Seeding shuffleBed with srand((unsigned)time(0)+(unsigned)getpid()); Thanks to Rob Long.

src/shuffleBed/shuffleBed.cpp

@@ -31,11 +31,8 @@ BedShuffle::BedShuffle(string &bedFile, string &genomeFile, string &excludeFile,
         srand(seed);
     }
     else {
-        timeval tim;
-        gettimeofday(&tim, NULL);
-        int t1=tim.tv_sec+tim.tv_usec;
-        
-        srand((unsigned)t1);
+        // thanks to Rob Long for the tip.
+        srand((unsigned)time(0)+(unsigned)getpid());
     }
 
     _bed         = new BedFile(bedFile);

src/shuffleBed/shuffleBed.h

@@ -19,7 +19,8 @@
 #include <cstdlib>
 #include <ctime>
 #include <sys/time.h>
-
+#include <unistd.h>
+#include <sys/types.h>
 using namespace std;
 
 const int MAX_TRIES = 1000000;