#include<cassert>
#include<string>
#include<vector>
+#include<stdint.h>
+
+typedef uint64_t HIT_INT_TYPE;
+typedef uint64_t READ_INT_TYPE;
const int STRLEN = 10005 ;
const double EPSILON = 1e-300;
const int OLEN = 25; // overlap length, number of bases must not be in poly(A) tails
const int NBITS = 32; // use unsigned int, 32 bits per variable
-bool verbose = true; // show detail intermediate outputs
+static bool verbose = true; // show detail intermediate outputs
inline bool isZero(double a) { return fabs(a) < 1e-8; }
inline bool isLongZero(double a) { return fabs(a) < 1e-30; }
return (fr <= to ? str.substr(fr, to - fr + 1) : "");
}
-void genReadFileNames(const char* readFN, int tagType, int read_type, int& s, char readFs[][STRLEN]){
+inline void genReadFileNames(const char* readFN, int tagType, int read_type, int& s, char readFs[][STRLEN]){
const char tags[3][STRLEN] = {"un", "alignable", "max"};
char suffix[STRLEN];
}
}
-void printTimeUsed(const time_t& a, const time_t& b, const char* program_name) {
+inline void printTimeUsed(const time_t& a, const time_t& b, const char* program_name) {
int hh = (b - a) / 3600;
int mm = (b - a) % 3600 / 60;
int ss = (b - a) % 60;