Antonie
Classes | Typedefs | Functions | Variables
dnamisc.hh File Reference
#include <string>
#include <vector>
#include <functional>
#include <stdlib.h>
#include <sstream>
#include "antonie.hh"

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Classes

class  Clusterer< T >
 Generic class to cluster objects that are 'close by'. More...
struct  Clusterer< T >::cluster
 Represents a cluster. More...

Typedefs

typedef std::function< void(void)> acgt_t

Functions

double qToErr (unsigned int i)
 convert a Sanger Q-score into an error probability. Uses a cache to be fast.
double getGCContent (const std::string &str)
 returns GC fraction of nucleotides in str
void acgtDo (char c, acgt_t aDo, acgt_t cDo, acgt_t gDo, acgt_t tDo)
void acgtxDo (char c, acgt_t aDo, acgt_t cDo, acgt_t gDo, acgt_t tDo, acgt_t xDo)
template<typename T >
const T::value_type & pickRandom (const T &t)
 Little utility to pick a random element from a container.
template<typename T >
std::string jsonVector (const std::vector< T > &v, const std::string &name, std::function< double(dnapos_t)> yAdjust=[](dnapos_t d){return 1.0 *d;}, std::function< double(int)> xAdjust=[](int i){return 1.0 *i;})
 returns v as a string in JSON format, where v is a vector of values, and we return it as an array of [offset,value] pairs.
template<typename T >
std::string jsonVectorD (const std::vector< T > &v, std::function< double(double)> yAdjust=[](double d){return d;}, std::function< double(int)> xAdjust=[](int i){return 1.0 *i;})
uint32_t kmerMapper (const std::string &str, int offset, int unsigned len)
 maps 'len' nucleotides from 'str' at offset offset to a 32 bit string. At most 16 nuclotides therefore!

Variables

const char * g_gitHash

Typedef Documentation

typedef std::function< void(void)> acgt_t

Function Documentation

void acgtDo ( char  c,
acgt_t  aDo,
acgt_t  cDo,
acgt_t  gDo,
acgt_t  tDo 
) [inline]
void acgtxDo ( char  c,
acgt_t  aDo,
acgt_t  cDo,
acgt_t  gDo,
acgt_t  tDo,
acgt_t  xDo 
) [inline]
double getGCContent ( const std::string &  str)

returns GC fraction of nucleotides in str

template<typename T >
std::string jsonVector ( const std::vector< T > &  v,
const std::string &  name 
)

returns v as a string in JSON format, where v is a vector of values, and we return it as an array of [offset,value] pairs.

v can be transformed inline ysing yAdjust and xAdjust

Parameters:
vVector of values
namename of JSON object
yAdjustfunction (or lambda) that transforms the values in v
xAdjustfunction (or lambda) that generates the offsets in our return vector. Gets passed this offset, returns a double
template<typename T >
std::string jsonVectorD ( const std::vector< T > &  v)
uint32_t kmerMapper ( const std::string &  str,
int  offset,
int unsigned  len 
)

maps 'len' nucleotides from 'str' at offset offset to a 32 bit string. At most 16 nuclotides therefore!

template<typename T >
const T::value_type& pickRandom ( const T &  t)

Little utility to pick a random element from a container.

double qToErr ( unsigned int  i)

convert a Sanger Q-score into an error probability. Uses a cache to be fast.


Variable Documentation

const char* g_gitHash
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