All Classes Namespaces Functions Variables Enumerations Enumerator

StatGen Software

o+Class List

|o*Alleles

|o*AnalyzeClass

|o*BamIndex

|o*BamInterface

|o*bamRecordStruct

|o*BaseAsciiMap

|o*BaseComposition

|o*BaseCount

|o*baseQualityConvertor

|o*BaseUtilities

|o*BasicHash

|o*BgzfFileType

|o*CharBuffer

|o*ChromosomeInfo

|o*Chunk

|o*Cigar

|o*Cigar::CigarOperator

|o*CigarRoller

|o*CigarRollerTest

|o*ColumnExtras

|o*defaultPileup< PILEUP_TYPE >

|o*DoubleParameter

|o*emptyGenericHeader

|o*ErrorHandler

|o*Family

|o*FastQ

|o*FastQFile

|o*FastQStatus

|o*FileType

|o*FortranFormat

|o*GenericSamInterface

|o*GenomeSequence

|o*genomeSequenceMmapHeader

|o*GenotypeList

|o*glfEntry

|o*GlfException

|o*GlfFile

|o*GlfFileReader

|o*GlfFileWriter

|o*glfHandler

|o*GlfHeader

|o*glfIndel

|o*GlfRecord

|o*GlfRefSection

|o*GlfStatus

|o*GlobalTestEnvironment

|o*GreedyTupleAligner< QueryType, ReferenceType, ReferenceIndex >

|o*GzipHeader

|o*HiddenDouble

|o*HiddenInteger

|o*HiddenString

|o*HiddenSwitch

|o*InputFile

|o*IntArray

|o*IntHash

|o*IntParameter

|o*ListParameter

|o*LongCounter

|o*LongHash< ObjectT >

|o*LongParameterList

|o*LongParameters

|o*MarkerInfo

|o*Matrix

|o*MemoryMap

|o*MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass >

|o*MemoryMapArrayHeader

|o*MemoryMapGenericHeader

|o*MiniDeflate

|o*MockGenomeSequence

|o*modify

|o*modifyVar

|o*OptionList

|o*PackedRead

|o*Parameter

|o*ParameterList

|o*Pedigree

|o*PedigreeDescription

|o*PedigreeGlobals

|o*PedigreeKey

|o*Person

|o*Pileup< PILEUP_TYPE, FUNC_CLASS >

|o*PileupElement

|o*PileupElementBaseQual

|o*QuickIndex

|o*Random

|o*ReadBase

|o*ReadInsertion

|o*RunningStat

|o*SamFile

|o*SamFileHeader

|o*SamFileReader

|o*SamFileWriter

|o*SamFilter

|o*SamFlag

|o*SamHeaderHD

|o*SamHeaderPG

|o*SamHeaderRecord

|o*SamHeaderRG

|o*SamHeaderSQ

|o*SamHeaderTag

|o*SamInterface

|o*SamQuerySeqWithRefIter

|o*SamRecord

|o*SamReferenceInfo

|o*SamSingleBaseMatchInfo

|o*SamStatistics

|o*SamStatus

|o*SamValidationError

|o*SamValidationErrors

|o*SamValidator

|o*SequenceCoverageReader

|o*SetParameter

|o*SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >

|o*SortedChunkList

|o*String

|o*StringArray

|o*StringDoubleHash

|o*StringHash

|o*StringIntHash

|o*StringIntMap

|o*StringMap

|o*StringParameter

|o*SwitchParameter

|o*TestWrite

|o*UncompressedFileType

|o*Vector

|o*VectorFunc

|o*SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::weight

|\*Weight

o+Class Hierarchy

|o*Alleles

|o*AnalyzeClass

|o*BamIndex

|o*bamRecordStruct

|o*BaseAsciiMap

|o*BaseComposition

|o*BaseCount

|o*baseQualityConvertor

|o*BaseUtilities

|o*BasicHash

|o*CharBuffer

|o*ChromosomeInfo

|o*Chunk

|o+Cigar

|o*Cigar::CigarOperator

