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unit: private static Stream initParametersPaired()
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unit: private static Stream initParameters()
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end line: 420
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McCabe index: 1
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id: 3
unit: def parse_arguments()
file: src/main/scripts/sc_rna_expression_cellranger_fastq.py
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end line: 0
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McCabe index: 43
number of parameters: 2

id: 4
unit: def annovar_annotation()
file: src/main/python/vcf_annovar_annotation.py
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end line: 0
size: 128 LOC
McCabe index: 2
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id: 5
unit: private static Stream initParametersNotNAAll()
file: src/integrationTest/java/com/epam/fonda/DnaAmpliconVarBamIntegrationTest.java
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end line: 281
size: 118 LOC
McCabe index: 1
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id: 6
unit: private static Stream initParametersSingle()
file: src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java
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end line: 240
size: 112 LOC
McCabe index: 12
number of parameters: 0

id: 7
unit: def snpsift_annotation()
file: src/main/python/vcf_snpeff_annotation.py
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end line: 0
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McCabe index: 2
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id: 8
unit: def parse_arguments()
file: src/main/scripts/dna_capture_var_fastq.py
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end line: 0
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number of parameters: 2

id: 9
unit: def parse_arguments()
file: src/main/scripts/rna_expression_fastq.py
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end line: 0
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McCabe index: 28
number of parameters: 2

id: 10
unit: def transvar_output()
file: src/main/python/vcf_snpeff_annotation.py
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end line: 0
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McCabe index: 5
number of parameters: 5

id: 11
unit: def transvar_output()
file: src/main/python/vcf_annovar_annotation.py
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end line: 0
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McCabe index: 5
number of parameters: 4

id: 12
unit: def variantScore()
file: src/main/python/vcf_snpeff_annotation.py
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end line: 0
size: 75 LOC
McCabe index: 5
number of parameters: 7

id: 13
unit: def variantScore()
file: src/main/python/vcf_annovar_annotation.py
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end line: 0
size: 75 LOC
McCabe index: 5
number of parameters: 7

id: 14
unit: def main()
file: src/main/scripts/sc_rna_expression_cellranger_fastq.py
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end line: 0
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McCabe index: 21
number of parameters: 2

id: 15
unit: def parse_arguments()
file: src/main/python/dna_rna_variant_qc_metrics.py
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end line: 0
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McCabe index: 2
number of parameters: 1

id: 16
unit: def variant_annotation()
file: src/main/python/vcf_snpeff_annotation.py
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end line: 0
size: 65 LOC
McCabe index: 3
number of parameters: 4

id: 17
unit: def variant_annotation()
file: src/main/python/vcf_annovar_annotation.py
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end line: 0
size: 65 LOC
McCabe index: 3
number of parameters: 4

id: 18
unit: def parse_arguments()
file: src/main/python/vcf_annovar_annotation.py
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end line: 0
size: 61 LOC
McCabe index: 6
number of parameters: 1

id: 19
unit: private static Stream initParametersNAAll()
file: src/integrationTest/java/com/epam/fonda/DnaAmpliconVarBamIntegrationTest.java
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end line: 161
size: 58 LOC
McCabe index: 1
number of parameters: 0

id: 20
unit: def parse_arguments()
file: src/main/python/vcf_snpeff_annotation.py
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end line: 0
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McCabe index: 6
number of parameters: 1

id: 21
unit: private XenomeFields constructFieldsByIndex()
file: src/main/java/com/epam/fonda/tools/impl/Xenome.java
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end line: 162
size: 54 LOC
McCabe index: 14
number of parameters: 1

id: 22
unit: private static Stream initParameters()
file: src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java
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end line: 294
size: 52 LOC
McCabe index: 6
number of parameters: 0

id: 23
unit: private VariantsVcfResult postMutect2Processing()
file: src/main/java/com/epam/fonda/workflow/stage/impl/SecondaryAnalysis.java
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end line: 261
size: 49 LOC
McCabe index: 2
number of parameters: 3

id: 24
unit: def main()
file: src/main/scripts/dna_capture_var_fastq.py
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end line: 0
size: 47 LOC
McCabe index: 13
number of parameters: 2

id: 25
unit: public static Flag buildFlags()
file: src/main/java/com/epam/fonda/workflow/impl/Flag.java
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end line: 110
size: 43 LOC
McCabe index: 1
number of parameters: 1

id: 26
unit: private static Stream streamOfGA5argumentsNASample()
file: src/integrationTest/java/com/epam/fonda/DnaWgsVarBamIntegrationTest.java
start line: 128
end line: 167
size: 40 LOC
McCabe index: 1
number of parameters: 0

id: 27
unit: private static Stream streamOfGA51argumentsNotNASample()
file: src/integrationTest/java/com/epam/fonda/DnaWgsVarBamIntegrationTest.java
start line: 169
end line: 209
size: 40 LOC
McCabe index: 1
number of parameters: 0

id: 28
unit: private static Stream streamOfGA52argumentsNotNASample()
file: src/integrationTest/java/com/epam/fonda/DnaWgsVarBamIntegrationTest.java
start line: 211
end line: 250
size: 40 LOC
McCabe index: 1
number of parameters: 0

id: 29
unit: public String buildScript()
file: src/main/java/com/epam/fonda/entity/configuration/orchestrator/MasterScript.java
start line: 73
end line: 113
size: 40 LOC
McCabe index: 5
number of parameters: 1

id: 30
unit: def create()
file: src/main/scripts/model/global_config.py
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end line: 0
size: 40 LOC
McCabe index: 10
number of parameters: 6

id: 31
unit: def variantType()
file: src/main/python/vcf_snpeff_annotation.py
start line: 0
end line: 0
size: 38 LOC
McCabe index: 18
number of parameters: 5

id: 32
unit: def variantType()
file: src/main/python/vcf_annovar_annotation.py
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end line: 0
size: 38 LOC
McCabe index: 18
number of parameters: 5

id: 33
unit: private CountFields constructFields()
file: src/main/java/com/epam/fonda/tools/impl/Count.java
start line: 104
end line: 140
size: 37 LOC
McCabe index: 5
number of parameters: 2

id: 34
unit: public BamResult process()
file: src/main/java/com/epam/fonda/workflow/stage/impl/PostAlignment.java
start line: 59
end line: 95
size: 37 LOC
McCabe index: 10
number of parameters: 4

id: 35
unit: def usage()
file: src/main/scripts/sc_rna_expression_cellranger_fastq.py
start line: 0
end line: 0
size: 37 LOC
McCabe index: 1
number of parameters: 0

id: 36
unit: private static Stream initParametersPairedSeqpurgeOptiType()
file: src/integrationTest/java/com/epam/fonda/HlaTypingFastqIntegrationTest.java
start line: 64
end line: 99
size: 36 LOC
McCabe index: 1
number of parameters: 0

id: 37
unit: private static Stream initParametersPairedTrimmQcXenomeYes()
file: src/integrationTest/java/com/epam/fonda/HlaTypingFastqIntegrationTest.java
start line: 102
end line: 137
size: 36 LOC
McCabe index: 1
number of parameters: 0

id: 38
unit: def parse_arguments()
file: src/main/python/rna_qc_metrics.py
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end line: 0
size: 36 LOC
McCabe index: 2
number of parameters: 1

id: 39
unit: private static Stream initParameters()
file: src/integrationTest/java/com/epam/fonda/RnaCaptureVarFastqIntegrationTest.java
start line: 46
end line: 79
size: 34 LOC
McCabe index: 1
number of parameters: 0

id: 40
unit: public static FastqResult mergeFastq()
file: src/main/java/com/epam/fonda/utils/PipelineUtils.java
start line: 231
end line: 264
size: 34 LOC
McCabe index: 4
number of parameters: 1

id: 41
unit: def main()
file: src/main/scripts/rna_expression_fastq.py
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end line: 0
size: 34 LOC
McCabe index: 10
number of parameters: 2

id: 42
unit: def launch()
file: src/main/scripts/launcher.py
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end line: 0
size: 34 LOC
McCabe index: 17
number of parameters: 8

id: 43
unit: public BamResult generate()
file: src/main/java/com/epam/fonda/tools/impl/Star.java
start line: 87
end line: 120
size: 33 LOC
McCabe index: 3
number of parameters: 2

id: 44
unit: public MetricsResult generate()
file: src/main/java/com/epam/fonda/tools/impl/DnaPicardQc.java
start line: 120
end line: 154
size: 33 LOC
McCabe index: 9
number of parameters: 2

id: 45
unit: public BamResult mapping()
file: src/main/java/com/epam/fonda/workflow/stage/impl/Alignment.java
start line: 97
end line: 128
size: 32 LOC
McCabe index: 9
number of parameters: 4

id: 46
unit: private QcSummaryFields constructFields()
file: src/main/java/com/epam/fonda/tools/impl/QcSummary.java
start line: 84
end line: 116
size: 31 LOC
McCabe index: 3
number of parameters: 2

id: 47
unit: private void processPostAlignment()
file: src/main/java/com/epam/fonda/workflow/impl/DnaVarFastqWorkflow.java
start line: 132
end line: 164
size: 31 LOC
McCabe index: 6
number of parameters: 4

id: 48
unit: public Workflow getWorkflow()
file: src/main/java/com/epam/fonda/workflow/WorkflowFactory.java
start line: 43
end line: 73
size: 31 LOC
McCabe index: 18
number of parameters: 2

id: 49
unit: private TrimmomaticFields constructFieldsByIndex()
file: src/main/java/com/epam/fonda/tools/impl/Trimmomatic.java
start line: 102
end line: 131
size: 30 LOC
McCabe index: 6
number of parameters: 1

id: 50
unit: def parse_arguments()
file: src/main/python/post_oncotator_cleanup.py
start line: 0
end line: 0
size: 29 LOC
McCabe index: 3
number of parameters: 1

id: 51
unit: private static Stream gSingleDnaAmpliconArguments()
file: src/integrationTest/java/com/epam/fonda/DnaAnalysisIntegrationTest.java
start line: 119
end line: 146
size: 28 LOC
McCabe index: 1
number of parameters: 0

id: 52
unit: private static Stream gSingleDnaCaptureArguments()
file: src/integrationTest/java/com/epam/fonda/DnaAnalysisIntegrationTest.java
start line: 148
end line: 175
size: 28 LOC
McCabe index: 1
number of parameters: 0

id: 53
unit: private String getValueForSpecificVar()
file: src/main/java/com/epam/fonda/tools/impl/QcSummary.java
start line: 138
end line: 167
size: 28 LOC
McCabe index: 10
number of parameters: 3

id: 54
unit: def parse_arguments()
file: src/main/python/rna_gene_annotation.py
start line: 0
end line: 0
size: 27 LOC
McCabe index: 5
number of parameters: 1

id: 55
unit: public StarFusionResult generate()
file: src/main/java/com/epam/fonda/tools/impl/StarFusion.java
start line: 80
end line: 106
size: 27 LOC
McCabe index: 2
number of parameters: 2

id: 56
unit: private MetricsFields constructMetricsForDnaCapturePicardQcAndDnaPicardQc()
file: src/main/java/com/epam/fonda/tools/impl/DnaPicardQc.java
start line: 301
end line: 327
size: 27 LOC
McCabe index: 1
number of parameters: 4

id: 57
unit: private MixcrFields constructMixcrFields()
file: src/main/java/com/epam/fonda/tools/impl/Mixcr.java
start line: 111
end line: 137
size: 27 LOC
McCabe index: 3
number of parameters: 2

id: 58
unit: private NovoalignSortFields constructFieldsForNovoalignSort()
file: src/main/java/com/epam/fonda/tools/impl/NovoalignSort.java
start line: 81
end line: 107
size: 27 LOC
McCabe index: 2
number of parameters: 1

id: 59
unit: public void addScript()
file: src/main/java/com/epam/fonda/entity/configuration/orchestrator/MasterScript.java
start line: 124
end line: 150
size: 27 LOC
McCabe index: 8
number of parameters: 3

id: 60
unit: void testDirTree()
file: src/integrationTest/java/com/epam/fonda/SCRnaExpressionBamIntegrationTest.java
start line: 175
end line: 200
size: 26 LOC
McCabe index: 1
number of parameters: 0

id: 61
unit: public MixcrResult generate()
file: src/main/java/com/epam/fonda/tools/impl/Mixcr.java
start line: 76
end line: 101
size: 26 LOC
McCabe index: 2
number of parameters: 2

id: 62
unit: private void alignFastq()
file: src/main/java/com/epam/fonda/workflow/impl/DnaVarFastqWorkflow.java
start line: 105
end line: 130
size: 26 LOC
McCabe index: 3
number of parameters: 7

id: 63
unit: public void run()
file: src/main/java/com/epam/fonda/workflow/impl/Bam2FastqWorkflow.java
start line: 55
end line: 81
size: 26 LOC
McCabe index: 5
number of parameters: 2

id: 64
unit: def parse_arguments()
file: src/main/python/convert_variant_for_annotation.py
start line: 0
end line: 0
size: 25 LOC
McCabe index: 5
number of parameters: 1

id: 65
unit: public Configuration parseArgs()
file: src/main/java/com/epam/fonda/CmdParser.java
start line: 51
end line: 78
size: 25 LOC
McCabe index: 1
number of parameters: 1

id: 66
unit: private Set filterToolset()
file: src/main/java/com/epam/fonda/tools/impl/DnaAnalysis.java
start line: 179
end line: 203
size: 25 LOC
McCabe index: 8
number of parameters: 1

id: 67
unit: private AdditionalStarFusionFields constructFieldsByIndex()
file: src/main/java/com/epam/fonda/tools/impl/StarFusion.java
start line: 115
end line: 139
size: 25 LOC
McCabe index: 1
number of parameters: 1

id: 68
unit: public void run()
file: src/main/java/com/epam/fonda/workflow/impl/TcrRepertoireFastqWorkflow.java
start line: 53
end line: 77
size: 25 LOC
McCabe index: 6
number of parameters: 2

id: 69
unit: public void run()
file: src/main/java/com/epam/fonda/workflow/impl/SCRnaExpressionCellRangerFastqWorkflow.java
start line: 57
end line: 82
size: 25 LOC
McCabe index: 5
number of parameters: 2

id: 70
unit: def usage()
file: src/main/scripts/dna_capture_var_fastq.py
start line: 0
end line: 0
size: 25 LOC
McCabe index: 1
number of parameters: 0

id: 71
unit: def usage()
file: src/main/scripts/rna_expression_fastq.py
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end line: 0
size: 25 LOC
McCabe index: 1
number of parameters: 0

id: 72
unit: private AdditionalFeatureCountFields initializeAdditionalFeatureCountFields()
file: src/main/java/com/epam/fonda/tools/impl/FeatureCount.java
start line: 119
end line: 142
size: 24 LOC
McCabe index: 1
number of parameters: 2

