epam / fonda
File Size

The distribution of size of files (measured in lines of code).

Intro
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File Size Overall
0% | 12% | 19% | 25% | 42%
Legend:
1001+
501-1000
201-500
101-200
1-100


explore: grouped by folders | grouped by size | sunburst | 3D view
File Size per Extension
1001+
501-1000
201-500
101-200
1-100
py0% | 36% | 29% | 20% | 13%
java0% | 5% | 16% | 26% | 50%
xml0% | 0% | 0% | 0% | 100%
File Size per Logical Decomposition
primary
1001+
501-1000
201-500
101-200
1-100
src0% | 12% | 19% | 25% | 42%
config0% | 0% | 0% | 0% | 100%
Longest Files (Top 50)
File# lines# units
DnaCaptureVarFastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 703 6
vcf_annovar_annotation.py
in src/main/python
 668 8
vcf_snpeff_annotation.py
in src/main/python
 609 9
455 4
RnaExpressionFastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 392 6
SecondaryAnalysis.java
in src/main/java/com/epam/fonda/workflow/stage/impl
 315 20
DnaPicardQc.java
in src/main/java/com/epam/fonda/tools/impl
 297 18
rna_qc_metrics.py
in src/main/python
 295 3
DnaWgsVarBamIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 272 8
270 3
DnaAmpliconVarBamIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 258 4
GlobalConfig.java
in src/main/java/com/epam/fonda/entity/configuration
 234 -
PipelineUtils.java
in src/main/java/com/epam/fonda/utils
 217 15
dna_capture_var_fastq.py
in src/main/scripts
 192 3
MasterScript.java
in src/main/java/com/epam/fonda/entity/configuration/orchestrator
 187 9
174 2
rna_expression_fastq.py
in src/main/scripts
 174 3
DnaAnalysisIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 173 6
DnaAmpliconVarFastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 170 10
post_oncotator_cleanup.py
in src/main/python
 169 2
SCRnaExpressionBamIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 164 7
DnaCaptureVarBamIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 149 7
Count.java
in src/main/java/com/epam/fonda/tools/impl
 149 5
DnaUtils.java
in src/main/java/com/epam/fonda/utils
 149 10
DnaAnalysis.java
in src/main/java/com/epam/fonda/tools/impl
 146 8
RNASeQC.java
in src/main/java/com/epam/fonda/tools/impl
 144 5
Alignment.java
in src/main/java/com/epam/fonda/workflow/stage/impl
 144 10
QcSummary.java
in src/main/java/com/epam/fonda/tools/impl
 140 4
DnaVarFastqWorkflow.java
in src/main/java/com/epam/fonda/workflow/impl
 137 5
SCRnaExpressionFastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 127 7
Xenome.java
in src/main/java/com/epam/fonda/tools/impl
 123 2
FeatureCount.java
in src/main/java/com/epam/fonda/tools/impl
 122 5
Star.java
in src/main/java/com/epam/fonda/tools/impl
 121 3
HlaTypingFastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 114 4
Bam2FastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 112 8
StarFusion.java
in src/main/java/com/epam/fonda/tools/impl
 112 3
SCRnaExpressionCellRangerFastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 109 8
GlobalConfigFormat.java
in src/main/java/com/epam/fonda/entity/configuration
 108 1
SCRnaAnalysis.java
in src/main/java/com/epam/fonda/tools/impl
 105 5
GatkHaplotypeCaller.java
in src/main/java/com/epam/fonda/tools/impl
 104 5
NovoalignSort.java
in src/main/java/com/epam/fonda/tools/impl
 103 4
ConfigurationUtils.java
in src/main/java/com/epam/fonda/utils
 99 9
Mixcr.java
in src/main/java/com/epam/fonda/tools/impl
 98 2
VcfSnpeffAnnotation.java
in src/main/java/com/epam/fonda/tools/impl
 95 5
TcrRepertoireFastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 94 5
AbstractIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 94 7
Hisat2.java
