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comparison fastx_toolkit-0.0.6/src/libfastx/fastx_args.c @ 3:997f5136985f draft default tip

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author xilinxu
date Thu, 14 Aug 2014 04:52:17 -0400
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2:dfe9332138cf 3:997f5136985f
1 /*
2 FASTX-toolkit - FASTA/FASTQ preprocessing tools.
3 Copyright (C) 2009 A. Gordon (gordon@cshl.edu)
4
5 This program is free software: you can redistribute it and/or modify
6 it under the terms of the GNU Affero General Public License as
7 published by the Free Software Foundation, either version 3 of the
8 License, or (at your option) any later version.
9
10 This program is distributed in the hope that it will be useful,
11 but WITHOUT ANY WARRANTY; without even the implied warranty of
12 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 GNU Affero General Public License for more details.
14
15 You should have received a copy of the GNU Affero General Public License
16 along with this program. If not, see <http://www.gnu.org/licenses/>.
17 */
18 #include <err.h>
19 #include <stdio.h>
20 #include <stdlib.h>
21 #include <unistd.h>
22 #include <sys/types.h>
23 #include <string.h>
24 #include <getopt.h>
25
26 #include "fastx_args.h"
27
28 /*
29 * Each program should specify its own usage string
30 */
31 extern char* usage;
32
33
34 /*
35 * globals.. yuck
36 *
37 * some day this will be a stand alone class
38 */
39 const char* input_filename = "-";
40 const char* output_filename = "-";
41 int verbose = 0;
42 int compress_output = 0 ;
43 FILE* report_file;
44
45 const char* get_input_filename()
46 {
47 return input_filename;
48 }
49
50 const char* get_output_filename()
51 {
52 return output_filename;
53 }
54
55 int verbose_flag()
56 {
57 return verbose;
58 }
59
60 int compress_output_flag()
61 {
62 return compress_output ;
63 }
64
65 FILE* get_report_file()
66 {
67 return report_file;
68 }
69
70 int fastx_parse_cmdline( int argc, char* argv[],
71 const char* program_options,
72 parse_argument_func program_parse_args )
73 {
74 int opt;
75
76 char combined_options_string[100];
77
78 strcpy(combined_options_string, "zhvi:o:");
79 strcat(combined_options_string, program_options);
80
81 report_file = stderr ; //since the default output is STDOUT, the report goes by default to STDERR
82
83 while ( (opt = getopt(argc, argv, combined_options_string) ) != -1 ) {
84
85 // Parse the program's custom options
86 if ( strchr(program_options, opt) != NULL ) {
87 if (!program_parse_args(optind, opt, optarg))
88 return 0;
89 continue;
90 }
91
92 //Parse the default options
93 switch(opt) {
94 case 'h':
95 printf("%s", usage);
96 exit(1);
97
98 case 'v':
99 verbose = 1 ;
100 break ;
101
102 case 'z':
103 compress_output = 1 ;
104 break ;
105
106
107 case 'i':
108 if (optarg==NULL)
109 errx(1,"[-i] option requires FILENAME argument");
110 input_filename = optarg;
111 break;
112
113 case 'o':
114 if (optarg==NULL)
115 errx(1,"[-o] option requires FILENAME argument");
116 output_filename = optarg;
117
118 //The user specified a specific output file, so the report can go to STDOUT
119 report_file = stdout;
120 break;
121
122 default:
123 printf("use '-h' for usage information.\n");
124 exit(1);
125 break;
126
127 }
128 }
129
130 return 1;
131 }
132