id: 73
unit: public BamResult generate()
file: src/main/java/com/epam/fonda/tools/impl/BwaSort.java
start line: 54
end line: 77
size: 24 LOC
McCabe index: 3
number of parameters: 2

id: 74
unit: private MetricsFields constructMetricsForDnaAmpliconPicardQc()
file: src/main/java/com/epam/fonda/tools/impl/DnaPicardQc.java
start line: 276
end line: 299
size: 24 LOC
McCabe index: 1
number of parameters: 3

id: 75
unit: private SeqPurgeFields constructFieldsByIndex()
file: src/main/java/com/epam/fonda/tools/impl/SeqPurge.java
start line: 102
end line: 125
size: 24 LOC
McCabe index: 3
number of parameters: 1

id: 76
unit: public OptiTypeResult generate()
file: src/main/java/com/epam/fonda/tools/impl/OptiType.java
start line: 75
end line: 98
size: 24 LOC
McCabe index: 2
number of parameters: 2

id: 77
unit: public PileupResult generate()
file: src/main/java/com/epam/fonda/tools/impl/Pileup.java
start line: 76
end line: 99
size: 24 LOC
McCabe index: 1
number of parameters: 2

id: 78
unit: public BamResult generate()
file: src/main/java/com/epam/fonda/tools/impl/NovoalignSort.java
start line: 56
end line: 79
size: 24 LOC
McCabe index: 3
number of parameters: 2

id: 79
unit: public static String checkPeriodicBamStatus()
file: src/main/java/com/epam/fonda/utils/DnaUtils.java
start line: 85
end line: 108
size: 24 LOC
McCabe index: 3
number of parameters: 5

id: 80
unit: public void run()
file: src/main/java/com/epam/fonda/workflow/impl/RnaExpressionFastqWorkflow.java
start line: 62
end line: 85
size: 24 LOC
McCabe index: 4
number of parameters: 2

id: 81
unit: public void run()
file: src/main/java/com/epam/fonda/workflow/impl/RnaFusionFastqWorkflow.java
start line: 62
end line: 85
size: 24 LOC
McCabe index: 4
number of parameters: 2

id: 82
unit: def write_from_list()
file: src/main/scripts/model/sample_manifest.py
start line: 0
end line: 0
size: 24 LOC
McCabe index: 10
number of parameters: 9

id: 83
unit: void testDirTreeNotNASample()
file: src/integrationTest/java/com/epam/fonda/DnaWgsVarBamIntegrationTest.java
start line: 267
end line: 289
size: 23 LOC
McCabe index: 1
number of parameters: 0

id: 84
unit: public void startAppWithConfigs()
file: src/integrationTest/java/com/epam/fonda/AbstractIntegrationTest.java
start line: 98
end line: 122
size: 23 LOC
McCabe index: 3
number of parameters: 3

id: 85
unit: def parse_arguments()
file: src/main/python/singlecell_doubletdetection.py
start line: 0
end line: 0
size: 23 LOC
McCabe index: 4
number of parameters: 1

id: 86
unit: def parse_arguments()
file: src/main/python/singlecell_scrublet.py
start line: 0
end line: 0
size: 23 LOC
McCabe index: 4
number of parameters: 1

id: 87
unit: public MetricsResult generate()
file: src/main/java/com/epam/fonda/tools/impl/RNASeQC.java
start line: 101
end line: 123
size: 23 LOC
McCabe index: 1
number of parameters: 2

id: 88
unit: public SalmonResult generate()
file: src/main/java/com/epam/fonda/tools/impl/Salmon.java
start line: 72
end line: 94
size: 23 LOC
McCabe index: 2
number of parameters: 2

id: 89
unit: public BamResult generate()
file: src/main/java/com/epam/fonda/tools/impl/Hisat2.java
start line: 76
end line: 98
size: 23 LOC
McCabe index: 2
number of parameters: 2

id: 90
unit: public static CommandLine parseInputArgumentsToOptions()
file: src/main/java/com/epam/fonda/utils/ConfigurationUtils.java
start line: 58
end line: 80
size: 23 LOC
McCabe index: 1
number of parameters: 1

id: 91
unit: private static Context buildContext()
file: src/main/java/com/epam/fonda/utils/DnaUtils.java
start line: 165
end line: 187
size: 23 LOC
McCabe index: 1
number of parameters: 5

id: 92
unit: public static void execute()
file: src/main/java/com/epam/fonda/Executor.java
start line: 53
end line: 77
size: 23 LOC
McCabe index: 4
number of parameters: 2

id: 93
unit: public void testFeatureCountCufflinksConversion()
file: src/integrationTest/java/com/epam/fonda/SCRnaExpressionFastqIntegrationTest.java
start line: 110
end line: 135
size: 22 LOC
McCabe index: 1
number of parameters: 0

id: 94
unit: private AdditionalStarFields initializeAdditionalFields()
file: src/main/java/com/epam/fonda/tools/impl/Star.java
start line: 129
end line: 150
size: 22 LOC
McCabe index: 2
number of parameters: 1

id: 95
unit: private CufflinksFields constructFields()
file: src/main/java/com/epam/fonda/tools/impl/Cufflinks.java
start line: 73
end line: 95
size: 22 LOC
McCabe index: 1
number of parameters: 2

id: 96
unit: public FastqResult generate()
file: src/main/java/com/epam/fonda/tools/impl/SamToFastq.java
start line: 68
end line: 89
size: 22 LOC
McCabe index: 4
number of parameters: 2

id: 97
unit: private ToolFields initToolFields()
file: src/main/java/com/epam/fonda/tools/impl/Mutect1.java
start line: 91
end line: 112
size: 22 LOC
McCabe index: 1
number of parameters: 1

id: 98
unit: public FusionCatcherResult generate()
file: src/main/java/com/epam/fonda/tools/impl/FusionCatcher.java
start line: 64
end line: 85
size: 22 LOC
McCabe index: 2
number of parameters: 2

id: 99
unit: private List replaceLast()
file: src/main/java/com/epam/fonda/entity/configuration/orchestrator/MasterScript.java
start line: 207
end line: 228
size: 22 LOC
McCabe index: 3
number of parameters: 2

id: 100
unit: public void run()
file: src/main/java/com/epam/fonda/workflow/impl/DnaVarBamWorkflow.java
start line: 58
end line: 81
size: 22 LOC
McCabe index: 6
number of parameters: 2

id: 101
unit: void testDirTreeDnaAmpliconVar()
file: src/integrationTest/java/com/epam/fonda/DnaAnalysisIntegrationTest.java
start line: 179
end line: 199
size: 21 LOC
McCabe index: 1
number of parameters: 1

id: 102
unit: public FeatureCountResult generate()
file: src/main/java/com/epam/fonda/tools/impl/FeatureCount.java
start line: 89
end line: 109
size: 21 LOC
McCabe index: 1
number of parameters: 2

id: 103
unit: public String generate()
file: src/main/java/com/epam/fonda/tools/impl/DnaAnalysis.java
start line: 79
end line: 101
size: 21 LOC
McCabe index: 6
number of parameters: 2

id: 104
unit: public BamResult generate()
file: src/main/java/com/epam/fonda/tools/impl/PicardMarkDuplicate.java
start line: 75
end line: 95
size: 21 LOC
McCabe index: 2
number of parameters: 2

id: 105
unit: public BamResult generate()
file: src/main/java/com/epam/fonda/tools/impl/PicardRemoveDuplicate.java
start line: 53
end line: 73
size: 21 LOC
McCabe index: 1
number of parameters: 2

id: 106
unit: private ToolFields initToolFields()
file: src/main/java/com/epam/fonda/tools/impl/Strelka2.java
start line: 93
end line: 113
size: 21 LOC
McCabe index: 3
number of parameters: 1

id: 107
unit: private SalmonFields constructFieldsForSalmon()
file: src/main/java/com/epam/fonda/tools/impl/Salmon.java
start line: 104
end line: 124
size: 21 LOC
McCabe index: 1
number of parameters: 2

id: 108
unit: public ContEstResult generate()
file: src/main/java/com/epam/fonda/tools/impl/ContEst.java
start line: 77
end line: 97
size: 21 LOC
McCabe index: 1
number of parameters: 2

id: 109
unit: public static String printShell()
file: src/main/java/com/epam/fonda/utils/PipelineUtils.java
start line: 176
end line: 199
size: 21 LOC
McCabe index: 4
number of parameters: 4

id: 110
unit: public void run()
file: src/main/java/com/epam/fonda/workflow/impl/HlaTypingFastqWorkflow.java
start line: 53
end line: 73
size: 21 LOC
McCabe index: 4
number of parameters: 2

id: 111
unit: private ToolFields initToolFields()
file: src/main/java/com/epam/fonda/tools/impl/Lofreq.java
start line: 91
end line: 110
size: 20 LOC
McCabe index: 2
number of parameters: 1

id: 112
unit: private BwaSortFields constructFieldsForBwaSort()
file: src/main/java/com/epam/fonda/tools/impl/BwaSort.java
start line: 79
end line: 99
size: 20 LOC
McCabe index: 1
number of parameters: 1

id: 113
unit: public VariantsVcfResult generate()
file: src/main/java/com/epam/fonda/tools/impl/Mutect2.java
start line: 73
end line: 92
size: 20 LOC
McCabe index: 1
number of parameters: 2

id: 114
unit: public FastqResult generate()
file: src/main/java/com/epam/fonda/tools/impl/SeqPurge.java
start line: 74
end line: 93
size: 20 LOC
McCabe index: 3
number of parameters: 2

id: 115
unit: public SequenzaResult generate()
file: src/main/java/com/epam/fonda/tools/impl/Sequenza.java
start line: 68
end line: 87
size: 20 LOC
McCabe index: 1
number of parameters: 2

id: 116
unit: private ToolFields initToolFields()
file: src/main/java/com/epam/fonda/tools/impl/Exomecnv.java
start line: 91
end line: 110
size: 20 LOC
McCabe index: 1
number of parameters: 1

id: 117
unit: public String process()
file: src/main/java/com/epam/fonda/workflow/stage/impl/SecondaryAnalysis.java
start line: 100
end line: 119
size: 20 LOC
McCabe index: 1
number of parameters: 3

id: 118
unit: def write()
file: src/main/scripts/model/sample_manifest.py
start line: 0
end line: 0
size: 20 LOC
McCabe index: 5
number of parameters: 6

id: 119
unit: private static Stream initParameters()
file: src/integrationTest/java/com/epam/fonda/RnaExpressionBamIntegrationTest.java
start line: 73
end line: 91
size: 19 LOC
McCabe index: 1
number of parameters: 0

id: 120
unit: public void testPairedPicard()
file: src/integrationTest/java/com/epam/fonda/Bam2FastqIntegrationTest.java
start line: 70
end line: 91
size: 19 LOC
McCabe index: 1
number of parameters: 0

id: 121
unit: public String generate()
file: src/main/java/com/epam/fonda/tools/impl/QcSummary.java
start line: 64
end line: 82
size: 19 LOC
McCabe index: 4
number of parameters: 2

id: 122
unit: private ToolFields initToolFields()
file: src/main/java/com/epam/fonda/tools/impl/Mutect2.java
start line: 94
end line: 112
size: 19 LOC
McCabe index: 2
number of parameters: 2

id: 123
unit: public String generate()
file: src/main/java/com/epam/fonda/tools/impl/RnaMutationAnalysis.java
start line: 45
end line: 63
size: 19 LOC
McCabe index: 4
number of parameters: 2

id: 124
unit: public StringtieResult generate()
file: src/main/java/com/epam/fonda/tools/impl/Stringtie.java
start line: 63
end line: 81
size: 19 LOC
McCabe index: 1
number of parameters: 2

id: 125
unit: private StringTieFields constructFields()
file: src/main/java/com/epam/fonda/tools/impl/Stringtie.java
start line: 83
end line: 102
size: 19 LOC
McCabe index: 1
number of parameters: 2

id: 126
unit: public CufflinksResult generate()
file: src/main/java/com/epam/fonda/tools/impl/Cufflinks.java
start line: 53
end line: 71
size: 19 LOC
McCabe index: 1
number of parameters: 2

id: 127
unit: public VariantsVcfResult generate()
file: src/main/java/com/epam/fonda/tools/impl/GatkHaplotypeCaller.java
start line: 82
end line: 100
size: 19 LOC
McCabe index: 2
number of parameters: 2

id: 128
unit: public RsemResult generate()
file: src/main/java/com/epam/fonda/tools/impl/RsemExpression.java
start line: 63
end line: 81
size: 19 LOC
McCabe index: 1
number of parameters: 2

id: 129
unit: def parse()
file: src/main/scripts/model/study_config.py
start line: 0
end line: 0
size: 19 LOC
McCabe index: 2
number of parameters: 2

id: 130
unit: void testDirTreeNASample()
file: src/integrationTest/java/com/epam/fonda/DnaWgsVarBamIntegrationTest.java
start line: 292
end line: 309
size: 18 LOC
McCabe index: 1
number of parameters: 0

id: 131
unit: private static Stream initTestFolderAndConfigs()
file: src/integrationTest/java/com/epam/fonda/DnaAmpliconVarFastqIntegrationTest.java
start line: 195
end line: 212
size: 18 LOC
McCabe index: 1
number of parameters: 0

id: 132
unit: public void testNoTumorOrCase()
file: src/integrationTest/java/com/epam/fonda/DnaCaptureVarBamIntegrationTest.java
start line: 137
end line: 156
size: 18 LOC
McCabe index: 1
number of parameters: 0

id: 133
unit: public BamResult generate()
file: src/main/java/com/epam/fonda/tools/impl/GatkSplitReads.java
start line: 52
end line: 69
size: 18 LOC
McCabe index: 1
number of parameters: 2

id: 134
unit: private ToolFields initToolFields()
file: src/main/java/com/epam/fonda/tools/impl/Vardict.java
start line: 89
end line: 106
size: 18 LOC
McCabe index: 3
number of parameters: 1

id: 135
unit: private String createLibraryCsvFile()
file: src/main/java/com/epam/fonda/tools/impl/Count.java
start line: 148
end line: 165
size: 18 LOC
McCabe index: 2
number of parameters: 2

id: 136
unit: private MetricsOutput buildMetricsOutput()
file: src/main/java/com/epam/fonda/tools/impl/DnaPicardQc.java
start line: 180
end line: 197
size: 18 LOC
McCabe index: 3
number of parameters: 0

id: 137
unit: public BamResult generate()
file: src/main/java/com/epam/fonda/tools/impl/GatkSortSam.java
start line: 54
end line: 71
size: 18 LOC
McCabe index: 1
number of parameters: 2

id: 138
unit: private ToolFields initToolFields()
file: src/main/java/com/epam/fonda/tools/impl/Sequenza.java
start line: 89
end line: 106
size: 18 LOC
McCabe index: 1
number of parameters: 1

