Fix QA warnings due to implicit declarations:
* filebuffer.c:123:34: warning: implicit declaration of function ‘toupper’ [-Wimplicit-function-declaration]
*      temp[i] = (strchr (alphabet, toupper ((char) i)) != 0) ?

--- a/src/filebuffer.c
+++ b/src/filebuffer.c
@@ -3,6 +3,7 @@
 #include <string.h>
 #include <stdio.h>
 #include <assert.h>
+#include <ctype.h>
 
 #ifdef CHAOS__FLAG
 char* alphabet = "ATCGNPCMHDEKRQSILVFYWX*";
--- a/src/mlagan.c
+++ b/src/mlagan.c
@@ -934,6 +934,7 @@
   return k;
 }
 
+int printXMFAAlign(FILE* outfile, align* myalign);
 
 int main(int argc, char** argv) {
   FileBuffer seqfile;
--- a/src/order.c
+++ b/src/order.c
@@ -398,6 +398,9 @@
   free(ends);
 }
 
+int printMFAAlign(char* seq1, char* seq2, align* myalign, char* n1, char* n2);
+int printXMFAAlign(char* seq1, char* seq2, align* myalign, char* n1, char* n2);
+
 void doAlign(dmat* mydm, seq* seq1, seq* seq2) {
   align *a = (align*) makeAlign(mydm, seq1->lets, seq2->lets);
   //  printf("into printing\n");
--- a/src/prolagan.c
+++ b/src/prolagan.c
@@ -949,6 +949,7 @@
   return k;
 }
 
+int printXMFAAlign(FILE* outfile, align* myalign);
 
 int main(int argc, char** argv) {
   FileBuffer seqfile;
--- a/src/utils/contigorder.c
+++ b/src/utils/contigorder.c
@@ -12,7 +12,7 @@
   int dummy, i;
   
   if (!(file = fopen (filename, "r"))){
-    fprintf (stderr, "contigorder: Error opening file: %s\n");
+    fprintf (stderr, "contigorder: Error opening file: %s\n", filename);
     exit (1);
   }
   
@@ -49,7 +49,7 @@
   }
 
   if (!(file = fopen (filename, "r"))){
-    fprintf (stderr, "contigorder: Error opening file: %s\n");
+    fprintf (stderr, "contigorder: Error opening file: %s\n", filename);
     exit (1);
   }
   
--- a/src/utils/cstat.c
+++ b/src/utils/cstat.c
@@ -3,6 +3,7 @@
 #include <string.h>
 #include <math.h>
 #include <assert.h>
+#include <ctype.h>
 
 #define MAX_SEQ 31
 #define MAX(a,b) ((a)>(b)?(a):(b))
--- a/src/utils/overlay.c
+++ b/src/utils/overlay.c
@@ -2,6 +2,7 @@
 #include <stdio.h>
 #include <assert.h>
 #include <string.h>
+#include <ctype.h>
 
 #define MAX_SEQS 63
 #define MIN2(y,z)        ((y)<(z))?(y):(z)
--- a/src/utils/scorecontigs.c
+++ b/src/utils/scorecontigs.c
@@ -3,6 +3,7 @@
 #include <string.h>
 #include <math.h>
 #include <assert.h>
+#include <ctype.h>
 
 #define MAX_SEQ 1024
 #define MAX(a,b) ((a)>(b)?(a):(b))