in src/main/java/com/epam/fonda/tools/impl
 94 3
Trimmomatic.java
in src/main/java/com/epam/fonda/tools/impl
 93 2
BwaSort.java
in src/main/java/com/epam/fonda/tools/impl
 92 3
Flag.java
in src/main/java/com/epam/fonda/workflow/impl
 92 1
Files With Most Units (Top 50)
File# lines# units
SecondaryAnalysis.java
in src/main/java/com/epam/fonda/workflow/stage/impl
 315 20
DnaPicardQc.java
in src/main/java/com/epam/fonda/tools/impl
 297 18
PipelineUtils.java
in src/main/java/com/epam/fonda/utils
 217 15
DnaAmpliconVarFastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 170 10
DnaUtils.java
in src/main/java/com/epam/fonda/utils
 149 10
Alignment.java
in src/main/java/com/epam/fonda/workflow/stage/impl
 144 10
vcf_snpeff_annotation.py
in src/main/python
 609 9
MasterScript.java
in src/main/java/com/epam/fonda/entity/configuration/orchestrator
 187 9
ConfigurationUtils.java
in src/main/java/com/epam/fonda/utils
 99 9
DnaWgsVarBamIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 272 8
SCRnaExpressionCellRangerFastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 109 8
Bam2FastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 112 8
vcf_annovar_annotation.py
in src/main/python
 668 8
DnaAnalysis.java
in src/main/java/com/epam/fonda/tools/impl
 146 8
AbstractIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 94 7
SCRnaExpressionBamIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 164 7
DnaCaptureVarBamIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 149 7
SCRnaExpressionFastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 127 7
RnaAnalysisUtils.java
in src/main/java/com/epam/fonda/utils
 88 7
sample_manifest.py
in src/main/scripts/model
 86 7
DnaCaptureVarFastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 703 6
RnaExpressionFastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 392 6
DnaAnalysisIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 173 6
TcrRepertoireFastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 94 5
TestTemplateUtils.java
in src/integrationTest/java/com/epam/fonda
 50 5
VcfSnpeffAnnotation.java
in src/main/java/com/epam/fonda/tools/impl
 95 5
FeatureCount.java
in src/main/java/com/epam/fonda/tools/impl
 122 5
RNASeQC.java
in src/main/java/com/epam/fonda/tools/impl
 144 5
Count.java
in src/main/java/com/epam/fonda/tools/impl
 149 5
SCRnaAnalysis.java
in src/main/java/com/epam/fonda/tools/impl
 105 5
GatkHaplotypeCaller.java
in src/main/java/com/epam/fonda/tools/impl
 104 5
ToolUtils.java
in src/main/java/com/epam/fonda/utils
 37 5
DnaVarFastqWorkflow.java
in src/main/java/com/epam/fonda/workflow/impl
 137 5
HlaTypingFastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 114 4
DnaAmpliconVarBamIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 258 4
455 4
GatkHaplotypeCallerRnaFilter.java
in src/main/java/com/epam/fonda/tools/impl
 72 4
QcSummary.java
in src/main/java/com/epam/fonda/tools/impl
 140 4
PicardMarkDuplicate.java
in src/main/java/com/epam/fonda/tools/impl
 90 4
SamToFastq.java
in src/main/java/com/epam/fonda/tools/impl
 90 4
NovoalignSort.java
in src/main/java/com/epam/fonda/tools/impl
 103 4
RnaFusionFastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 87 3
DnaWgsVarFastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 66 3
88 3
rna_qc_metrics.py
in src/main/python
 295 3
CmdParser.java
in src/main/java/com/epam/fonda
 68 3
Lofreq.java
in src/main/java/com/epam/fonda/tools/impl
 85 3
BwaSort.java
in src/main/java/com/epam/fonda/tools/impl
 92 3
Star.java
in src/main/java/com/epam/fonda/tools/impl
 121 3
Vdj.java
in src/main/java/com/epam/fonda/tools/impl
 85 3
Files With Long Lines (Top 10)

