Class Hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:

• cgatools::variants::Allele
• cgatools::variants::AlleleDiffSegment
• cgatools::mapping::AlleleSequenceAligner
• cgatools::reference::AmbiguousRegion
• cgatools::mapping::CacheOutStreams
• cgatools::variants::Call
• cgatools::variants::CallDiffResult
• cgatools::util::FileSinkDevice::category
• cgatools::util::FileDescriptorDevice::category
• cgatools::util::FileSourceDevice::category
• cgatools::mapping::Cigar
• cgatools::mapping::Cigar::CigarElement
• cgatools::cgdata::CnvSegmentData
• cgatools::command::Command
  • cgatools::command::CallDiff
  • cgatools::command::Crr2Fasta
  • cgatools::command::DecodeCrr
  • cgatools::command::Evidence2Cache
  • cgatools::command::Evidence2Sam
  • cgatools::command::Fasta2Crr
  • cgatools::command::Join
  • cgatools::command::JunctionCmp
  • cgatools::command::JunctionDiff
  • cgatools::command::JunctionType
  • cgatools::command::ListCrr
  • cgatools::command::ListVariants
  • cgatools::command::Map2Sam
  • cgatools::command::MergedMap2Sam
  • cgatools::command::SnpDiff
  • cgatools::command::TestVariants
  • cgatools::command::VarFileCombine
• cgatools::reference::CompactDnaSequence
• cgatools::util::GenericHistogram< Value, Index >::CompareBuckets
• cgatools::junctions::CompareJunctionsBySide
  • cgatools::junctions::CompareBySide
• cgatools::util::CompressedInputStream
• cgatools::util::CompressedOutputStream
• cgatools::junctions::CounterSet< Fields, Type >
• cgatools::reference::CrrFile
• cgatools::reference::CrrFileWriter
• cgatools::util::DelimitedFieldParser
  • cgatools::reference::ChromosomeIdField
  • cgatools::util::CharField
  • cgatools::util::DelimitedField
  • cgatools::util::IgnoreField
  • cgatools::util::SideField
  • cgatools::util::StrandField
  • cgatools::util::StringField
  • cgatools::util::ValueField< Value >
  • cgatools::util::ValueVectorField< Value >
• cgatools::util::DelimitedFile
• cgatools::util::DelimitedFileMetadata
• cgatools::util::DelimitedLineParser
• cgatools::cgdata::EvidenceReader::DnbRecord
  • cgatools::mapping::EvidenceCacheDnbRecord
  • cgatools::mapping::EvidenceDnbRecord
• cgatools::mapping::DnbSequenceIterator
• cgatools::cgdata::DnbStructure
• cgatools::command::Evidence2CacheConfig
• cgatools::command::Evidence2SamConfig
• cgatools::mapping::EvidenceCacheBuilder
• cgatools::mapping::EvidenceCacheReader
• cgatools::cgdata::EvidenceReader
• cgatools::util::Exception
• cgatools::util::FastRangeSet
• cgatools::util::FileDescriptorDevice
  • cgatools::util::FileSinkDevice
  • cgatools::util::FileSourceDevice
• cgatools::junctions::FullGenomeJunctionComparator
• cgatools::cgdata::HalfDnbStructure::Gap
• cgatools::mapping::GapAndConcordanceExtractor
  • cgatools::mapping::GapProbabilityAndConcordanceExtractor
• cgatools::mapping::GapEst::GapsEstimator
• cgatools::cgdata::GapTable< T >::GapsRecord
• cgatools::cgdata::GapTable< T >
• cgatools::reference::GeneDataStore
• cgatools::reference::GeneDescriptionData
• cgatools::util::GenericHistogram< Value, Index >
• cgatools::cgdata::GenomeMetadata
• cgatools::reference::GetRangeBoundary
• cgatools::cgdata::HalfDnbStructure
• cgatools::util::IndirectComparator< Container >
• cgatools::util::InputStream
• cgatools::cgdata::EvidenceReader::IntervalRecord
• cgatools::util::IntervalTree< TRange, TBoundary, TValue, Overlap, GetBoundary, BoundaryLess >
• cgatools::util::IntervalTree< reference::Range, reference::Location, CnvSegmentData, reference::RangeOverlap, reference::GetRangeBoundary >
• cgatools::util::IntervalTree< reference::Range, reference::Location, RepeatMaskerAnnotation, reference::RangeOverlap, reference::GetRangeBoundary >
• cgatools::junctions::JuctionStatisticsCollector
• cgatools::junctions::Junction
• cgatools::command::JunctionCmpConfig
• cgatools::junctions::JunctionCounterFields
• cgatools::command::JunctionDiffConfig
• cgatools::junctions::JunctionFile
• cgatools::junctions::JunctionRef
• cgatools::junctions::JunctionRefs
• cgatools::junctions::JunctionSideSection
• cgatools::mapping::LibraryData
• cgatools::cgdata::LibraryMetadata
• cgatools::mapping::LibraryMetadataContainer
• cgatools::cgdata::LibRecord
• cgatools::reference::Location
• cgatools::variants::Locus
• cgatools::mapping::Map2SamConfig
  • cgatools::mapping::MergedMap2SamConfig
• cgatools::mapping::Map2SamConverter
  • cgatools::mapping::MergedMap2SamConverter
• cgatools::util::Md5Context
• cgatools::util::Md5Digest
• cgatools::util::OutputStream
• cgatools::variants::PhasedAllele
• cgatools::variants::PhasedHypothesis
• cgatools::reference::Range
• cgatools::reference::RangeAnnotationStore< Derived, TValue >
• cgatools::reference::RangeAnnotationStore< CnvSegmentStore, CnvSegmentData >
  • cgatools::cgdata::CnvSegmentStore
• cgatools::reference::RangeAnnotationStore< RepeatMaskerStore, RepeatMaskerAnnotation >
  • cgatools::reference::RepeatMaskerStore
• cgatools::reference::RangeOverlap
• cgatools::util::FastRangeSet::RangeSet
• cgatools::cgdata::ReferenceSupportReader
• cgatools::reference::RepeatMaskerAnnotation
• cgatools::mapping::SamFileHeaderBlock
• cgatools::mapping::SamRecord
  • cgatools::mapping::EvidenceSamRecord
• cgatools::mapping::SamRecordGenerator
• cgatools::mapping::SamSequenceSplitter
• cgatools::mapping::SamStatistics
• cgatools::mapping::GapEst::SequenceRetriever
  • cgatools::mapping::GapEst::NoCallSequenceRetriever
  • cgatools::mapping::GapEst::TemplateSequenceRetriever< TSequence >
• cgatools::util::SimpleHistogram
• cgatools::util::StringSet
• cgatools::variants::Superlocus
• cgatools::variants::SuperlocusIterator
• cgatools::util::ValueParser< Value, IsSigned >
• cgatools::util::ValueParser< double, true >
• cgatools::util::ValueParser< float, true >
• cgatools::util::ValueParser< Value, false >
• cgatools::util::ValueParser< Value, true >
• cgatools::variants::VariantFileIterator