Path	Lines of Code
config/pmd/pmd-ruleset.xml	30
src/integrationTest/java/com/epam/fonda/AbstractIntegrationTest.java	94
src/integrationTest/java/com/epam/fonda/Bam2FastqIntegrationTest.java	112
src/integrationTest/java/com/epam/fonda/DnaAmpliconVarBamIntegrationTest.java	258
src/integrationTest/java/com/epam/fonda/DnaAmpliconVarFastqIntegrationTest.java	170
src/integrationTest/java/com/epam/fonda/DnaAnalysisIntegrationTest.java	173
src/integrationTest/java/com/epam/fonda/DnaCaptureVarBamIntegrationTest.java	149
src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java	703
src/integrationTest/java/com/epam/fonda/DnaWgsVarBamIntegrationTest.java	272
src/integrationTest/java/com/epam/fonda/DnaWgsVarFastqIntegrationTest.java	66
src/integrationTest/java/com/epam/fonda/HlaTypingFastqIntegrationTest.java	114
src/integrationTest/java/com/epam/fonda/RnaCaptureVarFastqIntegrationTest.java	58
src/integrationTest/java/com/epam/fonda/RnaExpressionBamIntegrationTest.java	70
src/integrationTest/java/com/epam/fonda/RnaExpressionFastqIntegrationTest.java	392
src/integrationTest/java/com/epam/fonda/RnaFusionFastqIntegrationTest.java	87
src/integrationTest/java/com/epam/fonda/SCRnaExpressionBamIntegrationTest.java	164
src/integrationTest/java/com/epam/fonda/SCRnaExpressionCellRangerFastqIntegrationTest.java	109
src/integrationTest/java/com/epam/fonda/SCRnaExpressionFastqIntegrationTest.java	127
src/integrationTest/java/com/epam/fonda/TcrRepertoireFastqIntegrationTest.java	94
src/integrationTest/java/com/epam/fonda/TestTemplateUtils.java	50
src/main/java/com/epam/fonda/CmdParser.java	68
src/main/java/com/epam/fonda/Executor.java	55
src/main/java/com/epam/fonda/FondaLauncher.java	21
src/main/java/com/epam/fonda/Main.java	32
src/main/java/com/epam/fonda/OptionName.java	18
src/main/java/com/epam/fonda/entity/command/AbstractCommand.java	22
src/main/java/com/epam/fonda/entity/command/BashCommand.java	13
src/main/java/com/epam/fonda/entity/configuration/CommonOutdir.java	25
src/main/java/com/epam/fonda/entity/configuration/Configuration.java	13
src/main/java/com/epam/fonda/entity/configuration/DirectoryManager.java	10
src/main/java/com/epam/fonda/entity/configuration/EOLConverter.java	13
src/main/java/com/epam/fonda/entity/configuration/EOLMarker.java	11
src/main/java/com/epam/fonda/entity/configuration/FlagXenomeConverter.java	13
src/main/java/com/epam/fonda/entity/configuration/GlobalConfig.java	234
src/main/java/com/epam/fonda/entity/configuration/GlobalConfigFormat.java	108
src/main/java/com/epam/fonda/entity/configuration/StudyConfig.java	28
src/main/java/com/epam/fonda/entity/configuration/StudyConfigFormat.java	15
src/main/java/com/epam/fonda/entity/configuration/ToolSetConverter.java	10
src/main/java/com/epam/fonda/entity/configuration/orchestrator/MasterScript.java	187
src/main/java/com/epam/fonda/entity/configuration/orchestrator/ScriptManager.java	15
src/main/java/com/epam/fonda/entity/configuration/orchestrator/ScriptType.java	4
src/main/java/com/epam/fonda/tools/PostProcessTool.java	7
src/main/java/com/epam/fonda/tools/Tool.java	7
src/main/java/com/epam/fonda/tools/impl/AbraRealign.java	81
