Updated README.md and WHAT_IS_NEW

[rsem.git] / utils.h

diff --git a/utils.h b/utils.h
index 4fa0750f9773cb5059c268d2d7ac7abac6557f10..137440ef82a42590460c965a1a61d7ead70e4af0 100644 (file)
--- a/utils.h
+++ b/utils.h
@@ -10,7 +10,10 @@
 #include<cassert>
 #include<string>
 #include<vector>
-#include<cerrno>
+#include<stdint.h>
+
+typedef uint64_t HIT_INT_TYPE;
+typedef uint64_t READ_INT_TYPE;
 
 const int STRLEN = 10005 ;
 const double EPSILON = 1e-300;
@@ -20,7 +23,7 @@ const int RANGE = 201;
 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; }
@@ -121,21 +124,7 @@ inline std::string cleanStr(const std::string& str) {
   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];
 
@@ -157,31 +146,12 @@ void genReadFileNames(const char* readFN, int tagType, int read_type, int& s, ch
        }
 }
 
-void exitWithError(const char* errmsg) {
-       fprintf(stderr, "%s\n", errmsg);
-       exit(-1);
-}
+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;
 
-void pthread_exception(int rc) {
-       switch(rc) {
-       case EAGAIN:
-               fprintf(stderr, "Error code: EAGAIN. Insufficient resources to create another thread, or a system-imposed limit on the number of threads was encountered.\n");
-               break;
-       case EINVAL:
-               fprintf(stderr, "Error code: EINVAL. Invalid settings in attr if pthread_create() is called. Or the implementation has detected that the value specified by thread_id does not refer to a joinable thread if pthread_join() is called.\n");
-               break;
-       case EPERM:
-               fprintf(stderr, "Error code: EPERM. No permission to set the scheduling policy and parameters specified in attr.\n");
-               break;
-       case EDEADLK:
-               fprintf(stderr, "Error code: EDEADLK. A deadlock was detected (e.g., two threads tried to join with each other); or thread_id specifies the calling thread.");
-               break;
-       case ESRCH:
-               fprintf(stderr, "Error code: ESRCH. No thread with thread_id could be found.\n");
-               break;
-       default: fprintf(stderr, "Unknown error code: %d\n", rc);
-       }
-       exit(-1);
+       printf("Time Used for %s : %d h %02d m %02d s\n", program_name, hh, mm, ss);
 }
 
 #endif