- g -

• gapCount() : cgatools::mapping::GapEst::GapsEstimator
• GapProbabilityAndConcordanceExtractor() : cgatools::mapping::GapProbabilityAndConcordanceExtractor
• getAlleleFreqs() : cgatools::variants::Allele
• getAlleles() : cgatools::variants::Locus
• getAlleleSequence() : cgatools::variants::Allele
• getAllXRef() : cgatools::variants::Locus
• getAmbiguousRegions() : cgatools::reference::CompactDnaSequence
• getAnnotation() : cgatools::variants::Locus
• getAnnotationIndex() : cgatools::variants::VariantFileIterator
• getAssemblyId() : cgatools::conv::VcfRecordSource , cgatools::copynumber::CnvFileVcfRecordSource , cgatools::junctions::JunctionVcfRecordSource , cgatools::mobileelement::MeiFileVcfRecordSource , cgatools::variants::VariantFileVcfRecordSource
• getBase() : cgatools::reference::CrrFile , cgatools::reference::CompactDnaSequence
• getBasePos() : cgatools::junctions::JunctionSideSection
• getBestOverlappingDetail() : cgatools::cgdata::CnvDetailStore
• getBestOverlappingSegment() : cgatools::cgdata::CnvSegmentStore
• getCallOffsets() : cgatools::variants::Allele
• getCalls() : cgatools::variants::Locus
• getChromosomeId() : cgatools::reference::CrrFile
• getChunkNumber() : cgatools::mapping::Map2SamConverter
• getCombinedVarFilter() : cgatools::variants::Allele
• getCompatibility() : cgatools::junctions::FullGenomeJunctionComparator
• getCompatible() : cgatools::junctions::FullGenomeJunctionComparator
• getCompatibleCombined() : cgatools::junctions::FullGenomeJunctionComparator
• getDigest() : cgatools::util::Md5Context
• getDir() : cgatools::junctions::JunctionSideSection
• getDistance() : cgatools::junctions::Junction
• getEvidenceScoreEAF() : cgatools::cgdata::EvidenceReader
• getEvidenceScoreVAF() : cgatools::cgdata::EvidenceReader
• getFields() : cgatools::util::DelimitedLineParser
• getFormatVersion() : cgatools::util::DelimitedFileMetadata
• getGapDistributionFileName() : cgatools::cgdata::LibraryMetadata
• getGapTuples() : cgatools::mapping::GapEst::GapsEstimator
• getHapLink() : cgatools::variants::Allele
• getHeader() : cgatools::variants::Call
• getId() : cgatools::junctions::JunctionRef , cgatools::variants::Locus , cgatools::variants::Superlocus
• getIncompatible() : cgatools::junctions::FullGenomeJunctionComparator
• getKeyValueHeaderRecords() : cgatools::conv::VcfRecordSource , cgatools::copynumber::CnvFileVcfRecordSource , cgatools::junctions::JunctionVcfRecordSource , cgatools::mobileelement::MeiFileVcfRecordSource , cgatools::variants::VariantFileVcfRecordSource
• getLaneDir() : cgatools::cgdata::GenomeMetadata
• getline() : cgatools::util::InputStream
• getLocation() : cgatools::conv::VcfRecordWriter , cgatools::copynumber::CnvFileVcfRecordWriter , cgatools::junctions::Junction , cgatools::junctions::JunctionVcfRecordWriter , cgatools::mobileelement::MeiFileVcfRecordWriter , cgatools::reference::CrrFile , cgatools::variants::VariantFileVcfRecordWriter
• getLoci() : cgatools::variants::Superlocus
• getMatchTypeString() : cgatools::variants::CallDiffResult
• getMaxDepth() : cgatools::util::IntervalTree< TRange, TBoundary, TValue, Overlap, GetBoundary, BoundaryLess >
• getMaxUniqueSequenceCoverage() : cgatools::cgdata::ReferenceSupportReader
• getMaxWeightedCoverage() : cgatools::cgdata::ReferenceSupportReader
• getMd5Digest() : cgatools::reference::CompactDnaSequence
• getMetadata() : cgatools::reference::RangeAnnotationStore< Derived, TValue >
• getMinScore() : cgatools::cgdata::ReferenceSupportReader
• getMinVarScoreEAF() : cgatools::variants::Allele
• getMinVarScoreVAF() : cgatools::variants::Allele
• getName() : cgatools::command::Command , cgatools::reference::CompactDnaSequence
• getPloidy() : cgatools::variants::Locus
• getPrecedingRefStart() : cgatools::variants::SuperlocusIterator
• getPrefiltered() : cgatools::junctions::FullGenomeJunctionComparator
• getProbability() : cgatools::mapping::GapEst::GapsEstimator
• getRange() : cgatools::variants::Locus , cgatools::variants::PhasedHypothesis , cgatools::variants::Superlocus
• getReadCounts() : cgatools::variants::VariantFileIterator
• getReference() : cgatools::variants::Locus
• getReferenceLength() : cgatools::mapping::Cigar
• getRefSequence() : cgatools::variants::Allele
• getSequence() : cgatools::reference::CompactDnaSequence , cgatools::mapping::GapEst::NoCallSequenceRetriever , cgatools::reference::CrrFile , cgatools::mapping::GapEst::SequenceRetriever , cgatools::mapping::GapEst::TemplateSequenceRetriever< TSequence >
• getSequenceLength() : cgatools::mapping::Cigar
• getShortDescription() : cgatools::command::Command
• getSimpleMatchTypeString() : cgatools::variants::CallDiffResult
• getSoftwareVersionString() : cgatools::util::DelimitedFileMetadata
• getSource() : cgatools::junctions::JunctionVcfRecordSource , cgatools::conv::VcfRecordSource , cgatools::copynumber::CnvFileVcfRecordSource , cgatools::variants::VariantFileVcfRecordSource , cgatools::mobileelement::MeiFileVcfRecordSource
• getSubFieldHeaderRecords() : cgatools::mobileelement::MeiFileVcfRecordSource , cgatools::variants::VariantFileVcfRecordSource , cgatools::copynumber::CnvFileVcfRecordSource , cgatools::conv::VcfRecordSource , cgatools::junctions::JunctionVcfRecordSource
• getType() : cgatools::variants::Locus
• getUnambiguousBase() : cgatools::reference::CompactDnaSequence
• getUnambiguousSequence() : cgatools::reference::CompactDnaSequence
• getVcfChromosomeName() : cgatools::conv::VcfRecordWriter
• getXRef() : cgatools::variants::Allele
• getZygosity() : cgatools::variants::Locus