Package org.broadinstitute.hellbender.utils.smithwaterman

Ignored tests

• SmithWatermanIntelAlignerUnitTest. testDegenerateAlignmentWithIndelsAtBothEnds
• SmithWatermanIntelAlignerUnitTest. testForIdenticalAlignmentsWithDifferingFlankLengths
• SmithWatermanIntelAlignerUnitTest. testIndelsAtStartAndEnd
• SmithWatermanIntelAlignerUnitTest. testOddNoAlignment[0](AAAGACTACTG, AACGGACACTG, org.broadinstitute.gatk.nativebindings.smithwaterman.SWParameters@6aa7b47b, 1, 2M2I3M1D4M)
• SmithWatermanIntelAlignerUnitTest. testOddNoAlignment[1](AAAGACTACTG, AACGGACACTG, org.broadinstitute.gatk.nativebindings.smithwaterman.SWParameters@3f3c7536, 0, 11M)
• SmithWatermanIntelAlignerUnitTest. testReadAlignedToRefComplexAlignment[0](AAAGGACTGACTG, ACTGACTGACTG, 1, 12M)
• SmithWatermanIntelAlignerUnitTest. testSubstringMatchLong[0](359, 7M, SOFTCLIP)
• SmithWatermanIntelAlignerUnitTest. testSubstringMatchLong[1](0, 1M358D6M29D, INDEL)
• SmithWatermanIntelAlignerUnitTest. testSubstringMatchLong[2](0, 1M1D6M, LEADING_INDEL)
• SmithWatermanIntelAlignerUnitTest. testSubstringMatchLong[3](359, 7M, IGNORE)
• SmithWatermanIntelAlignerUnitTest. testSubstringMatch[0](3, 5M, SOFTCLIP)
• SmithWatermanIntelAlignerUnitTest. testSubstringMatch[1](0, 3D5M, INDEL)
• SmithWatermanIntelAlignerUnitTest. testSubstringMatch[2](0, 3D5M, LEADING_INDEL)
• SmithWatermanIntelAlignerUnitTest. testSubstringMatch[3](3, 5M, IGNORE)

Classes