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| BaseAsciiMap.cpp |
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| BaseAsciiMap.h |
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| BaseQualityHelper.cpp |
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| BaseQualityHelper.h |
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| BaseUtilities.cpp |
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| BaseUtilities.h |
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| BasicHash.cpp |
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| BasicHash.h |
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| BgzfFileType.cpp |
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| BgzfFileType.h |
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| BgzfFileTypeRecovery.cpp |
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| BgzfFileTypeRecovery.h |
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| CharBuffer.cpp |
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| CharBuffer.h |
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| Chromosome.cpp |
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| Chromosome.h |
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| Cigar.cpp |
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| Cigar.h |
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| CigarRoller.cpp |
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| CigarRoller.h |
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| Constant.h |
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| CSG_MD5.h |
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| Error.cpp |
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| Error.h |
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| ErrorHandler.cpp |
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| ErrorHandler.h |
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| FileType.cpp |
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| FileType.h |
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| FortranFormat.cpp |
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| FortranFormat.h |
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| Generic.cpp |
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| Generic.h |
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| GenomeSequence.cpp |
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| GenomeSequence.h |
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| GenomeSequenceHelpers.h |
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| GenotypeLists.cpp |
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| GenotypeLists.h |
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| glfHandler.cpp |
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| glfHandler.h |
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| GreedyTupleAligner.h |
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| GzipFileType.cpp |
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| GzipFileType.h |
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| GzipHeader.cpp |
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| GzipHeader.h |
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| Hash.cpp |
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| Hash.h |
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| IndexBase.cpp |
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| IndexBase.h |
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| InplaceMerge.cpp |
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| InplaceMerge.h |
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| Input.cpp |
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| Input.h |
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| InputFile.cpp |
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| InputFile.h |
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| IntArray.cpp |
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| IntArray.h |
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| IntHash.cpp |
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| IntHash.h |
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| LongHash.h |
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| LongInt.h |
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| LongLongCounter.cpp |
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| LongLongCounter.h |
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| MapFunction.cpp |
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| MapFunction.h |
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| MathConstant.h |
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| MathMatrix.cpp |
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| MathMatrix.h |
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| MathVector.cpp |
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| MathVector.h |
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| MemoryAllocators.cpp |
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| MemoryAllocators.h |
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| MemoryInfo.cpp |
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| MemoryInfo.h |
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| MemoryMap.cpp |
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| MemoryMap.h |
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| MemoryMapArray.cpp |
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| MemoryMapArray.h |
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| MiniDeflate.cpp |
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| MiniDeflate.h |
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| NonOverlapRegions.cpp |
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| NonOverlapRegions.h |
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| PackedVector.h |
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| Parameters.cpp |
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| Parameters.h |
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| Pedigree.cpp |
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| Pedigree.h |
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| PedigreeAlleleFreq.cpp |
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| PedigreeAlleleFreq.h |
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| PedigreeAlleles.h |
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| PedigreeDescription.cpp |
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| PedigreeDescription.h |
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| PedigreeFamily.cpp |
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| PedigreeFamily.h |
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| PedigreeGlobals.cpp |
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| PedigreeGlobals.h |
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| PedigreeLoader.cpp |
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| PedigreePerson.cpp |
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| PedigreePerson.h |
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| PedigreeTrim.cpp |
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| PedigreeTwin.cpp |
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| Performance.h |
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| PhoneHome.cpp |
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| PhoneHome.h |
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| QuickIndex.cpp |
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| QuickIndex.h |
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| Random.cpp |
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| Random.h |
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| ReferenceSequence.cpp |
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| ReferenceSequence.h |
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| ReusableVector.h |
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| SimpleStats.h |
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| SmithWaterman.cpp |
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| SmithWaterman.h |
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| Sort.cpp |
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| Sort.h |
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| StatGenStatus.cpp |
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| StatGenStatus.h |
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| STLUtilities.cpp |
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| STLUtilities.h |
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| String.cpp |
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| StringAlias.cpp |
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| StringAlias.h |
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| StringArray.cpp |
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| StringArray.h |
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| StringBasics.cpp |
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| StringBasics.h |
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| StringHash.cpp |
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| StringHash.h |
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| StringMap.cpp |
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| StringMap.h |
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| Tabix.cpp |
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| Tabix.h |
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| TrimSequence.h |
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| UncompressedFileType.cpp |
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| UncompressedFileType.h |
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| UnitTest.h |
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