annotate src/getopt.R @ 1:7a520f7169e1 draft

"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"

# Copyright (c) 2008-2010 Allen Day
# Copyright (c) 2011-2013 Trevor L. Davis <[e-mail]>  
#  
# Modified by J.Vandel 2017 to consider situation of multiple identical flag
# and concatenate as a vector the set of parameter for the same flag instead of
# keeping only the last value as done by the previous version.
#
#  This file is free software: you may copy, redistribute and/or modify it  
#  under the terms of the GNU General Public License as published by the  
#  Free Software Foundation, either version 2 of the License, or (at your  
#  option) any later version.  
#  
#  This file is distributed in the hope that it will be useful, but  
#  WITHOUT ANY WARRANTY; without even the implied warranty of  
#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU  
#  General Public License for more details.  
#  
#  You should have received a copy of the GNU General Public License  
#  along with this program.  If not, see <http://www.gnu.org/licenses/>.  

#' C-like getopt behavior
#' 
#' getopt is primarily intended to be used with ``\link{Rscript}''.  It
#' facilitates writing ``\#!'' shebang scripts that accept short and long
#' flags/options.  It can also be used from ``R'' directly, but is probably less
#' useful in this context.
#' 
#' getopt() returns a \link{list} data structure containing \link{names} of the
#' flags that were present in the \link{character} \link{vector} passed in under
#' the \emph{opt} argument.  Each value of the \link{list} is coerced to the
#' data type specified according to the value of the \emph{spec} argument.  See
#' below for details.
#' 
#' Notes on naming convention:
#' 
#' 1. An \emph{option} is one of the shell-split input strings.
#' 
#' 2. A \emph{flag} is a type of \emph{option}.  a \emph{flag} can be defined as
#' having no \emph{argument} (defined below), a required \emph{argument}, or an
#' optional \emph{argument}.
#' 
#' 3. An \emph{argument} is a type of \emph{option}, and is the value associated
#' with a flag.
#' 
#' 4. A \emph{long flag} is a type of \emph{flag}, and begins with the string
#' ``--''.  If the \emph{long flag} has an associated \emph{argument}, it may be
#' delimited from the \emph{long flag} by either a trailing \emph{=}, or may be
#' the subsequent \emph{option}.
#' 
#' 5. A \emph{short flag} is a type of \emph{flag}, and begins with the string
#' ``-''.  If a \emph{short flag} has an associated \emph{argument}, it is the
#' subsequent \emph{option}.  \emph{short flags} may be bundled together,
#' sharing a single leading ``-'', but only the final \emph{short flag} is able
#' to have a corresponding \emph{argument}.
#'
#' Many users wonder whether they should use the getopt package, optparse package, 
#' or argparse package.
#' Here is some of the major differences:
#'
#' Features available in \code{getopt} unavailable in \code{optparse}
#'
#' 1. As well as allowing one to specify options that take either
#'      no argument or a required argument like \code{optparse},
#'    \code{getopt} also allows one to specify option with an optional argument.
#' 
#' Some features implemented in \code{optparse} package unavailable in \code{getopt}
#'
#' 1. Limited support for capturing positional arguments after the optional arguments
#' when \code{positional_arguments} set to TRUE in \code{parse_args} 
#'
#' 2. Automatic generation of an help option and printing of help text when encounters an "-h"
#' 
#' 3. Option to specify default arguments for options as well the
#'    variable name to store option values
#'
#' There is also new package \code{argparse} introduced in 2012 which contains
#' all the features of both getopt and optparse but which has a dependency on
#' Python 2.7 or 3.2+ and has not been used in production since 2008 or 2009
#' like the getopt and optparse packages.
#'
#' Some Features unlikely to be implemented in \code{getopt}:
#' 
#' 1. Support for multiple, identical flags, e.g. for "-m 3 -v 5 -v", the
#' trailing "-v" overrides the preceding "-v 5", result is v=TRUE (or equivalent
#' typecast).
#' 
#' 2. Support for multi-valued flags, e.g. "--libpath=/usr/local/lib
