Test
Methods
Passed
Scenarios
Passed
# skipped
# failed
Total
Time
Included
Groups
Excluded
Groups
Command line test
122
122
0
0
0.4 seconds
Class
Method
# of
Scenarios
Start
Time
(ms)
Command line test — passed
abra.ChromosomeRegexTest
testChr1
(unit)
1
1569241693339
7
testChrX
(unit)
1
1569241693347
0
testHg19Decoy
(unit)
1
1569241693347
0
testHg19Gl
(unit)
1
1569241693347
0
testRandom
(unit)
1
1569241693347
1
testUnplaced
(unit)
1
1569241693348
0
abra.CigarUtilsTest
testBeyondMultipleIndels
(unit)
1
1569241693349
2
testCompare
(unit)
1
1569241693351
1
testDeletion
(unit)
1
1569241693352
1
testExactMatch
(unit)
1
1569241693353
0
testExtendContig
(unit)
1
1569241693353
0
testHasNDM
(unit)
1
1569241693354
0
testInjectSplice
(unit)
1
1569241693354
0
testInjectSplices
(unit)
1
1569241693355
0
testInsertion
(unit)
1
1569241693355
0
testInsertionAtStart
(unit)
1
1569241693355
1
testInsertionPartialOverlapAtEnd
(unit)
1
1569241693356
0
testInsertionPartialOverlapAtStart
(unit)
1
1569241693356
0
testMatchSubset
(unit)
1
1569241693357
0
testMultipleIndels
(unit)
1
1569241693357
0
testReadBeyondDeletion
(unit)
1
1569241693358
0
testReadBeyondInsertion
(unit)
1
1569241693359
0
testSkipDeletionAtEnd
(unit)
1
1569241693359
0
testSkipDeletionAtStart
(unit)
1
1569241693359
1
abra.FeatureTest
testOverlaps
(unit)
1
1569241693360
1
abra.CigarUtilsTest
testSkipDeletionWithinStart
(unit)
1
1569241693360
0
testSkipInsertionAtEnd
(unit)
1
1569241693360
0
abra.cadabra.HomopolymerRunTest
testBasic
(unit)
1
1569241693361
2
testLeading
(unit)
1
1569241693363
0
testNone
(unit)
1
1569241693363
0
abra.IndelShifterTest
testShiftCigarLeft_basic
(unit)
1
1569241693363
3
abra.cadabra.HomopolymerRunTest
testTrailing
(unit)
1
1569241693363
0
abra.IndelShifterTest
testShiftCigarLeft_complex
(unit)
1
1569241693366
0
testShiftCigarLeft_insertAtTail
(unit)
1
1569241693366
0
testShiftCigarLeft_multipleIndels
(unit)
1
1569241693367
0
testShiftCigarLeft_softClipping
(unit)
1
1569241693367
0
testShiftDelLeft
(unit)
1
1569241693367
1
testShiftIndelsLeft
(unit)
1
1569241693369
27
testShiftIndelsLeft_LocalRef
(unit)
1
1569241693396
1
abra.JunctionUtilsTest
testCombineJunctions
(unit)
1
1569241693397
3
testGetRegionJunctions
(unit)
1
1569241693400
3
testLoadJunctionsFromGtf
(unit)
1
1569241693403
4
abra.MultiSamReaderTest
testReadTwoBams
(unit)
1
1569241693407
110
abra.ReAlignerOptionsTest
testBamParams
(unit)
1
1569241693517
37
testNoParams
(unit)
1
1569241693555
5
abra.ReadEvaluatorTest
testMapToMultipleContigsSynonymously
(unit)
1
1569241693561
5
testMultimapWithinContig
(unit)
1
1569241693566
1
testSelectBestAlignment
(unit)
1
1569241693567
0
testSingleAlignmentSingleContig
(unit)
1
1569241693567
1
testSingleAlignmentSingleContig_noImprovement
(unit)
1
1569241693568
0
testSingleAlignmentSingleContig_reverseComplement
(unit)
1
1569241693568
0
abra.RealignerTest
testCollapseRegions
(unit)
1
