#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? |
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read over all useless characters such as spaces, tabs and line breaks
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consider reverse complemented segments also?
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