    • PatientAnonymizer.kt
                    • ids
                      • CanonicalPatientId.kt
                      • PatientId.kt
                      • IdType.kt
                      • SampleId.kt
                    • AnonymizedPatients.kt
                    • Hash.kt
                    • AnonymizedRecord.kt
                    • HmfSampleIdRecord.kt
                    • AnonymizedSamples.kt
                    • Constants.kt
                    • SampleAnonymizer.kt
                    • anonymizedIds
                      • AnonymizedId.kt
                      • HmfPatientId.kt
                      • HashId.kt
                      • HmfSampleId.kt
                    • HmfSampleMappingRecord.kt
                    • SamplesInput.kt
        • test
          • kotlin
            • com
              • hartwig
                • hmftools
                  • idgenerator
                    • SampleAnonymizerTest.kt
                    • SamplesInputTest.kt
                    • ids
                      • SampleIdTest.kt
                      • PatientIdTest.kt
                    • AnonymizedSamplesTest.kt
                    • anonymizedIds
                      • HmfSampleIdTest.kt
                      • HmfPatientIdTest.kt
                    • IdGeneratorTest.kt
                    • PatientAnonymizerTest.kt
      • pom.xml
      • README.md
    • patient-reporter
      • src
        • main
          • resources
            • log4j2.xml
            • fonts
              • nimbus-sans
                • NimbusSansL-Regular.ttf
                • NimbusSansL-Bold.ttf
              • hmf-icons
                • hmf-icons.ttf
          • java
            • com
              • hartwig
                • hmftools
                  • patientreporter
                    • qcfail
                      • QCFailReporter.java
                      • QCFailReport.java
                      • QCFailReason.java
                      • QCFailReportData.java
                      • QCFailType.java
                    • AnalysedPatientReport.java
                    • SampleMetadata.java
                    • PatientReporterApplication.java
                    • viralInsertion
                      • ViralInsertionAnalyzer.java
                      • ViralInsertion.java
                    • SampleReportFactory.java
                    • AnalysedPatientReporter.java
                    • cfreport
                      • components
                        • Footer.java
                        • Header.java
                        • ReportSignature.java
                        • BarChart.java
                        • LineDivider.java
                        • DataLabel.java
                        • Icon.java
                        • TableUtil.java
                        • InlineBarChart.java
                        • TumorLocationAndTypeTable.java
                        • SidePanel.java
                        • BaseMarker.java
                      • ReportResources.java
                      • PageEventHandler.java
                      • CFReportWriter.java
                      • data
                        • DataUtil.java
                        • GeneDisruptions.java
                        • ClinicalTrials.java
                        • GainsAndLosses.java
                        • HomozygousDisruptions.java
                        • MutationalBurden.java
                        • SomaticVariants.java
                        • MicroSatelliteStatus.java
                        • GeneFusions.java
                        • GeneUtil.java
                        • MutationalLoad.java
                        • HrDeficiency.java
                        • EvidenceItems.java
                        • TumorPurity.java
                      • MathUtil.java
                      • chapters
                        • QCFailChapter.java
                        • GenomicAlterationsChapter.java
                        • SummaryChapter.java
                        • DetailsAndDisclaimerChapter.java
                        • TherapyDetailsChapterOffLabel.java
                        • ExplanationChapter.java
                        • TherapyDetailsChapterOnLabel.java
                        • ReportChapter.java
                        • TherapyDetailsChapterFunctions.java
                        • TumorCharacteristicsChapter.java
                        • CircosChapter.java
                    • OutputFileUtil.java
                    • variants
                      • DriverInterpretation.java
                      • germline
                        • BachelorFile.java
                        • GermlineReportingModel.java
                        • GermlineReportingFile.java
                        • FilterGermlineVariants.java
                        • GermlineVariant.java
                      • ReportVariantAnalysis.java
                      • somatic
                        • SomaticVariantAnalyzer.java
                        • SomaticVariantAnalysis.java
                      • ReportableVariant.java
                      • driver
                        • DriverGeneView.java
                        • DriverGeneViewFactory.java
                      • ReportableVariantAnalyzer.java
                      • ReportableGermlineVariant.java
                      • ReportableVariantFactory.java
                    • AnalysedReportDataLoader.java
                    • structural
                      • SvAnalysis.java
                      • ReportableGeneDisruption.java
                      • ReportableGeneDisruptionFactory.java
                      • SvAnalyzer.java
                    • QsFormNumber.java
                    • purple
                      • PurpleAnalyzer.java
