Test results
1 suite
abra.RealignerTest
testCollapseRegions
testPairJunctions
testPairJunctions_cannotAppearInSameContig
abra.ScoredContigTest
testConvertAndFilter
abra.cadabra.RepeatUtilsTest
testGetRepeatPeriod_HpRun
testGetRepeatPeriod_NoRepeat
testGetRepeatPeriod_NoRepeat1
testGetRepeatPeriod_Str1
testGetRepeatPeriod_Str2
testGetRepeatPeriod_Str3
testGetRepeatUnit_Homopolymer
testGetRepeatUnit_NearHomopolymer1
testGetRepeatUnit_NearHomopolymer2
testGetRepeatUnit_NearHomopolymer3
testGetRepeatUnit_NearStr1
testGetRepeatUnit_SingleNt
testGetRepeatUnit_Str1
testGetRepeatUnit_Str2
testGetRepeatUnit_Str3
abra.SAMRecordUtilsTest
testGetLeadingClips
testGetLeadingClips_empty
testGetMappedReadPortion
testGetTrailingClips
testGetTrailingClips_empty
testMergeSequences
testMergeSequences_discordantMismatch
testMergeSequences_multipleHeadHits
testMergeSequences_preferredMismatch
testMergeSequences_tooManyMismatches
testRemoveSoftClips_withDeletionAndSoftClipAtEnd
testRemoveSoftClips_withDeletionAndSoftClipAtStart
testSubsetCigar_deletion
testSubsetCigar_exact
testSubsetCigar_lessThan1Elem
testSubsetCigar_lessThan1Elem2
testSubsetCigar_lessThan1Elem3
testSubsetCigar_lessThanFirstElem
testSubsetCigar_long
testSubsetCigar_skipAndSpan1
testSubsetCigar_skipAndSpan2
testSubsetCigar_skipElem
testSubsetCigar_skipElem2
testSubsetCigar_spanAll1
testSubsetCigar_spanAll2
testSubsetCigar_spanAll3
testSubsetCigar_spanAll4
testSubsetCigar_spanElems1
testSubsetCigar_spanElems2
testSubsetCigar_spanElems3
abra.CigarUtilsTest
testBeyondMultipleIndels
testCompare
testDeletion
testExactMatch
testExtendContig
testHasNDM
testInjectSplice
testInjectSplices
testInsertion
testInsertionAtStart
testInsertionPartialOverlapAtEnd
testInsertionPartialOverlapAtStart
testMatchSubset
testMultipleIndels
testReadBeyondDeletion
testReadBeyondInsertion
testSkipDeletionAtEnd
testSkipDeletionAtStart
testSkipDeletionWithinStart
testSkipInsertionAtEnd
abra.MultiSamReaderTest
testReadTwoBams
abra.FeatureTest
testOverlaps
abra.ReadEvaluatorTest
testMapToMultipleContigsSynonymously
testMultimapWithinContig
testSelectBestAlignment
testSingleAlignmentSingleContig
testSingleAlignmentSingleContig_noImprovement
testSingleAlignmentSingleContig_reverseComplement
abra.ChromosomeRegexTest
testChr1
testChrX
testHg19Decoy
testHg19Gl
testRandom
testUnplaced
abra.cadabra.HomopolymerRunTest
testBasic
testLeading
testNone
testTrailing
abra.IndelShifterTest
testShiftCigarLeft_basic
testShiftCigarLeft_complex
testShiftCigarLeft_insertAtTail
testShiftCigarLeft_multipleIndels
testShiftCigarLeft_softClipping
testShiftDelLeft
testShiftIndelsLeft
testShiftIndelsLeft_LocalRef
abra.SimpleMapperTest
testMapAmbiguousMatch
testMapAmbiguousMatchWithMismatches
testMapExact
testMapFiveMismatches
testMapNoSeedMatch
testMapOneMismatch
testMapSixMismatches
testMapSixMismatchesIncreasedMismatchRate
testReverseComplement2Mismatches
testReverseComplementExact
testShortAmbiguousMatch
testSimple1Mismatch
abra.JunctionUtilsTest
testCombineJunctions
testGetRegionJunctions
