cgatools::util Namespace Reference

Namespace for general-purpose utilities. More...

Namespaces
namespace	baseutil
	DNA nucleotide (base) utility functions.
Classes
class	DelimitedFileMetadata
class	DelimitedFile
	Used to parse files delimited in the way found in a typical Complete Genomics data file. More...
class	DelimitedFieldParser
	Class that parses one field of a delimited line. More...
class	IgnoreField
	A no-op DelimitedFieldParser. More...
class	ValueField
	A DelimitedFieldParser that uses cgatools::util::parseValue to parse its value. More...
class	ValueVectorField
	DelimitedFieldParser that parses a variable length list of values separated by its own delimiter (distinct from the field delimiter). More...
class	StringField
	A DelimitedFieldParser that records a copy of the field. More...
class	CharField
	A DelimitedFieldParser that records a character (not an unsigned integer). More...
class	StrandField
class	SideField
class	DelimitedLineParser
	A class that parses delimited lines. More...
class	DelimitedField
class	Exception
	A basic exception type. More...
class	GenericHistogram
class	SimpleHistogram
class	IndirectComparator
class	Md5Digest
	The MD5 result type. More...
class	Md5Context
	A class to compute the MD5 hash of a sequence of bytes. More...
struct	ValueParser
struct	ValueParser< Value, true >
struct	ValueParser< Value, false >
struct	ValueParser< float, true >
struct	ValueParser< double, true >
class	IntervalTree
	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. More...
class	FastRangeSet
	the 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? More...
class	FileDescriptorDevice
struct	FileSourceDevice
struct	FileSinkDevice
class	InputStream
	A std::istream with good error messages. More...
class	OutputStream
	a std::ostream with good error messages, and which does fsync on close on UNIX. More...
class	CompressedInputStream
class	CompressedOutputStream
class	StringSet
	StringSet convenience class. More...
Typedefs
typedef std::vector< std::string >	StringVector
Functions
std::ostream &	operator<< (std::ostream &out, const DelimitedFileMetadata &meta)
template<class Value , class Index >
std::ostream &	operator<< (std::ostream &out, const GenericHistogram< Value, Index > &r)
bool	operator== (const Md5Digest &lhs, const Md5Digest &rhs)
bool	operator!= (const Md5Digest &lhs, const Md5Digest &rhs)
float	parseFloat (const char *first, const char *last)
double	parseDouble (const char *first, const char *last)
template<typename Value >
Value	parseValue (const char *first, const char *last)
	Parse the string to the given Value type.
template<typename Value >
Value	parseValue (const char *str)
	Parse the string to the given Value type.
template<typename Value >
Value	parseValue (const std::string &str)
	Parse the string to the given Value type.
void	parseTokenString (std::string const &inputString, char const *sep, std::vector< std::string > &tokens, bool trimWhitespace=false, bool compressEmpty=false)
	Parse a user-token-specified separated string The function can be used if the input string format is not strictly defined.
void	writeBinaryBool (std::ostream &out, bool val)
	Writes a '\0' for false or '\001' for true.
template<class IntType >
void	writeBinaryInt (std::ostream &out, IntType val)
	Writes the integer out in msb -> lsb order.
template<class IntType >
void	writeBinaryUIntZC (std::ostream &out, IntType val)
	Writes the integer out in "zero-compressed" format, suitable for reading in by cgatools::util::readBinaryUIntZC().
void	writeBinaryString (std::ostream &out, const std::string &val)
	Writes the string out in a binary format, suitable for reading in by cgatools::util::readBinaryString().
void	readBinaryBool (std::istream &in, bool *val)
	Reads one byte interpreted as a boolean, such that 0 is false and anything else is true.
template<class IntType >
void	readBinaryInt (std::istream &in, IntType *pVal)
	Reads the integer in msb -> lsb order.
template<class IntType >
void	readBinaryUIntZC (std::istream &in, IntType *pVal)
	Reads an integer stored in "zero-compressed" format.
void	readBinaryString (std::istream &in, std::string *val)
	Reads the string written out by cgatools::util::writeBinaryString().

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Detailed Description

Namespace for general-purpose utilities.

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Function Documentation

template<typename Value >

Value cgatools::util::parseValue

(

const std::string &

str

)

[inline]

Parse the string to the given Value type.

See also:

parseValue(const char*, const char*)

template<typename Value >

Value cgatools::util::parseValue

(

const char *

str

)

[inline]

Parse the string to the given Value type.

See also:

parseValue(const char*, const char*)

template<typename Value >

Value cgatools::util::parseValue	(	const char *	first,
		const char *	last
	)			[inline]

Parse the string to the given Value type.

Calling parseValue<Value>(str) is much like calling boost::lexical_cast<Value>(str), with the following exceptions:

• If Value is an 8-bit integer, boost may treat this as a string to character conversion, while parseValue still treats it as a string to integer conversion.
• Integer conversion by parseValue is very strict about only finding digits, possibly starting with a '-' character.
• This is much faster than boost::lexical_cast.
• This is only implemented for the following types:
  • cgatools::int8_t
  • cgatools::int16_t
  • cgatools::int32_t
  • cgatools::int64_t
  • cgatools::uint8_t
  • cgatools::uint16_t
  • cgatools::uint32_t
  • cgatools::uint64_t
  • float
  • double

void cgatools::util::readBinaryBool	(	std::istream &	in,
		bool *	val
	)

Reads one byte interpreted as a boolean, such that 0 is false and anything else is true.

template<class IntType >

void cgatools::util::readBinaryUIntZC	(	std::istream &	in,
		IntType *	pVal
	)			[inline]

Reads an integer stored in "zero-compressed" format.

At each iteration, a byte is read in, and the lsb 7 bits are or'd into val. If the msb is set, then the val is shifted left by 7, and the next byte must be read in.

void cgatools::util::writeBinaryString	(	std::ostream &	out,
		const std::string &	val
	)

Writes the string out in a binary format, suitable for reading in by cgatools::util::readBinaryString().

template<class IntType >

void cgatools::util::writeBinaryUIntZC	(	std::ostream &	out,
		IntType	val
	)			[inline]

Writes the integer out in "zero-compressed" format, suitable for reading in by cgatools::util::readBinaryUIntZC().

See cgatools::util::readBinaryUIntZC().