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