Move functions to libPATO

include/PATO/command_line_parser.h

@@ -0,0 +1,39 @@
+// MIT License
+//
+// Copyright (c) 2022-onwards Iñaki Amatria-Barral
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+
+#ifndef PATO_COMMAND_LINE_PARSER_H
+#define PATO_COMMAND_LINE_PARSER_H
+
+#include <PATO/options.h>
+
+#include <variant>
+
+namespace pato {
+
+using parse_result_t = std::variant<int, options_t>;
+
+parse_result_t parse_command_line(int argc, char *argv[], std::ostream &outs,
+                                  std::ostream &errs);
+
+} // namespace pato
+
+#endif // PATO_COMMAND_LINE_PARSER_H

include/PATO/tfo_finder.h

@@ -34,6 +34,8 @@ enum class find_tfo_motifs_result : unsigned {
 };
 
 find_tfo_motifs_result find_tfo_motifs(const options_t &opts);
+bool handle_find_tfo_motifs_result(find_tfo_motifs_result result,
+                                   std::ostream &errs, const options_t &opts);
 
 } // namespace pato
 

include/PATO/tpx_finder.h

@@ -35,6 +35,8 @@ enum class find_tpx_result : unsigned {
 };
 
 find_tpx_result find_tpxes(const options_t &opts);
+bool handle_find_tpx_result(find_tpx_result result, std::ostream &errs,
+                            const options_t &opts);
 
 } // namespace pato
 

include/PATO/tts_finder.h

@@ -34,6 +34,8 @@ enum class find_tts_motifs_result : unsigned {
 };
 
 find_tts_motifs_result find_tts_motifs(const options_t &opts);
+bool handle_find_tts_motifs_result(find_tts_motifs_result result,
+                                   std::ostream &errs, const options_t &opts);
 
 } // namespace pato
 

lib/PATO/CMakeLists.txt

@@ -1,4 +1,5 @@
 add_library(libPATO
+  command_line_parser.cpp
   guanine_filter.cpp
   output_writer.cpp
   repeat_filter.cpp