Path	Lines of Code
src/test/java/com/epam/fonda/CmdParserTest.java	259
src/test/java/com/epam/fonda/tools/impl/AbraRealignTest.java	97
src/test/java/com/epam/fonda/tools/impl/AbstractTest.java	22
src/test/java/com/epam/fonda/tools/impl/AmpliconGatkRealignTest.java	71
src/test/java/com/epam/fonda/tools/impl/AmpliconGatkRecalibrateTest.java	72
src/test/java/com/epam/fonda/tools/impl/BwaSortTest.java	101
src/test/java/com/epam/fonda/tools/impl/CalculateContaminationTest.java	47
src/test/java/com/epam/fonda/tools/impl/ContEstTest.java	66
src/test/java/com/epam/fonda/tools/impl/CountTest.java	142
src/test/java/com/epam/fonda/tools/impl/CufflinksTest.java	72
src/test/java/com/epam/fonda/tools/impl/DnaAnalysisTest.java	65
src/test/java/com/epam/fonda/tools/impl/DnaPicardQcTest.java	247
src/test/java/com/epam/fonda/tools/impl/ExomecnvTest.java	118
src/test/java/com/epam/fonda/tools/impl/FastqListAnalysisTest.java	96
src/test/java/com/epam/fonda/tools/impl/FeatureCountTest.java	74
src/test/java/com/epam/fonda/tools/impl/FilterAlignmentArtifactsTest.java	53
src/test/java/com/epam/fonda/tools/impl/FilterMutectCallsTest.java	66
src/test/java/com/epam/fonda/tools/impl/FreebayesTest.java	75
src/test/java/com/epam/fonda/tools/impl/FusionCatcherTest.java	61
src/test/java/com/epam/fonda/tools/impl/GatkHaplotypeCallerRnaFilterTest.java	57
src/test/java/com/epam/fonda/tools/impl/GatkHaplotypeCallerTest.java	79
src/test/java/com/epam/fonda/tools/impl/GatkSortSamTest.java	48
src/test/java/com/epam/fonda/tools/impl/GatkSplitReadsTest.java	56
src/test/java/com/epam/fonda/tools/impl/Hisat2Test.java	121
src/test/java/com/epam/fonda/tools/impl/LearnReadOrientationModelTest.java	47
src/test/java/com/epam/fonda/tools/impl/LofreqTest.java	96
src/test/java/com/epam/fonda/tools/impl/MixcrTest.java	145
src/test/java/com/epam/fonda/tools/impl/Mutect1Test.java	102
src/test/java/com/epam/fonda/tools/impl/Mutect2Test.java	102
src/test/java/com/epam/fonda/tools/impl/NovoalignSortTest.java	120
src/test/java/com/epam/fonda/tools/impl/OptiTypeTest.java	86
src/test/java/com/epam/fonda/tools/impl/PicardMarkDuplicateTest.java	69
src/test/java/com/epam/fonda/tools/impl/PicardMergeDnaBamTest.java	60
src/test/java/com/epam/fonda/tools/impl/PicardRemoveDuplicateTest.java	49
src/test/java/com/epam/fonda/tools/impl/PileupSummariesTest.java	57
src/test/java/com/epam/fonda/tools/impl/PileupTest.java	63
src/test/java/com/epam/fonda/tools/impl/QcSummaryTest.java	43
src/test/java/com/epam/fonda/tools/impl/RNASeQCTest.java	92
src/test/java/com/epam/fonda/tools/impl/RnaAnalysisTest.java	73
src/test/java/com/epam/fonda/tools/impl/RnaMutationAnalysisTest.java	62
src/test/java/com/epam/fonda/tools/impl/RsemAnnotationTest.java	45
src/test/java/com/epam/fonda/tools/impl/RsemExpressionTest.java	60
src/test/java/com/epam/fonda/tools/impl/SCRNASeqDoubletDetectionTest.java	79
src/test/java/com/epam/fonda/tools/impl/SCRnaAnalysisTest.java	92
src/test/java/com/epam/fonda/tools/impl/SalmonTest.java	65
src/test/java/com/epam/fonda/tools/impl/SamToFastqTest.java	63
src/test/java/com/epam/fonda/tools/impl/ScalpelTest.java	90
src/test/java/com/epam/fonda/tools/impl/SeqPurgeTest.java	63
src/test/java/com/epam/fonda/tools/impl/SequenzaTest.java	108
src/test/java/com/epam/fonda/tools/impl/SortBamByReadNameTest.java	50
src/test/java/com/epam/fonda/tools/impl/StarFusionTest.java	73
src/test/java/com/epam/fonda/tools/impl/StarTest.java	149
src/test/java/com/epam/fonda/tools/impl/Strelka2Test.java	108
src/test/java/com/epam/fonda/tools/impl/StringtieTest.java	53
src/test/java/com/epam/fonda/tools/impl/TrimmomaticTest.java	67
src/test/java/com/epam/fonda/tools/impl/VardictTest.java	96
src/test/java/com/epam/fonda/tools/impl/VcfSnpeffAnnotationTest.java	73
src/test/java/com/epam/fonda/tools/impl/VdjTest.java	71
src/test/java/com/epam/fonda/tools/impl/XenomeTest.java	103
src/test/java/com/epam/fonda/utils/CellRangerUtilsTest.java	44
src/test/java/com/epam/fonda/utils/ConfigurationUtilsTest.java	71
src/test/java/com/epam/fonda/utils/DnaUtilsTest.java	85
src/test/java/com/epam/fonda/utils/PipelineUtilsTest.java	128
src/test/java/com/epam/fonda/utils/RnaAnalysisUtilsTest.java	68
src/test/java/com/epam/fonda/workflow/WorkflowFactoryTest.java	40