|o*CigarRollerTest

|o*ColumnExtras

|o*defaultPileup< PILEUP_TYPE >

|o*ErrorHandler

|o*Family

|o*FastQ

|o*FastQFile

|o*FastQStatus

|o+FileType

|o*FortranFormat

|o+GenericSamInterface

|o*GenotypeList

|o*glfEntry

|o*GlfException

|o+GlfFile

|o*glfHandler

|o*GlfHeader

|o*glfIndel

|o*GlfRecord

|o*GlfRefSection

|o*GlfStatus

|o*GlobalTestEnvironment

|o*GreedyTupleAligner< QueryType, ReferenceType, ReferenceIndex >

|o*GzipHeader

|o*InputFile

|o+IntArray

|o*IntHash

|o*LongHash< ObjectT >

|o+LongHash< int >

|o*LongParameterList

|o*MarkerInfo

|o*Matrix

|o+MemoryMap

|o+MemoryMapArrayHeader

|o+MemoryMapGenericHeader

|o*MiniDeflate

|o*MockGenomeSequence

|o*modify

|o*modifyVar

|o*OptionList

|o*PackedRead

|o+Parameter

|o*ParameterList

|o+PedigreeGlobals

|o*PedigreeKey

|o*Pileup< PILEUP_TYPE, FUNC_CLASS >

|o+PileupElement

|o*Random

|o*ReadBase

|o*ReadInsertion

|o*RunningStat

|o+SamFile

|o*SamFileHeader

|o*SamFilter

|o*SamFlag

|o+SamHeaderRecord

|o*SamHeaderTag

|o*SamQuerySeqWithRefIter

|o*SamRecord

|o*SamReferenceInfo

|o*SamSingleBaseMatchInfo

|o*SamStatistics

|o*SamStatus

|o*SamValidationError

|o*SamValidationErrors

|o*SamValidator

|o*SequenceCoverageReader

|o*SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >

|o*SortedChunkList

|o*String

|o*StringArray

|o*StringDoubleHash

|o*StringHash

|o*StringIntHash

|o*StringIntMap

|o*StringMap

|o*TestWrite

|o*Vector

|o*VectorFunc

|o*SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::weight

|\*Weight

o*Class Members

o*Graphical Class Hierarchy

o+Namespace List

o*Namespace Members

o+File List

|o*lib/bam/BamIndex.cpp

|o*lib/bam/BamIndex.h

|o*lib/bam/BamInterface.cpp

|o*lib/bam/BamInterface.h

|o*lib/bam/ErrorHandler.cpp

|o*lib/bam/ErrorHandler.h

|o*lib/bam/GenericSamInterface.cpp

|o*lib/bam/GenericSamInterface.h

|o*lib/bam/Pileup.h

|o*lib/bam/PileupElement.cpp

|o*lib/bam/PileupElement.h

|o*lib/bam/PileupElementBaseQual.cpp

|o*lib/bam/PileupElementBaseQual.h

|o*lib/bam/PileupReader.cpp

|o*lib/bam/PileupReader.h

|o*lib/bam/SamFile.cpp

|o*lib/bam/SamFile.h

|o*lib/bam/SamFileHeader.cpp

|o*lib/bam/SamFileHeader.h

|o*lib/bam/SamFilter.cpp

|o*lib/bam/SamFilter.h

|o*lib/bam/SamFlag.cpp

|o*lib/bam/SamFlag.h

|o*lib/bam/SamHeaderHD.cpp

|o*lib/bam/SamHeaderHD.h

|o*lib/bam/SamHeaderPG.cpp

|o*lib/bam/SamHeaderPG.h

|o*lib/bam/SamHeaderRecord.cpp

|o*lib/bam/SamHeaderRecord.h

|o*lib/bam/SamHeaderRG.cpp

|o*lib/bam/SamHeaderRG.h

|o*lib/bam/SamHeaderSQ.cpp

|o*lib/bam/SamHeaderSQ.h

|o*lib/bam/SamHeaderTag.cpp

|o*lib/bam/SamHeaderTag.h

|o*lib/bam/SamInterface.cpp

|o*lib/bam/SamInterface.h

|o*lib/bam/SamQuerySeqWithRefHelper.cpp

|o*lib/bam/SamQuerySeqWithRefHelper.h

|o*lib/bam/SamRecord.cpp

|o*lib/bam/SamRecord.h

|o*lib/bam/SamReferenceInfo.cpp