id: 139
unit: public VariantsVcfResult generate()
file: src/main/java/com/epam/fonda/tools/impl/Mutect1.java
start line: 72
end line: 89
size: 18 LOC
McCabe index: 1
number of parameters: 2

id: 140
unit: public ExomecnvResult generate()
file: src/main/java/com/epam/fonda/tools/impl/Exomecnv.java
start line: 72
end line: 89
size: 18 LOC
McCabe index: 1
number of parameters: 2

id: 141
unit: public FastqResult generate()
file: src/main/java/com/epam/fonda/tools/impl/Trimmomatic.java
start line: 76
end line: 93
size: 18 LOC
McCabe index: 2
number of parameters: 2

id: 142
unit: private static Map initializeVariablesMap()
file: src/main/java/com/epam/fonda/utils/PipelineUtils.java
start line: 294
end line: 311
size: 18 LOC
McCabe index: 1
number of parameters: 3

id: 143
unit: public void testCreateRnaFusionFastqSpecificDirFusionCatcherStarFusionToolset()
file: src/integrationTest/java/com/epam/fonda/RnaFusionFastqIntegrationTest.java
start line: 77
end line: 93
size: 17 LOC
McCabe index: 1
number of parameters: 0

id: 144
unit: def usage()
file: src/main/python/dna_rna_variant_qc_metrics.py
start line: 0
end line: 0
size: 17 LOC
McCabe index: 1
number of parameters: 0

id: 145
unit: def usage()
file: src/main/python/vcf_annovar_annotation.py
start line: 0
end line: 0
size: 17 LOC
McCabe index: 1
number of parameters: 0

id: 146
unit: public VariantsVcfResult generate()
file: src/main/java/com/epam/fonda/tools/impl/Lofreq.java
start line: 73
end line: 89
size: 17 LOC
McCabe index: 1
number of parameters: 2

id: 147
unit: private void initializeVdjFields()
file: src/main/java/com/epam/fonda/tools/impl/Vdj.java
start line: 116
end line: 132
size: 17 LOC
McCabe index: 1
number of parameters: 1

id: 148
unit: public VariantsVcfResult generate()
file: src/main/java/com/epam/fonda/tools/impl/Freebayes.java
start line: 68
end line: 84
size: 17 LOC
McCabe index: 1
number of parameters: 2

id: 149
unit: private ToolFields initToolFields()
file: src/main/java/com/epam/fonda/tools/impl/Freebayes.java
start line: 86
end line: 102
size: 17 LOC
McCabe index: 1
number of parameters: 1

id: 150
unit: public VariantsVcfResult generate()
file: src/main/java/com/epam/fonda/tools/impl/Vardict.java
start line: 71
end line: 87
size: 17 LOC
McCabe index: 1
number of parameters: 2

id: 151
unit: public FastqResult generate()
file: src/main/java/com/epam/fonda/tools/impl/Xenome.java
start line: 83
end line: 99
size: 17 LOC
McCabe index: 1
number of parameters: 2

id: 152
unit: public VariantsVcfResult generate()
file: src/main/java/com/epam/fonda/tools/impl/Scalpel.java
start line: 68
end line: 84
size: 17 LOC
McCabe index: 1
number of parameters: 2

id: 153
unit: private ToolFields initToolFields()
file: src/main/java/com/epam/fonda/tools/impl/Scalpel.java
start line: 86
end line: 102
size: 17 LOC
McCabe index: 2
number of parameters: 1

id: 154
unit: public VariantsVcfResult generate()
file: src/main/java/com/epam/fonda/tools/impl/Strelka2.java
start line: 75
end line: 91
size: 17 LOC
McCabe index: 1
number of parameters: 2

id: 155
unit: private ToolFields initToolFields()
file: src/main/java/com/epam/fonda/tools/impl/FilterMutectCalls.java
start line: 82
end line: 98
size: 17 LOC
McCabe index: 1
number of parameters: 1

id: 156
unit: public static String getExecutionPath()
file: src/main/java/com/epam/fonda/utils/PipelineUtils.java
start line: 81
end line: 97
size: 17 LOC
McCabe index: 4
number of parameters: 1

id: 157
unit: public void run()
file: src/main/java/com/epam/fonda/workflow/impl/RnaExpressionBamWorkflow.java
start line: 54
end line: 71
size: 17 LOC
McCabe index: 2
number of parameters: 2

id: 158
unit: private void gatkHaplotypeCaller()
file: src/main/java/com/epam/fonda/workflow/stage/impl/SecondaryAnalysis.java
start line: 140
end line: 156
size: 17 LOC
McCabe index: 4
number of parameters: 4

id: 159
unit: public void testCreateDnaCaptureVarFastqSpecificDirExpressionFastqToolset()
file: src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java
start line: 111
end line: 126
size: 16 LOC
McCabe index: 1
number of parameters: 0

id: 160
unit: public void testStagesAndQcSummary()
file: src/integrationTest/java/com/epam/fonda/DnaAmpliconVarFastqIntegrationTest.java
start line: 126
end line: 144
size: 16 LOC
McCabe index: 1
number of parameters: 3

id: 161
unit: void testDir()
file: src/integrationTest/java/com/epam/fonda/DnaWgsVarFastqIntegrationTest.java
start line: 76
end line: 91
size: 16 LOC
McCabe index: 1
number of parameters: 0

id: 162
unit: public BamResult generate()
file: src/main/java/com/epam/fonda/tools/impl/Vdj.java
start line: 79
end line: 94
size: 16 LOC
McCabe index: 1
number of parameters: 2

id: 163
unit: private void periodicDnaMutationStatusCheck()
file: src/main/java/com/epam/fonda/tools/impl/DnaAnalysis.java
start line: 103
end line: 118
size: 16 LOC
McCabe index: 2
number of parameters: 4

id: 164
unit: private MetricFields initializeMetricsFields()
file: src/main/java/com/epam/fonda/tools/impl/RNASeQC.java
start line: 196
end line: 211
size: 16 LOC
McCabe index: 1
number of parameters: 1

id: 165
unit: private void checkValues()
file: src/main/java/com/epam/fonda/tools/impl/Count.java
start line: 173
end line: 188
size: 16 LOC
McCabe index: 1
number of parameters: 1

id: 166
unit: private MetricsFields initializeMetricsFields()
file: src/main/java/com/epam/fonda/tools/impl/DnaPicardQc.java
start line: 259
end line: 274
size: 16 LOC
McCabe index: 4
number of parameters: 0

id: 167
unit: private AdditionalFields initializeAdditionalFields()
file: src/main/java/com/epam/fonda/tools/impl/DnaPicardQc.java
start line: 336
end line: 351
size: 16 LOC
McCabe index: 3
number of parameters: 1

id: 168
unit: private OptiTypeFields constructFieldsForOptiType()
file: src/main/java/com/epam/fonda/tools/impl/OptiType.java
start line: 107
end line: 122
size: 16 LOC
McCabe index: 1
number of parameters: 1

id: 169
unit: private Set filterToolset()
file: src/main/java/com/epam/fonda/tools/impl/RnaAnalysis.java
start line: 71
end line: 86
size: 16 LOC
McCabe index: 5
number of parameters: 1

id: 170
unit: private AdditionalHisat2Fields initializeAdditionalFields()
file: src/main/java/com/epam/fonda/tools/impl/Hisat2.java
start line: 107
end line: 122
size: 16 LOC
McCabe index: 1
number of parameters: 1

id: 171
unit: private RsemExpressionFields constructFields()
file: src/main/java/com/epam/fonda/tools/impl/RsemExpression.java
start line: 90
end line: 105
size: 16 LOC
McCabe index: 1
number of parameters: 2

id: 172
unit: void testDnaCaptureVarFastqMaster()
file: src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java
start line: 92
end line: 108
size: 15 LOC
McCabe index: 1
number of parameters: 7

id: 173
unit: private String getExpectedMasterScript()
file: src/integrationTest/java/com/epam/fonda/RnaExpressionFastqIntegrationTest.java
start line: 182
end line: 196
size: 15 LOC
McCabe index: 1
number of parameters: 4

id: 174
unit: public void testAlignmentAndMergeMutation()
file: src/integrationTest/java/com/epam/fonda/DnaAmpliconVarFastqIntegrationTest.java
start line: 105
end line: 122
size: 15 LOC
McCabe index: 1
number of parameters: 3

id: 175
unit: public void cleanOutputDirForNextTest()
file: src/integrationTest/java/com/epam/fonda/AbstractIntegrationTest.java
start line: 74
end line: 88
size: 15 LOC
McCabe index: 3
number of parameters: 1

id: 176
unit: public static List getSamplesScripts()
file: src/integrationTest/java/com/epam/fonda/TestTemplateUtils.java
start line: 50
end line: 64
size: 15 LOC
McCabe index: 3
number of parameters: 3

id: 177
unit: public void testSortPairedNonPicard()
file: src/integrationTest/java/com/epam/fonda/Bam2FastqIntegrationTest.java
start line: 50
end line: 67
size: 15 LOC
McCabe index: 1
number of parameters: 0

id: 178
unit: public void testSinglePicard3Columns()
file: src/integrationTest/java/com/epam/fonda/Bam2FastqIntegrationTest.java
start line: 94
end line: 111
size: 15 LOC
McCabe index: 1
number of parameters: 0

id: 179
unit: public void testSinglePicard5Columns()
file: src/integrationTest/java/com/epam/fonda/Bam2FastqIntegrationTest.java
start line: 114
end line: 131
size: 15 LOC
McCabe index: 1
number of parameters: 0

id: 180
unit: private static Stream initGlobalConfigAndTemplatePath()
file: src/integrationTest/java/com/epam/fonda/RnaFusionFastqIntegrationTest.java
start line: 96
end line: 110
size: 15 LOC
McCabe index: 1
number of parameters: 0

id: 181
unit: def percentBaseCoverageRelative2Mean()
file: src/main/python/rna_qc_metrics.py
start line: 0
end line: 0
size: 15 LOC
McCabe index: 1
number of parameters: 2

id: 182
unit: def percentBaseCoverageRelative2Mean()
file: src/main/python/dna_rna_variant_qc_metrics.py
start line: 0
end line: 0
size: 15 LOC
McCabe index: 1
number of parameters: 2

id: 183
unit: def usage()
file: src/main/python/vcf_snpeff_annotation.py
start line: 0
end line: 0
size: 15 LOC
McCabe index: 1
number of parameters: 0

id: 184
unit: private DoubleDetectionFields constructFields()
file: src/main/java/com/epam/fonda/tools/impl/SCRNASeqDoubletDetection.java
start line: 89
end line: 103
size: 15 LOC
McCabe index: 1
number of parameters: 1

id: 185
unit: private DnaAnalysisFields constructDnaAnalysisFields()
file: src/main/java/com/epam/fonda/tools/impl/DnaAnalysis.java
start line: 146
end line: 160
size: 15 LOC
McCabe index: 1
number of parameters: 3

id: 186
unit: private ToolFields initializeToolFields()
file: src/main/java/com/epam/fonda/tools/impl/RNASeQC.java
start line: 132
end line: 146
size: 15 LOC
McCabe index: 1
number of parameters: 1

id: 187
unit: public BamResult generate()
file: src/main/java/com/epam/fonda/tools/impl/AmpliconGatkRecalibrate.java
start line: 61
end line: 75
size: 15 LOC
McCabe index: 1
number of parameters: 2

id: 188
unit: private ToolFields initializeToolFields()
file: src/main/java/com/epam/fonda/tools/impl/DnaPicardQc.java
start line: 206
end line: 220
size: 15 LOC
McCabe index: 3
number of parameters: 1

id: 189
unit: private String logFileScanningShellScript()
file: src/main/java/com/epam/fonda/tools/impl/SCRnaAnalysis.java
start line: 111
end line: 125
size: 15 LOC
McCabe index: 1
number of parameters: 4

id: 190
unit: String expressData()
file: src/main/java/com/epam/fonda/tools/impl/SCRnaAnalysis.java
start line: 133
end line: 148
size: 15 LOC
McCabe index: 1
number of parameters: 2

id: 191
unit: public CalculateContaminationResult generate()
file: src/main/java/com/epam/fonda/tools/impl/CalculateContamination.java
start line: 55
end line: 69
size: 15 LOC
McCabe index: 1
number of parameters: 2

id: 192
unit: public VariantsVcfResult generate()
file: src/main/java/com/epam/fonda/tools/impl/FilterAlignmentArtifacts.java
start line: 58
end line: 72
size: 15 LOC
McCabe index: 1
number of parameters: 2

id: 193
unit: public BamResult generate()
file: src/main/java/com/epam/fonda/tools/impl/SortBamByReadName.java
start line: 63
end line: 77
size: 15 LOC
McCabe index: 1
number of parameters: 2

id: 194
unit: public String generate()
file: src/main/java/com/epam/fonda/tools/impl/RnaAnalysis.java
start line: 48
end line: 62
size: 15 LOC
McCabe index: 2
number of parameters: 2

id: 195
unit: public VariantsVcfResult generate()
file: src/main/java/com/epam/fonda/tools/impl/FilterMutectCalls.java
start line: 66
end line: 80
size: 15 LOC
McCabe index: 1
number of parameters: 2

id: 196
unit: public static void executeScript()
file: src/main/java/com/epam/fonda/utils/PipelineUtils.java
start line: 208
end line: 223
size: 15 LOC
McCabe index: 4
number of parameters: 2

id: 197
unit: private static String logFileScanningShellScript()
file: src/main/java/com/epam/fonda/utils/RnaAnalysisUtils.java
start line: 114
end line: 128
size: 15 LOC
McCabe index: 1
number of parameters: 6

id: 198
unit: private static Stream initParameters()
file: src/integrationTest/java/com/epam/fonda/TcrRepertoireFastqIntegrationTest.java
start line: 74
end line: 87
size: 14 LOC
McCabe index: 1
number of parameters: 0

id: 199
unit: private static Stream streamOfGA5arguments()
file: src/integrationTest/java/com/epam/fonda/SCRnaExpressionBamIntegrationTest.java
start line: 129
end line: 142
size: 14 LOC
McCabe index: 1
number of parameters: 0

id: 200
unit: private static Stream streamOfGA51arguments()
file: src/integrationTest/java/com/epam/fonda/SCRnaExpressionBamIntegrationTest.java
start line: 144
end line: 157
size: 14 LOC
McCabe index: 1
number of parameters: 0

id: 201
unit: private static Stream streamOfGA52arguments()
file: src/integrationTest/java/com/epam/fonda/SCRnaExpressionBamIntegrationTest.java
start line: 159
end line: 172
size: 14 LOC
McCabe index: 1
number of parameters: 0