testLoadJunctionsFromGtf
abra.SemiGlobalAlignerTest
testBigDel
testDelete
testEndToEnd
testExactMatch
testInsert
testInsert2
testLeadingInsert
testMismatches
testTrailingInsert
testUnderflowBug
abra.ReAlignerOptionsTest
testBamParams
testNoParams
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE suite SYSTEM "http://testng.org/testng-1.0.dtd">
<suite name="Command line suite" verbose="0">
  <test name="Command line test" preserve-order="false">
    <classes>
      <class name="abra.SimpleMapperTest"/>
      <class name="abra.ReadEvaluatorTest"/>
      <class name="abra.ChromosomeRegexTest"/>
      <class name="abra.ReAlignerOptionsTest"/>
      <class name="abra.CigarUtilsTest"/>
      <class name="abra.SAMRecordUtilsTest"/>
      <class name="abra.FeatureTest"/>
      <class name="abra.IndelShifterTest"/>
      <class name="abra.RealignerTest"/>
      <class name="abra.cadabra.HomopolymerRunTest"/>
      <class name="abra.cadabra.RepeatUtilsTest"/>
      <class name="abra.ReverseComplementorTest"/>
      <class name="abra.JunctionUtilsTest"/>
      <class name="abra.MultiSamReaderTest"/>
      <class name="abra.ScoredContigTest"/>
      <class name="abra.SemiGlobalAlignerTest"/>
    </classes>
  </test> <!-- Command line test -->
</suite> <!-- Command line suite -->
            
Tests for Command line suite
  • Command line test (16 classes)
Groups for Command line suite
unit
testBamParams
testBasic
testBeyondMultipleIndels
testBigDel
testChr1
testChrX
testCollapseRegions
testCombineJunctions
testCompare
testConvertAndFilter
testDelete
testDeletion
testEndToEnd
testExactMatch
testExtendContig
testGetLeadingClips
testGetLeadingClips_empty
testGetMappedReadPortion
testGetRegionJunctions
testGetRepeatPeriod_HpRun
testGetRepeatPeriod_NoRepeat
testGetRepeatPeriod_NoRepeat1
testGetRepeatPeriod_Str1
testGetRepeatPeriod_Str2
testGetRepeatPeriod_Str3
testGetRepeatUnit_Homopolymer
testGetRepeatUnit_NearHomopolymer1
testGetRepeatUnit_NearHomopolymer2
testGetRepeatUnit_NearHomopolymer3
testGetRepeatUnit_NearStr1
testGetRepeatUnit_SingleNt
testGetRepeatUnit_Str1
testGetRepeatUnit_Str2
testGetRepeatUnit_Str3
testGetTrailingClips
testGetTrailingClips_empty
testHasNDM
testHg19Decoy
testHg19Gl
testInjectSplice
testInjectSplices
testInsert
testInsert2
testInsertion
testInsertionAtStart
testInsertionPartialOverlapAtEnd
testInsertionPartialOverlapAtStart
testLeading
testLeadingInsert
testLoadJunctionsFromGtf
testMapAmbiguousMatch
testMapAmbiguousMatchWithMismatches
testMapExact
testMapFiveMismatches
testMapNoSeedMatch
testMapOneMismatch
testMapSixMismatches
testMapSixMismatchesIncreasedMismatchRate
testMapToMultipleContigsSynonymously
testMatchSubset
testMergeSequences
testMergeSequences_discordantMismatch
testMergeSequences_multipleHeadHits
testMergeSequences_preferredMismatch
testMergeSequences_tooManyMismatches
testMismatches
testMultimapWithinContig
testMultipleIndels
testNoParams
testNone
testOverlaps
testPairJunctions
testPairJunctions_cannotAppearInSameContig
testRandom
testReadBeyondDeletion
testReadBeyondInsertion
