epam / fonda
File Change Frequency

File change frequency (churn) shows the distribution of file updates (days with at least one commit).

Overview
File Change Frequency Overall
  • There are 198 files with 15,525 lines of code.
    • 0 files changed more than 100 times (0 lines of code)
    • 0 files changed 51-100 times (0 lines of code)
    • 0 files changed 21-50 times (0 lines of code)
    • 33 files changed 6-20 times (5,329 lines of code)
    • 165 files changed 1-5 times (10,196 lines of code)
0% | 0% | 0% | 34% | 65%
Legend:
101+
51-100
21-50
6-20
1-5

explore: grouped by folders | grouped by update frequency | data
Contributors Count Frequency Overall
  • There are 198 files with 15,525 lines of code.
    • 0 files changed by more than 25 contributors (0 lines of code)
    • 0 files changed by 11-25 contributors (0 lines of code)
    • 2 files changed by 6-10 contributors (750 lines of code)
    • 64 files changed by 2-5 contributors (7,492 lines of code)
    • 132 files changed by 1 contributor (7,283 lines of code)
0% | 0% | 4% | 48% | 46%
Legend:
26+
11-25
6-10
2-5
1

explore: grouped by folders | grouped by contributors count | data
File Change Frequency per File Extension
txt, java, py, md, json, r, xml, properties, gradle, yaml, gitignore, bat
File Change Frequency per Extension
The number of recorded file updates
101+
51-100
21-50
6-20
1-5
java0% | 0% | 0% | 37% | 62%
py0% | 0% | 0% | 23% | 76%
xml0% | 0% | 0% | 0% | 100%
File Change Frequency per Logical Decomposition
primary
primary (file change frequency)
The number of recorded file updates
101+
51-100
21-50
6-20
1-5
src0% | 0% | 0% | 34% | 65%
config0% | 0% | 0% | 0% | 100%
Most Frequently Changed Files (Top 50)

See data for all files...