                      • PurpleAnalysis.java
                      • ReportableGainLoss.java
                      • ExtractReportableGainsAndLosses.java
                      • CheckEvidenceCnv.java
                      • PurpleSignatures.java
                    • homozygousdisruption
                      • HomozygousDisruptionAnalyzer.java
                      • ReportableHomozygousDisruption.java
                    • AnalysedReportData.java
                    • ReportWriter.java
                    • reportingdb
                      • ReportingDb.java
                      • ReportingEntry.java
                    • ReportData.java
                    • actionability
                      • ClinicalTrialFactory.java
                      • ReportableEvidenceItemFactory.java
                    • summary
                      • SummaryModel.java
                      • SummaryFile.java
                    • PatientReport.java
                    • SampleReport.java
                    • PatientReporterConfig.java
        • test
          • resources
            • germline
              • germline_genes_reporting.csv
            • test_run
              • chord
                • sample_chord_prediction.txt
              • linx
                • sample.linx.viral_inserts.tsv
                • sample.drivers.catalog.tsv
                • sample.linx.disruptions.tsv
                • sample.linx.reported_fusion.tsv
              • purple
                • plot
                • sample.purple.somatic.vcf
                • sample.purple.purity.tsv
                • sample.purple.cnv.gene.tsv
                • sample.purple.qc
              • bachelor
                • sample.bachelor.germline_variant.tsv
            • company_logo
              • hartwig_logo_test.jpg
            • rva_logo
              • rva_logo_test.jpg
            • reporting_db
              • reporting_db_example.tsv
            • sample_summary
              • sample_summary.tsv
            • signature
            • actionability
              • actionablePromiscuousThree.tsv
              • actionablePromiscuousFive.tsv
              • actionableVariants.tsv
              • knowledgebaseCancerTypes.tsv
              • actionableFusionPairs.tsv
              • actionableRanges.tsv
              • actionableCNVs.tsv
          • java
            • com
              • hartwig
                • hmftools
                  • patientreporter
                    • SampleReportFactoryTest.java
                    • viralInsertion
                      • ViralInsertionAnalyzerTest.java
                    • AnalysedPatientReporterTest.java
                    • cfreport
                      • MathUtilTest.java
                      • CFReportWriterTest.java
                      • data
                        • SomaticVariantsTest.java
                      • ReportResourcesTest.java
                      • chapters
                        • SummaryChapterTest.java
                    • variants
                      • germline
                        • GermlineReportingFileTest.java
                        • GermlineReportingModelTest.java
                        • FilterGermlineVariantsTest.java
                        • BachelorFileTest.java
                        • GermlineReportingModelTestFactory.java
                      • ReportableVariantAnalyzerTest.java
                      • somatic
                        • SomaticVariantAnalyzerTest.java
                    • PatientReporterTestFactory.java
                    • structural
                      • ReportableGeneDisruptionFactoryTest.java
                      • SvAnalysisDatamodelTestFactory.java
                      • SvAnalyzerTest.java
                    • purple
                      • CheckEvidenceCnvTest.java
                    • PatientReporterTestUtil.java
                    • homozygousdisruption
                      • HomozygousDisruptionAnalyzerTest.java
                    • ExampleAnalysisTestFactory.java
                    • reportingdb
                      • ReportingDbTest.java
                    • actionability
                      • ReportableEvidenceItemFactoryTest.java
                      • ClinicalTrialFactoryTest.java
                    • summary
                      • SummaryModelTest.java
                      • SummaryFileTest.java
      • pom.xml
    • isofox
      • src
        • main
          • resources
            • isofox.version
          • java
            • com
              • hartwig
                • hmftools
                  • isofox
                    • novel
                      • AltSpliceJunctionContext.java
                      • RetainedIntron.java
                      • RetainedIntronFinder.java
                      • cohort
                        • AltSpliceJunctionCohort.java
                        • SpliceVariantMatching.java
                        • SpliceVariant.java
                        • AltSpliceJuncCohortData.java
                      • AltSpliceJunction.java
                      • AltSpliceJunctionFinder.java
                      • AltSpliceJunctionType.java
                    • TaskType.java
                    • ChromosomeGeneTask.java
                    • results
                      • ResultsWriter.java
                      • GeneResult.java
                      • TranscriptResult.java
                      • SummaryStats.java
                    • IsofoxConfig.java
                    • Isofox.java
                    • BamFragmentAllocator.java
                    • IsofoxFunction.java
                    • common
                      • FragmentType.java
                      • BaseDepth.java
                      • GeneReadData.java
                      • RegionReadData.java
