Group name | Methods |
unit | IndelShifterTest.testShiftCigarLeft_basic()[pri:0, instance:abra.IndelShifterTest@61230f6a] RepeatUtilsTest.testGetRepeatUnit_Str2()[pri:0, instance:abra.cadabra.RepeatUtilsTest@10e92f8f] SAMRecordUtilsTest.testSubsetCigar_spanElems1()[pri:0, instance:abra.SAMRecordUtilsTest@22a637e7] IndelShifterTest.testShiftDelLeft()[pri:0, instance:abra.IndelShifterTest@61230f6a] SAMRecordUtilsTest.testSubsetCigar_spanElems2()[pri:0, instance:abra.SAMRecordUtilsTest@22a637e7] CigarUtilsTest.testInsertionPartialOverlapAtStart()[pri:0, instance:abra.CigarUtilsTest@76908cc0] SAMRecordUtilsTest.testSubsetCigar_spanElems3()[pri:0, instance:abra.SAMRecordUtilsTest@22a637e7] SAMRecordUtilsTest.testMergeSequences_preferredMismatch()[pri:0, instance:abra.SAMRecordUtilsTest@22a637e7] SimpleMapperTest.testReverseComplementExact()[pri:0, instance:abra.SimpleMapperTest@3c130745] IndelShifterTest.testShiftIndelsLeft()[pri:0, instance:abra.IndelShifterTest@61230f6a] SAMRecordUtilsTest.testSubsetCigar_skipAndSpan2()[pri:0, instance:abra.SAMRecordUtilsTest@22a637e7] SAMRecordUtilsTest.testGetMappedReadPortion()[pri:0, instance:abra.SAMRecordUtilsTest@22a637e7] SAMRecordUtilsTest.testSubsetCigar_skipAndSpan1()[pri:0, instance:abra.SAMRecordUtilsTest@22a637e7] HomopolymerRunTest.testLeading()[pri:0, instance:abra.cadabra.HomopolymerRunTest@418e7838] RepeatUtilsTest.testGetRepeatUnit_Str1()[pri:0, instance:abra.cadabra.RepeatUtilsTest@10e92f8f] SemiGlobalAlignerTest.testExactMatch()[pri:0, instance:abra.SemiGlobalAlignerTest@3e2e18f2] RepeatUtilsTest.testGetRepeatPeriod_Str2()[pri:0, instance:abra.cadabra.RepeatUtilsTest@10e92f8f] RepeatUtilsTest.testGetRepeatUnit_Str3()[pri:0, instance:abra.cadabra.RepeatUtilsTest@10e92f8f] RepeatUtilsTest.testGetRepeatPeriod_Str3()[pri:0, instance:abra.cadabra.RepeatUtilsTest@10e92f8f] SAMRecordUtilsTest.testGetTrailingClips_empty()[pri:0, instance:abra.SAMRecordUtilsTest@22a637e7] CigarUtilsTest.testHasNDM()[pri:0, instance:abra.CigarUtilsTest@76908cc0] SAMRecordUtilsTest.testSubsetCigar_spanAll1()[pri:0, instance:abra.SAMRecordUtilsTest@22a637e7] SAMRecordUtilsTest.testSubsetCigar_spanAll3()[pri:0, instance:abra.SAMRecordUtilsTest@22a637e7] RepeatUtilsTest.testGetRepeatPeriod_Str1()[pri:0, instance:abra.cadabra.RepeatUtilsTest@10e92f8f] SAMRecordUtilsTest.testSubsetCigar_spanAll2()[pri:0, instance:abra.SAMRecordUtilsTest@22a637e7] HomopolymerRunTest.testBasic()[pri:0, instance:abra.cadabra.HomopolymerRunTest@418e7838] SAMRecordUtilsTest.testSubsetCigar_lessThan1Elem2()[pri:0, instance:abra.SAMRecordUtilsTest@22a637e7] SemiGlobalAlignerTest.testMismatches()[pri:0, instance:abra.SemiGlobalAlignerTest@3e2e18f2] CigarUtilsTest.testSkipDeletionAtEnd()[pri:0, instance:abra.CigarUtilsTest@76908cc0] RepeatUtilsTest.testGetRepeatUnit_Homopolymer()[pri:0, instance:abra.cadabra.RepeatUtilsTest@10e92f8f] SAMRecordUtilsTest.testSubsetCigar_spanAll4()[pri:0, instance:abra.SAMRecordUtilsTest@22a637e7] CigarUtilsTest.testMultipleIndels()[pri:0, instance:abra.CigarUtilsTest@76908cc0] SimpleMapperTest.testMapSixMismatches()[pri:0, instance:abra.SimpleMapperTest@3c130745] ReadEvaluatorTest.testMultimapWithinContig()[pri:0, instance:abra.ReadEvaluatorTest@4a22f9e2] CigarUtilsTest.testSkipInsertionAtEnd()[pri:0, instance:abra.CigarUtilsTest@76908cc0] SAMRecordUtilsTest.testMergeSequences_discordantMismatch()[pri:0, instance:abra.SAMRecordUtilsTest@22a637e7] SAMRecordUtilsTest.testRemoveSoftClips_withDeletionAndSoftClipAtStart()[pri:0, instance:abra.SAMRecordUtilsTest@22a637e7] IndelShifterTest.testShiftCigarLeft_complex()[pri:0, instance:abra.IndelShifterTest@61230f6a] SimpleMapperTest.testMapOneMismatch()[pri:0, instance:abra.SimpleMapperTest@3c130745] SimpleMapperTest.testSimple1Mismatch()[pri:0, instance:abra.SimpleMapperTest@3c130745] SimpleMapperTest.testShortAmbiguousMatch()[pri:0, instance:abra.SimpleMapperTest@3c130745] RepeatUtilsTest.testGetRepeatUnit_SingleNt()[pri:0, instance:abra.cadabra.RepeatUtilsTest@10e92f8f] RepeatUtilsTest.testGetRepeatPeriod_NoRepeat()[pri:0, instance:abra.cadabra.RepeatUtilsTest@10e92f8f] SimpleMapperTest.testMapNoSeedMatch()[pri:0, instance:abra.SimpleMapperTest@3c130745] SemiGlobalAlignerTest.testLeadingInsert()[pri:0, instance:abra.SemiGlobalAlignerTest@3e2e18f2] CigarUtilsTest.testInsertionAtStart()[pri:0, instance:abra.CigarUtilsTest@76908cc0] SemiGlobalAlignerTest.testBigDel()[pri:0, instance:abra.SemiGlobalAlignerTest@3e2e18f2] ChromosomeRegexTest.testChr1()[pri:0, instance:abra.ChromosomeRegexTest@3c419631] ChromosomeRegexTest.testHg19Decoy()[pri:0, instance:abra.ChromosomeRegexTest@3c419631] JunctionUtilsTest.testGetRegionJunctions()[pri:0, instance:abra.JunctionUtilsTest@cd3fee8] HomopolymerRunTest.testNone()[pri:0, instance:abra.cadabra.HomopolymerRunTest@418e7838] SAMRecordUtilsTest.testMergeSequences_multipleHeadHits()[pri:0, instance:abra.SAMRecordUtilsTest@22a637e7] SimpleMapperTest.testMapAmbiguousMatch()[pri:0, instance:abra.SimpleMapperTest@3c130745] ReadEvaluatorTest.testSingleAlignmentSingleContig_reverseComplement()[pri:0, instance:abra.ReadEvaluatorTest@4a22f9e2] ReadEvaluatorTest.testSingleAlignmentSingleContig_noImprovement()[pri:0, instance:abra.ReadEvaluatorTest@4a22f9e2] CigarUtilsTest.testDeletion()[pri:0, instance:abra.CigarUtilsTest@76908cc0] SAMRecordUtilsTest.testMergeSequences()[pri:0, instance:abra.SAMRecordUtilsTest@22a637e7] SimpleMapperTest.testMapExact()[pri:0, instance:abra.SimpleMapperTest@3c130745] IndelShifterTest.testShiftCigarLeft_insertAtTail()[pri:0, instance:abra.IndelShifterTest@61230f6a] FeatureTest.testOverlaps()[pri:0, instance:abra.FeatureTest@3d680b5a] ChromosomeRegexTest.testUnplaced()[pri:0, instance:abra