cgatools::reference Namespace Reference

Namespace for reference-specific utilities. More...

Classes
class	ChromosomeIdField
struct	AmbiguousRegion
	Struct to describe an ambiguous region of reference, within a chromosome. More...
class	CompactDnaSequence
	Class to describe the DNA sequence of a chromosome, in a compact manner. More...
class	CrrFile
	Compact Randomly-accessible Reference file. More...
class	CrrFileWriter
	Writes a CrrFile to an output stream. More...
struct	GeneDescriptionData
class	GeneDataStore
class	Location
	Class representing a location in a CrrFile. More...
class	Range
	Class representing a range of sequence in a CrrFile. More...
struct	RangeOverlap
	Class that can be used as Overlap template parameter for an IntervalTree built on reference::Range. More...
struct	GetRangeBoundary
	Class that can be used as GetBoundary template parameter for an IntervalTree built on reference::Range. More...
class	RangeAnnotationStore
	Front end to IntervalTree based on reference ranges that allows to load annotations from a file. More...
struct	RepeatMaskerAnnotation
class	RepeatMaskerStore
Functions
bool	operator== (const Location &lhs, const Location &rhs)
bool	operator!= (const Location &lhs, const Location &rhs)
bool	operator< (const Location &lhs, const Location &rhs)
bool	operator<= (const Location &lhs, const Location &rhs)
bool	operator> (const Location &lhs, const Location &rhs)
bool	operator>= (const Location &lhs, const Location &rhs)
std::ostream &	operator<< (std::ostream &ostr, const Location &l)
bool	operator== (const Range &lhs, const Range &rhs)
bool	operator!= (const Range &lhs, const Range &rhs)
bool	operator< (const Range &lhs, const Range &rhs)
bool	operator<= (const Range &lhs, const Range &rhs)
bool	operator> (const Range &lhs, const Range &rhs)
bool	operator>= (const Range &lhs, const Range &rhs)

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Detailed Description

Namespace for reference-specific utilities.