epam / fondaDuplication

Intro

For duplication, we look at places in code where there are 6 or more lines of code that are exactly the same.
Before duplication is calculated, the code is cleaned to remove empty lines, comments, and frequently duplicated constructs such as imports.
You should aim at having as little as possible (<5%) of duplicated code as high-level of duplication can lead to maintenance difficulties, poor factoring, and logical contradictions.

Learn more...

Duplication Overall

20% duplication:

12,449 cleaned lines of cleaned code (without empty lines, comments, and frequently duplicated constructs such as imports)
2,576 duplicated lines

302 duplicates

dependency graphs: 2D graph | 3D graph | 3D graph (with duplicates)...

Duplication per Extension

Duplication per Component (primary)

Longest Duplicates

The list of 50 longest duplicates.

See data for all 302 duplicates...

Size	#	Folders	Files	Lines	Code
181	x 2	src/main/python src/main/python	vcf_annovar_annotation.py vcf_snpeff_annotation.py	128:327 (27%) 123:322 (29%)	view
86	x 2	src/main/python src/main/python	vcf_annovar_annotation.py vcf_snpeff_annotation.py	598:688 (12%) 586:676 (14%)	view
61	x 2	src/main/python src/main/python	vcf_annovar_annotation.py vcf_snpeff_annotation.py	339:404 (9%) 334:398 (10%)	view
33	x 2	src/main/python src/main/python	vcf_annovar_annotation.py vcf_snpeff_annotation.py	606:638 (4%) 644:676 (5%)	view
33	x 2	src/main/python src/main/python	vcf_annovar_annotation.py vcf_annovar_annotation.py	606:638 (4%) 656:688 (4%)	view
33	x 2	src/main/python src/main/python	vcf_snpeff_annotation.py vcf_snpeff_annotation.py	594:626 (5%) 644:676 (5%)	view
33	x 2	src/main/python src/main/python	vcf_annovar_annotation.py vcf_snpeff_annotation.py	656:688 (4%) 594:626 (5%)	view
30	x 2	src/main/python src/main/python	singlecell_doubletdetection.py singlecell_scrublet.py	25:66 (36%) 25:67 (44%)	view
27	x 2	src/main/python src/main/python	vcf_annovar_annotation.py vcf_snpeff_annotation.py	690:718 (4%) 679:707 (4%)	view
24	x 2	src/main/python src/main/python	dna_rna_variant_qc_metrics.py rna_qc_metrics.py	341:364 (5%) 262:285 (8%)	view
22	x 2	src/main/python src/main/python	convert_variant_for_annotation.py convert_variant_for_annotation.py	120:145 (12%) 147:172 (12%)	view
20	x 2	src/main/python src/main/python	dna_rna_variant_qc_metrics.py dna_rna_variant_qc_metrics.py	237:256 (4%) 308:327 (4%)	view
19	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	412:430 (2%) 475:493 (2%)	view
19	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	454:472 (2%) 475:493 (2%)	view
19	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	433:451 (2%) 454:472 (2%)	view
19	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	433:451 (2%) 475:493 (2%)	view
19	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	412:430 (2%) 454:472 (2%)	view
19	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	350:368 (2%) 475:493 (2%)	view
19	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	350:368 (2%) 454:472 (2%)	view
19	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	329:347 (2%) 454:472 (2%)	view
19	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	329:347 (2%) 475:493 (2%)	view
19	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	350:368 (2%) 391:409 (2%)	view
19	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	350:368 (2%) 433:451 (2%)	view
19	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	350:368 (2%) 412:430 (2%)	view
19	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	391:409 (2%) 433:451 (2%)	view
19	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	391:409 (2%) 412:430 (2%)	view
19	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	329:347 (2%) 350:368 (2%)	view
19	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	391:409 (2%) 475:493 (2%)	view
19	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	391:409 (2%) 454:472 (2%)	view
19	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	412:430 (2%) 433:451 (2%)	view
19	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	329:347 (2%) 391:409 (2%)	view
19	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	329:347 (2%) 412:430 (2%)	view
19	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	329:347 (2%) 433:451 (2%)	view
18	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	576:593 (2%) 696:713 (2%)	view
18	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	576:593 (2%) 676:693 (2%)	view
18	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	516:533 (2%) 676:693 (2%)	view
18	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	516:533 (2%) 696:713 (2%)	view
18	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	371:388 (2%) 434:451 (2%)	view
18	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	556:573 (2%) 596:613 (2%)	view
18	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	371:388 (2%) 476:493 (2%)	view
18	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	636:653 (2%) 696:713 (2%)	view
18	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	556:573 (2%) 576:593 (2%)	view
18	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	351:368 (2%) 371:388 (2%)	view
18	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	371:388 (2%) 455:472 (2%)	view
18	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	330:347 (2%) 371:388 (2%)	view
18	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	371:388 (2%) 392:409 (2%)	view
18	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	371:388 (2%) 413:430 (2%)	view
18	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	596:613 (2%) 676:693 (2%)	view
18	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	596:613 (2%) 696:713 (2%)	view
18	x 2	src/integrationTest/java/com/epam/fonda src/integrationTest/java/com/epam/fonda	DnaCaptureVarFastqIntegrationTest.java DnaCaptureVarFastqIntegrationTest.java	516:533 (2%) 536:553 (2%)	view

Duplicated Units

The list of top 4 duplicated units.

See data for all 4 unit duplicates...

Size	#	Folders	Files	Lines	Code
23	x 2	src/main/python src/main/python	singlecell_doubletdetection.py singlecell_scrublet.py	0:0 0:0	view
9	x 2	src/main/java/com/epam/fonda/tools/impl src/main/java/com/epam/fonda/tools/impl	Star.java StarFusion.java	159:169 141:151	view
8	x 2	src/main/java/com/epam/fonda/tools/impl src/main/java/com/epam/fonda/tools/impl	PicardMarkDuplicate.java PicardMergeDnaBam.java	122:131 93:102	view
6	x 2	src/main/java/com/epam/fonda/tools/impl src/main/java/com/epam/fonda/tools/impl	GatkHaplotypeCallerRnaFilter.java GatkSplitReads.java	72:79 79:86	view