Fix a bug in block order string where a bad index was used while outp…

…utting paths
edawson · Apr 5, 2018 · 28325fc · 28325fc
1 parent ad47105
commit 28325fc
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Showing 2 changed files with 24 additions and 7 deletions.
diff --git a/src/gfakluge.cpp b/src/gfakluge.cpp
@@ -250,6 +250,8 @@ namespace gfak{
         this->version = v;
         verz.val = std::to_string((double) this->version).substr(0,3);
         this->header[verz.key] = verz;
+        //gfa_1_ize();
+        //gfa_2_ize();
     }
     void GFAKluge::set_version(){
         header_elem verz;
@@ -896,6 +898,10 @@ namespace gfak{
     }
 
     std::string GFAKluge::block_order_string(){
+
+        this->gfa_1_ize();
+        this->gfa_2_ize();
+
         if (version >= 2.0){
             return block_order_string_2();
         }
@@ -960,7 +966,7 @@ namespace gfak{
                     vector<string> ovec;
                     for (int oi = 0; oi < pt->second.segment_names.size(); oi++){
                         stringstream o_str;
-                        o_str << pt->second.segment_names[oi] << (pt->second.orientations[i] ? "-" : "+");
+                        o_str << pt->second.segment_names[oi] << (pt->second.orientations[oi] ? "-" : "+");
                         ovec.push_back(o_str.str());
                     }
                     pat << join(ovec, ",");

diff --git a/src/main.cpp b/src/main.cpp
@@ -278,7 +278,7 @@ int diff_main(int argc, char** argv){
 int convert_main(int argc, char** argv){
     string gfa_file = "";
     bool block_order = false;
-    double spec_version = 0.1;
+    double spec_version = 2.0;
     bool use_paths = true;
 
     if (argc < 3){
@@ -538,7 +538,7 @@ int merge_main(int argc, char** argv){
 int sort_main(int argc, char** argv){
     string gfa_file = "";
     bool block_order = true;
-    double spec = 0.0;
+    double spec_version = 2.0;
 
     if (argc <= 2){
         sort_help(argv);
@@ -574,7 +574,7 @@ int sort_main(int argc, char** argv){
                 exit(1);
 
             case 'S':
-                spec = stod(optarg);
+                spec_version = stod(optarg);
                 break;
 
             default:
@@ -586,10 +586,21 @@ int sort_main(int argc, char** argv){
     GFAKluge gg;
     gg.parse_gfa_file(gfa_file);
 
-    if (spec != 0){
-        gg.set_version(spec);
+    if (spec_version == 0.1){
+        gg.set_version(0.1);
     }
-
+    else if (spec_version == 1.0){
+        gg.set_version(1.0);
+    }
+    else if (spec_version == 2.0){
+        gg.set_version(2.0);
+    }
+    else if (spec_version != 0.0){
+        cerr << "Invalid specification number: " << spec_version << endl
+        << "Please provide one of [0.1, 1.0, 2.0]." << endl;
+        exit(22);
+    }
+
     cout << gg.block_order_string();