Refactor --gcf option to take a trees file. --help usage for concorda…

…nce factor analysis.

main/phyloanalysis.cpp

@@ -3945,7 +3945,7 @@ void assignBranchSupportNew(Params &params) {
     string prefix = (params.out_prefix) ? params.out_prefix : params.user_file;
     string str = prefix + ".cf.tree";
     tree->printTree(str.c_str());
-    cout << "Tree with assigned branch supports written to " << str << endl;
+    cout << "Tree with concordance factors written to " << str << endl;
     if (verbose_mode >= VB_DEBUG)
         tree->drawTree(cout);
     str = prefix + ".cf.branch";
@@ -3983,7 +3983,7 @@ void assignBranchSupportNew(Params &params) {
         out << '\t' << label << '\t' << length << endl;
     }
     out.close();
-    cout << "Concordance factors printed to " << filename << endl;
+    cout << "Concordance factors per branch printed to " << filename << endl;
     if (!params.site_concordance_partition || !tree->isSuperTree())
         return;
     // print partition-wise concordant/discordant sites
@@ -4017,7 +4017,7 @@ void assignBranchSupportNew(Params &params) {
         }
     }
     out.close();
-    cout << "Concordance factors for loci printed to " << filename << endl;
+    cout << "Concordance factors per branch and locus printed to " << filename << endl;
 }
 
 

utils/tools.cpp

@@ -1518,6 +1518,10 @@ void parseArg(int argc, char *argv[], Params &params) {
 
             if (strcmp(argv[cnt], "--gcf") == 0) {
 				params.consensus_type = CT_ASSIGN_SUPPORT_EXTENDED;
+                cnt++;
+                if (cnt >= argc)
+                    throw "Use --gcf <user_trees_file>";
+                params.treeset_file = argv[cnt];
 				continue;
 			}
             if (strcmp(argv[cnt], "--scf") == 0) {
@@ -4153,6 +4157,15 @@ void usage_iqtree(char* argv[], bool full_command) {
     << "  --bisymtest-pval NUMER    P-value cutoff (default: 0.05)" << endl
     << "  --bisymtest-keep-zero     Keep NAs in the tests" << endl
     << "  --permsymtest NUMBER      Replicates for permutation tests of symmetry" << endl
+
+    << endl << "CONCORDANCE FACTOR ANALYSIS:" << endl
+    << "  -t FILE              Reference tree to assign concordance factor" << endl
+    << "  --gcf FILE           Set of trees gene concordance factor (gCF)" << endl
+    << "  --scf NUMBER         Number of quartets for site concordance factor (sCF)" << endl
+    << "  -s FILE              Sequence alignment for --scf" << endl
+    << "  -p FILE|DIR          Partition file or directory for --scf" << endl
+    << "  --scf-part           Write sCF per partition to .cf.stat2 file" << endl
+
     << endl;