#' --libpath=/tmp/foo".
#' 
#' 3. Support for lists, e.g. "--define os=linux --define os=redhat" would
#' set result$os$linux=TRUE and result$os$redhat=TRUE.
#' 
#' 4. Support for incremental, argument-less flags, e.g. "/path/to/script
#' -vvv" should set v=3.
#' 
#' 5. Support partial-but-unique string match on options, e.g. "--verb" and
#' "--verbose" both match long flag "--verbose".
#' 
#' 6. No support for mixing in positional arguments or extra arguments that
#' don't match any options.  For example, you can't do "my.R --arg1 1 foo bar
#' baz" and recover "foo", "bar", "baz" as a list.  Likewise for "my.R foo
#' --arg1 1 bar baz".
#' 
#' @aliases getopt getopt-package
#' @param spec The getopt specification, or spec of what options are considered
#' valid.  The specification must be either a 4-5 column \link{matrix}, or a
#' \link{character} \link{vector} coercible into a 4 column \link{matrix} using
#' \link{matrix}(x,ncol=4,byrow=TRUE) command.  The \link{matrix}/\link{vector}
#' contains:
#' 
#' Column 1: the \emph{long flag} name.  A multi-\link{character} string.
#' 
#' Column 2: \emph{short flag} alias of Column 1.  A single-\link{character}
#' string.
#' 
#' Column 3: \emph{Argument} mask of the \emph{flag}.  An \link{integer}.
#' Possible values: 0=no argument, 1=required argument, 2=optional argument.
#' 
#' Column 4: Data type to which the \emph{flag}'s argument shall be cast using
#' \link{storage.mode}.  A multi-\link{character} string.  This only considered
#' for same-row Column 3 values of 1,2.  Possible values: \link{logical},
#' \link{integer}, \link{double}, \link{complex}, \link{character}.
#' If \link{numeric} is encountered then it will be converted to double.
#' 
#' Column 5 (optional): A brief description of the purpose of the option.
#' 
#' The terms \emph{option}, \emph{flag}, \emph{long flag}, \emph{short flag},
#' and \emph{argument} have very specific meanings in the context of this
#' document.  Read the ``Description'' section for definitions.
#' @param opt This defaults to the return value of \link{commandArgs}(TRUE).
#' 
#' If R was invoked directly via the ``R'' command, this corresponds to all
#' arguments passed to R after the ``--args'' flag.
#' 
#' If R was invoked via the ``\link{Rscript}'' command, this corresponds to all
#' arguments after the name of the R script file.
#' 
#' Read about \link{commandArgs} and \link{Rscript} to learn more.
#' @param command The string to use in the usage message as the name of the
#' script.  See argument \emph{usage}.
#' @param usage If TRUE, argument \emph{opt} will be ignored and a usage
#' statement (character string) will be generated and returned from \emph{spec}.
#' @param debug This is used internally to debug the getopt() function itself.
#' @author Allen Day
#' @seealso \code{\link{getopt}}
#' @keywords data
#' @export
#' @examples
#'
#' #!/path/to/Rscript
#' library('getopt');
#' #get options, using the spec as defined by the enclosed list.
#' #we read the options from the default: commandArgs(TRUE).
#' spec = matrix(c(
#'   'verbose', 'v', 2, "integer",
#'   'help'   , 'h', 0, "logical",
#'   'count'  , 'c', 1, "integer",
#'   'mean'   , 'm', 1, "double",
#'   'sd'     , 's', 1, "double"
#' ), byrow=TRUE, ncol=4);
#' opt = getopt(spec);
#' 
#' # if help was asked for print a friendly message 
#' # and exit with a non-zero error code
#' if ( !is.null(opt$help) ) {
#'   cat(getopt(spec, usage=TRUE));
#'   q(status=1);
#' }
#' 
#' #set some reasonable defaults for the options that are needed,
#' #but were not specified.
#' if ( is.null(opt$mean    ) ) { opt$mean    = 0     }
#' if ( is.null(opt$sd      ) ) { opt$sd      = 1     }
#' if ( is.null(opt$count   ) ) { opt$count   = 10    }
#' if ( is.null(opt$verbose ) ) { opt$verbose = FALSE }
#' 
#' #print some progress messages to stderr, if requested.
#' if ( opt$verbose ) { write("writing...",stderr()); }
#' 
#' #do some operation based on user input.
#' cat(paste(rnorm(opt$count,mean=opt$mean,sd=opt$sd),collapse="\n"));
#' cat("\n");
#' 
#' #signal success and exit.
#' #q(status=0);
getopt = function (spec=NULL,opt=commandArgs(TRUE),command=get_Rscript_filename(),usage=FALSE,debug=FALSE) {