File# lines# unitscreatedlast modified# changes
(days)		# contributorsfirst
contributor		latest
contributor
270 3 2020-05-27 2021-09-14 15 2 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
WorkflowFactory.java
in src/main/java/com/epam/fonda/workflow
 47 1 2019-12-10 2021-05-20 12 6 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
dna_capture_var_fastq.py
in src/main/scripts
 192 3 2020-05-27 2021-06-02 12 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
PipelineUtils.java
in src/main/java/com/epam/fonda/utils
 217 15 2019-12-10 2021-05-20 12 3 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
QcSummary.java
in src/main/java/com/epam/fonda/tools/impl
 140 4 2019-12-10 2021-04-08 10 2 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
DnaCaptureVarFastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 703 6 2019-12-18 2021-08-09 10 6 ekaterina_kazachkova@epam.com yulia_kamyshova@epam.com
AbstractIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 94 7 2019-12-10 2021-06-15 9 4 yulia_kamyshova@epam.com 81816946+alekseizaichenkov@...
SCRnaExpressionCellRangerFastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 109 8 2019-12-10 2021-04-08 9 3 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
RNASeQC.java
in src/main/java/com/epam/fonda/tools/impl
 144 5 2019-12-10 2021-05-20 9 2 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Count.java
in src/main/java/com/epam/fonda/tools/impl
 149 5 2019-12-10 2021-09-14 9 2 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
rna_expression_fastq.py
in src/main/scripts
 174 3 2020-05-27 2021-04-12 9 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
GlobalConfig.java
in src/main/java/com/epam/fonda/entity/configuration
 234 - 2019-12-10 2021-05-18 9 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
DnaPicardQc.java
in src/main/java/com/epam/fonda/tools/impl
 297 18 2019-12-10 2021-05-20 9 3 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
launcher.py
in src/main/scripts
 45 2 2020-05-27 2021-04-26 8 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
RnaExpressionBamWorkflow.java
in src/main/java/com/epam/fonda/workflow/impl
 59 2 2019-12-10 2021-05-20 8 4 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Star.java
in src/main/java/com/epam/fonda/tools/impl
 121 3 2019-12-10 2021-05-20 8 3 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Alignment.java
in src/main/java/com/epam/fonda/workflow/stage/impl
 144 10 2019-12-10 2020-07-24 8 4 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
SecondaryAnalysis.java
in src/main/java/com/epam/fonda/workflow/stage/impl
 315 20 2019-12-10 2021-05-20 8 3 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
RnaExpressionFastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 392 6 2019-12-10 2021-08-09 8 4 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
PipelineType.java
in src/main/java/com/epam/fonda/workflow
 37 2 2019-12-10 2020-07-24 7 4 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
PostAlignment.java
in src/main/java/com/epam/fonda/workflow/stage/impl
 65 2 2019-12-10 2021-05-18 7 4 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
SCRnaAnalysis.java
in src/main/java/com/epam/fonda/tools/impl
 105 5 2019-12-10 2021-04-08 7 3 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
GlobalConfigFormat.java
in src/main/java/com/epam/fonda/entity/configuration
 108 1 2019-12-10 2021-05-18 7 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
DnaAmpliconVarFastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 170 10 2019-12-10 2021-04-08 7 3 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
global_config.py
in src/main/scripts/model
 52 2 2020-05-27 2021-05-18 6 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
RnaFusionFastqWorkflow.java
in src/main/java/com/epam/fonda/workflow/impl
 60 2 2019-12-10 2021-04-08 6 3 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
PicardMergeDnaBam.java
in src/main/java/com/epam/fonda/tools/impl
 72 3 2019-12-10 2021-05-20 6 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
sample_manifest.py
in src/main/scripts/model
 86 7 2020-05-27 2021-04-12 6 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
NovoalignSort.java
in src/main/java/com/epam/fonda/tools/impl
 103 4 2019-12-10 2021-05-20 6 2 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
GatkHaplotypeCaller.java
in src/main/java/com/epam/fonda/tools/impl
 104 5 2019-12-10 2021-05-20 6 2 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
StarFusion.java
in src/main/java/com/epam/fonda/tools/impl
 112 3 2019-12-10 2021-05-20 6 2 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
DnaVarFastqWorkflow.java
in src/main/java/com/epam/fonda/workflow/impl
 137 5 2019-12-18 2021-05-20 6 3 ekaterina_kazachkova@epam.com yulia_kamyshova@epam.com
DnaWgsVarBamIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 272 8 2020-01-17 2021-05-18 6 3 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
RsemAnnotation.java
in src/main/java/com/epam/fonda/tools/impl
 50 2 2019-12-10 2020-03-12 5 2 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
SCRNASeqDoubletDetection.java
in src/main/java/com/epam/fonda/tools/impl
 65 3 2019-12-10 2020-07-24 5 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Bam2FastqWorkflow.java
in src/main/java/com/epam/fonda/workflow/impl
 70 2 2020-01-24 2021-05-20 5 2 33068870+ilya-ugr@users.nor... yulia_kamyshova@epam.com
DnaVarBamWorkflow.java
in src/main/java/com/epam/fonda/workflow/impl
 81 3 2020-01-17 2021-05-20 5 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
RnaAnalysisUtils.java
in src/main/java/com/epam/fonda/utils
 88 7 2019-12-10 2020-03-12 5 2 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
PicardMarkDuplicate.java
in src/main/java/com/epam/fonda/tools/impl
 90 4 2019-12-10 2021-05-20 5 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Flag.java
in src/main/java/com/epam/fonda/workflow/impl
 92 1 2019-12-10 2020-06-16 5 4 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
BwaSort.java
in src/main/java/com/epam/fonda/tools/impl
 92 3 2019-12-10 2021-05-20 5 2 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Trimmomatic.java
in src/main/java/com/epam/fonda/tools/impl
 93 2 2019-12-10 2020-02-17 5 3 yulia_kamyshova@epam.com 33068870+ilya-ugr@users.nor...
Hisat2.java
in src/main/java/com/epam/fonda/tools/impl
 94 3 2019-12-10 2021-05-20 5 2 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
VcfSnpeffAnnotation.java
in src/main/java/com/epam/fonda/tools/impl
 95 5 2019-12-10 2020-04-17 5 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Bam2FastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 112 8 2020-01-24 2021-04-08 5 3 33068870+ilya-ugr@users.nor... yulia_kamyshova@epam.com
FeatureCount.java
in src/main/java/com/epam/fonda/tools/impl
 122 5 2019-12-10 2021-05-20 5 2 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
DnaAnalysis.java
in src/main/java/com/epam/fonda/tools/impl
 146 8 2019-12-10 2021-04-08 5 2 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
DnaUtils.java
in src/main/java/com/epam/fonda/utils
 149 10 2019-12-10 2020-02-20 5 2 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
DnaAnalysisIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 173 6 2019-12-10 2021-04-08 5 4 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
DnaAmpliconVarBamIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 258 4 2020-01-17 2021-04-08 5 3 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Files With Most Contributors (Top 50)
Based on the number of unique email addresses found in commits.

See data for all files...