src/main/java/com/epam/fonda/tools/impl/AmpliconGatkRealign.java	56
src/main/java/com/epam/fonda/tools/impl/AmpliconGatkRecalibrate.java	54
src/main/java/com/epam/fonda/tools/impl/BwaSort.java	92
src/main/java/com/epam/fonda/tools/impl/CalculateContamination.java	58
src/main/java/com/epam/fonda/tools/impl/ContEst.java	89
src/main/java/com/epam/fonda/tools/impl/Count.java	149
src/main/java/com/epam/fonda/tools/impl/Cufflinks.java	78
src/main/java/com/epam/fonda/tools/impl/DnaAnalysis.java	146
src/main/java/com/epam/fonda/tools/impl/DnaPicardQc.java	297
src/main/java/com/epam/fonda/tools/impl/Exomecnv.java	84
src/main/java/com/epam/fonda/tools/impl/FastqListAnalysis.java	73
src/main/java/com/epam/fonda/tools/impl/FeatureCount.java	122
src/main/java/com/epam/fonda/tools/impl/FilterAlignmentArtifacts.java	64
src/main/java/com/epam/fonda/tools/impl/FilterMutectCalls.java	76
src/main/java/com/epam/fonda/tools/impl/Freebayes.java	73
src/main/java/com/epam/fonda/tools/impl/FusionCatcher.java	71
src/main/java/com/epam/fonda/tools/impl/GatkHaplotypeCaller.java	104
src/main/java/com/epam/fonda/tools/impl/GatkHaplotypeCallerRnaFilter.java	72
src/main/java/com/epam/fonda/tools/impl/GatkSortSam.java	51
src/main/java/com/epam/fonda/tools/impl/GatkSplitReads.java	57
src/main/java/com/epam/fonda/tools/impl/Hisat2.java	94
src/main/java/com/epam/fonda/tools/impl/LearnReadOrientationModel.java	55
src/main/java/com/epam/fonda/tools/impl/Lofreq.java	85
src/main/java/com/epam/fonda/tools/impl/Mixcr.java	98
src/main/java/com/epam/fonda/tools/impl/Mutect1.java	82
src/main/java/com/epam/fonda/tools/impl/Mutect2.java	84
src/main/java/com/epam/fonda/tools/impl/NovoalignSort.java	103
src/main/java/com/epam/fonda/tools/impl/OptiType.java	84
src/main/java/com/epam/fonda/tools/impl/PicardMarkDuplicate.java	90
src/main/java/com/epam/fonda/tools/impl/PicardMergeDnaBam.java	72
src/main/java/com/epam/fonda/tools/impl/PicardRemoveDuplicate.java	44
src/main/java/com/epam/fonda/tools/impl/Pileup.java	87
src/main/java/com/epam/fonda/tools/impl/PileupSummaries.java	62
src/main/java/com/epam/fonda/tools/impl/QcSummary.java	140
src/main/java/com/epam/fonda/tools/impl/RNASeQC.java	144
src/main/java/com/epam/fonda/tools/impl/RnaAnalysis.java	59
src/main/java/com/epam/fonda/tools/impl/RnaMutationAnalysis.java	47
src/main/java/com/epam/fonda/tools/impl/RsemAnnotation.java	50
src/main/java/com/epam/fonda/tools/impl/RsemExpression.java	68
src/main/java/com/epam/fonda/tools/impl/SCRNASeqDoubletDetection.java	65
src/main/java/com/epam/fonda/tools/impl/SCRnaAnalysis.java	105
src/main/java/com/epam/fonda/tools/impl/Salmon.java	85
src/main/java/com/epam/fonda/tools/impl/SamToFastq.java	90
src/main/java/com/epam/fonda/tools/impl/Scalpel.java	77
src/main/java/com/epam/fonda/tools/impl/SeqPurge.java	87
src/main/java/com/epam/fonda/tools/impl/Sequenza.java	80
src/main/java/com/epam/fonda/tools/impl/SortBamByReadName.java	67
src/main/java/com/epam/fonda/tools/impl/Star.java	121
src/main/java/com/epam/fonda/tools/impl/StarFusion.java	112
src/main/java/com/epam/fonda/tools/impl/Strelka2.java	87
src/main/java/com/epam/fonda/tools/impl/Stringtie.java	71
