Updated startup message.

Author: bbuchfink

.dockerignore

@@ -0,0 +1,3 @@
+.git
+.vs
+out

Dockerfile

@@ -6,7 +6,7 @@ WORKDIR /opt/diamond
 ADD . .
 
 WORKDIR build
-RUN cmake -G Ninja -DCMAKE_BUILD_TYPE=Release -DCMAKE_BUILD_MARCH=x86-64 ..
+RUN cmake -G Ninja -DCMAKE_BUILD_TYPE=Release ..
 RUN ninja && ninja install
 
 FROM alpine:latest

src/basic/config.cpp

@@ -77,7 +77,7 @@ Config::Config(int argc, const char **argv)
 		.add_command("split", "")
 		.add_command("upgma", "")
 		.add_command("upgmamc", "")
-		.add_command("test", "Run regression test.")
+		.add_command("test", "")
 		.add_command("reverse", "")
 		.add_command("compute-medoids", "")
 		.add_command("mutate", "");
@@ -396,9 +396,8 @@ Config::Config(int argc, const char **argv)
 	}
 
 	ostream &header_out = command == Config::help ? cout : cerr;
-	header_out << Const::program_name << " v" << Const::version_string << "." << (unsigned)Const::build_version << " | by Benjamin Buchfink <[email protected]>" << endl;
-	header_out << "Licensed under the GNU GPL <https://www.gnu.org/licenses/gpl.txt>" << endl;
-	header_out << "Check http://github.com/bbuchfink/diamond for updates." << endl << endl;
+	header_out << Const::program_name << " v" << Const::version_string << "." << (unsigned)Const::build_version << " (C) Max Planck Society for the Advancement of Science" << endl;
+	header_out << "Documentation, support and updates available at http://www.diamondsearch.org" << endl << endl;
 	log_stream << Const::program_name << " v" << Const::version_string << "." << (unsigned)Const::build_version << endl;
 #ifndef NDEBUG
 	verbose_stream << "Assertions enabled." << endl;

src/test/simulate.cpp

@@ -77,8 +77,10 @@ void mutate() {
 	input_value_traits = value_traits = nucleotide_traits;
 	OutputFile out(config.output_file);
 	std::minstd_rand0 random_engine;
+	std::uniform_real_distribution<double> id_dist(0.3, 1.0);
 	while (FASTA_format().get_seq(id, seq, in)) {
-		Util::Sequence::format(sequence(seq), std::string(id.data(), id.size()).c_str(), nullptr, out, "fasta", nucleotide_traits);
+		const double i = id_dist(random_engine);
+		Util::Sequence::format(sequence(simulate_homolog(sequence(seq), i, random_engine)), std::to_string(int(i*100)).c_str(), nullptr, out, "fasta", nucleotide_traits);
 	}
 	out.close();
 	in.close();

src/util/command_line_parser.cpp

@@ -119,4 +119,5 @@ void Command_line_parser::print_help()
 		}
 		cout << endl;
 	}
+	cout << "Online documentation at http://www.diamondsearch.org" << endl;
 }