File# lines# unitscreatedlast modified# changes
(days)		# contributorsfirst
contributor		latest
contributor
WorkflowFactory.java
in src/main/java/com/epam/fonda/workflow
 47 1 2019-12-10 2021-05-20 12 6 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
DnaCaptureVarFastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 703 6 2019-12-18 2021-08-09 10 6 ekaterina_kazachkova@epam.com yulia_kamyshova@epam.com
AbstractIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 94 7 2019-12-10 2021-06-15 9 4 yulia_kamyshova@epam.com 81816946+alekseizaichenkov@...
RnaExpressionFastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 392 6 2019-12-10 2021-08-09 8 4 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
RnaExpressionBamWorkflow.java
in src/main/java/com/epam/fonda/workflow/impl
 59 2 2019-12-10 2021-05-20 8 4 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Alignment.java
in src/main/java/com/epam/fonda/workflow/stage/impl
 144 10 2019-12-10 2020-07-24 8 4 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
PipelineType.java
in src/main/java/com/epam/fonda/workflow
 37 2 2019-12-10 2020-07-24 7 4 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
PostAlignment.java
in src/main/java/com/epam/fonda/workflow/stage/impl
 65 2 2019-12-10 2021-05-18 7 4 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
DnaAnalysisIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 173 6 2019-12-10 2021-04-08 5 4 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Flag.java
in src/main/java/com/epam/fonda/workflow/impl
 92 1 2019-12-10 2020-06-16 5 4 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
PipelineUtils.java
in src/main/java/com/epam/fonda/utils
 217 15 2019-12-10 2021-05-20 12 3 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
SCRnaExpressionCellRangerFastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 109 8 2019-12-10 2021-04-08 9 3 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
DnaPicardQc.java
in src/main/java/com/epam/fonda/tools/impl
 297 18 2019-12-10 2021-05-20 9 3 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Star.java
in src/main/java/com/epam/fonda/tools/impl
 121 3 2019-12-10 2021-05-20 8 3 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
SecondaryAnalysis.java
in src/main/java/com/epam/fonda/workflow/stage/impl
 315 20 2019-12-10 2021-05-20 8 3 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
DnaAmpliconVarFastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 170 10 2019-12-10 2021-04-08 7 3 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
SCRnaAnalysis.java
in src/main/java/com/epam/fonda/tools/impl
 105 5 2019-12-10 2021-04-08 7 3 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
DnaWgsVarBamIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 272 8 2020-01-17 2021-05-18 6 3 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
DnaVarFastqWorkflow.java
in src/main/java/com/epam/fonda/workflow/impl
 137 5 2019-12-18 2021-05-20 6 3 ekaterina_kazachkova@epam.com yulia_kamyshova@epam.com
RnaFusionFastqWorkflow.java
in src/main/java/com/epam/fonda/workflow/impl
 60 2 2019-12-10 2021-04-08 6 3 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
DnaAmpliconVarBamIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 258 4 2020-01-17 2021-04-08 5 3 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Bam2FastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 112 8 2020-01-24 2021-04-08 5 3 33068870+ilya-ugr@users.nor... yulia_kamyshova@epam.com
Trimmomatic.java
in src/main/java/com/epam/fonda/tools/impl
 93 2 2019-12-10 2020-02-17 5 3 yulia_kamyshova@epam.com 33068870+ilya-ugr@users.nor...
RnaExpressionBamIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 70 2 2019-12-10 2021-04-08 4 3 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
TcrRepertoireFastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 94 5 2020-02-17 2021-04-08 3 3 49245254+karimmagomedov@use... yulia_kamyshova@epam.com
HlaTypingFastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 114 4 2020-02-18 2021-04-08 3 3 30953718+yurysukhorukov@use... yulia_kamyshova@epam.com
SCRnaExpressionBamIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 164 7 2020-02-21 2021-04-08 3 3 49245254+karimmagomedov@use... yulia_kamyshova@epam.com
Mixcr.java
in src/main/java/com/epam/fonda/tools/impl
 98 2 2020-01-29 2020-02-13 3 3 49954060+dtegai@users.norep... 49245254+karimmagomedov@use...
270 3 2020-05-27 2021-09-14 15 2 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
QcSummary.java
in src/main/java/com/epam/fonda/tools/impl
 140 4 2019-12-10 2021-04-08 10 2 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
RNASeQC.java
in src/main/java/com/epam/fonda/tools/impl
 144 5 2019-12-10 2021-05-20 9 2 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Count.java
in src/main/java/com/epam/fonda/tools/impl
 149 5 2019-12-10 2021-09-14 9 2 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
StarFusion.java
in src/main/java/com/epam/fonda/tools/impl
 112 3 2019-12-10 2021-05-20 6 2 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
GatkHaplotypeCaller.java
in src/main/java/com/epam/fonda/tools/impl
 104 5 2019-12-10 2021-05-20 6 2 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
NovoalignSort.java
in src/main/java/com/epam/fonda/tools/impl
 103 4 2019-12-10 2021-05-20 6 2 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
FeatureCount.java
in src/main/java/com/epam/fonda/tools/impl
 122 5 2019-12-10 2021-05-20 5 2 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
BwaSort.java
in src/main/java/com/epam/fonda/tools/impl
 92 3 2019-12-10 2021-05-20 5 2 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
DnaAnalysis.java
in src/main/java/com/epam/fonda/tools/impl
 146 8 2019-12-10 2021-04-08 5 2 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
RsemAnnotation.java
in src/main/java/com/epam/fonda/tools/impl
 50 2 2019-12-10 2020-03-12 5 2 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Hisat2.java
in src/main/java/com/epam/fonda/tools/impl
 94 3 2019-12-10 2021-05-20 5 2 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
RnaAnalysisUtils.java
in src/main/java/com/epam/fonda/utils
 88 7 2019-12-10 2020-03-12 5 2 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
DnaUtils.java
in src/main/java/com/epam/fonda/utils
 149 10 2019-12-10 2020-02-20 5 2 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Bam2FastqWorkflow.java
in src/main/java/com/epam/fonda/workflow/impl
 70 2 2020-01-24 2021-05-20 5 2 33068870+ilya-ugr@users.nor... yulia_kamyshova@epam.com
DnaCaptureVarBamIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 149 7 2020-01-17 2021-04-08 4 2 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
RnaFusionFastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 87 3 2019-12-10 2021-04-08 4 2 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
DnaWgsVarFastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 66 3 2020-02-26 2021-04-08 4 2 49245254+karimmagomedov@use... yulia_kamyshova@epam.com
GatkSplitReads.java
in src/main/java/com/epam/fonda/tools/impl
 57 2 2020-01-29 2021-05-20 4 2 33068870+ilya-ugr@users.nor... yulia_kamyshova@epam.com
Xenome.java
in src/main/java/com/epam/fonda/tools/impl
 123 2 2019-12-10 2020-05-12 4 2 yulia_kamyshova@epam.com 62957240+syansanofi@users.n...
Strelka2.java
in src/main/java/com/epam/fonda/tools/impl
 87 3 2019-12-10 2020-02-11 4 2 yulia_kamyshova@epam.com 49954060+dtegai@users.norep...
SortBamByReadName.java
in src/main/java/com/epam/fonda/tools/impl
 67 3 2019-12-24 2021-05-20 4 2 33068870+ilya-ugr@users.nor... yulia_kamyshova@epam.com
Files With Least Contributors (Top 50)
Based on the number of unique email addresses found in commits.