There are 10 files with lines longer than 120 characters. In total, there are 81 long lines.

File# lines# units# long lines
455 4 23
vcf_annovar_annotation.py
in src/main/python
 668 8 19
vcf_snpeff_annotation.py
in src/main/python
 609 9 13
post_oncotator_cleanup.py
in src/main/python
 169 2 10
rna_qc_metrics.py
in src/main/python
 295 3 6
174 2 5
rna_expression_fastq.py
in src/main/scripts
 174 3 2
88 3 1
singlecell_scrublet.py
in src/main/python
 73 2 1
rna_gene_annotation.py
in src/main/python
 54 2 1
Correlations

File Size vs. Commits (all time): 198 points

src/main/java/com/epam/fonda/tools/impl/Count.java x: 9 commits (all time) y: 149 lines of code src/main/scripts/sc_rna_expression_cellranger_fastq.py x: 16 commits (all time) y: 270 lines of code src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java x: 10 commits (all time) y: 703 lines of code src/integrationTest/java/com/epam/fonda/RnaExpressionFastqIntegrationTest.java x: 8 commits (all time) y: 392 lines of code src/integrationTest/java/com/epam/fonda/TestTemplateUtils.java x: 2 commits (all time) y: 50 lines of code src/main/java/com/epam/fonda/entity/configuration/orchestrator/MasterScript.java x: 3 commits (all time) y: 187 lines of code src/integrationTest/java/com/epam/fonda/AbstractIntegrationTest.java x: 10 commits (all time) y: 94 lines of code src/main/java/com/epam/fonda/entity/configuration/orchestrator/ScriptManager.java x: 2 commits (all time) y: 15 lines of code src/main/java/com/epam/fonda/workflow/Workflow.java x: 4 commits (all time) y: 29 lines of code src/main/scripts/dna_capture_var_fastq.py x: 13 commits (all time) y: 192 lines of code src/main/java/com/epam/fonda/tools/impl/AbraRealign.java x: 2 commits (all time) y: 81 lines of code src/main/java/com/epam/fonda/tools/impl/AmpliconGatkRealign.java x: 3 commits (all time) y: 56 lines of code src/main/java/com/epam/fonda/tools/impl/AmpliconGatkRecalibrate.java x: 4 commits (all time) y: 54 lines of code src/main/java/com/epam/fonda/tools/impl/BwaSort.java x: 5 commits (all time) y: 92 lines of code src/main/java/com/epam/fonda/tools/impl/ContEst.java x: 4 commits (all time) y: 89 lines of code src/main/java/com/epam/fonda/tools/impl/DnaPicardQc.java x: 9 commits (all time) y: 297 lines of code src/main/java/com/epam/fonda/tools/impl/Exomecnv.java x: 3 commits (all time) y: 84 lines of code src/main/java/com/epam/fonda/tools/impl/FeatureCount.java x: 5 commits (all time) y: 122 lines of code src/main/java/com/epam/fonda/tools/impl/FusionCatcher.java x: 4 commits (all time) y: 71 lines of code src/main/java/com/epam/fonda/tools/impl/GatkHaplotypeCaller.java x: 6 commits (all time) y: 104 lines of code src/main/java/com/epam/fonda/tools/impl/GatkSplitReads.java x: 4 commits (all time) y: 57 lines of code src/main/java/com/epam/fonda/tools/impl/Mutect1.java x: 3 commits (all time) y: 82 lines of code src/main/java/com/epam/fonda/tools/impl/PicardMarkDuplicate.java x: 5 commits (all time) y: 90 lines of code src/main/java/com/epam/fonda/tools/impl/PicardMergeDnaBam.java x: 6 commits (all time) y: 72 lines of code src/main/java/com/epam/fonda/tools/impl/PicardRemoveDuplicate.java x: 4 commits (all time) y: 44 lines of code src/main/java/com/epam/fonda/tools/impl/RNASeQC.java x: 10 commits (all time) y: 144 lines of code src/main/java/com/epam/fonda/tools/impl/Sequenza.java x: 3 commits (all time) y: 80 lines of code src/main/java/com/epam/fonda/tools/impl/SortBamByReadName.java x: 4 commits (all time) y: 67 lines of code src/main/java/com/epam/fonda/tools/impl/Star.java x: 8 commits (all time) y: 121 lines of code src/main/java/com/epam/fonda/tools/impl/StarFusion.java x: 6 commits (all time) y: 112 lines of code src/main/java/com/epam/fonda/utils/PipelineUtils.java x: 14 commits (all time) y: 217 lines of code src/main/java/com/epam/fonda/workflow/WorkflowFactory.java x: 13 commits (all time) y: 47 lines of code src/main/java/com/epam/fonda/workflow/impl/Bam2FastqWorkflow.java x: 5 commits (all time) y: 70 lines of code src/main/java/com/epam/fonda/workflow/impl/DnaVarBamWorkflow.java x: 5 commits (all time) y: 81 lines of code src/main/java/com/epam/fonda/workflow/impl/DnaVarFastqWorkflow.java x: 6 commits (all time) y: 137 lines of code src/main/java/com/epam/fonda/workflow/impl/RnaExpressionBamWorkflow.java x: 8 commits (all time) y: 59 lines of code src/main/java/com/epam/fonda/workflow/stage/impl/SecondaryAnalysis.java x: 9 commits (all time) y: 315 lines of code src/main/scripts/model/global_config.py