  # littler compatibility - map argv vector to opt
  if (exists("argv", where = .GlobalEnv, inherits = FALSE)) {
    opt = get("argv", envir = .GlobalEnv);
  }

  ncol=4;
  maxcol=6;
  col.long.name    = 1;
  col.short.name   = 2;
  col.has.argument = 3;
  col.mode         = 4;
  col.description  = 5;

  flag.no.argument = 0;
  flag.required.argument = 1;
  flag.optional.argument = 2;

  result = list();
  result$ARGS = vector(mode="character");

  #no spec.  fail.
  if ( is.null(spec) ) {
    stop('argument "spec" must be non-null.');

  #spec is not a matrix.  attempt to coerce, if possible.  issue a warning.
  } else if ( !is.matrix(spec) ) {
    if ( length(spec)/4 == as.integer(length(spec)/4) ) {
      warning('argument "spec" was coerced to a 4-column (row-major) matrix.  use a matrix to prevent the coercion');
      spec = matrix( spec, ncol=ncol, byrow=TRUE );
    } else {
      stop('argument "spec" must be a matrix, or a character vector with length divisible by 4, rtfm.');
    }

  #spec is a matrix, but it has too few columns.
  } else if ( dim(spec)[2] < ncol ) {
    stop(paste('"spec" should have at least ",ncol," columns.',sep=''));

  #spec is a matrix, but it has too many columns.
  } else if ( dim(spec)[2] > maxcol ) {
    stop(paste('"spec" should have no more than ",maxcol," columns.',sep=''));

  #spec is a matrix, and it has some optional columns.
  } else if ( dim(spec)[2] != ncol ) {
    ncol = dim(spec)[2];
  }

  #sanity check.  make sure long names are unique, and short names are unique.
  if ( length(unique(spec[,col.long.name])) != length(spec[,col.long.name]) ) {
    stop(paste('redundant long names for flags (column ',col.long.name,').',sep=''));
  }
  if ( length(na.omit(unique(spec[,col.short.name]))) != length(na.omit(spec[,col.short.name])) ) {
    stop(paste('redundant short names for flags (column ',col.short.name,').',sep=''));
  }
  # convert numeric type to double type
  spec[,4] <- gsub("numeric", "double", spec[,4])

  # if usage=TRUE, don't process opt, but generate a usage string from the data in spec
  if ( usage ) {
    ret = '';
    ret = paste(ret,"Usage: ",command,sep='');
    for ( j in 1:(dim(spec))[1] ) {
      ret = paste(ret,' [-[-',spec[j,col.long.name],'|',spec[j,col.short.name],']',sep='');
      if (spec[j,col.has.argument] == flag.no.argument) {
        ret = paste(ret,']',sep='');
      } else if (spec[j,col.has.argument] == flag.required.argument) {
        ret = paste(ret,' <',spec[j,col.mode],'>]',sep='');
      } else if (spec[j,col.has.argument] == flag.optional.argument) {
        ret = paste(ret,' [<',spec[j,col.mode],'>]]',sep='');
      }
    }
    # include usage strings
    if ( ncol >= 5 ) {
      max.long = max(apply(cbind(spec[,col.long.name]),1,function(x)length(strsplit(x,'')[[1]])));
      ret = paste(ret,"\n",sep='');
      for (j in 1:(dim(spec))[1] ) {
        ret = paste(ret,sprintf(paste("    -%s|--%-",max.long,"s    %s\n",sep=''),
          spec[j,col.short.name],spec[j,col.long.name],spec[j,col.description]
        ),sep='');
      }
    }
    else {
      ret = paste(ret,"\n",sep='');
    }
    return(ret);
  }

  #XXX check spec validity here.  e.g. column three should be convertible to integer

  i = 1;

  while ( i <= length(opt) ) {
    if ( debug ) print(paste("processing",opt[i]));

    current.flag = 0; #XXX use NA
    optstring = opt[i];