id: 202
unit: private void startAppWithIncompatibleTools()
file: src/integrationTest/java/com/epam/fonda/SCRnaExpressionFastqIntegrationTest.java
start line: 154
end line: 169
size: 14 LOC
McCabe index: 2
number of parameters: 2

id: 203
unit: private Configuration buildConfiguration()
file: src/main/java/com/epam/fonda/CmdParser.java
start line: 94
end line: 107
size: 14 LOC
McCabe index: 1
number of parameters: 4

id: 204
unit: private ToolFields initToolFields()
file: src/main/java/com/epam/fonda/tools/impl/PileupSummaries.java
start line: 70
end line: 83
size: 14 LOC
McCabe index: 1
number of parameters: 1

id: 205
unit: private AdditionalQcFields initializeAdditionalFields()
file: src/main/java/com/epam/fonda/tools/impl/RNASeQC.java
start line: 174
end line: 187
size: 14 LOC
McCabe index: 1
number of parameters: 1

id: 206
unit: public String generate()
file: src/main/java/com/epam/fonda/tools/impl/SCRnaAnalysis.java
start line: 71
end line: 84
size: 14 LOC
McCabe index: 4
number of parameters: 2

id: 207
unit: public BamResult generate()
file: src/main/java/com/epam/fonda/tools/impl/AbraRealign.java
start line: 77
end line: 90
size: 14 LOC
McCabe index: 1
number of parameters: 2

id: 208
unit: private AdditionalFields initializeAdditionalFields()
file: src/main/java/com/epam/fonda/tools/impl/AbraRealign.java
start line: 115
end line: 128
size: 14 LOC
McCabe index: 1
number of parameters: 1

id: 209
unit: public BamResult generate()
file: src/main/java/com/epam/fonda/tools/impl/AmpliconGatkRealign.java
start line: 62
end line: 75
size: 14 LOC
McCabe index: 1
number of parameters: 2

id: 210
unit: public String generate()
file: src/main/java/com/epam/fonda/tools/impl/FastqListAnalysis.java
start line: 51
end line: 64
size: 14 LOC
McCabe index: 1
number of parameters: 2

id: 211
unit: private AdditionalFields initializeAdditionalFields()
file: src/main/java/com/epam/fonda/tools/impl/ContEst.java
start line: 108
end line: 121
size: 14 LOC
McCabe index: 1
number of parameters: 1

id: 212
unit: private FusionCatcherFields constructFieldsByIndex()
file: src/main/java/com/epam/fonda/tools/impl/FusionCatcher.java
start line: 93
end line: 106
size: 14 LOC
McCabe index: 1
number of parameters: 1

id: 213
unit: public LearnReadOrientationModelResult generate()
file: src/main/java/com/epam/fonda/tools/impl/LearnReadOrientationModel.java
start line: 54
end line: 67
size: 14 LOC
McCabe index: 1
number of parameters: 2

id: 214
unit: private static Map initializeVariablesMap()
file: src/main/java/com/epam/fonda/entity/configuration/orchestrator/MasterScript.java
start line: 185
end line: 198
size: 14 LOC
McCabe index: 1
number of parameters: 1

id: 215
unit: private static void printInfo()
file: src/main/java/com/epam/fonda/utils/ConfigurationUtils.java
start line: 122
end line: 136
size: 14 LOC
McCabe index: 5
number of parameters: 3

id: 216
unit: static
file: src/main/java/com/epam/fonda/utils/MessageConstant.java
start line: 41
end line: 55
size: 14 LOC
McCabe index: 3
number of parameters: 0

id: 217
unit: public void run()
file: src/main/java/com/epam/fonda/workflow/impl/DnaVarFastqWorkflow.java
start line: 68
end line: 82
size: 14 LOC
McCabe index: 2
number of parameters: 2

id: 218
unit: private void rsem()
file: src/main/java/com/epam/fonda/workflow/stage/impl/SecondaryAnalysis.java
start line: 311
end line: 324
size: 14 LOC
McCabe index: 3
number of parameters: 4

id: 219
unit: public static void main()
file: src/main/java/com/epam/fonda/Main.java
start line: 38
end line: 51
size: 14 LOC
McCabe index: 3
number of parameters: 1

id: 220
unit: def write_from_dir()
file: src/main/scripts/model/sample_manifest.py
start line: 0
end line: 0
size: 14 LOC
McCabe index: 5
number of parameters: 6

id: 221
unit: public void testCreateRnaExpressionFastqSpecificDirExpressionFastqToolset()
file: src/integrationTest/java/com/epam/fonda/RnaExpressionFastqIntegrationTest.java
start line: 168
end line: 180
size: 13 LOC
McCabe index: 1
number of parameters: 0

id: 222
unit: private static Stream initTaskAndTemplateNotNAAllTasks()
file: src/integrationTest/java/com/epam/fonda/DnaCaptureVarBamIntegrationTest.java
start line: 173
end line: 185
size: 13 LOC
McCabe index: 1
number of parameters: 0

id: 223
unit: public VcfScnpeffAnnonationResult generate()
file: src/main/java/com/epam/fonda/tools/impl/VcfSnpeffAnnotation.java
start line: 78
end line: 90
size: 13 LOC
McCabe index: 1
number of parameters: 2

id: 224
unit: public BamResult generate()
file: src/main/java/com/epam/fonda/tools/impl/Count.java
start line: 83
end line: 95
size: 13 LOC
McCabe index: 2
number of parameters: 2

id: 225
unit: private DatabaseFields initializeDatabaseFields()
file: src/main/java/com/epam/fonda/tools/impl/DnaPicardQc.java
start line: 229
end line: 241
size: 13 LOC
McCabe index: 1
number of parameters: 1

id: 226
unit: private ToolFields initToolFields()
file: src/main/java/com/epam/fonda/tools/impl/FilterAlignmentArtifacts.java
start line: 74
end line: 86
size: 13 LOC
McCabe index: 1
number of parameters: 1

id: 227
unit: public BamResult generate()
file: src/main/java/com/epam/fonda/tools/impl/PicardMergeDnaBam.java
start line: 72
end line: 84
size: 13 LOC
McCabe index: 1
number of parameters: 2

id: 228
unit: private void putScript()
file: src/main/java/com/epam/fonda/entity/configuration/orchestrator/MasterScript.java
start line: 152
end line: 164
size: 13 LOC
McCabe index: 3
number of parameters: 3

id: 229
unit: private static AdditionalFields initializeAdditionalFields()
file: src/main/java/com/epam/fonda/utils/DnaUtils.java
start line: 200
end line: 212
size: 13 LOC
McCabe index: 2
number of parameters: 4

id: 230
unit: public void postProcess()
file: src/main/java/com/epam/fonda/workflow/impl/RnaExpressionFastqWorkflow.java
start line: 88
end line: 100
size: 13 LOC
McCabe index: 2
number of parameters: 2

id: 231
unit: private void mutect2()
file: src/main/java/com/epam/fonda/workflow/stage/impl/SecondaryAnalysis.java
start line: 199
end line: 211
size: 13 LOC
McCabe index: 2
number of parameters: 4

id: 232
unit: public Alignment()
file: src/main/java/com/epam/fonda/workflow/stage/impl/Alignment.java
start line: 74
end line: 86
size: 13 LOC
McCabe index: 1
number of parameters: 2

id: 233
unit: public BamResult estimating()
file: src/main/java/com/epam/fonda/workflow/stage/impl/Alignment.java
start line: 139
end line: 152
size: 13 LOC
McCabe index: 4
number of parameters: 4

id: 234
unit: private AbstractCommand mergeCommands()
file: src/main/java/com/epam/fonda/workflow/stage/impl/Alignment.java
start line: 154
end line: 166
size: 13 LOC
McCabe index: 1
number of parameters: 1

id: 235
unit: def get_sample_name()
file: src/main/scripts/model/sample_utilities.py
start line: 0
end line: 0
size: 13 LOC
McCabe index: 8
number of parameters: 2

id: 236
unit: void testNoTumorOrCase()
file: src/integrationTest/java/com/epam/fonda/DnaWgsVarBamIntegrationTest.java
start line: 253
end line: 264
size: 12 LOC
McCabe index: 1
number of parameters: 0

id: 237
unit: private static Stream initTaskAndTemplateNAAllTasks()
file: src/integrationTest/java/com/epam/fonda/DnaCaptureVarBamIntegrationTest.java
start line: 159
end line: 170
size: 12 LOC
McCabe index: 1
number of parameters: 0

id: 238
unit: public void testAlignmentAndRsem()
file: src/integrationTest/java/com/epam/fonda/SCRnaExpressionFastqIntegrationTest.java
start line: 67
end line: 81
size: 12 LOC
McCabe index: 1
number of parameters: 2

id: 239
unit: public void testStarWithoutRsem()
file: src/integrationTest/java/com/epam/fonda/SCRnaExpressionFastqIntegrationTest.java
start line: 84
end line: 98
size: 12 LOC
McCabe index: 1
number of parameters: 0

id: 240
unit: String getCommand()
file: src/main/java/com/epam/fonda/tools/impl/SCRNASeqDoubletDetection.java
start line: 70
end line: 81
size: 12 LOC
McCabe index: 3
number of parameters: 3

id: 241
unit: private AdditionalMkDupFields initializeAdditionalFields()
file: src/main/java/com/epam/fonda/tools/impl/PicardMarkDuplicate.java
start line: 102
end line: 113
size: 12 LOC
McCabe index: 1
number of parameters: 0

id: 242
unit: private RsemAnnotationFields constructFields()
file: src/main/java/com/epam/fonda/tools/impl/RsemAnnotation.java
start line: 75
end line: 86
size: 12 LOC
McCabe index: 1
number of parameters: 1

id: 243
unit: public static String createStaticShell()
file: src/main/java/com/epam/fonda/utils/PipelineUtils.java
start line: 110
end line: 121
size: 12 LOC
McCabe index: 1
number of parameters: 4

id: 244
unit: public static boolean createDir()
file: src/main/java/com/epam/fonda/utils/PipelineUtils.java
start line: 272
end line: 283
size: 12 LOC
McCabe index: 3
number of parameters: 1

id: 245
unit: private static void extract()
file: src/main/java/com/epam/fonda/utils/CellRangerUtils.java
start line: 54
end line: 65
size: 12 LOC
McCabe index: 3
number of parameters: 2

id: 246
unit: public static AmpliconGatkDatabaseFields init()
file: src/main/java/com/epam/fonda/utils/AmpliconGatkDatabaseFields.java
start line: 41
end line: 52
size: 12 LOC
McCabe index: 1
number of parameters: 1

id: 247
unit: public static TemplateEngine init()
file: src/main/java/com/epam/fonda/utils/TemplateEngineUtils.java
start line: 29
end line: 40
size: 12 LOC
McCabe index: 1
number of parameters: 0

id: 248
unit: private static Context buildContext()
file: src/main/java/com/epam/fonda/utils/RnaAnalysisUtils.java
start line: 152
end line: 163
size: 12 LOC
McCabe index: 1
number of parameters: 2

id: 249
unit: public static String periodicIndexBamStatusCheckForFastqList()
file: src/main/java/com/epam/fonda/utils/DnaUtils.java
start line: 128
end line: 139
size: 12 LOC
McCabe index: 2
number of parameters: 4

id: 250
unit: public void postProcess()
file: src/main/java/com/epam/fonda/workflow/impl/DnaVarBamWorkflow.java
start line: 84
end line: 95
size: 12 LOC
McCabe index: 3
number of parameters: 2

id: 251
unit: private void sequenza()
file: src/main/java/com/epam/fonda/workflow/stage/impl/SecondaryAnalysis.java
start line: 168
end line: 179
size: 12 LOC
McCabe index: 3
number of parameters: 4

id: 252
unit: private void createCustomToolShell()
file: src/main/java/com/epam/fonda/workflow/stage/impl/SecondaryAnalysis.java
start line: 352
end line: 363
size: 12 LOC
McCabe index: 3
number of parameters: 4

id: 253
unit: public FastqResult process()
file: src/main/java/com/epam/fonda/workflow/stage/impl/PreAlignment.java
start line: 55
end line: 66
size: 12 LOC
McCabe index: 5
number of parameters: 4

id: 254
unit: public static Optional getExecutorResult()
file: src/main/java/com/epam/fonda/Executor.java
start line: 83
end line: 94
size: 12 LOC
McCabe index: 2
number of parameters: 0

id: 255
unit: void testRnaExpressionFastqMaster()
file: src/integrationTest/java/com/epam/fonda/RnaExpressionFastqIntegrationTest.java
start line: 153
end line: 165
size: 11 LOC
McCabe index: 1
number of parameters: 7

id: 256
unit: private static Stream initControlSampleAllTasks()
file: src/integrationTest/java/com/epam/fonda/DnaAmpliconVarFastqIntegrationTest.java
start line: 168
end line: 178
size: 11 LOC
McCabe index: 1
number of parameters: 0

id: 257
unit: void testDirTree()
file: src/integrationTest/java/com/epam/fonda/TcrRepertoireFastqIntegrationTest.java
start line: 101
end line: 111
size: 11 LOC
McCabe index: 1
number of parameters: 1

id: 258
unit: public void testPeriodicDnaMutationStatusCheck()
file: src/integrationTest/java/com/epam/fonda/DnaAnalysisIntegrationTest.java
start line: 100
end line: 112
size: 11 LOC
McCabe index: 1
number of parameters: 5

id: 259
unit: public VariantsVcfResult generate()
file: src/main/java/com/epam/fonda/tools/impl/GatkHaplotypeCallerRnaFilter.java
start line: 52
end line: 62
size: 11 LOC
McCabe index: 1
number of parameters: 2

id: 260
unit: private DatabaseFields initializeDatabaseFields()
file: src/main/java/com/epam/fonda/tools/impl/VcfSnpeffAnnotation.java
start line: 117
end line: 127
size: 11 LOC
McCabe index: 1
number of parameters: 1

id: 261
unit: private ToolFields initializeToolFields()
file: src/main/java/com/epam/fonda/tools/impl/Star.java
start line: 159
end line: 169
size: 11 LOC
McCabe index: 1
number of parameters: 1

id: 262
unit: private ToolFields initializeToolFields()
file: src/main/java/com/epam/fonda/tools/impl/StarFusion.java
start line: 141
end line: 151
size: 11 LOC
McCabe index: 1
number of parameters: 1

id: 263
unit: public PileupSummariesResult generate()
file: src/main/java/com/epam/fonda/tools/impl/PileupSummaries.java
start line: 58
end line: 68
size: 11 LOC
McCabe index: 1
number of parameters: 2

id: 264
unit: private Context buildContext()
file: src/main/java/com/epam/fonda/tools/impl/DnaPicardQc.java
start line: 163
end line: 173
size: 11 LOC
McCabe index: 1
number of parameters: 3

id: 265
unit: private ToolFields initializeToolFields()
file: src/main/java/com/epam/fonda/tools/impl/SortBamByReadName.java
start line: 95
end line: 105
size: 11 LOC
McCabe index: 1
number of parameters: 1