1569241693569
0
testPairJunctions
(unit)
1
1569241693569
6
abra.cadabra.RepeatUtilsTest
testGetRepeatPeriod_HpRun
(unit)
1
1569241693575
1
abra.RealignerTest
testPairJunctions_cannotAppearInSameContig
(unit)
1
1569241693575
0
abra.cadabra.RepeatUtilsTest
testGetRepeatPeriod_NoRepeat
(unit)
1
1569241693576
0
testGetRepeatPeriod_NoRepeat1
(unit)
1
1569241693576
0
testGetRepeatPeriod_Str1
(unit)
1
1569241693576
0
testGetRepeatPeriod_Str2
(unit)
1
1569241693577
0
testGetRepeatPeriod_Str3
(unit)
1
1569241693577
0
testGetRepeatUnit_Homopolymer
(unit)
1
1569241693577
0
testGetRepeatUnit_NearHomopolymer1
(unit)
1
1569241693577
0
testGetRepeatUnit_NearHomopolymer2
(unit)
1
1569241693577
0
testGetRepeatUnit_NearHomopolymer3
(unit)
1
1569241693578
0
testGetRepeatUnit_NearStr1
(unit)
1
1569241693578
0
testGetRepeatUnit_SingleNt
(unit)
1
1569241693578
0
testGetRepeatUnit_Str1
(unit)
1
1569241693578
0
testGetRepeatUnit_Str2
(unit)
1
1569241693578
1
abra.SAMRecordUtilsTest
testGetLeadingClips
(unit)
1
1569241693579
0
testGetLeadingClips_empty
(unit)
1
1569241693579
0
testGetMappedReadPortion
(unit)
1
1569241693579
0
abra.cadabra.RepeatUtilsTest
testGetRepeatUnit_Str3
(unit)
1
1569241693579
0
abra.SAMRecordUtilsTest
testGetTrailingClips
(unit)
1
1569241693580
0
testGetTrailingClips_empty
(unit)
1
1569241693580
0
testMergeSequences
(unit)
1
1569241693580
1
testMergeSequences_discordantMismatch
(unit)
1
1569241693581
0
testMergeSequences_multipleHeadHits
(unit)
1
1569241693581
0
testMergeSequences_preferredMismatch
(unit)
1
1569241693582
0
testMergeSequences_tooManyMismatches
(unit)
1
1569241693582
0
testRemoveSoftClips_withDeletionAndSoftClipAtEnd
(unit)
1
1569241693582
0
testRemoveSoftClips_withDeletionAndSoftClipAtStart
(unit)
1
1569241693582
0
testSubsetCigar_deletion
(unit)
1
1569241693582
1
testSubsetCigar_exact
(unit)
1
1569241693583
0
testSubsetCigar_lessThan1Elem
(unit)
1
1569241693583
0
testSubsetCigar_lessThan1Elem2
(unit)
1
1569241693583
0
testSubsetCigar_lessThan1Elem3
(unit)
1
1569241693583
0
testSubsetCigar_lessThanFirstElem
(unit)
1
1569241693584
0
testSubsetCigar_long
(unit)
1
1569241693584
0
testSubsetCigar_skipAndSpan1
(unit)
1
1569241693584
0
testSubsetCigar_skipAndSpan2
(unit)
1
1569241693585
0
testSubsetCigar_skipElem
(unit)
1
1569241693585
0
testSubsetCigar_skipElem2
(unit)
1
1569241693585
0
testSubsetCigar_spanAll1
(unit)
1
1569241693585
0
testSubsetCigar_spanAll2
(unit)
1
1569241693585
0
testSubsetCigar_spanAll3
(unit)
1
1569241693586
0
testSubsetCigar_spanAll4
(unit)
1
1569241693586
0
testSubsetCigar_spanElems1
(unit)
1
1569241693586
0
testSubsetCigar_spanElems2
(unit)
1
1569241693586
0
testSubsetCigar_spanElems3
(unit)
1
1569241693586
1
abra.ScoredContigTest
testConvertAndFilter
(unit)
1
1569241693587
1
abra.SemiGlobalAlignerTest
testBigDel
(unit)
1
1569241693588
7
testDelete
(unit)
1
1569241693595
0
testEndToEnd
(unit)
1
1569241693595
0
