Class name Method name Groups
abra.FeatureTest   
@Test
  testOverlaps unit
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
abra.SAMRecordUtilsTest   
@Test
  testSubsetCigar_lessThan1Elem unit
  testSubsetCigar_spanAll1 unit
  testSubsetCigar_spanAll2 unit
  testSubsetCigar_spanAll3 unit
  testSubsetCigar_spanAll4 unit
  testMergeSequences unit
  testSubsetCigar_deletion unit
  testSubsetCigar_lessThan1Elem2 unit
  testGetLeadingClips_empty unit
  testSubsetCigar_lessThan1Elem3 unit
  testGetLeadingClips unit
  testRemoveSoftClips_withDeletionAndSoftClipAtStart unit
  testGetTrailingClips unit
  testRemoveSoftClips_withDeletionAndSoftClipAtEnd unit
  testMergeSequences_discordantMismatch unit
  testSubsetCigar_exact unit
  testSubsetCigar_spanElems3 unit
  testSubsetCigar_spanElems1 unit
  testSubsetCigar_spanElems2 unit
  testSubsetCigar_long unit
  testMergeSequences_preferredMismatch unit
  testSubsetCigar_lessThanFirstElem unit
  testSubsetCigar_skipAndSpan2 unit
  testSubsetCigar_skipAndSpan1 unit
  testSubsetCigar_skipElem unit
  testGetMappedReadPortion unit
  testSubsetCigar_skipElem2 unit
  testMergeSequences_tooManyMismatches unit
  testGetTrailingClips_empty unit
  testMergeSequences_multipleHeadHits unit
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
abra.IndelShifterTest   
@Test
  testShiftCigarLeft_insertAtTail unit
  testShiftIndelsLeft unit
  testShiftCigarLeft_complex unit
  testShiftCigarLeft_basic unit
  testShiftIndelsLeft_LocalRef unit
  testShiftCigarLeft_multipleIndels unit
  testShiftDelLeft unit
  testShiftCigarLeft_softClipping unit
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
abra.RealignerTest   
@Test
  testPairJunctions unit
  testPairJunctions_cannotAppearInSameContig unit
  testCollapseRegions unit
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
abra.ReadEvaluatorTest   
@Test
  testMultimapWithinContig unit
  testSingleAlignmentSingleContig_reverseComplement unit
  testSelectBestAlignment unit
  testMapToMultipleContigsSynonymously unit
  testSingleAlignmentSingleContig_noImprovement unit
  testSingleAlignmentSingleContig unit
@BeforeClass
@BeforeMethod
  setUp  
@AfterMethod
@AfterClass
abra.MultiSamReaderTest   
@Test
  testReadTwoBams unit
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
abra.cadabra.RepeatUtilsTest   
@Test
  testGetRepeatUnit_NearHomopolymer1 unit
  testGetRepeatUnit_NearHomopolymer2 unit
  testGetRepeatUnit_NearHomopolymer3 unit
  testGetRepeatUnit_SingleNt unit
  testGetRepeatPeriod_HpRun unit
  testGetRepeatPeriod_NoRepeat1 unit
  testGetRepeatPeriod_NoRepeat unit
  testGetRepeatPeriod_Str1 unit
  testGetRepeatUnit_Str2 unit
  testGetRepeatUnit_NearStr1 unit
  testGetRepeatUnit_Str1 unit
  testGetRepeatPeriod_Str3 unit
  testGetRepeatPeriod_Str2 unit
  testGetRepeatUnit_Str3 unit
  testGetRepeatUnit_Homopolymer unit
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
abra.ScoredContigTest   
@Test
  testConvertAndFilter unit
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
abra.cadabra.HomopolymerRunTest   
@Test
  testNone unit
  testBasic unit
  testLeading unit
  testTrailing unit
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
abra.SemiGlobalAlignerTest   
@Test
  testDelete unit
  testMismatches unit
  testTrailingInsert unit
  testBigDel unit
  testInsert2 unit
  testEndToEnd unit
  testUnderflowBug unit
  testInsert unit
  testExactMatch unit
  testLeadingInsert unit
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
abra.SimpleMapperTest   
@Test
  testMapOneMismatch unit
  testMapSixMismatches unit
  testReverseComplement2Mismatches unit
  testSimple1Mismatch unit
  testShortAmbiguousMatch unit
  testMapSixMismatchesIncreasedMismatchRate unit
  testMapExact unit
  testMapAmbiguousMatchWithMismatches unit
  testMapAmbiguousMatch unit
  testReverseComplementExact unit
  testMapFiveMismatches unit
  testMapNoSeedMatch unit
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
abra.CigarUtilsTest   
@Test
  testMultipleIndels unit
  testSkipInsertionAtEnd unit
  testHasNDM unit
  testExtendContig unit
  testInsertionAtStart unit
  testSkipDeletionWithinStart unit
  testBeyondMultipleIndels unit
  testInjectSplices unit
  testExactMatch unit
  testSkipDeletionAtStart unit
  testSkipDeletionAtEnd unit
  testDeletion unit
  testMatchSubset unit
  testInsertionPartialOverlapAtStart unit
  testCompare unit
  testReadBeyondDeletion unit
  testInsertionPartialOverlapAtEnd unit
  testInjectSplice unit
  testReadBeyondInsertion unit
  testInsertion unit
@BeforeClass
@BeforeMethod
  beforeTest  
@AfterMethod
@AfterClass
abra.ReAlignerOptionsTest   
@Test
  testNoParams unit
  testBamParams unit
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
abra.JunctionUtilsTest   
@Test
  testGetRegionJunctions unit
  testLoadJunctionsFromGtf unit
  testCombineJunctions unit
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
abra.ChromosomeRegexTest   
@Test
  testChrX unit
  testUnplaced unit
  testHg19Decoy unit
  testChr1 unit
  testRandom unit
  testHg19Gl unit
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass