Groups used for this test run

Group nameMethods
unitIndelShifterTest.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]