Command line test

Tests passed/Failed/Skipped:122/0/0
Started on:Mon Sep 23 14:28:13 CEST 2019
Total time:0 seconds (378 ms)
Included groups:
Excluded groups:

(Hover the method name to see the test class name)

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