    #long flag
    if ( substr(optstring, 1, 2) == '--' ) {
      if ( debug ) print(paste("  long option:",opt[i]));

      optstring = substring(optstring,3);

      this.flag = NA;
      this.argument = NA;
      kv = strsplit(optstring, '=')[[1]];
      if ( !is.na(kv[2]) ) {
        this.flag = kv[1];
        this.argument = paste(kv[-1], collapse="=");
      } else {
        this.flag = optstring;
      }

      rowmatch = grep( this.flag, spec[,col.long.name],fixed=TRUE );

      #long flag is invalid, matches no options
      if ( length(rowmatch) == 0 ) {
        stop(paste('long flag "', this.flag, '" is invalid', sep=''));

      #long flag is ambiguous, matches too many options
      } else if ( length(rowmatch) > 1 ) {
        # check if there is an exact match and use that
        rowmatch = which(this.flag == spec[,col.long.name])
        if(length(rowmatch) == 0) {
          stop(paste('long flag "', this.flag, '" is ambiguous', sep=''));
        }
      }

      #if we have an argument
      if ( !is.na(this.argument) ) {
        #if we can't accept the argument, bail out
        if ( spec[rowmatch, col.has.argument] == flag.no.argument ) {
          stop(paste('long flag "', this.flag, '" accepts no arguments', sep=''));

        #otherwise assign the argument to the flag
        } else {
          storage.mode(this.argument) = spec[rowmatch, col.mode];
          #don't need here to remove the last value of the vector as argument is in the same string as
          #the flag name "--flag=argument" so no spurious TRUE was added
          result[[spec[rowmatch, col.long.name]]] = c(result[[spec[rowmatch, col.long.name]]],this.argument);
	  i = i + 1;
	  next;
        }

      #otherwise, we don't have an argument
      } else {
        #if we require an argument, bail out
        ###if ( spec[rowmatch, col.has.argument] == flag.required.argument ) {
        ###  stop(paste('long flag "', this.flag, '" requires an argument', sep=''));

        #long flag has no attached argument. set flag as present.  set current.flag so we can peek ahead later and consume the argument if it's there
        ###} else {
          result[[spec[rowmatch, col.long.name]]] = c(result[[spec[rowmatch, col.long.name]]],TRUE);
          current.flag = rowmatch;
        ###}
      }

    #short flag(s)
    } else if ( substr(optstring, 1, 1) == '-' ) {
      if ( debug ) print(paste("  short option:",opt[i]));

      these.flags = strsplit(optstring,'')[[1]];

      done = FALSE;
      for ( j in 2:length(these.flags) ) {
        this.flag = these.flags[j];
        rowmatch = grep( this.flag, spec[,col.short.name],fixed=TRUE );

        #short flag is invalid, matches no options
        if ( length(rowmatch) == 0 ) {
          stop(paste('short flag "', this.flag, '" is invalid', sep=''));

        #short flag is ambiguous, matches too many options
        } else if ( length(rowmatch) > 1 ) {
          stop(paste('short flag "', this.flag, '" is ambiguous', sep=''));

        #short flag has an argument, but is not the last in a compound flag string
        } else if ( j < length(these.flags) & spec[rowmatch,col.has.argument] == flag.required.argument ) {
          stop(paste('short flag "', this.flag, '" requires an argument, but has none', sep=''));

        #short flag has no argument, flag it as present
        } else if ( spec[rowmatch,col.has.argument] == flag.no.argument ) {
          result[[spec[rowmatch, col.long.name]]] = c(result[[spec[rowmatch, col.long.name]]],TRUE);
	  done = TRUE;

        #can't definitively process this flag yet, need to see if next option is an argument or not
        } else {
          result[[spec[rowmatch, col.long.name]]] = c(result[[spec[rowmatch, col.long.name]]],TRUE);
          current.flag = rowmatch;
          done = FALSE;
        }
      }
      if ( done ) {
        i = i + 1;
        next;
      }
    }

    #invalid opt
    if ( current.flag == 0 ) {
      stop(paste('"', optstring, '" is not a valid option, or does not support an argument', sep=''));
      #TBD support for positional args
      #if ( debug ) print(paste('"', optstring, '" not a valid option.  It is appended to getopt(...)$ARGS', sep=''));
      #result$ARGS = append(result$ARGS, optstring);