id: 266
unit: private AdditionalFields initializeAdditionalFields()
file: src/main/java/com/epam/fonda/tools/impl/GatkHaplotypeCaller.java
start line: 119
end line: 129
size: 11 LOC
McCabe index: 2
number of parameters: 1

id: 267
unit: private FastqOutput buildFastqOutput()
file: src/main/java/com/epam/fonda/tools/impl/SamToFastq.java
start line: 100
end line: 110
size: 11 LOC
McCabe index: 2
number of parameters: 3

id: 268
unit: private ToolFields initializeToolFields()
file: src/main/java/com/epam/fonda/tools/impl/SamToFastq.java
start line: 119
end line: 129
size: 11 LOC
McCabe index: 1
number of parameters: 1

id: 269
unit: private FastqListAnalysisFields initFastqListAnalysisFields()
file: src/main/java/com/epam/fonda/tools/impl/FastqListAnalysis.java
start line: 105
end line: 115
size: 11 LOC
McCabe index: 1
number of parameters: 1

id: 270
unit: private ToolFields initializeToolFields()
file: src/main/java/com/epam/fonda/tools/impl/Hisat2.java
start line: 131
end line: 141
size: 11 LOC
McCabe index: 1
number of parameters: 1

id: 271
unit: public static FastqFileSample extractFastqDir()
file: src/main/java/com/epam/fonda/utils/CellRangerUtils.java
start line: 37
end line: 47
size: 11 LOC
McCabe index: 2
number of parameters: 1

id: 272
unit: def add_sample()
file: src/main/scripts/model/sample_manifest.py
start line: 0
end line: 0
size: 11 LOC
McCabe index: 4
number of parameters: 6

id: 273
unit: void testControlSample()
file: src/integrationTest/java/com/epam/fonda/DnaWgsVarBamIntegrationTest.java
start line: 109
end line: 120
size: 10 LOC
McCabe index: 1
number of parameters: 7

id: 274
unit: void testConversion()
file: src/integrationTest/java/com/epam/fonda/SCRnaExpressionBamIntegrationTest.java
start line: 111
end line: 122
size: 10 LOC
McCabe index: 1
number of parameters: 0

id: 275
unit: void setup()
file: src/integrationTest/java/com/epam/fonda/SCRnaExpressionCellRangerFastqIntegrationTest.java
start line: 70
end line: 79
size: 10 LOC
McCabe index: 1
number of parameters: 0

id: 276
unit: private static Stream initParameters()
file: src/integrationTest/java/com/epam/fonda/SCRnaExpressionCellRangerFastqIntegrationTest.java
start line: 109
end line: 118
size: 10 LOC
McCabe index: 1
number of parameters: 0

id: 277
unit: public void testControlSampleNotNAAllTasksOutputDir()
file: src/integrationTest/java/com/epam/fonda/DnaCaptureVarBamIntegrationTest.java
start line: 124
end line: 134
size: 10 LOC
McCabe index: 1
number of parameters: 0

id: 278
unit: private static Stream initParameters()
file: src/integrationTest/java/com/epam/fonda/DnaWgsVarFastqIntegrationTest.java
start line: 64
end line: 73
size: 10 LOC
McCabe index: 1
number of parameters: 0

id: 279
unit: def usage()
file: src/main/python/rna_qc_metrics.py
start line: 0
end line: 0
size: 10 LOC
McCabe index: 1
number of parameters: 0

id: 280
unit: private ToolFields initializeToolFields()
file: src/main/java/com/epam/fonda/tools/impl/VcfSnpeffAnnotation.java
start line: 99
end line: 108
size: 10 LOC
McCabe index: 1
number of parameters: 1

id: 281
unit: private ToolFields initializeToolFields()
file: src/main/java/com/epam/fonda/tools/impl/PicardMarkDuplicate.java
start line: 122
end line: 131
size: 10 LOC
McCabe index: 1
number of parameters: 1

id: 282
unit: private ToolFields initToolFields()
file: src/main/java/com/epam/fonda/tools/impl/CalculateContamination.java
start line: 71
end line: 80
size: 10 LOC
McCabe index: 1
number of parameters: 1

id: 283
unit: private AdditionalFields initializeAdditionalFields()
file: src/main/java/com/epam/fonda/tools/impl/AmpliconGatkRealign.java
start line: 82
end line: 91
size: 10 LOC
McCabe index: 1
number of parameters: 0

id: 284
unit: private AdditionaPileuplFields initializeAdditionalFields()
file: src/main/java/com/epam/fonda/tools/impl/Pileup.java
start line: 108
end line: 117
size: 10 LOC
McCabe index: 1
number of parameters: 1

id: 285
unit: private ToolFields initializeToolFields()
file: src/main/java/com/epam/fonda/tools/impl/PicardMergeDnaBam.java
start line: 93
end line: 102
size: 10 LOC
McCabe index: 1
number of parameters: 1

id: 286
unit: public static boolean validateOldPicardVersion()
file: src/main/java/com/epam/fonda/utils/ToolUtils.java
start line: 51
end line: 60
size: 10 LOC
McCabe index: 3
number of parameters: 1

id: 287
unit: private static LogFileFields initializeLogFields()
file: src/main/java/com/epam/fonda/utils/DnaUtils.java
start line: 189
end line: 198
size: 10 LOC
McCabe index: 2
number of parameters: 2

id: 288
unit: public void postProcess()
file: src/main/java/com/epam/fonda/workflow/impl/DnaVarFastqWorkflow.java
start line: 85
end line: 94
size: 10 LOC
McCabe index: 2
number of parameters: 2

id: 289
unit: private BamResult buildBamResult()
file: src/main/java/com/epam/fonda/workflow/impl/DnaVarBamWorkflow.java
start line: 97
end line: 106
size: 10 LOC
McCabe index: 1
number of parameters: 1

id: 290
unit: public void postProcess()
file: src/main/java/com/epam/fonda/workflow/impl/Bam2FastqWorkflow.java
start line: 84
end line: 93
size: 10 LOC
McCabe index: 1
number of parameters: 2

id: 291
unit: private void featureCount()
file: src/main/java/com/epam/fonda/workflow/stage/impl/SecondaryAnalysis.java
start line: 326
end line: 335
size: 10 LOC
McCabe index: 2
number of parameters: 4

id: 292
unit: private void qcCheck()
file: src/main/java/com/epam/fonda/workflow/stage/impl/Alignment.java
start line: 177
end line: 186
size: 10 LOC
McCabe index: 4
number of parameters: 4

id: 293
unit: private static Stream initParamsOfDirs()
file: src/integrationTest/java/com/epam/fonda/TcrRepertoireFastqIntegrationTest.java
start line: 114
end line: 122
size: 9 LOC
McCabe index: 1
number of parameters: 0

id: 294
unit: void testCreateRnaCellRangerFastqSpecificDir()
file: src/integrationTest/java/com/epam/fonda/SCRnaExpressionCellRangerFastqIntegrationTest.java
start line: 87
end line: 97
size: 9 LOC
McCabe index: 1
number of parameters: 0

id: 295
unit: public static List getSamplesScripts()
file: src/integrationTest/java/com/epam/fonda/TestTemplateUtils.java
start line: 66
end line: 74
size: 9 LOC
McCabe index: 1
number of parameters: 2

id: 296
unit: public void testControlSampleNAAllTasksOutputDir()
file: src/integrationTest/java/com/epam/fonda/DnaCaptureVarBamIntegrationTest.java
start line: 99
end line: 108
size: 9 LOC
McCabe index: 1
number of parameters: 0

id: 297
unit: def snpsift_dbsnp()
file: src/main/python/vcf_snpeff_annotation.py
start line: 0
end line: 0
size: 9 LOC
McCabe index: 1
number of parameters: 4

id: 298
unit: private AdditionalFields initializeAdditionalFields()
file: src/main/java/com/epam/fonda/tools/impl/VcfSnpeffAnnotation.java
start line: 137
end line: 145
size: 9 LOC
McCabe index: 1
number of parameters: 1

id: 299
unit: private QueueParametersFields initializeQueueParametersFields()
file: src/main/java/com/epam/fonda/tools/impl/FeatureCount.java
start line: 150
end line: 158
size: 9 LOC
McCabe index: 1
number of parameters: 1

id: 300
unit: private DatabaseFields initializeDatabaseFields()
file: src/main/java/com/epam/fonda/tools/impl/RNASeQC.java
start line: 155
end line: 165
size: 9 LOC
McCabe index: 1
number of parameters: 1

id: 301
unit: public RsemResult generate()
file: src/main/java/com/epam/fonda/tools/impl/RsemAnnotation.java
start line: 59
end line: 67
size: 9 LOC
McCabe index: 1
number of parameters: 2

id: 302
unit: private DatabaseFields initializeDatabaseFields()
file: src/main/java/com/epam/fonda/tools/impl/GatkHaplotypeCaller.java
start line: 109
end line: 117
size: 9 LOC
McCabe index: 2
number of parameters: 1

id: 303
unit: private AdditionalFields initializeAdditionalFields()
file: src/main/java/com/epam/fonda/tools/impl/PicardMergeDnaBam.java
start line: 108
end line: 116
size: 9 LOC
McCabe index: 1
number of parameters: 0

id: 304
unit: private ToolFields initToolFields()
file: src/main/java/com/epam/fonda/tools/impl/LearnReadOrientationModel.java
start line: 69
end line: 77
size: 9 LOC
McCabe index: 1
number of parameters: 1

id: 305
unit: public static String cleanUpTmpDir()
file: src/main/java/com/epam/fonda/utils/PipelineUtils.java
start line: 157
end line: 165
size: 9 LOC
McCabe index: 2
number of parameters: 1

id: 306
unit: public void postProcess()
file: src/main/java/com/epam/fonda/workflow/impl/SCRnaExpressionCellRangerFastqWorkflow.java
start line: 85
end line: 93
size: 9 LOC
McCabe index: 2
number of parameters: 2

id: 307
unit: private void contEst()
file: src/main/java/com/epam/fonda/workflow/stage/impl/SecondaryAnalysis.java
start line: 121
end line: 129
size: 9 LOC
McCabe index: 3
number of parameters: 4

id: 308
unit: private void exomecnv()
file: src/main/java/com/epam/fonda/workflow/stage/impl/SecondaryAnalysis.java
start line: 158
end line: 166
size: 9 LOC
McCabe index: 3
number of parameters: 4

id: 309
unit: private void vardict()
file: src/main/java/com/epam/fonda/workflow/stage/impl/SecondaryAnalysis.java
start line: 281
end line: 289
size: 9 LOC
McCabe index: 2
number of parameters: 4

id: 310
unit: private void stringtie()
file: src/main/java/com/epam/fonda/workflow/stage/impl/SecondaryAnalysis.java
start line: 291
end line: 299
size: 9 LOC
McCabe index: 2
number of parameters: 4

id: 311
unit: private void cufflinks()
file: src/main/java/com/epam/fonda/workflow/stage/impl/SecondaryAnalysis.java
start line: 301
end line: 309
size: 9 LOC
McCabe index: 2
number of parameters: 4

id: 312
unit: def __init__()
file: src/main/scripts/model/study_config.py
start line: 0
end line: 0
size: 9 LOC
McCabe index: 1
number of parameters: 8

id: 313
unit: public void testControlSampleAllTasksXenomeNo()
file: src/integrationTest/java/com/epam/fonda/DnaAmpliconVarFastqIntegrationTest.java
start line: 83
end line: 92
size: 8 LOC
McCabe index: 1
number of parameters: 2

id: 314
unit: private static Stream initConfigsTestPostAlignment()
file: src/integrationTest/java/com/epam/fonda/DnaAmpliconVarFastqIntegrationTest.java
start line: 158
end line: 165
size: 8 LOC
McCabe index: 1
number of parameters: 0

id: 315
unit: private static Stream initConfigsTestAlignmentAndMergeMutation()
file: src/integrationTest/java/com/epam/fonda/DnaAmpliconVarFastqIntegrationTest.java
start line: 181
end line: 188
size: 8 LOC
McCabe index: 1
number of parameters: 0

id: 316
unit: void testDir()
file: src/integrationTest/java/com/epam/fonda/TcrRepertoireFastqIntegrationTest.java
start line: 90
end line: 97
size: 8 LOC
McCabe index: 1
number of parameters: 0

id: 317
unit: public void testFeatureCountRsemCufflinksStringtie()
file: src/integrationTest/java/com/epam/fonda/RnaExpressionBamIntegrationTest.java
start line: 63
end line: 70
size: 8 LOC
McCabe index: 1
number of parameters: 2

id: 318
unit: public void testControlSampleNAAllTasks()
file: src/integrationTest/java/com/epam/fonda/DnaCaptureVarBamIntegrationTest.java
start line: 87
end line: 96
size: 8 LOC
McCabe index: 1
number of parameters: 2

id: 319
unit: public void testControlSampleNotNAAllTasks()
file: src/integrationTest/java/com/epam/fonda/DnaCaptureVarBamIntegrationTest.java
start line: 112
end line: 121
size: 8 LOC
McCabe index: 1
number of parameters: 2

id: 320
unit: public void testWorkflowOutput()
file: src/integrationTest/java/com/epam/fonda/RnaFusionFastqIntegrationTest.java
start line: 65
end line: 74
size: 8 LOC
McCabe index: 1
number of parameters: 2

id: 321
unit: private void assertDirectories()
file: src/integrationTest/java/com/epam/fonda/SCRnaExpressionFastqIntegrationTest.java
start line: 145
end line: 152
size: 8 LOC
McCabe index: 1
number of parameters: 0

id: 322
unit: private ToolFields initializeToolFields()
file: src/main/java/com/epam/fonda/tools/impl/GatkHaplotypeCallerRnaFilter.java
start line: 72
end line: 79
size: 8 LOC
McCabe index: 1
number of parameters: 1

id: 323
unit: private AdditionalFields initializeAdditionalFields()
file: src/main/java/com/epam/fonda/tools/impl/GatkHaplotypeCallerRnaFilter.java
start line: 81
end line: 88
size: 8 LOC
McCabe index: 1
number of parameters: 0

id: 324
unit: private Context buildContext()
file: src/main/java/com/epam/fonda/tools/impl/VcfSnpeffAnnotation.java
start line: 155
end line: 162
size: 8 LOC
McCabe index: 1
number of parameters: 2

id: 325
unit: private ToolFields initializeToolFields()
file: src/main/java/com/epam/fonda/tools/impl/GatkSplitReads.java
start line: 79
end line: 86
size: 8 LOC
McCabe index: 1
number of parameters: 1

id: 326
unit: private AdditionalFields initializeAdditionalFields()
file: src/main/java/com/epam/fonda/tools/impl/AmpliconGatkRecalibrate.java
start line: 82
end line: 89
size: 8 LOC
McCabe index: 1
number of parameters: 0

