epam / fonda
File Age & Freshness

File age measurements show the distribution of file ages (days since the first commit) and the file freshness (days since the latest commit).

Summary
File Change History Overall
File Age Distribution Overall
Days since first update
  • There are 198 files with 15,525 lines of code in files.
    • 198 files that are 366+ days old (15,525 lines of code)
    • 0 files that are 181-365 days old (0 lines of code)
    • 0 files that are 91-180 days old (0 lines of code)
    • 0 files that are 31-90 days old (0 lines of code)
    • 0 files that are 1-30 days old (0 lines of code)
100% | 0% | 0% | 0% | 0%
Legend:
366+
181-365
91-180
31-90
1-30

explore: grouped by folders | grouped by age
File Freshness Distribution Overall
Days since last update
  • There are 198 files with 15,525 lines of code in files.
    • 198 files have been last changed 366+ days ago (15,525 lines of code)
    • 0 files have been last changed 181-365 days ago (0 lines of code)
    • 0 files have been last changed 91-180 days ago (0 lines of code)
    • 0 files have been last changed 31-90 days ago (0 lines of code)
    • 0 files have been last changed 1-30 days ago (0 lines of code)
100% | 0% | 0% | 0% | 0%
Legend:
366+
181-365
91-180
31-90
1-30

explore: grouped by folders | grouped by freshness
File Change History per File Extension
txt, java, py, md, json, r, xml, properties, gradle, yaml, gitignore, bat
File Age Distribution per Extension
Days since first update
366+
181-365
91-180
31-90
1-30
java100% | 0% | 0% | 0% | 0%
py100% | 0% | 0% | 0% | 0%
xml100% | 0% | 0% | 0% | 0%
File Freshness Distribution per Extension
Days since last update
366+
181-365
91-180
31-90
1-30
java100% | 0% | 0% | 0% | 0%
py100% | 0% | 0% | 0% | 0%
xml100% | 0% | 0% | 0% | 0%
File Change History per Logical Decomposition
primary
primary (file age distribution)
Days since first update
366+
181-365
91-180
31-90
1-30
src100% | 0% | 0% | 0% | 0%
config100% | 0% | 0% | 0% | 0%
primary (file freshness distribution)
Days since last update
366+
181-365
91-180
31-90
1-30
src100% | 0% | 0% | 0% | 0%
config100% | 0% | 0% | 0% | 0%
Oldest Files (Top 50)
File# lines# unitscreatedlast modified# changes
(days)		# contributorsfirst
contributor		latest
contributor
pmd-ruleset.xml
in config/pmd
 30 - 2019-12-09 2019-12-09 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
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
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
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
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
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
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
174 2 2019-12-10 2019-12-10 1 1 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
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
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
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
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
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
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
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
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
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...
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
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
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
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
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
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
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
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
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@...
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
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...
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
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
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
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
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
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
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...
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
Files Not Recently Changed (Top 50)
File# lines# unitscreatedlast modified# changes
(days)		# contributorsfirst
contributor		latest
contributor
pmd-ruleset.xml
in config/pmd
 30 - 2019-12-09 2019-12-09 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
__init__.py
in src/main/python
 1 - 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Stage.java
in src/main/java/com/epam/fonda/workflow/stage
 3 - 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Result.java
in src/main/java/com/epam/fonda/tools/results
 3 - 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Tool.java
in src/main/java/com/epam/fonda/tools
 7 - 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
VcfScnpeffAnnotationOutput.java
in src/main/java/com/epam/fonda/tools/results
 8 - 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
FastqOutput.java
in src/main/java/com/epam/fonda/tools/results
 9 - 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
ToolSetConverter.java
in src/main/java/com/epam/fonda/entity/configuration
 10 1 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
DirectoryManager.java
in src/main/java/com/epam/fonda/entity/configuration
 10 1 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
FastqResult.java
in src/main/java/com/epam/fonda/tools/results
 10 - 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
ContEstResult.java
in src/main/java/com/epam/fonda/tools/results
 10 - 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
VcfScnpeffAnnonationResult.java
in src/main/java/com/epam/fonda/tools/results
 10 - 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
PileupResult.java
in src/main/java/com/epam/fonda/tools/results
 10 - 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
RsemResult.java
in src/main/java/com/epam/fonda/tools/results