src/main/java/com/epam/fonda/tools/impl/Trimmomatic.java	93
src/main/java/com/epam/fonda/tools/impl/Vardict.java	80
src/main/java/com/epam/fonda/tools/impl/VcfSnpeffAnnotation.java	95
src/main/java/com/epam/fonda/tools/impl/Vdj.java	85
src/main/java/com/epam/fonda/tools/impl/Xenome.java	123
src/main/java/com/epam/fonda/tools/results/BamOutput.java	19
src/main/java/com/epam/fonda/tools/results/BamResult.java	11
src/main/java/com/epam/fonda/tools/results/CalculateContaminationOutput.java	9
src/main/java/com/epam/fonda/tools/results/CalculateContaminationResult.java	10
src/main/java/com/epam/fonda/tools/results/ContEstOutput.java	17
src/main/java/com/epam/fonda/tools/results/ContEstResult.java	10
src/main/java/com/epam/fonda/tools/results/CufflinksOutput.java	17
src/main/java/com/epam/fonda/tools/results/CufflinksResult.java	11
src/main/java/com/epam/fonda/tools/results/ExomecnvOutput.java	17
src/main/java/com/epam/fonda/tools/results/ExomecnvResult.java	11
src/main/java/com/epam/fonda/tools/results/FastqOutput.java	9
src/main/java/com/epam/fonda/tools/results/FastqResult.java	10
src/main/java/com/epam/fonda/tools/results/FeatureCountOutput.java	16
src/main/java/com/epam/fonda/tools/results/FeatureCountResult.java	11
src/main/java/com/epam/fonda/tools/results/FusionCatcherOutput.java	17
src/main/java/com/epam/fonda/tools/results/FusionCatcherResult.java	11
src/main/java/com/epam/fonda/tools/results/LearnReadOrientationModelOutput.java	8
src/main/java/com/epam/fonda/tools/results/LearnReadOrientationModelResult.java	10
src/main/java/com/epam/fonda/tools/results/MetricsOutput.java	20
src/main/java/com/epam/fonda/tools/results/MetricsResult.java	11
src/main/java/com/epam/fonda/tools/results/MixcrOutput.java	19
src/main/java/com/epam/fonda/tools/results/MixcrResult.java	11
src/main/java/com/epam/fonda/tools/results/OptiTypeOutput.java	17
src/main/java/com/epam/fonda/tools/results/OptiTypeResult.java	11
src/main/java/com/epam/fonda/tools/results/PileupOutput.java	17
src/main/java/com/epam/fonda/tools/results/PileupResult.java	10
src/main/java/com/epam/fonda/tools/results/PileupSummariesResult.java	10
src/main/java/com/epam/fonda/tools/results/Result.java	3
src/main/java/com/epam/fonda/tools/results/RsemOutput.java	17
src/main/java/com/epam/fonda/tools/results/RsemResult.java	11
src/main/java/com/epam/fonda/tools/results/SalmonOutput.java	17
src/main/java/com/epam/fonda/tools/results/SalmonResult.java	11
src/main/java/com/epam/fonda/tools/results/SequenzaOutput.java	19
src/main/java/com/epam/fonda/tools/results/SequenzaResult.java	11
src/main/java/com/epam/fonda/tools/results/StarFusionOutput.java	16
src/main/java/com/epam/fonda/tools/results/StarFusionResult.java	11
src/main/java/com/epam/fonda/tools/results/StringtieOutput.java	17
src/main/java/com/epam/fonda/tools/results/StringtieResult.java	11
src/main/java/com/epam/fonda/tools/results/VariantsVcfOutput.java	24
src/main/java/com/epam/fonda/tools/results/VariantsVcfResult.java	11
src/main/java/com/epam/fonda/tools/results/VcfScnpeffAnnonationResult.java	10
src/main/java/com/epam/fonda/tools/results/VcfScnpeffAnnotationOutput.java	8