See data for all files...

File# lines# unitscreatedlast modified# changes
(days)		# contributorsfirst
contributor		latest
contributor
vcf_annovar_annotation.py
in src/main/python
 668 8 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
vcf_snpeff_annotation.py
in src/main/python
 609 9 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
455 4 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
rna_qc_metrics.py
in src/main/python
 295 3 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
GlobalConfig.java
in src/main/java/com/epam/fonda/entity/configuration
 234 - 2019-12-10 2021-05-18 9 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
dna_capture_var_fastq.py
in src/main/scripts
 192 3 2020-05-27 2021-06-02 12 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
174 2 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
rna_expression_fastq.py
in src/main/scripts
 174 3 2020-05-27 2021-04-12 9 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
post_oncotator_cleanup.py
in src/main/python
 169 2 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
GlobalConfigFormat.java
in src/main/java/com/epam/fonda/entity/configuration
 108 1 2019-12-10 2021-05-18 7 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
ConfigurationUtils.java
in src/main/java/com/epam/fonda/utils
 99 9 2019-12-10 2021-04-08 3 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
VcfSnpeffAnnotation.java
in src/main/java/com/epam/fonda/tools/impl
 95 5 2019-12-10 2020-04-17 5 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
PicardMarkDuplicate.java
in src/main/java/com/epam/fonda/tools/impl
 90 4 2019-12-10 2021-05-20 5 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
ContEst.java
in src/main/java/com/epam/fonda/tools/impl
 89 3 2019-12-10 2021-05-20 4 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
88 3 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
SeqPurge.java
in src/main/java/com/epam/fonda/tools/impl
 87 2 2019-12-10 2020-06-04 4 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Pileup.java
in src/main/java/com/epam/fonda/tools/impl
 87 3 2019-12-10 2020-02-04 4 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
sample_manifest.py
in src/main/scripts/model
 86 7 2020-05-27 2021-04-12 6 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Lofreq.java
in src/main/java/com/epam/fonda/tools/impl
 85 3 2019-12-10 2020-02-04 3 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Vdj.java
in src/main/java/com/epam/fonda/tools/impl
 85 3 2019-12-10 2020-07-24 4 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Salmon.java
in src/main/java/com/epam/fonda/tools/impl
 85 2 2019-12-10 2020-02-04 3 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Mutect2.java
in src/main/java/com/epam/fonda/tools/impl
 84 2 2019-12-10 2021-05-18 4 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Exomecnv.java
in src/main/java/com/epam/fonda/tools/impl
 84 3 2019-12-10 2021-05-20 3 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Mutect1.java
in src/main/java/com/epam/fonda/tools/impl
 82 2 2019-12-10 2021-05-20 3 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
DnaVarBamWorkflow.java
in src/main/java/com/epam/fonda/workflow/impl
 81 3 2020-01-17 2021-05-20 5 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Vardict.java
in src/main/java/com/epam/fonda/tools/impl
 80 3 2019-12-10 2020-02-04 2 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Sequenza.java
in src/main/java/com/epam/fonda/tools/impl
 80 3 2019-12-10 2021-05-20 3 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Cufflinks.java
in src/main/java/com/epam/fonda/tools/impl
 78 2 2019-12-10 2020-02-04 3 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Scalpel.java
in src/main/java/com/epam/fonda/tools/impl
 77 3 2019-12-10 2020-02-04 2 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
FilterMutectCalls.java
in src/main/java/com/epam/fonda/tools/impl
 76 2 2021-05-18 2021-05-18 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
singlecell_scrublet.py
in src/main/python
 73 2 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Freebayes.java
in src/main/java/com/epam/fonda/tools/impl
 73 2 2019-12-10 2020-02-04 3 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
PicardMergeDnaBam.java
in src/main/java/com/epam/fonda/tools/impl
 72 3 2019-12-10 2021-05-20 6 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Stringtie.java
in src/main/java/com/epam/fonda/tools/impl
 71 2 2019-12-10 2020-02-04 3 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
FusionCatcher.java
in src/main/java/com/epam/fonda/tools/impl
 71 2 2019-12-10 2021-05-20 4 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
SCRnaExpressionCellRangerFastqWorkflow.java
in src/main/java/com/epam/fonda/workflow/impl
 70 2 2019-12-10 2021-04-08 4 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
CmdParser.java
in src/main/java/com/epam/fonda
 68 3 2019-12-10 2021-04-08 2 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
SCRNASeqDoubletDetection.java
in src/main/java/com/epam/fonda/tools/impl
 65 3 2019-12-10 2020-07-24 5 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
FilterAlignmentArtifacts.java
in src/main/java/com/epam/fonda/tools/impl
 64 2 2021-05-18 2021-05-18 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
PileupSummaries.java
in src/main/java/com/epam/fonda/tools/impl
 62 2 2021-05-18 2021-05-18 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
RnaAnalysis.java
in src/main/java/com/epam/fonda/tools/impl
 59 2 2019-12-10 2021-04-08 2 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
CalculateContamination.java
in src/main/java/com/epam/fonda/tools/impl
 58 2 2021-05-18 2021-05-18 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
AmpliconGatkRealign.java
in src/main/java/com/epam/fonda/tools/impl
 56 2 2019-12-10 2021-05-20 3 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
LearnReadOrientationModel.java
in src/main/java/com/epam/fonda/tools/impl
 55 2 2021-05-18 2021-05-18 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Executor.java
in src/main/java/com/epam/fonda
 55 3 2019-12-10 2021-04-26 2 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
rna_gene_annotation.py
in src/main/python
 54 2 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
AmpliconGatkRecalibrate.java
in src/main/java/com/epam/fonda/tools/impl
 54 2 2019-12-10 2021-05-20 4 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
global_config.py
in src/main/scripts/model
 52 2 2020-05-27 2021-05-18 6 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
GatkSortSam.java
in src/main/java/com/epam/fonda/tools/impl
 51 1 2021-05-18 2021-05-18 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
RnaMutationAnalysis.java
in src/main/java/com/epam/fonda/tools/impl
 47 2 2019-12-10 2021-04-08 2 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Correlations