id: 327
unit: private ToolFields initializeToolFields()
file: src/main/java/com/epam/fonda/tools/impl/AbraRealign.java
start line: 99
end line: 106
size: 8 LOC
McCabe index: 1
number of parameters: 1

id: 328
unit: private ToolFields constructFieldsForPileup()
file: src/main/java/com/epam/fonda/tools/impl/Pileup.java
start line: 119
end line: 126
size: 8 LOC
McCabe index: 1
number of parameters: 1

id: 329
unit: private Context buildContext()
file: src/main/java/com/epam/fonda/tools/impl/SortBamByReadName.java
start line: 79
end line: 86
size: 8 LOC
McCabe index: 1
number of parameters: 4

id: 330
unit: private Context buildContext()
file: src/main/java/com/epam/fonda/tools/impl/GatkHaplotypeCaller.java
start line: 131
end line: 138
size: 8 LOC
McCabe index: 1
number of parameters: 2

id: 331
unit: private Context buildContext()
file: src/main/java/com/epam/fonda/tools/impl/SamToFastq.java
start line: 91
end line: 98
size: 8 LOC
McCabe index: 1
number of parameters: 4

id: 332
unit: private ToolFields constructFieldsForContEst()
file: src/main/java/com/epam/fonda/tools/impl/ContEst.java
start line: 99
end line: 106
size: 8 LOC
McCabe index: 1
number of parameters: 1

id: 333
unit: public Boolean convert()
file: src/main/java/com/epam/fonda/entity/configuration/FlagXenomeConverter.java
start line: 27
end line: 34
size: 8 LOC
McCabe index: 3
number of parameters: 1

id: 334
unit: public static Properties getProperties()
file: src/main/java/com/epam/fonda/utils/ConfigurationUtils.java
start line: 95
end line: 102
size: 8 LOC
McCabe index: 1
number of parameters: 0

id: 335
unit: public static String getSampleFileListReference()
file: src/main/java/com/epam/fonda/utils/RnaAnalysisUtils.java
start line: 63
end line: 70
size: 8 LOC
McCabe index: 3
number of parameters: 1

id: 336
unit: public static String periodicStatusCheck()
file: src/main/java/com/epam/fonda/utils/RnaAnalysisUtils.java
start line: 81
end line: 88
size: 8 LOC
McCabe index: 1
number of parameters: 5

id: 337
unit: private boolean determineReadType()
file: src/main/java/com/epam/fonda/workflow/impl/DnaVarFastqWorkflow.java
start line: 96
end line: 103
size: 8 LOC
McCabe index: 3
number of parameters: 1

id: 338
unit: public void postProcess()
file: src/main/java/com/epam/fonda/workflow/impl/RnaExpressionBamWorkflow.java
start line: 74
end line: 81
size: 8 LOC
McCabe index: 2
number of parameters: 2

id: 339
unit: private void freebayes()
file: src/main/java/com/epam/fonda/workflow/stage/impl/SecondaryAnalysis.java
start line: 131
end line: 138
size: 8 LOC
McCabe index: 3
number of parameters: 4

id: 340
unit: private void lofreq()
file: src/main/java/com/epam/fonda/workflow/stage/impl/SecondaryAnalysis.java
start line: 181
end line: 188
size: 8 LOC
McCabe index: 2
number of parameters: 4

id: 341
unit: private void scalpel()
file: src/main/java/com/epam/fonda/workflow/stage/impl/SecondaryAnalysis.java
start line: 190
end line: 197
size: 8 LOC
McCabe index: 2
number of parameters: 4

id: 342
unit: private void mutect1()
file: src/main/java/com/epam/fonda/workflow/stage/impl/SecondaryAnalysis.java
start line: 263
end line: 270
size: 8 LOC
McCabe index: 3
number of parameters: 4

id: 343
unit: private void strelka2()
file: src/main/java/com/epam/fonda/workflow/stage/impl/SecondaryAnalysis.java
start line: 272
end line: 279
size: 8 LOC
McCabe index: 2
number of parameters: 4

id: 344
unit: private BamResult markDuplicate()
file: src/main/java/com/epam/fonda/workflow/stage/impl/Alignment.java
start line: 168
end line: 175
size: 8 LOC
McCabe index: 3
number of parameters: 4

id: 345
unit: default void process()
file: src/main/java/com/epam/fonda/workflow/Workflow.java
start line: 37
end line: 44
size: 8 LOC
McCabe index: 2
number of parameters: 1

id: 346
unit: private static int processResult()
file: src/main/java/com/epam/fonda/Main.java
start line: 57
end line: 64
size: 8 LOC
McCabe index: 3
number of parameters: 1

id: 347
unit: public void testPostAlignment()
file: src/integrationTest/java/com/epam/fonda/DnaAmpliconVarFastqIntegrationTest.java
start line: 148
end line: 155
size: 7 LOC
McCabe index: 1
number of parameters: 3

id: 348
unit: void testWorkflow()
file: src/integrationTest/java/com/epam/fonda/SCRnaExpressionBamIntegrationTest.java
start line: 102
end line: 108
size: 7 LOC
McCabe index: 1
number of parameters: 3

id: 349
unit: public static Context getContextForMaster()
file: src/integrationTest/java/com/epam/fonda/TestTemplateUtils.java
start line: 42
end line: 48
size: 7 LOC
McCabe index: 1
number of parameters: 3

id: 350
unit: private void assertDirectories()
file: src/integrationTest/java/com/epam/fonda/Bam2FastqIntegrationTest.java
start line: 137
end line: 143
size: 7 LOC
McCabe index: 1
number of parameters: 0

id: 351
unit: private Context buildContext()
file: src/main/java/com/epam/fonda/tools/impl/GatkHaplotypeCallerRnaFilter.java
start line: 64
end line: 70
size: 7 LOC
McCabe index: 1
number of parameters: 2

id: 352
unit: private Integer defaultOrSpecifiedPeriod()
file: src/main/java/com/epam/fonda/tools/impl/QcSummary.java
start line: 122
end line: 130
size: 7 LOC
McCabe index: 2
number of parameters: 1

id: 353
unit: private DirectoryFields initializeDirectoryFields()
file: src/main/java/com/epam/fonda/tools/impl/FeatureCount.java
start line: 168
end line: 174
size: 7 LOC
McCabe index: 1
number of parameters: 2

id: 354
unit: private Map constructCufflinksLibraryTypeTofeatureCountMap()
file: src/main/java/com/epam/fonda/tools/impl/FeatureCount.java
start line: 180
end line: 186
size: 7 LOC
McCabe index: 1
number of parameters: 0

id: 355
unit: private SampleFields initializeSampleFields()
file: src/main/java/com/epam/fonda/tools/impl/Vdj.java
start line: 101
end line: 107
size: 7 LOC
McCabe index: 1
number of parameters: 1

id: 356
unit: public String generate()
file: src/main/java/com/epam/fonda/tools/impl/SCRNASeqDoubletDetection.java
start line: 53
end line: 59
size: 7 LOC
McCabe index: 1
number of parameters: 2

id: 357
unit: private String passSampleToConstructDnaAnalysisFields()
file: src/main/java/com/epam/fonda/tools/impl/DnaAnalysis.java
start line: 129
end line: 135
size: 7 LOC
McCabe index: 1
number of parameters: 4

id: 358
unit: private OutputDirFields initializeOutputDirFields()
file: src/main/java/com/epam/fonda/tools/impl/DnaPicardQc.java
start line: 246
end line: 252
size: 7 LOC
McCabe index: 1
number of parameters: 0

id: 359
unit: private boolean checkWorkflow()
file: src/main/java/com/epam/fonda/tools/impl/DnaPicardQc.java
start line: 377
end line: 383
size: 7 LOC
McCabe index: 6
number of parameters: 0

id: 360
unit: private boolean isRnaWorkflow()
file: src/main/java/com/epam/fonda/tools/impl/DnaPicardQc.java
start line: 385
end line: 391
size: 7 LOC
McCabe index: 2
number of parameters: 1

id: 361
unit: String periodicStatusCheck()
file: src/main/java/com/epam/fonda/tools/impl/SCRnaAnalysis.java
start line: 94
end line: 100
size: 7 LOC
McCabe index: 1
number of parameters: 2

id: 362
unit: private List buildToolFieldsList()
file: src/main/java/com/epam/fonda/tools/impl/FastqListAnalysis.java
start line: 90
end line: 96
size: 7 LOC
McCabe index: 1
number of parameters: 0

id: 363
unit: default void launchScript()
file: src/main/java/com/epam/fonda/entity/configuration/orchestrator/ScriptManager.java
start line: 31
end line: 37
size: 7 LOC
McCabe index: 2
number of parameters: 1

id: 364
unit: public static String addTask()
file: src/main/java/com/epam/fonda/utils/PipelineUtils.java
start line: 143
end line: 149
size: 7 LOC
McCabe index: 1
number of parameters: 3

id: 365
unit: private static String constructFilenameIfSampleNotNull()
file: src/main/java/com/epam/fonda/utils/PipelineUtils.java
start line: 324
end line: 330
size: 7 LOC
McCabe index: 2
number of parameters: 4

id: 366
unit: public static Map parseConfigFileLinesToMap()
file: src/main/java/com/epam/fonda/utils/ConfigurationUtils.java
start line: 87
end line: 93
size: 7 LOC
McCabe index: 1
number of parameters: 1

id: 367
unit: private void processVcfTool()
file: src/main/java/com/epam/fonda/workflow/stage/impl/SecondaryAnalysis.java
start line: 337
end line: 343
size: 7 LOC
McCabe index: 1
number of parameters: 4

id: 368
unit: static void unsafe()
file: src/main/java/com/epam/fonda/workflow/Workflow.java
start line: 56
end line: 62
size: 7 LOC
McCabe index: 2
number of parameters: 1

id: 369
unit: public void launch()
file: src/main/java/com/epam/fonda/FondaLauncher.java
start line: 42
end line: 48
size: 7 LOC
McCabe index: 1
number of parameters: 0

id: 370
unit: def __init__()
file: src/main/scripts/model/global_config.py
start line: 0
end line: 0
size: 7 LOC
McCabe index: 1
number of parameters: 6

id: 371
unit: void testRnaCaptureVarFastq()
file: src/integrationTest/java/com/epam/fonda/RnaCaptureVarFastqIntegrationTest.java
start line: 38
end line: 43
size: 6 LOC
McCabe index: 1
number of parameters: 4

id: 372
unit: void testDnaCaptureVarFastq()
file: src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java
start line: 83
end line: 88
size: 6 LOC
McCabe index: 1
number of parameters: 4

id: 373
unit: void testRnaExpressionFastq()
file: src/integrationTest/java/com/epam/fonda/RnaExpressionFastqIntegrationTest.java
start line: 144
end line: 149
size: 6 LOC
McCabe index: 1
number of parameters: 3

id: 374
unit: private List getFieldsToClean()
file: src/integrationTest/java/com/epam/fonda/RnaExpressionFastqIntegrationTest.java
start line: 198
end line: 203
size: 6 LOC
McCabe index: 1
number of parameters: 2

id: 375
unit: public void testControlSampleAllTasksXenomeNoOutput()
file: src/integrationTest/java/com/epam/fonda/DnaAmpliconVarFastqIntegrationTest.java
start line: 95
end line: 101
size: 6 LOC
McCabe index: 1
number of parameters: 0

id: 376
unit: public void setUp()
file: src/integrationTest/java/com/epam/fonda/AbstractIntegrationTest.java
start line: 56
end line: 61
size: 6 LOC
McCabe index: 1
number of parameters: 0

id: 377
unit: public String getCmd()
file: src/integrationTest/java/com/epam/fonda/AbstractIntegrationTest.java
start line: 134
end line: 139
size: 6 LOC
McCabe index: 1
number of parameters: 1

id: 378
unit: void testHlaTypingPairedSeqpurgeOptiType()
file: src/integrationTest/java/com/epam/fonda/HlaTypingFastqIntegrationTest.java
start line: 47
end line: 52
size: 6 LOC
McCabe index: 1
number of parameters: 2

id: 379
unit: void testHlaTypingPairedTrimmQcXenomeYes()
file: src/integrationTest/java/com/epam/fonda/HlaTypingFastqIntegrationTest.java
start line: 56
end line: 61
size: 6 LOC
McCabe index: 1
number of parameters: 2

id: 380
unit: void testDnaAmpliconVarBamNAAll()
file: src/integrationTest/java/com/epam/fonda/DnaAmpliconVarBamIntegrationTest.java
start line: 87
end line: 92
size: 6 LOC
McCabe index: 1
number of parameters: 4

id: 381
unit: void testDnaAmpliconVarBamNotNAAll()
file: src/integrationTest/java/com/epam/fonda/DnaAmpliconVarBamIntegrationTest.java
start line: 96
end line: 101
size: 6 LOC
McCabe index: 1
number of parameters: 4

id: 382
unit: void testCount()
file: src/integrationTest/java/com/epam/fonda/SCRnaExpressionCellRangerFastqIntegrationTest.java
start line: 101
end line: 106
size: 6 LOC
McCabe index: 1
number of parameters: 2

id: 383
unit: void testExtractFastqDirFastq1Fastq2()
file: src/integrationTest/java/com/epam/fonda/SCRnaExpressionCellRangerFastqIntegrationTest.java
start line: 137
end line: 143
size: 6 LOC
McCabe index: 1
number of parameters: 0

id: 384
unit: private static Stream initParametersForDirTesting()
file: src/integrationTest/java/com/epam/fonda/DnaAnalysisIntegrationTest.java
start line: 202
end line: 207
size: 6 LOC
McCabe index: 1
number of parameters: 0

id: 385
unit: public void testRsemHisat2incompatibility()
file: src/integrationTest/java/com/epam/fonda/SCRnaExpressionFastqIntegrationTest.java
start line: 101
end line: 107
size: 6 LOC
McCabe index: 1
number of parameters: 0

id: 386
unit: private static Stream initForAlignmentAndRsem()
file: src/integrationTest/java/com/epam/fonda/SCRnaExpressionFastqIntegrationTest.java
start line: 138
end line: 143
size: 6 LOC
McCabe index: 1
number of parameters: 0

id: 387
unit: def usage()
file: src/main/python/post_oncotator_cleanup.py
start line: 0
end line: 0
size: 6 LOC
McCabe index: 1
number of parameters: 0

id: 388
unit: def usage()
file: src/main/python/convert_variant_for_annotation.py
start line: 0
end line: 0
size: 6 LOC
McCabe index: 1
number of parameters: 0

id: 389
unit: def usage()
file: src/main/python/rna_gene_annotation.py
start line: 0
end line: 0
size: 6 LOC
McCabe index: 1
number of parameters: 0