x: 6 commits (all time) y: 52 lines of code src/integrationTest/java/com/epam/fonda/DnaWgsVarBamIntegrationTest.java x: 6 commits (all time) y: 272 lines of code src/main/java/com/epam/fonda/entity/configuration/GlobalConfig.java x: 10 commits (all time) y: 234 lines of code src/main/java/com/epam/fonda/entity/configuration/GlobalConfigFormat.java x: 8 commits (all time) y: 108 lines of code src/main/java/com/epam/fonda/tools/impl/CalculateContamination.java x: 1 commits (all time) y: 58 lines of code src/main/java/com/epam/fonda/tools/impl/FilterAlignmentArtifacts.java x: 1 commits (all time) y: 64 lines of code src/main/java/com/epam/fonda/tools/impl/FilterMutectCalls.java x: 1 commits (all time) y: 76 lines of code src/main/java/com/epam/fonda/tools/impl/GatkSortSam.java x: 1 commits (all time) y: 51 lines of code src/main/java/com/epam/fonda/tools/impl/LearnReadOrientationModel.java x: 1 commits (all time) y: 55 lines of code src/main/java/com/epam/fonda/tools/impl/Mutect2.java x: 4 commits (all time) y: 84 lines of code src/main/java/com/epam/fonda/tools/impl/PileupSummaries.java x: 1 commits (all time) y: 62 lines of code src/main/java/com/epam/fonda/tools/results/CalculateContaminationOutput.java x: 1 commits (all time) y: 9 lines of code src/main/java/com/epam/fonda/tools/results/LearnReadOrientationModelOutput.java x: 1 commits (all time) y: 8 lines of code src/main/java/com/epam/fonda/tools/results/VariantsVcfOutput.java x: 3 commits (all time) y: 24 lines of code src/main/java/com/epam/fonda/workflow/stage/impl/PostAlignment.java x: 7 commits (all time) y: 65 lines of code src/main/java/com/epam/fonda/Executor.java x: 2 commits (all time) y: 55 lines of code src/main/scripts/launcher.py x: 10 commits (all time) y: 45 lines of code src/main/scripts/model/bam_sample_manifest.py x: 3 commits (all time) y: 13 lines of code src/main/scripts/model/fastq_sample_manifest.py x: 4 commits (all time) y: 15 lines of code src/main/scripts/model/sample_manifest.py x: 6 commits (all time) y: 86 lines of code src/main/scripts/rna_expression_fastq.py x: 10 commits (all time) y: 174 lines of code src/integrationTest/java/com/epam/fonda/Bam2FastqIntegrationTest.java x: 5 commits (all time) y: 112 lines of code src/integrationTest/java/com/epam/fonda/DnaAmpliconVarBamIntegrationTest.java x: 5 commits (all time) y: 258 lines of code src/integrationTest/java/com/epam/fonda/DnaAmpliconVarFastqIntegrationTest.java x: 7 commits (all time) y: 170 lines of code src/integrationTest/java/com/epam/fonda/DnaAnalysisIntegrationTest.java x: 5 commits (all time) y: 173 lines of code src/integrationTest/java/com/epam/fonda/DnaCaptureVarBamIntegrationTest.java x: 5 commits (all time) y: 149 lines of code src/integrationTest/java/com/epam/fonda/DnaWgsVarFastqIntegrationTest.java x: 4 commits (all time) y: 66 lines of code src/integrationTest/java/com/epam/fonda/HlaTypingFastqIntegrationTest.java x: 3 commits (all time) y: 114 lines of code src/integrationTest/java/com/epam/fonda/RnaCaptureVarFastqIntegrationTest.java x: 2 commits (all time) y: 58 lines of code src/integrationTest/java/com/epam/fonda/RnaFusionFastqIntegrationTest.java x: 4 commits (all time) y: 87 lines of code src/integrationTest/java/com/epam/fonda/SCRnaExpressionBamIntegrationTest.java x: 3 commits (all time) y: 164 lines of code src/integrationTest/java/com/epam/fonda/SCRnaExpressionCellRangerFastqIntegrationTest.java x: 9 commits (all time) y: 109 lines of code src/integrationTest/java/com/epam/fonda/SCRnaExpressionFastqIntegrationTest.java x: 2 commits (all time) y: 127 lines of code src/integrationTest/java/com/epam/fonda/TcrRepertoireFastqIntegrationTest.java x: 3 commits (all time) y: 94 lines of code src/main/java/com/epam/fonda/CmdParser.java x: 2 commits (all time) y: 68 lines of code src/main/java/com/epam/fonda/OptionName.java x: 2 commits (all time) y: 18 lines of code src/main/java/com/epam/fonda/entity/configuration/Configuration.java x: 2 commits (all time) y: 13 lines of code src/main/java/com/epam/fonda/entity/configuration/orchestrator/ScriptType.java x: 1 commits (all time) y: 4 lines of code src/main/java/com/epam/fonda/tools/PostProcessTool.java x: 2 commits (all time) y: 7 lines of code src/main/java/com/epam/fonda/tools/impl/DnaAnalysis.java x: 5 commits (all time) y: 146 lines of code src/main/java/com/epam/fonda/tools/impl/FastqListAnalysis.java x: 4 commits (all time) y: 73 lines of code src/main/java/com/epam/fonda/tools/impl/QcSummary.java x: 