improved output

[RADS]
-added gop/gep information to output
-added hidden option to makeRadsDB to print only file name not path (for servers)

[makeRadsDB]
-added rads version and commandline to sql database into info table

CHANGELOG

-v. 2.0.0
-- Initial release
+v. 2.1.3
+- added gop/gep information to output file
+- added commandline and rads version to databse file in additional table
+
+v. 2.1.2
+- improved error reporting in case of input format problems
+
+v. 2.1.1
+- fixed sorting in makeDB on InterPro data
 
 v. 2.1.0
 - fixed problem in the score calculation (problem in BSDL)
 - added the time the program was run to the output file
 - added database file, query file and matrix information to the output file
 
-v. 2.1.1
-- fixed sorting in makeDB on InterPro data
-
-v. 2.1.2
-- improved error reporting in case of input format problems
+v. 2.0.0
+- Initial release

CMakeLists.txt

@@ -4,7 +4,7 @@ cmake_minimum_required(VERSION 2.6)
 project (RADS C CXX)
 SET(MAJOR_VERSION 2)
 SET(MINOR_VERSION 1)
-SET(PATCH_VERSION 2)
+SET(PATCH_VERSION 3)
 
 
 SET(CMAKE_CXX_FLAGS_COVERAGE

src/makeRadsDB.cpp

@@ -97,6 +97,14 @@ shortenNumber(std::string &number)
 int
 main(int argc, char *argv[])
 {
+	std::string input_command;
+	for (int i = 0; i < argc; i++)
+	{
+    	input_command += argv[i];
+		if (i < (argc-1))
+			input_command += " ";
+	}
+
 	std::string version(std::string(STR(MAJOR_VERSION)) + "." + std::string(STR(MINOR_VERSION)) + "." + std::string(STR(PATCH_VERSION)));
 	po::options_description allOpts("makeRadsDB " + version + " (C) 2016-2018  Carsten Kemena\nThis program comes with ABSOLUTELY NO WARRANTY;\n\nAllowed options are displayed below.");
 
@@ -122,7 +130,7 @@ main(int argc, char *argv[])
 		("threshold,t", po::value<unsigned int>(&threshold)->default_value(10), "Maximal number of allowed overlap")
 	;
 	allOpts.add(general).add(filterOpts);
-
+	
 
 	try
 	{
@@ -157,6 +165,7 @@ main(int argc, char *argv[])
 
 	// Create tables
 	db.exec("CREATE TABLE IF NOT EXISTS domain('id' INT PRIMARY KEY, 'accession' VARCHAR(45) NULL,'position' INT NULL)");
+	db.exec("CREATE TABLE IF NOT EXISTS info('id' INT PRIMARY KEY, 'version' VARCHAR(20), 'command' VARCHAR(200) NULL)");
 	db.startTransaction();
 
 	std::set<std::string> empty;
@@ -335,6 +344,7 @@ main(int argc, char *argv[])
 
 		// write the databaes to files
 		size_t nSeqs = 0;
+		db.exec("INSERT INTO info VALUES(NULL,'"+ version + "','" + input_command + "')");
 		for (auto &arrangements : dbContent)
 		{
 

src/rads.cpp

@@ -227,7 +227,6 @@ main(int argc, char *argv[])
 	vector<std::string> q, domains;
 
 	unsigned short nThreads;
-	po::options_description allOpts("rads " + version + " (C) 2015-2018  Carsten Kemena\nThis program comes with ABSOLUTELY NO WARRANTY;\n\nAllowed options are displayed below.");
 	po::options_description general("General options");
 	general.add_options()
 		("help,h", "Produces this help message")
@@ -261,14 +260,24 @@ main(int argc, char *argv[])
 		("min-score,M", po::value<int>(&minScore)->default_value(0), "The minimum alignment score to list")
 	;
 
-	allOpts.add(general).add(queryOpts).add(scoreOpts).add(filterOpts);
+	bool print_filename_only;
+	po::options_description hiddenOpts("Server Options");
+	hiddenOpts.add_options()
+	 	("print_filename_only", po::value<bool>(&print_filename_only)->default_value(false)->zero_tokens(), "Print the file name only in parameters (no path)")
+	;
+
+	po::options_description visibleOpts("rads " + version + " (C) 2015-2018  Carsten Kemena\nThis program comes with ABSOLUTELY NO WARRANTY;\n\nAllowed options are displayed below.");
+	visibleOpts.add(general).add(queryOpts).add(scoreOpts).add(filterOpts);
+	
+	po::options_description allOpts("Everything");
+	allOpts.add(general).add(queryOpts).add(scoreOpts).add(filterOpts).add(hiddenOpts);
 	try
 	{
 		po::variables_map vm;
 		po::store(po::command_line_parser(argc, argv).options(allOpts).run(), vm);
 		if (vm.count("help"))
 		{
-			cout << allOpts<< "\n";
+			cout << visibleOpts<< "\n";
 			return EXIT_SUCCESS;
 		}
 		po::notify(vm);
@@ -355,13 +364,17 @@ main(int argc, char *argv[])
 
 	string qPath = querySeqFile.empty() ? "-" : fs::canonical(querySeqFile).string();
 
+	string print_matrix_name = (print_filename_only) ? matrixName.stem().string() : fs::canonical(matrixName).string();
+	string print_db_name = (print_filename_only) ? fs::change_extension(daFile, "").stem().string() : fs::change_extension(fs::canonical(daFile), "").string();
 	// print output header
 	outS << "# RADS version " + version + "\n"
 	     << "# RADS Output v1\n"
 		 << "# run at " << ctime (&tt) << "#\n"
 		 << "# query file: " << qPath << "\n"
-		 << "# database: " << fs::change_extension(fs::canonical(daFile), "").string() << "\n"
-		 << "# matrix: " << fs::canonical(matrixName).string() << "\n"
+		 << "# database: " << print_db_name << "\n"
+		 << "# gap open penalty " << std::to_string(gop) << "\n"
+		 << "# gap extension penalty " << std::to_string(gep) << "\n"
+		 << "# matrix: " << print_matrix_name << "\n"
 		 << "# ******************************************************************\n"
 		 << "\n";