    # some dangling flag, handle it
    } else if ( current.flag > 0 ) {
      if ( debug ) print('    dangling flag');
      if ( length(opt) > i ) {
        peek.optstring = opt[i + 1];
        if ( debug ) print(paste('      peeking ahead at: "',peek.optstring,'"',sep=''));

        #got an argument.  attach it, increment the index, and move on to the next option.  we don't allow arguments beginning with '-' UNLESS
	#specfile indicates the value is an "integer" or "double", in which case we allow a leading dash (and verify trailing digits/decimals).
        if ( substr(peek.optstring, 1, 1) != '-' |
	  #match negative double
	  ( substr(peek.optstring, 1, 1) == '-'
	  & regexpr('^-[0123456789]*\\.?[0123456789]+$',peek.optstring) > 0
	  & spec[current.flag, col.mode]== 'double'
	  ) |
	  #match negative integer
	  ( substr(peek.optstring, 1, 1) == '-'
	  & regexpr('^-[0123456789]+$',peek.optstring) > 0
	  & spec[current.flag, col.mode]== 'integer'
	  )
	) {
          if ( debug ) print(paste('        consuming argument *',peek.optstring,'*',sep=''));
          storage.mode(peek.optstring) = spec[current.flag, col.mode];
          #remove the last argument put in result for current.flag that should be a TRUE and concatenate argument with previous ones
          result[[spec[current.flag, col.long.name]]] = c(result[[spec[current.flag, col.long.name]]][-length(result[[spec[current.flag, col.long.name]]])],peek.optstring);
          i = i + 1;

	#a lone dash
	} else if ( substr(peek.optstring, 1, 1) == '-' & length(strsplit(peek.optstring,'')[[1]]) == 1 ) {
          if ( debug ) print('        consuming "lone dash" argument');
          storage.mode(peek.optstring) = spec[current.flag, col.mode];
          #remove the last argument put in result for current.flag that should be a TRUE and concatenate argument with previous ones
          result[[spec[current.flag, col.long.name]]] =c(result[[spec[current.flag, col.long.name]]][-length(result[[spec[current.flag, col.long.name]]])],peek.optstring);
          i = i + 1;

        #no argument
        } else {
          if ( debug ) print('        no argument!');

          #if we require an argument, bail out
          if ( spec[current.flag, col.has.argument] == flag.required.argument ) {
            stop(paste('flag "', this.flag, '" requires an argument', sep=''));

          #otherwise set flag as present.
          } else if (
	    spec[current.flag, col.has.argument] == flag.optional.argument |
	    spec[current.flag, col.has.argument] == flag.no.argument 
	  ) {
  	    x = TRUE;
  	    storage.mode(x) = spec[current.flag, col.mode];
            result[[spec[current.flag, col.long.name]]] = c(result[[spec[current.flag, col.long.name]]],x);
          } else {
            stop(paste("This should never happen.",
              "Is your spec argument correct?  Maybe you forgot to set",
              "ncol=4, byrow=TRUE in your matrix call?"));
	  }
        }
      #trailing flag without required argument
      } else if ( spec[current.flag, col.has.argument] == flag.required.argument ) {
        stop(paste('flag "', this.flag, '" requires an argument', sep=''));

      #trailing flag without optional argument
      } else if ( spec[current.flag, col.has.argument] == flag.optional.argument ) {
        x = TRUE;
        storage.mode(x) = spec[current.flag, col.mode];
        result[[spec[current.flag, col.long.name]]] = c(result[[spec[current.flag, col.long.name]]],x);

      #trailing flag without argument
      } else if ( spec[current.flag, col.has.argument] == flag.no.argument ) {
        x = TRUE;
        storage.mode(x) = spec[current.flag, col.mode];
        result[[spec[current.flag, col.long.name]]] = c(result[[spec[current.flag, col.long.name]]],x);
      } else {
        stop("this should never happen (2).  please inform the author.");
      }
    #no dangling flag, nothing to do.
    } else {
    }

    i = i+1;
  }
  return(result);
}



#########################
#set a modified version using only long named parameters 

getoptLong = function (spec=NULL,opt=commandArgs(TRUE),command=get_Rscript_filename(),usage=FALSE,debug=FALSE) {
  