10 commits (all time) y: 140 lines of code src/main/java/com/epam/fonda/tools/impl/RnaAnalysis.java x: 2 commits (all time) y: 59 lines of code src/main/java/com/epam/fonda/tools/impl/RnaMutationAnalysis.java x: 2 commits (all time) y: 47 lines of code src/main/java/com/epam/fonda/tools/impl/SCRnaAnalysis.java x: 7 commits (all time) y: 105 lines of code src/main/java/com/epam/fonda/utils/ConfigurationUtils.java x: 3 commits (all time) y: 99 lines of code src/main/java/com/epam/fonda/utils/MessageConstant.java x: 3 commits (all time) y: 36 lines of code src/main/java/com/epam/fonda/workflow/impl/RnaExpressionFastqWorkflow.java x: 4 commits (all time) y: 79 lines of code src/main/java/com/epam/fonda/workflow/impl/RnaFusionFastqWorkflow.java x: 6 commits (all time) y: 60 lines of code src/main/java/com/epam/fonda/workflow/impl/TcrRepertoireFastqWorkflow.java x: 4 commits (all time) y: 59 lines of code src/main/scripts/model/sample_utilities.py x: 3 commits (all time) y: 14 lines of code src/main/java/com/epam/fonda/tools/impl/SCRNASeqDoubletDetection.java x: 5 commits (all time) y: 65 lines of code src/main/java/com/epam/fonda/workflow/PipelineType.java x: 7 commits (all time) y: 37 lines of code src/main/java/com/epam/fonda/workflow/stage/impl/Alignment.java x: 8 commits (all time) y: 144 lines of code src/main/scripts/model/study_config.py x: 2 commits (all time) y: 32 lines of code src/main/scripts/__init__.py x: 1 commits (all time) y: 1 lines of code src/main/java/com/epam/fonda/tools/impl/Xenome.java x: 4 commits (all time) y: 123 lines of code src/main/java/com/epam/fonda/tools/impl/SamToFastq.java x: 3 commits (all time) y: 90 lines of code src/main/java/com/epam/fonda/tools/impl/VcfSnpeffAnnotation.java x: 5 commits (all time) y: 95 lines of code src/main/java/com/epam/fonda/tools/impl/RsemAnnotation.java x: 5 commits (all time) y: 50 lines of code src/main/java/com/epam/fonda/utils/RnaAnalysisUtils.java x: 5 commits (all time) y: 88 lines of code src/main/java/com/epam/fonda/tools/impl/GatkHaplotypeCallerRnaFilter.java x: 3 commits (all time) y: 72 lines of code src/main/java/com/epam/fonda/Main.java x: 3 commits (all time) y: 32 lines of code src/main/java/com/epam/fonda/entity/command/AbstractCommand.java x: 2 commits (all time) y: 22 lines of code src/main/java/com/epam/fonda/tools/impl/Scalpel.java x: 2 commits (all time) y: 77 lines of code src/main/java/com/epam/fonda/tools/impl/Stringtie.java x: 3 commits (all time) y: 71 lines of code src/main/java/com/epam/fonda/tools/impl/Vardict.java x: 2 commits (all time) y: 80 lines of code src/main/java/com/epam/fonda/workflow/TaskContainer.java x: 1 commits (all time) y: 20 lines of code src/main/java/com/epam/fonda/tools/results/MixcrOutput.java x: 1 commits (all time) y: 19 lines of code src/main/java/com/epam/fonda/utils/AmpliconGatkDatabaseFields.java x: 2 commits (all time) y: 26 lines of code src/main/java/com/epam/fonda/entity/command/BashCommand.java x: 1 commits (all time) y: 13 lines of code src/main/java/com/epam/fonda/entity/configuration/CommonOutdir.java x: 1 commits (all time) y: 25 lines of code src/main/java/com/epam/fonda/entity/configuration/StudyConfig.java x: 1 commits (all time) y: 28 lines of code src/main/java/com/epam/fonda/entity/configuration/StudyConfigFormat.java x: 1 commits (all time) y: 15 lines of code src/main/java/com/epam/fonda/utils/CellRangerUtils.java x: 1 commits (all time) y: 35 lines of code src/main/java/com/epam/fonda/workflow/stage/impl/PreAlignment.java x: 1 commits (all time) y: 36 lines of code src/main/python/convert_variant_for_annotation.py x: 1 commits (all time) y: 174 lines of code src/main/python/dna_rna_variant_qc_metrics.py x: 1 commits (all time) y: 455 lines of code src/main/python/post_oncotator_cleanup.py x: 1 commits (all time) y: 169 lines of code src/main/python/rna_qc_metrics.py x: 1 commits (all time) y: 295 lines of code src/main/python/singlecell_doubletdetection.py x: 1 commits (all time) y: 88 lines of code src/main/python/singlecell_scrublet.py x: 1 commits (all time) y: 73 lines of code src/main/python/vcf_annovar_annotation.py x: 1 commits (all time) y: 668 lines of code src/main/python/vcf_snpeff_annotation.py x: 1 commits (all time) y: 609 lines of code
703.0
lines of code
  min: 1.0
  average: 78.41
  25th percentile: 16.0
  median: 57.5
  75th percentile: 92.0
  max: 703.0
0 16.0
commits (all time)
min: 1.0 | average: 3.32 | 25th percentile: 1.0 | median: 2.0 | 75th percentile: 5.0 | max: 16.0

