Updated README.md and WHAT_IS_NEW

[rsem.git] / utils.h

diff --git a/utils.h b/utils.h
index e3f8bcba1306fc7116550a292767895b6c2d9544..137440ef82a42590460c965a1a61d7ead70e4af0 100644 (file)
--- a/utils.h
+++ b/utils.h
@@ -10,6 +10,10 @@
 #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;
@@ -19,7 +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; }
@@ -120,7 +124,7 @@ inline std::string cleanStr(const std::string& str) {
   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];
 
@@ -142,7 +146,7 @@ void genReadFileNames(const char* readFN, int tagType, int read_type, int& s, ch
        }
 }
 
-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;