1 /*  sam_opts.c -- utilities to aid parsing common command line options.
2 
3     Copyright (C) 2015, 2019 Genome Research Ltd.
4 
5     Author: James Bonfield <jkb@sanger.ac.uk>
6 
7 Permission is hereby granted, free of charge, to any person obtaining a copy
8 of this software and associated documentation files (the "Software"), to deal
9 in the Software without restriction, including without limitation the rights
10 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
11 copies of the Software, and to permit persons to whom the Software is
12 furnished to do so, subject to the following conditions:
13 
14 The above copyright notice and this permission notice shall be included in
15 all copies or substantial portions of the Software.
16 
17 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
18 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
19 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
20 THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
21 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
22 FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
23 DEALINGS IN THE SOFTWARE.  */
24 
25 #include <config.h>
26 
27 #include <stdio.h>
28 #include <stdlib.h>
29 #include <string.h>
30 #include "sam_opts.h"
31 
32 /*
33  * Processes a standard "global" samtools long option.
34  *
35  * The 'c' value is the return value from a getopt_long() call.  It is checked
36  * against the lopt[] array to find the corresponding value as this may have
37  * been reassigned by the individual subcommand.
38  *
39  * Having found the entry, the corresponding long form is used to apply the
40  * option, storing the setting in sam_global_args *ga.
41  *
42  * Returns 0 on success,
43  *        -1 on failure.
44  */
parse_sam_global_opt(int c,const char * optarg,const struct option * lopt,sam_global_args * ga)45 int parse_sam_global_opt(int c, const char *optarg, const struct option *lopt,
46                          sam_global_args *ga) {
47     int r = 0;
48 
49     while (lopt->name) {
50         if (c != lopt->val) {
51             lopt++;
52             continue;
53         }
54 
55         if (strcmp(lopt->name, "input-fmt") == 0) {
56             r = hts_parse_format(&ga->in, optarg);
57             break;
58         } else if (strcmp(lopt->name, "input-fmt-option") == 0) {
59             r = hts_opt_add((hts_opt **)&ga->in.specific, optarg);
60             break;
61         } else if (strcmp(lopt->name, "output-fmt") == 0) {
62             r = hts_parse_format(&ga->out, optarg);
63             break;
64         } else if (strcmp(lopt->name, "output-fmt-option") == 0) {
65             r = hts_opt_add((hts_opt **)&ga->out.specific, optarg);
66             break;
67         } else if (strcmp(lopt->name, "reference") == 0) {
68             char *ref = malloc(10 + strlen(optarg) + 1);
69 
70             if (!ref) {
71                 fprintf(stderr, "Unable to allocate memory in "
72                                 "parse_sam_global_opt.\n");
73 
74                 return -1;
75             }
76 
77             sprintf(ref, "reference=%s", optarg);
78 
79             if (!(ga->reference = strdup(optarg))) {
80                 fprintf(stderr, "Unable to allocate memory in "
81                                 "parse_sam_global_opt.\n");
82 
83                 return -1;
84             }
85 
86             r  = hts_opt_add((hts_opt **)&ga->in.specific, ref);
87             r |= hts_opt_add((hts_opt **)&ga->out.specific, ref);
88             free(ref);
89             break;
90         } else if (strcmp(lopt->name, "threads") == 0) {
91             ga->nthreads = atoi(optarg);
92             break;
93         } else if (strcmp(lopt->name, "write-index") == 0) {
94             ga->write_index = 1;
95             break;
96         } else if (strcmp(lopt->name, "verbosity") == 0) {
97             hts_verbose = atoi(optarg);
98             break;
99         }
100     }
101 
102     if (!lopt->name) {
103         fprintf(stderr, "Unexpected global option.\n");
104         return -1;
105     }
106 
107     /*
108      * SAM format with compression enabled implies SAM.bgzf
109      */
110     if (ga->out.format == sam) {
111         hts_opt *opts = (hts_opt *)ga->out.specific;
112         while (opts) {
113             if (opts->opt == HTS_OPT_COMPRESSION_LEVEL)
114                 ga->out.compression = bgzf;
115             opts = opts->next;
116         }
117     }
118 
119     return r;
120 }
121 
122 /*
123  * Report the usage for global options.
124  *
125  * This accepts a string with one character per SAM_OPT_GLOBAL_OPTIONS option
126  * to determine which options need to be printed and how.
127  * Each character should be one of:
128  * '.'    No short option has been assigned. Use --long-opt only.
129  * '-'    The long (and short) option has been disabled.
130  * <c>    Otherwise the short option is character <c>.
131  */
sam_global_opt_help(FILE * fp,const char * shortopts)132 void sam_global_opt_help(FILE *fp, const char *shortopts) {
133     int i = 0;
134 
135     static const struct option lopts[] = {
136         SAM_OPT_GLOBAL_OPTIONS(0,0,0,0,0,0),
137         { NULL, 0, NULL, 0 }
138     };
139 
140     for (i = 0; shortopts && shortopts[i] && lopts[i].name; i++) {
141         if (shortopts[i] == '-')
142             continue;
143 
144         if (shortopts[i] == '.')
145             fprintf(fp, "      --");
146         else
147             fprintf(fp, "  -%c, --", shortopts[i]);
148 
149         if (strcmp(lopts[i].name, "input-fmt") == 0)
150             fprintf(fp,"input-fmt FORMAT[,OPT[=VAL]]...\n"
151                     "               Specify input format (SAM, BAM, CRAM)\n");
152         else if (strcmp(lopts[i].name, "input-fmt-option") == 0)
153             fprintf(fp,"input-fmt-option OPT[=VAL]\n"
154                     "               Specify a single input file format option in the form\n"
155                     "               of OPTION or OPTION=VALUE\n");
156         else if (strcmp(lopts[i].name, "output-fmt") == 0)
157             fprintf(fp,"output-fmt FORMAT[,OPT[=VAL]]...\n"
158                     "               Specify output format (SAM, BAM, CRAM)\n");
159         else if (strcmp(lopts[i].name, "output-fmt-option") == 0)
160             fprintf(fp,"output-fmt-option OPT[=VAL]\n"
161                     "               Specify a single output file format option in the form\n"
162                     "               of OPTION or OPTION=VALUE\n");
163         else if (strcmp(lopts[i].name, "reference") == 0)
164             fprintf(fp,"reference FILE\n"
165                     "               Reference sequence FASTA FILE [null]\n");
166         else if (strcmp(lopts[i].name, "threads") == 0)
167             fprintf(fp,"threads INT\n"
168                     "               Number of additional threads to use [0]\n");
169         else if (strcmp(lopts[i].name, "write-index") == 0)
170             fprintf(fp,"write-index\n"
171                     "               Automatically index the output files [off]\n");
172         else if (strcmp(lopts[i].name, "verbosity") == 0)
173             fprintf(fp,"verbosity INT\n"
174                     "               Set level of verbosity\n");
175     }
176 }
177 
sam_global_args_init(sam_global_args * ga)178 void sam_global_args_init(sam_global_args *ga) {
179     if (!ga)
180         return;
181 
182     memset(ga, 0, sizeof(*ga));
183 }
184 
sam_global_args_free(sam_global_args * ga)185 void sam_global_args_free(sam_global_args *ga) {
186     if (ga->in.specific)
187         hts_opt_free(ga->in.specific);
188 
189     if (ga->out.specific)
190         hts_opt_free(ga->out.specific);
191 
192     if (ga->reference)
193         free(ga->reference);
194 }
195