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 |