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+\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}