File Size vs. Contributors (all time): 198 points

src/main/java/com/epam/fonda/tools/impl/Count.java x: 2 contributors (all time) y: 149 lines of code src/main/scripts/sc_rna_expression_cellranger_fastq.py x: 2 contributors (all time) y: 270 lines of code src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java x: 6 contributors (all time) y: 703 lines of code src/integrationTest/java/com/epam/fonda/RnaExpressionFastqIntegrationTest.java x: 4 contributors (all time) y: 392 lines of code src/integrationTest/java/com/epam/fonda/TestTemplateUtils.java x: 2 contributors (all time) y: 50 lines of code src/main/java/com/epam/fonda/entity/configuration/orchestrator/MasterScript.java x: 2 contributors (all time) y: 187 lines of code src/integrationTest/java/com/epam/fonda/AbstractIntegrationTest.java x: 4 contributors (all time) y: 94 lines of code src/main/java/com/epam/fonda/entity/configuration/orchestrator/ScriptManager.java x: 1 contributors (all time) y: 15 lines of code src/main/java/com/epam/fonda/workflow/Workflow.java x: 1 contributors (all time) y: 29 lines of code src/main/scripts/dna_capture_var_fastq.py x: 1 contributors (all time) y: 192 lines of code src/main/java/com/epam/fonda/tools/impl/AbraRealign.java x: 2 contributors (all time) y: 81 lines of code src/main/java/com/epam/fonda/tools/impl/AmpliconGatkRealign.java x: 1 contributors (all time) y: 56 lines of code src/main/java/com/epam/fonda/tools/impl/AmpliconGatkRecalibrate.java x: 1 contributors (all time) y: 54 lines of code src/main/java/com/epam/fonda/tools/impl/BwaSort.java x: 2 contributors (all time) y: 92 lines of code src/main/java/com/epam/fonda/tools/impl/ContEst.java x: 1 contributors (all time) y: 89 lines of code src/main/java/com/epam/fonda/tools/impl/DnaPicardQc.java x: 3 contributors (all time) y: 297 lines of code src/main/java/com/epam/fonda/tools/impl/Exomecnv.java x: 1 contributors (all time) y: 84 lines of code src/main/java/com/epam/fonda/tools/impl/FeatureCount.java x: 2 contributors (all time) y: 122 lines of code src/main/java/com/epam/fonda/tools/impl/FusionCatcher.java x: 1 contributors (all time) y: 71 lines of code src/main/java/com/epam/fonda/tools/impl/GatkHaplotypeCaller.java x: 2 contributors (all time) y: 104 lines of code src/main/java/com/epam/fonda/tools/impl/GatkSplitReads.java x: 2 contributors (all time) y: 57 lines of code src/main/java/com/epam/fonda/tools/impl/Mutect1.java x: 1 contributors (all time) y: 82 lines of code src/main/java/com/epam/fonda/tools/impl/PicardMergeDnaBam.java x: 1 contributors (all time) y: 72 lines of code src/main/java/com/epam/fonda/tools/impl/PicardRemoveDuplicate.java x: 1 contributors (all time) y: 44 lines of code src/main/java/com/epam/fonda/tools/impl/RNASeQC.java x: 2 contributors (all time) y: 144 lines of code src/main/java/com/epam/fonda/tools/impl/Sequenza.java x: 1 contributors (all time) y: 80 lines of code src/main/java/com/epam/fonda/tools/impl/SortBamByReadName.java x: 2 contributors (all time) y: 67 lines of code src/main/java/com/epam/fonda/tools/impl/Star.java x: 3 contributors (all time) y: 121 lines of code src/main/java/com/epam/fonda/tools/impl/StarFusion.java x: 2 contributors (all time) y: 112 lines of code src/main/java/com/epam/fonda/utils/PipelineUtils.java x: 3 contributors (all time) y: 217 lines of code src/main/java/com/epam/fonda/workflow/WorkflowFactory.java x: 6 contributors (all time) y: 47 lines of code src/main/java/com/epam/fonda/workflow/impl/Bam2FastqWorkflow.java x: 2 contributors (all time) y: 70 lines of code src/main/java/com/epam/fonda/workflow/impl/DnaVarFastqWorkflow.java x: 3 contributors (all time) y: 137 lines of code src/main/java/com/epam/fonda/workflow/impl/RnaExpressionBamWorkflow.java x: 4 contributors (all time) y: 59 lines of code src/main/java/com/epam/fonda/workflow/stage/impl/SecondaryAnalysis.java x: 3 contributors (all time) y: 315 lines of code src/main/scripts/model/global_config.py x: 1 contributors (all time) y: 52 lines of code src/integrationTest/java/com/epam/fonda/DnaWgsVarBamIntegrationTest.java x: 3 contributors (all time) y: 272 lines of code src/main/java/com/epam/fonda/entity/configuration/GlobalConfig.java x: 1 contributors (all time) y: 234 lines of code src/main/java/com/epam/fonda/entity/configuration/GlobalConfigFormat.java x: 1 contributors (all time) y: 108 lines of code src/main/java/com/epam/fonda/tools/impl/FilterAlignmentArtifacts.java x: 1 contributors (all time) y: 64 lines of code src/main/java/com/epam/fonda/tools/impl/FilterMutectCalls.java x: 1 contributors (all time) y: 76 lines of code src/main/java/com/epam/fonda/tools/impl/PileupSummaries.java x: 1 contributors (all time) y: 62 lines of code src/main/java/com/epam/fonda/tools/results/CalculateContaminationOutput.java x: 1 contributors (all time) y: 9 lines of code src/main/java/com/epam/fonda/tools/results/LearnReadOrientationModelOutput.java x: 1 contributors (all time) y: 8 lines of code src/main/java/com/epam/fonda/tools/results/VariantsVcfOutput.java x: 2 contributors (all time) y: 24 lines of code src/main/java/com/epam/fonda/workflow/stage/impl/PostAlignment.java x: 4 contributors (all time) y: 65 lines of code src/main/scripts/launcher.py x: 1 contributors (all time) y: 45 lines of code src/main/scripts/model/bam_sample_manifest.py x: 1 contributors (all time) y: 13 lines of code src/main/scripts/model/sample_manifest.py x: 1 contributors (all time) y: 86 lines of code src/main/scripts/rna_expression_fastq.py x: 1 contributors (all time) y: 174 lines of code src/integrationTest/java/com/epam/fonda/Bam2FastqIntegrationTest.java x: 3 contributors (all time) y: 112 lines of code src/integrationTest/java/com/epam/fonda/DnaAmpliconVarBamIntegrationTest.java x: 3 contributors (all time) y: 258 lines of code src/integrationTest/java/com/epam/fonda/DnaAmpliconVarFastqIntegrationTest.java x: 3 contributors (all time) y: 170 lines of code src/integrationTest/java/com/epam/fonda/DnaAnalysisIntegrationTest.java x: 4 contributors (all time) y: 173 lines of code src/integrationTest/java/com/epam/fonda/DnaWgsVarFastqIntegrationTest.java x: 2 contributors (all time) y: 66 lines of code src/integrationTest/java/com/epam/fonda/HlaTypingFastqIntegrationTest.java x: 3 contributors (all time) y: 114 lines of code src/integrationTest/java/com/epam/fonda/RnaExpressionBamIntegrationTest.java x: 3 contributors (all time) y: 70 lines of code src/integrationTest/java/com/epam/fonda/RnaFusionFastqIntegrationTest.java x: 2 contributors (all time) y: 87 lines of code src/integrationTest/java/com/epam/fonda/SCRnaExpressionBamIntegrationTest.java x: 3 contributors (all time) y: 164 lines of code src/integrationTest/java/com/epam/fonda/SCRnaExpressionCellRangerFastqIntegrationTest.java x: 3 contributors (all time) y: 109 lines of code src/integrationTest/java/com/epam/fonda/SCRnaExpressionFastqIntegrationTest.java x: 2 contributors (all time) y: 127 lines of code src/integrationTest/java/com/epam/fonda/TcrRepertoireFastqIntegrationTest.java x: 3 contributors (all time) y: 94 lines of code src/main/java/com/epam/fonda/CmdParser.java x: 1 contributors (all time) y: 68 lines of code src/main/java/com/epam/fonda/OptionName.java x: 1 contributors (all time) y: 18 lines of code