TestMethods
Passed		Scenarios
Passed		# skipped# failedTotal
Time		Included
Groups		Excluded
Groups
Command line test122122000.4 seconds
ClassMethod# of
Scenarios		StartTime
(ms)
Command line test — passed
abra.ChromosomeRegexTesttestChr1 (unit) 115692416933397
testChrX (unit) 115692416933470
testHg19Decoy (unit) 115692416933470
testHg19Gl (unit) 115692416933470
testRandom (unit) 115692416933471
testUnplaced (unit) 115692416933480
abra.CigarUtilsTesttestBeyondMultipleIndels (unit) 115692416933492
testCompare (unit) 115692416933511
testDeletion (unit) 115692416933521
testExactMatch (unit) 115692416933530
testExtendContig (unit) 115692416933530
testHasNDM (unit) 115692416933540
testInjectSplice (unit) 115692416933540
testInjectSplices (unit) 115692416933550
testInsertion (unit) 115692416933550
testInsertionAtStart (unit) 115692416933551
testInsertionPartialOverlapAtEnd (unit) 115692416933560
testInsertionPartialOverlapAtStart (unit) 115692416933560
testMatchSubset (unit) 115692416933570
testMultipleIndels (unit) 115692416933570
testReadBeyondDeletion (unit) 115692416933580
testReadBeyondInsertion (unit) 115692416933590
testSkipDeletionAtEnd (unit) 115692416933590
testSkipDeletionAtStart (unit) 115692416933591
abra.FeatureTesttestOverlaps (unit) 115692416933601
abra.CigarUtilsTesttestSkipDeletionWithinStart (unit) 115692416933600
testSkipInsertionAtEnd (unit) 115692416933600
abra.cadabra.HomopolymerRunTesttestBasic (unit) 115692416933612
testLeading (unit) 115692416933630
testNone (unit) 115692416933630
abra.IndelShifterTesttestShiftCigarLeft_basic (unit) 115692416933633
abra.cadabra.HomopolymerRunTesttestTrailing (unit) 115692416933630
abra.IndelShifterTesttestShiftCigarLeft_complex (unit) 115692416933660
testShiftCigarLeft_insertAtTail (unit) 115692416933660
testShiftCigarLeft_multipleIndels (unit) 115692416933670
testShiftCigarLeft_softClipping (unit) 115692416933670
testShiftDelLeft (unit) 115692416933671
testShiftIndelsLeft (unit) 1156924169336927
testShiftIndelsLeft_LocalRef (unit) 115692416933961
abra.JunctionUtilsTesttestCombineJunctions (unit) 115692416933973
testGetRegionJunctions (unit) 115692416934003
testLoadJunctionsFromGtf (unit) 115692416934034
abra.MultiSamReaderTesttestReadTwoBams (unit) 11569241693407110
abra.ReAlignerOptionsTesttestBamParams (unit) 1156924169351737
testNoParams (unit) 115692416935555
abra.ReadEvaluatorTesttestMapToMultipleContigsSynonymously (unit) 115692416935615
testMultimapWithinContig (unit) 115692416935661
testSelectBestAlignment (unit) 115692416935670
testSingleAlignmentSingleContig (unit) 115692416935671
testSingleAlignmentSingleContig_noImprovement (unit) 115692416935680
testSingleAlignmentSingleContig_reverseComplement (unit) 115692416935680
abra.RealignerTesttestCollapseRegions (unit) 115692416935690
testPairJunctions (unit) 115692416935696
abra.cadabra.RepeatUtilsTesttestGetRepeatPeriod_HpRun (unit) 115692416935751
abra.RealignerTesttestPairJunctions_cannotAppearInSameContig (unit) 115692416935750
abra.cadabra.RepeatUtilsTesttestGetRepeatPeriod_NoRepeat (unit) 115692416935760
testGetRepeatPeriod_NoRepeat1 (unit) 115692416935760
testGetRepeatPeriod_Str1 (unit) 115692416935760
testGetRepeatPeriod_Str2 (unit) 115692416935770
