gatb::core::kmer Namespace Reference

Package for genomic databases management. More...

Namespaces
	impl
	Implementation for genomic databases management.

Classes
class	ICountProcessor
	Interface that uses kmer counting information. More...

Enumerations

Functions
std::string	toString (Strand s)
char	ascii (Nucleotide nt)
Nucleotide	reverse (Nucleotide nt)

Detailed Description

Package for genomic databases management.

Enumeration Type Documentation

enum KmerMode

enumeration giving the way the kmers are computed.

Enumerator
KMER_DIRECT	Kmer from direct strand
KMER_REVCOMP	Kmer as reverse complement
KMER_CANONICAL	Kmer as minimum between the direct and reverse complement

enum Nucleotide

Enumeration for nucleotides.

Enumerator
NUCL_A	enum for the A nucleotide
NUCL_C	enum for the C nucleotide
NUCL_T	enum for the T nucleotide
NUCL_G	enum for the G nucleotide

enum Strand

Enumeration for strand.

Enumerator
STRAND_FORWARD	enum for the forward strand
STRAND_REVCOMP	enum for the reverse strand

Function Documentation

char gatb::core::kmer::ascii ( Nucleotide  nt )

inline

Ascii representation of a Nucleotide object ('A', 'C', 'T' or 'G')

Parameters

[in]

nt

: the nucleotide

Returns

the Ascii representation

Nucleotide gatb::core::kmer::reverse ( Nucleotide  nt )

inline

Reverse complement of a nucleotide (A->T, C->G, T->A, G->C)

Parameters

[in]

nt

: the nucleotide to be reversed

Returns

the reversed nucleotide

std::string gatb::core::kmer::toString ( Strand  s )

inline

Ascii representation of a Strand object ("FWD" or "REV")

Parameters

[in]

s

: the strand

Returns

the Ascii representation