BaseUtil.hpp File Reference

File containing definition of the BaseUtil class. More...

#include "cgatools/core.hpp"
#include <string>

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Namespaces
namespace	cgatools
	Namespace containing the libcgatools API.
namespace	cgatools::util
	Namespace for general-purpose utilities.
namespace	cgatools::util::baseutil
	DNA nucleotide (base) utility functions.
Defines
#define	CGATOOLS_UTIL_BASEUTIL_HPP_   1
Functions
bool	cgatools::util::baseutil::isValidBase (char base)
bool	cgatools::util::baseutil::isCalledSequence (const std::string &sequence)
	Returns true if all the bases in the sequence are valid.
bool	cgatools::util::baseutil::isCalledSequence (const std::string &sequence, size_t start, size_t end)
	Returns true if all the bases in the subsequence are valid.
bool	cgatools::util::baseutil::isValidIupacCode (char iupacCode)
	Returns true if iupacCode is a valid IUPAC (base ambiguity) code.
uint32_t	cgatools::util::baseutil::pack (char base)
	Returns an integer corresponding to the given base, or throws an exception if the base is invalid.
char	cgatools::util::baseutil::unpack (uint32_t packedBase)
	Returns the unpacked base call.
char	cgatools::util::baseutil::disambiguate (char iupacCode)
	Returns an unambiguous base call that is consistent with the given iupacCode.
bool	cgatools::util::baseutil::isConsistent (char lhs, char rhs)
	Returns true if the given IUPAC codes are consistent.
bool	cgatools::util::baseutil::isConsistent (const std::string &lhs, const std::string &rhs)
	Returns true if lhs and rhs are consistent.
bool	cgatools::util::baseutil::isConsistent (const std::string &lhs, size_t lhsStart, size_t lhsEnd, const std::string &rhs, size_t rhsStart, size_t rhsEnd)
	Returns true if lhs and rhs are consistent for the given range of posistions.
char	cgatools::util::baseutil::complement (char iupacCode)
	Returns the complement of the given IUPAC code.
std::string	cgatools::util::baseutil::reverseComplement (const std::string &sequence)
	Returns the reverse complement of the given sequence of IUPAC codes.

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Detailed Description

File containing definition of the BaseUtil class.