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#ifndef __MISC_HPP__
#define __MISC_HPP__
//#define _GNU_SOURCE
#include <string.h>
#include <assert.h>
#include <algorithm>
// IO manipulator for substrings
class substr {
public:
const char * const _str;
size_t const _len;
substr(const char *str, size_t len) :
_str(str), _len(len) {}
substr(const char *str, const char *end) :
_str(str), _len(end > str ? end - str : 0) {}
};
inline bool is_base(const char c) {
switch(c) {
case 'A': case 'C': case 'G': case 'T':
case 'a': case 'c': case 'g': case 't':
return true;
default:
return false;
}
}
inline bool not_base(const char c) { return !is_base(c); }
inline std::ostream & operator<<(std::ostream &os, const substr &ss) {
assert(std::count_if(ss._str, ss._str+ss._len, not_base) == 0);
return os.write(ss._str, ss._len);
}
template<typename T>
int getFldsFromLine(char *line, T &res) {
char *saveptr;
res.clear();
char *tok = strtok_r(line, " \t\n", &saveptr);
while(tok) {
res.push_back(tok);
tok = strtok_r(0, " \t\n", &saveptr);
}
return res.size();
}
template<typename T>
int appendFldsFromLine(char *line, T &res) {
char *saveptr;
int numFlds = 0;
char *tok = strtok_r(line, " \t\n", &saveptr);
while(tok) {
res.push_back(tok);
++numFlds;
tok = strtok_r(0, " \t\n", &saveptr);
}
return numFlds;
}
#include <signal.h>
#define BREAKPOINT raise(SIGINT);
#endif
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