|o*lib/bam/SamReferenceInfo.h

|o*lib/bam/SamStatistics.cpp

|o*lib/bam/SamStatistics.h

|o*lib/bam/SamStatus.cpp

|o*lib/bam/SamStatus.h

|o*lib/bam/SamValidation.cpp

|o*lib/bam/SamValidation.h

|o*lib/bam/examples/Main.cpp

|o*lib/bam/test/BamIndexTest.cpp

|o*lib/bam/test/BamIndexTest.h

|o*lib/bam/test/Main.cpp

|o*lib/bam/test/Modify.cpp

|o*lib/bam/test/Modify.h

|o*lib/bam/test/ModifyVar.cpp

|o*lib/bam/test/ModifyVar.h

|o*lib/bam/test/ReadFiles.cpp

|o*lib/bam/test/ReadFiles.h

|o*lib/bam/test/SamFileTest.cpp

|o*lib/bam/test/SamFileTest.h

|o*lib/bam/test/Validate.cpp

|o*lib/bam/test/Validate.h

|o*lib/bam/test/ValidationTest.cpp

|o*lib/bam/test/ValidationTest.h

|o*lib/bam/test/WriteFiles.cpp

|o*lib/bam/test/WriteFiles.h

|o*lib/fastq/BaseComposition.cpp

|o*lib/fastq/BaseComposition.h

|o*lib/fastq/BaseCount.cpp

|o*lib/fastq/BaseCount.h

|o*lib/fastq/FastQFile.cpp

|o*lib/fastq/FastQFile.h

|o*lib/fastq/FastQStatus.cpp

|o*lib/fastq/FastQStatus.h

|o*lib/fastq/FastQValidator.cpp

|o*lib/fastq/test/FastQFileTest.cpp

|o*lib/general/BaseAsciiMap.cpp

|o*lib/general/BaseAsciiMap.h

|o*lib/general/BaseQualityHelper.cpp

|o*lib/general/BaseQualityHelper.h

|o*lib/general/BaseUtilities.cpp

|o*lib/general/BaseUtilities.h

|o*lib/general/BasicHash.cpp

|o*lib/general/BasicHash.h

|o*lib/general/BgzfFileType.cpp

|o*lib/general/BgzfFileType.h

|o*lib/general/CharBuffer.cpp

|o*lib/general/CharBuffer.h

|o*lib/general/Cigar.cpp

|o*lib/general/Cigar.h

|o*lib/general/CigarRoller.cpp

|o*lib/general/CigarRoller.h

|o*lib/general/Constant.h

|o*lib/general/Error.cpp

|o*lib/general/Error.h

|o*lib/general/FastQ.cpp

|o*lib/general/FastQ.h

|o*lib/general/FileType.cpp

|o*lib/general/FileType.h

|o*lib/general/FortranFormat.cpp

|o*lib/general/FortranFormat.h

|o*lib/general/Generic.cpp

|o*lib/general/Generic.h

|o*lib/general/GenomeSequence.cpp

|o*lib/general/GenomeSequence.h

|o*lib/general/GenotypeLists.cpp

|o*lib/general/GenotypeLists.h

|o*lib/general/glfHandler.cpp

|o*lib/general/glfHandler.h

|o*lib/general/GreedyTupleAligner.h

|o*lib/general/GzipFileType.cpp

|o*lib/general/GzipFileType.h

|o*lib/general/GzipHeader.cpp

|o*lib/general/GzipHeader.h

|o*lib/general/Hash.cpp

|o*lib/general/Hash.h

|o*lib/general/InplaceMerge.cpp

|o*lib/general/InplaceMerge.h

|o*lib/general/Input.cpp

|o*lib/general/Input.h

|o*lib/general/InputFile.cpp

|o*lib/general/InputFile.h

|o*lib/general/IntArray.cpp

|o*lib/general/IntArray.h

|o*lib/general/IntHash.cpp

|o*lib/general/IntHash.h

|o*lib/general/LongHash.cpp

|o*lib/general/LongHash.h

|o*lib/general/LongInt.h

|o*lib/general/LongLongCounter.cpp

|o*lib/general/LongLongCounter.h

|o*lib/general/MapFunction.cpp

|o*lib/general/MapFunction.h

|o*lib/general/MathConstant.h