  # littler compatibility - map argv vector to opt
  if (exists("argv", where = .GlobalEnv, inherits = FALSE)) {
    opt = get("argv", envir = .GlobalEnv);
  }
  
  ncol=4;
  maxcol=6;
  col.long.name    = 1;
  #col.short.name   = 2;
  col.has.argument = 3;
  col.mode         = 4;
  col.description  = 5;
  
  flag.no.argument = 0;
  flag.required.argument = 1;
  flag.optional.argument = 2;
  
  result = list();
  result$ARGS = vector(mode="character");
  
  #no spec.  fail.
  if ( is.null(spec) ) {
    stop('argument "spec" must be non-null.');
    
    #spec is not a matrix.  attempt to coerce, if possible.  issue a warning.
  } else if ( !is.matrix(spec) ) {
    if ( length(spec)/4 == as.integer(length(spec)/4) ) {
      warning('argument "spec" was coerced to a 4-column (row-major) matrix.  use a matrix to prevent the coercion');
      spec = matrix( spec, ncol=ncol, byrow=TRUE );
    } else {
      stop('argument "spec" must be a matrix, or a character vector with length divisible by 4, rtfm.');
    }
    
    #spec is a matrix, but it has too few columns.
  } else if ( dim(spec)[2] < ncol ) {
    stop(paste('"spec" should have at least ",ncol," columns.',sep=''));
    
    #spec is a matrix, but it has too many columns.
  } else if ( dim(spec)[2] > maxcol ) {
    stop(paste('"spec" should have no more than ",maxcol," columns.',sep=''));
    
    #spec is a matrix, and it has some optional columns.
  } else if ( dim(spec)[2] != ncol ) {
    ncol = dim(spec)[2];
  }
  
  #sanity check.  make sure long names are unique, and short names are unique.
  if ( length(unique(spec[,col.long.name])) != length(spec[,col.long.name]) ) {
    stop(paste('redundant long names for flags (column ',col.long.name,').',sep=''));
  }
  # if ( length(na.omit(unique(spec[,col.short.name]))) != length(na.omit(spec[,col.short.name])) ) {
  #   stop(paste('redundant short names for flags (column ',col.short.name,').',sep=''));
  # }
  # convert numeric type to double type
  spec[,4] <- gsub("numeric", "double", spec[,4])
  
  # if usage=TRUE, don't process opt, but generate a usage string from the data in spec
  if ( usage ) {
    ret = '';
    ret = paste(ret,"Usage: ",command,sep='');
    for ( j in 1:(dim(spec))[1] ) {
      ret = paste(ret,' [-[-',spec[j,col.long.name],']',sep='');
      if (spec[j,col.has.argument] == flag.no.argument) {
        ret = paste(ret,']',sep='');
      } else if (spec[j,col.has.argument] == flag.required.argument) {
        ret = paste(ret,' <',spec[j,col.mode],'>]',sep='');
      } else if (spec[j,col.has.argument] == flag.optional.argument) {
        ret = paste(ret,' [<',spec[j,col.mode],'>]]',sep='');
      }
    }
    # include usage strings
    if ( ncol >= 5 ) {
      max.long = max(apply(cbind(spec[,col.long.name]),1,function(x)length(strsplit(x,'')[[1]])));
      ret = paste(ret,"\n",sep='');
      for (j in 1:(dim(spec))[1] ) {
        ret = paste(ret,sprintf(paste("--%-",max.long,"s    %s\n",sep='')
                                ,spec[j,col.long.name],spec[j,col.description]
        ),sep='');
      }
    }
    else {
      ret = paste(ret,"\n",sep='');
    }
    return(ret);
  }
  
  #XXX check spec validity here.  e.g. column three should be convertible to integer
  
  i = 1;
  
  while ( i <= length(opt) ) {
    if ( debug ) print(paste("processing",opt[i]));
    
    current.flag = 0; #XXX use NA
    optstring = opt[i];
    