                      • FragmentTracker.java
                      • GeneCollection.java
                      • TransMatchType.java
                      • DuplicateReadTracker.java
                      • FragmentMatchType.java
                      • RnaUtils.java
                      • BamSlicer.java
                      • TransExonRef.java
                      • ReadRecord.java
                      • RegionMatchType.java
                    • IsofoxConstants.java
                    • cohort
                      • CohortAnalyser.java
                      • SampleRoutines.java
                      • CohortConfig.java
                      • SampleDataCache.java
                      • CohortAnalysisType.java
                    • adjusts
                      • GcRatioCounts.java
                      • GcTranscriptCalculator.java
                      • FragmentSizeCalcs.java
                    • expression
                      • CategoryCountsData.java
                      • GeneCollectionSummary.java
                      • ExpectedRatesData.java
                      • cohort
                        • TransExpressionData.java
                        • GeneExpressionDistribution.java
                        • GeneCohortData.java
                        • SampleGenePercentiles.java
                        • TransExpressionDistribution.java
                      • ExpectationMaxFit.java
                      • ExpectedRatesGenerator.java
                      • TranscriptExpression.java
                      • ExpectedCountsCache.java
                    • fusion
                      • FusionFragmentBuilder.java
                      • FusionFragmentType.java
                      • SupplementaryReadData.java
                      • FusionUtils.java
                      • FusionFragment.java
                      • FusionFinder.java
                      • FusionConfig.java
                      • FusionConstants.java
                      • cohort
                        • FusionCohort.java
                        • FusionCohortConfig.java
                        • KnownGeneType.java
                        • FusionCohortTask.java
                        • FusionCollection.java
                        • FusionData.java
                        • FusionCohortData.java
                        • FusionFilters.java
                        • ExternalFusionCompare.java
                        • ExternalFusionData.java
                      • FusionTask.java
                      • FusionReadData.java
                      • ChimericReadTracker.java
                      • FusionWriter.java
                      • FusionJunctionType.java
                      • ChimericStats.java
        • test
          • java
            • com
              • hartwig
                • hmftools
                  • isofox
                    • NovelJunctionsTest.java
                    • FusionFragmentsTest.java
                    • FusionDataTest.java
                    • TestUtils.java
                    • SpliceVariantTest.java
                    • MiscTest.java
                    • GcBiasTest.java
                    • ExpectedRatesTest.java
                    • ChimericReadTest.java
                    • ReadCountsTest.java
      • pom.xml
      • README.md
    • README.md
    • bam-slicer
      • src
        • main
          • resources
            • log4j2.xml
          • java
            • com
              • hartwig
                • hmftools
                  • bamslicer
                    • S3UrlGenerator.java
                    • CachingSeekableHTTPStream.java
                    • BamSlicerApplication.java
                    • ChunkHttpBuffer.java
                    • SlicerHttpClient.java
      • pom.xml
    • serve
      • src
        • main
          • resources
            • log4j2.xml
          • java
            • com
              • hartwig
                • hmftools
                  • serve
                    • AllGenomicEvents.java
                    • output
                      • GeneratingOutputFiles.java
                    • GenomicEvents.java
                    • util
                      • ProteinKeyFormatter.java
                      • HgvsConstants.java
                      • AminoAcidFunctions.java
                    • transvar
                      • TransvarTestApplication.java
                      • Transvar.java
                      • TransvarConverter.java
                      • TransvarProcess.java
                      • datamodel
                        • TransvarAnnotation.java
                        • TransvarRecord.java
                        • TransvarInsertion.java
                        • TransvarDeletion.java
                        • TransvarSnvMnv.java
                        • TransvarComplexInsertDelete.java
                        • TransvarDuplication.java
                      • TransvarProcessImpl.java
                      • TransvarInterpreter.java
                    • compassionateuse
                      • CompassionateUseProgram.java
                      • CompassionateUseProgramFile.java
                    • KnowledgebaseGeneratorApplication.java
                    • RefGenomeVersion.java
                    • vicc
                      • copynumber
                        • ActionableAmplificationDeletion.java
                        • KnownAmplificationDeletion.java
                        • CopyNumberExtractor.java
                      • ViccEventTypeExtractorTestApplication.java
                      • signatures
                        • Signatures.java
                        • SignaturesExtractor.java
                      • ViccExtractionResult.java
                      • hotspot
