| cgatools::variants::Allele | A class that corresponds to a single allele within a locus in a Complete Genomics variant file |
| cgatools::variants::AlleleDiffSegment | Structure to keep track of a segment the reference, as well as calls aligned to that segment for two calldiff files |
| cgatools::mapping::AlleleSequenceAligner | The class is used to iterate through the bases of a variation allele from an evidenceInterval file operator[] returns either a base from the allele or a reference base if the index points outside of the allele range |
| cgatools::reference::AmbiguousRegion | Struct to describe an ambiguous region of reference, within a chromosome |
| cgatools::mapping::CacheOutStreams | |
| cgatools::variants::Call | A struct that corresponds to a single line of a Complete Genomics variant file |
| cgatools::command::CallDiff | |
| cgatools::variants::CallDiffResult | Class to hold the result of diffing two superloci |
| cgatools::util::FileSinkDevice::category | |
| cgatools::util::FileDescriptorDevice::category | |
| cgatools::util::FileSourceDevice::category | |
| cgatools::util::CharField | A DelimitedFieldParser that records a character (not an unsigned integer) |
| cgatools::reference::ChromosomeIdField | |
| cgatools::mapping::Cigar | Provides support for manipulations on SAM/BAM and CGI Evidence CIGAR |
| cgatools::mapping::Cigar::CigarElement | |
| cgatools::cgdata::CnvSegmentData | Per-segment CNV data |
| cgatools::cgdata::CnvSegmentStore | Loads CNV segment data from a file and caches it in memory |
| cgatools::command::Command | The base class for writing new commands |
| cgatools::reference::CompactDnaSequence | Class to describe the DNA sequence of a chromosome, in a compact manner |
| cgatools::util::GenericHistogram< Value, Index >::CompareBuckets | |
| cgatools::junctions::CompareBySide | |
| cgatools::junctions::CompareJunctionsBySide | Compares two junctions by a given side Uses the other side and then junction id as secondary keys |
| cgatools::util::CompressedInputStream | |
| cgatools::util::CompressedOutputStream | |
| cgatools::junctions::CounterSet< Fields, Type > | |
| cgatools::command::Crr2Fasta | |
| cgatools::reference::CrrFile | Compact Randomly-accessible Reference file |
| cgatools::reference::CrrFileWriter | Writes a CrrFile to an output stream |
| cgatools::command::DecodeCrr | |
| cgatools::util::DelimitedField | |
| cgatools::util::DelimitedFieldParser | Class that parses one field of a delimited line |
| cgatools::util::DelimitedFile | Used to parse files delimited in the way found in a typical Complete Genomics data file |
| cgatools::util::DelimitedFileMetadata | |
| cgatools::util::DelimitedLineParser | A class that parses delimited lines |
| cgatools::cgdata::EvidenceReader::DnbRecord | |
| cgatools::mapping::DnbSequenceIterator | An iterator through an aligned read sequence The iterator is able to return bases in reverse order or/and complimented |
| cgatools::cgdata::DnbStructure | |
| cgatools::command::Evidence2Cache | |
| cgatools::command::Evidence2CacheConfig | |
| cgatools::command::Evidence2Sam | |
| cgatools::command::Evidence2SamConfig | |
| cgatools::mapping::EvidenceCacheBuilder | |
| cgatools::mapping::EvidenceCacheDnbRecord | |
| cgatools::mapping::EvidenceCacheReader | |
| cgatools::mapping::EvidenceDnbRecord | |
| cgatools::cgdata::EvidenceReader | |
| cgatools::mapping::EvidenceSamRecord | |
| cgatools::util::Exception | A basic exception type |
| cgatools::command::Fasta2Crr | |
| cgatools::util::FastRangeSet | Class is designed to support a relatively small set of ranges and answer the questions:
- does a given range intersect one of the ranges in the FastRangeSet?
- is a given location contained by one of the ranges in the FastRangeSet?