testGetRepeatPeriod_Str3 (unit) 115692416935770
testGetRepeatUnit_Homopolymer (unit) 115692416935770
testGetRepeatUnit_NearHomopolymer1 (unit) 115692416935770
testGetRepeatUnit_NearHomopolymer2 (unit) 115692416935770
testGetRepeatUnit_NearHomopolymer3 (unit) 115692416935780
testGetRepeatUnit_NearStr1 (unit) 115692416935780
testGetRepeatUnit_SingleNt (unit) 115692416935780
testGetRepeatUnit_Str1 (unit) 115692416935780
testGetRepeatUnit_Str2 (unit) 115692416935781
abra.SAMRecordUtilsTesttestGetLeadingClips (unit) 115692416935790
testGetLeadingClips_empty (unit) 115692416935790
testGetMappedReadPortion (unit) 115692416935790
abra.cadabra.RepeatUtilsTesttestGetRepeatUnit_Str3 (unit) 115692416935790
abra.SAMRecordUtilsTesttestGetTrailingClips (unit) 115692416935800
testGetTrailingClips_empty (unit) 115692416935800
testMergeSequences (unit) 115692416935801
testMergeSequences_discordantMismatch (unit) 115692416935810
testMergeSequences_multipleHeadHits (unit) 115692416935810
testMergeSequences_preferredMismatch (unit) 115692416935820
testMergeSequences_tooManyMismatches (unit) 115692416935820
testRemoveSoftClips_withDeletionAndSoftClipAtEnd (unit) 115692416935820
testRemoveSoftClips_withDeletionAndSoftClipAtStart (unit) 115692416935820
testSubsetCigar_deletion (unit) 115692416935821
testSubsetCigar_exact (unit) 115692416935830
testSubsetCigar_lessThan1Elem (unit) 115692416935830
testSubsetCigar_lessThan1Elem2 (unit) 115692416935830
testSubsetCigar_lessThan1Elem3 (unit) 115692416935830
testSubsetCigar_lessThanFirstElem (unit) 115692416935840
testSubsetCigar_long (unit) 115692416935840
testSubsetCigar_skipAndSpan1 (unit) 115692416935840
testSubsetCigar_skipAndSpan2 (unit) 115692416935850
testSubsetCigar_skipElem (unit) 115692416935850
testSubsetCigar_skipElem2 (unit) 115692416935850
testSubsetCigar_spanAll1 (unit) 115692416935850
testSubsetCigar_spanAll2 (unit) 115692416935850
testSubsetCigar_spanAll3 (unit) 115692416935860
testSubsetCigar_spanAll4 (unit) 115692416935860
testSubsetCigar_spanElems1 (unit) 115692416935860
testSubsetCigar_spanElems2 (unit) 115692416935860
testSubsetCigar_spanElems3 (unit) 115692416935861
abra.ScoredContigTesttestConvertAndFilter (unit) 115692416935871
abra.SemiGlobalAlignerTesttestBigDel (unit) 115692416935887
testDelete (unit) 115692416935950
testEndToEnd (unit) 115692416935950
testExactMatch (unit) 115692416935960
testInsert (unit) 115692416935960
testInsert2 (unit) 115692416935963
testLeadingInsert (unit) 115692416935991
testMismatches (unit) 115692416936000
testTrailingInsert (unit) 115692416936001
testUnderflowBug (unit) 11569241693601100
abra.SimpleMapperTesttestMapAmbiguousMatch (unit) 115692416937011
testMapAmbiguousMatchWithMismatches (unit) 115692416937020
testMapExact (unit) 115692416937021
testMapFiveMismatches (unit) 115692416937030
testMapNoSeedMatch (unit) 115692416937031
testMapOneMismatch (unit) 115692416937040
testMapSixMismatches (unit) 115692416937041
testMapSixMismatchesIncreasedMismatchRate (unit) 115692416937050
testReverseComplement2Mismatches (unit) 115692416937051
testReverseComplementExact (unit) 115692416937060
testShortAmbiguousMatch (unit) 115692416937060
testSimple1Mismatch (unit) 115692416937060

