add: README

CMakeLists.txt

@@ -0,0 +1,12 @@
+cmake_minimum_required(VERSION 3.0)
+
+project(tnt_script)
+SET( CMAKE_EXPORT_COMPILE_COMMANDS ON )
+
+set(CMAKE_CXX_STANDARD 11)
+
+add_executable(gene_marker gene_marker.cpp)
+add_executable(trim_marker trim_marker.cpp)
+	
+target_compile_options(gene_marker PRIVATE -Wall -Wextra -pedantic -O3)
+target_compile_options(trim_marker PRIVATE -Wall -Wextra -pedantic -O3)

README.md

@@ -0,0 +1,24 @@
+
+- Author: Guoyi Zhang
+
+- License: GPLv2
+
+## gene_marker
+
+Generate fasta file which `m` means selected position by Gblocks from Gblocks html report file.
+
+Usage:
+
+```
+gene_marker <input_file> <output_file>
+```
+
+## trim_marker
+
+Trim the multi-sequence-alignment based on the marker which `m` indicates selected position.
+
+Usage:
+
+```
+trim_marker <marker_fasta_file> <input_fasta_file> <output_file>
+```

gene_marker.cpp

@@ -15,7 +15,7 @@
 bool checkArguments(int argc, char* argv[]) {
 	if (argc != 3) {
 		std::cerr << "Usage: " << argv[0]
-			  << " input_file output_file\n";
+			  << " <input_file> <output_file>\n";
 		return false;
 	}
 	return true;

trim_marker.cpp

@@ -58,7 +58,7 @@ void extract_characters(const std::string& line, const std::string& file,
 			const std::vector<int> positions) {
 	std::ofstream outfile(file, std::ios::app);
 	std::string new_line;
-	for (int pos : positions) {
+	for (unsigned long pos : positions) {
 		if (pos <= line.length()) {
 			new_line += line[pos - 1];  // start from 0
 		}