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SamFile
SamFile
SamFile::SamFile()
SamFile::SamFile(ErrorHandler::HandlingType errorHandlingType)
SamFile::SamFile(const char *filename, OpenType mode)
SamFile::SamFile(const char *filename, OpenType mode, ErrorHandler::HandlingType errorHandlingType)
SamFileHeader
SamFileReader
SamFileReader
SamFileReader::SamFileReader()
SamFileReader::SamFileReader(const char *filename)
SamFileWriter
SamFileWriter
SamFileWriter::SamFileWriter()
SamFileWriter::SamFileWriter(const char *filename)
SamFilter
SamFlag
SamHeaderHD
SamHeaderPG
SamHeaderRecord
SamHeaderRG
SamHeaderSQ
SamHeaderTag
SamInterface
SamQuerySeqWithRefIter
SamRecord
SamRecord
SamRecord::SamRecord()
SamRecord::SamRecord(ErrorHandler::HandlingType errorHandlingType)
SamReferenceInfo
SamSingleBaseMatchInfo
SamStatistics
SamStatus
SamValidationError
SamValidationErrors
SamValidator
SequenceCoverageReader
setApplication
GenomeSequence
setDeletionIndel1
GlfRecord
setDeletionIndel2
GlfRecord
setHeaderTextString
GlfHeader
setInsertionIndel1
GlfRecord
setInsertionIndel2
GlfRecord
setLk
GlfRecord
setLkHet
GlfRecord
setLkHom1
GlfRecord
setLkHom2
GlfRecord
setMinDepth
GlfRecord
setMinLk
GlfRecord
setName
GlfRefSection
setOffset
GlfRecord
SetParameter
setReadDepth
GlfRecord
SetReadSection
SamFile::SetReadSection(int32_t refID)
SamFile::SetReadSection(const char *refName)
SamFile::SetReadSection(int32_t refID, int32_t start, int32_t end)
SamFile::SetReadSection(const char *refName, int32_t start, int32_t end)
setRecordType
GlfRecord
setRefBaseInt
GlfRecord
setReferenceName
GenomeSequence
setRefLen
GlfRefSection
setRmsMapQ
GlfRecord
setRtypeRef
GlfRecord
setSortedValidation
SamFile
setStatus
GlfStatus
SmithWaterman
SortedChunkList
SortedType
SamFile
Status
GlfStatus
STLUtilities
String
StringArray
StringDoubleHash
StringHash
StringIntHash
StringIntMap
StringMap
StringParameter
SUCCESS
GlfStatus
SwitchParameter
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