File Size vs. Number of Changes: 198 points

src/main/java/com/epam/fonda/tools/impl/Count.java x: 149 lines of code y: 9 # changes src/main/scripts/sc_rna_expression_cellranger_fastq.py x: 270 lines of code y: 15 # changes src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java x: 703 lines of code y: 10 # changes src/integrationTest/java/com/epam/fonda/RnaExpressionFastqIntegrationTest.java x: 392 lines of code y: 8 # changes src/integrationTest/java/com/epam/fonda/TestTemplateUtils.java x: 50 lines of code y: 2 # changes src/main/java/com/epam/fonda/entity/configuration/orchestrator/MasterScript.java x: 187 lines of code y: 3 # changes src/integrationTest/java/com/epam/fonda/AbstractIntegrationTest.java x: 94 lines of code y: 9 # changes src/main/java/com/epam/fonda/entity/configuration/orchestrator/ScriptManager.java x: 15 lines of code y: 2 # changes src/main/java/com/epam/fonda/workflow/Workflow.java x: 29 lines of code y: 4 # changes src/main/scripts/dna_capture_var_fastq.py x: 192 lines of code y: 12 # changes src/main/java/com/epam/fonda/tools/impl/AbraRealign.java x: 81 lines of code y: 2 # changes src/main/java/com/epam/fonda/tools/impl/AmpliconGatkRealign.java x: 56 lines of code y: 3 # changes src/main/java/com/epam/fonda/tools/impl/AmpliconGatkRecalibrate.java x: 54 lines of code y: 4 # changes src/main/java/com/epam/fonda/tools/impl/BwaSort.java x: 92 lines of code y: 5 # changes src/main/java/com/epam/fonda/tools/impl/ContEst.java x: 89 lines of code y: 4 # changes src/main/java/com/epam/fonda/tools/impl/DnaPicardQc.java x: 297 lines of code y: 9 # changes src/main/java/com/epam/fonda/tools/impl/Exomecnv.java x: 84 lines of code y: 3 # changes src/main/java/com/epam/fonda/tools/impl/FeatureCount.java x: 122 lines of code y: 5 # changes src/main/java/com/epam/fonda/tools/impl/FusionCatcher.java x: 71 lines of code y: 4 # changes src/main/java/com/epam/fonda/tools/impl/GatkHaplotypeCaller.java x: 104 lines of code y: 6 # changes src/main/java/com/epam/fonda/tools/impl/GatkSplitReads.java x: 57 lines of code y: 4 # changes src/main/java/com/epam/fonda/tools/impl/Hisat2.java x: 94 lines of code y: 5 # changes src/main/java/com/epam/fonda/tools/impl/Mutect1.java x: 82 lines of code y: 3 # changes src/main/java/com/epam/fonda/tools/impl/PicardMarkDuplicate.java x: 90 lines of code y: 5 # changes src/main/java/com/epam/fonda/tools/impl/PicardMergeDnaBam.java x: 72 lines of code y: 6 # changes src/main/java/com/epam/fonda/tools/impl/PicardRemoveDuplicate.java x: 44 lines of code y: 4 # changes src/main/java/com/epam/fonda/tools/impl/RNASeQC.java x: 144 lines of code y: 9 # changes src/main/java/com/epam/fonda/tools/impl/Sequenza.java x: 80 lines of code y: 3 # changes src/main/java/com/epam/fonda/tools/impl/SortBamByReadName.java x: 67 lines of code y: 4 # changes src/main/java/com/epam/fonda/tools/impl/Star.java x: 121 lines of code y: 8 # changes src/main/java/com/epam/fonda/tools/impl/StarFusion.java x: 112 lines of code y: 6 # changes src/main/java/com/epam/fonda/utils/PipelineUtils.java x: 217 lines of code y: 12 # changes src/main/java/com/epam/fonda/workflow/WorkflowFactory.java x: 47 lines of code y: 12 # changes src/main/java/com/epam/fonda/workflow/impl/Bam2FastqWorkflow.java x: 70 lines of code y: 5 # changes src/main/java/com/epam/fonda/workflow/impl/DnaVarBamWorkflow.java x: 81 lines of code y: 5 # changes src/main/java/com/epam/fonda/workflow/impl/DnaVarFastqWorkflow.java x: 137 lines of code y: 6 # changes src/main/java/com/epam/fonda/workflow/impl/RnaExpressionBamWorkflow.java x: 59 lines of code y: 8 # changes src/main/java/com/epam/fonda/workflow/stage/impl/SecondaryAnalysis.java x: 315 lines of code y: 8 # changes src/main/scripts/model/global_config.py x: 52 lines of code y: 6 # changes src/integrationTest/java/com/epam/fonda/DnaWgsVarBamIntegrationTest.java x: 272 lines of code y: 6 # changes src/main/java/com/epam/fonda/entity/configuration/GlobalConfig.java x: 234 lines of code y: 9 # changes src/main/java/com/epam/fonda/entity/configuration/GlobalConfigFormat.java x: 108 lines of code y: 7 # changes src/main/java/com/epam/fonda/tools/impl/CalculateContamination.java x: 58 lines of code y: 1 # changes src/main/java/com/epam/fonda/tools/impl/FilterAlignmentArtifacts.java x: 64 lines of code y: 1 # changes src/main/java/com/epam/fonda/tools/impl/FilterMutectCalls.java