                        • HotspotExtractor.java
                        • HotspotAnnotation.java
                        • ProteinResolver.java
                      • eventtype
                        • EventTypeAnalyzer.java
                        • DetermineEventOfGenomicMutation.java
                        • EventType.java
                      • ViccExtractorTestApplication.java
                      • curation
                        • FeatureCurator.java
                        • CurationKey.java
                        • CurationFactory.java
                      • ViccExtractor.java
                      • FeatureIgnoreUtil.java
                      • range
                        • GeneRangeExtractor.java
                        • GeneLevelEventExtractor.java
                      • ViccKnowledgebaseGeneratorTestApplication.java
                      • fusion
                        • KnownFusions.java
                        • FusionExtractor.java
                    • actionability
                      • variant
                        • ActionableVariant.java
                        • VariantEvidenceAnalyzerFactory.java
                        • VariantEvidenceAnalyzer.java
                      • ActionabilityAnalyzer.java
                      • gene
                        • GeneEvidenceAnalyzerFactory.java
                        • GeneEvidenceAnalyzer.java
                        • ActionableGene.java
                      • range
                        • ActionableRange.java
                        • RangeEvidenceAnalyzer.java
                        • RangeEvidenceAnalyzerFactory.java
                      • signature
                        • ActionableSignature.java
                        • SignatureEvidenceAnalyzer.java
                        • SignatureEvidenceAnalyzerFactory.java
                      • fusion
                        • FusionEvidenceAnalyzer.java
                        • ActionableFusion.java
                        • FusionEvidenceAnalyzerFactory.java
                    • ServeAnnotatedHotspotVCFChecker.java
        • test
          • resources
            • compassionateuse
              • example.tsv
            • refgenome
              • ref.fasta.fai
              • ref.fasta
              • ref.fasta.dict
            • actionability
              • actionableSignatures.tsv
              • actionableVariants.tsv
              • actionableRanges.tsv
              • actionableFusions.tsv
              • actionableGenes.tsv
          • java
            • com
              • hartwig
                • hmftools
                  • serve
                    • util
                      • AminoAcidFunctionsTest.java
                    • transvar
                      • TransvarConverterTest.java
                      • TransvarTest.java
                      • TransvarTestFactory.java
                      • TransvarInterpreterTest.java
                    • compassionateuse
                      • CompassionateUseProgramFileTest.java
                    • GenomicEventsTest.java
                    • vicc
                      • hotspot
                        • HotspotExtractorTest.java
                      • ViccTestFactory.java
                      • eventtype
                        • DetermineEventOfGenomicMutationTest.java
                        • EventTypeAnalyzerTest.java
                      • curation
                        • FeatureCuratorTest.java
                    • actionability
                      • ActionabilityAnalyzerTest.java
      • pom.xml
      • README.md
    • iclusion-importer
      • src
        • main
          • resources
            • log4j2.xml
          • java
            • com
              • hartwig
                • hmftools
                  • iclusion
                    • IclusionImporterApplication.java
                    • qc
                      • IclusionTrialChecker.java
                    • api
                      • IclusionObjectVariant.java
                      • IclusionApi.java
                      • IclusionObjectIndication.java
                      • IclusionObjectGene.java
                      • IclusionApiMain.java
                      • IclusionApiObjectMapper.java
                      • IclusionResponseAdapter.java
                      • IclusionToken.java
                      • IclusionObjectMutation.java
                      • IclusionObjectStudy.java
                    • IclusionCredentials.java
                    • data
                      • IclusionMutation.java
                      • IclusionTumorLocation.java
                      • IclusionTrial.java
                    • io
                      • IclusionTrialFile.java
        • test
          • java
            • com
              • hartwig
                • hmftools
                  • iclusion
                    • api
                      • IclusionApiObjectMapperTest.java
                    • io
                      • IclusionTrialFileTest.java
      • pom.xml
    • .gitignore
    • hmf_code_scheme.xml
    • count-bam-lines
      • src
        • main
          • resources
            • log4j2.xml
            • cobalt.version
            • r
              • ratioSegmentation.R
          • java
            • com
              • hartwig
                • hmftools
                  • cobalt
                    • CountBamLinesApplication.java
                    • count
                      • CountSupplier.java
                      • ChromosomeReadCount.java
                    • CobaltConfig.java
                    • ratio
                      • GCRatioSupplier.java
                      • RollingMedian.java
                      • DiploidRatioSupplier.java