testReadTwoBams
testRemoveSoftClips_withDeletionAndSoftClipAtEnd
testRemoveSoftClips_withDeletionAndSoftClipAtStart
testReverseComplement2Mismatches
testReverseComplementExact
testSelectBestAlignment
testShiftCigarLeft_basic
testShiftCigarLeft_complex
testShiftCigarLeft_insertAtTail
testShiftCigarLeft_multipleIndels
testShiftCigarLeft_softClipping
testShiftDelLeft
testShiftIndelsLeft
testShiftIndelsLeft_LocalRef
testShortAmbiguousMatch
testSimple1Mismatch
testSingleAlignmentSingleContig
testSingleAlignmentSingleContig_noImprovement
testSingleAlignmentSingleContig_reverseComplement
testSkipDeletionAtEnd
testSkipDeletionAtStart
testSkipDeletionWithinStart
testSkipInsertionAtEnd
testSubsetCigar_deletion
testSubsetCigar_exact
testSubsetCigar_lessThan1Elem
testSubsetCigar_lessThan1Elem2
testSubsetCigar_lessThan1Elem3
testSubsetCigar_lessThanFirstElem
testSubsetCigar_long
testSubsetCigar_skipAndSpan1
testSubsetCigar_skipAndSpan2
testSubsetCigar_skipElem
testSubsetCigar_skipElem2
testSubsetCigar_spanAll1
testSubsetCigar_spanAll2
testSubsetCigar_spanAll3
testSubsetCigar_spanAll4
testSubsetCigar_spanElems1
testSubsetCigar_spanElems2
testSubsetCigar_spanElems3
testTrailing
testTrailingInsert
testUnderflowBug
testUnplaced
Times for Command line suite
Total running time: 347 ms
Reporter output for Command line suite
0 ignored methods
Methods in chronological order
abra.ChromosomeRegexTest
testChr1 0 ms
testChrX 8 ms
testHg19Decoy 8 ms
testHg19Gl 8 ms
testRandom 8 ms
abra.CigarUtilsTest
beforeTest 9 ms
abra.ChromosomeRegexTest
testUnplaced 9 ms
abra.CigarUtilsTest
testBeyondMultipleIndels 10 ms
beforeTest 12 ms
testCompare 12 ms
beforeTest 13 ms
testDeletion 13 ms
beforeTest 14 ms
beforeTest 14 ms
testExactMatch 14 ms
testExtendContig 14 ms
beforeTest 15 ms
beforeTest 15 ms
testHasNDM 15 ms
testInjectSplice 15 ms
beforeTest 16 ms
beforeTest 16 ms
beforeTest 16 ms
testInjectSplices 16 ms
testInsertion 16 ms
testInsertionAtStart 16 ms
beforeTest 17 ms
beforeTest 17 ms
testInsertionPartialOverlapAtEnd 17 ms
testInsertionPartialOverlapAtStart 17 ms
beforeTest 18 ms
beforeTest 18 ms
beforeTest 18 ms
testMatchSubset 18 ms
testMultipleIndels 18 ms
beforeTest 19 ms
testReadBeyondDeletion 19 ms
beforeTest 20 ms
beforeTest 20 ms
testReadBeyondInsertion 20 ms
testSkipDeletionAtEnd 20 ms
testSkipDeletionAtStart 20 ms
beforeTest 21 ms
beforeTest 21 ms
abra.FeatureTest
testOverlaps 21 ms
abra.CigarUtilsTest
testSkipDeletionWithinStart 21 ms
testSkipInsertionAtEnd 21 ms
abra.cadabra.HomopolymerRunTest
testBasic 22 ms
testLeading 24 ms
testNone 24 ms
abra.IndelShifterTest
testShiftCigarLeft_basic 24 ms
abra.cadabra.HomopolymerRunTest
testTrailing 24 ms
abra.IndelShifterTest
testShiftCigarLeft_complex 27 ms
testShiftCigarLeft_insertAtTail 27 ms
testShiftCigarLeft_multipleIndels 28 ms
testShiftCigarLeft_softClipping 28 ms
testShiftDelLeft 28 ms
testShiftIndelsLeft 30 ms
testShiftIndelsLeft_LocalRef 57 ms
abra.JunctionUtilsTest
testCombineJunctions 58 ms
testGetRegionJunctions 61 ms
testLoadJunctionsFromGtf 64 ms