src/main/java/com/epam/fonda/tools/results/VdjOutput.java	16
src/main/java/com/epam/fonda/tools/results/VdjResult.java	11
src/main/java/com/epam/fonda/utils/AmpliconGatkDatabaseFields.java	26
src/main/java/com/epam/fonda/utils/AmpliconGatkToolFields.java	18
src/main/java/com/epam/fonda/utils/CellRangerUtils.java	35
src/main/java/com/epam/fonda/utils/ConfigurationUtils.java	99
src/main/java/com/epam/fonda/utils/DnaUtils.java	149
src/main/java/com/epam/fonda/utils/MessageConstant.java	36
src/main/java/com/epam/fonda/utils/PipelineUtils.java	217
src/main/java/com/epam/fonda/utils/RnaAnalysisUtils.java	88
src/main/java/com/epam/fonda/utils/TemplateEngineUtils.java	21
src/main/java/com/epam/fonda/utils/ToolUtils.java	37
src/main/java/com/epam/fonda/workflow/BamWorkflow.java	13
src/main/java/com/epam/fonda/workflow/FastqWorkflow.java	13
src/main/java/com/epam/fonda/workflow/PipelineType.java	37
src/main/java/com/epam/fonda/workflow/TaskContainer.java	20
src/main/java/com/epam/fonda/workflow/Workflow.java	29
src/main/java/com/epam/fonda/workflow/WorkflowFactory.java	47
src/main/java/com/epam/fonda/workflow/impl/Bam2FastqWorkflow.java	70
src/main/java/com/epam/fonda/workflow/impl/DnaVarBamWorkflow.java	81
src/main/java/com/epam/fonda/workflow/impl/DnaVarFastqWorkflow.java	137
src/main/java/com/epam/fonda/workflow/impl/Flag.java	92
src/main/java/com/epam/fonda/workflow/impl/HlaTypingFastqWorkflow.java	55
src/main/java/com/epam/fonda/workflow/impl/RnaExpressionBamWorkflow.java	59
src/main/java/com/epam/fonda/workflow/impl/RnaExpressionFastqWorkflow.java	79
src/main/java/com/epam/fonda/workflow/impl/RnaFusionFastqWorkflow.java	60
src/main/java/com/epam/fonda/workflow/impl/SCRnaExpressionCellRangerFastqWorkflow.java	70
src/main/java/com/epam/fonda/workflow/impl/TcrRepertoireFastqWorkflow.java	59
src/main/java/com/epam/fonda/workflow/stage/Stage.java	3
src/main/java/com/epam/fonda/workflow/stage/impl/Alignment.java	144
src/main/java/com/epam/fonda/workflow/stage/impl/PostAlignment.java	65
src/main/java/com/epam/fonda/workflow/stage/impl/PreAlignment.java	36
src/main/java/com/epam/fonda/workflow/stage/impl/SecondaryAnalysis.java	315
src/main/python/__init__.py	1
src/main/python/convert_variant_for_annotation.py	174
src/main/python/dna_rna_variant_qc_metrics.py	455
src/main/python/post_oncotator_cleanup.py	169
src/main/python/rna_gene_annotation.py	54
src/main/python/rna_qc_metrics.py	295
src/main/python/singlecell_doubletdetection.py	88
src/main/python/singlecell_scrublet.py	73
src/main/python/vcf_annovar_annotation.py	668
src/main/python/vcf_snpeff_annotation.py	609
src/main/resources/log4j2.xml	21
src/main/scripts/__init__.py	1
src/main/scripts/dna_capture_var_fastq.py	192
src/main/scripts/launcher.py	45
src/main/scripts/model/__init__.py	1
src/main/scripts/model/bam_sample_manifest.py	13
src/main/scripts/model/fastq_sample_manifest.py	15
src/main/scripts/model/global_config.py	52
src/main/scripts/model/sample_manifest.py	86
src/main/scripts/model/sample_utilities.py	14
src/main/scripts/model/study_config.py	32
src/main/scripts/rna_expression_fastq.py	174
src/main/scripts/sc_rna_expression_cellranger_fastq.py	270