int main( int argc, char *argv[] ) {
int exit_status = EXIT_SUCCESS;
const char *i_file = NULL;
const char *o_file = NULL;
FILE *fp = NULL;
if( argc < 2 ) { // absolute minimum args: <executable name> <input matrix>
_print_usage( argv[0], stdout, USAGE_SHORT );
exit( EXIT_SUCCESS );
}
_jit_initialization();
do {
static const char *CHAR_OPTIONS
#ifdef HAVE_LUA
= "s:hrt:N:C:P:n:x:c:DM:p:f:q:v:?X";
#else
= "hrt:N:C:P:n:x:DM:p:f:q:v:?X";
#endif
static struct option LONG_OPTIONS[] = {
#ifdef HAVE_LUA
{"script", required_argument, 0,'s'},
#endif
{"no-header", no_argument, 0,'h'},
{"no-row-labels", no_argument, 0,'r'},
{"type-parser", required_argument, 0,'t'},
{"na-regex", required_argument, 0,'N'},
{"crossprod", required_argument, 0,'C'},
{"pair", required_argument, 0,'P'},
{"by-name", required_argument, 0,'n'},
{"by-index", required_argument, 0,'x'},
#ifdef HAVE_LUA
{"coroutine", required_argument, 0,'c'},
#endif
{"dry-run", no_argument, 0,'D'},
{"min-ct-cell", required_argument, 0, 256 }, // no short equivalents
{"min-mx-cell", required_argument, 0, 257 }, // no short equivalents
{"min-samples", required_argument, 0,'M'},
{"p-value", required_argument, 0,'p'},
{"format", required_argument, 0,'f'},
{"fdr", required_argument, 0,'q'},
{"verbosity", required_argument, 0,'v'},
#ifdef _DEBUG
{"debug", required_argument, 0, 258 }, // no short equivalents
#endif
{"help", no_argument, 0,'?'},
{ NULL, 0, 0, 0 }
};
int arg_index = 0;
const int c
= getopt_long( argc, argv, CHAR_OPTIONS, LONG_OPTIONS, &arg_index );
switch (c) {
case 's': // script
opt_script = optarg;
break;
case 'h': // no-header
opt_header = false;
break;
case 'r': // no-row-labels
opt_row_labels = false;
break;
case 't': // type-parser
opt_type_parser = optarg;
break;
case 'N': // na-regex
opt_na_regex = optarg;
break;
case 'C': // cross-product of matrices
opt_preproc_matrix = optarg;
break;
case 'P': // pair
opt_single_pair = optarg;
break;
case 'n': // by-name
opt_pairlist_source = optarg;
opt_by_name = true;
break;
case 'x': // by-index
opt_pairlist_source = optarg;
opt_by_name = false;
break;
case 'c': // coroutine
opt_coroutine = optarg;
break;
case 'D': // dry-run
opt_dry_run = true;
break;
////////////////////////////////////////////////////////////////////
case 256: // ...because I haven't defined a short form for this
arg_min_cell_count = atoi( optarg );
break;
case 257: // ...because I haven't defined a short form for this
arg_min_mixb_count = atoi( optarg );
break;
case 'M':
arg_min_sample_count = atoi( optarg );
if( arg_min_sample_count < 2 ) {
warnx( "Seriously...%d samples is acceptable?\n"
"I don't think so... ;)\n",
arg_min_sample_count );
exit( EXIT_FAILURE );
}
break;
////////////////////////////////////////////////////////////////////
case 'p':
opt_p_value = atof( optarg );
if( ! ( 0 < opt_p_value ) ) {
warnx( "specified p-value %.3f will preclude all output.\n",
opt_p_value );
abort();
} else
if( ! ( opt_p_value < 1.0 ) ) {
warnx( "p-value %.3f will filter nothing.\n"
"\tIs this really what you want?\n",
opt_p_value );
}
break;
case 'J': // JSON format
case 'f': // tabular format
// Check for magic-value strings first
if( strcmp( MAGIC_FORMAT_ID_STD, optarg ) == 0 )
_emit = format_standard;
else
if( strcmp( MAGIC_FORMAT_ID_TCGA, optarg ) == 0 )
_emit = format_tcga;
else {
const char *specifier
= emit_config( optarg, c=='J' ? FORMAT_JSON : FORMAT_TABULAR );
if( specifier ) {
errx( -1, "invalid specifier \"%s\"", specifier );
}
_emit = emit_exec;
}
break;
case 'q':
arg_q_value = atof( optarg );
_analyze = _fdr_cache;
break;
case 'v': // verbosity
opt_verbosity = atoi( optarg );
break;
case '?': // help
_print_usage( argv[0], stdout, USAGE_SHORT );
exit( EXIT_SUCCESS );
break;
case 'X': // help
_print_usage( argv[0], stdout, USAGE_LONG );
exit( EXIT_SUCCESS );
break;
#ifdef _DEBUG
case 258:
if( strchr( optarg, 'X' ) != NULL ) {
// Turn OFF all filtering to turn on "exhaustive"
// output mode.
opt_status_mask = 0;
opt_p_value = 1.0;
}
dbg_silent = strchr( optarg, 'S' ) != NULL;
break;
#endif
case -1: // ...signals no more options.
break;
default:
printf ("error: unknown option: %c\n", c );
exit( EXIT_FAILURE );
}
if( -1 == c ) break;
} while( true );
int main(int argc, const char *argv[])
{
int is_config = (argc == 2) && (strcmp(argv[1], "config") == 0);
return is_config ? emit_config() : emit_fetch();
}
