duplicated block id: 1 size: 181 cleaned lines of code in 2 files: - src/main/python/vcf_annovar_annotation.py (128:327) - src/main/python/vcf_snpeff_annotation.py (123:322) duplicated block id: 2 size: 86 cleaned lines of code in 2 files: - src/main/python/vcf_annovar_annotation.py (598:688) - src/main/python/vcf_snpeff_annotation.py (586:676) duplicated block id: 3 size: 61 cleaned lines of code in 2 files: - src/main/python/vcf_annovar_annotation.py (339:404) - src/main/python/vcf_snpeff_annotation.py (334:398) duplicated block id: 4 size: 33 cleaned lines of code in 2 files: - src/main/python/vcf_annovar_annotation.py (606:638) - src/main/python/vcf_snpeff_annotation.py (644:676) duplicated block id: 5 size: 33 cleaned lines of code in 2 files: - src/main/python/vcf_annovar_annotation.py (606:638) - src/main/python/vcf_annovar_annotation.py (656:688) duplicated block id: 6 size: 33 cleaned lines of code in 2 files: - src/main/python/vcf_snpeff_annotation.py (594:626) - src/main/python/vcf_snpeff_annotation.py (644:676) duplicated block id: 7 size: 33 cleaned lines of code in 2 files: - src/main/python/vcf_annovar_annotation.py (656:688) - src/main/python/vcf_snpeff_annotation.py (594:626) duplicated block id: 8 size: 30 cleaned lines of code in 2 files: - src/main/python/singlecell_doubletdetection.py (25:66) - src/main/python/singlecell_scrublet.py (25:67) duplicated block id: 9 size: 27 cleaned lines of code in 2 files: - src/main/python/vcf_annovar_annotation.py (690:718) - src/main/python/vcf_snpeff_annotation.py (679:707) duplicated block id: 10 size: 24 cleaned lines of code in 2 files: - src/main/python/dna_rna_variant_qc_metrics.py (341:364) - src/main/python/rna_qc_metrics.py (262:285) duplicated block id: 11 size: 22 cleaned lines of code in 2 files: - src/main/python/convert_variant_for_annotation.py (120:145) - src/main/python/convert_variant_for_annotation.py (147:172) duplicated block id: 12 size: 20 cleaned lines of code in 2 files: - src/main/python/dna_rna_variant_qc_metrics.py (237:256) - src/main/python/dna_rna_variant_qc_metrics.py (308:327) duplicated block id: 13 size: 19 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (412:430) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (475:493) duplicated block id: 14 size: 19 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (454:472) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (475:493) duplicated block id: 15 size: 19 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (433:451) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (454:472) duplicated block id: 16 size: 19 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (433:451) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (475:493) duplicated block id: 17 size: 19 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (412:430) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (454:472) duplicated block id: 18 size: 19 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (350:368) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (475:493) duplicated block id: 19 size: 19 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (350:368) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (454:472) duplicated block id: 20 size: 19 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (329:347) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (454:472) duplicated block id: 21 size: 19 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (329:347) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (475:493) duplicated block id: 22 size: 19 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (350:368) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (391:409) duplicated block id: 23 size: 19 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (350:368) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (433:451) duplicated block id: 24 size: 19 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (350:368) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (412:430) duplicated block id: 25 size: 19 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (391:409) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (433:451) duplicated block id: 26 size: 19 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (391:409) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (412:430) duplicated block id: 27 size: 19 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (329:347) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (350:368) duplicated block id: 28 size: 19 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (391:409) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (475:493) duplicated block id: 29 size: 19 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (391:409) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (454:472) duplicated block id: 30 size: 19 