lib/bam/BamIndex.cpp
lib/bam/BamIndex.h
lib/bam/BamInterface.cpp
lib/bam/BamInterface.h
lib/bam/ErrorHandler.cpp
lib/bam/ErrorHandler.h
lib/bam/GenericSamInterface.cpp
lib/bam/GenericSamInterface.h
lib/bam/Pileup.h
lib/bam/PileupElement.cpp
lib/bam/PileupElement.h
lib/bam/PileupElementBaseQual.cpp
lib/bam/PileupElementBaseQual.h
lib/bam/PileupReader.cpp
lib/bam/PileupReader.h
lib/bam/SamFile.cpp
lib/bam/SamFile.h
lib/bam/SamFileHeader.cpp
lib/bam/SamFileHeader.h
lib/bam/SamFilter.cpp
lib/bam/SamFilter.h
lib/bam/SamFlag.cpp
lib/bam/SamFlag.h
lib/bam/SamHeaderHD.cpp
lib/bam/SamHeaderHD.h
lib/bam/SamHeaderPG.cpp
lib/bam/SamHeaderPG.h
lib/bam/SamHeaderRecord.cpp
lib/bam/SamHeaderRecord.h
lib/bam/SamHeaderRG.cpp
lib/bam/SamHeaderRG.h
lib/bam/SamHeaderSQ.cpp
lib/bam/SamHeaderSQ.h
lib/bam/SamHeaderTag.cpp
lib/bam/SamHeaderTag.h
lib/bam/SamInterface.cpp
lib/bam/SamInterface.h
lib/bam/SamQuerySeqWithRefHelper.cpp
lib/bam/SamQuerySeqWithRefHelper.h
lib/bam/SamRecord.cpp
lib/bam/SamRecord.h
lib/bam/SamReferenceInfo.cpp
lib/bam/SamReferenceInfo.h
lib/bam/SamStatistics.cpp
lib/bam/SamStatistics.h
lib/bam/SamStatus.cpp
lib/bam/SamStatus.h
lib/bam/SamValidation.cpp
lib/bam/SamValidation.h
lib/bam/examples/Main.cpp
lib/bam/test/BamIndexTest.cpp
lib/bam/test/BamIndexTest.h
lib/bam/test/Main.cpp
lib/bam/test/Modify.cpp
lib/bam/test/Modify.h
lib/bam/test/ModifyVar.cpp
lib/bam/test/ModifyVar.h
lib/bam/test/ReadFiles.cpp
lib/bam/test/ReadFiles.h
lib/bam/test/SamFileTest.cpp
lib/bam/test/SamFileTest.h
lib/bam/test/Validate.cpp
lib/bam/test/Validate.h
lib/bam/test/ValidationTest.cpp
lib/bam/test/ValidationTest.h
lib/bam/test/WriteFiles.cpp
lib/bam/test/WriteFiles.h
lib/fastq/BaseComposition.cpp
lib/fastq/BaseComposition.h
lib/fastq/BaseCount.cpp
lib/fastq/BaseCount.h
lib/fastq/FastQFile.cpp
lib/fastq/FastQFile.h
lib/fastq/FastQStatus.cpp
lib/fastq/FastQStatus.h
lib/fastq/FastQValidator.cpp
lib/fastq/test/FastQFileTest.cpp
lib/general/BaseAsciiMap.cpp
lib/general/BaseAsciiMap.h
lib/general/BaseQualityHelper.cpp
lib/general/BaseQualityHelper.h
lib/general/BaseUtilities.cpp
lib/general/BaseUtilities.h
lib/general/BasicHash.cpp
lib/general/BasicHash.h
lib/general/BgzfFileType.cpp
lib/general/BgzfFileType.h
lib/general/CharBuffer.cpp
lib/general/CharBuffer.h
lib/general/Cigar.cpp
lib/general/Cigar.h
lib/general/CigarRoller.cpp
lib/general/CigarRoller.h
lib/general/Constant.h
lib/general/Error.cpp
lib/general/Error.h
lib/general/FastQ.cpp
lib/general/FastQ.h
lib/general/FileType.cpp
lib/general/FileType.h
lib/general/FortranFormat.cpp
lib/general/FortranFormat.h
lib/general/Generic.cpp
lib/general/Generic.h
lib/general/GenomeSequence.cpp
lib/general/GenomeSequence.h
lib/general/GenotypeLists.cpp
lib/general/GenotypeLists.h
lib/general/glfHandler.cpp
lib/general/glfHandler.h
lib/general/GreedyTupleAligner.h
lib/general/GzipFileType.cpp
lib/general/GzipFileType.h
lib/general/GzipHeader.cpp
lib/general/GzipHeader.h
