path	# lines of code	# active days	days since first update	days since last update	# commits	# contributors	first updated	last updated	first contributor	last contributor
config/pmd/pmd-ruleset.xml	30	1	1860	1860	1	1	2019-12-09	2019-12-09	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/integrationTest/java/com/epam/fonda/RnaCaptureVarFastqIntegrationTest.java	58	2	1774	1374	2	2	2020-03-04	2021-04-08	33068870+ilya-ugr@users.noreply.github.com	yulia_kamyshova@epam.com
src/integrationTest/java/com/epam/fonda/DnaCaptureVarFastqIntegrationTest.java	703	10	1851	1251	10	6	2019-12-18	2021-08-09	ekaterina_kazachkova@epam.com	yulia_kamyshova@epam.com
src/integrationTest/java/com/epam/fonda/DnaWgsVarBamIntegrationTest.java	272	6	1821	1334	6	3	2020-01-17	2021-05-18	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/integrationTest/java/com/epam/fonda/RnaExpressionFastqIntegrationTest.java	392	8	1859	1251	8	4	2019-12-10	2021-08-09	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/integrationTest/java/com/epam/fonda/DnaAmpliconVarFastqIntegrationTest.java	170	7	1859	1374	7	3	2019-12-10	2021-04-08	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/integrationTest/java/com/epam/fonda/TcrRepertoireFastqIntegrationTest.java	94	3	1790	1374	3	3	2020-02-17	2021-04-08	49245254+karimmagomedov@users.noreply.github.com	yulia_kamyshova@epam.com
src/integrationTest/java/com/epam/fonda/RnaExpressionBamIntegrationTest.java	70	4	1859	1374	4	3	2019-12-10	2021-04-08	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/integrationTest/java/com/epam/fonda/AbstractIntegrationTest.java	94	9	1859	1306	10	4	2019-12-10	2021-06-15	yulia_kamyshova@epam.com	81816946+alekseizaichenkov@users.noreply.github.com
src/integrationTest/java/com/epam/fonda/HlaTypingFastqIntegrationTest.java	114	3	1789	1374	3	3	2020-02-18	2021-04-08	30953718+yurysukhorukov@users.noreply.github.com	yulia_kamyshova@epam.com
src/integrationTest/java/com/epam/fonda/DnaAmpliconVarBamIntegrationTest.java	258	5	1821	1374	5	3	2020-01-17	2021-04-08	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/integrationTest/java/com/epam/fonda/SCRnaExpressionBamIntegrationTest.java	164	3	1786	1374	3	3	2020-02-21	2021-04-08	49245254+karimmagomedov@users.noreply.github.com	yulia_kamyshova@epam.com
src/integrationTest/java/com/epam/fonda/SCRnaExpressionCellRangerFastqIntegrationTest.java	109	9	1859	1374	9	3	2019-12-10	2021-04-08	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/integrationTest/java/com/epam/fonda/TestTemplateUtils.java	50	2	1304	1251	2	2	2021-06-17	2021-08-09	81816946+alekseizaichenkov@users.noreply.github.com	yulia_kamyshova@epam.com
src/integrationTest/java/com/epam/fonda/DnaAnalysisIntegrationTest.java	173	5	1859	1374	5	4	2019-12-10	2021-04-08	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/integrationTest/java/com/epam/fonda/DnaCaptureVarBamIntegrationTest.java	149	4	1821	1374	5	2	2020-01-17	2021-04-08	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/integrationTest/java/com/epam/fonda/Bam2FastqIntegrationTest.java	112	5	1814	1374	5	3	2020-01-24	2021-04-08	33068870+ilya-ugr@users.noreply.github.com	yulia_kamyshova@epam.com
src/integrationTest/java/com/epam/fonda/RnaFusionFastqIntegrationTest.java	87	4	1859	1374	4	2	2019-12-10	2021-04-08	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/integrationTest/java/com/epam/fonda/SCRnaExpressionFastqIntegrationTest.java	127	2	1776	1374	2	2	2020-03-02	2021-04-08	49954060+dtegai@users.noreply.github.com	yulia_kamyshova@epam.com
src/integrationTest/java/com/epam/fonda/DnaWgsVarFastqIntegrationTest.java	66	4	1781	1374	4	2	2020-02-26	2021-04-08	49245254+karimmagomedov@users.noreply.github.com	yulia_kamyshova@epam.com
src/main/python/singlecell_doubletdetection.py	88	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/python/rna_qc_metrics.py	295	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/python/post_oncotator_cleanup.py	169	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/python/dna_rna_variant_qc_metrics.py	455	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/python/vcf_snpeff_annotation.py	609	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/python/vcf_annovar_annotation.py	668	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/python/__init__.py	1	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/python/convert_variant_for_annotation.py	174	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/python/singlecell_scrublet.py	73	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/python/rna_gene_annotation.py	54	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/resources/log4j2.xml	21	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/CmdParser.java	68	2	1859	1374	2	1	2019-12-10	2021-04-08	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/Lofreq.java	85	3	1859	1803	3	1	2019-12-10	2020-02-04	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/GatkHaplotypeCallerRnaFilter.java	72	3	1804	1774	3	2	2020-02-03	2020-03-04	33068870+ilya-ugr@users.noreply.github.com	33068870+ilya-ugr@users.noreply.github.com
