bbq Implementation Documentation
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cluster_fragments.cpp File Reference

#include <ctype.h>
#include <iostream>
#include <fstream>
#include <list>
#include <stdio.h>
#include <map>
#include <string>
#include <set>

Defines

#define CHUNK_SIZE   4096

Functions

void fill_reverse_segments ()
void skip (std::ifstream &ifs)
 read over all useless characters such as spaces, tabs and line breaks

bool read_parameters (int argc, char **argv)
void read_data (int argc, char **argv)
void free_all ()
bool matches (int i, int j)
void process_data ()
void write_output ()
void print_help ()
int main (int argc, char **argv)

Variables

bool params_good
int num_of_opts
char ** s
char ** s_names
int * n
int * m
int L
int k
int kappa
int K
std::set< std::string > groups
std::map< std::string, std::list<
int > > 		group_members
bool reverse
 consider reverse complemented segments also?

Define Documentation

#define CHUNK_SIZE   4096
 

Function Documentation

void fill_reverse_segments (   ) 
 

void free_all (   ) 
 

int main (  int  argc,
char **  argv
) 
 

bool matches (  int  i,
int  j
) 
 

void print_help (   ) 
 

void process_data (   ) 
 

void read_data (  int  argc,
char **  argv
) 
 

bool read_parameters (  int  argc,
char **  argv
) 
 

void skip (  std::ifstream &  ifs  ) 
 

read over all useless characters such as spaces, tabs and line breaks

void write_output (   ) 
 

Variable Documentation

std::map< std::string,std::list<int> > group_members
 

std::set<std::string> groups
 

int K
 

int k
 

int kappa
 

int L
 

int* m
 

int* n
 

int num_of_opts
 

bool params_good
 

bool reverse
 

consider reverse complemented segments also?

char** s
 

char** s_names
 

bbq Implementation Documentation
Axel Mosig, Bioinformatics, University of Leipzig