Command line test

abra.cadabra.RepeatUtilsTest:testGetRepeatUnit_NearHomopolymer3

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abra.CigarUtilsTest:testMultipleIndels

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abra.JunctionUtilsTest:testLoadJunctionsFromGtf

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abra.CigarUtilsTest:testSkipDeletionAtEnd

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abra.SAMRecordUtilsTest:testSubsetCigar_skipAndSpan2

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abra.MultiSamReaderTest:testReadTwoBams

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abra.SAMRecordUtilsTest:testRemoveSoftClips_withDeletionAndSoftClipAtStart

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abra.SAMRecordUtilsTest:testSubsetCigar_skipAndSpan1

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abra.IndelShifterTest:testShiftCigarLeft_complex

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abra.CigarUtilsTest:testReadBeyondDeletion

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abra.cadabra.RepeatUtilsTest:testGetRepeatPeriod_HpRun

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abra.SAMRecordUtilsTest:testGetTrailingClips_empty

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abra.SemiGlobalAlignerTest:testMismatches

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abra.SAMRecordUtilsTest:testRemoveSoftClips_withDeletionAndSoftClipAtEnd

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abra.SemiGlobalAlignerTest:testLeadingInsert

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abra.SimpleMapperTest:testMapFiveMismatches

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abra.SAMRecordUtilsTest:testGetLeadingClips_empty

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abra.SimpleMapperTest:testShortAmbiguousMatch

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abra.ReAlignerOptionsTest:testBamParams

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abra.cadabra.HomopolymerRunTest:testLeading

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abra.cadabra.RepeatUtilsTest:testGetRepeatPeriod_Str2

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abra.ChromosomeRegexTest:testUnplaced

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abra.CigarUtilsTest:testReadBeyondInsertion

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abra.cadabra.RepeatUtilsTest:testGetRepeatPeriod_Str3

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abra.SemiGlobalAlignerTest:testExactMatch

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abra.SAMRecordUtilsTest:testSubsetCigar_spanAll1

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abra.CigarUtilsTest:testInsertion

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abra.SAMRecordUtilsTest:testMergeSequences

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abra.ChromosomeRegexTest:testChrX

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abra.SAMRecordUtilsTest:testSubsetCigar_long

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abra.SemiGlobalAlignerTest:testInsert2

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abra.CigarUtilsTest:testInjectSplice

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abra.ReadEvaluatorTest:testSingleAlignmentSingleContig_noImprovement

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abra.SAMRecordUtilsTest:testSubsetCigar_lessThan1Elem2

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abra.CigarUtilsTest:testHasNDM

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abra.ReadEvaluatorTest:testMapToMultipleContigsSynonymously

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abra.CigarUtilsTest:testCompare

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abra.SAMRecordUtilsTest:testSubsetCigar_spanAll2

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abra.CigarUtilsTest:testInsertionAtStart

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abra.SemiGlobalAlignerTest:testDelete

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abra.IndelShifterTest:testShiftCigarLeft_softClipping

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abra.SimpleMapperTest:testReverseComplement2Mismatches

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abra.IndelShifterTest:testShiftIndelsLeft_LocalRef

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abra.SimpleMapperTest:testMapNoSeedMatch

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abra.SimpleMapperTest:testMapOneMismatch

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abra.JunctionUtilsTest:testGetRegionJunctions

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abra.cadabra.RepeatUtilsTest:testGetRepeatUnit_Homopolymer

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abra.SAMRecordUtilsTest:testSubsetCigar_skipElem2

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abra.SAMRecordUtilsTest:testSubsetCigar_deletion

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abra.cadabra.RepeatUtilsTest:testGetRepeatUnit_NearHomopolymer1

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abra.ReadEvaluatorTest:testMultimapWithinContig

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abra.CigarUtilsTest:testExactMatch

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abra.cadabra.RepeatUtilsTest:testGetRepeatUnit_Str3

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abra.ReadEvaluatorTest:testSingleAlignmentSingleContig_reverseComplement

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abra.SemiGlobalAlignerTest:testTrailingInsert

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abra.JunctionUtilsTest:testCombineJunctions

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abra.SAMRecordUtilsTest:testMergeSequences_discordantMismatch

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abra.RealignerTest:testPairJunctions

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abra.ScoredContigTest:testConvertAndFilter

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abra.SAMRecordUtilsTest:testSubsetCigar_lessThan1Elem

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abra.SAMRecordUtilsTest:testSubsetCigar_lessThan1Elem3

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abra.cadabra.HomopolymerRunTest:testBasic

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abra.CigarUtilsTest:testExtendContig