src/main/java/com/epam/fonda/tools/impl/QcSummary.java	140	10	1859	1374	10	2	2019-12-10	2021-04-08	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/VcfSnpeffAnnotation.java	95	5	1859	1730	5	1	2019-12-10	2020-04-17	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/FeatureCount.java	122	5	1859	1332	5	2	2019-12-10	2021-05-20	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/BwaSort.java	92	5	1859	1332	5	2	2019-12-10	2021-05-20	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/Star.java	121	8	1859	1332	8	3	2019-12-10	2021-05-20	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/GatkSplitReads.java	57	4	1809	1332	4	2	2020-01-29	2021-05-20	33068870+ilya-ugr@users.noreply.github.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/Vdj.java	85	4	1859	1632	4	1	2019-12-10	2020-07-24	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/Mutect2.java	84	4	1859	1334	4	1	2019-12-10	2021-05-18	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/SCRNASeqDoubletDetection.java	65	5	1859	1632	5	1	2019-12-10	2020-07-24	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/Freebayes.java	73	3	1859	1803	3	1	2019-12-10	2020-02-04	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/Vardict.java	80	2	1859	1803	2	1	2019-12-10	2020-02-04	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/DnaAnalysis.java	146	5	1859	1374	5	2	2019-12-10	2021-04-08	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/PicardMarkDuplicate.java	90	5	1859	1332	5	1	2019-12-10	2021-05-20	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/RnaMutationAnalysis.java	47	2	1859	1374	2	1	2019-12-10	2021-04-08	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/StarFusion.java	112	6	1859	1332	6	2	2019-12-10	2021-05-20	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/PileupSummaries.java	62	1	1334	1334	1	1	2021-05-18	2021-05-18	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/RNASeQC.java	144	9	1859	1332	10	2	2019-12-10	2021-05-20	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/AmpliconGatkRecalibrate.java	54	4	1859	1332	4	1	2019-12-10	2021-05-20	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/Count.java	149	9	1859	1215	9	2	2019-12-10	2021-09-14	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/DnaPicardQc.java	297	9	1859	1332	9	3	2019-12-10	2021-05-20	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/Mixcr.java	98	3	1809	1794	3	3	2020-01-29	2020-02-13	49954060+dtegai@users.noreply.github.com	49245254+karimmagomedov@users.noreply.github.com
src/main/java/com/epam/fonda/tools/impl/SeqPurge.java	87	4	1859	1682	4	1	2019-12-10	2020-06-04	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/OptiType.java	84	3	1809	1793	3	2	2020-01-29	2020-02-14	30953718+yurysukhorukov@users.noreply.github.com	30953718+yurysukhorukov@users.noreply.github.com
src/main/java/com/epam/fonda/tools/impl/PicardRemoveDuplicate.java	44	4	1859	1332	4	1	2019-12-10	2021-05-20	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/Xenome.java	123	4	1859	1705	4	2	2019-12-10	2020-05-12	yulia_kamyshova@epam.com	62957240+syansanofi@users.noreply.github.com
src/main/java/com/epam/fonda/tools/impl/SCRnaAnalysis.java	105	7	1859	1374	7	3	2019-12-10	2021-04-08	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/Scalpel.java	77	2	1859	1803	2	1	2019-12-10	2020-02-04	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/RsemAnnotation.java	50	5	1859	1766	5	2	2019-12-10	2020-03-12	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/AbraRealign.java	81	2	1786	1332	2	2	2020-02-21	2021-05-20	49245254+karimmagomedov@users.noreply.github.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/Stringtie.java	71	3	1859	1803	3	1	2019-12-10	2020-02-04	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/GatkSortSam.java	51	1	1334	1334	1	1	2021-05-18	2021-05-18	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/CalculateContamination.java	58	1	1334	1334	1	1	2021-05-18	2021-05-18	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/AmpliconGatkRealign.java	56	3	1859	1332	3	1	2019-12-10	2021-05-20	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/FilterAlignmentArtifacts.java	64	1	1334	1334	1	1	2021-05-18	2021-05-18	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/Pileup.java	87	4	1859	1803	4	1	2019-12-10	2020-02-04	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/Strelka2.java	87	4	1859	1796	4	2	2019-12-10	2020-02-11	yulia_kamyshova@epam.com	49954060+dtegai@users.noreply.github.com
