CMakeLists.txt

@@ -1,12 +0,0 @@
-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

@@ -1,24 +0,0 @@
-
-- 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 (unsigned long pos : positions) {
+	for (int pos : positions) {
 		if (pos <= line.length()) {
 			new_line += line[pos - 1];  // start from 0
 		}