id: 390
unit: private void parseFieldsFromMapToConfigClass()
file: src/main/java/com/epam/fonda/CmdParser.java
start line: 80
end line: 85
size: 6 LOC
McCabe index: 1
number of parameters: 2

id: 391
unit: private String constructFieldRG()
file: src/main/java/com/epam/fonda/tools/impl/BwaSort.java
start line: 101
end line: 106
size: 6 LOC
McCabe index: 2
number of parameters: 2

id: 392
unit: private void checkConfiguration()
file: src/main/java/com/epam/fonda/tools/impl/SCRnaAnalysis.java
start line: 150
end line: 155
size: 6 LOC
McCabe index: 1
number of parameters: 1

id: 393
unit: private ToolFields initializeToolFields()
file: src/main/java/com/epam/fonda/tools/impl/GatkHaplotypeCaller.java
start line: 102
end line: 107
size: 6 LOC
McCabe index: 1
number of parameters: 1

id: 394
unit: public EOLMarker convert()
file: src/main/java/com/epam/fonda/entity/configuration/EOLConverter.java
start line: 29
end line: 34
size: 6 LOC
McCabe index: 2
number of parameters: 1

id: 395
unit: public void resetScript()
file: src/main/java/com/epam/fonda/entity/configuration/orchestrator/MasterScript.java
start line: 116
end line: 121
size: 6 LOC
McCabe index: 1
number of parameters: 0

id: 396
unit: private void processScripts()
file: src/main/java/com/epam/fonda/entity/configuration/orchestrator/MasterScript.java
start line: 200
end line: 205
size: 6 LOC
McCabe index: 2
number of parameters: 2

id: 397
unit: public CommonOutdir()
file: src/main/java/com/epam/fonda/entity/configuration/CommonOutdir.java
start line: 37
end line: 42
size: 6 LOC
McCabe index: 1
number of parameters: 4

id: 398
unit: public static AmpliconGatkToolFields init()
file: src/main/java/com/epam/fonda/utils/AmpliconGatkToolFields.java
start line: 39
end line: 44
size: 6 LOC
McCabe index: 1
number of parameters: 1

id: 399
unit: public static boolean matchesCaptureLibraryTypeCondition()
file: src/main/java/com/epam/fonda/utils/ToolUtils.java
start line: 62
end line: 67
size: 6 LOC
McCabe index: 9
number of parameters: 1

id: 400
unit: private static boolean isValidLine()
file: src/main/java/com/epam/fonda/utils/ConfigurationUtils.java
start line: 104
end line: 109
size: 6 LOC
McCabe index: 4
number of parameters: 1

id: 401
unit: private static Pair parseConfigLine()
file: src/main/java/com/epam/fonda/utils/ConfigurationUtils.java
start line: 111
end line: 116
size: 6 LOC
McCabe index: 2
number of parameters: 1

id: 402
unit: public static String dnaRnaMutationAnalysis()
file: src/main/java/com/epam/fonda/utils/RnaAnalysisUtils.java
start line: 138
end line: 143
size: 6 LOC
McCabe index: 1
number of parameters: 3

id: 403
unit: public static Set getTasks()
file: src/main/java/com/epam/fonda/workflow/TaskContainer.java
start line: 16
end line: 21
size: 6 LOC
McCabe index: 2
number of parameters: 0

id: 404
unit: private void createVcfToolShell()
file: src/main/java/com/epam/fonda/workflow/stage/impl/SecondaryAnalysis.java
start line: 345
end line: 350
size: 6 LOC
McCabe index: 1
number of parameters: 4

id: 405
unit: public Alignment()
file: src/main/java/com/epam/fonda/workflow/stage/impl/Alignment.java
start line: 63
end line: 68
size: 6 LOC
McCabe index: 1
number of parameters: 0

id: 406
unit: void testTcrRepertoireFastqWorkflow()
file: src/integrationTest/java/com/epam/fonda/TcrRepertoireFastqIntegrationTest.java
start line: 67
end line: 71
size: 5 LOC
McCabe index: 1
number of parameters: 2

id: 407
unit: public void cleanUp()
file: src/integrationTest/java/com/epam/fonda/AbstractIntegrationTest.java
start line: 64
end line: 68
size: 5 LOC
McCabe index: 1
number of parameters: 0

id: 408
unit: void testExtractFastqDirFastq1()
file: src/integrationTest/java/com/epam/fonda/SCRnaExpressionCellRangerFastqIntegrationTest.java
start line: 121
end line: 126
size: 5 LOC
McCabe index: 1
number of parameters: 0

id: 409
unit: void testExtractFastqDirFastq1Length1()
file: src/integrationTest/java/com/epam/fonda/SCRnaExpressionCellRangerFastqIntegrationTest.java
start line: 129
end line: 134
size: 5 LOC
McCabe index: 1
number of parameters: 0

id: 410
unit: public static String trimNotImportant()
file: src/integrationTest/java/com/epam/fonda/TestTemplateUtils.java
start line: 36
end line: 40
size: 5 LOC
McCabe index: 1
number of parameters: 1

id: 411
unit: void testControlSample()
file: src/integrationTest/java/com/epam/fonda/DnaWgsVarFastqIntegrationTest.java
start line: 57
end line: 61
size: 5 LOC
McCabe index: 1
number of parameters: 2

id: 412
unit: def usage()
file: src/main/python/singlecell_doubletdetection.py
start line: 0
end line: 0
size: 5 LOC
McCabe index: 1
number of parameters: 0

id: 413
unit: def usage()
file: src/main/python/singlecell_scrublet.py
start line: 0
end line: 0
size: 5 LOC
McCabe index: 1
number of parameters: 0

id: 414
unit: private boolean removeFeatureRefFlag()
file: src/main/java/com/epam/fonda/tools/impl/Count.java
start line: 142
end line: 146
size: 5 LOC
McCabe index: 3
number of parameters: 1

id: 415
unit: private String constructFieldRG()
file: src/main/java/com/epam/fonda/tools/impl/NovoalignSort.java
start line: 109
end line: 113
size: 5 LOC
McCabe index: 2
number of parameters: 2

id: 416
unit: public List getDirs()
file: src/main/java/com/epam/fonda/tools/results/VariantsVcfOutput.java
start line: 39
end line: 43
size: 5 LOC
McCabe index: 2
number of parameters: 0

id: 417
unit: public static String dataAnalysis()
file: src/main/java/com/epam/fonda/utils/RnaAnalysisUtils.java
start line: 98
end line: 102
size: 5 LOC
McCabe index: 1
number of parameters: 3

id: 418
unit: private static String getLogFileScanningShellScript()
file: src/main/java/com/epam/fonda/utils/DnaUtils.java
start line: 159
end line: 163
size: 5 LOC
McCabe index: 1
number of parameters: 5

id: 419
unit: def create_by_list()
file: src/main/scripts/model/fastq_sample_manifest.py
start line: 0
end line: 0
size: 5 LOC
McCabe index: 1
number of parameters: 8

id: 420
unit: private static Stream initParameters()
file: src/integrationTest/java/com/epam/fonda/DnaWgsVarBamIntegrationTest.java
start line: 123
end line: 126
size: 4 LOC
McCabe index: 1
number of parameters: 0

id: 421
unit: private String getTestFastqFileString()
file: src/integrationTest/java/com/epam/fonda/Bam2FastqIntegrationTest.java
start line: 149
end line: 152
size: 4 LOC
McCabe index: 1
number of parameters: 1

id: 422
unit: def stddev()
file: src/main/python/dna_rna_variant_qc_metrics.py
start line: 0
end line: 0
size: 4 LOC
McCabe index: 2
number of parameters: 1

id: 423
unit: private String outputFile()
file: src/main/java/com/epam/fonda/tools/impl/Lofreq.java
start line: 112
end line: 115
size: 4 LOC
McCabe index: 2
number of parameters: 2

id: 424
unit: private String outputFile()
file: src/main/java/com/epam/fonda/tools/impl/Vardict.java
start line: 108
end line: 111
size: 4 LOC
McCabe index: 2
number of parameters: 2

id: 425
unit: private Integer defaultOrSpecifiedPeriod()
file: src/main/java/com/epam/fonda/tools/impl/DnaAnalysis.java
start line: 174
end line: 177
size: 4 LOC
McCabe index: 1
number of parameters: 1

id: 426
unit: private boolean checkToolset()
file: src/main/java/com/epam/fonda/tools/impl/DnaAnalysis.java
start line: 205
end line: 208
size: 4 LOC
McCabe index: 7
number of parameters: 1

id: 427
unit: private boolean checkToolset()
file: src/main/java/com/epam/fonda/tools/impl/RnaMutationAnalysis.java
start line: 65
end line: 68
size: 4 LOC
McCabe index: 7
number of parameters: 1

id: 428
unit: private String outputFile()
file: src/main/java/com/epam/fonda/tools/impl/Scalpel.java
start line: 104
end line: 107
size: 4 LOC
McCabe index: 2
number of parameters: 2

id: 429
unit: private String outputFile()
file: src/main/java/com/epam/fonda/tools/impl/Strelka2.java
start line: 115
end line: 118
size: 4 LOC
McCabe index: 2
number of parameters: 2

id: 430
unit: private boolean isDnaAmpliconWorkflow()
file: src/main/java/com/epam/fonda/tools/impl/NovoalignSort.java
start line: 115
end line: 118
size: 4 LOC
McCabe index: 1
number of parameters: 1

id: 431
unit: public Set setTempDirs()
file: src/main/java/com/epam/fonda/entity/command/AbstractCommand.java
start line: 48
end line: 51
size: 4 LOC
McCabe index: 1
number of parameters: 1

id: 432
unit: private static String normalize()
file: src/main/java/com/epam/fonda/utils/PipelineUtils.java
start line: 340
end line: 343
size: 4 LOC
McCabe index: 2
number of parameters: 2

id: 433
unit: public static String validate()
file: src/main/java/com/epam/fonda/utils/ToolUtils.java
start line: 41
end line: 44
size: 4 LOC
McCabe index: 1
number of parameters: 2

id: 434
unit: public static boolean matchesExomeLibraryTypeCondition()
file: src/main/java/com/epam/fonda/utils/ToolUtils.java
start line: 69
end line: 72
size: 4 LOC
McCabe index: 5
number of parameters: 1

id: 435
unit: public static Integer getDefaultOrSpecifiedPeriod()
file: src/main/java/com/epam/fonda/utils/DnaUtils.java
start line: 114
end line: 117
size: 4 LOC
McCabe index: 1
number of parameters: 1

id: 436
unit: default List provideSample()
file: src/main/java/com/epam/fonda/workflow/FastqWorkflow.java
start line: 38
end line: 41
size: 4 LOC
McCabe index: 1
number of parameters: 1

id: 437
unit: default List provideSample()
file: src/main/java/com/epam/fonda/workflow/BamWorkflow.java
start line: 38
end line: 41
size: 4 LOC
McCabe index: 1
number of parameters: 1

id: 438
unit: public static PipelineType getByName()
file: src/main/java/com/epam/fonda/workflow/PipelineType.java
start line: 66
end line: 69
size: 4 LOC
McCabe index: 1
number of parameters: 1

id: 439
unit: private boolean isScRnaExpressionFastq()
file: src/main/java/com/epam/fonda/workflow/stage/impl/Alignment.java
start line: 188
end line: 191
size: 4 LOC
McCabe index: 1
number of parameters: 1

id: 440
unit: private boolean isRnaCaptureVarFastq()
file: src/main/java/com/epam/fonda/workflow/stage/impl/Alignment.java
start line: 193
end line: 196
size: 4 LOC
McCabe index: 1
number of parameters: 1

id: 441
unit: private boolean skipTool()
file: src/main/java/com/epam/fonda/workflow/stage/impl/PreAlignment.java
start line: 68
end line: 71
size: 4 LOC
McCabe index: 2
number of parameters: 1

id: 442
unit: def __init__()
file: src/main/scripts/model/sample_manifest.py
start line: 0
end line: 0
size: 4 LOC
McCabe index: 1
number of parameters: 3

id: 443
unit: private String getTestTemplate()
file: src/integrationTest/java/com/epam/fonda/DnaAmpliconVarFastqIntegrationTest.java
start line: 190
end line: 192
size: 3 LOC
McCabe index: 1
number of parameters: 3

id: 444
unit: public void startAppWithConfigs()
file: src/integrationTest/java/com/epam/fonda/AbstractIntegrationTest.java
start line: 94
end line: 96
size: 3 LOC
McCabe index: 1
number of parameters: 2

id: 445
unit: private boolean checkOption()
file: src/integrationTest/java/com/epam/fonda/AbstractIntegrationTest.java
start line: 124
end line: 126
size: 3 LOC
McCabe index: 2
number of parameters: 2

id: 446
unit: private static Stream initParameters()
file: src/integrationTest/java/com/epam/fonda/SCRnaExpressionBamIntegrationTest.java
start line: 125
end line: 127
size: 3 LOC
McCabe index: 1
number of parameters: 0

id: 447
unit: public void cleanUp()
file: src/integrationTest/java/com/epam/fonda/SCRnaExpressionCellRangerFastqIntegrationTest.java
start line: 82
end line: 84
size: 3 LOC
McCabe index: 1
number of parameters: 0

id: 448
unit: private static Stream initParameters()
file: src/integrationTest/java/com/epam/fonda/DnaAnalysisIntegrationTest.java
start line: 115
end line: 117
size: 3 LOC
McCabe index: 1
number of parameters: 0

id: 449
unit: private String getTemplate()
file: src/integrationTest/java/com/epam/fonda/Bam2FastqIntegrationTest.java
start line: 133
end line: 135
size: 3 LOC
McCabe index: 1
number of parameters: 2

id: 450
unit: private String getOutputFastqFileString()
file: src/integrationTest/java/com/epam/fonda/Bam2FastqIntegrationTest.java
start line: 145
end line: 147
size: 3 LOC
McCabe index: 1
number of parameters: 0

id: 451
unit: def run()
file: src/main/python/singlecell_doubletdetection.py
start line: 0
end line: 0
size: 3 LOC
McCabe index: 1
number of parameters: 1

id: 452
unit: def run()
file: src/main/python/vcf_snpeff_annotation.py
start line: 0
end line: 0
size: 3 LOC
McCabe index: 1
number of parameters: 1

id: 453
unit: def run()
file: src/main/python/vcf_annovar_annotation.py
start line: 0
end line: 0
size: 3 LOC
McCabe index: 1
number of parameters: 1

id: 454
unit: private boolean checkSampleType()
file: src/main/java/com/epam/fonda/tools/impl/DnaAnalysis.java
start line: 166
end line: 168
size: 3 LOC
McCabe index: 2
number of parameters: 1

id: 455
unit: private boolean isAmplicon()
file: src/main/java/com/epam/fonda/tools/impl/PicardMarkDuplicate.java
start line: 133
end line: 135
size: 3 LOC
McCabe index: 1
number of parameters: 1