src/main/java/com/epam/fonda/tools/impl/SortBamByReadName.java	67	4	1845	1332	4	2	2019-12-24	2021-05-20	33068870+ilya-ugr@users.noreply.github.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/Sequenza.java	80	3	1859	1332	3	1	2019-12-10	2021-05-20	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/Salmon.java	85	3	1859	1803	3	1	2019-12-10	2020-02-04	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/Cufflinks.java	78	3	1859	1803	3	1	2019-12-10	2020-02-04	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/GatkHaplotypeCaller.java	104	6	1859	1332	6	2	2019-12-10	2021-05-20	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/RnaAnalysis.java	59	2	1859	1374	2	1	2019-12-10	2021-04-08	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/SamToFastq.java	90	3	1850	1709	3	2	2019-12-19	2020-05-08	33068870+ilya-ugr@users.noreply.github.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/Mutect1.java	82	3	1859	1332	3	1	2019-12-10	2021-05-20	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/PicardMergeDnaBam.java	72	6	1859	1332	6	1	2019-12-10	2021-05-20	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/NovoalignSort.java	103	6	1859	1332	6	2	2019-12-10	2021-05-20	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/FastqListAnalysis.java	73	4	1822	1374	4	2	2020-01-16	2021-04-08	33068870+ilya-ugr@users.noreply.github.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/ContEst.java	89	4	1859	1332	4	1	2019-12-10	2021-05-20	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/FusionCatcher.java	71	4	1859	1332	4	1	2019-12-10	2021-05-20	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/Exomecnv.java	84	3	1859	1332	3	1	2019-12-10	2021-05-20	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/FilterMutectCalls.java	76	1	1334	1334	1	1	2021-05-18	2021-05-18	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/Hisat2.java	94	5	1859	1332	5	2	2019-12-10	2021-05-20	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/LearnReadOrientationModel.java	55	1	1334	1334	1	1	2021-05-18	2021-05-18	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/impl/RsemExpression.java	68	4	1859	1786	4	2	2019-12-10	2020-02-21	yulia_kamyshova@epam.com	49245254+karimmagomedov@users.noreply.github.com
src/main/java/com/epam/fonda/tools/impl/Trimmomatic.java	93	5	1859	1790	5	3	2019-12-10	2020-02-17	yulia_kamyshova@epam.com	33068870+ilya-ugr@users.noreply.github.com
src/main/java/com/epam/fonda/tools/results/FeatureCountOutput.java	16	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/VdjOutput.java	16	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/BamOutput.java	19	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/MixcrResult.java	11	1	1809	1809	1	1	2020-01-29	2020-01-29	49954060+dtegai@users.noreply.github.com	49954060+dtegai@users.noreply.github.com
src/main/java/com/epam/fonda/tools/results/MetricsResult.java	11	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/StarFusionResult.java	11	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/CufflinksResult.java	11	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/StarFusionOutput.java	16	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/CufflinksOutput.java	17	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/MetricsOutput.java	20	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/MixcrOutput.java	19	1	1809	1809	1	1	2020-01-29	2020-01-29	49954060+dtegai@users.noreply.github.com	49954060+dtegai@users.noreply.github.com
src/main/java/com/epam/fonda/tools/results/VdjResult.java	11	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/FeatureCountResult.java	11	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/BamResult.java	11	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/StringtieResult.java	11	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/SequenzaResult.java	11	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/VariantsVcfResult.java	11	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/FusionCatcherResult.java	11	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/RsemOutput.java	17	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/PileupResult.java	10	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/SalmonResult.java	11	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/OptiTypeOutput.java	17	1	1809	1809	1	1	2020-01-29	2020-01-29	30953718+yurysukhorukov@users.noreply.github.com	30953718+yurysukhorukov@users.noreply.github.com