.ChromosomeRegexTest@3c419631] HomopolymerRunTest.testTrailing()[pri:0, instance:abra.cadabra.HomopolymerRunTest@418e7838] IndelShifterTest.testShiftCigarLeft_multipleIndels()[pri:0, instance:abra.IndelShifterTest@61230f6a] ChromosomeRegexTest.testChrX()[pri:0, instance:abra.ChromosomeRegexTest@3c419631] SAMRecordUtilsTest.testRemoveSoftClips_withDeletionAndSoftClipAtEnd()[pri:0, instance:abra.SAMRecordUtilsTest@22a637e7] CigarUtilsTest.testInsertionPartialOverlapAtEnd()[pri:0, instance:abra.CigarUtilsTest@76908cc0] ReadEvaluatorTest.testSingleAlignmentSingleContig()[pri:0, instance:abra.ReadEvaluatorTest@4a22f9e2] CigarUtilsTest.testMatchSubset()[pri:0, instance:abra.CigarUtilsTest@76908cc0] CigarUtilsTest.testSkipDeletionAtStart()[pri:0, instance:abra.CigarUtilsTest@76908cc0] IndelShifterTest.testShiftIndelsLeft_LocalRef()[pri:0, instance:abra.IndelShifterTest@61230f6a] RealignerTest.testPairJunctions()[pri:0, instance:abra.RealignerTest@460d0a57] SAMRecordUtilsTest.testSubsetCigar_long()[pri:0, instance:abra.SAMRecordUtilsTest@22a637e7] SAMRecordUtilsTest.testSubsetCigar_skipElem()[pri:0, instance:abra.SAMRecordUtilsTest@22a637e7] SimpleMapperTest.testMapAmbiguousMatchWithMismatches()[pri:0, instance:abra.SimpleMapperTest@3c130745] CigarUtilsTest.testExactMatch()[pri:0, instance:abra.CigarUtilsTest@76908cc0] JunctionUtilsTest.testCombineJunctions()[pri:0, instance:abra.JunctionUtilsTest@cd3fee8] ReadEvaluatorTest.testMapToMultipleContigsSynonymously()[pri:0, instance:abra.ReadEvaluatorTest@4a22f9e2] SemiGlobalAlignerTest.testTrailingInsert()[pri:0, instance:abra.SemiGlobalAlignerTest@3e2e18f2] ChromosomeRegexTest.testHg19Gl()[pri:0, instance:abra.ChromosomeRegexTest@3c419631] CigarUtilsTest.testInsertion()[pri:0, instance:abra.CigarUtilsTest@76908cc0] CigarUtilsTest.testReadBeyondInsertion()[pri:0, instance:abra.CigarUtilsTest@76908cc0] RepeatUtilsTest.testGetRepeatPeriod_HpRun()[pri:0, instance:abra.cadabra.RepeatUtilsTest@10e92f8f] CigarUtilsTest.testCompare()[pri:0, instance:abra.CigarUtilsTest@76908cc0] IndelShifterTest.testShiftCigarLeft_softClipping()[pri:0, instance:abra.IndelShifterTest@61230f6a] RepeatUtilsTest.testGetRepeatUnit_NearHomopolymer2()[pri:0, instance:abra.cadabra.RepeatUtilsTest@10e92f8f] RepeatUtilsTest.testGetRepeatUnit_NearHomopolymer1()[pri:0, instance:abra.cadabra.RepeatUtilsTest@10e92f8f] SemiGlobalAlignerTest.testEndToEnd()[pri:0, instance:abra.SemiGlobalAlignerTest@3e2e18f2] RepeatUtilsTest.testGetRepeatUnit_NearHomopolymer3()[pri:0, instance:abra.cadabra.RepeatUtilsTest@10e92f8f] SAMRecordUtilsTest.testSubsetCigar_deletion()[pri:0, instance:abra.SAMRecordUtilsTest@22a637e7] SAMRecordUtilsTest.testGetLeadingClips_empty()[pri:0, instance:abra.SAMRecordUtilsTest@22a637e7] SimpleMapperTest.testReverseComplement2Mismatches()[pri:0, instance:abra.SimpleMapperTest@3c130745] RepeatUtilsTest.testGetRepeatUnit_NearStr1()[pri:0, instance:abra.cadabra.RepeatUtilsTest@10e92f8f] ScoredContigTest.testConvertAndFilter()[pri:0, instance:abra.ScoredContigTest@6ef888f6] SimpleMapperTest.testMapSixMismatchesIncreasedMismatchRate()[pri:0, instance:abra.SimpleMapperTest@3c130745] CigarUtilsTest.testSkipDeletionWithinStart()[pri:0, instance:abra.CigarUtilsTest@76908cc0] SAMRecordUtilsTest.testGetTrailingClips()[pri:0, instance:abra.SAMRecordUtilsTest@22a637e7] SemiGlobalAlignerTest.testDelete()[pri:0, instance:abra.SemiGlobalAlignerTest@3e2e18f2] JunctionUtilsTest.testLoadJunctionsFromGtf()[pri:0, instance:abra.JunctionUtilsTest@cd3fee8] RealignerTest.testPairJunctions_cannotAppearInSameContig()[pri:0, instance:abra.RealignerTest@460d0a57] RepeatUtilsTest.testGetRepeatPeriod_NoRepeat1()[pri:0, instance:abra.cadabra.RepeatUtilsTest@10e92f8f] SAMRecordUtilsTest.testSubsetCigar_lessThanFirstElem()[pri:0, instance:abra.SAMRecordUtilsTest@22a637e7] ReadEvaluatorTest.testSelectBestAlignment()[pri:0, instance:abra.ReadEvaluatorTest@4a22f9e2] SAMRecordUtilsTest.testSubsetCigar_lessThan1Elem3()[pri:0, instance:abra.SAMRecordUtilsTest@22a637e7] ChromosomeRegexTest.testRandom()[pri:0, instance:abra.ChromosomeRegexTest@3c419631] CigarUtilsTest.testBeyondMultipleIndels()[pri:0, instance:abra.CigarUtilsTest@76908cc0] MultiSamReaderTest.testReadTwoBams()[pri:0, instance:abra.MultiSamReaderTest@4b5d6a01] SAMRecordUtilsTest.testSubsetCigar_skipElem2()[pri:0, instance:abra.SAMRecordUtilsTest@22a637e7] SAMRecordUtilsTest.testSubsetCigar_exact()[pri:0, instance:abra.SAMRecordUtilsTest@22a637e7] ReAlignerOptionsTest.testNoParams()[pri:0, instance:abra.ReAlignerOptionsTest@470f1802] SimpleMapperTest.testMapFiveMismatches()[pri:0, instance:abra.SimpleMapperTest@3c130745] SAMRecordUtilsTest.testMergeSequences_tooManyMismatches()[pri:0, instance:abra.SAMRecordUtilsTest@22a637e7] CigarUtilsTest.testInjectSplice()[pri:0, instance:abra.CigarUtilsTest@76908cc0] SAMRecordUtilsTest.testSubsetCigar_lessThan1Elem()[pri:0, instance:abra.SAMRecordUtilsTest@22a637e7] SemiGlobalAlignerTest.testInsert()[pri:0, instance:abra.SemiGlobalAlignerTest@3e2e18f2] RealignerTest.testCollapseRegions()[pri:0, instance:abra.RealignerTest@460d0a57] CigarUtilsTest.testReadBeyondDeletion()[pri:0, instance:abra.CigarUtilsTest@76908cc0] SemiGlobalAlignerTest.testUnderflowBug()[pri:0, instance:abra.SemiGlobalAlignerTest@3e2e18f2] CigarUtilsTest.testInjectSplices()[pri:0, instance:abra.CigarUtilsTest@76908cc0] SemiGlobalAlignerTest.testInsert2()[pri:0, instance:abra.SemiGlobalAlignerTest@3e2e18f2] SAMRecordUtilsTest.testGetLeadingClips()[pri:0, instance:abra.SAMRecordUtilsTest@22a637e7] CigarUtilsTest.testExtendContig()[pri:0, instance:abra.CigarUtilsTest@76908cc0] ReAlignerOptionsTest.testBamParams()[pri:0, instance:abra.ReAlignerOptionsTest@470f1802] |