gatb.core-API-1.4.2
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