void *list_actions(void *args) {
t_args_plug *a;
a = (t_args_plug*) args;
if (strcmp(a->name, "volumes") == 0)
list_volumes(a->general_info, a->commands[0]);
else if (strcmp(a->name, "plugins") == 0)
list_plugins(a->general_info, a->commands[0]);
else if (strcmp(a->name, "help") == 0)
printf("Usage; list [plugins | volumes] --verbose\n");
return (NULL);
}
int main_plugin(int argc, char *argv[])
{
int c;
args_t *args = (args_t*) calloc(1,sizeof(args_t));
args->argc = argc; args->argv = argv;
args->files = bcf_sr_init();
args->output_fname = "-";
args->output_type = FT_VCF;
args->nplugin_paths = -1;
int regions_is_file = 0, targets_is_file = 0, plist_only = 0;
if ( argc==1 ) usage(args);
char *plugin_name = NULL;
if ( argv[1][0]!='-' ) { plugin_name = argv[1]; argc--; argv++; }
static struct option loptions[] =
{
{"verbose",0,0,'v'},
{"help",0,0,'h'},
{"list-plugins",0,0,'l'},
{"output",1,0,'o'},
{"output-type",1,0,'O'},
{"include",1,0,'i'},
{"exclude",1,0,'e'},
{"regions",1,0,'r'},
{"regions-file",1,0,'R'},
{"targets",1,0,'t'},
{"targets-file",1,0,'T'},
{0,0,0,0}
};
while ((c = getopt_long(argc, argv, "h?o:O:r:R:li:e:v",loptions,NULL)) >= 0)
{
switch (c) {
case 'v': args->verbose = 1; break;
case 'o': args->output_fname = optarg; break;
case 'O':
switch (optarg[0]) {
case 'b': args->output_type = FT_BCF_GZ; break;
case 'u': args->output_type = FT_BCF; break;
case 'z': args->output_type = FT_VCF_GZ; break;
case 'v': args->output_type = FT_VCF; break;
default: error("The output type \"%s\" not recognised\n", optarg);
};
break;
case 'e': args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break;
case 'i': args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break;
case 'r': args->regions_list = optarg; break;
case 'R': args->regions_list = optarg; regions_is_file = 1; break;
case 't': args->targets_list = optarg; break;
case 'T': args->targets_list = optarg; targets_is_file = 1; break;
case 'l': plist_only = 1; break;
case '?':
case 'h': load_plugin(args, plugin_name, 1, &args->plugin); fprintf(stderr,"%s",args->plugin.usage()); return 0; break;
default: error("Unknown argument: %s\n", optarg);
}
}
if ( plist_only ) return list_plugins(args);
char *fname = NULL;
if ( optind>=argc || argv[optind][0]=='-' )
{
if ( !isatty(fileno((FILE *)stdin)) ) fname = "-"; // reading from stdin
else usage(args);
args->plugin.argc = argc - optind + 1;
args->plugin.argv = argv + optind - 1;
}
else
{
fname = argv[optind];
args->plugin.argc = argc - optind;
args->plugin.argv = argv + optind;
}
optind = 0;
args->plugin.argv[0] = plugin_name;
load_plugin(args, plugin_name, 1, &args->plugin);
if ( args->regions_list )
{
if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
error("Failed to read the regions: %s\n", args->regions_list);
}
if ( args->targets_list )
{
if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file, 0)<0 )
error("Failed to read the targets: %s\n", args->targets_list);
args->files->collapse |= COLLAPSE_SOME;
}
if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to open or the file not indexed: %s\n", fname);
init_data(args);
while ( bcf_sr_next_line(args->files) )
{
bcf1_t *line = bcf_sr_get_line(args->files,0);
if ( args->filter )
{
int pass = filter_test(args->filter, line, NULL);
if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1;
if ( !pass ) continue;
}
line = args->plugin.process(line);
if ( line ) bcf_write1(args->out_fh, args->hdr_out, line);
}
destroy_data(args);
bcf_sr_destroy(args->files);
free(args);
return 0;
}
int main(int carg, char *varg[])
{
size_t i;
char *filename;
char *dir;
char *metafile;
pup_mode_t mode;
plugin_t *p;
filename = NULL;
dir = NULL;
metafile = NULL;
mode = NONE;
p = NULL;
for(i = 1; i < carg; i++)
{
if (strcmp(varg[i], "--plugin") == 0)
{
i++;