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (412:430) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (433:451) duplicated block id: 31 size: 19 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (329:347) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (391:409) duplicated block id: 32 size: 19 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (329:347) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (412:430) duplicated block id: 33 size: 19 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (329:347) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (433:451) duplicated block id: 34 size: 18 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (576:593) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (696:713) duplicated block id: 35 size: 18 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (576:593) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (676:693) duplicated block id: 36 size: 18 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (516:533) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (676:693) duplicated block id: 37 size: 18 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (516:533) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (696:713) duplicated block id: 38 size: 18 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (371:388) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (434:451) duplicated block id: 39 size: 18 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (556:573) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (596:613) duplicated block id: 40 size: 18 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (371:388) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (476:493) duplicated block id: 41 size: 18 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (636:653) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (696:713) duplicated block id: 42 size: 18 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (556:573) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (576:593) duplicated block id: 43 size: 18 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (351:368) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (371:388) duplicated block id: 44 size: 18 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (371:388) - 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src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (596:613) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (696:713) duplicated block id: 50 size: 18 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (516:533) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (536:553) duplicated block id: 51 size: 18 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (536:553) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (676:693) duplicated block id: 52 size: 18 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (536:553) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (696:713) duplicated block id: 53 size: 18 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (576:593) - 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src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (556:573) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (636:653) duplicated block id: 59 size: 18 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (616:633) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (656:673) duplicated block id: 60 size: 18 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (576:593) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (636:653) duplicated block id: 61 size: 18 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (596:613) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (636:653) duplicated block id: 62 size: 18 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (556:573) - 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src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (536:553) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (576:593) duplicated block id: 68 size: 18 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (536:553) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (596:613) duplicated block id: 69 size: 18 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (536:553) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (636:653) duplicated block id: 70 size: 17 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (597:613) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (657:673) duplicated block id: 71 size: 17 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (657:673) - 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src/main/python/vcf_annovar_annotation.py (54:75) - src/main/python/vcf_snpeff_annotation.py (53:74) duplicated block id: 77 size: 17 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (577:593) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (657:673) duplicated block id: 78 size: 17 