resolve issues with parseArgs and Subcall base class to ensure usabil…

…ity without redundancy

cli/include/Index.hpp

@@ -12,6 +12,7 @@ class Index : public Subcall {
     public:
         cxxopts::ParseResult parseArgs(int argc, char** argv) override;
         void execute(const cxxopts::ParseResult& args) override;
+
 };
 
-#endif //GENOGROVE_INDEX_HPP
+#endif //GENOGROVE_INDEX_HPP

cli/include/Overlap.hpp

@@ -14,6 +14,11 @@ class Overlap : public Subcall {
     public:
         cxxopts::ParseResult parseArgs(int argc, char** argv) override;
         void execute(const cxxopts::ParseResult& args) override;
+
+        // getter & setter
+        cxxopts::Options getOptions();
+        void setOptions(cxxopts::Options options);
+
 };
 
 #endif //GENOGROVE_OVERLAP_HPP

cli/include/Subcall.hpp

@@ -8,6 +8,7 @@ class Subcall {
         virtual cxxopts::ParseResult parseArgs(int argc, char** argv) = 0;
         virtual void execute(const cxxopts::ParseResult& args) = 0;
         virtual ~Subcall() = default;
+
 };
 
 #endif //GENOGROVE_SUBCALL_HPP

cli/src/Index.cpp

@@ -5,15 +5,23 @@ cxxopts::ParseResult Index::parseArgs(int argc, char** argv) {
     options.add_options()
             ("inputfile", "The input file to be indexed",
                     cxxopts::value<std::string>())
-            ("-o, outputfile", "Write the index to the specified file",
+            ("o, outputfile", "Write the index to the specified file",
                     cxxopts::value<std::string>())
             ("k, order", "The order of the tree (default: 3)",
                     cxxopts::value<int>()->default_value("3"))
+            ("h, help", "Print help")
+
             ;
     options.parse_positional({"inputfile"});
-    return options.parse(argc, argv);
+    cxxopts::ParseResult args = options.parse(argc, argv);
+
+    if(args.count("help")) {
+        options.help();
+    }
+    return args;
 }
 
+
 void Index::execute(const cxxopts::ParseResult& args) {
     if(args.count("inputfile")) {
         std::string inputfile = args["inputfile"].as<std::string>();
@@ -24,4 +32,4 @@ void Index::execute(const cxxopts::ParseResult& args) {
         std::string outputfile = args["outputfile"].as<std::string>();
         std::cout << "Writing index to file: " << outputfile << std::endl;
     }
-}
+}

cli/src/Overlap.cpp

@@ -1,25 +1,28 @@
 #include "Overlap.hpp"
 
 cxxopts::ParseResult Overlap::parseArgs(int argc, char** argv) {
-    cxxopts::Options options("overlap", "Search for interval overlaps in the index");
+    cxxopts::Options options("index", "Index an Interval File");
     options.add_options()
-            ("input", "The search string or file to search for",
-                    cxxopts::value<std::string>())
-            ("o, output", "The output file to store the overlaps",
-                    cxxopts::value<std::string>())
+            ("inputfile", "The input file to be indexed",
+             cxxopts::value<std::string>())
+            ("-o, outputfile", "Write the index to the specified file",
+             cxxopts::value<std::string>()->default_value(""))
+            ("k, order", "The order of the tree (default: 3)",
+             cxxopts::value<int>()->default_value("3"))
             ;
-    options.parse_positional({"input"});
+    options.parse_positional({"inputfile"});
     return options.parse(argc, argv);
 }
 
+
 void Overlap::execute(const cxxopts::ParseResult& args) {
-    if(args.count("input")) {
-        std::string input = args["input"].as<std::string>();
-        std::cout << "Searching for overlaps in file: " << input << std::endl;
+    if(args.count("inputfile")) {
+        std::string inputfile = args["inputfile"].as<std::string>();
+        std::cout << "Indexing file: " << inputfile << std::endl;
     }
 
-    if(args.count("output")) {
-        std::string output = args["output"].as<std::string>();
-        std::cout << "Writing overlaps to file: " << output << std::endl;
+    if(args.count("outputfile")) {
+        std::string outputfile = args["outputfile"].as<std::string>();
+        std::cout << "Writing index to file: " << outputfile << std::endl;
     }
-}
+}

cli/src/main.cpp

@@ -56,11 +56,7 @@ int main(int argc, char** argv) {
     }
 
     // parse additional options for the subcommand
-    auto subcallArgs = command->parseArgs(argc, argv);
-    if(subcallArgs.count("help")) {
-
-        command->printHelp(options);
-        return 0;
-    }
+    cxxopts::ParseResult subcallArgs = command->parseArgs(argc, argv);
+    command->execute(subcallArgs);
 }