cgatools::variants Namespace Reference

Namespace for variant file processing utilities. More...

Classes
class	Allele
	A class that corresponds to a single allele within a locus in a Complete Genomics variant file. More...
struct	AlleleDiffSegment
	Structure to keep track of a segment the reference, as well as calls aligned to that segment for two calldiff files. More...
struct	Call
	A struct that corresponds to a single line of a Complete Genomics variant file. More...
struct	CallDiffResult
	Class to hold the result of diffing two superloci. More...
class	Locus
	A class that corresponds to a single locus in a Complete Genomics variant file. More...
class	PhasedAllele
	Class to hold allele-specific information for a PhasedHypothesis. More...
class	PhasedHypothesis
	Class to hold a single possible phasing of loci in a Superlocus. More...
class	Superlocus
	The Superlocus class. More...
class	SuperlocusIterator
	A class to iterate through one or more variant files at a time, enabling access to a stream of Superlocus. More...
class	VariantFileIterator
Functions
void	upgradeOldFieldValues (Call &c)
	Convert some field values that exist only in old variation files to their contemporary equivalents.
std::ostream &	operator<< (std::ostream &out, const Locus &locus)

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Detailed Description

Namespace for variant file processing utilities.