    
    #long flag
    if ( substr(optstring, 1, 2) == '--' ) {
      if ( debug ) print(paste("  long option:",opt[i]));
      
      optstring = substring(optstring,3);
      
      this.flag = NA;
      this.argument = NA;
      kv = strsplit(optstring, '=')[[1]];
      if ( !is.na(kv[2]) ) {
        this.flag = kv[1];
        this.argument = paste(kv[-1], collapse="=");
      } else {
        this.flag = optstring;
      }
      
      rowmatch = grep( this.flag, spec[,col.long.name],fixed=TRUE );
      
      #long flag is invalid, matches no options
      if ( length(rowmatch) == 0 ) {
        stop(paste('long flag "', this.flag, '" is invalid', sep=''));
        
        #long flag is ambiguous, matches too many options
      } else if ( length(rowmatch) > 1 ) {
        # check if there is an exact match and use that
        rowmatch = which(this.flag == spec[,col.long.name])
        if(length(rowmatch) == 0) {
          stop(paste('long flag "', this.flag, '" is ambiguous', sep=''));
        }
      }
      
      #if we have an argument
      if ( !is.na(this.argument) ) {
        #if we can't accept the argument, bail out
        if ( spec[rowmatch, col.has.argument] == flag.no.argument ) {
          stop(paste('long flag "', this.flag, '" accepts no arguments', sep=''));
          
          #otherwise assign the argument to the flag
        } else {
          storage.mode(this.argument) = spec[rowmatch, col.mode];
          #don't need here to remove the last value of the vector as argument is in the same string as
          #the flag name "--flag=argument" so no spurious TRUE was added
          result[[spec[rowmatch, col.long.name]]] = c(result[[spec[rowmatch, col.long.name]]],this.argument);
          i = i + 1;
          next;
        }
        
        #otherwise, we don't have an argument
      } else {
        #if we require an argument, bail out
        ###if ( spec[rowmatch, col.has.argument] == flag.required.argument ) {
        ###  stop(paste('long flag "', this.flag, '" requires an argument', sep=''));
        
        #long flag has no attached argument. set flag as present.  set current.flag so we can peek ahead later and consume the argument if it's there
        ###} else {
        result[[spec[rowmatch, col.long.name]]] = c(result[[spec[rowmatch, col.long.name]]],TRUE);
        current.flag = rowmatch;
        ###}
      }
      
      #short flag(s)
    } 
    #else if ( substr(optstring, 1, 1) == '-' ) {
    #   if ( debug ) print(paste("  short option:",opt[i]));
    #   
    #   these.flags = strsplit(optstring,'')[[1]];
    #   
    #   done = FALSE;
    #   for ( j in 2:length(these.flags) ) {
    #     this.flag = these.flags[j];
    #     rowmatch = grep( this.flag, spec[,col.short.name],fixed=TRUE );
    #     
    #     #short flag is invalid, matches no options
    #     if ( length(rowmatch) == 0 ) {
    #       stop(paste('short flag "', this.flag, '" is invalid', sep=''));
    #       
    #       #short flag is ambiguous, matches too many options
    #     } else if ( length(rowmatch) > 1 ) {
    #       stop(paste('short flag "', this.flag, '" is ambiguous', sep=''));
    #       
    #       #short flag has an argument, but is not the last in a compound flag string
    #     } else if ( j < length(these.flags) & spec[rowmatch,col.has.argument] == flag.required.argument ) {
    #       stop(paste('short flag "', this.flag, '" requires an argument, but has none', sep=''));
    #       
    #       #short flag has no argument, flag it as present
    #     } else if ( spec[rowmatch,col.has.argument] == flag.no.argument ) {
    #       result[[spec[rowmatch, col.long.name]]] = c(result[[spec[rowmatch, col.long.name]]],TRUE);
    #       done = TRUE;
    #       
    #       #can't definitively process this flag yet, need to see if next option is an argument or not
    #     } else {
    #       result[[spec[rowmatch, col.long.name]]] = c(result[[spec[rowmatch, col.long.name]]],TRUE);
    #       current.flag = rowmatch;
    #       done = FALSE;
    #     }
    #   }
    #   if ( done ) {
    #     i = i + 1;
    #     next;
    #   }
    # }
    