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abra.cadabra.RepeatUtilsTest:testGetRepeatUnit_NearHomopolymer2

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abra.CigarUtilsTest:testMatchSubset

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abra.cadabra.RepeatUtilsTest:testGetRepeatUnit_NearStr1

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abra.SemiGlobalAlignerTest:testInsert

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abra.CigarUtilsTest:testSkipDeletionWithinStart

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abra.CigarUtilsTest:testInsertionPartialOverlapAtEnd

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abra.ReadEvaluatorTest:testSingleAlignmentSingleContig

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abra.SimpleMapperTest:testMapAmbiguousMatchWithMismatches

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abra.SAMRecordUtilsTest:testMergeSequences_multipleHeadHits

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abra.cadabra.HomopolymerRunTest:testTrailing

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abra.SemiGlobalAlignerTest:testUnderflowBug

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abra.ChromosomeRegexTest:testRandom

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abra.SAMRecordUtilsTest:testSubsetCigar_lessThanFirstElem

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abra.SAMRecordUtilsTest:testSubsetCigar_spanElems2

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abra.IndelShifterTest:testShiftCigarLeft_insertAtTail

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abra.SimpleMapperTest:testReverseComplementExact

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abra.CigarUtilsTest:testSkipInsertionAtEnd

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abra.cadabra.RepeatUtilsTest:testGetRepeatPeriod_NoRepeat

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abra.IndelShifterTest:testShiftCigarLeft_multipleIndels

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abra.FeatureTest:testOverlaps

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abra.cadabra.RepeatUtilsTest:testGetRepeatUnit_SingleNt

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abra.RealignerTest:testCollapseRegions

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abra.cadabra.RepeatUtilsTest:testGetRepeatUnit_Str1

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abra.SAMRecordUtilsTest:testSubsetCigar_skipElem

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abra.ReadEvaluatorTest:testSelectBestAlignment

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abra.IndelShifterTest:testShiftIndelsLeft

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abra.SimpleMapperTest:testMapSixMismatchesIncreasedMismatchRate

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abra.cadabra.RepeatUtilsTest:testGetRepeatPeriod_NoRepeat1

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abra.SAMRecordUtilsTest:testSubsetCigar_spanAll4

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abra.CigarUtilsTest:testInsertionPartialOverlapAtStart

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abra.SAMRecordUtilsTest:testSubsetCigar_spanAll3

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abra.SimpleMapperTest:testMapSixMismatches

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abra.SAMRecordUtilsTest:testMergeSequences_tooManyMismatches

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abra.ChromosomeRegexTest:testHg19Decoy

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abra.CigarUtilsTest:testDeletion

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abra.SemiGlobalAlignerTest:testBigDel

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abra.SAMRecordUtilsTest:testGetMappedReadPortion

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abra.CigarUtilsTest:testBeyondMultipleIndels

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abra.cadabra.RepeatUtilsTest:testGetRepeatUnit_Str2

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abra.SAMRecordUtilsTest:testSubsetCigar_exact

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abra.ChromosomeRegexTest:testHg19Gl

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abra.ChromosomeRegexTest:testChr1

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abra.SimpleMapperTest:testSimple1Mismatch

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abra.SAMRecordUtilsTest:testSubsetCigar_spanElems3

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abra.CigarUtilsTest:testSkipDeletionAtStart

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abra.SAMRecordUtilsTest:testMergeSequences_preferredMismatch

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abra.SimpleMapperTest:testMapExact

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abra.IndelShifterTest:testShiftCigarLeft_basic

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abra.cadabra.RepeatUtilsTest:testGetRepeatPeriod_Str1

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abra.RealignerTest:testPairJunctions_cannotAppearInSameContig

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abra.SemiGlobalAlignerTest:testEndToEnd

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abra.ReAlignerOptionsTest:testNoParams

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abra.IndelShifterTest:testShiftDelLeft

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abra.SAMRecordUtilsTest:testGetTrailingClips

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abra.CigarUtilsTest:testInjectSplices

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abra.SAMRecordUtilsTest:testGetLeadingClips

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abra.SAMRecordUtilsTest:testSubsetCigar_spanElems1

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abra.SimpleMapperTest:testMapAmbiguousMatch

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abra.cadabra.HomopolymerRunTest:testNone

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