|
| cgatools::util::FileDescriptorDevice | |
| cgatools::util::FileSinkDevice | |
| cgatools::util::FileSourceDevice | |
| cgatools::junctions::FullGenomeJunctionComparator | |
| cgatools::cgdata::HalfDnbStructure::Gap | |
| cgatools::mapping::GapAndConcordanceExtractor | The class scans a given alignment for a given allele, provided by AlleleSequenceAligner in the constructor |
| cgatools::mapping::GapProbabilityAndConcordanceExtractor | The class extends GapAndConcordanceExtractor by computing the probablility of sequence-dependent gaps in addition to the metrics computed by the parent class |
| cgatools::mapping::GapEst::GapsEstimator | Estimates wobble (small) gap probabilities, based on the sequence at a particular offset from the end of the clone |
| cgatools::cgdata::GapTable< T >::GapsRecord | |
| cgatools::cgdata::GapTable< T > | The class contains simple gap estimation table template |
| cgatools::reference::GeneDataStore | |
| cgatools::reference::GeneDescriptionData | |
| cgatools::util::GenericHistogram< Value, Index > | |
| cgatools::cgdata::GenomeMetadata | |
| cgatools::reference::GetRangeBoundary | Class that can be used as GetBoundary template parameter for an IntervalTree built on reference::Range |
| cgatools::cgdata::HalfDnbStructure | |
| cgatools::util::IgnoreField | A no-op DelimitedFieldParser |
| cgatools::util::IndirectComparator< Container > | |
| cgatools::util::InputStream | A std::istream with good error messages |
| cgatools::cgdata::EvidenceReader::IntervalRecord | |
| cgatools::util::IntervalTree< TRange, TBoundary, TValue, Overlap, GetBoundary, BoundaryLess > | Class that maintains a mapping from key to value, where the key is a type with range semantics, for the purpose of finding the intersection of a range to a set of ranges |
| cgatools::command::Join | |
| cgatools::junctions::JuctionStatisticsCollector | |
| cgatools::junctions::Junction | Main class describing a single Junction |
| cgatools::command::JunctionCmp | |
| cgatools::command::JunctionCmpConfig | |
| cgatools::junctions::JunctionCounterFields | |
| cgatools::command::JunctionDiff | |
| cgatools::command::JunctionDiffConfig | |
| cgatools::junctions::JunctionFile | Class describing a Junction file |
| cgatools::junctions::JunctionRef | A utility class used as a lightweight reference to a junction record and might contain a list of references to associated junctions |
| cgatools::junctions::JunctionRefs | |
| cgatools::junctions::JunctionSideSection | Class describing the left or right side of a junction |
| cgatools::command::JunctionType | |
| cgatools::mapping::LibraryData | |
| cgatools::cgdata::LibraryMetadata | |
| cgatools::mapping::LibraryMetadataContainer | |
| cgatools::cgdata::LibRecord | |
| cgatools::command::ListCrr | |
| cgatools::command::ListVariants | |
| cgatools::reference::Location | Class representing a location in a CrrFile |
| cgatools::variants::Locus | A class that corresponds to a single locus in a Complete Genomics variant file |
| cgatools::command::Map2Sam | |
| cgatools::mapping::Map2SamConfig | |
| cgatools::mapping::Map2SamConverter | |
| cgatools::util::Md5Context | A class to compute the MD5 hash of a sequence of bytes |
| cgatools::util::Md5Digest | The MD5 result type |
| cgatools::command::MergedMap2Sam | |
| cgatools::mapping::MergedMap2SamConfig | |
| cgatools::mapping::MergedMap2SamConverter | |
| cgatools::mapping::GapEst::NoCallSequenceRetriever | Retrieves all no-calls |
| cgatools::util::OutputStream | Std::ostream with good error messages, and which does fsync on close on UNIX |
| cgatools::variants::PhasedAllele | Class to hold allele-specific information for a PhasedHypothesis |
| cgatools::variants::PhasedHypothesis | Class to hold a single possible phasing of loci in a Superlocus |
| cgatools::reference::Range | Class representing a range of sequence in a CrrFile |
| cgatools::reference::RangeAnnotationStore< Derived, TValue > | Front end to IntervalTree based on reference ranges that allows to load annotations from a file |
| cgatools::reference::RangeOverlap | Class that can be used as Overlap template parameter for an IntervalTree built on reference::Range |
| cgatools::util::FastRangeSet::RangeSet | |
| cgatools::cgdata::ReferenceSupportReader | Sequential reader for CGI reference support files provided as a part of the genome data package |
| cgatools::reference::RepeatMaskerAnnotation | |
| cgatools::reference::RepeatMaskerStore | |
| cgatools::mapping::SamFileHeaderBlock | Used to manage sections of the SAM file header use "operator <<" to serialize the content into a SAM file |
| cgatools::mapping::SamRecord | |
| cgatools::mapping::SamRecordGenerator | Generates a SAM file record based on a given mapping record The final logic defining what goes into the output file is defined here |
| cgatools::mapping::SamSequenceSplitter | |
| cgatools::mapping::SamStatistics | |
| cgatools::mapping::GapEst::SequenceRetriever | Retrieves sequence at a given offset from the end of the clone |
| cgatools::util::SideField | |
| cgatools::util::SimpleHistogram | |
| cgatools::command::SnpDiff | |
| cgatools::util::StrandField | |
| cgatools::util::StringField | A DelimitedFieldParser that records a copy of the field |
| cgatools::util::StringSet | StringSet convenience class |
| cgatools::variants::Superlocus | The Superlocus class |
| cgatools::variants::SuperlocusIterator | A class to iterate through one or more variant files at a time, enabling access to a stream of Superlocus |
| cgatools::mapping::GapEst::TemplateSequenceRetriever< TSequence > | Retrieves sequence at a given offset from the end of the clone |
| cgatools::command::TestVariants | |
| cgatools::util::ValueField< Value > | A DelimitedFieldParser that uses cgatools::util::parseValue to parse its value |
| 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::util::ValueVectorField< Value > | DelimitedFieldParser that parses a variable length list of values separated by its own delimiter (distinct from the field delimiter) |
| cgatools::command::VarFileCombine | |
| cgatools::variants::VariantFileIterator | |
1.6.2