id: 456
unit: private boolean isWorkflowDnaCapture()
file: src/main/java/com/epam/fonda/tools/impl/DnaPicardQc.java
start line: 353
end line: 355
size: 3 LOC
McCabe index: 1
number of parameters: 0

id: 457
unit: private boolean isWorkflowDnaAmplicon()
file: src/main/java/com/epam/fonda/tools/impl/DnaPicardQc.java
start line: 357
end line: 359
size: 3 LOC
McCabe index: 1
number of parameters: 0

id: 458
unit: private boolean isWorkflowDnaWgs()
file: src/main/java/com/epam/fonda/tools/impl/DnaPicardQc.java
start line: 361
end line: 363
size: 3 LOC
McCabe index: 1
number of parameters: 0

id: 459
unit: private boolean isWorkflowRna()
file: src/main/java/com/epam/fonda/tools/impl/DnaPicardQc.java
start line: 365
end line: 367
size: 3 LOC
McCabe index: 1
number of parameters: 0

id: 460
unit: private boolean isCaptureWorkflowTargetType()
file: src/main/java/com/epam/fonda/tools/impl/DnaPicardQc.java
start line: 369
end line: 371
size: 3 LOC
McCabe index: 2
number of parameters: 1

id: 461
unit: private String replaceBamOutdirWithQcOutdir()
file: src/main/java/com/epam/fonda/tools/impl/DnaPicardQc.java
start line: 373
end line: 375
size: 3 LOC
McCabe index: 1
number of parameters: 3

id: 462
unit: private String format()
file: src/main/java/com/epam/fonda/tools/impl/Sequenza.java
start line: 108
end line: 110
size: 3 LOC
McCabe index: 1
number of parameters: 2

id: 463
unit: private String format()
file: src/main/java/com/epam/fonda/tools/impl/Exomecnv.java
start line: 112
end line: 114
size: 3 LOC
McCabe index: 1
number of parameters: 2

id: 464
unit: public List getDirs()
file: src/main/java/com/epam/fonda/tools/results/FeatureCountOutput.java
start line: 33
end line: 35
size: 3 LOC
McCabe index: 1
number of parameters: 0

id: 465
unit: public List getDirs()
file: src/main/java/com/epam/fonda/tools/results/VdjOutput.java
start line: 33
end line: 35
size: 3 LOC
McCabe index: 1
number of parameters: 0

id: 466
unit: public List getDirs()
file: src/main/java/com/epam/fonda/tools/results/StarFusionOutput.java
start line: 33
end line: 35
size: 3 LOC
McCabe index: 1
number of parameters: 0

id: 467
unit: public List getDirs()
file: src/main/java/com/epam/fonda/tools/results/CufflinksOutput.java
start line: 34
end line: 36
size: 3 LOC
McCabe index: 1
number of parameters: 0

id: 468
unit: public List getDirs()
file: src/main/java/com/epam/fonda/tools/results/MixcrOutput.java
start line: 36
end line: 38
size: 3 LOC
McCabe index: 1
number of parameters: 0

id: 469
unit: public List getDirs()
file: src/main/java/com/epam/fonda/tools/results/RsemOutput.java
start line: 34
end line: 36
size: 3 LOC
McCabe index: 1
number of parameters: 0

id: 470
unit: public List getDirs()
file: src/main/java/com/epam/fonda/tools/results/OptiTypeOutput.java
start line: 34
end line: 36
size: 3 LOC
McCabe index: 1
number of parameters: 0

id: 471
unit: public List getDirs()
file: src/main/java/com/epam/fonda/tools/results/ExomecnvOutput.java
start line: 34
end line: 36
size: 3 LOC
McCabe index: 1
number of parameters: 0

id: 472
unit: public List getDirs()
file: src/main/java/com/epam/fonda/tools/results/ContEstOutput.java
start line: 34
end line: 36
size: 3 LOC
McCabe index: 1
number of parameters: 0

id: 473
unit: public List getDirs()
file: src/main/java/com/epam/fonda/tools/results/PileupOutput.java
start line: 34
end line: 36
size: 3 LOC
McCabe index: 1
number of parameters: 0

id: 474
unit: public List getDirs()
file: src/main/java/com/epam/fonda/tools/results/SalmonOutput.java
start line: 34
end line: 36
size: 3 LOC
McCabe index: 1
number of parameters: 0

id: 475
unit: public List getDirs()
file: src/main/java/com/epam/fonda/tools/results/FusionCatcherOutput.java
start line: 34
end line: 36
size: 3 LOC
McCabe index: 1
number of parameters: 0

id: 476
unit: public List getDirs()
file: src/main/java/com/epam/fonda/tools/results/SequenzaOutput.java
start line: 37
end line: 39
size: 3 LOC
McCabe index: 1
number of parameters: 0

id: 477
unit: public List getDirs()
file: src/main/java/com/epam/fonda/tools/results/StringtieOutput.java
start line: 34
end line: 36
size: 3 LOC
McCabe index: 1
number of parameters: 0

id: 478
unit: default void createDirectory()
file: src/main/java/com/epam/fonda/entity/configuration/DirectoryManager.java
start line: 32
end line: 34
size: 3 LOC
McCabe index: 1
number of parameters: 0

id: 479
unit: public LinkedHashSet convert()
file: src/main/java/com/epam/fonda/entity/configuration/ToolSetConverter.java
start line: 30
end line: 32
size: 3 LOC
McCabe index: 1
number of parameters: 1

id: 480
unit: private MasterScript()
file: src/main/java/com/epam/fonda/entity/configuration/orchestrator/MasterScript.java
start line: 64
end line: 66
size: 3 LOC
McCabe index: 1
number of parameters: 0

id: 481
unit: public static MasterScript getInstance()
file: src/main/java/com/epam/fonda/entity/configuration/orchestrator/MasterScript.java
start line: 68
end line: 70
size: 3 LOC
McCabe index: 1
number of parameters: 0

id: 482
unit: public CommonOutdir()
file: src/main/java/com/epam/fonda/entity/configuration/CommonOutdir.java
start line: 44
end line: 46
size: 3 LOC
McCabe index: 1
number of parameters: 1

id: 483
unit: public List getDirs()
file: src/main/java/com/epam/fonda/entity/configuration/CommonOutdir.java
start line: 49
end line: 51
size: 3 LOC
McCabe index: 1
number of parameters: 0

id: 484
unit: public static BashCommand withTool()
file: src/main/java/com/epam/fonda/entity/command/BashCommand.java
start line: 29
end line: 31
size: 3 LOC
McCabe index: 1
number of parameters: 1

id: 485
unit: public BashCommand()
file: src/main/java/com/epam/fonda/entity/command/BashCommand.java
start line: 33
end line: 35
size: 3 LOC
McCabe index: 1
number of parameters: 1

id: 486
unit: public static void writeToFile()
file: src/main/java/com/epam/fonda/utils/PipelineUtils.java
start line: 130
end line: 132
size: 3 LOC
McCabe index: 1
number of parameters: 3

id: 487
unit: public static boolean isPaired()
file: src/main/java/com/epam/fonda/utils/PipelineUtils.java
start line: 320
end line: 322
size: 3 LOC
McCabe index: 2
number of parameters: 1

id: 488
unit: public static boolean checkSampleType()
file: src/main/java/com/epam/fonda/utils/PipelineUtils.java
start line: 336
end line: 338
size: 3 LOC
McCabe index: 2
number of parameters: 1

id: 489
unit: private static String getValue()
file: src/main/java/com/epam/fonda/utils/ConfigurationUtils.java
start line: 118
end line: 120
size: 3 LOC
McCabe index: 2
number of parameters: 2

id: 490
unit: private static File getFile()
file: src/main/java/com/epam/fonda/utils/ConfigurationUtils.java
start line: 138
end line: 140
size: 3 LOC
McCabe index: 1
number of parameters: 1

id: 491
unit: public static boolean isNotCaseOrTumor()
file: src/main/java/com/epam/fonda/utils/DnaUtils.java
start line: 146
end line: 148
size: 3 LOC
McCabe index: 2
number of parameters: 1

id: 492
unit: public static boolean isWgsWorkflow()
file: src/main/java/com/epam/fonda/utils/DnaUtils.java
start line: 155
end line: 157
size: 3 LOC
McCabe index: 1
number of parameters: 1

id: 493
unit: static
file: src/main/java/com/epam/fonda/workflow/PipelineType.java
start line: 52
end line: 54
size: 3 LOC
McCabe index: 1
number of parameters: 0

id: 494
unit: private TaskContainer()
file: src/main/java/com/epam/fonda/workflow/TaskContainer.java
start line: 12
end line: 14
size: 3 LOC
McCabe index: 1
number of parameters: 0

id: 495
unit: public static void addTasks()
file: src/main/java/com/epam/fonda/workflow/TaskContainer.java
start line: 23
end line: 25
size: 3 LOC
McCabe index: 1
number of parameters: 1

id: 496
unit: public Alignment()
file: src/main/java/com/epam/fonda/workflow/stage/impl/Alignment.java
start line: 70
end line: 72
size: 3 LOC
McCabe index: 1
number of parameters: 1

id: 497
unit: private boolean isCapture()
file: src/main/java/com/epam/fonda/workflow/stage/impl/PostAlignment.java
start line: 97
end line: 99
size: 3 LOC
McCabe index: 1
number of parameters: 1

id: 498
unit: public PreAlignment()
file: src/main/java/com/epam/fonda/workflow/stage/impl/PreAlignment.java
start line: 42
end line: 44
size: 3 LOC
McCabe index: 1
number of parameters: 1

id: 499
unit: public String getName()
file: src/main/java/com/epam/fonda/OptionName.java
start line: 41
end line: 43
size: 3 LOC
McCabe index: 1
number of parameters: 0

id: 500
unit: def create_by_folder()
file: src/main/scripts/model/bam_sample_manifest.py
start line: 0
end line: 0
size: 3 LOC
McCabe index: 4
number of parameters: 4

id: 501
unit: def create_by_list()
file: src/main/scripts/model/bam_sample_manifest.py
start line: 0
end line: 0
size: 3 LOC
McCabe index: 1
number of parameters: 6

id: 502
unit: def create_by_folder()
file: src/main/scripts/model/fastq_sample_manifest.py
start line: 0
end line: 0
size: 3 LOC
McCabe index: 5
number of parameters: 4

id: 503
unit: private TestTemplateUtils()
file: src/integrationTest/java/com/epam/fonda/TestTemplateUtils.java
start line: 33
end line: 34
size: 2 LOC
McCabe index: 1
number of parameters: 0

id: 504
unit: private GlobalConfigFormat()
file: src/main/java/com/epam/fonda/entity/configuration/GlobalConfigFormat.java
start line: 23
end line: 24
size: 2 LOC
McCabe index: 1
number of parameters: 0

id: 505
unit: private PipelineUtils()
file: src/main/java/com/epam/fonda/utils/PipelineUtils.java
start line: 66
end line: 67
size: 2 LOC
McCabe index: 1
number of parameters: 0

id: 506
unit: private ToolUtils()
file: src/main/java/com/epam/fonda/utils/ToolUtils.java
start line: 31
end line: 33
size: 2 LOC
McCabe index: 1
number of parameters: 0

id: 507
unit: private TemplateEngineUtils()
file: src/main/java/com/epam/fonda/utils/TemplateEngineUtils.java
start line: 26
end line: 27
size: 2 LOC
McCabe index: 1
number of parameters: 0

id: 508
unit: private ConfigurationUtils()
file: src/main/java/com/epam/fonda/utils/ConfigurationUtils.java
start line: 49
end line: 50
size: 2 LOC
McCabe index: 1
number of parameters: 0

id: 509
unit: private DnaUtils()
file: src/main/java/com/epam/fonda/utils/DnaUtils.java
start line: 74
end line: 75
size: 2 LOC
McCabe index: 1
number of parameters: 0

id: 510
unit: public void postProcess()
file: src/main/java/com/epam/fonda/workflow/impl/TcrRepertoireFastqWorkflow.java
start line: 80
end line: 82
size: 2 LOC
McCabe index: 1
number of parameters: 2

id: 511
unit: public void postProcess()
file: src/main/java/com/epam/fonda/workflow/impl/HlaTypingFastqWorkflow.java
start line: 76
end line: 78
size: 2 LOC
McCabe index: 1
number of parameters: 2

id: 512
unit: public void postProcess()
file: src/main/java/com/epam/fonda/workflow/impl/RnaFusionFastqWorkflow.java
start line: 93
end line: 95
size: 2 LOC
McCabe index: 1
number of parameters: 2

id: 513
unit: def create_by_folder()
file: src/main/scripts/model/sample_manifest.py
start line: 0
end line: 0
size: 2 LOC
McCabe index: 1
number of parameters: 4

id: 514
unit: def create_by_list()
file: src/main/scripts/model/sample_manifest.py
start line: 0
end line: 0
size: 2 LOC
McCabe index: 1
number of parameters: 5

id: 515
unit: def __init__()
file: src/main/scripts/model/bam_sample_manifest.py
start line: 0
end line: 0
size: 2 LOC
McCabe index: 1
number of parameters: 1

id: 516
unit: def __init__()
file: src/main/scripts/model/fastq_sample_manifest.py
start line: 0
end line: 0
size: 2 LOC
McCabe index: 1
number of parameters: 2

id: 517
unit: def __init__()
file: src/main/scripts/launcher.py
start line: 0
end line: 0
size: 2 LOC
McCabe index: 1
number of parameters: 1

id: 518
unit: private StudyConfigFormat()
file: src/main/java/com/epam/fonda/entity/configuration/StudyConfigFormat.java
start line: 23
end line: 23
size: 1 LOC
McCabe index: 1
number of parameters: 0

id: 519
unit: private CellRangerUtils()
file: src/main/java/com/epam/fonda/utils/CellRangerUtils.java
start line: 31
end line: 31
size: 1 LOC
McCabe index: 1
number of parameters: 0

id: 520
unit: private RnaAnalysisUtils()
file: src/main/java/com/epam/fonda/utils/RnaAnalysisUtils.java
start line: 40
end line: 40
size: 1 LOC
McCabe index: 1
number of parameters: 0

id: 521
unit: private MessageConstant()
file: src/main/java/com/epam/fonda/utils/MessageConstant.java
start line: 59
end line: 59
size: 1 LOC
McCabe index: 1
number of parameters: 0

id: 522
unit: private Main()
file: src/main/java/com/epam/fonda/Main.java
start line: 31
end line: 31
size: 1 LOC
McCabe index: 1
number of parameters: 0

id: 523
unit: private Executor()
file: src/main/java/com/epam/fonda/Executor.java
start line: 40
end line: 40
size: 1 LOC
McCabe index: 1
number of parameters: 0