| 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::reference::AmbiguousRegion | Struct to describe an ambiguous region of reference, within a chromosome |
| 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::FileDescriptorDevice::category | |
| cgatools::util::FileSourceDevice::category | |
| cgatools::util::FileSinkDevice::category | |
| cgatools::util::CharField | A DelimitedFieldParser that records a character (not an unsigned integer) |
| cgatools::reference::ChromosomeIdField | |
| cgatools::command::Cigar | Provides support for manipulations on SAM/BAM and CGI Evidence CIGAR |
| cgatools::command::Cigar::CigarElement | |
| 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::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::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 export file |
| cgatools::util::DelimitedFileMetadata | |
| cgatools::util::DelimitedLineParser | A class that parses delimited lines |
| cgatools::command::Evidence2Sam | |
| cgatools::command::Evidence2SamConfig | |
| cgatools::cgdata::EvidenceIntervalsReader | |
| cgatools::util::Exception | A basic exception type |
| cgatools::command::Fasta2Crr | |
| cgatools::util::FileDescriptorDevice | |
| cgatools::util::FileSinkDevice | |
| cgatools::util::FileSourceDevice | |
| cgatools::junctions::FullGenomeJunctionComparator | |
| cgatools::util::GenericHistogram< Value, Index > | |
| cgatools::cgdata::GenomeMetadata | |
| cgatools::util::IgnoreField | A no-op DelimitedFieldParser |
| cgatools::util::IndirectComparator< Container > | |
| cgatools::util::InputStream | A std::istream with good error messages |
| cgatools::junctions::InvalidJunction | |
| cgatools::command::Join | |
| cgatools::junctions::JuctionStatisticsCollector | |
| cgatools::junctions::Junction | |
| cgatools::junctions::JunctionComparatorWithinContig | |
| cgatools::junctions::JunctionCounterFields | |
| cgatools::command::JunctionDiff | |
| cgatools::command::JunctionDiffConfig | |
| cgatools::junctions::JunctionFile | |
| cgatools::junctions::JunctionId | |
| cgatools::junctions::JunctionIdGenerator | |
| cgatools::junctions::JunctionIt | |
| cgatools::junctions::JunctionIts | |
| cgatools::junctions::JunctionScore | |
| cgatools::junctions::JunctionSideSection | |
| cgatools::junctions::JunctionTransitionSection | |
| 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::command::Map2SamConfig | |
| cgatools::util::Md5Context | A class to compute the MD5 hash of a sequence of bytes |
| cgatools::util::Md5Digest | The MD5 result type |
| 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::junctions::Range | |
| cgatools::util::RangeIntersector< TRange, TValue, Overlap, Less > | Class that maintains a mapping from key -> 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::util::RangeSet | |
| cgatools::cgdata::ReferenceSupportReader | Sequential reader for CGI reference support files provided as a part of the genome data package |
| cgatools::command::SamSequenceSplitter | |
| 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::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::variants::VariantFileIterator | |
1.6.2