testExactMatch
(unit)
1
1569241693596
0
testInsert
(unit)
1
1569241693596
0
testInsert2
(unit)
1
1569241693596
3
testLeadingInsert
(unit)
1
1569241693599
1
testMismatches
(unit)
1
1569241693600
0
testTrailingInsert
(unit)
1
1569241693600
1
testUnderflowBug
(unit)
1
1569241693601
100
abra.SimpleMapperTest
testMapAmbiguousMatch
(unit)
1
1569241693701
1
testMapAmbiguousMatchWithMismatches
(unit)
1
1569241693702
0
testMapExact
(unit)
1
1569241693702
1
testMapFiveMismatches
(unit)
1
1569241693703
0
testMapNoSeedMatch
(unit)
1
1569241693703
1
testMapOneMismatch
(unit)
1
1569241693704
0
testMapSixMismatches
(unit)
1
1569241693704
1
testMapSixMismatchesIncreasedMismatchRate
(unit)
1
1569241693705
0
testReverseComplement2Mismatches
(unit)
1
1569241693705
1
testReverseComplementExact
(unit)
1
1569241693706
0
testShortAmbiguousMatch
(unit)
1
1569241693706
0
testSimple1Mismatch
(unit)
1
1569241693706
0
Command line test
abra.cadabra.RepeatUtilsTest:testGetRepeatUnit_NearHomopolymer3
back to summary
abra.CigarUtilsTest:testMultipleIndels
back to summary
abra.JunctionUtilsTest:testLoadJunctionsFromGtf
back to summary
abra.CigarUtilsTest:testSkipDeletionAtEnd
back to summary
abra.SAMRecordUtilsTest:testSubsetCigar_skipAndSpan2
back to summary
abra.MultiSamReaderTest:testReadTwoBams
back to summary
abra.SAMRecordUtilsTest:testRemoveSoftClips_withDeletionAndSoftClipAtStart
back to summary
abra.SAMRecordUtilsTest:testSubsetCigar_skipAndSpan1
back to summary
abra.IndelShifterTest:testShiftCigarLeft_complex
back to summary
abra.CigarUtilsTest:testReadBeyondDeletion
back to summary
abra.cadabra.RepeatUtilsTest:testGetRepeatPeriod_HpRun
back to summary
abra.SAMRecordUtilsTest:testGetTrailingClips_empty
back to summary
abra.SemiGlobalAlignerTest:testMismatches
back to summary
abra.SAMRecordUtilsTest:testRemoveSoftClips_withDeletionAndSoftClipAtEnd
back to summary
abra.SemiGlobalAlignerTest:testLeadingInsert
back to summary
abra.SimpleMapperTest:testMapFiveMismatches
back to summary
abra.SAMRecordUtilsTest:testGetLeadingClips_empty
back to summary
abra.SimpleMapperTest:testShortAmbiguousMatch
back to summary
abra.ReAlignerOptionsTest:testBamParams
back to summary
abra.cadabra.HomopolymerRunTest:testLeading
back to summary
abra.cadabra.RepeatUtilsTest:testGetRepeatPeriod_Str2
back to summary
abra.ChromosomeRegexTest:testUnplaced
back to summary
abra.CigarUtilsTest:testReadBeyondInsertion
back to summary
abra.cadabra.RepeatUtilsTest:testGetRepeatPeriod_Str3
back to summary
abra.SemiGlobalAlignerTest:testExactMatch
back to summary
abra.SAMRecordUtilsTest:testSubsetCigar_spanAll1
back to summary
abra.CigarUtilsTest:testInsertion
back to summary
abra.SAMRecordUtilsTest:testMergeSequences
back to summary
abra.ChromosomeRegexTest:testChrX
back to summary
abra.SAMRecordUtilsTest:testSubsetCigar_long
back to summary
abra.SemiGlobalAlignerTest:testInsert2
back to summary
