minor main change

@@ -250,21 +250,21 @@ void outputCliques (
 void usage()
 void usage()
 {
 {
     std::cout << "C-RCPred (Constrained RNA Complex Prediction)" << std::endl
     std::cout << "C-RCPred (Constrained RNA Complex Prediction)" << std::endl
-              << " -f:       Input fasta file" << std::endl
-              << " -s:       Input secondary structure files," << std::endl
-              << " -i:       Input interaction secondary structure files," << std::endl
-              << " -c:       Constraint files where constraints are in the same order than the secondary structure and interaction files" << std::endl
-              << " -p:       Probing data file for each RNA, in the same order than the fasta files (if no data for an RNA, an empty file is needed)" << std::endl
-              << " -o:       Format of output \"d\" (dot-parenthesis, default), \"j\" (JSON) or \"b\" (base pair list format)" << std::endl
-              << " -e:       Energy model (0: No energy model; use energies computed by upstream tools, 1: ViennaRNA package model; default, 2: NUPACK model)" << std::endl
-              << " -t:       Threshold for compatibility RNA (0->100, default 100)" << std::endl
-              << " -l:       Lower probing threshold (0->100, if not specified, probing values between 0% and the upper threshold once normalized will not be taken into account)" << std::endl
-              << " -u:       Upper probing threshold  (0->100, if not specified, probing values between the lower threshold and 100% once normalized will not be taken into account)" << std::endl
-              << " -g:       Output graph file" << std::endl
-              << " -k:       Output cliques predicted" << std::endl
-              << " -q:       Output cliques predicted without duplicates" << std::endl
-              << " -m:       Maximum number of structures to output" << std::endl
-              << " -h:       Shows this message" << std::endl;
+              << " -f       Input fasta file" << std::endl
+              << " -s       Input secondary structure files," << std::endl
+              << " -i       Input interaction secondary structure files," << std::endl
+              << " -c       Constraint files where constraints are in the same order than the secondary structure and interaction files" << std::endl
+              << " -p       Probing data file for each RNA, in the same order than the fasta files (if no data for an RNA, an empty file is needed)" << std::endl
+              << " -o       Format of output \"d\" (dot-parenthesis, default), \"j\" (JSON) or \"b\" (base pair list format)" << std::endl
+              << " -e       Energy model (0: No energy model; use energies computed by upstream tools, 1: ViennaRNA package model; default, 2: NUPACK model)" << std::endl
+              << " -t       Threshold for compatibility RNA (0->100, default 100)" << std::endl
+              << " -l       Lower probing threshold (0->100, if not specified, probing values between 0% and the upper threshold once normalized will not be taken into account)" << std::endl
+              << " -u       Upper probing threshold  (0->100, if not specified, probing values between the lower threshold and 100% once normalized will not be taken into account)" << std::endl
+              << " -g       Output graph file" << std::endl
+              << " -k       Output cliques predicted" << std::endl
+              << " -q       Output cliques predicted without duplicates" << std::endl
+              << " -m       Maximum number of structures to output" << std::endl
+              << " -h       Shows this message" << std::endl;
 }
 }
 
 
 // Main
 // Main
@@ -279,7 +279,7 @@ int main(int argc, char *argv[]) {
     if(argc > 1) {
     if(argc > 1) {
         // Parse options
         // Parse options
         char ch;
         char ch;
-        while ((ch=char(getopt(argc, argv, "f:s:i:c:o:t:e:p:l:u:g:k:q:m:h:?")))!=-1) {
+        while ((ch=char(getopt(argc, argv, "hf:s:i:c:o:t:e:p:l:u:g:k:q:m:?")))!=-1) {
             switch (ch) {
             switch (ch) {
             case 'f':
             case 'f':
                 SEQfile = optarg;
                 SEQfile = optarg;