if ((i < carg) && (strncmp(varg[i], "--", 2) != 0))
p = select_plugin(varg[i]);
}
else if (strcmp(varg[i], "--pack") == 0)
{
mode = PACK;
i++;
if ((i < carg) && (strncmp(varg[i], "--", 2) != 0))
filename = varg[i];
i++;
if ((i < carg) && (strncmp(varg[i], "--", 2) != 0))
dir = varg[i];
i++;
if ((i < carg) && (strncmp(varg[i], "--", 2) != 0))
metafile = varg[i];
}
else if (strcmp(varg[i], "--unpack") == 0)
{
mode = UNPACK;
i++;
if ((i < carg) && (strncmp(varg[i], "--", 2) != 0))
filename = varg[i];
i++;
if ((i < carg) && (strncmp(varg[i], "--", 2) != 0))
dir = varg[i];
i++;
if ((i < carg) && (strncmp(varg[i], "--", 2) != 0))
metafile = varg[i];
}
else if (strcmp(varg[i], "--print") == 0)
{
mode = PRINT;
i++;
if ((i < carg) && (strncmp(varg[i], "--", 2) != 0))
filename = varg[i];
}
else if (strcmp(varg[i], "--savemeta") == 0)
{
mode = SAVEMETA;
i++;
if ((i < carg) && (strncmp(varg[i], "--", 2) != 0))
filename = varg[i];
i++;
if ((i < carg) && (strncmp(varg[i], "--", 2) != 0))
metafile = varg[i];
}
else if (strcmp(varg[i], "--list") == 0)
mode = LIST;
else
{
fprintf(stderr, "Unknown option: %s\n", varg[i]);
return 1;
}
}
if ((filename == NULL) && ((mode == PACK) || (mode == UNPACK) || (mode == PRINT) || (mode == SAVEMETA)))
{
fprintf(stderr, "You must specify filename for this mode.\n");
return 2;
}
if ((metafile == NULL) && (mode == SAVEMETA))
{
fprintf(stderr, "You must specify metafile for this mode.\n");
return 2;
}
if (mode == LIST)
list_plugins();
else if (mode == PACK)
{
if (pack(p, filename, dir, metafile) == FALSE)
return 3;
}
else if (mode == UNPACK)
{
if (unpack(p, filename, dir, metafile) == FALSE)
return 4;
}
else if (mode == SAVEMETA)
{
if (savemeta(p, filename, metafile) == FALSE)
return 5;
}
else if (mode == PRINT)
{
if (print(p, filename) == FALSE)
return 7;
}
else
{
fprintf(stdout, "Usage: pup --list\n"
" pup --plugin <plugin> --pack <file> [<dir> [<meta>]]\n"
" pup [--plugin <plugin>] --unpack <file> [<dir> [<meta>]]\n"
" pup [--plugin <plugin>] --savemeta <file> [<meta>]\n"
" pup [--plugin <plugin>] --print <file>\n"
"Options:\n"
" --plugin <plugin>\t\t - specify certain plugin\n");
fprintf(stdout, "Modes:\n"
" --list\t\t\t\t - list of all supported plugins\n"
" --pack <file> [<dir> [<meta>]]\t - packing dir to specified file\n"
" --unpack <file> [<dir> [<meta>]]\t - unpacking specified file to dir\n"
" --savemeta <file> [<meta>]\t - only save metadata to specified metafile\n"
" --print <file>\t\t\t - print technical information to stdout\n");
return 8;
}
return 0;
}
int main(int argc, char *argv[])
{
int c, cmd, ret;
conf_info_t info = {0};
char *config = DEFAULT_INTERNAL;
xmlKeepBlanksDefault(0);
xmlTreeIndentString = "\t";
if (argc < 2) {
usage(argv[0]);
return 1;
}
cmd = command_decode(argv[1]);
/* parse params */
while ((c = getopt_long(argc, argv, OPTSTRING, long_opts, NULL)) != -1) {
switch (c) {
case 'h':
usage(argv[0]);
return 0;
case 'c':
config = optarg;
break;
case 'p':
switch (optarg[0]) {
case 'i': case 'I':
info.type = PL_INPUT;
break;
case 'm': case 'M':
info.type = PL_INTERMEDIATE;
break;
case 'o': case 'O':
info.type = PL_OUTPUT;
break;
default:
fprintf(stderr, "Unknown plugin type '%c'\n", optarg[0]);
return 1;
}
break;
case 'n':
info.name = optarg;
break;
case 's':
info.sofile = optarg;
break;
case 't':
info.thread = optarg;
break;
case 'f':
info.force = 1;
break;
default:
return 1;
}
}
ret = open_xml(&info, config);
if (ret != 0) {
return 1;
}
switch (cmd) {
case CMD_ADD:
ret = add_plugin(&info);
break;
case CMD_REMOVE:
ret = remove_plugin(&info);
break;
case CMD_LIST:
ret = list_plugins(&info);
break;
default:
fprintf(stderr, "Unknown command '%s'\n", argv[1]);
ret = 1;
break;
}
if (ret == 0 && cmd != CMD_LIST) {
save_xml(&info, config);
}
close_xml(&info);
return ret;
}