x: 76 lines of code y: 1 # changes src/main/java/com/epam/fonda/tools/impl/GatkSortSam.java x: 51 lines of code y: 1 # changes src/main/java/com/epam/fonda/tools/impl/LearnReadOrientationModel.java x: 55 lines of code y: 1 # changes src/main/java/com/epam/fonda/tools/impl/Mutect2.java x: 84 lines of code y: 4 # changes src/main/java/com/epam/fonda/tools/impl/PileupSummaries.java x: 62 lines of code y: 1 # changes src/main/java/com/epam/fonda/tools/results/CalculateContaminationOutput.java x: 9 lines of code y: 1 # changes src/main/java/com/epam/fonda/tools/results/LearnReadOrientationModelOutput.java x: 8 lines of code y: 1 # changes src/main/java/com/epam/fonda/tools/results/VariantsVcfOutput.java x: 24 lines of code y: 3 # changes src/main/java/com/epam/fonda/workflow/stage/impl/PostAlignment.java x: 65 lines of code y: 7 # changes src/main/java/com/epam/fonda/Executor.java x: 55 lines of code y: 2 # changes src/main/scripts/launcher.py x: 45 lines of code y: 8 # changes src/main/scripts/model/bam_sample_manifest.py x: 13 lines of code y: 3 # changes src/main/scripts/model/fastq_sample_manifest.py x: 15 lines of code y: 4 # changes src/main/scripts/model/sample_manifest.py x: 86 lines of code y: 6 # changes src/main/scripts/rna_expression_fastq.py x: 174 lines of code y: 9 # changes src/integrationTest/java/com/epam/fonda/Bam2FastqIntegrationTest.java x: 112 lines of code y: 5 # changes src/integrationTest/java/com/epam/fonda/DnaAmpliconVarBamIntegrationTest.java x: 258 lines of code y: 5 # changes src/integrationTest/java/com/epam/fonda/DnaAmpliconVarFastqIntegrationTest.java x: 170 lines of code y: 7 # changes src/integrationTest/java/com/epam/fonda/DnaAnalysisIntegrationTest.java x: 173 lines of code y: 5 # changes src/integrationTest/java/com/epam/fonda/DnaCaptureVarBamIntegrationTest.java x: 149 lines of code y: 4 # changes src/integrationTest/java/com/epam/fonda/HlaTypingFastqIntegrationTest.java x: 114 lines of code y: 3 # changes src/integrationTest/java/com/epam/fonda/RnaCaptureVarFastqIntegrationTest.java x: 58 lines of code y: 2 # changes src/integrationTest/java/com/epam/fonda/RnaFusionFastqIntegrationTest.java x: 87 lines of code y: 4 # changes src/integrationTest/java/com/epam/fonda/SCRnaExpressionBamIntegrationTest.java x: 164 lines of code y: 3 # changes src/integrationTest/java/com/epam/fonda/SCRnaExpressionCellRangerFastqIntegrationTest.java x: 109 lines of code y: 9 # changes src/integrationTest/java/com/epam/fonda/SCRnaExpressionFastqIntegrationTest.java x: 127 lines of code y: 2 # changes src/integrationTest/java/com/epam/fonda/TcrRepertoireFastqIntegrationTest.java x: 94 lines of code y: 3 # changes src/main/java/com/epam/fonda/CmdParser.java x: 68 lines of code y: 2 # changes src/main/java/com/epam/fonda/OptionName.java x: 18 lines of code y: 2 # changes src/main/java/com/epam/fonda/entity/configuration/Configuration.java x: 13 lines of code y: 2 # changes src/main/java/com/epam/fonda/entity/configuration/orchestrator/ScriptType.java x: 4 lines of code y: 1 # changes src/main/java/com/epam/fonda/tools/PostProcessTool.java x: 7 lines of code y: 2 # changes src/main/java/com/epam/fonda/tools/impl/DnaAnalysis.java x: 146 lines of code y: 5 # changes src/main/java/com/epam/fonda/tools/impl/FastqListAnalysis.java x: 73 lines of code y: 4 # changes src/main/java/com/epam/fonda/tools/impl/QcSummary.java x: 140 lines of code y: 10 # changes src/main/java/com/epam/fonda/tools/impl/RnaAnalysis.java x: 59 lines of code y: 2 # changes src/main/java/com/epam/fonda/tools/impl/RnaMutationAnalysis.java x: 47 lines of code y: 2 # changes src/main/java/com/epam/fonda/tools/impl/SCRnaAnalysis.java x: 105 lines of code y: 7 # changes src/main/java/com/epam/fonda/utils/ConfigurationUtils.java x: 99 lines of code y: 3 # changes src/main/java/com/epam/fonda/utils/MessageConstant.java x: 36 lines of code y: 3 # changes src/main/java/com/epam/fonda/workflow/impl/HlaTypingFastqWorkflow.java x: 55 lines of code y: 4 # changes src/main/java/com/epam/fonda/workflow/impl/RnaExpressionFastqWorkflow.java x: 79 lines of code y: 4 # changes src/main/java/com/epam/fonda/workflow/impl/RnaFusionFastqWorkflow.java x: 60 lines of code y: 6 # changes src/main/java/com/epam/fonda/workflow/impl/TcrRepertoireFastqWorkflow.java x: 59 lines of code y: 4 # changes src/main/java/com/epam/fonda/utils/ToolUtils.java