lib/general/Hash.cpp
lib/general/Hash.h
lib/general/InplaceMerge.cpp
lib/general/InplaceMerge.h
lib/general/Input.cpp
lib/general/Input.h
lib/general/InputFile.cpp
lib/general/InputFile.h
lib/general/IntArray.cpp
lib/general/IntArray.h
lib/general/IntHash.cpp
lib/general/IntHash.h
lib/general/LongHash.cpp
lib/general/LongHash.h
lib/general/LongInt.h
lib/general/LongLongCounter.cpp
lib/general/LongLongCounter.h
lib/general/MapFunction.cpp
lib/general/MapFunction.h
lib/general/MathConstant.h
lib/general/MathMatrix.cpp
lib/general/MathMatrix.h
lib/general/MathVector.cpp
lib/general/MathVector.h
lib/general/MemoryAllocators.cpp
lib/general/MemoryAllocators.h
lib/general/MemoryInfo.cpp
lib/general/MemoryInfo.h
lib/general/MemoryMap.cpp
lib/general/MemoryMap.h
lib/general/MemoryMapArray.cpp
lib/general/MemoryMapArray.h
lib/general/MiniDeflate.cpp
lib/general/MiniDeflate.h
lib/general/Parameters.cpp
lib/general/Parameters.h
lib/general/Pedigree.cpp
lib/general/Pedigree.h
lib/general/PedigreeAlleleFreq.cpp
lib/general/PedigreeAlleleFreq.h
lib/general/PedigreeAlleles.h
lib/general/PedigreeDescription.cpp
lib/general/PedigreeDescription.h
lib/general/PedigreeFamily.cpp
lib/general/PedigreeFamily.h
lib/general/PedigreeGlobals.cpp
lib/general/PedigreeGlobals.h
lib/general/PedigreeLoader.cpp
lib/general/PedigreePerson.cpp
lib/general/PedigreePerson.h
lib/general/PedigreeTrim.cpp
lib/general/PedigreeTwin.cpp
lib/general/QuickIndex.cpp
lib/general/QuickIndex.h
lib/general/Random.cpp
lib/general/Random.h
lib/general/SimpleStats.h
lib/general/SmithWaterman.cpp
lib/general/SmithWaterman.h
lib/general/Sort.cpp
lib/general/Sort.h
lib/general/STLUtilities.cpp
lib/general/STLUtilities.h
lib/general/String.cpp
lib/general/String.h
lib/general/StringArray.cpp
lib/general/StringArray.h
lib/general/StringBasics.cpp
lib/general/StringBasics.h
lib/general/StringHash.cpp
lib/general/StringHash.h
lib/general/StringMap.cpp
lib/general/StringMap.h
lib/general/TrimSequence.cpp
lib/general/TrimSequence.h
lib/general/UncompressedFileType.cpp
lib/general/UncompressedFileType.h
lib/general/WindowsHelper.cpp
lib/general/WindowsHelper.h
lib/general/test/GenomeSequence_test.cpp
lib/general/test/GreedyTupleAligner_test.cpp
lib/general/test/gtest.cpp
lib/general/test/STLUtilities_test.cpp
lib/general/test/TrimSequence_test.cpp
lib/general/test/cigar/CigarRollerTest.cpp
lib/general/test/cigar/CigarRollerTest.h
lib/general/test/inputFileTest/InputFileTest.cpp
lib/general/test/inputFileTest/InputFileTest.h
lib/glf/GlfException.cpp
lib/glf/GlfException.h
lib/glf/GlfFile.cpp
lib/glf/GlfFile.h
lib/glf/GlfHeader.cpp
lib/glf/GlfHeader.h
lib/glf/GlfRecord.cpp
lib/glf/GlfRecord.h
lib/glf/GlfRefSection.cpp
lib/glf/GlfRefSection.h
lib/glf/GlfStatus.cpp
lib/glf/GlfStatus.h
lib/glf/test/Main.cpp
lib/glf/test/ReadFiles.cpp
lib/glf/test/ReadFiles.h
lib/glf/test/Validate.cpp
lib/glf/test/Validate.h
lib/glf/test/WriteFiles.cpp
lib/glf/test/WriteFiles.h