deps/kb_meme/meme-5.0.1/src/tomtom.c
/*****************************************************************************
 * Print a usage message with an optional reason for failure.
 *****************************************************************************/
Print a usage message with an optional reason for failure.
Print a usage message with an optional reason for failure .
static void usage(char *format, ...) {
  va_list argp;
  char *usage = 
    "\n"
    "Usage:\n"
    "  tomtom [options] <query file> <target file>+\n"
    "Options:\n"
    "  -o <output dir>  Name of directory for output files;\n"
    "                    will not replace existing directory\n"
    "  -oc <output dir> Name of directory for output files;\n"
    "                    will replace existing directory\n"
    "  -xalph           Convert the alphabet of the target motif databases\n"
    "                    to the alphabet of the query motif database\n"
    "                    assuming the core symbols of the target motif\n"
    "                    alphabet are a subset; default: reject differences\n"
    "  -bfile <background file>\n"
    "                   Name of background file;\n"
    "                    default: use the background from the query\n"
    "                    motif database\n"
    "  -motif-pseudo <pseudo count>\n"
    "                   Apply the pseudocount to the query and target motifs;\n"
    "                    default: apply a pseudocount of 0.1\n"
    "  -m <id>          Use only query motifs with a specified id;\n"
    "                    may be repeated\n"
    "  -mi <index>      Use only query motifs with a specifed index;\n"
    "                    may be repeated\n"
    "  -thresh <float>  Significance threshold; default: 0.5\n"
    "  -evalue          Use E-value threshold; default: q-value\n"
    "  -dist allr|ed|kullback|pearson|sandelin|blic1|blic5|llr1|llr5\n"
    "                   Distance metric for scoring alignments;\n"
    "                    default: pearson\n"
    "  -internal        Only allow internal alignments;\n"
    "                    default: allow overhangs\n"
    "  -min-overlap <int>\n"
    "                   Minimum overlap between query and target;\n"
    "                    default: 1\n"
    "  -norc            Do not score the reverse complements of targets\n"
    "  -incomplete-scores\n"
    "                   Ignore unaligned columns in computing scores\n"
    "                    default: use complete set of columns\n"
    "  -text            Output in text format (default is HTML)\n"
    "  -png             Create PNG logos; default: don't create PNG logos\n"
    "  -eps             Create EPS logos; default: don't create EPS logos\n"
    "  -no-ssc          Don't apply small-sample correction to logos;\n"
    "                    default: use small-sample correction\n"
    "  -verbosity [1|2|3|4]\n"
    "                   Set the verbosity of the program; default: 2 (normal)\n"
    "  -version         Print the version and exit\n"
    ;
  if (format) {
    va_start(argp, format);
    vfprintf(stderr, format, argp);
    va_end(argp);
    fprintf(stderr, "\n");
    fputs(usage, stderr);
    fflush(stderr);
  } else {
    fputs(usage, stderr);
  }
  exit(1);
}
static void usage ( char * format , ... ) { va_list argp ; char * usage = " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " " \n " ; if ( format ) { va_start ( argp , format ) ; vfprintf ( stderr , format , argp ) ; va_end ( argp ) ; fprintf ( stderr , " \n " ) ; fputs ( usage , stderr ) ; fflush ( stderr ) ; } else { fputs ( usage , stderr ) ; } exit ( 1 ) ; }
Print a usage message with an optional reason for failure.
Print a usage message with an optional reason for failure .