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (557:573) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (657:673) duplicated block id: 79 size: 17 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (517:533) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (657:673) duplicated block id: 80 size: 17 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (637:653) - 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src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (617:633) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (637:653) duplicated block id: 86 size: 17 cleaned lines of code in 2 files: - src/main/python/dna_rna_variant_qc_metrics.py (200:216) - src/main/python/dna_rna_variant_qc_metrics.py (276:292) duplicated block id: 87 size: 17 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (597:613) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (617:633) duplicated block id: 88 size: 16 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (433:448) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (496:511) duplicated block id: 89 size: 16 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (475:490) - 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src/main/java/com/epam/fonda/tools/impl/Scalpel.java (41:48) - src/main/java/com/epam/fonda/tools/impl/Strelka2.java (44:51) duplicated block id: 200 size: 7 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/tools/impl/Freebayes.java (74:80) - src/main/java/com/epam/fonda/tools/impl/Vardict.java (77:83) duplicated block id: 201 size: 7 cleaned lines of code in 2 files: - src/main/scripts/rna_expression_fastq.py (53:61) - src/main/scripts/sc_rna_expression_cellranger_fastq.py (67:75) duplicated block id: 202 size: 7 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/tools/impl/Freebayes.java (74:80) - src/main/java/com/epam/fonda/tools/impl/Scalpel.java (74:80) duplicated block id: 203 size: 7 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/tools/impl/Freebayes.java (74:80) - src/main/java/com/epam/fonda/tools/impl/Lofreq.java (79:85) duplicated block id: 204 size: 7 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/HlaTypingFastqIntegrationTest.java (87:93) - 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src/main/java/com/epam/fonda/tools/impl/Lofreq.java (79:85) - src/main/java/com/epam/fonda/tools/impl/Vardict.java (77:83) duplicated block id: 210 size: 7 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/tools/impl/Lofreq.java (52:58) - src/main/java/com/epam/fonda/tools/impl/Scalpel.java (50:56) duplicated block id: 211 size: 6 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (164:169) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (174:179) duplicated block id: 212 size: 6 cleaned lines of code in 2 files: - src/main/python/vcf_annovar_annotation.py (264:269) - src/main/python/vcf_annovar_annotation.py (640:645) duplicated block id: 213 size: 6 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/RnaExpressionFastqIntegrationTest.java (281:286) - src/integrationTest/java/com/epam/fonda/RnaExpressionFastqIntegrationTest.java (291:296) duplicated block id: 214 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/workflow/impl/HlaTypingFastqWorkflow.java (46:53) - src/main/java/com/epam/fonda/workflow/impl/TcrRepertoireFastqWorkflow.java (46:53) duplicated block id: 215 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/tools/impl/Scalpel.java (92:97) - src/main/java/com/epam/fonda/tools/impl/Vardict.java (95:100) duplicated block id: 216 size: 6 cleaned lines of code in 2 files: - src/main/python/vcf_annovar_annotation.py (611:616) - src/main/python/vcf_snpeff_annotation.py (455:460) duplicated block id: 217 size: 6 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/RnaExpressionFastqIntegrationTest.java (356:361) - src/integrationTest/java/com/epam/fonda/RnaExpressionFastqIntegrationTest.java (366:371) duplicated block id: 218 size: 6 cleaned lines of code in 2 files: - src/main/python/vcf_snpeff_annotation.py (455:460) - src/main/python/vcf_snpeff_annotation.py (649:654) duplicated block id: 219 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/workflow/impl/SCRnaExpressionCellRangerFastqWorkflow.java (50:57) - src/main/java/com/epam/fonda/workflow/impl/TcrRepertoireFastqWorkflow.java (46:53) duplicated block id: 220 size: 6 cleaned lines of code in 2 files: - src/main/python/post_oncotator_cleanup.py (41:48) - src/main/python/rna_gene_annotation.py (36:43) duplicated block id: 221 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/tools/impl/AmpliconGatkRealign.java (72:84) - src/main/java/com/epam/fonda/tools/impl/AmpliconGatkRecalibrate.java (72:84) duplicated block id: 222 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/tools/impl/Mixcr.java (44:50) - src/main/java/com/epam/fonda/tools/impl/OptiType.java (47:53) duplicated block id: 223 size: 6 cleaned lines of