 11 - 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
ExomecnvResult.java
in src/main/java/com/epam/fonda/tools/results
 11 - 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
SalmonResult.java
in src/main/java/com/epam/fonda/tools/results
 11 - 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
FusionCatcherResult.java
in src/main/java/com/epam/fonda/tools/results
 11 - 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
VariantsVcfResult.java
in src/main/java/com/epam/fonda/tools/results
 11 - 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
SequenzaResult.java
in src/main/java/com/epam/fonda/tools/results
 11 - 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
StringtieResult.java
in src/main/java/com/epam/fonda/tools/results
 11 - 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
BamResult.java
in src/main/java/com/epam/fonda/tools/results
 11 - 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
FeatureCountResult.java
in src/main/java/com/epam/fonda/tools/results
 11 - 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
VdjResult.java
in src/main/java/com/epam/fonda/tools/results
 11 - 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
CufflinksResult.java
in src/main/java/com/epam/fonda/tools/results
 11 - 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
StarFusionResult.java
in src/main/java/com/epam/fonda/tools/results
 11 - 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
MetricsResult.java
in src/main/java/com/epam/fonda/tools/results
 11 - 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
BamWorkflow.java
in src/main/java/com/epam/fonda/workflow
 13 1 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
FastqWorkflow.java
in src/main/java/com/epam/fonda/workflow
 13 1 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
BashCommand.java
in src/main/java/com/epam/fonda/entity/command
 13 2 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
FlagXenomeConverter.java
in src/main/java/com/epam/fonda/entity/configuration
 13 1 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
StudyConfigFormat.java
in src/main/java/com/epam/fonda/entity/configuration
 15 1 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
StarFusionOutput.java
in src/main/java/com/epam/fonda/tools/results
 16 1 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
VdjOutput.java
in src/main/java/com/epam/fonda/tools/results
 16 1 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
FeatureCountOutput.java
in src/main/java/com/epam/fonda/tools/results
 16 1 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
StringtieOutput.java
in src/main/java/com/epam/fonda/tools/results
 17 1 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
FusionCatcherOutput.java
in src/main/java/com/epam/fonda/tools/results
 17 1 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
SalmonOutput.java
in src/main/java/com/epam/fonda/tools/results
 17 1 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
PileupOutput.java
in src/main/java/com/epam/fonda/tools/results
 17 1 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
ContEstOutput.java
in src/main/java/com/epam/fonda/tools/results
 17 1 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
ExomecnvOutput.java
in src/main/java/com/epam/fonda/tools/results
 17 1 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
RsemOutput.java
in src/main/java/com/epam/fonda/tools/results
 17 1 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
CufflinksOutput.java
in src/main/java/com/epam/fonda/tools/results
 17 1 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
SequenzaOutput.java
in src/main/java/com/epam/fonda/tools/results
 19 1 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
BamOutput.java
in src/main/java/com/epam/fonda/tools/results
 19 - 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
MetricsOutput.java
in src/main/java/com/epam/fonda/tools/results
 20 - 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
FondaLauncher.java
in src/main/java/com/epam/fonda
 21 1 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
TemplateEngineUtils.java
in src/main/java/com/epam/fonda/utils
 21 2 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
log4j2.xml
in src/main/resources
 21 - 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
CommonOutdir.java
in src/main/java/com/epam/fonda/entity/configuration
 25 3 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
StudyConfig.java
in src/main/java/com/epam/fonda/entity/configuration
 28 - 2019-12-10 2019-12-10 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
Most Recently Created Files (Top 50)
File# lines# unitscreatedlast modified# changes
(days)		# contributorsfirst
contributor		latest
contributor
TestTemplateUtils.java
in src/integrationTest/java/com/epam/fonda
 50 5 2021-06-17 2021-08-09 2 2 81816946+alekseizaichenkov@... 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
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
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
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
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
LearnReadOrientationModelResult.java
in src/main/java/com/epam/fonda/tools/results
 10 - 2021-05-18 2021-05-18 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
CalculateContaminationResult.java
in src/main/java/com/epam/fonda/tools/results
 10 - 2021-05-18 2021-05-18 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
PileupSummariesResult.java
in src/main/java/com/epam/fonda/tools/results
 10 - 2021-05-18 2021-05-18 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
CalculateContaminationOutput.java
in src/main/java/com/epam/fonda/tools/results
 9 - 2021-05-18 2021-05-18 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
LearnReadOrientationModelOutput.java
in src/main/java/com/epam/fonda/tools/results
 8 - 2021-05-18 2021-05-18 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
MasterScript.java
in src/main/java/com/epam/fonda/entity/configuration/orchestrator
 187 9 2021-04-08 2021-06-17 3 2 yulia_kamyshova@epam.com 81816946+alekseizaichenkov@...