abra.CigarUtilsTest:testInjectSplice
back to summary
abra.ReadEvaluatorTest:testSingleAlignmentSingleContig_noImprovement
back to summary
abra.SAMRecordUtilsTest:testSubsetCigar_lessThan1Elem2
back to summary
abra.CigarUtilsTest:testHasNDM
back to summary
abra.ReadEvaluatorTest:testMapToMultipleContigsSynonymously
back to summary
abra.CigarUtilsTest:testCompare
back to summary
abra.SAMRecordUtilsTest:testSubsetCigar_spanAll2
back to summary
abra.CigarUtilsTest:testInsertionAtStart
back to summary
abra.SemiGlobalAlignerTest:testDelete
back to summary
abra.IndelShifterTest:testShiftCigarLeft_softClipping
back to summary
abra.SimpleMapperTest:testReverseComplement2Mismatches
back to summary
abra.IndelShifterTest:testShiftIndelsLeft_LocalRef
back to summary
abra.SimpleMapperTest:testMapNoSeedMatch
back to summary
abra.SimpleMapperTest:testMapOneMismatch
back to summary
abra.JunctionUtilsTest:testGetRegionJunctions
back to summary
abra.cadabra.RepeatUtilsTest:testGetRepeatUnit_Homopolymer
back to summary
abra.SAMRecordUtilsTest:testSubsetCigar_skipElem2
back to summary
abra.SAMRecordUtilsTest:testSubsetCigar_deletion
back to summary
abra.cadabra.RepeatUtilsTest:testGetRepeatUnit_NearHomopolymer1
back to summary
abra.ReadEvaluatorTest:testMultimapWithinContig
back to summary
abra.CigarUtilsTest:testExactMatch
back to summary
abra.cadabra.RepeatUtilsTest:testGetRepeatUnit_Str3
back to summary
abra.ReadEvaluatorTest:testSingleAlignmentSingleContig_reverseComplement
back to summary
abra.SemiGlobalAlignerTest:testTrailingInsert
back to summary
abra.JunctionUtilsTest:testCombineJunctions
back to summary
abra.SAMRecordUtilsTest:testMergeSequences_discordantMismatch
back to summary
abra.RealignerTest:testPairJunctions
back to summary
abra.ScoredContigTest:testConvertAndFilter
back to summary
abra.SAMRecordUtilsTest:testSubsetCigar_lessThan1Elem
back to summary
abra.SAMRecordUtilsTest:testSubsetCigar_lessThan1Elem3
back to summary
abra.cadabra.HomopolymerRunTest:testBasic
back to summary
abra.CigarUtilsTest:testExtendContig
back to summary
abra.cadabra.RepeatUtilsTest:testGetRepeatUnit_NearHomopolymer2
back to summary
abra.CigarUtilsTest:testMatchSubset
back to summary
abra.cadabra.RepeatUtilsTest:testGetRepeatUnit_NearStr1
back to summary
abra.SemiGlobalAlignerTest:testInsert
back to summary
abra.CigarUtilsTest:testSkipDeletionWithinStart
back to summary
abra.CigarUtilsTest:testInsertionPartialOverlapAtEnd
back to summary
abra.ReadEvaluatorTest:testSingleAlignmentSingleContig
back to summary
abra.SimpleMapperTest:testMapAmbiguousMatchWithMismatches
back to summary
abra.SAMRecordUtilsTest:testMergeSequences_multipleHeadHits
back to summary
abra.cadabra.HomopolymerRunTest:testTrailing
back to summary
abra.SemiGlobalAlignerTest:testUnderflowBug
back to summary
abra.ChromosomeRegexTest:testRandom
back to summary
abra.SAMRecordUtilsTest:testSubsetCigar_lessThanFirstElem