code in 2 files: - src/main/python/rna_gene_annotation.py (36:43) - src/main/python/vcf_annovar_annotation.py (54:61) duplicated block id: 224 size: 6 cleaned lines of code in 2 files: - src/main/python/vcf_annovar_annotation.py (532:537) - src/main/python/vcf_snpeff_annotation.py (455:460) duplicated block id: 225 size: 6 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/RnaExpressionFastqIntegrationTest.java (252:257) - src/integrationTest/java/com/epam/fonda/RnaExpressionFastqIntegrationTest.java (272:277) duplicated block id: 226 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/workflow/impl/RnaFusionFastqWorkflow.java (48:62) - src/main/java/com/epam/fonda/workflow/impl/SCRnaExpressionCellRangerFastqWorkflow.java (50:57) duplicated block id: 227 size: 6 cleaned lines of code in 2 files: - src/main/python/vcf_annovar_annotation.py (640:645) - src/main/python/vcf_snpeff_annotation.py (259:264) duplicated block id: 228 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/tools/impl/Freebayes.java (43:49) - src/main/java/com/epam/fonda/tools/impl/Mutect1.java (43:49) duplicated block id: 229 size: 6 cleaned lines of code in 2 files: - src/main/python/vcf_annovar_annotation.py (744:749) - src/main/python/vcf_annovar_annotation.py (764:769) duplicated block id: 230 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/tools/impl/Trimmomatic.java (87:92) - src/main/java/com/epam/fonda/tools/impl/Xenome.java (93:98) duplicated block id: 231 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/tools/impl/Scalpel.java (42:48) - src/main/java/com/epam/fonda/tools/impl/Vardict.java (44:50) duplicated block id: 232 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/tools/impl/AbraRealign.java (63:77) - src/main/java/com/epam/fonda/tools/impl/Vdj.java (64:79) duplicated block id: 233 size: 6 cleaned lines of code in 2 files: - src/main/python/vcf_annovar_annotation.py (478:483) - src/main/python/vcf_annovar_annotation.py (539:544) duplicated block id: 234 size: 6 cleaned lines of code in 2 files: - src/main/scripts/dna_capture_var_fastq.py (68:73) - src/main/scripts/rna_expression_fastq.py (65:70) duplicated block id: 235 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/tools/impl/RNASeQC.java (132:137) - src/main/java/com/epam/fonda/tools/impl/Star.java (159:164) duplicated block id: 236 size: 6 cleaned lines of code in 2 files: - src/main/python/dna_rna_variant_qc_metrics.py (52:59) - src/main/python/rna_qc_metrics.py (41:48) duplicated block id: 237 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/tools/impl/AbraRealign.java (63:77) - src/main/java/com/epam/fonda/tools/impl/AmpliconGatkRealign.java (48:62) duplicated block id: 238 size: 6 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaWgsVarBamIntegrationTest.java (186:191) - src/integrationTest/java/com/epam/fonda/DnaWgsVarBamIntegrationTest.java (195:200) duplicated block id: 239 size: 6 cleaned lines of code in 2 files: - src/main/python/vcf_annovar_annotation.py (661:666) - src/main/python/vcf_snpeff_annotation.py (455:460) duplicated block id: 240 size: 6 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (154:159) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (174:179) duplicated block id: 241 size: 6 cleaned lines of code in 2 files: - src/main/python/vcf_snpeff_annotation.py (455:460) - src/main/python/vcf_snpeff_annotation.py (521:526) duplicated block id: 242 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/tools/impl/RNASeQC.java (132:137) - src/main/java/com/epam/fonda/tools/impl/StarFusion.java (141:146) duplicated block id: 243 size: 6 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (320:325) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (342:347) duplicated block id: 244 size: 6 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaAnalysisIntegrationTest.java (181:186) - src/integrationTest/java/com/epam/fonda/DnaWgsVarFastqIntegrationTest.java (78:83) duplicated block id: 245 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/workflow/impl/RnaFusionFastqWorkflow.java (48:62) - src/main/java/com/epam/fonda/workflow/impl/TcrRepertoireFastqWorkflow.java (46:53) duplicated block id: 246 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/workflow/impl/HlaTypingFastqWorkflow.java (46:53) - src/main/java/com/epam/fonda/workflow/impl/SCRnaExpressionCellRangerFastqWorkflow.java (50:57) duplicated block id: 247 size: 6 cleaned lines of code in 2 files: - src/main/python/vcf_snpeff_annotation.py (455:460) - src/main/python/vcf_snpeff_annotation.py (599:604) duplicated block id: 248 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/tools/impl/Lofreq.java (44:50) - src/main/java/com/epam/fonda/tools/impl/Vardict.java (44:50) duplicated block id: 249 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/tools/impl/Strelka2.java (45:51) - src/main/java/com/epam/fonda/tools/impl/Vardict.java (44:50) duplicated block id: 250 size: 6 cleaned lines of code in 2 files: - src/main/python/convert_variant_for_annotation.py (40:47) - src/main/python/vcf_annovar_annotation.py (54:61) duplicated block id: 251 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/tools/impl/SeqPurge.java (87:92) - src/main/java/com/epam/fonda/tools/impl/Xenome.java (93:98) duplicated block id: 252 size: 6 cleaned lines of code in 2 files: - src/main/python/vcf_annovar_annotation.py (331:337) - src/main/python/vcf_snpeff_annotation.py (326:332) duplicated block id: 253 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/tools/impl/FilterAlignmentArtifacts.java (54:61) - src/main/java/com/epam/fonda/tools/impl/FilterMutectCalls.java (62:69) duplicated block id: 254 size: 6 cleaned lines of code in 2 files: - src/main/python/vcf_annovar_annotation.py (77:83) - src/main/python/vcf_snpeff_annotation.py (79:85) duplicated block id: 255 size: 6 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaWgsVarBamIntegrationTest.java (177:182) - src/integrationTest/java/com/epam/fonda/DnaWgsVarBamIntegrationTest.java (195:200) duplicated block id: 256 size: 6 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaWgsVarBamIntegrationTest.java (177:182) - src/integrationTest/java/com/epam/fonda/DnaWgsVarBamIntegrationTest.java (186:191) duplicated block id: 257 size: 6 cleaned lines of code in 2 files: - src/main/python/vcf_annovar_annotation.py (696:701) - src/main/python/vcf_snpeff_annotation.py (701:706) duplicated block id: 258 size: 6 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (194:199) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (204:209) duplicated block id: 259 size: 6 cleaned lines of code in 2 files: - src/main/python/convert_variant_for_annotation.py (40:47) - src/main/python/vcf_snpeff_annotation.py (53:60) duplicated block id: 260 size: 6 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (320:325) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (425:430) duplicated block id: 261 size: 6 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (320:325) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (404:409) duplicated block id: 262 size: 6 cleaned lines of code in 2 files: - src/main/python/rna_gene_annotation.py (36:43) - src/main/python/vcf_snpeff_annotation.py (53:60) duplicated block id: 263 size: 6 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaWgsVarBamIntegrationTest.java (228:233) - src/integrationTest/java/com/epam/fonda/DnaWgsVarBamIntegrationTest.java (237:242) duplicated block id: 264 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/tools/impl/BwaSort.java (41:54) - src/main/java/com/epam/fonda/tools/impl/NovoalignSort.java (43:56) duplicated block id: 265 size: 6 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/RnaExpressionFastqIntegrationTest.java (347:352) - src/integrationTest/java/com/epam/fonda/RnaExpressionFastqIntegrationTest.java (366:371) duplicated block id: 266 size: 6 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (320:325) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (446:451) duplicated block id: 267 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/tools/impl/SeqPurge.java (87:92) - src/main/java/com/epam/fonda/tools/impl/Trimmomatic.java (87:92) duplicated block id: 268 size: 6 cleaned lines of code in 2 files: - src/main/python/vcf_annovar_annotation.py (113:120) - src/main/python/vcf_snpeff_annotation.py (108:115) duplicated block id: 269 size: 6 cleaned lines of code in 2 files: - src/main/python/vcf_annovar_annotation.py (471:476) - src/main/python/vcf_snpeff_annotation.py (455:460) duplicated block id: 270 size: 6 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (184:189) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (204:209) duplicated block id: 271 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/tools/impl/Scalpel.java (50:55) - src/main/java/com/epam/fonda/tools/impl/Strelka2.java (54:59) duplicated block id: 272 size: 6 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (320:325) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (383:388) duplicated block id: 273 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/workflow/impl/DnaVarBamWorkflow.java (51:58) - src/main/java/com/epam/fonda/workflow/impl/RnaExpressionBamWorkflow.java (47:54) duplicated block id: 274 size: 6 cleaned lines of code in 2 files: - src/main/python/singlecell_doubletdetection.py (118:124) - src/main/python/singlecell_scrublet.py (100:106) duplicated block id: 275 size: 6 cleaned lines of code in 2 files: - src/main/python/vcf_annovar_annotation.py (264:269) - src/main/python/vcf_snpeff_annotation.py (628:633) duplicated block id: 276 size: 6 cleaned lines of code in 2 files: - src/main/python/vcf_annovar_annotation.py (493:499) - src/main/python/vcf_annovar_annotation.py (550:556) duplicated block id: 277 size: 6 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (320:325) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (363:368) duplicated block id: 278 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/tools/impl/GatkHaplotypeCallerRnaFilter.java (90:95) - src/main/java/com/epam/fonda/tools/impl/GatkSplitReads.java (71:76) duplicated block id: 279 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/tools/impl/PicardMarkDuplicate.java (89:94) - src/main/java/com/epam/fonda/tools/impl/PicardRemoveDuplicate.java (67:72) duplicated block id: 280 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/tools/impl/SeqPurge.java (59:73) - src/main/java/com/epam/fonda/tools/impl/Xenome.java (68:82) duplicated block id: 281 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/tools/impl/Lofreq.java (52:57) - src/main/java/com/epam/fonda/tools/impl/Vardict.java (52:57) duplicated block id: 282 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/tools/impl/SamToFastq.java (42:47) - src/main/java/com/epam/fonda/tools/impl/SortBamByReadName.java (40:45) duplicated block id: 283 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/tools/impl/Hisat2.java (62:76) - src/main/java/com/epam/fonda/tools/impl/Star.java (73:87) duplicated block id: 284 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/tools/impl/AmpliconGatkRealign.java (48:62) - src/main/java/com/epam/fonda/tools/impl/Vdj.java (64:79) duplicated block id: 285 size: 6 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/RnaExpressionFastqIntegrationTest.java (262:267) - src/integrationTest/java/com/epam/fonda/RnaExpressionFastqIntegrationTest.java (272:277) duplicated block id: 286 size: 6 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaWgsVarBamIntegrationTest.java (219:224) - src/integrationTest/java/com/epam/fonda/DnaWgsVarBamIntegrationTest.java (228:233) duplicated block id: 287 size: 6 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaWgsVarBamIntegrationTest.java (219:224) - src/integrationTest/java/com/epam/fonda/DnaWgsVarBamIntegrationTest.java (237:242) duplicated block id: 288 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/tools/impl/Lofreq.java (52:57) - src/main/java/com/epam/fonda/tools/impl/Strelka2.java (54:59) duplicated block id: 289 size: 6 cleaned lines of code in 2 files: - src/main/python/vcf_snpeff_annotation.py (685:690) - src/main/python/vcf_snpeff_annotation.py (701:706) duplicated block id: 290 size: 6 cleaned lines of code in 2 files: - src/main/python/vcf_annovar_annotation.py (712:717) - src/main/python/vcf_snpeff_annotation.py (685:690) duplicated block id: 291 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/tools/impl/Trimmomatic.java (61:75) - src/main/java/com/epam/fonda/tools/impl/Xenome.java (68:82) duplicated block id: 292 size: 6 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (320:325) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (467:472) duplicated block id: 293 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/tools/impl/PicardMarkDuplicate.java (122:127) - src/main/java/com/epam/fonda/tools/impl/RNASeQC.java (132:137) duplicated block id: 294 size: 6 cleaned lines of code in 2 files: - src/main/python/vcf_annovar_annotation.py (696:701) - src/main/python/vcf_annovar_annotation.py (712:717) duplicated block id: 295 size: 6 cleaned lines of code in 2 files: - src/main/scripts/dna_capture_var_fastq.py (148:153) - src/main/scripts/rna_expression_fastq.py (147:152) duplicated block id: 296 size: 6 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaWgsVarBamIntegrationTest.java (145:150) - src/integrationTest/java/com/epam/fonda/DnaWgsVarBamIntegrationTest.java (154:159) duplicated block id: 297 size: 6 cleaned lines of code in 2 files: - src/main/python/vcf_snpeff_annotation.py (259:264) - src/main/python/vcf_snpeff_annotation.py (628:633) duplicated block id: 298 size: 6 cleaned lines of code in 2 files: - src/main/java/com/epam/fonda/tools/impl/Scalpel.java (50:55) - src/main/java/com/epam/fonda/tools/impl/Vardict.java (52:57) duplicated block id: 299 size: 6 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (320:325) - src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java (488:493) duplicated block id: 300 size: 6 cleaned lines of code in 2 files: - src/main/python/convert_variant_for_annotation.py (40:47) - src/main/python/post_oncotator_cleanup.py (41:48) duplicated block id: 301 size: 6 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaWgsVarBamIntegrationTest.java (136:141) - src/integrationTest/java/com/epam/fonda/DnaWgsVarBamIntegrationTest.java (145:150) duplicated block id: 302 size: 6 cleaned lines of code in 2 files: - src/integrationTest/java/com/epam/fonda/DnaWgsVarBamIntegrationTest.java (136:141) - src/integrationTest/java/com/epam/fonda/DnaWgsVarBamIntegrationTest.java (154:159)