keep_gff_id.patch

diff --git a/src/extended/gff3_visitor.c b/src/extended/gff3_visitor.c
index 8246680..9e87612 100644
--- a/src/extended/gff3_visitor.c
+++ b/src/extended/gff3_visitor.c
@@ -197,32 +197,52 @@ static int store_ids(GtGenomeNode *gn, void *data, GtError *err)
   AddIDInfo add_id_info;
   int had_err = 0;
   GtStr *id;
+  /* Q: is this const ok? */
+  const char *idstring;
+  int has_id = 0;
 
   gt_error_check(err);
   gt_assert(gn && gf && gff3_visitor);
+  idstring = gt_feature_node_get_attribute(gf, "ID");
 
-  if (gt_genome_node_has_children(gn) || gt_feature_node_is_multi(gf)) {
-    if (gt_feature_node_is_multi(gf)) {
-      id = gt_hashmap_get(gff3_visitor->gt_feature_node_to_unique_id_str,
+  if (idstring) {
+    id = gt_str_new_cstr(idstring);
+    has_id = 1;
+  }
+  else {
+    if (gt_feature_node_is_multi(gf) || gt_genome_node_has_children(gn) ) {
+      if (gt_feature_node_get_multi_representative(gf) != gf) {
+        id = gt_hashmap_get(gff3_visitor->gt_feature_node_to_unique_id_str,
                           gt_feature_node_get_multi_representative(gf));
-      if (!id) { /* the representative does not have its own id */
-        id = create_unique_id(gff3_visitor,
-                              gt_feature_node_get_multi_representative(gf));
+        has_id = 1;
       }
-      if (gt_feature_node_get_multi_representative(gf) != gf) {
-        gt_hashmap_add(gff3_visitor->gt_feature_node_to_unique_id_str, gf,
-                       gt_str_ref(id));
+      /*
+      else {
+        id = create_unique_id(gff3_visitor, gf);
+        has_id = 1;
       }
+      */
     }
-    else
-      id = create_unique_id(gff3_visitor, gf);
+    /* if it has a parent, get id from parent */
+    /* Q: better way to test for parent ? */
+    else if ( ! gt_feature_node_get_attribute(gf, "Parent")) {
+        id = create_unique_id(gff3_visitor, gf);
+        has_id = 1;
+    }
+
+  }
+  if (has_id == 1) {
+    gt_hashmap_add(gff3_visitor->gt_feature_node_to_unique_id_str, gf,
+               gt_str_ref(id));
 
     /* for each child -> store the parent feature in the hash map */
     add_id_info.gt_feature_node_to_id_array =
-      gff3_visitor->gt_feature_node_to_id_array,
+       gff3_visitor->gt_feature_node_to_id_array,
     add_id_info.id = gt_str_get(id);
     had_err = gt_genome_node_traverse_direct_children(gn, &add_id_info, add_id,
                                                       err);
+    /* Q: needed? */
+    gt_str_delete(id);
   }
   return had_err;
 }
@@ -262,8 +282,8 @@ static int gff3_visitor_feature_node(GtNodeVisitor *gv, GtFeatureNode *fn,
 
   /* show terminator, if the feature has children (otherwise it is clear that
      the feature is complete, because no ID attribute has been shown) */
-  if (gt_genome_node_has_children((GtGenomeNode*) fn))
-    gt_genfile_xprintf(gff3_visitor->outfp, "%s\n", GFF_TERMINATOR);
+  /* if (gt_genome_node_has_children((GtGenomeNode*) fn)) */
+  gt_genfile_xprintf(gff3_visitor->outfp, "%s\n", GFF_TERMINATOR);
 
   return had_err;
 }
diff --git a/testsuite/gt_gff3_include.rb b/testsuite/gt_gff3_include.rb
index 89d6e41..5e589b9 100644
--- a/testsuite/gt_gff3_include.rb
+++ b/testsuite/gt_gff3_include.rb
@@ -15,6 +15,7 @@ end
 Name "gt gff3 short test (stdin)"
 Keywords "gt_gff3"
 Test do
+  puts "#{$bin}gt gff3 < #{$testdata}gff3_file_1_short.txt"
   run_test "#{$bin}gt gff3 < #{$testdata}gff3_file_1_short.txt"
   run "env LC_ALL=C sort #{$last_stdout}"
   run "diff #{$last_stdout} #{$testdata}gff3_file_1_short_sorted.txt"