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