x: 37 lines of code y: 3 # changes src/main/scripts/model/sample_utilities.py x: 14 lines of code y: 3 # changes src/main/java/com/epam/fonda/tools/impl/SCRNASeqDoubletDetection.java x: 65 lines of code y: 5 # changes src/main/java/com/epam/fonda/workflow/PipelineType.java x: 37 lines of code y: 7 # changes src/main/java/com/epam/fonda/workflow/stage/impl/Alignment.java x: 144 lines of code y: 8 # changes src/main/scripts/model/study_config.py x: 32 lines of code y: 2 # changes src/main/scripts/__init__.py x: 1 lines of code y: 1 # changes src/main/java/com/epam/fonda/tools/impl/Xenome.java x: 123 lines of code y: 4 # changes src/main/java/com/epam/fonda/tools/impl/SamToFastq.java x: 90 lines of code y: 3 # changes src/main/java/com/epam/fonda/entity/configuration/EOLMarker.java x: 11 lines of code y: 1 # changes src/main/java/com/epam/fonda/tools/impl/RsemAnnotation.java x: 50 lines of code y: 5 # changes src/main/java/com/epam/fonda/utils/RnaAnalysisUtils.java x: 88 lines of code y: 5 # changes src/main/java/com/epam/fonda/tools/impl/GatkHaplotypeCallerRnaFilter.java x: 72 lines of code y: 3 # changes src/main/java/com/epam/fonda/Main.java x: 32 lines of code y: 3 # changes src/main/java/com/epam/fonda/tools/impl/RsemExpression.java x: 68 lines of code y: 4 # changes src/main/java/com/epam/fonda/utils/DnaUtils.java x: 149 lines of code y: 5 # changes src/main/java/com/epam/fonda/tools/impl/Trimmomatic.java x: 93 lines of code y: 5 # changes src/main/java/com/epam/fonda/tools/impl/Mixcr.java x: 98 lines of code y: 3 # changes src/main/java/com/epam/fonda/entity/command/AbstractCommand.java x: 22 lines of code y: 2 # changes src/main/java/com/epam/fonda/tools/impl/Cufflinks.java x: 78 lines of code y: 3 # changes src/main/java/com/epam/fonda/tools/impl/Freebayes.java x: 73 lines of code y: 3 # changes src/main/java/com/epam/fonda/tools/impl/Scalpel.java x: 77 lines of code y: 2 # changes src/main/java/com/epam/fonda/tools/impl/Stringtie.java x: 71 lines of code y: 3 # changes src/main/java/com/epam/fonda/workflow/TaskContainer.java x: 20 lines of code y: 1 # changes src/main/java/com/epam/fonda/tools/results/MixcrOutput.java x: 19 lines of code y: 1 # changes src/main/java/com/epam/fonda/tools/results/OptiTypeOutput.java x: 17 lines of code y: 1 # changes src/main/java/com/epam/fonda/utils/AmpliconGatkDatabaseFields.java x: 26 lines of code y: 2 # changes src/main/java/com/epam/fonda/FondaLauncher.java x: 21 lines of code y: 1 # changes src/main/java/com/epam/fonda/entity/command/BashCommand.java x: 13 lines of code y: 1 # changes src/main/java/com/epam/fonda/entity/configuration/CommonOutdir.java x: 25 lines of code y: 1 # changes src/main/java/com/epam/fonda/entity/configuration/StudyConfig.java x: 28 lines of code y: 1 # changes src/main/java/com/epam/fonda/entity/configuration/StudyConfigFormat.java x: 15 lines of code y: 1 # changes src/main/java/com/epam/fonda/tools/Tool.java x: 7 lines of code y: 1 # changes src/main/java/com/epam/fonda/tools/results/FeatureCountOutput.java x: 16 lines of code y: 1 # changes src/main/java/com/epam/fonda/tools/results/Result.java x: 3 lines of code y: 1 # changes src/main/java/com/epam/fonda/utils/CellRangerUtils.java x: 35 lines of code y: 1 # changes src/main/java/com/epam/fonda/workflow/stage/impl/PreAlignment.java x: 36 lines of code y: 1 # changes src/main/python/convert_variant_for_annotation.py x: 174 lines of code y: 1 # changes src/main/python/dna_rna_variant_qc_metrics.py x: 455 lines of code y: 1 # changes src/main/python/post_oncotator_cleanup.py x: 169 lines of code y: 1 # changes src/main/python/rna_gene_annotation.py x: 54 lines of code y: 1 # changes src/main/python/rna_qc_metrics.py x: 295 lines of code y: 1 # changes src/main/python/singlecell_doubletdetection.py x: 88 lines of code y: 1 # changes src/main/python/singlecell_scrublet.py x: 73 lines of code y: 1 # changes src/main/python/vcf_annovar_annotation.py x: 668 lines of code y: 1 # changes src/main/python/vcf_snpeff_annotation.py x: 609 lines of code y: 1 # changes config/pmd/pmd-ruleset.xml x: 30 lines of code y: 1 # changes
15.0
# changes
  min: 1.0
  average: 3.25
  25th percentile: 1.0
  median: 2.0
  75th percentile: 5.0
  max: 15.0
0 703.0
lines of code
min: 1.0 | average: 78.41 | 25th percentile: 16.0 | median: 57.5 | 75th percentile: 92.0 | max: 703.0

