ConstantLengthKmerHelper< keyType, valueType > Class Template Reference

IOHelper for Constant-Length Kmers. More...

#include <io_helper.h>

Inheritance diagram for ConstantLengthKmerHelper< keyType, valueType >:

Collaboration diagram for ConstantLengthKmerHelper< keyType, valueType >:

Public Member Functions
	ConstantLengthKmerHelper (uint8_t _kmerlength, uint8_t _splitbit)
bool	convert (char *s, keyType *k, valueType *v)
	convert a input-style line to key/value pair. More...
bool	convert (char *s, keyType *k)
	skip the value.
void	splitgrp (const keyType &key, uint32_t &grp, keyType &keyInGroup)
	split a keyTypeype value into two parts: groupID/keyInGroup by the highest splitbit bits.
void	combgrp (keyType &key, uint32_t &grp, keyType &keyInGroup)
	combine groupID/keyInGroup to the origional key

Public Attributes
uint8_t	kmerlength
	Assume all kmers are of the same length.
uint8_t	splitbit
	group the keys according to the highest bits.

Detailed Description

template<typename keyType, typename valueType>
class ConstantLengthKmerHelper< keyType, valueType >

IOHelper for Constant-Length Kmers.

Note

Each Kmer is a string of length KMERLENGTH,
We consider string as a base-4 number. [A=0,C=1,G=2,T=3].
Kmers are grouped according to the highest splitbit bits.

Member Function Documentation

template<typename keyType, typename valueType>

bool ConstantLengthKmerHelper< keyType, valueType >::convert ( char *  s, keyType *  T, valueType *  V  )

inlinevirtual

convert a input-style line to key/value pair.

Parameters

[in]	char	*s, a line from the input.
[out]	keyType*	T, converted key.
[out]	valueType*	V, converted value.

Return values

boolean

return true if convert is success.

Implements IOHelper< keyType, valueType >.

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The documentation for this class was generated from the following file:

• io_helper.h