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

-debug problem with relative path hard-coded in vidjil
-if you want to give a relative path in vidjil command imagine you are at the vidjil root

algo/core/germline.h

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

algo/vidjil.cpp

@@ -30,6 +30,8 @@
 #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"
@@ -292,6 +294,17 @@ 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)