






<?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