I added #include <getopt.h> to two files and #include <unistd.h> to msa.cc. (#20)

Author: BenjaminSchwessinger

detect_collinear_tandem_arrays.cc

@@ -1,5 +1,5 @@
 #include "detect_collinear_tandem_arrays.h"
-
+#include <getopt.h>
 void read_gff(char* path)
 {
     if (!ifstream(path))

dissect_multiple_alignment.cc

@@ -1,5 +1,5 @@
 #include "dissect_multiple_alignment.h"
-
+#include <getopt.h>
 void read_gff(char* path)
 {
     if (!ifstream(path))

msa.cc

@@ -2,6 +2,7 @@
  * This is the new code for generating and printing multiple alignment based on progressive alignment 
 */
 #include "msa.h"
+#include <unistd.h>
 
 static vector <New_endpoint> endpoints;
 int max_level;