Revert "vidjil.cpp : force current working directory to be the vidjil program directory"

This reverts commit 88044a01.
We do not want to chdir, the user may legitimately want to run vidjil from any directory.

algo/core/germline.h

@@ -8,7 +8,6 @@
 #include "kmerstore.h"
 #include "stats.h"
 
-
 using namespace std;
 
 class Germline {

algo/vidjil.cpp

@@ -30,8 +30,6 @@
 #include <sys/stat.h>
 #include <sys/types.h>
 #include <unistd.h>
-#include <limits.h>
-#include <stdio.h>
 
 #include "core/tools.h"
 #include "core/json.h"
@@ -294,17 +292,6 @@ int main (int argc, char **argv)
   //JsonArray which contains the Levenshtein distances
   JsonArray jsonLevenshtein;
 
-  //replace working directory to avoid relative path problem
-  char dest[PATH_MAX];
-  char path[PATH_MAX] = "/proc/self/exe";
-  
-  if (readlink(path, dest, PATH_MAX) == -1)
-    perror("readlink");
-  string dest2(dest);
-  string dest3 = dest2.substr(0, dest2.find_last_of("\\/"));
-  cout << chdir(dest3.c_str())<<endl;
-  
-  
   //$$ options: getopt
 
   while ((c = getopt(argc, argv, "AhagG:V:D:J:k:r:vw:e:C:t:l:dc:m:M:N:s:p:Sn:o:L%:Z:y:z:uU")) != EOF)