|o*lib/general/MathMatrix.cpp

|o*lib/general/MathMatrix.h

|o*lib/general/MathVector.cpp

|o*lib/general/MathVector.h

|o*lib/general/MemoryAllocators.cpp

|o*lib/general/MemoryAllocators.h

|o*lib/general/MemoryInfo.cpp

|o*lib/general/MemoryInfo.h

|o*lib/general/MemoryMap.cpp

|o*lib/general/MemoryMap.h

|o*lib/general/MemoryMapArray.cpp

|o*lib/general/MemoryMapArray.h

|o*lib/general/MiniDeflate.cpp

|o*lib/general/MiniDeflate.h

|o*lib/general/Parameters.cpp

|o*lib/general/Parameters.h

|o*lib/general/Pedigree.cpp

|o*lib/general/Pedigree.h

|o*lib/general/PedigreeAlleleFreq.cpp

|o*lib/general/PedigreeAlleleFreq.h

|o*lib/general/PedigreeAlleles.h

|o*lib/general/PedigreeDescription.cpp

|o*lib/general/PedigreeDescription.h

|o*lib/general/PedigreeFamily.cpp

|o*lib/general/PedigreeFamily.h

|o*lib/general/PedigreeGlobals.cpp

|o*lib/general/PedigreeGlobals.h

|o*lib/general/PedigreeLoader.cpp

|o*lib/general/PedigreePerson.cpp

|o*lib/general/PedigreePerson.h

|o*lib/general/PedigreeTrim.cpp

|o*lib/general/PedigreeTwin.cpp

|o*lib/general/QuickIndex.cpp

|o*lib/general/QuickIndex.h

|o*lib/general/Random.cpp

|o*lib/general/Random.h

|o*lib/general/SimpleStats.h

|o*lib/general/SmithWaterman.cpp

|o*lib/general/SmithWaterman.h

|o*lib/general/Sort.cpp

|o*lib/general/Sort.h

|o*lib/general/STLUtilities.cpp

|o*lib/general/STLUtilities.h

|o*lib/general/String.cpp

|o*lib/general/String.h

|o*lib/general/StringArray.cpp

|o*lib/general/StringArray.h

|o*lib/general/StringBasics.cpp

|o*lib/general/StringBasics.h

|o*lib/general/StringHash.cpp

|o*lib/general/StringHash.h

|o*lib/general/StringMap.cpp

|o*lib/general/StringMap.h

|o*lib/general/TrimSequence.cpp

|o*lib/general/TrimSequence.h

|o*lib/general/UncompressedFileType.cpp

|o*lib/general/UncompressedFileType.h

|o*lib/general/WindowsHelper.cpp

|o*lib/general/WindowsHelper.h

|o*lib/general/test/GenomeSequence_test.cpp

|o*lib/general/test/GreedyTupleAligner_test.cpp

|o*lib/general/test/gtest.cpp

|o*lib/general/test/STLUtilities_test.cpp

|o*lib/general/test/TrimSequence_test.cpp

|o*lib/general/test/cigar/CigarRollerTest.cpp

|o*lib/general/test/cigar/CigarRollerTest.h

|o*lib/general/test/inputFileTest/InputFileTest.cpp

|o*lib/general/test/inputFileTest/InputFileTest.h

|o*lib/glf/GlfException.cpp

|o*lib/glf/GlfException.h

|o*lib/glf/GlfFile.cpp

|o*lib/glf/GlfFile.h

|o*lib/glf/GlfHeader.cpp

|o*lib/glf/GlfHeader.h

|o*lib/glf/GlfRecord.cpp

|o*lib/glf/GlfRecord.h

|o*lib/glf/GlfRefSection.cpp

|o*lib/glf/GlfRefSection.h

|o*lib/glf/GlfStatus.cpp

|o*lib/glf/GlfStatus.h

|o*lib/glf/test/Main.cpp

|o*lib/glf/test/ReadFiles.cpp

|o*lib/glf/test/ReadFiles.h

|o*lib/glf/test/Validate.cpp

|o*lib/glf/test/Validate.h

|o*lib/glf/test/WriteFiles.cpp

|\*lib/glf/test/WriteFiles.h

\+Directory Hierarchy