src/main/java/com/epam/fonda/entity/configuration/orchestrator/ScriptType.java x: 1 contributors (all time) y: 4 lines of code src/main/java/com/epam/fonda/tools/impl/FastqListAnalysis.java x: 2 contributors (all time) y: 73 lines of code src/main/java/com/epam/fonda/tools/impl/QcSummary.java x: 2 contributors (all time) y: 140 lines of code src/main/java/com/epam/fonda/tools/impl/RnaAnalysis.java x: 1 contributors (all time) y: 59 lines of code src/main/java/com/epam/fonda/tools/impl/SCRnaAnalysis.java x: 3 contributors (all time) y: 105 lines of code src/main/java/com/epam/fonda/utils/ConfigurationUtils.java x: 1 contributors (all time) y: 99 lines of code src/main/java/com/epam/fonda/utils/MessageConstant.java x: 1 contributors (all time) y: 36 lines of code src/main/java/com/epam/fonda/workflow/impl/HlaTypingFastqWorkflow.java x: 2 contributors (all time) y: 55 lines of code src/main/java/com/epam/fonda/workflow/impl/RnaExpressionFastqWorkflow.java x: 2 contributors (all time) y: 79 lines of code src/main/java/com/epam/fonda/workflow/impl/RnaFusionFastqWorkflow.java x: 3 contributors (all time) y: 60 lines of code src/main/java/com/epam/fonda/workflow/impl/TcrRepertoireFastqWorkflow.java x: 2 contributors (all time) y: 59 lines of code src/main/java/com/epam/fonda/workflow/PipelineType.java x: 4 contributors (all time) y: 37 lines of code src/main/java/com/epam/fonda/workflow/stage/impl/Alignment.java x: 4 contributors (all time) y: 144 lines of code src/main/scripts/model/study_config.py x: 1 contributors (all time) y: 32 lines of code src/main/scripts/__init__.py x: 1 contributors (all time) y: 1 lines of code src/main/java/com/epam/fonda/tools/impl/SamToFastq.java x: 2 contributors (all time) y: 90 lines of code src/main/java/com/epam/fonda/tools/impl/VcfSnpeffAnnotation.java x: 1 contributors (all time) y: 95 lines of code src/main/java/com/epam/fonda/Main.java x: 2 contributors (all time) y: 32 lines of code src/main/java/com/epam/fonda/tools/impl/OptiType.java x: 2 contributors (all time) y: 84 lines of code src/main/java/com/epam/fonda/tools/impl/Mixcr.java x: 3 contributors (all time) y: 98 lines of code src/main/java/com/epam/fonda/entity/command/AbstractCommand.java x: 2 contributors (all time) y: 22 lines of code src/main/java/com/epam/fonda/workflow/TaskContainer.java x: 1 contributors (all time) y: 20 lines of code src/main/java/com/epam/fonda/utils/AmpliconGatkDatabaseFields.java x: 1 contributors (all time) y: 26 lines of code src/main/java/com/epam/fonda/utils/CellRangerUtils.java x: 1 contributors (all time) y: 35 lines of code src/main/python/dna_rna_variant_qc_metrics.py x: 1 contributors (all time) y: 455 lines of code src/main/python/post_oncotator_cleanup.py x: 1 contributors (all time) y: 169 lines of code src/main/python/rna_qc_metrics.py x: 1 contributors (all time) y: 295 lines of code src/main/python/vcf_annovar_annotation.py x: 1 contributors (all time) y: 668 lines of code src/main/python/vcf_snpeff_annotation.py x: 1 contributors (all time) y: 609 lines of code
703.0
lines of code
  min: 1.0
  average: 78.41
  25th percentile: 16.0
  median: 57.5
  75th percentile: 92.0
  max: 703.0
0 6.0
contributors (all time)
min: 1.0 | average: 1.55 | 25th percentile: 1.0 | median: 1.0 | 75th percentile: 2.0 | max: 6.0

File Size vs. Commits (30 days): 0 points

No data for "commits (30d)" vs. "lines of code".

File Size vs. Contributors (30 days): 0 points

No data for "contributors (30d)" vs. "lines of code".

File Size vs. Commits (90 days): 0 points

No data for "commits (90d)" vs. "lines of code".

File Size vs. Contributors (90 days): 0 points

No data for "contributors (90d)" vs. "lines of code".