Merge remote-tracking branch 'origin/report-taxon-root-dist' into sin…

…k-action

tools/taxonomy-parser.cpp

@@ -69,6 +69,7 @@ variables_map parse_cmd_line(int argc,char* argv[]) {
         ("extinct-to-incert,E","Adds an incertae_sedis flag to every extinct taxa (use with write-taxonomy)")
         ("children,C",value<long>(),"Show the children of node <arg>")
         ("parent,P",value<OttId>(),"Show the parent taxon of node <arg>")
+        ("report-dist-to-root","Report the number of nodes between from the root to each OTT ID (the root reports 1)")
         ("high-degree-nodes",value<int>(),"Show the top <arg> high-degree nodes")
         ("write-tree,T","Write out the result as a tree")
         ("write-taxonomy",value<string>(),"Write out the result as a taxonomy to directory 'arg'")
@@ -283,6 +284,11 @@ std::function<bool(tax_flags)> get_flags_match(variables_map& args) {
     }
 }
 
+void report_dist_to_root(std::ostream & out, const Taxonomy & taxonomy) {
+    for (auto & rec : taxonomy) {
+        out << rec.id << '\t' << rec.depth << '\n';
+    }
+}
 
 int main(int argc, char* argv[])
 {
@@ -391,6 +397,9 @@ int main(int argc, char* argv[])
         if (args.count("version")) {
             std::cout << taxonomy.get_version() << std::endl;
         }
+        if (args.count("report-dist-to-root")) {
+            report_dist_to_root(std::cout, taxonomy);
+        }
     } catch (std::exception& e) {
         cerr << "otc-taxonomy-parser: Error! " << e.what() << std::endl;
         return 1;