src/main/java/com/epam/fonda/tools/results/LearnReadOrientationModelResult.java	10	1	1334	1334	1	1	2021-05-18	2021-05-18	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/FastqOutput.java	9	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/CalculateContaminationResult.java	10	1	1334	1334	1	1	2021-05-18	2021-05-18	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/ExomecnvOutput.java	17	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/ContEstOutput.java	17	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/VcfScnpeffAnnonationResult.java	10	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/PileupSummariesResult.java	10	1	1334	1334	1	1	2021-05-18	2021-05-18	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/VcfScnpeffAnnotationOutput.java	8	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/Result.java	3	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/CalculateContaminationOutput.java	9	1	1334	1334	1	1	2021-05-18	2021-05-18	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/ExomecnvResult.java	11	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/ContEstResult.java	10	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/PileupOutput.java	17	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/LearnReadOrientationModelOutput.java	8	1	1334	1334	1	1	2021-05-18	2021-05-18	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/OptiTypeResult.java	11	1	1809	1809	1	1	2020-01-29	2020-01-29	30953718+yurysukhorukov@users.noreply.github.com	30953718+yurysukhorukov@users.noreply.github.com
src/main/java/com/epam/fonda/tools/results/FastqResult.java	10	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/SalmonOutput.java	17	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/FusionCatcherOutput.java	17	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/SequenzaOutput.java	19	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/StringtieOutput.java	17	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/VariantsVcfOutput.java	24	3	1859	1334	3	2	2019-12-10	2021-05-18	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/results/RsemResult.java	11	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/Tool.java	7	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/tools/PostProcessTool.java	7	2	1859	1374	2	1	2019-12-10	2021-04-08	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/entity/configuration/StudyConfig.java	28	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/entity/configuration/StudyConfigFormat.java	15	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/entity/configuration/DirectoryManager.java	10	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/entity/configuration/EOLMarker.java	11	1	1766	1766	1	1	2020-03-12	2020-03-12	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/entity/configuration/ToolSetConverter.java	10	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/entity/configuration/Configuration.java	13	2	1859	1374	2	1	2019-12-10	2021-04-08	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/entity/configuration/EOLConverter.java	13	2	1766	1762	2	1	2020-03-12	2020-03-16	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/entity/configuration/FlagXenomeConverter.java	13	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/entity/configuration/GlobalConfigFormat.java	108	7	1859	1334	8	1	2019-12-10	2021-05-18	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/entity/configuration/orchestrator/MasterScript.java	187	3	1374	1304	3	2	2021-04-08	2021-06-17	yulia_kamyshova@epam.com	81816946+alekseizaichenkov@users.noreply.github.com
src/main/java/com/epam/fonda/entity/configuration/orchestrator/ScriptType.java	4	1	1374	1374	1	1	2021-04-08	2021-04-08	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/entity/configuration/orchestrator/ScriptManager.java	15	2	1374	1314	2	1	2021-04-08	2021-06-07	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/entity/configuration/CommonOutdir.java	25	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/entity/configuration/GlobalConfig.java	234	9	1859	1334	10	1	2019-12-10	2021-05-18	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/entity/command/AbstractCommand.java	22	2	1859	1803	2	2	2019-12-10	2020-02-04	yulia_kamyshova@epam.com	49954060+dtegai@users.noreply.github.com
src/main/java/com/epam/fonda/entity/command/BashCommand.java	13	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/utils/PipelineUtils.java	217	12	1859	1332	14	3	2019-12-10	2021-05-20	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/utils/AmpliconGatkToolFields.java	18	2	1859	1814	2	1	2019-12-10	2020-01-24	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/utils/ToolUtils.java	37	3	1859	1536	3	1	2019-12-10	2020-10-28	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/utils/CellRangerUtils.java	35	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/utils/AmpliconGatkDatabaseFields.java	26	2	1859	1814	2	1	2019-12-10	2020-01-24	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/utils/TemplateEngineUtils.java	21	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/utils/ConfigurationUtils.java	99	3	1859	1374	3	1	2019-12-10	2021-04-08	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/utils/RnaAnalysisUtils.java	88	5	1859	1766	5	2	2019-12-10	2020-03-12	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/utils/DnaUtils.java	149	5	1859	1787	5	2	2019-12-10	2020-02-20	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/utils/MessageConstant.java	36	3	1859	1374	3	1	2019-12-10	2021-04-08	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/workflow/impl/Flag.java	92	5	1859	1670	5	4	2019-12-10	2020-06-16	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/workflow/impl/DnaVarFastqWorkflow.java	137	6	1851	1332	6	3	2019-12-18	2021-05-20	ekaterina_kazachkova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/workflow/impl/TcrRepertoireFastqWorkflow.java	59	4	1790	1374	4	2	2020-02-17	2021-04-08	49245254+karimmagomedov@users.noreply.github.