back to summary
abra.SAMRecordUtilsTest:testSubsetCigar_spanElems2
back to summary
abra.IndelShifterTest:testShiftCigarLeft_insertAtTail
back to summary
abra.SimpleMapperTest:testReverseComplementExact
back to summary
abra.CigarUtilsTest:testSkipInsertionAtEnd
back to summary
abra.cadabra.RepeatUtilsTest:testGetRepeatPeriod_NoRepeat
back to summary
abra.IndelShifterTest:testShiftCigarLeft_multipleIndels
back to summary
abra.FeatureTest:testOverlaps
back to summary
abra.cadabra.RepeatUtilsTest:testGetRepeatUnit_SingleNt
back to summary
abra.RealignerTest:testCollapseRegions
back to summary
abra.cadabra.RepeatUtilsTest:testGetRepeatUnit_Str1
back to summary
abra.SAMRecordUtilsTest:testSubsetCigar_skipElem
back to summary
abra.ReadEvaluatorTest:testSelectBestAlignment
back to summary
abra.IndelShifterTest:testShiftIndelsLeft
back to summary
abra.SimpleMapperTest:testMapSixMismatchesIncreasedMismatchRate
back to summary
abra.cadabra.RepeatUtilsTest:testGetRepeatPeriod_NoRepeat1
back to summary
abra.SAMRecordUtilsTest:testSubsetCigar_spanAll4
back to summary
abra.CigarUtilsTest:testInsertionPartialOverlapAtStart
back to summary
abra.SAMRecordUtilsTest:testSubsetCigar_spanAll3
back to summary
abra.SimpleMapperTest:testMapSixMismatches
back to summary
abra.SAMRecordUtilsTest:testMergeSequences_tooManyMismatches
back to summary
abra.ChromosomeRegexTest:testHg19Decoy
back to summary
abra.CigarUtilsTest:testDeletion
back to summary
abra.SemiGlobalAlignerTest:testBigDel
back to summary
abra.SAMRecordUtilsTest:testGetMappedReadPortion
back to summary
abra.CigarUtilsTest:testBeyondMultipleIndels
back to summary
abra.cadabra.RepeatUtilsTest:testGetRepeatUnit_Str2
back to summary
abra.SAMRecordUtilsTest:testSubsetCigar_exact
back to summary
abra.ChromosomeRegexTest:testHg19Gl
back to summary
abra.ChromosomeRegexTest:testChr1
back to summary
abra.SimpleMapperTest:testSimple1Mismatch
back to summary
abra.SAMRecordUtilsTest:testSubsetCigar_spanElems3
back to summary
abra.CigarUtilsTest:testSkipDeletionAtStart
back to summary
abra.SAMRecordUtilsTest:testMergeSequences_preferredMismatch
back to summary
abra.SimpleMapperTest:testMapExact
back to summary
abra.IndelShifterTest:testShiftCigarLeft_basic
back to summary
abra.cadabra.RepeatUtilsTest:testGetRepeatPeriod_Str1
back to summary
abra.RealignerTest:testPairJunctions_cannotAppearInSameContig
back to summary
abra.SemiGlobalAlignerTest:testEndToEnd
back to summary
abra.ReAlignerOptionsTest:testNoParams
back to summary
abra.IndelShifterTest:testShiftDelLeft
back to summary
abra.SAMRecordUtilsTest:testGetTrailingClips
back to summary
abra.CigarUtilsTest:testInjectSplices
back to summary
abra.SAMRecordUtilsTest:testGetLeadingClips
back to summary
abra.SAMRecordUtilsTest:testSubsetCigar_spanElems1
back to summary
abra.SimpleMapperTest:testMapAmbiguousMatch
back to summary
abra.cadabra.HomopolymerRunTest:testNone
back to summary