Number of Contributors vs. Number of Changes: 198 points

src/main/java/com/epam/fonda/tools/impl/Count.java x: 2 # contributors y: 9 # changes src/main/scripts/sc_rna_expression_cellranger_fastq.py x: 2 # contributors y: 15 # changes src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java x: 6 # contributors y: 10 # changes src/integrationTest/java/com/epam/fonda/RnaExpressionFastqIntegrationTest.java x: 4 # contributors y: 8 # changes src/integrationTest/java/com/epam/fonda/TestTemplateUtils.java x: 2 # contributors y: 2 # changes src/main/java/com/epam/fonda/entity/configuration/orchestrator/MasterScript.java x: 2 # contributors y: 3 # changes src/integrationTest/java/com/epam/fonda/AbstractIntegrationTest.java x: 4 # contributors y: 9 # changes src/main/java/com/epam/fonda/entity/configuration/orchestrator/ScriptManager.java x: 1 # contributors y: 2 # changes src/main/java/com/epam/fonda/workflow/Workflow.java x: 1 # contributors y: 4 # changes src/main/scripts/dna_capture_var_fastq.py x: 1 # contributors y: 12 # changes src/main/java/com/epam/fonda/tools/impl/AmpliconGatkRealign.java x: 1 # contributors y: 3 # changes src/main/java/com/epam/fonda/tools/impl/BwaSort.java x: 2 # contributors y: 5 # changes src/main/java/com/epam/fonda/tools/impl/DnaPicardQc.java x: 3 # contributors y: 9 # changes src/main/java/com/epam/fonda/tools/impl/GatkHaplotypeCaller.java x: 2 # contributors y: 6 # changes src/main/java/com/epam/fonda/tools/impl/GatkSplitReads.java x: 2 # contributors y: 4 # changes src/main/java/com/epam/fonda/tools/impl/PicardMarkDuplicate.java x: 1 # contributors y: 5 # changes src/main/java/com/epam/fonda/tools/impl/PicardMergeDnaBam.java x: 1 # contributors y: 6 # changes src/main/java/com/epam/fonda/tools/impl/Star.java x: 3 # contributors y: 8 # changes src/main/java/com/epam/fonda/utils/PipelineUtils.java x: 3 # contributors y: 12 # changes src/main/java/com/epam/fonda/workflow/WorkflowFactory.java x: 6 # contributors y: 12 # changes src/main/java/com/epam/fonda/workflow/impl/DnaVarFastqWorkflow.java x: 3 # contributors y: 6 # changes src/main/java/com/epam/fonda/entity/configuration/GlobalConfig.java x: 1 # contributors y: 9 # changes src/main/java/com/epam/fonda/entity/configuration/GlobalConfigFormat.java x: 1 # contributors y: 7 # changes src/main/java/com/epam/fonda/tools/impl/CalculateContamination.java x: 1 # contributors y: 1 # changes src/main/java/com/epam/fonda/workflow/stage/impl/PostAlignment.java x: 4 # contributors y: 7 # changes src/main/scripts/launcher.py x: 1 # contributors y: 8 # changes src/integrationTest/java/com/epam/fonda/Bam2FastqIntegrationTest.java x: 3 # contributors y: 5 # changes src/integrationTest/java/com/epam/fonda/DnaAmpliconVarFastqIntegrationTest.java x: 3 # contributors y: 7 # changes src/integrationTest/java/com/epam/fonda/DnaAnalysisIntegrationTest.java x: 4 # contributors y: 5 # changes src/integrationTest/java/com/epam/fonda/HlaTypingFastqIntegrationTest.java x: 3 # contributors y: 3 # changes src/integrationTest/java/com/epam/fonda/RnaExpressionBamIntegrationTest.java x: 3 # contributors y: 4 # changes src/main/java/com/epam/fonda/tools/impl/QcSummary.java x: 2 # contributors y: 10 # changes
15.0
# changes
  min: 1.0
  average: 3.25
  25th percentile: 1.0
  median: 2.0
  75th percentile: 5.0
  max: 15.0
0 6.0
# contributors
min: 1.0 | average: 1.55 | 25th percentile: 1.0 | median: 1.0 | 75th percentile: 2.0 | max: 6.0

Number of Contributors vs. File Size: 198 points

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