                      • DiploidRatioNormalization.java
                      • RatioSupplier.java
                      • GCRatioNormalization.java
                    • RatioSegmentation.java
        • test
          • java
            • com
              • hartwig
                • hmftools
                  • cobalt
                    • ratio
                      • DiploidRatioNormalizationTest.java
                      • RollingMedianTest.java
      • pom.xml
      • README.md
    • protect
      • src
        • main
          • resources
            • log4j2.xml
          • java
            • com
              • hartwig
                • hmftools
                  • protect
                    • ClinicalEvidenceDAOProtect.java
                    • ProtectDataLoader.java
                    • report
                      • chord
                        • ChordStatus.java
                        • ChordFileReader.java
                        • ChordAnalysis.java
                    • conclusion
                      • TemplateConclusionFile.java
                      • ConclusionFactory.java
                      • TemplateConclusion.java
                    • ProtectActionability.java
                    • common
                      • DriverInterpretation.java
                      • BachelorFile.java
                      • GermlineReportingModel.java
                      • CopyNumberAnalyzer.java
                      • DriverGeneView.java
                      • GenomicData.java
                      • ActionabilityFile.java
                      • HomozygousDisruptionAnalyzer.java
                      • DriverGeneViewFactory.java
                      • GermlineReportingFile.java
                      • ReportableHomozygousDisruption.java
                      • SomaticVariantAnalyzer.java
                      • GermlineVariant.java
                      • ReportableVariant.java
                      • ReportableVariantAnalysis.java
                      • ReportableGermlineVariant.java
                      • CopyNumberAnalysis.java
                      • ReportableGainLoss.java
                      • ExtractReportableGainsAndLosses.java
                      • SomaticVariantAnalysis.java
                    • actionability
                      • Actionable.java
                      • EvidenceItem.java
                      • ClinicalTrial.java
                      • variant
                        • ActionableVariant.java
                        • ActionableRange.java
                        • VariantEvidenceAnalyzerFactory.java
                        • VariantEvidenceAnalyzer.java
                      • ActionabilityAnalyzer.java
                      • util
                        • MultiDrugCurator.java
                      • EvidenceLevel.java
                      • panel
                        • ActionablePanelFile.java
                        • ActionablePanelBuilder.java
                        • ActionablePanel.java
                      • cancertype
                        • CancerTypeAnalyzer.java
                        • PrimaryTumorToDOIDMapper.java
                        • CancerTypeToDOIDMappingEntry.java
                        • CancerTypeToDOIDMapper.java
                      • cnv
                        • CopyNumberEvidenceAnalyzer.java
                        • ActionableCopyNumber.java
                        • CopyNumberType.java
                        • SignificantGeneCopyNumberFilter.java
                        • CopyNumberEvidenceAnalyzerFactory.java
                      • ActionabilitySource.java
                      • fusion
                        • FusionEvidenceAnalyzer.java
                        • ActionableFusion.java
                        • ActionablePromiscuous.java
                        • FusionEvidenceAnalyzerFactory.java
                      • drup
                        • DrupActionabilityModelFactory.java
                        • DrupActionabilityModel.java
        • test
          • resources
            • report
              • chord
                • sample_chord_prediction.txt
            • actionability
              • actionablePromiscuousThree.tsv
              • actionablePromiscuousFive.tsv
              • actionableVariants.tsv
              • knowledgebaseCancerTypes.tsv
              • actionableTumorCharacteristics
              • drup_genes.csv
              • actionableFusionPairs.tsv
              • actionableRanges.tsv
              • actionableCNVs.tsv
          • java
            • com
              • hartwig
                • hmftools
                  • protect
                    • report
                      • chord
                        • ChordFileReaderTest.java
                    • actionability
                      • ActionabilityAnalyzerTest.java
                      • variant
                        • VariantEvidenceAnalyzerTest.java
                      • util
                        • MultiDrugCuratorTest.java
                      • cancertype
                        • CancerTypeAnalyzerTestFactory.java
                        • PrimaryTumorToDOIDMapperTest.java
                        • CancerTypeAnalyzerTest.java
                      • cnv
                        • CopyNumberEvidenceAnalyzerTest.java
                        • SignificantGeneCopyNumberFilterTest.java
                      • fusion
                        • FusionEvidenceAnalyzerTest.java
                      • drup
                        • DrupActionabilityModelFactoryTest.java
      • pom.xml
      • README.md
    • purity-ploidy-estimator
      • src
        • main
          • resources
            • purple.version
            • log4j2.xml
            • readme
            • circos
              • input.template