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/workflow/impl/DnaVarBamWorkflow.java	81	5	1821	1332	5	1	2020-01-17	2021-05-20	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/workflow/impl/SCRnaExpressionCellRangerFastqWorkflow.java	70	4	1859	1374	4	1	2019-12-10	2021-04-08	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/workflow/impl/RnaExpressionBamWorkflow.java	59	8	1859	1332	8	4	2019-12-10	2021-05-20	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/workflow/impl/HlaTypingFastqWorkflow.java	55	4	1789	1374	4	2	2020-02-18	2021-04-08	30953718+yurysukhorukov@users.noreply.github.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/workflow/impl/RnaExpressionFastqWorkflow.java	79	4	1859	1374	4	2	2019-12-10	2021-04-08	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/workflow/impl/Bam2FastqWorkflow.java	70	5	1814	1332	5	2	2020-01-24	2021-05-20	33068870+ilya-ugr@users.noreply.github.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/workflow/impl/RnaFusionFastqWorkflow.java	60	6	1859	1374	6	3	2019-12-10	2021-04-08	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/workflow/FastqWorkflow.java	13	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/workflow/BamWorkflow.java	13	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/workflow/PipelineType.java	37	7	1859	1632	7	4	2019-12-10	2020-07-24	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/workflow/TaskContainer.java	20	1	1803	1803	1	1	2020-02-04	2020-02-04	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/workflow/WorkflowFactory.java	47	12	1859	1332	13	6	2019-12-10	2021-05-20	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/workflow/stage/impl/SecondaryAnalysis.java	315	8	1859	1332	9	3	2019-12-10	2021-05-20	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/workflow/stage/impl/Alignment.java	144	8	1859	1632	8	4	2019-12-10	2020-07-24	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/workflow/stage/impl/PostAlignment.java	65	7	1859	1334	7	4	2019-12-10	2021-05-18	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/workflow/stage/impl/PreAlignment.java	36	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/workflow/stage/Stage.java	3	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/workflow/Workflow.java	29	4	1859	1314	4	1	2019-12-10	2021-06-07	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/Main.java	32	3	1859	1786	3	2	2019-12-10	2020-02-21	yulia_kamyshova@epam.com	49245254+karimmagomedov@users.noreply.github.com
src/main/java/com/epam/fonda/Executor.java	55	2	1859	1356	2	1	2019-12-10	2021-04-26	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/FondaLauncher.java	21	1	1859	1859	1	1	2019-12-10	2019-12-10	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/java/com/epam/fonda/OptionName.java	18	2	1859	1374	2	1	2019-12-10	2021-04-08	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/scripts/__init__.py	1	1	1690	1690	1	1	2020-05-27	2020-05-27	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/scripts/sc_rna_expression_cellranger_fastq.py	270	15	1690	1215	16	2	2020-05-27	2021-09-14	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/scripts/dna_capture_var_fastq.py	192	12	1690	1319	13	1	2020-05-27	2021-06-02	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/scripts/rna_expression_fastq.py	174	9	1690	1370	10	1	2020-05-27	2021-04-12	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/scripts/model/sample_manifest.py	86	6	1690	1370	6	1	2020-05-27	2021-04-12	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/scripts/model/study_config.py	32	2	1690	1688	2	1	2020-05-27	2020-05-29	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/scripts/model/global_config.py	52	6	1690	1334	6	1	2020-05-27	2021-05-18	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/scripts/model/__init__.py	1	1	1690	1690	1	1	2020-05-27	2020-05-27	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/scripts/model/sample_utilities.py	14	3	1688	1562	3	1	2020-05-29	2020-10-02	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/scripts/model/bam_sample_manifest.py	13	3	1690	1370	3	1	2020-05-27	2021-04-12	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/scripts/model/fastq_sample_manifest.py	15	4	1690	1370	4	1	2020-05-27	2021-04-12	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com
src/main/scripts/launcher.py	45	8	1690	1356	10	1	2020-05-27	2021-04-26	yulia_kamyshova@epam.com	yulia_kamyshova@epam.com