\name{GmapSnps-class}
 \Rdversion{1.1}
 \docType{class}
 \alias{GmapSnps-class}
 \alias{directory,GmapSnps-method}

 \alias{GmapSnps}

 
 \title{Class \code{"GmapSnps"}}
 \description{
   This class represents a set of SNPs (single nucleotide polymorphisms)
   for use with GMAP and GSNAP (typically for SNP-tolerant alignment.)
 }
 \section{Objects from the Class}{
   ##TODO: doc these args
 Objects can be created by calls of the form \code{GmapSnps(snps,
   directory, name, create)}.
 }

 
 \usage{GmapSnps(snps, directory, name = snps, create = FALSE, ...)}
 
 \arguments{
   \item{snps}{A path to a VCF file}
   \item{directory}{The directory to create the IIT files used by GMAP
   and GSNAP}
   \item{name}{If provided, the name to give the database of SNPs. If not
   provided, defauts to the \code{snps} argument.}
   \item{create}{If the directory provided in the \code{directory}

     argument does not exist, create it.}
   \item{...}{Additional arguments to be passed to the SNPs
     replacement method.}
 }

   
 \section{Accessors}{
     \describe{
       \item{}{\code{name(x)}: returns the name of the \code{GmapSnps} object}
       \item{}{\code{directory(x)}: returns the \code{GmapGenomeDirectory}
 	that is the parent of the directory containing the index files for
 	this \code{GmapSnps} object.}
     }
 }

 \section{Methods}{
   \describe{
     \item{directory}{\code{signature(x = "GmapSnps")}: ... }
   }
 }
 \author{
   Michael Lawrence
 }
 \keyword{classes}