From 579237709ab8c71691f0e60c1b44de30f8b40ea0 Mon Sep 17 00:00:00 2001
From: riasc <richard.schaefer@zoho.com>
Date: Fri, 15 Nov 2024 12:16:48 -0600
Subject: [PATCH] added workflow to call help on subcall

---
 cli/include/Index.hpp   |  5 ++++-
 cli/include/Overlap.hpp |  2 +-
 cli/include/Subcall.hpp |  2 +-
 cli/src/Index.cpp       | 12 ++++--------
 cli/src/Overlap.cpp     |  4 ++--
 cli/src/main.cpp        |  9 +++++++--
 6 files changed, 19 insertions(+), 15 deletions(-)

diff --git a/cli/include/Index.hpp b/cli/include/Index.hpp
index c287110..b4d81b4 100644
--- a/cli/include/Index.hpp
+++ b/cli/include/Index.hpp
@@ -1,6 +1,9 @@
 #ifndef GENOGROVE_INDEX_HPP
 #define GENOGROVE_INDEX_HPP
 
+// Standard
+#include <cstdlib>
+
 // Class
 #include "genogrove/all.hpp"
 #include "Subcall.hpp"
@@ -10,7 +13,7 @@
 
 class Index : public Subcall {
     public:
-        cxxopts::ParseResult parseArgs(int argc, char** argv) override;
+        cxxopts::Options parseArgs(int argc, char** argv) override;
         void execute(const cxxopts::ParseResult& args) override;
 
 };
diff --git a/cli/include/Overlap.hpp b/cli/include/Overlap.hpp
index 6bca6f6..d1433d3 100644
--- a/cli/include/Overlap.hpp
+++ b/cli/include/Overlap.hpp
@@ -12,7 +12,7 @@
 
 class Overlap : public Subcall {
     public:
-        cxxopts::ParseResult parseArgs(int argc, char** argv) override;
+        cxxopts::Options parseArgs(int argc, char** argv) override;
         void execute(const cxxopts::ParseResult& args) override;
 
         // getter & setter
diff --git a/cli/include/Subcall.hpp b/cli/include/Subcall.hpp
index ff325c7..6da2ca2 100644
--- a/cli/include/Subcall.hpp
+++ b/cli/include/Subcall.hpp
@@ -5,7 +5,7 @@
 
 class Subcall {
     public:
-        virtual cxxopts::ParseResult parseArgs(int argc, char** argv) = 0;
+        virtual cxxopts::Options parseArgs(int argc, char** argv) = 0;
         virtual void execute(const cxxopts::ParseResult& args) = 0;
         virtual ~Subcall() = default;
 
diff --git a/cli/src/Index.cpp b/cli/src/Index.cpp
index 277fb58..d5e130f 100644
--- a/cli/src/Index.cpp
+++ b/cli/src/Index.cpp
@@ -1,7 +1,7 @@
 #include "Index.hpp"
 
-cxxopts::ParseResult Index::parseArgs(int argc, char** argv) {
-    cxxopts::Options options("index", "Index an Interval File");
+cxxopts::Options Index::parseArgs(int argc, char** argv) {
+    cxxopts::Options options("genogrove index", "Index an Interval File");
     options.add_options()
             ("inputfile", "The input file to be indexed",
                     cxxopts::value<std::string>())
@@ -13,15 +13,11 @@ cxxopts::ParseResult Index::parseArgs(int argc, char** argv) {
 
             ;
     options.parse_positional({"inputfile"});
-    cxxopts::ParseResult args = options.parse(argc, argv);
+    options.positional_help("inputfile");
 
-    if(args.count("help")) {
-        options.help();
-    }
-    return args;
+    return options;
 }
 
-
 void Index::execute(const cxxopts::ParseResult& args) {
     if(args.count("inputfile")) {
         std::string inputfile = args["inputfile"].as<std::string>();
diff --git a/cli/src/Overlap.cpp b/cli/src/Overlap.cpp
index e1b88e6..5680636 100644
--- a/cli/src/Overlap.cpp
+++ b/cli/src/Overlap.cpp
@@ -1,6 +1,6 @@
 #include "Overlap.hpp"
 
-cxxopts::ParseResult Overlap::parseArgs(int argc, char** argv) {
+cxxopts::Options Overlap::parseArgs(int argc, char** argv) {
     cxxopts::Options options("index", "Index an Interval File");
     options.add_options()
             ("inputfile", "The input file to be indexed",
@@ -11,7 +11,7 @@ cxxopts::ParseResult Overlap::parseArgs(int argc, char** argv) {
              cxxopts::value<int>()->default_value("3"))
             ;
     options.parse_positional({"inputfile"});
-    return options.parse(argc, argv);
+    return options;
 }
 
 
diff --git a/cli/src/main.cpp b/cli/src/main.cpp
index 4e845fa..280bef3 100644
--- a/cli/src/main.cpp
+++ b/cli/src/main.cpp
@@ -56,7 +56,12 @@ int main(int argc, char** argv) {
     }
 
     // parse additional options for the subcommand
-    cxxopts::ParseResult subcallArgs = command->parseArgs(argc, argv);
-    command->execute(subcallArgs);
+    cxxopts::Options subcallOptions = command->parseArgs(argc, argv);
+    cxxopts::ParseResult subcallArgs = subcallOptions.parse(argc, argv);
+
+    if(subcallArgs.count("help")) {
+        std::cout << subcallOptions.help() << "\n";
+        return 0;
+    }
 }