--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastx_toolkit-0.0.6/src/libfastx/fastx_args.c	Thu Aug 14 04:52:17 2014 -0400
@@ -0,0 +1,132 @@
+/*
+    FASTX-toolkit - FASTA/FASTQ preprocessing tools.
+    Copyright (C) 2009  A. Gordon (gordon@cshl.edu)
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU Affero General Public License as
+    published by the Free Software Foundation, either version 3 of the
+    License, or (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU Affero General Public License for more details.
+
+    You should have received a copy of the GNU Affero General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+*/
+#include <err.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <sys/types.h>
+#include <string.h>
+#include <getopt.h>
+
+#include "fastx_args.h"
+
+/*
+ * Each program should specify its own usage string
+ */
+extern char* usage;
+
+
+/*
+ * globals.. yuck
+ *
+ * some day this will be a stand alone class
+ */
+const char* input_filename = "-";
+const char* output_filename = "-";
+int verbose = 0;
+int compress_output = 0 ;
+FILE* report_file;
+
+const char* get_input_filename()
+{
+	return input_filename;
+}
+
+const char* get_output_filename()
+{
+	return output_filename;
+}
+
+int verbose_flag()
+{
+	return verbose;
+}
+
+int compress_output_flag()
+{
+	return compress_output ;
+}
+
+FILE* get_report_file()
+{
+	return report_file;
+}
+
+int fastx_parse_cmdline( int argc, char* argv[],
+			 const char* program_options,
+			 parse_argument_func program_parse_args ) 
+{
+	int opt;
+
+	char combined_options_string[100];
+
+	strcpy(combined_options_string, "zhvi:o:");
+	strcat(combined_options_string, program_options);
+	
+	report_file = stderr ; //since the default output is STDOUT, the report goes by default to STDERR
+
+	while ( (opt = getopt(argc, argv, combined_options_string) ) != -1 ) {
+		
+		// Parse the program's custom options
+		if ( strchr(program_options, opt) != NULL ) {
+			if (!program_parse_args(optind, opt, optarg))
+				return 0;
+			continue;
+		}
+
+		//Parse the default options
+		switch(opt) {
+		case 'h':
+			printf("%s", usage);
+			exit(1);
+		
+		case 'v':
+			verbose = 1 ;
+			break ;
+
+		case 'z':
+			compress_output = 1 ;
+			break ;
+
+
+		case 'i':
+			if (optarg==NULL)
+				errx(1,"[-i] option requires FILENAME argument");
+			input_filename = optarg;
+			break;
+
+		case 'o':
+			if (optarg==NULL)
+				errx(1,"[-o] option requires FILENAME argument");
+			output_filename = optarg;
+			
+			//The user specified a specific output file, so the report can go to STDOUT
+			report_file = stdout;
+			break;
+			
+		default:
+			printf("use '-h' for usage information.\n");
+			exit(1);
+			break;
+
+		}
+	}
+
+	return 1;
+}
+