    #invalid opt
    if ( current.flag == 0 ) {
      stop(paste('"', optstring, '" is not a valid option, or does not support an argument', sep=''));
      #TBD support for positional args
      #if ( debug ) print(paste('"', optstring, '" not a valid option.  It is appended to getopt(...)$ARGS', sep=''));
      #result$ARGS = append(result$ARGS, optstring);
      
      # some dangling flag, handle it
    } else if ( current.flag > 0 ) {
      if ( debug ) print('    dangling flag');
      if ( length(opt) > i ) {
        peek.optstring = opt[i + 1];
        if ( debug ) print(paste('      peeking ahead at: "',peek.optstring,'"',sep=''));
        
        #got an argument.  attach it, increment the index, and move on to the next option.  we don't allow arguments beginning with '-' UNLESS
        #specfile indicates the value is an "integer" or "double", in which case we allow a leading dash (and verify trailing digits/decimals).
        if ( substr(peek.optstring, 1, 1) != '-' |
             #match negative double
             ( substr(peek.optstring, 1, 1) == '-'
               & regexpr('^-[0123456789]*\\.?[0123456789]+$',peek.optstring) > 0
               & spec[current.flag, col.mode]== 'double'
             ) |
             #match negative integer
             ( substr(peek.optstring, 1, 1) == '-'
               & regexpr('^-[0123456789]+$',peek.optstring) > 0
               & spec[current.flag, col.mode]== 'integer'
             )
        ) {
          if ( debug ) print(paste('        consuming argument *',peek.optstring,'*',sep=''));
          storage.mode(peek.optstring) = spec[current.flag, col.mode];
          #remove the last argument put in result for current.flag that should be a TRUE and concatenate argument with previous ones
          result[[spec[current.flag, col.long.name]]] = c(result[[spec[current.flag, col.long.name]]][-length(result[[spec[current.flag, col.long.name]]])],peek.optstring);
          i = i + 1;
          
          #a lone dash
        } else if ( substr(peek.optstring, 1, 1) == '-' & length(strsplit(peek.optstring,'')[[1]]) == 1 ) {
          if ( debug ) print('        consuming "lone dash" argument');
          storage.mode(peek.optstring) = spec[current.flag, col.mode];
          #remove the last argument put in result for current.flag that should be a TRUE and concatenate argument with previous ones
          result[[spec[current.flag, col.long.name]]] =c(result[[spec[current.flag, col.long.name]]][-length(result[[spec[current.flag, col.long.name]]])],peek.optstring);
          i = i + 1;
          
          #no argument
        } else {
          if ( debug ) print('        no argument!');
          
          #if we require an argument, bail out
          if ( spec[current.flag, col.has.argument] == flag.required.argument ) {
            stop(paste('flag "', this.flag, '" requires an argument', sep=''));
            
            #otherwise set flag as present.
          } else if (
            spec[current.flag, col.has.argument] == flag.optional.argument |
            spec[current.flag, col.has.argument] == flag.no.argument 
          ) {
            x = TRUE;
            storage.mode(x) = spec[current.flag, col.mode];
            result[[spec[current.flag, col.long.name]]] = c(result[[spec[current.flag, col.long.name]]],x);
          } else {
            stop(paste("This should never happen.",
                       "Is your spec argument correct?  Maybe you forgot to set",
                       "ncol=4, byrow=TRUE in your matrix call?"));
          }
        }
        #trailing flag without required argument
      } else if ( spec[current.flag, col.has.argument] == flag.required.argument ) {
        stop(paste('flag "', this.flag, '" requires an argument', sep=''));
        
        #trailing flag without optional argument
      } else if ( spec[current.flag, col.has.argument] == flag.optional.argument ) {
        x = TRUE;
        storage.mode(x) = spec[current.flag, col.mode];
        result[[spec[current.flag, col.long.name]]] = c(result[[spec[current.flag, col.long.name]]],x);
        
        #trailing flag without argument
      } else if ( spec[current.flag, col.has.argument] == flag.no.argument ) {
        x = TRUE;
        storage.mode(x) = spec[current.flag, col.mode];
        result[[spec[current.flag, col.long.name]]] = c(result[[spec[current.flag, col.long.name]]],x);
      } else {
        stop("this should never happen (2).  please inform the author.");
      }
      #no dangling flag, nothing to do.
    } else {
    }
    
    i = i+1;
  }
  return(result);
}