ScriptManager.java
in src/main/java/com/epam/fonda/entity/configuration/orchestrator
 15 1 2021-04-08 2021-06-07 2 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
ScriptType.java
in src/main/java/com/epam/fonda/entity/configuration/orchestrator
 4 - 2021-04-08 2021-04-08 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
sample_utilities.py
in src/main/scripts/model
 14 1 2020-05-29 2020-10-02 3 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
270 3 2020-05-27 2021-09-14 15 2 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
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
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
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
launcher.py
in src/main/scripts
 45 2 2020-05-27 2021-04-26 8 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
study_config.py
in src/main/scripts/model
 32 2 2020-05-27 2020-05-29 2 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
fastq_sample_manifest.py
in src/main/scripts/model
 15 3 2020-05-27 2021-04-12 4 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
bam_sample_manifest.py
in src/main/scripts/model
 13 3 2020-05-27 2021-04-12 3 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
__init__.py
in src/main/scripts
 1 - 2020-05-27 2020-05-27 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
__init__.py
in src/main/scripts/model
 1 - 2020-05-27 2020-05-27 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
EOLConverter.java
in src/main/java/com/epam/fonda/entity/configuration
 13 1 2020-03-12 2020-03-16 2 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
EOLMarker.java
in src/main/java/com/epam/fonda/entity/configuration
 11 - 2020-03-12 2020-03-12 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
RnaCaptureVarFastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 58 2 2020-03-04 2021-04-08 2 2 33068870+ilya-ugr@users.nor... yulia_kamyshova@epam.com
SCRnaExpressionFastqIntegrationTest.java
in src/integrationTest/java/com/epam/fonda
 127 7 2020-03-02 2021-04-08 2 2 49954060+dtegai@users.norep... 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
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
AbraRealign.java
in src/main/java/com/epam/fonda/tools/impl
 81 3 2020-02-21 2021-05-20 2 2 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
HlaTypingFastqWorkflow.java
in src/main/java/com/epam/fonda/workflow/impl
 55 2 2020-02-18 2021-04-08 4 2 30953718+yurysukhorukov@use... 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
TcrRepertoireFastqWorkflow.java
in src/main/java/com/epam/fonda/workflow/impl
 59 2 2020-02-17 2021-04-08 4 2 49245254+karimmagomedov@use... yulia_kamyshova@epam.com
TaskContainer.java
in src/main/java/com/epam/fonda/workflow
 20 3 2020-02-04 2020-02-04 1 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
GatkHaplotypeCallerRnaFilter.java
in src/main/java/com/epam/fonda/tools/impl
 72 4 2020-02-03 2020-03-04 3 2 33068870+ilya-ugr@users.nor... 33068870+ilya-ugr@users.nor...
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...
OptiType.java
in src/main/java/com/epam/fonda/tools/impl
 84 2 2020-01-29 2020-02-14 3 2 30953718+yurysukhorukov@use... 30953718+yurysukhorukov@use...
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
MixcrOutput.java
in src/main/java/com/epam/fonda/tools/results
 19 1 2020-01-29 2020-01-29 1 1 49954060+dtegai@users.norep... 49954060+dtegai@users.norep...
OptiTypeOutput.java
in src/main/java/com/epam/fonda/tools/results
 17 1 2020-01-29 2020-01-29 1 1 30953718+yurysukhorukov@use... 30953718+yurysukhorukov@use...
MixcrResult.java
in src/main/java/com/epam/fonda/tools/results
 11 - 2020-01-29 2020-01-29 1 1 49954060+dtegai@users.norep... 49954060+dtegai@users.norep...
OptiTypeResult.java
in src/main/java/com/epam/fonda/tools/results
 11 - 2020-01-29 2020-01-29 1 1 30953718+yurysukhorukov@use... 30953718+yurysukhorukov@use...
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
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
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
Most Recently Changed Files (Top 50)
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
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
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
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
TestTemplateUtils.java
in src/integrationTest/java/com/epam/fonda
 50 5 2021-06-17 2021-08-09 2 2 81816946+alekseizaichenkov@... yulia_kamyshova@epam.com
MasterScript.java
in src/main/java/com/epam/fonda/entity/configuration/orchestrator
 187 9 2021-04-08 2021-06-17 3 2 yulia_kamyshova@epam.com 81816946+alekseizaichenkov@...
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@...
Workflow.java
in src/main/java/com/epam/fonda/workflow
 29 2 2019-12-10 2021-06-07 4 1 yulia_kamyshova@epam.com yulia_kamyshova@epam.com
ScriptManager.java
in src/main/java/com/epam/fonda/entity/configuration/orchestrator
 15 1 2021-04-08 2021-06-07 2 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
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
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
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
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
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
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
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
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
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
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
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
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
AbraRealign.java
in src/main/java/com/epam/fonda/tools/impl
 81 3 2020-02-21 2021-05-20 2 2 49245254+karimmagomedov@use... 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
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
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
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
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
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
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
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
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
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
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
PicardRemoveDuplicate.java
in src/main/java/com/epam/fonda/tools/impl
 44 1 2019-12-10 2021-05-20 4 1 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
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
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
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
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
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
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
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
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
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