deps/kb_meme/meme-5.0.1/src/mast.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: mast [options] <motif file> <sequence file>\n"
    "\n"
    "   Options:\n"
    "     -bfile <bf>    read background frequencies from <bf>\n"
    "     -dblist        the file specified as database contains a list of databases\n"
    "     -o <dir>       directory to output mast results\n"
    "     -oc <dir>      directory to output mast results with overwriting allowed\n"
    "     -hit_list      print only a list of non-overlapping hits to stdout\n"
    "     -remcorr       remove highly correlated motifs from query\n"
    "     -m <id>        use only motif(s) named <id> (overrides -mev);\n"
    "                      can be repeated\n"
    "     -mi <m>        use only motif(s) numbered <m> (overrides -mev);\n"
    "                      can be repeated\n"
    "     -c <count>     only use the first <count> motifs or all motifs\n"
    "                      when <count> is zero\n"
    "     -mev <mev>     use only motifs with E-values less than <mev>\n"
    "     -diag <diag>   nominal order and spacing of motifs\n"
    "     -norc          do not score reverse complement DNA strand\n"
    "     -sep           score reverse complement DNA strand as a separate sequence\n"
    "     -dna           translate DNA sequences to protein\n"
    "     -comp          adjust p-values and E-values for sequence composition\n"
    "     -ev <ev>       print results for sequences with E-value < <ev>;\n"
    "                      default: %g\n"
    "     -mt <mt>       show motif matches with p-value < mt; default: %g\n"
    "     -w             show weak matches (mt < p-value < mt*10) in angle brackets\n"
    "     -best          include only the best motif in diagrams;\n"
    "                      hit_list mode only\n"
    "     -seqp          use SEQUENCE p-values for motif thresholds\n"
    "                      default: use POSITION p-values\n"
    "     -mv <mf>       in results use <mf> as motif file name\n"
    "     -df <df>       in results use <df> as database name; ignored when\n"
    "                      option -dblist is specified\n"
    "     -dl <dl>       in results use <dl> as link to search sequence names;\n"
    "                      ignored when -dblist specified\n"
    "     -minseqs <ms>  lower bound on number of sequences in db\n"
    "     -nostatus      do not print progress report\n"
    "     -notext        do not generate text output\n"
    "     -nohtml        do not generate html output\n"
    "     -version       print the version and exit\n"
    ;
  if (format) {
    va_start(argp, format);
    vfprintf(stderr, format, argp);
    va_end(argp);
    fprintf(stderr, "\n");
  }
  fprintf(stderr, usage, EXPECT, MOTIF_THRESH_DEFAULT);
  fflush(stderr);
  exit(EXIT_FAILURE);
}
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 " ; if ( format ) { va_start ( argp , format ) ; vfprintf ( stderr , format , argp ) ; va_end ( argp ) ; fprintf ( stderr , " \n " ) ; } fprintf ( stderr , usage , EXPECT , MOTIF_THRESH_DEFAULT ) ; fflush ( stderr ) ; exit ( EXIT_FAILURE ) ; }
Print a usage message with an optional reason for failure.
Print a usage message with an optional reason for failure .