\title{Class \code{"GsnapOutput"}}
  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.

  In the code snippets below, \code{x} is a GsnapOutput object.
       \code{as(x, BamFile)},
       \code{as(x, BamFileList)}:

       Returns either a BamFile or BamFileList object containing paths
     to the output of GSNAP.

     converts all gsnap SAM files to BAM files and creates the .bai
     index files.

  Michael Lawrence