abra.MultiSamReaderTest
testReadTwoBams 68 ms
abra.ReAlignerOptionsTest
testBamParams 178 ms
testNoParams 216 ms
abra.ReadEvaluatorTest
setUp 221 ms
testMapToMultipleContigsSynonymously 222 ms
setUp 227 ms
testMultimapWithinContig 227 ms
setUp 228 ms
setUp 228 ms
testSelectBestAlignment 228 ms
testSingleAlignmentSingleContig 228 ms
setUp 229 ms
setUp 229 ms
testSingleAlignmentSingleContig_noImprovement 229 ms
testSingleAlignmentSingleContig_reverseComplement 229 ms
abra.RealignerTest
testCollapseRegions 230 ms
testPairJunctions 230 ms
abra.cadabra.RepeatUtilsTest
testGetRepeatPeriod_HpRun 236 ms
abra.RealignerTest
testPairJunctions_cannotAppearInSameContig 236 ms
abra.cadabra.RepeatUtilsTest
testGetRepeatPeriod_NoRepeat 237 ms
testGetRepeatPeriod_NoRepeat1 237 ms
testGetRepeatPeriod_Str1 237 ms
testGetRepeatPeriod_Str2 238 ms
testGetRepeatPeriod_Str3 238 ms
testGetRepeatUnit_Homopolymer 238 ms
testGetRepeatUnit_NearHomopolymer1 238 ms
testGetRepeatUnit_NearHomopolymer2 238 ms
testGetRepeatUnit_NearHomopolymer3 239 ms
testGetRepeatUnit_NearStr1 239 ms
testGetRepeatUnit_SingleNt 239 ms
testGetRepeatUnit_Str1 239 ms
testGetRepeatUnit_Str2 239 ms
abra.SAMRecordUtilsTest
testGetLeadingClips 240 ms
testGetLeadingClips_empty 240 ms
testGetMappedReadPortion 240 ms
abra.cadabra.RepeatUtilsTest
testGetRepeatUnit_Str3 240 ms
abra.SAMRecordUtilsTest
testGetTrailingClips 241 ms
testGetTrailingClips_empty 241 ms
testMergeSequences 241 ms
testMergeSequences_discordantMismatch 242 ms
testMergeSequences_multipleHeadHits 242 ms
testMergeSequences_preferredMismatch 243 ms
testMergeSequences_tooManyMismatches 243 ms
testRemoveSoftClips_withDeletionAndSoftClipAtEnd 243 ms
testRemoveSoftClips_withDeletionAndSoftClipAtStart 243 ms
testSubsetCigar_deletion 243 ms
testSubsetCigar_exact 244 ms
testSubsetCigar_lessThan1Elem 244 ms
testSubsetCigar_lessThan1Elem2 244 ms
testSubsetCigar_lessThan1Elem3 244 ms
testSubsetCigar_lessThanFirstElem 245 ms
testSubsetCigar_long 245 ms
testSubsetCigar_skipAndSpan1 245 ms
testSubsetCigar_skipAndSpan2 246 ms
testSubsetCigar_skipElem 246 ms
testSubsetCigar_skipElem2 246 ms
testSubsetCigar_spanAll1 246 ms
testSubsetCigar_spanAll2 246 ms
testSubsetCigar_spanAll3 247 ms
testSubsetCigar_spanAll4 247 ms
testSubsetCigar_spanElems1 247 ms
testSubsetCigar_spanElems2 247 ms
testSubsetCigar_spanElems3 247 ms
abra.ScoredContigTest
testConvertAndFilter 248 ms
abra.SemiGlobalAlignerTest
testBigDel 249 ms
testDelete 256 ms
testEndToEnd 256 ms
testExactMatch 257 ms
testInsert 257 ms
testInsert2 257 ms
testLeadingInsert 260 ms
testMismatches 261 ms
testTrailingInsert 261 ms
testUnderflowBug 262 ms
abra.SimpleMapperTest
testMapAmbiguousMatch 362 ms
testMapAmbiguousMatchWithMismatches 363 ms
testMapExact 363 ms
testMapFiveMismatches 364 ms
testMapNoSeedMatch 364 ms
testMapOneMismatch 365 ms
testMapSixMismatches 365 ms
testMapSixMismatchesIncreasedMismatchRate 366 ms
testReverseComplement2Mismatches 366 ms
testReverseComplementExact 367 ms
testShortAmbiguousMatch 367 ms
testSimple1Mismatch 367 ms