\name{GsnapOutput-class}
 \Rdversion{1.1}
 \docType{class}
 \alias{GsnapOutput-class}
 \alias{bamPaths,GsnapOutput-method}
 \alias{path,GsnapOutput-method}
 \alias{GsnapOutput}
 
 \title{Class \code{"GsnapOutput"}}
 \description{
   A \code{GsnapOutput} object stores locations of data output by the
   GSNAP alignment algorithm.
 }
 
 \section{Objects from the Class}{
   \code{GsnapOutput} objects are created from the \link{gsnap} function,
   though the function \code{GsnapOutput} can also be used as a constructor.
 }
 
 \section{Coercion}{
   In the code snippets below, \code{x} is a GsnapOutput object.
   
    \describe{
      \item{}{
        \code{as(x, BamFile)},
        \code{as(x, BamFileList)}:
 
        Returns either a BamFile or BamFileList object containing paths
      to the output of GSNAP.
    }
    \item{}{
      \code{asBam(x)}:
 
      converts all gsnap SAM files to BAM files and creates the .bai
      index files.
    }
  }
 }
 
 \author{
   Michael Lawrence
 }
 \seealso{
 \code{\link{gsnap}}
 }
 \keyword{classes}