diff snp_caller/src/args.h @ 0:0fd352f62446 draft default tip

planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snp_caller/src/args.h	Sun Feb 21 06:05:24 2016 -0500
@@ -0,0 +1,62 @@
+#ifndef ARGS_H
+#define ARGS_H
+
+#include <string>
+#include <vector>
+
+void static usage() {
+        fprintf(stderr, "\n");
+        fprintf(stderr, "Program: SNP Finder \n");
+        fprintf(stderr, "Contact: Chris Dean <[e-mail]>\n\n");
+        fprintf(stderr, "Usage: snp [options] <fasta_file> <sam_file> <best> <output_file>\n\n");
+        fprintf(stderr, "Options:\n\n");
+        fprintf(stderr, "   -amr_fp STRING             amr database\n");
+        fprintf(stderr, "   -samse STRING           single-end alignments\n");
+        fprintf(stderr, "   -sampe STRING           paired-end alignments\n");
+        fprintf(stderr, "   -b BOOLEAN              filter on unique alignments\n");
+        fprintf(stderr, "   -out_fp STRING               output path or(file)\n\n");
+}
+
+struct cmd_args {
+	std::string amr_fp;
+	std::string sam_fp;
+	std::string out_fp;
+
+	bool best = false;
+	bool samse = false;
+	bool sampe = false;
+};
+
+static inline cmd_args
+parse_command_line(int argc, const char *argv[]) {
+	std::vector<std::string> args(argv, argv+argc);
+	
+	cmd_args arg;
+
+	for(int i = 1; i < argc; i++) {
+		if(args[i] == "-amr_fp") {
+			arg.amr_fp = args[++i];
+		}
+		else if(args[i] == "-samse") {
+			arg.sam_fp = argv[++i];		
+			arg.samse = true;
+		}
+		else if(args[i] == "-sampe") {
+			arg.sam_fp = argv[++i];
+			arg.sampe = true;
+		}
+		else if(args[i] == "-out_fp") {
+			arg.out_fp = argv[++i];
+		}
+		else if(args[i] == "-b") {
+			arg.best = true;		
+		}
+		else {
+			usage();
+			exit(EXIT_FAILURE);						
+		}
+	}
+	return arg;
+}
+
+#endif //ARGS_H