#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 printTimeUsed(const time_t& a, const time_t& b, const char* filename = "") {
- int hh = (b - a) / 3600;
- int mm = (b - a) % 3600 / 60;
- int ss = (b - a) % 60;
-
- printf("Time Used : %d h %02d m %02d s\n", hh, mm, ss);
-
- if (strcmp(filename, "")) {
- FILE *fo = fopen(filename, "w");
- fprintf(fo, "Time Used : %d h %02d m %02d s\n", hh, mm, ss);
- fclose(fo);
- }
-}
-
-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];
}
}
+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;
+
+ printf("Time Used for %s : %d h %02d m %02d s\n", program_name, hh, mm, ss);
+}
+
#endif